Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold179
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2991183
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.31
Warning! 65816 characters in sequence are not A, C, G, or T
File 4 of 18
Found at i:479478 original size:41 final size:41
Alignment explanation
Indices: 479421--479514 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
479411 CTGCCAAGAA
479421 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
479462 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
479503 ATGTATCGATAC
1 ATGTATCGATAC
479515 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:481982 original size:13 final size:13
Alignment explanation
Indices: 481964--482002 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
481954 ATAATCACCC
*
481964 TGTATCGATACAG
1 TGTATCGATACAA
481977 TGTATCGATACAA
1 TGTATCGATACAA
*
481990 TGTATCAATACAA
1 TGTATCGATACAA
482003 AGAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:482013 original size:20 final size:20
Alignment explanation
Indices: 481988--482026 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
481978 GTATCGATAC
481988 AATGTATCAATACAAAGAAA
1 AATGTATCAATACAAAGAAA
* *
482008 AATGTATCGATACATAGAA
1 AATGTATCAATACAAAGAA
482027 TTTCCAGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.23
Consensus pattern (20 bp):
AATGTATCAATACAAAGAAA
Found at i:485944 original size:21 final size:21
Alignment explanation
Indices: 485915--485959 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
485905 AAGTTTTCAT
*
485915 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
485935 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
485957 TTT
1 TTT
485960 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:488192 original size:13 final size:13
Alignment explanation
Indices: 488174--488199 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
488164 AATTTTTTTG
488174 TGTATCGATACAT
1 TGTATCGATACAT
488187 TGTATCGATACAT
1 TGTATCGATACAT
488200 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:488283 original size:20 final size:20
Alignment explanation
Indices: 488238--488310 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
488228 CTGCCAAGAA
***
488238 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGAATC
488259 ATGTATCGATACATTGCAA-C
1 ATGTATCGATACATTG-AATC
* *
488279 ATGTATCGATACTTTGAATT
1 ATGTATCGATACATTGAATC
488299 ATGTATCGATAC
1 ATGTATCGATAC
488311 TTTTAAGGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 29 0.64
21 14 0.31
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTGAATC
Found at i:488311 original size:20 final size:20
Alignment explanation
Indices: 488258--488313 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
488248 ACATCTTTTT
*
488258 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
488278 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
488297 TTATGTATCGATACTTT
1 -CATGTATCGATACTTT
488314 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:493384 original size:21 final size:22
Alignment explanation
Indices: 493351--493392 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
493341 ATTAATACCA
493351 ATGCATAAGGTATCAATACATC
1 ATGCATAAGGTATCAATACATC
* *
493373 ATGCA-AATGTATCGATACAT
1 ATGCATAAGGTATCAATACAT
493393 TTGCTTCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (22 bp):
ATGCATAAGGTATCAATACATC
Found at i:495543 original size:29 final size:29
Alignment explanation
Indices: 495511--495568 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
495501 ATTAATAATT
* * *
495511 ATTTTTAAGAGTTAAAAAATTATTTTTAA
1 ATTTTTAAGAATAAAAAAATTATCTTTAA
495540 ATTTTTAAGAATAAAAAAATTATCTTTAA
1 ATTTTTAAGAATAAAAAAATTATCTTTAA
495569 TAGTTATCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (29 bp):
ATTTTTAAGAATAAAAAAATTATCTTTAA
Found at i:496728 original size:2 final size:2
Alignment explanation
Indices: 496721--496754 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
496711 CTCTATATTT
496721 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
496755 CATGGATAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:498372 original size:2 final size:2
Alignment explanation
Indices: 498365--498391 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
498355 ATTTTCTTGC
498365 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
498392 AAAGTTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:502651 original size:20 final size:21
Alignment explanation
Indices: 502628--502680 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
502618 ATTTCAAATG
*
502628 TGTATCAATACATT-CACTTA-
1 TGTATCGATACATTAC-CTTAT
*
502648 TGTAGCGATACATTACCTTAT
1 TGTATCGATACATTACCTTAT
502669 TGTATCGATACA
1 TGTATCGATACA
502681 AATTGCTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTACCTTAT
Found at i:502677 original size:21 final size:20
Alignment explanation
Indices: 502606--502680 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 20
502596 CTGCATGGTC
* **
502606 TTGTATCGATACATTTCAAA
1 TTGTATCGATACATTCCTTA
*
502626 TGTGTATCAATACATTCACTTA
1 T-TGTATCGATACATTC-CTTA
*
502648 -TGTAGCGATACATTACCTTA
1 TTGTATCGATACATT-CCTTA
502668 TTGTATCGATACA
1 TTGTATCGATACA
502681 AATTGCTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
20 17 0.39
21 25 0.57
22 2 0.05
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATTCCTTA
Found at i:506725 original size:13 final size:13
Alignment explanation
Indices: 506707--506731 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
506697 ATTACTCAAA
506707 TGTATCGATACAT
1 TGTATCGATACAT
506720 TGTATCGATACA
1 TGTATCGATACA
506732 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:506796 original size:52 final size:52
Alignment explanation
Indices: 506740--506864 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
506730 CACTGATCTT
* *
506740 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
*
506792 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
*
506844 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
506865 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
Found at i:513970 original size:52 final size:52
Alignment explanation
Indices: 513885--514009 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
513875 ATATGAAAAG
* *
513885 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
513937 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
513989 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
514010 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:514022 original size:52 final size:51
Alignment explanation
Indices: 513885--514030 Score: 213
Period size: 52 Copynumber: 2.8 Consensus size: 51
513875 ATATGAAAAG
*
513885 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
513937 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
513989 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACAT
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACAT
514031 TTGAGTAATG
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:514111 original size:13 final size:13
Alignment explanation
Indices: 514093--514117 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
514083 CAAAAAAATA
514093 TGTATCGATACAT
1 TGTATCGATACAT
514106 TGTATCGATACA
1 TGTATCGATACA
514118 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:514113 original size:33 final size:33
Alignment explanation
Indices: 514071--514137 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
514061 AGTAGCTTAA
514071 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
514104 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
514137 A
1 A
514138 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:515019 original size:42 final size:42
Alignment explanation
Indices: 514972--515091 Score: 168
Period size: 42 Copynumber: 2.9 Consensus size: 42
514962 CTTCTTCTCT
* * * *
514972 CCTCCTCTTGTCATCCTTCCTCTCTCTATTATCTCTCCTGTC
1 CCTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTC
*
515014 CCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTC
1 CCTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTC
* * *
515056 TCTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CCTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
515092 TTGAGGGCTA
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CCTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTC
Found at i:515057 original size:18 final size:18
Alignment explanation
Indices: 514989--515058 Score: 50
Period size: 18 Copynumber: 3.6 Consensus size: 18
514979 TTGTCATCCT
* *
514989 TCCTCTCTCTATTATCTC
1 TCCTGTCTCTACTATCTC
*
515007 TCCTGTCCCTCCTCCTATCATCCC
1 TCCTGT--CT-CTACTATC-T--C
*
515031 TCCTATCTCTACTATCTC
1 TCCTGTCTCTACTATCTC
515049 TCCTGTCTCT
1 TCCTGTCTCT
515059 CCTCCTATCA
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
18 15 0.38
20 3 0.08
21 13 0.32
22 3 0.08
24 6 0.15
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.43
Consensus pattern (18 bp):
TCCTGTCTCTACTATCTC
Found at i:515076 original size:24 final size:24
Alignment explanation
Indices: 514997--515082 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
514987 CTTCCTCTCT
* * *
514997 CTATTATCTCTCCTGTCCCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
515021 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
515042 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
515063 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
515083 TCTTTCTCTT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 4 0.08
24 21 0.44
ACGTcount: A:0.10, C:0.47, G:0.02, T:0.41
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:519381 original size:158 final size:156
Alignment explanation
Indices: 519111--519564 Score: 563
Period size: 156 Copynumber: 2.9 Consensus size: 156
519101 TCAAAAGTAT
* * * * *
519111 TAATTAAATTTAATTTTATTTATTTTCGACAATACTATTTCGTACCCCAGTGGAAGCCCGAAAGG
1 TAATTCAATTTAATTTTATTTATTTTCGAAAATACCATTTCGTACCCTAATGGAAGCCCGAAAGG
* *
519176 ATACGAAATATTTTTGAAATCTTTTATACCTCTACGGATGCCAATAAGAATATAAAAGATTAGAC
66 ATACGAAATATTTTTGAAATCTTTTATACCCCTACGGATGCCCATAAGAATATAAAAGATTAGA-
519241 AAAAAAATAGAATTTATACC-GAAAATAC
130 AAAAAAATA-AATTTAT-CCTGAAAATAC
* ** * * * *
519269 TAATTCAATTTAATTTTAATTATTTTTAAAAATACCATTTCATACCCTAATGAAAGTCTGAAAGG
1 TAATTCAATTTAATTTTATTTATTTTCGAAAATACCATTTCGTACCCTAATGGAAGCCCGAAAGG
** *
519334 ATACGAAAGGTTTTTGAAATCTTTTATACCCCTACGGATGCCCATAAGAATATAAAAGATTATAA
66 ATACGAAATATTTTTGAAATCTTTTATACCCCTACGGATGCCCATAAGAATATAAAAGATTAGAA
* * *
519399 AAGAATTAAATTTATCCTGAAAATAT
131 AAAAAATAAATTTATCCTGAAAATAC
** * * ** *
519425 TAATTCACCTTAATTTTATTTACTTTCGAAAATAGCA-TTCGTACTTTAACTGGAAGCCCGAAAT
1 TAATTCAATTTAATTTTATTTATTTTCGAAAATACCATTTCGTACCCTAA-TGGAAGCCCGAAAG
* * * *
519489 GATACGAAATATTTTTGAAATCTTTTATACCCCTACAGATACCCATAGGAATATAAGAGATTA-A
65 GATACGAAATATTTTTGAAATCTTTTATACCCCTACGGATGCCCATAAGAATATAAAAGATTAGA
519553 AAAAATAATAAA
130 AAAAA-AATAAA
519565 CATGGAAATA
Statistics
Matches: 251, Mismatches: 42, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
155 16 0.06
156 116 0.46
157 7 0.03
158 112 0.45
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.33
Consensus pattern (156 bp):
TAATTCAATTTAATTTTATTTATTTTCGAAAATACCATTTCGTACCCTAATGGAAGCCCGAAAGG
ATACGAAATATTTTTGAAATCTTTTATACCCCTACGGATGCCCATAAGAATATAAAAGATTAGAA
AAAAAATAAATTTATCCTGAAAATAC
Found at i:521392 original size:12 final size:11
Alignment explanation
Indices: 521372--521396 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
521362 TTTTTTGAGT
521372 TTTTCAAAAAA
1 TTTTCAAAAAA
521383 TTTTCAAAAAA
1 TTTTCAAAAAA
521394 TTT
1 TTT
521397 CTAAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (11 bp):
TTTTCAAAAAA
Found at i:523295 original size:79 final size:79
Alignment explanation
Indices: 523000--523308 Score: 313
Period size: 79 Copynumber: 3.9 Consensus size: 79
522990 TGGAGATGAC
* * ** *
523000 AACGGGGCTGGAGTATCCCCTGACTAT-AGAAAATTGGCGTTTT-GAAAATAAAATCGGGGTTGG
1 AACGGGGTTGGAGTATCCCC-GATTATGA-AAAATTGATGTTTTAG-AAATAAAACCGGGGTTGG
* *
523063 AGTATCTCCTCGAAAAT
63 AGTATCCCCTCAAAAAT
* * * * ** *
523080 AACGGGGTTGAAGTATCCCCGATTATGGAAAATCGATGCTTTAGAAATAAGGCAGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGT
*
523145 AT-CCCTGCCAAAAT
66 ATCCCCT-CAAAAAT
* * * * * *
523159 AATGGGGTTGGAGTATCCCCGATTGTGAGAAA-TAATATTTTAGAAATAAAAGTCGGGGTTGGAG
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAA-CCGGGGTTGGAG
*
523223 AATCCCCTCAAAAAT
65 TATCCCCTCAAAAAT
* *
523238 AA-GGGGATTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGCTAGAG
1 AACGGGG-TTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAG
523302 TATCCCC
65 TATCCCC
523309 GAGATGAAAA
Statistics
Matches: 185, Mismatches: 37, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
78 20 0.11
79 125 0.68
80 40 0.22
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (79 bp):
AACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGT
ATCCCCTCAAAAAT
Found at i:523330 original size:50 final size:50
Alignment explanation
Indices: 523248--523371 Score: 167
Period size: 50 Copynumber: 2.5 Consensus size: 50
523238 AAGGGGATTG
* ** * *
523248 GAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGCTA
1 GAGTATCCCCGA-GATGAAAAATCAATATTTTAGAAATAAAACCGGAGCTA
* *
523299 GAGTATCCCCGAGATGAAAAATCAATATTTTAGAAATAAAGCCGGAGTTA
1 GAGTATCCCCGAGATGAAAAATCAATATTTTAGAAATAAAACCGGAGCTA
*
523349 GAGTATCCCCGAGATAAAAAATC
1 GAGTATCCCCGAGATGAAAAATC
523372 TAGAAGTTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 53 0.82
51 12 0.18
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.24
Consensus pattern (50 bp):
GAGTATCCCCGAGATGAAAAATCAATATTTTAGAAATAAAACCGGAGCTA
Found at i:526237 original size:7 final size:6
Alignment explanation
Indices: 526201--526253 Score: 52
Period size: 6 Copynumber: 8.0 Consensus size: 6
526191 GTTTTTACTA
*
526201 TTTTTC TTTTTT TTTCTTGC TTTTTC TTTTCTC TTTTCTC TATTTTC TTTTTC
1 TTTTTC TTTTTC TTT-TT-C TTTTTC TTTT-TC TTTT-TC T-TTTTC TTTTTC
526254 AGCTGAACAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 18 0.44
7 17 0.41
8 6 0.15
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTTTC
Found at i:534179 original size:22 final size:22
Alignment explanation
Indices: 534132--534194 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
534122 ATGTGAAAAT
*
534132 AAATTTTTTATAAAGGA--A-T
1 AAATTTTTTATAAAGGAGGAGA
* *
534151 AAATTTTTTATAACGGGGGAGA
1 AAATTTTTTATAAAGGAGGAGA
534173 AAATTTTTTATAAAGGAGGAGA
1 AAATTTTTTATAAAGGAGGAGA
534195 TAATCGTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
19 15 0.42
21 1 0.03
22 20 0.56
ACGTcount: A:0.43, C:0.02, G:0.21, T:0.35
Consensus pattern (22 bp):
AAATTTTTTATAAAGGAGGAGA
Found at i:534772 original size:13 final size:13
Alignment explanation
Indices: 534754--534780 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
534744 ACATGCTACT
534754 TTGTATCGATACA
1 TTGTATCGATACA
534767 TTGTATCGATACA
1 TTGTATCGATACA
534780 T
1 T
534781 GTTCACTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:534815 original size:20 final size:19
Alignment explanation
Indices: 534764--534820 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
534754 TTGTATCGAT
*
534764 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
* * *
534783 TCACTGCATCGATACATGG
1 ACATTGTATCGATACATGG
534802 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
534821 AAACTGGCAG
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:534886 original size:13 final size:13
Alignment explanation
Indices: 534865--534895 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
534855 CGATACATGG
*
534865 TACAATGTATCGA
1 TACATTGTATCGA
534878 TACATTGTATCGA
1 TACATTGTATCGA
534891 TACAT
1 TACAT
534896 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:534891 original size:33 final size:32
Alignment explanation
Indices: 534849--534915 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 32
534839 CTATCACTAT
534849 TTGTATCGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
534882 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
534915 T
1 T
534916 AGCTTGTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:536635 original size:167 final size:167
Alignment explanation
Indices: 536291--536636 Score: 393
Period size: 167 Copynumber: 2.1 Consensus size: 167
536281 TTTAGAAAAA
* * * *
536291 AAAAGGATTTCAAAGG--AAAAATTCCAAAATTTATGAAAATGAATTAATCTTTTAAAACTAATT
1 AAAAGAATTTC-AAGGAAAAAAATTCAAAAATTTATGAAAATGAATGAATCTTTTAAAACTAATA
** * * * *
536354 TAATATGAGTTAAAAGATGATATTTGATGAATTTTAAAAATTTTAAACCAAGAAAAATTCCCTCG
65 TAATATGAAATAAAAGATAATACTTGATGAATTTTAAAAATTTAAAACCAAGAAAAATTCCCTCC
* *
536419 AAAAAATTTACGGAGTAAAGAACACCTAATTTTGAAAT
130 AAAAAATTTACGGAGTAAAAAACACCTAATTTTGAAAC
*** * * *
536457 TGGAGAATTTCAAGGAAAAAAATTTAAAAATTTATGAAAATGAATGAATTTTTTAAAACTGATAT
1 AAAAGAATTTCAAGGAAAAAAATTCAAAAATTTATGAAAATGAATGAATCTTTTAAAACTAATAT
*
536522 AATATGAAATAAATA-ATAATACTTGATGAATTTTGAAAATTTAAAACCAAGAAAAA-T-CCTCC
66 AATATGAAATAAA-AGATAATACTTGATGAATTTTAAAAATTTAAAACCAAGAAAAATTCCCT-C
*
536584 CAAAAATTTTACGGAG-AAGAAAAC-CCATAA-TTTGAAAAC
129 CAAAAAATTTACGGAGTAA-AAAACACC-TAATTTTG-AAAC
536623 AAAAGAAATTTCAA
1 AAAAG-AATTTCAA
536637 AAGAAAATCA
Statistics
Matches: 149, Mismatches: 23, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
165 15 0.10
166 35 0.23
167 98 0.66
168 1 0.01
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (167 bp):
AAAAGAATTTCAAGGAAAAAAATTCAAAAATTTATGAAAATGAATGAATCTTTTAAAACTAATAT
AATATGAAATAAAAGATAATACTTGATGAATTTTAAAAATTTAAAACCAAGAAAAATTCCCTCCA
AAAAATTTACGGAGTAAAAAACACCTAATTTTGAAAC
Found at i:539648 original size:20 final size:19
Alignment explanation
Indices: 539625--539696 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
539615 CACACCCAGA
* *
539625 TGTATCGATACATTATGCTT
1 TGTATCGATACATGAT-CAT
539645 TGTATCGATACATGATCAT
1 TGTATCGATACATGATCAT
*
539664 TGTATCCATACATGGA-CAAT
1 TGTATCGATACAT-GATC-AT
539684 TGTATCGATACAT
1 TGTATCGATACAT
539697 TAAACTGGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 15 0.33
20 31 0.67
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGATCAT
Found at i:539755 original size:20 final size:20
Alignment explanation
Indices: 539730--539779 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
539720 CACCGTTTGC
*
539730 ATCGATACATGGT-ATATTGT
1 ATCGATACATGATGA-ATTGT
539750 ATCGATACATGATGAATTGT
1 ATCGATACATGATGAATTGT
539770 ATCGATACAT
1 ATCGATACAT
539780 TACTTGTAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (20 bp):
ATCGATACATGATGAATTGT
Found at i:541382 original size:9 final size:9
Alignment explanation
Indices: 541365--541398 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
541355 GTCAACCATC
541365 AATGATGAT
1 AATGATGAT
541374 GAA-GATGAT
1 -AATGATGAT
541383 AATGATGAT
1 AATGATGAT
541392 AATGATG
1 AATGATG
541399 GTGACTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.09
9 19 0.83
10 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.29
Consensus pattern (9 bp):
AATGATGAT
Found at i:546143 original size:20 final size:21
Alignment explanation
Indices: 546107--546145 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
546097 TTACAAATTT
*
546107 CTTCATTTTTACTTCAAAACA
1 CTTCATTTTTACATCAAAACA
546128 CTTCATTTTT-CATCAAAA
1 CTTCATTTTTACATCAAAA
546146 TGACCAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.44
Consensus pattern (21 bp):
CTTCATTTTTACATCAAAACA
Found at i:556592 original size:79 final size:79
Alignment explanation
Indices: 556430--556643 Score: 218
Period size: 79 Copynumber: 2.7 Consensus size: 79
556420 AATGTTCTAC
* ** *
556430 AAATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGCA-TCTATGATTATAGG
1 AAATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATTC-CCGATTATAGA
* * **
556494 AAGTTGGCATTTTTA
65 AAATTGGAAGCTTTA
* * *
556509 AAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATTCCCGATTGT-GAA
1 AAATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATTCCCGATTATAG-A
556573 AAATT-GAAGCTTTA
65 AAATTGGAAGCTTTA
*** * * * *
556587 GAAATAAGGCCGGGGTTGGAGTATCCCCGCCAAAATAACGGGGTTGGAGTATCCCCG
1 -AAATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATTCCCG
556644 CCAAAATAAC
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
78 7 0.06
79 104 0.92
80 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (79 bp):
AAATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATTCCCGATTATAGAA
AATTGGAAGCTTTA
Found at i:556631 original size:28 final size:28
Alignment explanation
Indices: 556597--556668 Score: 144
Period size: 28 Copynumber: 2.6 Consensus size: 28
556587 GAAATAAGGC
556597 CGGGGTTGGAGTATCCCCGCCAAAATAA
1 CGGGGTTGGAGTATCCCCGCCAAAATAA
556625 CGGGGTTGGAGTATCCCCGCCAAAATAA
1 CGGGGTTGGAGTATCCCCGCCAAAATAA
556653 CGGGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
556669 TCGATTGTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.25, C:0.24, G:0.32, T:0.19
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGCCAAAATAA
Found at i:556632 original size:107 final size:107
Alignment explanation
Indices: 556521--556746 Score: 289
Period size: 107 Copynumber: 2.1 Consensus size: 107
556511 ATAAAATCGA
* * * *
556521 GGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATTCC-CGATTGTGAAAAATTGAA-GCT
1 GGTTGGAGTATCCCCGCCAAAATAACAGGGTTGGAGTA-TCCTCGATTGTGAAAAA-TCAATACT
* *
556584 TTAGAAATAAGGC-CGGGGTTGGAGTATCCCCGCCA-AAATAACGG
64 TTAGAAATAA-ACTCGGGGTTAGAGTAT-CCCGCCAGAAATAACGG
* * *
556628 GGTTGGAGTATCCCCGCCAAAATAACGGGGTTGGAGTATCCTCGATTGTGAGAAATCAATATTTT
1 GGTTGGAGTATCCCCGCCAAAATAACAGGGTTGGAGTATCCTCGATTGTGAAAAATCAATACTTT
**
556693 AGAAATAAACTCGGGGTTAGAGTATCCCTTCAGAAATAACGG
66 AGAAATAAACTCGGGGTTAGAGTATCCCGCCAGAAATAACGG
556735 GGTTGGAGTATC
1 GGTTGGAGTATC
556747 TTCGTTTATG
Statistics
Matches: 104, Mismatches: 11, Indels: 8
0.85 0.09 0.07
Matches are distributed among these distances:
106 12 0.12
107 92 0.88
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (107 bp):
GGTTGGAGTATCCCCGCCAAAATAACAGGGTTGGAGTATCCTCGATTGTGAAAAATCAATACTTT
AGAAATAAACTCGGGGTTAGAGTATCCCGCCAGAAATAACGG
Found at i:556708 original size:79 final size:79
Alignment explanation
Indices: 556625--556800 Score: 230
Period size: 79 Copynumber: 2.2 Consensus size: 79
556615 GCCAAAATAA
* * *
556625 CGGGGTTGGAGTATCCCCGCCA-AAATAACGGGGTTGGAGTATCCTCGATTGTGAGAAATCAATA
1 CGGGGTTAGAGTATCCCCGCCAGAAATAACGGGGTTGGAGTATCCTCGATTATGAAAAATCAATA
*
556689 TTTTAGAAATAAAC
66 TTTTAGAAAAAAAC
** * * **
556703 TCGGGGTTAGAGTAT-CCCTTCAGAAATAACGGGGTTGGAGTATCTTCGTTTATGAAAAATTGAT
1 -CGGGGTTAGAGTATCCCCGCCAGAAATAACGGGGTTGGAGTATCCTCGATTATGAAAAATCAAT
*
556767 GTTTTAGAAAAAAAC
65 ATTTTAGAAAAAAAC
556782 CGGGGTTAGAGTATCCCCG
1 CGGGGTTAGAGTATCCCCG
556801 AGATGAAAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
78 19 0.23
79 64 0.77
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (79 bp):
CGGGGTTAGAGTATCCCCGCCAGAAATAACGGGGTTGGAGTATCCTCGATTATGAAAAATCAATA
TTTTAGAAAAAAAC
Found at i:556821 original size:49 final size:50
Alignment explanation
Indices: 556754--556862 Score: 157
Period size: 50 Copynumber: 2.2 Consensus size: 50
556744 ATCTTCGTTT
** * *
556754 ATGAAAAATTGATGTTTTAGAAA-AAAACCGGGGTTAGAGTATCCCCGAG
1 ATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTAGAGTATCCCCAAG
* *
556803 ATGAAAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCAAG
1 ATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTAGAGTATCCCCAAG
556853 ATGAAAAATC
1 ATGAAAAATC
556863 TAGAAATTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
49 20 0.38
50 33 0.62
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.24
Consensus pattern (50 bp):
ATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTAGAGTATCCCCAAG
Found at i:557892 original size:13 final size:13
Alignment explanation
Indices: 557874--557898 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
557864 CATAAAGTGT
557874 TGTATCGATACAA
1 TGTATCGATACAA
557887 TGTATCGATACA
1 TGTATCGATACA
557899 TATTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:557981 original size:13 final size:13
Alignment explanation
Indices: 557963--557987 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
557953 ATTACTCAAA
557963 TGTATCGATACAT
1 TGTATCGATACAT
557976 TGTATCGATACA
1 TGTATCGATACA
557988 CTAATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:563415 original size:40 final size:41
Alignment explanation
Indices: 563369--563722 Score: 206
Period size: 42 Copynumber: 8.5 Consensus size: 41
563359 AAGGAAGGGA
**
563369 GCGTCCTGCTCTTTGAGGATTAAGGAAAAAGAGAA-AAAAT
1 GCGTCCTGCTCTTTGAGGACAAAGGAAAAAGAGAATAAAAT
* * * *
563409 GGGTCCTGCTCCTTGGGGACTAAGGAAAAA-AGGAAATAAAAT
1 GCGTCCTGCTCTTTGAGGACAAAGGAAAAAGA-G-AATAAAAT
* * * * * *
563451 GCATCCTACCCTTCGAAGACAAAGGAAAAAG-GAAATTAAAT
1 GCGTCCTGCTCTTTGAGGACAAAGGAAAAAGAG-AATAAAAT
* * * *
563492 GTGTCCTGCTTTTTGAGGACAAAGAAGAAAAGAGAATAAAGT
1 GCGTCCTGCTCTTTGAGGACAAAGGA-AAAAGAGAATAAAAT
* * * *
563534 -CTGTCTTGCTCTTTTAGAACTAGAAGGGAAAAGAAGGAAATAAAAT
1 GC-GTCCTGCTCTTTGAGGAC-A-AAGGAAAAAG-A-G-AATAAAAT
* * *
563580 GCGTCCTGCTTTTTGAGGATAAAGGAAAATAGA-AA-AAAAG
1 GCGTCCTGCTCTTTGAGGACAAAGGAAAA-AGAGAATAAAAT
* * * *
563620 GCATCGTGCTCTTTGAGGACAAAAGGGAAAAAAAGGAAATGAAAT
1 GCGTCCTGCTCTTTGAGGAC-AAA-GGAAAAAGA-G-AATAAAAT
* * * * *
563665 GTGTCATGGTCTTTGAGGACAAA-G---AAGAGAAGGAAAAG
1 GCGTCCTGCTCTTTGAGGACAAAGGAAAAAGAGAA-TAAAAT
563703 GCGTCCTGCTCTTTGAGGAC
1 GCGTCCTGCTCTTTGAGGAC
563723 TAAAAAGTGT
Statistics
Matches: 236, Mismatches: 57, Indels: 44
0.70 0.17 0.13
Matches are distributed among these distances:
37 2 0.01
38 21 0.09
39 4 0.02
40 47 0.20
41 36 0.15
42 58 0.25
43 7 0.03
44 17 0.07
45 23 0.10
46 20 0.08
47 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.26, T:0.21
Consensus pattern (41 bp):
GCGTCCTGCTCTTTGAGGACAAAGGAAAAAGAGAATAAAAT
Found at i:563513 original size:41 final size:41
Alignment explanation
Indices: 563369--563722 Score: 222
Period size: 41 Copynumber: 8.5 Consensus size: 41
563359 AAGGAAGGGA
**
563369 GCGTCCTGCTCTTTGAGGATTAAGGAAAAA-GAGAA-AAAAT
1 GCGTCCTGCTCTTTGAGGACAAAGGAAAAAGGA-AATAAAAT
* * * *
563409 GGGTCCTGCTCCTTGGGGACTAAGGAAAAAAGGAAATAAAAT
1 GCGTCCTGCTCTTTGAGGACAAAGG-AAAAAGGAAATAAAAT
* * * * * *
563451 GCATCCTACCCTTCGAAGACAAAGGAAAAAGGAAATTAAAT
1 GCGTCCTGCTCTTTGAGGACAAAGGAAAAAGGAAATAAAAT
* * * *
563492 GTGTCCTGCTTTTTGAGGACAAA-GAAGAAAAGAGAATAAAGT
1 GCGTCCTGCTCTTTGAGGACAAAGGAA-AAAGGA-AATAAAAT
* * *
563534 -CTGTCTTGCTCTTTTAGAACTAGAAGGGAAAAGAAGGAAATAAAAT
1 GC-GTCCTGCTCTTTGAGGAC-A-AA-GG-AAA-AAGGAAATAAAAT
* * *
563580 GCGTCCTGCTTTTTGAGGATAAAGGAAAATA-GAAA-AAAAG
1 GCGTCCTGCTCTTTGAGGACAAAGGAAAA-AGGAAATAAAAT
* * *
563620 GCATCGTGCTCTTTGAGGACAAAAGGGAAAAAAAGGAAATGAAAT
1 GCGTCCTGCTCTTTGAGGAC-AAA-GG--AAAAAGGAAATAAAAT
* * * * ** *
563665 GTGTCATGGTCTTTGAGGACAAA-G-AAGA-GAAGGAAAAG
1 GCGTCCTGCTCTTTGAGGACAAAGGAAAAAGGAAATAAAAT
563703 GCGTCCTGCTCTTTGAGGAC
1 GCGTCCTGCTCTTTGAGGAC
563723 TAAAAAGTGT
Statistics
Matches: 239, Mismatches: 55, Indels: 42
0.71 0.16 0.12
Matches are distributed among these distances:
38 23 0.10
39 3 0.01
40 44 0.18
41 51 0.21
42 50 0.21
43 4 0.02
44 15 0.06
45 20 0.08
46 22 0.09
47 7 0.03
ACGTcount: A:0.40, C:0.13, G:0.26, T:0.21
Consensus pattern (41 bp):
GCGTCCTGCTCTTTGAGGACAAAGGAAAAAGGAAATAAAAT
Found at i:563680 original size:85 final size:85
Alignment explanation
Indices: 563476--563727 Score: 267
Period size: 85 Copynumber: 2.9 Consensus size: 85
563466 AAGACAAAGG
* * * *
563476 AAAAAGGAAATTAAATGTGTCCTGCTTTTTGAGGACAAAGAAGAAAAGAGAATAAAGTCTGTCTT
1 AAAAAGGAAATAAAATGTGTCCTGCTTTTTGAGGACAAAGAA-AAAAGA-AAAAAAGGC-GTCCT
* * *
563541 GCTCTTTTAGAACTAGAAGGGAA
63 GCTCTTTGAGGACTAAAAGGGAA
* * * * * *
563564 AAGAAGGAAATAAAATGCGTCCTGCTTTTTGAGGATAAAGGAAAATAGAAAAAAAGGCATCGTGC
1 AAAAAGGAAATAAAATGTGTCCTGCTTTTTGAGGACAAA-GAAAAAAGAAAAAAAGGCGTCCTGC
563629 TCTTTGAGGAC-AAAAGGGAA
65 TCTTTGAGGACTAAAAGGGAA
* * * * * *
563649 AAAAAGGAAATGAAATGTGTCATGGTCTTTGAGGACAAAG--AAGAGAAGGAAAAGGCGTCCTGC
1 AAAAAGGAAATAAAATGTGTCCTGCTTTTTGAGGACAAAGAAAAAAGAA-AAAAAGGCGTCCTGC
563712 TCTTTGAGGACTAAAA
65 TCTTTGAGGACTAAAA
563728 AGTGTTACCA
Statistics
Matches: 138, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
82 6 0.04
83 23 0.17
84 5 0.04
85 40 0.29
86 14 0.10
87 7 0.05
88 40 0.29
89 3 0.02
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.22
Consensus pattern (85 bp):
AAAAAGGAAATAAAATGTGTCCTGCTTTTTGAGGACAAAGAAAAAAGAAAAAAAGGCGTCCTGCT
CTTTGAGGACTAAAAGGGAA
Found at i:563799 original size:61 final size:61
Alignment explanation
Indices: 563694--564244 Score: 639
Period size: 61 Copynumber: 9.1 Consensus size: 61
563684 CAAAGAAGAG
** * ** **
563694 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGTTACCAACTCATGTGGGCTTTGAA
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT-AA
*
563756 AA-GAAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCA
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT-AA
* * *
563817 AA-GAGAAA-GCATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTCAA
1 AAGGA-AAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAA
* * * * * * * * *
563877 AGGGAGAAGGCGTCCTGCTCCTTGAAGATTGAAAAGTGCCACCAACTTGTGCGGTCTTTAA
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAA
* * *
563938 AAGGAGAAA-GCATCCTGCTC-TTGAGGACTAGAAGGTGCCACCAATTTGTGTGGGCTTTAA
1 AAGGA-AAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAA
* * * *
563998 AAGGAAAAGGCGTCTTGCTCTTTAAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAA
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GGAAGGTGCCACCAACTTGTGTGGGCTTTAA
* * **
564060 AAGGAAAAGGTGTCCTACTCTTTGAGGACT-GAAGGCCCCACCAACTTGTGTGGGCTTTAA
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAA
*** * *
564120 AAGGAAAAATTGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAA
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAA
* ** * *
564181 AAGGAAAAGGCATCCTGCTCTTTGAGGA-TTAAAGGTGCCACCAGCTTGTGTGGGCTTTGA
1 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAA
564241 AAGG
1 AAGG
564245 CATCTTGCTC
Statistics
Matches: 416, Mismatches: 65, Indels: 18
0.83 0.13 0.04
Matches are distributed among these distances:
59 3 0.01
60 134 0.32
61 219 0.53
62 60 0.14
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (61 bp):
AAGGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAA
Found at i:564137 original size:243 final size:243
Alignment explanation
Indices: 563694--564244 Score: 693
Period size: 243 Copynumber: 2.3 Consensus size: 243
563684 CAAAGAAGAG
* * ** **
563694 AAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGTTACCAACTCATGTGGGCTTTGAAAA-
1 AAGGAAAAGGCATCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG
* * * *
563758 GAAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGA
64 GAAAAGGCGTCCTGCTCTTTAAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAGA
* ** * * *
563823 AAGCATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTCAAAGGGAGAAGGC
129 AAGCATCCTACTCTTTGAGGACTGGAAGGCCCCACCAACTTGTGTAGGCTTCAAAAGGAAAAAGC
* *
563888 GTCCTGCTCCTTGAAGA-TTGAAAAGTGCCACCAACTTGTGCGGTCTTTAA
194 GTCCTGCTCCTTGAAGACTAG-AAAGTGCCACCAACTTGTGCGGGCTTTAA
*
563938 AAGGAGAAA-GCATCCTGCTC-TTGAGGACTAGAAGGTGCCACCAATTTGTGTGGGCTTTAAAAG
1 AAGGA-AAAGGCATCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
*
564001 GAAAAGGCGTCTTGCTCTTTAAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAG-G
64 GAAAAGGCGTCCTGCTCTTTAAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAG
** * *
564064 AAAAGGTGTCCTACTCTTTGAGGACT-GAAGGCCCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
128 -AAA-GCATCCTACTCTTTGAGGACTGGAAGGCCCCACCAACTTGTGTAGGCTTCAAAAGGAAAA
** * * *
564128 ATTGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAA
191 AGCGTCCTGCTCCTTGAAGACTAGAAAGTGCCACCAACTTGTGCGGGCTTTAA
* * *
564181 AAGGAAAAGGCATCCTGCTCTTTGAGGATTAAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAGG
1 AAGGAAAAGGCATCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG
564245 CATCTTGCTC
Statistics
Matches: 265, Mismatches: 33, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
242 9 0.03
243 182 0.69
244 71 0.27
245 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (243 bp):
AAGGAAAAGGCATCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
AAAGGCGTCCTGCTCTTTAAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAGAAA
GCATCCTACTCTTTGAGGACTGGAAGGCCCCACCAACTTGTGTAGGCTTCAAAAGGAAAAAGCGT
CCTGCTCCTTGAAGACTAGAAAGTGCCACCAACTTGTGCGGGCTTTAA
Found at i:564301 original size:55 final size:54
Alignment explanation
Indices: 564132--564323 Score: 181
Period size: 55 Copynumber: 3.4 Consensus size: 54
564122 GGAAAAATTG
* * *
564132 TCCTGCTCTTTGAGGACTAGAA-AGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGATTA-AAGA-TACCACCAACTGGTGTGGGCTTT-----G-AAAGGCA
* * * *
564193 TCCTGCTCTTTGAGGATTAAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAGGCA
1 TCCTGCTCTTTGAGGATTAAAGATACCACCAACTGGTGTGGGCTTTGAAAGGCA
* *
564247 TCTTGCTCTTTGAGGATTGGAAA-ATACCACCAACTGGTGTGGGTTTTGAAAGGCA
1 TCCTGCTCTTTGAGGATT--AAAGATACCACCAACTGGTGTGGGCTTTGAAAGGCA
* *
564302 TCCTACTCTTTGAGGACTAAAG
1 TCCTGCTCTTTGAGGATTAAAG
564324 GGTGAAAGGA
Statistics
Matches: 115, Mismatches: 12, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
53 3 0.03
54 24 0.21
55 43 0.37
56 3 0.03
60 24 0.21
61 18 0.16
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.29
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGATTAAAGATACCACCAACTGGTGTGGGCTTTGAAAGGCA
Found at i:565417 original size:1 final size:1
Alignment explanation
Indices: 565397--565449 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
565387 AAGCAGGTTC
* * * * * *
565397 TTTTCTTTTCTTTCTTTTTTTTTCTTTTTTTTTTTATTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
565450 AAAAAAGAAG
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.02, C:0.08, G:0.02, T:0.89
Consensus pattern (1 bp):
T
Found at i:565421 original size:19 final size:17
Alignment explanation
Indices: 565397--565449 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 17
565387 AAGCAGGTTC
565397 TTTTCTTTTCTTTCTTTTT
1 TTTTCTTTT-TTT-TTTTT
565416 TTTTCTTTTTTTTTTTAT
1 TTTTCTTTTTTTTTTT-T
565434 TTTT-TTTGTTTTTTTT
1 TTTTCTTT-TTTTTTTT
565450 AAAAAAGAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.22
18 16 0.50
19 9 0.28
ACGTcount: A:0.02, C:0.08, G:0.02, T:0.89
Consensus pattern (17 bp):
TTTTCTTTTTTTTTTTT
Found at i:565429 original size:10 final size:10
Alignment explanation
Indices: 565397--565449 Score: 63
Period size: 10 Copynumber: 5.3 Consensus size: 10
565387 AAGCAGGTTC
565397 TTTTC-TTTT
1 TTTTCTTTTT
*
565406 CTTTCTTTTT
1 TTTTCTTTTT
565416 TTTTCTTTTT
1 TTTTCTTTTT
*
565426 TTTTTTATTTT
1 TTTTCT-TTTT
*
565437 TTTTGTTTTT
1 TTTTCTTTTT
565447 TTT
1 TTT
565450 AAAAAAGAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
9 4 0.11
10 25 0.66
11 9 0.24
ACGTcount: A:0.02, C:0.08, G:0.02, T:0.89
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:574170 original size:79 final size:79
Alignment explanation
Indices: 574067--574412 Score: 330
Period size: 79 Copynumber: 4.4 Consensus size: 79
574057 ATTGGTGCTC
* * * * **
574067 TAGAAATAAAATCGGGGTTAGAGTATCCCCTCGAAAATAACAGGGTTAGAGTATCCTTGATTAT-
1 TAGAAATAAAACCGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATTATG
574131 AGGAAATCGATATTT
66 A-GAAATCGATATTT
* *
574146 T-GAAAATAAAATCGAGGTTGGAGTATCCCCTTGAAAATAACAGGGTTGGAGTATCCCCGATTAT
1 TAG-AAATAAAACCGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATTAT
* *
574210 G-GAAAATCGAAACTT
65 GAG-AAATCGATATTT
** * * * ** *
574225 TAGAAATAAGGCCG-GCGTTGGAGTATCCCCGCCAAAATAACAAGGTTGGAGTATCCTTGATTGT
1 TAGAAATAAAACCGAG-GTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATTAT
*
574289 GAGAAATCAATATTT
65 GAGAAATCGATATTT
* * *
574304 TAGAAATAAAGCC-ATGGTTGGAGTATCCTCTC-AGAAATAAC-GGGATTGAAGTATCCCCGATT
1 TAGAAATAAAACCGA-GGTTGGAGTATCCCCTCGA-AAATAACAGGG-TTGGAGTATCCCCGATT
* *
574366 ATGAAAAATTGATGATTT
63 ATGAGAAATCGAT-ATTT
* *
574384 T-GTAATAAAACCGAGGTTAGAGTATCCCC
1 TAGAAATAAAACCGAGGTTGGAGTATCCCC
574413 GAGATGAAAA
Statistics
Matches: 219, Mismatches: 36, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
78 6 0.03
79 204 0.93
80 9 0.04
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (79 bp):
TAGAAATAAAACCGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATTATG
AGAAATCGATATTT
Found at i:574183 original size:31 final size:28
Alignment explanation
Indices: 574145--574203 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 28
574135 AATCGATATT
574145 TTGAAAATAAAATCGAGGTTGGAGTATCCCC
1 TTGAAAATAAAA--G-GGTTGGAGTATCCCC
*
574176 TTGAAAATAACAGGGTTGGAGTATCCCC
1 TTGAAAATAAAAGGGTTGGAGTATCCCC
574204 GATTATGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 15 0.56
29 1 0.04
31 11 0.41
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (28 bp):
TTGAAAATAAAAGGGTTGGAGTATCCCC
Found at i:574391 original size:158 final size:158
Alignment explanation
Indices: 574067--574413 Score: 393
Period size: 158 Copynumber: 2.2 Consensus size: 158
574057 ATTGGTGCTC
* * * * *
574067 TAGAAATAAAATCGGGGTTAGAGTATCCCCTCGAAAATAACAGGGTTAGAGTATCCTTGATTATA
1 TAGAAATAAAACCGAGGTTAGAGTATCCCCGCCAAAATAACAAGGTTAGAGTATCCTTGATTATA
* * * * *
574132 GGAAATCGATATTTTGAAAATAAAATCGAGGTTGGAGTATCCCCTTGAAAATAACAGGGTTGGAG
66 GGAAATCAATATTTTGAAAATAAAAGCCAGGTTGGAGTATCCCCTAGAAAATAACAGGGTTGAAG
*
574197 TATCCCCGATTATGGAAAATCGAAACTT
131 TATCCCCGATTATGAAAAATCGAAACTT
** * * *
574225 TAGAAATAAGGCCG-GCGTTGGAGTATCCCCGCCAAAATAACAAGGTTGGAGTATCCTTGATTGT
1 TAGAAATAAAACCGAG-GTTAGAGTATCCCCGCCAAAATAACAAGGTTAGAGTATCCTTGATTAT
*
574289 -GAGAAATCAATATTTT-AGAAAT-AAAGCCATGGTTGGAGTATCCTCTCAG-AAATAAC-GGGA
65 AG-GAAATCAATATTTTGA-AAATAAAAGCCA-GGTTGGAGTATCCCCT-AGAAAATAACAGGG-
* *
574349 TTGAAGTATCCCCGATTATGAAAAATTGATGA-TT
125 TTGAAGTATCCCCGATTATGAAAAATCGA-AACTT
* *
574383 TTGTAATAAAACCGAGGTTAGAGTATCCCCG
1 TAGAAATAAAACCGAGGTTAGAGTATCCCCG
574414 AGATGAAAAA
Statistics
Matches: 158, Mismatches: 23, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
157 11 0.07
158 144 0.91
159 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.27
Consensus pattern (158 bp):
TAGAAATAAAACCGAGGTTAGAGTATCCCCGCCAAAATAACAAGGTTAGAGTATCCTTGATTATA
GGAAATCAATATTTTGAAAATAAAAGCCAGGTTGGAGTATCCCCTAGAAAATAACAGGGTTGAAG
TATCCCCGATTATGAAAAATCGAAACTT
Found at i:576854 original size:62 final size:63
Alignment explanation
Indices: 576757--576884 Score: 179
Period size: 62 Copynumber: 2.0 Consensus size: 63
576747 AAAATGCCTG
*
576757 AATGTATCGATACATTAAAAAATTTATCAATACATCTAGGT-AAACCCAGAATGTATCAATAC
1 AATGTATCGATACATTAAAAAATGTATCAATACATCTAGGTAAAACCCAGAATGTATCAATAC
** * * *
576819 AATGTATCGATACAATT-AACGATGTATCGATACATCTGGGTAAAACCCAGAATGTATCGATAC
1 AATGTATCGATAC-ATTAAAAAATGTATCAATACATCTAGGTAAAACCCAGAATGTATCAATAC
576882 AAT
1 AAT
576885 AAATAATGTA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
62 32 0.55
63 26 0.45
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.28
Consensus pattern (63 bp):
AATGTATCGATACATTAAAAAATGTATCAATACATCTAGGTAAAACCCAGAATGTATCAATAC
Found at i:580167 original size:31 final size:31
Alignment explanation
Indices: 580106--580169 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
580096 CTTTAGTTTT
* *
580106 AAAATGACAAAAACAAAAAAAACGTTATAAA
1 AAAATGACAAAAACAAAAAAAACATAATAAA
580137 AAAATGA-AAAAATCGAAAAAAAA-ATAATAAA
1 AAAATGACAAAAA-C-AAAAAAAACATAATAAA
580168 AA
1 AA
580170 CAAATCAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 5 0.17
31 16 0.55
32 8 0.28
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.12
Consensus pattern (31 bp):
AAAATGACAAAAACAAAAAAAACATAATAAA
Found at i:584409 original size:52 final size:52
Alignment explanation
Indices: 584325--584498 Score: 303
Period size: 52 Copynumber: 3.3 Consensus size: 52
584315 TGAAACTTTA
* * * * *
584325 CCTGCATGTATCGATACATTTAATAGTATATCGACACATCTGGGTAAATTTG
1 CCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTG
584377 CCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTG
1 CCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTG
584429 CCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTG
1 CCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTG
584481 CCTGCATGTATCGATACA
1 CCTGCATGTATCGATACA
584499 AAGATCAGTG
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 117 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
CCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTG
Found at i:584511 original size:104 final size:104
Alignment explanation
Indices: 584325--584518 Score: 291
Period size: 104 Copynumber: 1.9 Consensus size: 104
584315 TGAAACTTTA
* *
584325 CCTGCATGTATCGATACATTTAATAGTATATCGACACATCTGGGTAAATTTGCCTGCATGTATCG
1 CCTGCATGTATCGATACATTTAATAATATATCGACACATCTGGGCAAATTTGCCTGCATGTATCG
***
584390 ATACATTTTATAATGTATCGATACATCTGGGCAAATTTG
66 ATACATAAGATAATGTATCGATACATCTGGGCAAATTTG
* * *
584429 CCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCG
1 CCTGCATGTATCGATACATTTAATAATATATCGACACATCTGGGCAAATTTGCCTGCATGTATCG
*
584494 ATACA-AAGATCAGTGTATCGATACA
66 ATACATAAGAT-AATGTATCGATACA
584519 ATGTATCGAT
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
103 2 0.03
104 78 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (104 bp):
CCTGCATGTATCGATACATTTAATAATATATCGACACATCTGGGCAAATTTGCCTGCATGTATCG
ATACATAAGATAATGTATCGATACATCTGGGCAAATTTG
Found at i:584525 original size:13 final size:13
Alignment explanation
Indices: 584507--584531 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
584497 CAAAGATCAG
584507 TGTATCGATACAA
1 TGTATCGATACAA
584520 TGTATCGATACA
1 TGTATCGATACA
584532 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:584599 original size:22 final size:22
Alignment explanation
Indices: 584574--584629 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
584564 TAGCTTAAAT
584574 TGTATCGATACAAAAAAATATA
1 TGTATCGATACAAAAAAATATA
* * *
584596 TGTATCGATAC--AACACTTTA
1 TGTATCGATACAAAAAAATATA
584616 TGTATCGATACAAA
1 TGTATCGATACAAA
584630 TCGTTGAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 17 0.59
22 12 0.41
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (22 bp):
TGTATCGATACAAAAAAATATA
Found at i:585641 original size:92 final size:92
Alignment explanation
Indices: 585447--586556 Score: 1669
Period size: 92 Copynumber: 12.0 Consensus size: 92
585437 AGGATAAGAA
* *
585447 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGTAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG---AAGGTGCCAAT
* * *
585512 ATGTTGATTCAAGGCCAACTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCGATATTGGACTT
*
585543 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
585608 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
*
585635 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
585700 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
*
585727 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
585792 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
*
585819 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
585884 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
*
585911 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
585976 TGATTCAAGGCCAGCGATAATGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
586003 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
586068 TGATTCAAGGCCAGCTATATTAGG-CTT
66 TGATTCAAGGCCAGCGATATT-GGACTT
* *
586095 AGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* *
586160 TGATTCAAGGCCAGCTATATTGAACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * *
586187 AAAGGTGCGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGT-CAGGTGCCAATGT
1 AAAGGT--GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATAT
* *
586251 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
64 GCTGATTCAAGGCCAGCGATATTGGAC-T-----T
* * * * *
586286 AAAGGTGCCAATATGCTGATTTAAGGCCAGCTATAATGGACTT----A--AAGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* * *
586345 TGAGTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * *
586372 AAAGGTGAGGTGCCAATGTGCTGATTCAAGGCCAACTGCATTGGAATTAAAGATGAAGGTGCCAA
1 -AA----AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAA
* *
586437 TATGCTGATTCAGGGCTAGCGATATTGGACTT
61 TATGCTGATTCAAGGCCAGCGATATTGGACTT
* *
586469 AAAGGTGCCAATGTGCTGTTTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
586534 TGATTCAAGGCCAGCTATATTGG
66 TGATTCAAGGCCAGCGATATTGG
586557 GTTTAGAAGG
Statistics
Matches: 945, Mismatches: 48, Indels: 46
0.91 0.05 0.04
Matches are distributed among these distances:
86 1 0.00
87 2 0.00
91 36 0.04
92 699 0.74
93 38 0.04
94 42 0.04
95 44 0.05
96 7 0.01
97 69 0.07
99 7 0.01
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTT
Found at i:586236 original size:22 final size:22
Alignment explanation
Indices: 586211--586283 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
586201 GTGCTGATTC
586211 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTACATTGGACTTA
* * * *
586233 AAGGTCAGGTGCCAATGTGCTGA-TTC
1 AAGGCCAGCT-AC-AT-TG--GACTTA
586259 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTACATTGGACTTA
586281 AAG
1 AAG
586284 ATAAAGGTGC
Statistics
Matches: 37, Mismatches: 8, Indels: 12
0.65 0.14 0.21
Matches are distributed among these distances:
21 2 0.05
22 13 0.35
23 3 0.08
24 4 0.11
25 3 0.08
26 10 0.27
27 2 0.05
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (22 bp):
AAGGCCAGCTACATTGGACTTA
Found at i:586604 original size:33 final size:33
Alignment explanation
Indices: 586561--586763 Score: 299
Period size: 33 Copynumber: 6.2 Consensus size: 33
586551 TATTGGGTTT
586561 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
586594 AGAATGGTTGCCACCAACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
586627 AG-AGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
586659 AAGAA-GGTTGCCACAGACTTGTGTGGGCTTTAG
1 -AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
586692 -GAAGAAGGTTGCCACCAACTTGTGTGGGCTTTAG
1 AGAAG--GGTTGCCACCGACTTGTGTGGGCTTTAG
586726 -GAAGGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
586757 GGAAGGG
1 AGAAGGG
586764 AGAAAGATGC
Statistics
Matches: 156, Mismatches: 8, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
31 4 0.03
32 59 0.38
33 62 0.40
34 31 0.20
ACGTcount: A:0.20, C:0.17, G:0.36, T:0.27
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:586639 original size:65 final size:64
Alignment explanation
Indices: 586554--586755 Score: 295
Period size: 65 Copynumber: 3.1 Consensus size: 64
586544 CCAGCTATAT
586554 TGGG-TTTAGA-AGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAATGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAA-GGTTGCCACCAACTTGTG
586617 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAGAAGGTTGCCA-CAGACTTGT
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAG-AGAAGGTTGCCACCA-ACTTGT
586681 G
64 G
* * *
586682 TGGGCTTTAGGAAGAAGGTTGCCACCAACTTGTGTGGGCTTTAG-GAAGGGTTGCCACCGACTTG
1 TGGGCTTTA-G-AGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAA-GGTTGCCACCAACTTG
586746 TG
63 TG
586748 TGGGCTTT
1 TGGGCTTT
586756 GGGAAGGGAG
Statistics
Matches: 128, Mismatches: 3, Indels: 13
0.89 0.02 0.09
Matches are distributed among these distances:
63 4 0.03
64 8 0.06
65 57 0.45
66 28 0.22
67 31 0.24
ACGTcount: A:0.19, C:0.17, G:0.35, T:0.29
Consensus pattern (64 bp):
TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGTTGCCACCAACTTGTG
Found at i:586732 original size:99 final size:96
Alignment explanation
Indices: 586554--586755 Score: 329
Period size: 99 Copynumber: 2.1 Consensus size: 96
586544 CCAGCTATAT
*
586554 TGGG-TTTAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAATGGTTGCCACCAACTTGTGT
1 TGGGCTTTAGAAGGGTTGCCACAGACTTGTGTGGGCTTTAGAGAATGGTTGCCACCAACTTGTGT
586618 GGGCTTTAGAGAGGGTTGCCACCGACTTGTG
66 GGGCTTTAGAGAGGGTTGCCACCGACTTGTG
586649 TGGGCTTTAGAAGAAGGTTGCCACAGACTTGTGTGGGCTTTAGGAAGAA-GGTTGCCACCAACTT
1 TGGGCTTTAGAAG--GGTTGCCACAGACTTGTGTGGGCTTTA-G-AGAATGGTTGCCACCAACTT
586713 GTGTGGGCTTTAG-GAAGGGTTGCCACCGACTTGTG
62 GTGTGGGCTTTAGAG-AGGGTTGCCACCGACTTGTG
586748 TGGGCTTT
1 TGGGCTTT
586756 GGGAAGGGAG
Statistics
Matches: 100, Mismatches: 1, Indels: 8
0.92 0.01 0.07
Matches are distributed among these distances:
95 4 0.04
96 8 0.08
98 27 0.27
99 57 0.57
100 4 0.04
ACGTcount: A:0.19, C:0.17, G:0.35, T:0.29
Consensus pattern (96 bp):
TGGGCTTTAGAAGGGTTGCCACAGACTTGTGTGGGCTTTAGAGAATGGTTGCCACCAACTTGTGT
GGGCTTTAGAGAGGGTTGCCACCGACTTGTG
Found at i:586804 original size:34 final size:34
Alignment explanation
Indices: 586766--588029 Score: 1060
Period size: 34 Copynumber: 37.8 Consensus size: 34
586756 GGGAAGGGAG
* *
586766 AAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAA-GGAA
* *
586800 AAAGAGTGCCACGGAGTTGTGCGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
586835 AACGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
586869 AAAGGTGCCACGGAGTTATGGGCTTTGAAAA-AAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGAA
*
586903 AAAGGTTGCCACGGAATTGTGGGCTTTAAAA-G--
1 AAAGG-TGCCACGGAGTTGTGGGCTTTAAAAGGAA
* * *
586935 ---GGTGCCACGGAGTTGTGGACTTAAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
*
586966 AAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-GGAA
* *
587002 AAAGAATGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
587037 AAA-GTGCCACGGAGTGGTGGGCTTTGAGAA-GAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGAA
* * *
587070 AAATGTTGCCACGGAATTGTGGGTTTTAAAA-G--
1 AAA-GGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* * *
587102 ---GGTACCACAGAGTTGTGGAC-TTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* * *
587132 CAAGGTGCCACGGAGTTGTGGACTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
587166 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-GG-AA
*
587203 AAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-GG-AA
*
587240 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGAA
*
587275 AAAGGTGCCACGGAGTTATGGGCTTTGAAAA-G--
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGAA
* *
587307 -AAGGTGCCACGGAGTCGTGGAC-TTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* * * *
587339 CAAGGTGCCACGGGGTTGTGGACTTTAAAAGGGGA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAA-GGAA
* *
587374 AAAGAGTGCCACAGAGTTGTGGAC-TT---A-G--
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* * * * *
587402 AAGGGTGCCATGGAATTATGGAC-TTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAA-GGAA
* * *
587436 AAAGAGTGACACAGAGTTGTGGGCTTTGAAAGGGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTT-AAAAGGAA
* *
587472 AAAGAGTGTCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGAA
*
587507 AAA-GTGCCACGGAGTGGTGGGCTTTAAGAA-GAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAA-AAGGAA
*
587540 AAAGGTTGCCACGGAATTGTGGGCTTTAAAA-G--
1 AAAGG-TGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
587572 ---GGTGCCACGGAGTTGTGGAC-TTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* * *
587602 CAAGGTGTCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
587636 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-GGAA
*
587672 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGAA
587707 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-G--
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGAA
* *
587739 -AAGGTGCCACGGAGTCGTGGAC-TTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* * * * * *
587771 CATGGTGCGACGGGGTTGTGGACTTTAAAAGGGGA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAA-GGAA
*
587806 AAAGAGTGCCACGGAGTTGTGGAC-TT---A-G--
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* * * *
587834 AAGGGTGCCATGGAATTGTGGAC-TTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAA-GGAA
** * *
587868 AAAGAGTGCCACAAAGTTCTGGGCTTTGAAAGGGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTT-AAAAGGAA
*
587904 AAAGAGTGCCACAGAGTTGTGGGCTTTGAAAA-G--
1 AAAG-GTGCCACGGAGTTGTGGGCTTT-AAAAGGAA
* *
587937 -AAGGTGCCACGGAGTCGTGGAC-TTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* * * *
587969 CAAGGTGCCACGGGGTCGTGGAC-TTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
*
588002 CAAAGAGTGCCACAGAGTTGTGGGCTTT
1 -AAAG-GTGCCACGGAGTTGTGGGCTTT
588030 GAAGAAAAAA
Statistics
Matches: 1029, Mismatches: 118, Indels: 164
0.78 0.09 0.13
Matches are distributed among these distances:
27 48 0.05
28 60 0.06
29 17 0.02
30 13 0.01
31 55 0.05
32 7 0.01
33 159 0.15
34 234 0.23
35 189 0.18
36 132 0.13
37 93 0.09
38 22 0.02
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.20
Consensus pattern (34 bp):
AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
Found at i:586942 original size:28 final size:28
Alignment explanation
Indices: 586901--586961 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
586891 CTTTGAAAAA
* *
586901 AAAAAGGTTGCCACGGAATTGTGGGCTT
1 AAAAAGGGTGCCACGGAATTGTGGACTT
* *
586929 TAAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAAGGGTGCCACGGAATTGTGGACTT
586957 AAAAA
1 AAAAA
586962 AGAAAAAGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.33, C:0.13, G:0.31, T:0.23
Consensus pattern (28 bp):
AAAAAGGGTGCCACGGAATTGTGGACTT
Found at i:587084 original size:167 final size:166
Alignment explanation
Indices: 586771--588029 Score: 1023
Period size: 167 Copynumber: 7.5 Consensus size: 166
586761 GGGAGAAAGA
** *
586771 TGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGCGCTTTAAAAAGAAA
1 TGCCACGGAGTTGTGGACTTAAAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
* * *
586836 ACGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTATGGGCTTTGAAAAA
65 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG
*
586901 AAAAAGGTTGCCACGGAATTGTGGGCTTTAAAAG-GG
130 AAAAAGGGTGCCACGGAATTGTGGGCTTTAAAAGAGG
* *
586937 TGCCACGGAGTTGTGGACTTAAAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAA
1 TGCCACGGAGTTGTGGACTTAAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-AGAA
* * *
587002 AAAGAATGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA-GTGCCACGGAGTGGTGGGCTTTGAGA
64 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAA
* * *
587066 AGAAAAATGTTGCCACGGAATTGTGGGTTTTAAAAG-GG
128 AGAAAAAGGGTGCCACGGAATTGTGGGCTTTAAAAGAGG
* * * * *
587104 TACCACAGAGTTGTGGACTT-AAAAGGAACAAGGTGCCACGGAGTTGTGGACTTTAAAAAGAAAA
1 TGCCACGGAGTTGTGGACTTAAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAA
* *
587168 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAA
66 AGGTGCCACGGAGTTGTGGGCTTT-AAAA-AG-AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAA
* *
587233 AGGGAAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGG
128 A--G-AAAAAGGGTGCCACGGAATTGTGGGCTTT-AAAAG----AGG
* * ** * * * *
587280 TGCCACGGAGTTATGGGCTTTGAAAAG---AAGGTGCCACGGAGTCGTGGAC-TTAAAAGGAACA
1 TGCCACGGAGTTGTGGACTTAAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAA
* * * * * *
587341 AGGTGCCACGGGGTTGTGGACTTTAAAAGGGGAAAAGAGTGCCACAGAGTTGTGGAC-TT----A
66 AGGTGCCACGGAGTTGTGGGCTTTAAAA-AGAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAAA
* * *
587401 G---AAGGGTGCCATGGAATTATGGAC-TTAAAAGGGAAAAAGAG
129 GAAAAAGGGTGCCACGGAATTGTGGGCTTTAAAA--G----AG-G
* * * * ** *
587442 TGACACAGAGTTGTGGGCTTTGAAAGGGAAAAAGAGTGTCACGGAGTTGTGGGCTTTAAAAAGAA
1 TGCCACGGAGTTGTGGAC-TTAAAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* * *
587507 AAA-GTGCCACGGAGTGGTGGGCTTTAAGAAGAAAAAGGTTGCCACGGAATTGTGGGCTTT----
64 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGG-TGCCACGGAGTTGTGGGCTTTGAAA
* * *
587567 ---AAAAGGGTGCCACGGAGTTGTGGACTTAAAAAGAACAAGG
128 AGAAAAAGGGTGCCACGGAATTGTGGGCTTTAAAAG----AGG
* * * *
587607 TGTCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 TGCCACGGAGTTGTGGACTTAAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-AGAA
587672 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAA
64 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAA
* * *
587737 AG---AA-GGTGCCACGGAGTCGTGGAC-TTAAAAGGAACATGG
128 AGAAAAAGGGTGCCACGGAATTGTGGGCTTTAAAA-G---A-GG
* * ** * *
587776 TGCGACGGGGTTGTGGACTTTAAAAGGGGAAAAGAGTGCCACGGAGTTGTGGAC-TT----AG--
1 TGCCACGGAGTTGTGGAC-TTAAAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* * * * * ** *
587834 AAGGGTGCCATGGAATTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACAAAGTTCTGGGCTTTGAA
64 AAAGGTGCCACGGAGTTGTGGGCTTTAAAA-AGAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAA
* * * *
587898 AGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGG
127 A-AGAAAAAGGGTGCCACGGAATTGTGGGCTTT-AAAAG-AGG
* * * * * * *
587941 TGCCACGGAGTCGTGGACTT-AAAAGGAACAAGGTGCCACGGGGTCGTGGAC-TTAAAAGGAACA
1 TGCCACGGAGTTGTGGACTTAAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA-A
*
588004 AAGAGTGCCACAGAGTTGTGGGCTTT
65 AAG-GTGCCACGGAGTTGTGGGCTTT
588030 GAAGAAAAAA
Statistics
Matches: 902, Mismatches: 127, Indels: 123
0.78 0.11 0.11
Matches are distributed among these distances:
159 4 0.00
160 8 0.01
161 48 0.05
162 61 0.07
163 57 0.06
164 30 0.03
165 67 0.07
166 124 0.14
167 217 0.24
168 58 0.06
169 44 0.05
170 54 0.06
171 31 0.03
172 24 0.03
173 32 0.04
174 21 0.02
176 18 0.02
177 4 0.00
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (166 bp):
TGCCACGGAGTTGTGGACTTAAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAA
AGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGA
AAAAGGGTGCCACGGAATTGTGGGCTTTAAAAGAGG
Found at i:587470 original size:470 final size:470
Alignment explanation
Indices: 586746--587831 Score: 1520
Period size: 470 Copynumber: 2.3 Consensus size: 470
586736 CACCGACTTG
** * * *
586746 TGTGGGCTTTGGGAAGGGAGAAAGA-TGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGC
1 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA-AGAAAAAG-GTGC
* * *
586809 CACGGAGTTGTGCGCTTTAAAAAGAAAACGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGG
64 CACGGAGTTGTGGGCTTT-AAAAG-AAACGGTGCCACGGAGTTGTGGACTTT-AAAAGGAAAAGG
* * * *
586874 TGCCACGGAGTTATGGGCTTTGAAAAAAAAAAGGTTGCCACGGAATTGTGGGCTTTAAAAGGGTG
126 TGCCACGGAGTTGTGGACTTTGAAAAAAAAAAGGTTGCCACAGAATTGTGGACTTTAAAAGGGTG
* * *
586939 CCACGGAGTTGTGGACTTAAAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAAAA
191 CCACGGAATTATGGACTTAAAAAAGAAAAAGGTGACACAGAGTTGTGGGCTTTGAAAAGGGAAAA
*
587004 AGAATGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGCCACGGAGTGGTGGGCTTTGAGAAGA
256 AGAATGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGCCACGGAGTGGTGGGCTTTAAGAAGA
* * *
587069 AAAATGTTGCCACGGAATTGTGGGTTTTAAAAGGGTACCACAGAGTTGTGGACTTAAAAGGAACA
321 AAAAGGTTGCCACGGAATTGTGGGCTTTAAAAGGGTACCACAGAGTTGTGGACTTAAAAAGAACA
587134 AGGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGG
386 AGGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGG
587199 GAAAAAAAGTGCCACGGAGT
451 GAAAAAAAGTGCCACGGAGT
587219 TGTGGGCTTTGAAAAGGGAAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCC
1 TGTGGGCTTTGAAAAGGG-AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCC
* *
587284 ACGGAGTTATGGGCTTTGAAAAG-AA-GGTGCCACGGAGTCGTGGAC-TTAAAAGGAACAAGGTG
65 ACGGAGTTGTGGGCTTT-AAAAGAAACGGTGCCACGGAGTTGTGGACTTTAAAAGGAA-AAGGTG
* ** * *
587346 CCACGGGGTTGTGGACTTT-AAAAGGGGAAAAGAG-TGCCACAGAGTTGTGGAC-TTAGAAGGGT
128 CCACGGAGTTGTGGACTTTGAAAA--AAAAAAG-GTTGCCACAGAATTGTGGACTTTAAAAGGGT
* **
587408 GCCATGGAATTATGGACTTAAAAGGGAAAAAGAGTGACACAGAGTTGTGGGCTTTG-AAAGGGAA
190 GCCACGGAATTATGGACTTAAAAAAGAAAAAG-GTGACACAGAGTTGTGGGCTTTGAAAAGGGAA
* *
587472 AAAGAGTGTCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGCCACGGAGTGGTGGGCTTTAAGAA
254 AAAGAATGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGCCACGGAGTGGTGGGCTTTAAGAA
* *
587537 GAAAAAGGTTGCCACGGAATTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAAGAA
319 GAAAAAGGTTGCCACGGAATTGTGGGCTTTAAAAGGGTACCACAGAGTTGTGGACTTAAAAAGAA
* *
587602 CAAGGTGTCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
384 CAAGGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
*
587667 GGGAAAAAGAGTGCCACGGAGT
449 GGGAAAAAAAGTGCCACGGAGT
* *
587689 TGTGGGCTTT-AAAA-AGAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAG---AAGGTGCCA
1 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCA
* * * * *
587748 CGGAGTCGTGGAC-TTAAAAGGAACATGGTGCGACGGGGTTGTGGACTTTAAAAGGGGAAAAGAG
66 CGGAGTTGTGGGCTTTAAAA-GAA-ACGGTGCCACGGAGTTGTGGACTTTAAAA--GGAAAAG-G
587812 TGCCACGGAGTTGTGGACTT
126 TGCCACGGAGTTGTGGACTT
587832 AGAAGGGTGC
Statistics
Matches: 551, Mismatches: 46, Indels: 37
0.87 0.07 0.06
Matches are distributed among these distances:
461 4 0.01
462 3 0.01
463 20 0.04
464 1 0.00
465 17 0.03
466 33 0.06
467 9 0.02
468 25 0.05
469 15 0.03
470 284 0.52
471 60 0.11
472 3 0.01
473 16 0.03
474 31 0.06
475 24 0.04
476 6 0.01
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (470 bp):
TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCA
CGGAGTTGTGGGCTTTAAAAGAAACGGTGCCACGGAGTTGTGGACTTTAAAAGGAAAAGGTGCCA
CGGAGTTGTGGACTTTGAAAAAAAAAAGGTTGCCACAGAATTGTGGACTTTAAAAGGGTGCCACG
GAATTATGGACTTAAAAAAGAAAAAGGTGACACAGAGTTGTGGGCTTTGAAAAGGGAAAAAGAAT
GCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGCCACGGAGTGGTGGGCTTTAAGAAGAAAAAG
GTTGCCACGGAATTGTGGGCTTTAAAAGGGTACCACAGAGTTGTGGACTTAAAAAGAACAAGGTG
CCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAA
AAAGTGCCACGGAGT
Found at i:587635 original size:96 final size:96
Alignment explanation
Indices: 586771--587751 Score: 544
Period size: 96 Copynumber: 9.8 Consensus size: 96
586761 GGGAGAAAGA
* * *
586771 TGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGCGCTTTAAAAAGAA
1 TGCCACGGAGTTGTGGGCTTTAAAA-AG-AAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* * *
586835 AACGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGG
63 AAAGGTGCCACGGAATTGTGGGCTTT-----GAAAAGGG
* * *
586874 TGCCACGGAGTTATGGGCTTTGAAAAAAAAAAGGTTGCCACGGAATTGTGGGCTTT-AAAAG---
1 TGCCACGGAGTTGTGGGCTTT-AAAAAGAAAAGG-TGCCACGGAGTTGTGGGCTTTAAAAAGAAA
* * * *
586935 --GGTGCCACGGAGTTGTGGACTTAAAAAAGAAAAAGG
64 AAGGTGCCACGGAATTGTGGGCTT-----TGAAAAGGG
* * *
586971 TGCCACAGAGTTGTGGGCTTTGAAAAGGGAAAAAGAATGCCACGGAGTTGTGGGCTTTAAAAAGA
1 TGCCACGGAGTTGTGGGCTTT-AAAA-AG-AAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGA
* * * *
587036 AAAA-GTGCCACGGAGTGGTGGGCTTTGAGAAGAAAAATGT
62 AAAAGGTGCCACGGAATTGTGGGCTTT-----G-AAAAGGG
* * * * * * *
587076 TGCCACGGAATTGTGGG-TTTTAAAAG----GGTACCACAGAGTTGTGGAC-TTAAAAGGAACAA
1 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
* * *
587135 GGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGG
66 GGTGCCACGGAATTGTGGGCTTT-----GAAAAGGG
* * *
587171 TGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGG
1 TGCCACGGAGTTGTGGGCTTT-AAAA---AGAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-A
* *
587236 GAAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGG
60 G-AAAAAG-GTGCCACGGAATTGTGGGCTTT-----GAAAAGGG
* * * * * *
587280 TGCCACGGAGTTATGGGCTTTGAAAAG--AAGGTGCCACGGAGTCGTGGAC-TTAAAAGGAACAA
1 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
** * *
587342 GGTGCCACGGGGTTGTGGACTTTAAAAGGGGAAAAGAG
66 GGTGCCACGGAATTGTGGGCTTT-------GAAAAGGG
* * * * * * * *
587380 TGCCACAGAGTTGTGGAC-TT----AG-AAGGGTGCCATGGAATTATGGAC-TTAAAAGGGAAAA
1 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA-AGAAAA
* * * *
587438 AGAGTGACACAGAGTTGTGGGCTTTGAAAGGGAAAAAGAG
65 AG-GTGCCACGGAATTGTGGGCTTT------G-AAAAGGG
* * * *
587478 TGTCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGCCACGGAGTGGTGGGCTTTAAGAAGAAAAA
1 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
587543 GGTTGCCACGGAATTGTGGGCTTT-AAAAGGG
66 GG-TGCCACGGAATTGTGGGCTTTGAAAAGGG
* *
587574 TGCCACGGAGTTGTGGAC-TTAAAAAGAACAAGGTGTCACGGAGTTGTGGGCTTTAAAAAGAAAA
1 TGCCACGGAGTTGTGGGCTTTAAAAAGAA-AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAA
*
587638 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAG
65 AGGTGCCACGGAATTGTGGGCTTTGAAAA--G-----G-G
*
587678 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG---A
1 TGCCACGGAGTTGTGGGCTTTAAAAAG-AAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAA
587740 AGGTGCCACGGA
65 AGGTGCCACGGA
587752 GTCGTGGACT
Statistics
Matches: 715, Mismatches: 99, Indels: 129
0.76 0.10 0.14
Matches are distributed among these distances:
95 64 0.09
96 125 0.17
97 69 0.10
98 61 0.09
99 34 0.05
100 31 0.04
101 4 0.01
102 22 0.03
103 66 0.09
104 100 0.14
105 69 0.10
106 6 0.01
107 2 0.00
108 8 0.01
109 54 0.08
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.21
Consensus pattern (96 bp):
TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
GGTGCCACGGAATTGTGGGCTTTGAAAAGGG
Found at i:587732 original size:432 final size:434
Alignment explanation
Indices: 586766--588000 Score: 1561
Period size: 432 Copynumber: 2.8 Consensus size: 434
586756 GGGAAGGGAG
* * *
586766 AAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGCGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
* * ** *
586829 AAAGAAAACGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTATGGGCTT
66 AAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG---AAGGTGCCACGGAGTCGTGGAC-T
* * ** *
586894 TGAAAA-AAAAAAGGTTGCCACGGAATTGTGGGCTTTAAAA---G----G-GTGCCACGGAGTTG
127 T-AAAAGGAACAAGG-TGCCACGGGGTTGTGGACTTTAAAAGGGGAAAAGAGTGCCACGGAGTTG
* ** * * * *
586950 TGGACTTAAAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAAAAAGAATGCCACG
190 TGGACTT-----AG--AAGGGTGCCATGGAATTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACA
** * *
587015 GAGTTGTGGGCTTT-AAAAAG-AAAA-AGTGCCACGGAGTGGTGGGCTTTGAGAAGAAAAATGTT
246 GAGTTGTGGGCTTTGAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAA-G-T
* * * * * *
587077 GCCACGGAATTGTGGGTTTTAAAAG----GGTACCACAGAGTTGTGGACTTAAAAGGAACAAGGT
309 GCCACGGAGTCGTGGGCTTTAAAAGAAAAGGTGCCACGGAATTGTGGACTTAAAAGG----AGGT
*
587138 GCCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAA
370 GCCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAGAAA
*
587203 AAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGG-AAAAAGAGTGCCACGGAGTTGTGGGCTTTA
*
587268 AAAAGAAAAAGGTGCCACGGAGTTATGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAA
65 AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAA
*
587333 AAGGAACAAGGTGCCACGGGGTTGTGGACTTTAAAAGGGGAAAAGAGTGCCACAGAGTTGTGGAC
130 AAGGAACAAGGTGCCACGGGGTTGTGGACTTTAAAAGGGGAAAAGAGTGCCACGGAGTTGTGGAC
* *
587398 TTAGAAGGGTGCCATGGAATTATGGACTTAAAAGGGAAAAAGAGTGACACAGAGTTGTGGGCTTT
195 TTAGAAGGGTGCCATGGAATTGTGGACTTAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
* * *
587463 GAAAGGGAAAAAGAGTGTCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGCCACGGAGTGGTGGG
260 GAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGTGCCACGGAGTCGTGGG
*
587528 CTTTAAGAAGAAAAAGGTTGCCACGGAATTGTGGGCTTTAAAA-G-GGTGCCACGGAGTTGTGGA
325 CTTTAA-AAG-AAAAGG-TGCCACGGAATTGTGGAC-TTAAAAGGAGGTGCCACGGAGTTGTGGA
* *
587591 C-TTAAAAAGAACAAGGTGTCACGGAGTTGTGGGCTTT-AAAA-AG-AA
386 CTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAGAAA
587636 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
587701 AAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAAA
66 AAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAAA
* *
587766 AGGAACATGGTGCGACGGGGTTGTGGACTTTAAAAGGGGAAAAGAGTGCCACGGAGTTGTGGACT
131 AGGAACAAGGTGCCACGGGGTTGTGGACTTTAAAAGGGGAAAAGAGTGCCACGGAGTTGTGGACT
* *
587831 TAGAAGGGTGCCATGGAATTGTGGACTTAAAAGGGAAAAAGAGTGCCACAAAGTTCTGGGCTTTG
196 TAGAAGGGTGCCATGGAATTGTGGACTTAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTG
* * *
587896 AAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAAAG--AAGGTGCCACGGAGTCGTGGAC
261 AAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGTGCCACGGAGTCGTGGGC
** *
587959 -TTAAAAGGAACAAGGTGCCACGGGGTCGTGGACTTAAAAGGA
326 TTTAAAA-GAA-AAGGTGCCACGGAATTGTGGACTTAAAAGGA
588001 ACAAAGAGTG
Statistics
Matches: 711, Mismatches: 60, Indels: 62
0.85 0.07 0.07
Matches are distributed among these distances:
427 6 0.01
428 19 0.03
429 9 0.01
430 19 0.03
432 256 0.36
433 35 0.05
434 34 0.05
435 56 0.08
436 67 0.09
437 89 0.13
438 5 0.01
439 7 0.01
440 65 0.09
441 2 0.00
442 16 0.02
443 26 0.04
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (434 bp):
AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
AAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAAA
AGGAACAAGGTGCCACGGGGTTGTGGACTTTAAAAGGGGAAAAGAGTGCCACGGAGTTGTGGACT
TAGAAGGGTGCCATGGAATTGTGGACTTAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTG
AAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGTGCCACGGAGTCGTGGGC
TTTAAAAGAAAAGGTGCCACGGAATTGTGGACTTAAAAGGAGGTGCCACGGAGTTGTGGACTTTA
AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAGAAA
Found at i:587852 original size:27 final size:27
Alignment explanation
Indices: 587805--587865 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
587795 TTAAAAGGGG
* *
587805 AAAAGAGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAATTGTGGACTT
* *
587832 AGAAGGGTGCCATGGAATTGTGGACTT
1 AAAAGGGTGCCACGGAATTGTGGACTT
587859 AAAAGGG
1 AAAAGGG
587866 AAAAAGAGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.31, C:0.11, G:0.36, T:0.21
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAATTGTGGACTT
Found at i:587921 original size:98 final size:98
Alignment explanation
Indices: 587567--588059 Score: 453
Period size: 98 Copynumber: 4.9 Consensus size: 98
587557 TGTGGGCTTT
* * * * * * *
587567 AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAAGAACAAG-GTGTCACGGAGTTGTGGGCTTTAA
1 AAAAAGGTGCCACGGAGTTCTGGACTTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTGA
* *
587630 AAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGG
66 AAAG----AGGTGCCACGGAGTCGTGGAC-TT-AAAA-GG
* * * *
587670 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTTG
1 AAAAAG-GTGCCACGGAGTTCTGGACTTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTG
587734 AAAAGAAGGTGCCACGGAGTCGTGGACTTAAAAGG
65 AAAAG-AGGTGCCACGGAGTCGTGGACTTAAAAGG
* * * * * * * *
587769 AACATGGTGCGACGGGGTTGTGGACTTTAAAAGGGGAAAAGAGTGCCACGGAGTTGTGGAC-TT-
1 AAAAAGGTGCCACGGAGTTCTGGACTTTAAAA-GGAAAAAGAGTGCCACAGAGTTGTGGGCTTTG
* * * *
587832 AGAAG-GGTGCCATGGAATTGTGGACTTAAAAGGG
65 AAAAGAGGTGCCACGGAGTCGTGGACTTAAAA-GG
** * *
587866 AAAAAGAGTGCCACAAAGTTCTGGGCTTTGAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
1 AAAAAG-GTGCCACGGAGTTCTGGACTTT-AAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
587931 GAAAAGAAGGTGCCACGGAGTCGTGGACTTAAAAGG
64 GAAAAG-AGGTGCCACGGAGTCGTGGACTTAAAAGG
* *
587967 AACAAGGTGCCACGG-GGTCGTGGAC-TTAAAAGGAACAAAGAGTGCCACAGAGTTGTGGGCTTT
1 AAAAAGGTGCCACGGAGTTC-TGGACTTTAAAAGGAA-AAAGAGTGCCACAGAGTTGTGGGCTTT
* ** * *
588030 GAAGAAAAAATGCCACTGATTCGTGGACTT
64 GAA-AAGAGGTGCCACGGAGTCGTGGACTT
588060 TGAGACAAAA
Statistics
Matches: 330, Mismatches: 46, Indels: 32
0.81 0.11 0.08
Matches are distributed among these distances:
96 23 0.07
97 6 0.02
98 75 0.23
99 73 0.22
100 39 0.12
101 9 0.03
102 43 0.13
103 5 0.02
104 18 0.05
105 39 0.12
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.20
Consensus pattern (98 bp):
AAAAAGGTGCCACGGAGTTCTGGACTTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTGA
AAAGAGGTGCCACGGAGTCGTGGACTTAAAAGG
Found at i:587939 original size:198 final size:197
Alignment explanation
Indices: 587452--588033 Score: 623
Period size: 198 Copynumber: 2.9 Consensus size: 197
587442 TGACACAGAG
* * ** *
587452 TTGTGGGCTTTG-AAAGGGAAAAAGAGTGTCACGGAGTTGTGGGCTTTAAAAAGAAAAA-GTGCC
1 TTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACAAAGTTCTGGGCTTTAAAAAGAAAAAGGTGCC
* * * * * *
587515 ACGGAGTGGTGGGCTTTAAGAAGAAAAAGGTTGCCACGGAATTGTGGGCTTTAAAA-G-----GG
66 ACAGAGTTGTGGGCTTT--GAA-AAGAAGG-TGCCACGGAGTCGTGGAC-TTAAAAGGAACAAGG
* * * * * *
587574 TGCCACGGAGTTGTGGACTTAAAAAGAAC-AAG-GTGTCACGGAGTTGTGGGCTTTAAAAAGAAA
126 TGCCACGGGGTCGTGGACTTAAAAGGAACAAAGAGTGCCACAGAGTTGTGGAC-TT----AG--A
* *
587637 AAGGTGCCACGGAG
184 AGGGTGCCACGGAA
* ** *
587651 TTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCC
1 TTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACAAAGTTCTGGGCTTTAAAAAGAAAAAGGTGCC
* * *
587716 ACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAAAAGGAACATGGTGCGA
66 ACAGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAAAAGGAACAAGGTGCCA
* * * *
587781 CGGGGTTGTGGACTTTAAAAGGGGA-AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGGTGCCAT
131 CGGGGTCGTGGAC-TTAAAA-GGAACAAAGAGTGCCACAGAGTTGTGGACTTAGAAGGGTGCCAC
587845 GGAA
194 GGAA
**
587849 TTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACAAAGTTCTGGGCTTTGAAAGGGAAAAAGAGTG
1 TTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACAAAGTTCTGGGCTTT-AAAAAGAAAAAG-GTG
587912 CCACAGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAAAAGGAACAAGGTGC
64 CCACAGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAAAAGGAACAAGGTGC
* *
587977 CACGGGGTCGTGGACTTAAAAGGAACAAAGAGTGCCACAGAGTTGTGGGCTTTGAAG
129 CACGGGGTCGTGGACTTAAAAGGAACAAAGAGTGCCACAGAGTTGTGGACTTAGAAG
588034 AAAAAATGCC
Statistics
Matches: 339, Mismatches: 29, Indels: 32
0.85 0.07 0.08
Matches are distributed among these distances:
196 42 0.12
197 62 0.18
198 104 0.31
199 15 0.04
200 47 0.14
201 21 0.06
202 18 0.05
203 6 0.02
204 7 0.02
205 17 0.05
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.21
Consensus pattern (197 bp):
TTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACAAAGTTCTGGGCTTTAAAAAGAAAAAGGTGCC
ACAGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAAAAGGAACAAGGTGCCA
CGGGGTCGTGGACTTAAAAGGAACAAAGAGTGCCACAGAGTTGTGGACTTAGAAGGGTGCCACGG
AA
Found at i:587945 original size:31 final size:34
Alignment explanation
Indices: 587865--588173 Score: 151
Period size: 31 Copynumber: 9.6 Consensus size: 34
587855 ACTTAAAAGG
* *
587865 GAAAAAGAGTGCCACAAAGTTCTGGGCTTTGAAA
1 GAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAA
587899 GGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTG-AA
1 --GAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAA
* * * * *
587934 -AAGAAG-GTGCCACGGAGTCGTGGAC-TTAAAA
1 GAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAA
* * * * * *
587965 GGAACAAG-GTGCCACGGGGTCGTGGAC-TTAAAA
1 -GAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAA
587998 GGAACAAAGAGTGCCACAGAGTTGTGGGCTTTG-AA
1 -GAA-AAAGAGTGCCACAGAGTTGTGGGCTTTGAAA
* *
588033 GAAAAA-A-TGCCACTGA-TTCGTGGACTTTG--A
1 GAAAAAGAGTGCCACAGAGTT-GTGGGCTTTGAAA
* * * *
588063 GACAAA-A-TGCCACTGAGTCGTGGACTTTG-AA
1 GAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAA
* * *
588094 GAAAAA-A-TGCCACTGAGTCGTGGACTTTG--A
1 GAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAA
* * * *
588124 GACAAA-A-TGCCACTGAGTCGTGGACTTTG-AA
1 GAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAA
* *
588155 GAAAAGGA-TGCCACTGAGT
1 GAAAAAGAGTGCCACAGAGT
588174 CATGGACTTC
Statistics
Matches: 239, Mismatches: 23, Indels: 26
0.83 0.08 0.09
Matches are distributed among these distances:
30 59 0.25
31 70 0.29
32 18 0.08
33 36 0.15
34 6 0.03
35 19 0.08
36 31 0.13
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.20
Consensus pattern (34 bp):
GAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAA
Found at i:588096 original size:61 final size:64
Alignment explanation
Indices: 587941--588343 Score: 475
Period size: 63 Copynumber: 6.4 Consensus size: 64
587931 GAAAAGAAGG
* ** * * ** *
587941 TGCCACGGAGTCGTGGACTTAAAAGGAACAAGG-TGCCACGGGGTCGTGGACTTAAAAGGAACAA
1 TGCCACTGAGTCGTGGACTTTGAA-GAA-AAGGATGCCACTGAGTCGTGGACTT-TGA-G-ACAG
*
588005 AGAG
61 AGAT
* * * * * *
588009 TGCCACAGAGTTGTGGGCTTTGAAGAAAA-AATGCCACTGATTCGTGGACTTTGAGACA-A-AA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGACAGAGAT
* *
588070 TGCCACTGAGTCGTGGACTTTGAAGAAAA-AATGCCACTGAGTCGTGGACTTTGAGACA-A-AA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGACAGAGAT
* * *
588131 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCATGGACTTCGTG-CAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGACAGAGAT
*
588194 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTCGAG-CAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGACAGAGAT
* *
588257 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCATTGAGTCGTGGACTTTGATA-AGAGAT
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGACAGAGAT
*
588320 TGCCACTGAGTCGTGGGCTTTGAA
1 TGCCACTGAGTCGTGGACTTTGAA
588344 AAGAGATTTC
Statistics
Matches: 303, Mismatches: 27, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
61 89 0.29
62 24 0.08
63 147 0.49
64 1 0.00
65 1 0.00
66 19 0.06
67 3 0.01
68 19 0.06
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.23
Consensus pattern (64 bp):
TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGACAGAGAT
Found at i:588341 original size:31 final size:31
Alignment explanation
Indices: 588003--588342 Score: 382
Period size: 31 Copynumber: 10.9 Consensus size: 31
587993 TAAAAGGAAC
* * * *
588003 AAAGAGTGCCACAGAGTTGTGGGCTTTGAAGA
1 AAAGAATGCCACTGAGTCGTGGACTTTG-AGA
*
588035 AAA-AATGCCACTGATTCGTGGACTTTGAGA
1 AAAGAATGCCACTGAGTCGTGGACTTTGAGA
*
588065 CAA-AATGCCACTGAGTCGTGGACTTTGAAGA
1 AAAGAATGCCACTGAGTCGTGGACTTTG-AGA
588096 AAA-AATGCCACTGAGTCGTGGACTTTGAGA
1 AAAGAATGCCACTGAGTCGTGGACTTTGAGA
*
588126 CAA-AATGCCACTGAGTCGTGGACTTTGAAGA
1 AAAGAATGCCACTGAGTCGTGGACTTTG-AGA
* * * * *
588157 AAAGGATGCCACTGAGTCATGGACTTCGTGC
1 AAAGAATGCCACTGAGTCGTGGACTTTGAGA
* *
588188 AGAGATTGCCACTGAGTCGTGGACTTTGAAGA
1 AAAGAATGCCACTGAGTCGTGGACTTTG-AGA
* * *
588220 AAAGGATGCCACTGAGTCGTGGACTTCGAGC
1 AAAGAATGCCACTGAGTCGTGGACTTTGAGA
* *
588251 AGAGATTGCCACTGAGTCGTGGACTTTGAAGA
1 AAAGAATGCCACTGAGTCGTGGACTTTG-AGA
* * *
588283 AAAGGATGCCATTGAGTCGTGGACTTTGATA
1 AAAGAATGCCACTGAGTCGTGGACTTTGAGA
* * *
588314 AGAGATTGCCACTGAGTCGTGGGCTTTGA
1 AAAGAATGCCACTGAGTCGTGGACTTTGA
588343 AAAGAGATTT
Statistics
Matches: 261, Mismatches: 42, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
30 57 0.22
31 129 0.49
32 75 0.29
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.24
Consensus pattern (31 bp):
AAAGAATGCCACTGAGTCGTGGACTTTGAGA
Found at i:588351 original size:31 final size:30
Alignment explanation
Indices: 587904--588343 Score: 343
Period size: 31 Copynumber: 14.0 Consensus size: 30
587894 TGAAAGGGAA
* * * *
587904 AAAGAGTGCCACAGAGTTGTGGGCTTTGAAA
1 AAAGA-TGCCACTGAGTCGTGGACTTTGAAG
* * **
587935 AGAAGGTGCCACGGAGTCGTGGACTTAAAAGG
1 A-AAGATGCCACTGAGTCGTGGACTTTGAA-G
* * * * *
587967 AACAAGGTGCCACGGGGTCGTGGACTTAAAAGGAAC
1 -A-AAGATGCCACTGAGTCGTGGACTT----TGAAG
* * *
588003 AAAGAGTGCCACAGAGTTGTGGGCTTTGAAG
1 AAAGA-TGCCACTGAGTCGTGGACTTTGAAG
* *
588034 AAAAAATGCCACTGATTCGTGGACTTTG-AG
1 -AAAGATGCCACTGAGTCGTGGACTTTGAAG
*
588064 ACAAAATGCCACTGAGTCGTGGACTTTGAAG
1 A-AAGATGCCACTGAGTCGTGGACTTTGAAG
*
588095 AAAAAATGCCACTGAGTCGTGGACTTTG-AG
1 -AAAGATGCCACTGAGTCGTGGACTTTGAAG
*
588125 ACAAAATGCCACTGAGTCGTGGACTTTGAAG
1 A-AAGATGCCACTGAGTCGTGGACTTTGAAG
* *
588156 AAAAGGATGCCACTGAGTCATGGACTTCGTGCAG
1 -AAA-GATGCCACTGAGTCGTGGACTT--TGAAG
588190 --AGATTGCCACTGAGTCGTGGACTTTGAAG
1 AAAGA-TGCCACTGAGTCGTGGACTTTGAAG
*
588219 AAAAGGATGCCACTGAGTCGTGGACTTCG-AG
1 -AAA-GATGCCACTGAGTCGTGGACTTTGAAG
*
588250 CAGAGATTGCCACTGAGTCGTGGACTTTGAAG
1 -AAAGA-TGCCACTGAGTCGTGGACTTTGAAG
*
588282 AAAAGGATGCCATTGAGTCGTGGACTTTGATA-
1 -AAA-GATGCCACTGAGTCGTGGACTTTGA-AG
* *
588314 AGAGATTGCCACTGAGTCGTGGGCTTTGAA
1 AAAGA-TGCCACTGAGTCGTGGACTTTGAA
588344 AAGAGATTTC
Statistics
Matches: 341, Mismatches: 40, Indels: 57
0.78 0.09 0.13
Matches are distributed among these distances:
29 6 0.02
30 62 0.18
31 141 0.41
32 77 0.23
33 29 0.09
34 7 0.02
35 17 0.05
37 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (30 bp):
AAAGATGCCACTGAGTCGTGGACTTTGAAG
Found at i:589293 original size:12 final size:12
Alignment explanation
Indices: 589276--589317 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
589266 TGAAAAGGGA
589276 TTTTTCGTTTTT
1 TTTTTCGTTTTT
*
589288 TTTTTCCTTTTT
1 TTTTTCGTTTTT
589300 TGTTTT-GTTTCTT
1 T-TTTTCGTTT-TT
589313 TTTTT
1 TTTTT
589318 GGAAAAGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 19 0.73
13 7 0.27
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (12 bp):
TTTTTCGTTTTT
Found at i:589310 original size:17 final size:17
Alignment explanation
Indices: 589285--589318 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
589275 ATTTTTCGTT
*
589285 TTTTTTTTCCTTTTTTG
1 TTTTGTTTCCTTTTTTG
*
589302 TTTTGTTTCTTTTTTTG
1 TTTTGTTTCCTTTTTTG
589319 GAAAAGAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (17 bp):
TTTTGTTTCCTTTTTTG
Found at i:596583 original size:52 final size:52
Alignment explanation
Indices: 596505--596737 Score: 394
Period size: 52 Copynumber: 4.5 Consensus size: 52
596495 CGAAATATGA
* * * * *
596505 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATTTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGAGC
*
596557 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGAGC
*
596609 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTCAGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGAGC
*
596661 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTTAGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGAGC
596713 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
596738 AAGATCAATG
Statistics
Matches: 174, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 174 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGAGC
Found at i:599849 original size:55 final size:54
Alignment explanation
Indices: 599765--600057 Score: 183
Period size: 60 Copynumber: 5.0 Consensus size: 54
599755 AGGACGCCTT
* * *
599765 CGCCTTTCAAAGCCTACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGTAGGA
1 CGCCTTTCAAAGCCCACACAAGCTGGTGGCACTTT-CAATCCTCAAAGAGTAGGA
* *
599820 CGCCTTTCAAAGCCCACATAAGCTGGTGGCACTTTCAGTCCTCAAAGAGTAGGACA
1 CGCCTTTCAAAGCCCACACAAGCTGGTGGCACTTTCAATCCTCAAAGAGTAGG--A
* * * * * *
599876 TCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTC-AAGAAGCAAGA
1 -C---GCCTTTCAAAGCCCACACAAGCTGGTGGCAC-TTTCAATCCTCAAAG-AGTAGGA
* * *
599935 CGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGA
1 CGCC-TTT-C----AAAGCCCACACAAGCTGGTGGCAC-TTTC-AATCCTCAAAGAGTAGGA
* * *** * *
599997 TGCCTTTTCCTTTCAAAGCCCACGCAAGCTAAAGGCACCTTCAGTCCTCAAAGAGTAGGA
1 ---C---GCCTTTCAAAGCCCACACAAGCTGGTGGCACTTTCAATCCTCAAAGAGTAGGA
600057 C
1 C
600058 ACTTTTTCCT
Statistics
Matches: 194, Mismatches: 22, Indels: 42
0.75 0.09 0.16
Matches are distributed among these distances:
54 17 0.09
55 33 0.17
56 4 0.02
57 2 0.01
58 1 0.01
59 1 0.01
60 47 0.24
61 47 0.24
62 32 0.16
63 3 0.02
65 1 0.01
66 1 0.01
67 3 0.02
68 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (54 bp):
CGCCTTTCAAAGCCCACACAAGCTGGTGGCACTTTCAATCCTCAAAGAGTAGGA
Found at i:600053 original size:183 final size:182
Alignment explanation
Indices: 599741--600207 Score: 581
Period size: 183 Copynumber: 2.6 Consensus size: 182
599731 CGTCGCAACA
* * ** * * * *
599741 AGTCCTCAAAGAGTAGGACGCCTTCGCCTTTCAAAGCCTACACAAGTTGGTGGCATTTTCCAATC
1 AGTCCTCAAAGAGCAAGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTC
* * * *** *
599806 CTCAAAGAGTAGGA--C---GCCTTTCAAAGCCCACATAAGCTGGTGGCACTTTCAGTCCTCAAA
66 CTCAAAGAGCAGGAGCCTTTTCCTTTCAAAGCCCACACAAGCTAAAGGCACCTTCAGTCCTCAAA
599866 GAGTAGGACA-TCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-
131 GAGTAGGACACT-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCT
599917 AGTCCTC-AAGAAGCAAGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAG
1 AGTCCTCAAAG-AGCAAGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCTAG
*
599981 TCCTCAAAGAGCAGGATGCCTTTTCCTTTCAAAGCCCACGCAAGCTAAAGGCACCTTCAGTCCTC
64 TCCTCAAAGAGCAGGA-GCCTTTTCCTTTCAAAGCCCACACAAGCTAAAGGCACCTTCAGTCCTC
600046 AAAGAGTAGGACACTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCT
128 AAAGAGTAGGACACTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCT
* * * * * * * *
600101 AGTCCTTAAAGAGCATGATGCCTTTTCCTTTTAAAACACACACAAGTCGGTGGCATCTTCTAGTT
1 AGTCCTCAAAGAGCAAGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTC
* * **
600166 CTCAAAGAGCAAGACGCCTTTTCCTTTTACGGCCCACACAAG
66 CTCAAAGAGCAGGA-GCCTTTTCCTTTCAAAGCCCACACAAG
600208 TTGGTGGCAC
Statistics
Matches: 250, Mismatches: 30, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
175 3 0.01
176 45 0.18
177 21 0.08
180 1 0.00
183 131 0.52
184 46 0.18
185 3 0.01
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (182 bp):
AGTCCTCAAAGAGCAAGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTC
CTCAAAGAGCAGGAGCCTTTTCCTTTCAAAGCCCACACAAGCTAAAGGCACCTTCAGTCCTCAAA
GAGTAGGACACTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCT
Found at i:600241 original size:61 final size:61
Alignment explanation
Indices: 599741--600237 Score: 528
Period size: 61 Copynumber: 8.2 Consensus size: 61
599731 CGTCGCAACA
* ** * * *
599741 AGTCCTCAAAGAGTAGGACGCCTTCGCCTTTCAAAGCCTACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCC
* * * *
599802 AATCCTCAAAGAGTAGGACGCC-TTT-C----AAAGCCCACATAAGCTGGTGGCACTTT-C
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCC
* ** *
599856 AGTCCTCAAAGAGTAGGACATCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCC
* *
599917 AGTCCTC-AAGAAGCAAGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCT
1 AGTCCTCAAAG-AGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCC
* * * * *** *
599979 AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTCAAAGCCCACGCAAGCTAAAGGCACCTT-C
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCC
* * * *
600039 AGTCCTCAAAGAGTAGGACACTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCC
* * * * * * *
600101 AGTCCTTAAAGAGCATGATGCCTTTTCCTTTTAAAACACACACAAGTCGGTGGCA-TCTTCT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACT-TTCC
* * ** *
600162 AGTTCTCAAAGAGCAAGACGCCTTTTCCTTTTACGGCCCACACAAGTTGGTGGCACTTCCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCC
600223 AGTCCTCAAAGAGCA
1 AGTCCTCAAAGAGCA
600238 AGACTGCTCT
Statistics
Matches: 361, Mismatches: 61, Indels: 28
0.80 0.14 0.06
Matches are distributed among these distances:
54 20 0.06
55 26 0.07
56 1 0.00
59 1 0.00
60 76 0.21
61 140 0.39
62 94 0.26
63 3 0.01
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (61 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCC
Found at i:600359 original size:62 final size:60
Alignment explanation
Indices: 600265--600464 Score: 267
Period size: 61 Copynumber: 3.3 Consensus size: 60
600255 CACCTTTTAG
* *
600265 TCCTCAAAGAACATGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTATA
1 TCCTCAAAGAGCAGGACG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTATA
* **
600326 GTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCGA
1 -TCCTCAAAGAGCAGGACG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTATA
* * * *
600388 TCCTCAAAGAGTAGGATGCTTTCTCCTTGTAAAGCCCATACAAGTTGGTGGCACCTTTTA-A
1 TCCTCAAAGAGCAGGACGCTTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTTATA
600449 TCCTCAAAGAGCAGGA
1 TCCTCAAAGAGCAGGA
600465 TGCCCCCTTC
Statistics
Matches: 123, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
60 4 0.03
61 60 0.49
62 59 0.48
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (60 bp):
TCCTCAAAGAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTATA
Found at i:600369 original size:163 final size:161
Alignment explanation
Indices: 600100--600415 Score: 436
Period size: 163 Copynumber: 2.0 Consensus size: 161
600090 GGCACTTTTC
* * * *
600100 TAGTCCTTAAAGAGCATGATGCCTTTTCCTTTTAAAACACACACAAGTCGGTGGCATCTTCTAGT
1 TAGTCCTCAAAGAACATGACGCCTTTTCCTTTTAAAACACACACAAGTCGGTGGCATCTTATAGT
* **
600165 TCTCAAAGAGCAAGACGCCTTTTCCTTTTACGGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCT
66 CCTCAAAGAGCAAGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCCA-TCCT
600229 CAAAGAGCAAGACTGCTCTCTCCTTTCACCTTT
130 CAAAGAGCAAGA-TGCTCTCTCCTTTCACCTTT
* * * * *
600262 TAGTCCTCAAAGAACATGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTATAG
1 TAGTCCTCAAAGAACATGACGCCTTTTCCTTTTAAAACACACACAAGTCGGTGGCA-TCTTATAG
* * *
600327 TCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCGATCCT
65 TCCTCAAAGAGCAAGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCCATCCT
* * *
600392 CAAAGAGTAGGATGCTTTCTCCTT
130 CAAAGAGCAAGATGCTCTCTCCTT
600416 GTAAAGCCCA
Statistics
Matches: 134, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
162 60 0.45
163 69 0.51
164 5 0.04
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (161 bp):
TAGTCCTCAAAGAACATGACGCCTTTTCCTTTTAAAACACACACAAGTCGGTGGCATCTTATAGT
CCTCAAAGAGCAAGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCCATCCTC
AAAGAGCAAGATGCTCTCTCCTTTCACCTTT
Found at i:601074 original size:13 final size:13
Alignment explanation
Indices: 601056--601085 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
601046 ATACATTATT
601056 CATTGTATCAATA
1 CATTGTATCAATA
*
601069 CATTGTATCGATA
1 CATTGTATCAATA
601082 CATT
1 CATT
601086 CTGGGTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTGTATCAATA
Found at i:603578 original size:79 final size:75
Alignment explanation
Indices: 603416--603803 Score: 285
Period size: 79 Copynumber: 4.9 Consensus size: 75
603406 TTTTCATCTT
* * * *
603416 AGGGATACTCAAACCCCAGCTTTATTTCTAAAATATCAATTTTTCATCTCGGGGATACTCCAACC
1 AGGGATACTCCAA-CCCAGCTTTATTTCTAAAATATCGATTTTACAAC-CGGGGATACTCCAACC
603481 CCGTTATTTTCG
64 CCGTTATTTTCG
*
603493 AGGGGATACTCCAACACCAGCTTTATTTCTAAAATATTGATTCCTTACAACCGGGGATACTCCAA
1 A-GGGATACTCCAAC-CCAGCTTTATTTCTAAAATATCGATT--TTACAACCGGGGATACTCCAA
*
603558 CCCCGTTATTTTGG
62 CCCCGTTATTTTCG
* * * ** *
603572 TAGGGATACTCCTAACCTCGGCCTTATTACTAAAGCATCGATTTTCCACTAATCGGGGATACTCC
1 -AGGGATACTCC-AACC-CAGCTTTATTTCTAAAATATCGATTTT--AC-AACCGGGGATACTCC
*
603637 AACCCTGTTATTTTCG
60 AACCCCGTTATTTTCG
** ** * * * *
603653 AGAGGATACTCCAACCTCAATTTTATTT-TCAAAACGTCGATTTTCTATAATCAGGGATACTCTA
1 AG-GGATACTCCAACC-CAGCTTTATTTCT-AAAATATCGA-TTT-TACAACCGGGGATACTCCA
*
603717 ACCCTGTTA-TTTCTG
61 ACCCCGTTATTTTC-G
* * * * * * * * *
603732 AGGGGATACTCCAACCCTGATTTTATTTTTAGAACACCGATTTTCCATAATCGGGGATACTCCAG
1 A-GGGATACTCCAACCCAG-CTTTATTTCTAAAATATCGATTTT--ACAACCGGGGATACTCCAA
603797 CCCCGTT
62 CCCCGTT
603804 GTTATCCCCA
Statistics
Matches: 257, Mismatches: 34, Indels: 38
0.78 0.10 0.12
Matches are distributed among these distances:
77 3 0.01
78 45 0.18
79 114 0.44
80 54 0.21
81 40 0.16
82 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (75 bp):
AGGGATACTCCAACCCAGCTTTATTTCTAAAATATCGATTTTACAACCGGGGATACTCCAACCCC
GTTATTTTCG
Found at i:603712 original size:160 final size:158
Alignment explanation
Indices: 603464--603803 Score: 370
Period size: 160 Copynumber: 2.1 Consensus size: 158
603454 ATTTTTCATC
* * *
603464 TCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACACCAGCTTTATTTCTAAAATA
1 TCGGGGATACTCCAACCCCGTTATTTTCGAGAGGATACTCCAACACCAACTTTATTTCTAAAACA
* *
603529 TTGATTCCTTACAACCGGGGATACTCCAACCCCGTTATTT-TG-GTAGGGATACTCCTAA-CCTC
66 TCGATTCCTTACAACCAGGGATACTCCAACCCCGTTATTTCTGAG--GGGATACTCC-AACCCT-
* *
603591 GGCCTTATTACTA-AAGCATCGATTTTCCACTAA
127 GACCTTATTACTAGAA-CACCGATTTTCCA-TAA
* *
603624 TCGGGGATACTCCAACCCTGTTATTTTCGAGAGGATACTCCAAC-CTCAATTTTATTT-TCAAAA
1 TCGGGGATACTCCAACCCCGTTATTTTCGAGAGGATACTCCAACAC-CAACTTTATTTCT-AAAA
* * * * * *
603687 CGTCGATT-TTCTATAATCAGGGATACTCTAACCCTGTTATTTCTGAGGGGATACTCCAACCCTG
64 CATCGATTCCT-TACAACCAGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCTG
** **
603751 ATTTTATTTTTAGAACACCGATTTTCCATAA
128 ACCTTATTACTAGAACACCGATTTTCCATAA
*
603782 TCGGGGATACTCCAGCCCCGTT
1 TCGGGGATACTCCAACCCCGTT
603804 GTTATCCCCA
Statistics
Matches: 152, Mismatches: 21, Indels: 16
0.80 0.11 0.08
Matches are distributed among these distances:
158 23 0.15
159 25 0.16
160 101 0.66
161 2 0.01
162 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (158 bp):
TCGGGGATACTCCAACCCCGTTATTTTCGAGAGGATACTCCAACACCAACTTTATTTCTAAAACA
TCGATTCCTTACAACCAGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCTGACC
TTATTACTAGAACACCGATTTTCCATAA
Found at i:607403 original size:13 final size:13
Alignment explanation
Indices: 607385--607468 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
607375 AGCTTCGTAG
607385 CGATACATTGTAT
1 CGATACATTGTAT
607398 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
607417 CGATACATTGTAT
1 CGATACATTGTAT
607430 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
607449 CGATACATTGTAT
1 CGATACATTGTAT
607462 CGATACA
1 CGATACA
607469 ACACTTATGT
Statistics
Matches: 59, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
13 26 0.44
14 1 0.02
15 2 0.03
16 8 0.14
17 2 0.03
18 1 0.02
19 19 0.32
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:607417 original size:19 final size:18
Alignment explanation
Indices: 607393--607489 Score: 97
Period size: 19 Copynumber: 5.8 Consensus size: 18
607383 AGCGATACAT
607393 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
607412 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
607425 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
607444 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
607457 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
607476 TGTATCGATACAAA
1 TGTATCGATACAAA
607490 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 3 0.05
19 35 0.53
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:607426 original size:32 final size:32
Alignment explanation
Indices: 607385--607487 Score: 197
Period size: 32 Copynumber: 3.2 Consensus size: 32
607375 AGCTTCGTAG
*
607385 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
607417 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
607449 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
607481 CGATACA
1 CGATACA
607488 AATCGTTGAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:607566 original size:21 final size:22
Alignment explanation
Indices: 607519--607566 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
607509 TTGACCGTTG
*
607519 GGACATTGTATCGATACATTCT
1 GGACAATGTATCGATACATTCT
*
607541 -AACAATGTATCGATACATT-T
1 GGACAATGTATCGATACATTCT
607561 GGACAA
1 GGACAA
607567 AAATGTGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (22 bp):
GGACAATGTATCGATACATTCT
Found at i:610377 original size:13 final size:13
Alignment explanation
Indices: 610359--610384 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
610349 TACACAAAGT
610359 ATGTATCGATACA
1 ATGTATCGATACA
610372 ATGTATCGATACA
1 ATGTATCGATACA
610385 CAAAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:612641 original size:21 final size:22
Alignment explanation
Indices: 612608--612657 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
612598 TTGCAAGTTG
* **
612608 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAAAAA
*
612630 AAATAATG-AGTTAGCTAAAAA
1 AAATAAAGAAGTTAGCTAAAAA
612651 AAATAAA
1 AAATAAA
612658 AACTTGCATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.58, C:0.04, G:0.16, T:0.22
Consensus pattern (22 bp):
AAATAAAGAAGTTAGCTAAAAA
Found at i:614475 original size:15 final size:15
Alignment explanation
Indices: 614455--614485 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
614445 TAAAAATGTC
*
614455 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
614470 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
614485 C
1 C
614486 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:616581 original size:13 final size:13
Alignment explanation
Indices: 616563--616601 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
616553 CATTTTTCTT
616563 TGTATCGATACAA
1 TGTATCGATACAA
*
616576 TGTATCGATACAC
1 TGTATCGATACAA
616589 TGTATCGATACAA
1 TGTATCGATACAA
616602 GGGGATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:616764 original size:20 final size:20
Alignment explanation
Indices: 616721--616766 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
616711 AAATCTTTTG
616721 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
616742 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
616762 CAAAA
1 CAAAA
616767 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:621026 original size:25 final size:25
Alignment explanation
Indices: 620998--621068 Score: 70
Period size: 31 Copynumber: 2.6 Consensus size: 25
620988 TTGGTTCAAT
*
620998 GTTAATATAATTTCTAATTTATTTA
1 GTTAATATAATTTATAATTTATTTA
621023 GTTAATCATAATATAATTTATAATTTATTTA
1 G----T--TAATATAATTTATAATTTATTTA
*
621054 GTTAATATGATTTAT
1 GTTAATATAATTTAT
621069 TTAAGCTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
25 13 0.34
27 1 0.03
29 1 0.03
31 23 0.61
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.54
Consensus pattern (25 bp):
GTTAATATAATTTATAATTTATTTA
Found at i:621035 original size:31 final size:31
Alignment explanation
Indices: 621000--621059 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
620990 GGTTCAATGT
*
621000 TAATATAATTTCTAATTTATTTAGTTAATCA
1 TAATATAATTTATAATTTATTTAGTTAATCA
621031 TAATATAATTTATAATTTATTTAGTTAAT
1 TAATATAATTTATAATTTATTTAGTTAAT
621060 ATGATTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (31 bp):
TAATATAATTTATAATTTATTTAGTTAATCA
Found at i:624457 original size:4 final size:4
Alignment explanation
Indices: 624448--624484 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
624438 CTATTCATGA
624448 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
624485 TATGGATTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:625267 original size:2 final size:2
Alignment explanation
Indices: 625260--625290 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
625250 AATCTTTATT
625260 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
625291 TCTCATGACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:626973 original size:12 final size:13
Alignment explanation
Indices: 626936--626973 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
626926 ATAATATATC
*
626936 TAAAATTTAAATA
1 TAAAATTAAAATA
*
626949 TAAAATTATAATA
1 TAAAATTAAAATA
626962 -AAAATTAAAATA
1 TAAAATTAAAATA
626974 CTTAATGTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
TAAAATTAAAATA
Found at i:628718 original size:37 final size:37
Alignment explanation
Indices: 628676--628751 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
628666 TTGGATAAAC
*
628676 AACATATTCATGTTGCAAGAAGACATAAGTTTTTTCA
1 AACATATTCACGTTGCAAGAAGACATAAGTTTTTTCA
**
628713 AACATATTCACGTTGCAAGAAGATGTAAGTTTTTTCA
1 AACATATTCACGTTGCAAGAAGACATAAGTTTTTTCA
628750 AA
1 AA
628752 ACCTCTTTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (37 bp):
AACATATTCACGTTGCAAGAAGACATAAGTTTTTTCA
Found at i:630259 original size:4 final size:4
Alignment explanation
Indices: 630244--630287 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
630234 AAATTCCAAC
* *
630244 AAGA ATGA AAGA AAGA AA-A AAAA AAGA AAGA AAGA AAG- AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
630288 CTCAAGTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
3 6 0.17
4 29 0.83
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.02
Consensus pattern (4 bp):
AAGA
Found at i:630271 original size:15 final size:15
Alignment explanation
Indices: 630251--630287 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
630241 AACAAGAATG
630251 AAAGAAAGAAAAAAA
1 AAAGAAAGAAAAAAA
*
630266 AAAGAAAGAAAGAAA
1 AAAGAAAGAAAAAAA
*
630281 GAAGAAA
1 AAAGAAA
630288 CTCAAGTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAAAAAA
Found at i:630754 original size:28 final size:27
Alignment explanation
Indices: 630702--630754 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
630692 TCTAATATAA
*
630702 ATCTAAAATTGAAAATAAAACATAAGT
1 ATCTAAAATTAAAAATAAAACATAAGT
630729 ATCTAAAA-TAAAAATAGAAAACATAA
1 ATCTAAAATTAAAAAT--AAAACATAA
630755 CAAAAACTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 8 0.35
28 9 0.39
ACGTcount: A:0.64, C:0.08, G:0.06, T:0.23
Consensus pattern (27 bp):
ATCTAAAATTAAAAATAAAACATAAGT
Found at i:636676 original size:15 final size:15
Alignment explanation
Indices: 636643--636676 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
636633 GAAGTATTGT
*
636643 TATTTTGATGACTCT
1 TATTTTGATGACTCA
*
636658 TATTTTGATGAGTCA
1 TATTTTGATGACTCA
636673 TATT
1 TATT
636677 AATAATGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.53
Consensus pattern (15 bp):
TATTTTGATGACTCA
Found at i:638238 original size:76 final size:74
Alignment explanation
Indices: 638130--638301 Score: 179
Period size: 76 Copynumber: 2.3 Consensus size: 74
638120 TCTTCACTTT
** * * * * *
638130 CTATCAATGACCAAAGCAAACTGATAATAAGCTGAAGTAGAATATCATAATGGGGAATATGT-GA
1 CTATCAACAACCAAAACAAACTGATAACAAGCT--AG-AGAATAAC-CAATGGGGAATATATAG-
*
638194 TTT-TATAA-TTTC
61 TTTCTAAAATTTTC
638206 CTATCAACAACCAAAACAAACTGATAACAAGCTAGAGAATAACCAATGGGGAATATATAGTTTCT
1 CTATCAACAACCAAAACAAACTGATAACAAGCTAGAGAATAACCAATGGGGAATATATAGTTTCT
638271 AAAATTTTC
66 AAAATTTTC
* **
638280 CCATCAACAGTCAAAACAAACT
1 CTATCAACAACCAAAACAAACT
638302 AGTAATGAGC
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
72 16 0.20
73 12 0.15
74 25 0.30
76 29 0.35
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (74 bp):
CTATCAACAACCAAAACAAACTGATAACAAGCTAGAGAATAACCAATGGGGAATATATAGTTTCT
AAAATTTTC
Found at i:638296 original size:74 final size:75
Alignment explanation
Indices: 638139--638301 Score: 181
Period size: 74 Copynumber: 2.2 Consensus size: 75
638129 TCTATCAATG
* * * * * *
638139 ACCAAAGCAAACTGATAATAAGCTGAAGTAGAATATCATAATGGGGAATATGTGATTTTATAATT
1 ACCAAAACAAACTGATAACAAGCT-AAGTAGAATAACACAATGGGGAATATATGATTTTAAAATT
*
638204 TCCTATCAACA
65 TCCCATCAACA
638215 ACCAAAACAAACTGATAACAAGCT-AG-AGAATAAC-CAATGGGGAATATAT-AGTTTCTAAAAT
1 ACCAAAACAAACTGATAACAAGCTAAGTAGAATAACACAATGGGGAATATATGA-TTT-TAAAA-
638276 TTTCCCATCAACA
63 TTTCCCATCAACA
**
638289 GTCAAAACAAACT
1 ACCAAAACAAACT
638302 AGTAATGAGC
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
71 1 0.01
72 16 0.21
73 11 0.15
74 25 0.33
76 22 0.29
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.25
Consensus pattern (75 bp):
ACCAAAACAAACTGATAACAAGCTAAGTAGAATAACACAATGGGGAATATATGATTTTAAAATTT
CCCATCAACA
Found at i:641228 original size:33 final size:33
Alignment explanation
Indices: 641186--641250 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
641176 TTAGAAGCAA
*
641186 TGTATCGATACAAT-TCATCATGTATCGATACAT
1 TGTATCGATACAATGT-ACCATGTATCGATACAT
*
641219 TGTATCGATATAATGTACCATGTATCGATACA
1 TGTATCGATACAATGTACCATGTATCGATACA
641251 AGCATAATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATGTACCATGTATCGATACAT
Found at i:647074 original size:61 final size:60
Alignment explanation
Indices: 646936--647855 Score: 884
Period size: 61 Copynumber: 15.1 Consensus size: 60
646926 GAGCATGACA
* * * * * * **
646936 CCTTTCAAAGCCCACACAAGCTGGTGGCACTTTTCTAGTCCTCAAAAAGTAGGACACCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCCAGTCCTCAAAGAGCAGGA-TGCTTTT
* * * *
646998 CCTTTTAAAGTCCACACAAGTTGGTGGCACCTTCCAATCCTCAAAAAGCAGGATGCTTTCG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCTTT-T
* **
647059 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGTGGGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATG-CTTTT
* * * * * *
647119 CTTTTTAAAGCCCACACGAGTTGGTGGCACTTTTCAGTCCTTAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATG-CTTTT
* * * * *
647180 CCTTTTAAAGCCCACACAAGCTGGTGGCACTTTTCTAGTCCTCAAAAAGCAGGATACCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCCAGTCCTCAAAGAGCAGGAT-GCTTTT
** * * *
647242 CCTTTTAAAGTTCACACAAGTTGGTGGCACCTTCCAGTTCTCAAAGAGTATGATG-TTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCTTTT
* * * **
647301 CACATTTCAAAGCCCACACAAGCTGGTGGCACCTT-CAGTCCTCAAATAGTGGGATGCCTTTT
1 C-C-TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATG-CTTTT
* * * *
647363 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAGGAGCAGGACGCATTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGC-TTTT
* * * *
647424 -CTTTTAAAGCCCACACAAGCTGGTAGCACTTTTCTAGTCCTCAAAGAGCAGGACAT-CTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCCAGTCCTCAAAGAGCAGG--ATGCTTTT
* * * *
647485 CCTTTTAAAGTCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGGATGCTTTCG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCTTT-T
* *** * * * * *
647546 CCTTTCAAAGCTTGCACAAGCTGGTGGTACCTT-CAGTCCTTAAAGAGCGGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATG-CTTTT
* ** * *
647606 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAGGAGTAGGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATG-CTTTT
* * * **
647667 CCTTTCAAAGCCCACACAAGCTGATGGCACCTT-CAGTCCTCAAAGAGCAGGACACCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGA-TGCTTTT
* * * * * *
647727 TCTTTTCAAAGCCCGCACAAGTTGGTGACACC-TCTTAGTCCTCAAAGAGCAGGACGCCTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTC-CAGTCCTCAAAGAGCAGGATGCTTTT
* * * * *
647788 CCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTCAATCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATG-CTTTT
647850 CCTTTT
1 CCTTTT
647856 CTCCTTTGTC
Statistics
Matches: 707, Mismatches: 126, Indels: 50
0.80 0.14 0.06
Matches are distributed among these distances:
59 7 0.01
60 196 0.28
61 364 0.51
62 139 0.20
63 1 0.00
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (60 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCTTTT
Found at i:647554 original size:243 final size:244
Alignment explanation
Indices: 646936--647855 Score: 1301
Period size: 244 Copynumber: 3.8 Consensus size: 244
646926 GAGCATGACA
*
646936 CCTTTCAAAGCCCACACAAGCTGGTGGCACTTTTCTAGTCCTCAAAAAGTAGGACACCTTTTCCT
1 CCTTTCAAAGCCCACACAAGCTGGTGGCACTTTTCTAGTCCTCAAAAAGCAGGACACCTTTTCCT
* *
647001 TTTAAAGTCCACACAAGTTGGTGGCACCTTCCAATCCTCAAAAAGCAGGATGCTTTCGCCTTTCA
66 TTTAAAGTCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCTTTCGCCTTTCA
* * * *
647066 AAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGTGGGATGCCTTTTCTTTTTAAAGCC
131 AAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCCTTTTAAAGCC
* * *
647131 CACACGAGTTGGTGGCACTTTTCAGTCCTTAAAGAGCAGGACGCCTTTT
196 CACACAAGTTGGTGGCACTTTTCAGTCCTCAAGGAGCAGGACGCCTTTT
* *
647180 CCTTTTAAAGCCCACACAAGCTGGTGGCACTTTTCTAGTCCTCAAAAAGCAGGATACCTTTTCCT
1 CCTTTCAAAGCCCACACAAGCTGGTGGCACTTTTCTAGTCCTCAAAAAGCAGGACACCTTTTCCT
* * * * * * *
647245 TTTAAAGTTCACACAAGTTGGTGGCACCTTCCAGTTCTCAAAGAGTATGATGTTTTCACATTTCA
66 TTTAAAGTCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCTTTCGCCTTTCA
* * *
647310 AAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAATAGTGGGATGCCTTTTCCTTTTAAAGCC
131 AAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCCTTTTAAAGCC
*
647375 CACACAAGTTGGTGGCACTTTTCAGTCCTCAAGGAGCAGGACGCATTTT
196 CACACAAGTTGGTGGCACTTTTCAGTCCTCAAGGAGCAGGACGCCTTTT
* * * *
647424 -CTTTTAAAGCCCACACAAGCTGGTAGCACTTTTCTAGTCCTCAAAGAGCAGGACATCTTTTCCT
1 CCTTTCAAAGCCCACACAAGCTGGTGGCACTTTTCTAGTCCTCAAAAAGCAGGACACCTTTTCCT
* *
647488 TTTAAAGTCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGGATGCTTTCGCCTTTCA
66 TTTAAAGTCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCTTTCGCCTTTCA
*** * *
647553 AAGCTTGCACAAGCTGGTGGTACCTTCAGTCCTTAAAGAGCGGGACGCCTTTTCCTTTTAAAGCC
131 AAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCCTTTTAAAGCC
* * *
647618 CACACAAGTTGGTGGCACTTTTTAGTCCTCAAGGAGTAGGATGCCTTTT
196 CACACAAGTTGGTGGCACTTTTCAGTCCTCAAGGAGCAGGACGCCTTTT
* * * *
647667 CCTTTCAAAGCCCACACAAGCTGATGGCAC-CTTC-AGTCCTCAAAGAGCAGGACACCTTTTTCT
1 CCTTTCAAAGCCCACACAAGCTGGTGGCACTTTTCTAGTCCTCAAAAAGCAGGACACCTTTTCCT
* * * * * *
647730 TTTCAAAGCCCGCACAAGTTGGTGACACC-TCTTAGTCCTCAAAGAGCAGGACGCCTTTC-CTTT
66 TTT-AAAGTCCACACAAGTTGGTGGCACCTTC-CAGTCCTCAAAGAGCAGGATG-CTTTCGCCTT
* * * * *
647793 TCAAAGCCCACACGAGTTGGTGGCACTTTTCAATCCTCAAAGAGCAGGACGCCTTTTCCTTTT
128 TCAAAGCCCACACAAGCTGGTGGCAC-CTTCAGTCCTCAAAGAGCGGGACGCCTTTTCCTTTT
647856 CTCCTTTGTC
Statistics
Matches: 607, Mismatches: 64, Indels: 10
0.89 0.09 0.01
Matches are distributed among these distances:
242 32 0.05
243 287 0.47
244 288 0.47
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (244 bp):
CCTTTCAAAGCCCACACAAGCTGGTGGCACTTTTCTAGTCCTCAAAAAGCAGGACACCTTTTCCT
TTTAAAGTCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCTTTCGCCTTTCA
AAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCCTTTTAAAGCC
CACACAAGTTGGTGGCACTTTTCAGTCCTCAAGGAGCAGGACGCCTTTT
Found at i:647954 original size:42 final size:42
Alignment explanation
Indices: 647905--648139 Score: 188
Period size: 42 Copynumber: 5.5 Consensus size: 42
647895 TCTTTTCCCT
* *
647905 TTTGTCCTCAAAGAGTAGGATGC-CTTTTTTTTTCTTTTTTCC
1 TTTGTCCTCAAAGAGCAGGATGCAC-TTTATTTTCTTTTTTCC
* *
647947 TTTGTCCTCAAAGAGCAGGACGCACTTTATTTCCTTATTTTGCC
1 TTTGTCCTCAAAGAGCAGGATGCACTTTATTTTCTT-TTTT-CC
* * * *
647991 TTCTAGTTCTCAAAGAGCAAGATGCACTTTATTCTCCTTTTTCC
1 TT-T-GTCCTCAAAGAGCAGGATGCACTTTATTTTCTTTTTTCC
* * * * *
648035 TTTGTCCTCAGAAAAAGTA-GA-ACACATTTAATTTCCTTTTTCC
1 TTTGTCCTC--AAAGAGCAGGATGCAC-TTTATTTTCTTTTTTCC
* * * * *
648078 TTTGTCTTCAAAGGGCACGATGCATTTTATTTCCTTTTTTCC
1 TTTGTCCTCAAAGAGCAGGATGCACTTTATTTTCTTTTTTCC
* * *
648120 TTAGTCCCCAAGGAGCAGGA
1 TTTGTCCTCAAAGAGCAGGA
648140 CCTATTTCAT
Statistics
Matches: 152, Mismatches: 31, Indels: 20
0.75 0.15 0.10
Matches are distributed among these distances:
41 5 0.03
42 68 0.45
43 33 0.22
44 14 0.09
45 5 0.03
46 27 0.18
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (42 bp):
TTTGTCCTCAAAGAGCAGGATGCACTTTATTTTCTTTTTTCC
Found at i:647980 original size:87 final size:85
Alignment explanation
Indices: 647847--648140 Score: 256
Period size: 87 Copynumber: 3.4 Consensus size: 85
647837 CAGGACGCCT
* * * **
647847 TTTCCTTTTCTCCTTTGTCCTTAAAGAGCATGACACATTTCGTTTCCCTCTTTTCCCTTTTGTCC
1 TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTAATTTCCCT-TTTT-CCTTTTGTCC
* * *
647912 TCAAAGAGTAGGATGCCTTTTT
64 TCAAAGAGCAAGATGCCTTTTA
* * * *
647934 TTTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTT-ATTTCCTTATTTTGCCTTCTAGT
1 TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACACA-TTTAATTTCCCT-TTTT-CCTT-TTGT
*
647998 TCTCAAAGAGCAAGATGCAC-TTTA
62 CCTCAAAGAGCAAGATGC-CTTTTA
* * *
648022 TTCTCC-TTTTTCCTTTGTCCTCAGAAAAAGTAGAACACATTTAATTT-CCTTTTTCC-TTTGTC
1 TT-TCCTTTTTTCCTTTGTCCTC--AAAGAGCAGGACACATTTAATTTCCCTTTTTCCTTTTGTC
* * * *
648084 TTCAAAGGGCACGATGCATTTTA
63 CTCAAAGAGCAAGATGCCTTTTA
* * *
648107 TTTCCTTTTTTCCTTAGTCCCCAAGGAGCAGGAC
1 TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGAC
648141 CTATTTCATT
Statistics
Matches: 166, Mismatches: 32, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
83 8 0.05
84 3 0.02
85 37 0.22
86 1 0.01
87 48 0.29
88 46 0.28
89 8 0.05
90 15 0.09
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.42
Consensus pattern (85 bp):
TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTAATTTCCCTTTTTCCTTTTGTCCTC
AAAGAGCAAGATGCCTTTTA
Found at i:648863 original size:49 final size:50
Alignment explanation
Indices: 648753--648883 Score: 176
Period size: 49 Copynumber: 2.7 Consensus size: 50
648743 TCACAATTTC
* * * *
648753 TATCTATACATGGTTCATTGTATCGATACATTCTGAGTTTTACCCGGATG
1 TATCGATACATTGTTCATTGTATCGATACATTCTGAGGTTTACCCAGATG
* *
648803 TGTCGATACATTGTTCATTTTATCGATACATTCTG-GGTTTACCCAGATG
1 TATCGATACATTGTTCATTGTATCGATACATTCTGAGGTTTACCCAGATG
* *
648852 TATCGATACATTTTTCAATGTATCGAT-CATTC
1 TATCGATACATTGTTCATTGTATCGATACATTC
648884 ATGCATTTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
48 5 0.07
49 35 0.49
50 31 0.44
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.41
Consensus pattern (50 bp):
TATCGATACATTGTTCATTGTATCGATACATTCTGAGGTTTACCCAGATG
Found at i:650398 original size:13 final size:13
Alignment explanation
Indices: 650380--650436 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
650370 CATAAAGTGT
650380 TGTATCGATACAA
1 TGTATCGATACAA
650393 TGTATCGATACATAA
1 TGTATCGATAC--AA
650408 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
650425 TGTATCGATACA
1 TGTATCGATACA
650437 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:650415 original size:32 final size:32
Alignment explanation
Indices: 650360--650457 Score: 178
Period size: 32 Copynumber: 3.0 Consensus size: 32
650350 TTCAACGATT
650360 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
650393 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
650425 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
650457 T
1 T
650458 TTAAGCTACT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 51 0.80
33 13 0.20
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Done.