Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold57
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: 4071704
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82236 characters in sequence are not A, C, G, or T
File 5 of 27
Found at i:503420 original size:19 final size:19
Alignment explanation
Indices: 503375--503474 Score: 76
Period size: 19 Copynumber: 5.3 Consensus size: 19
503365 AGGGTCACAT
* *
503375 AATATGATTACATTCAACC
1 AATATAATTACATTCAAAC
* *
503394 TA-ATAATTACATTTAAAC
1 AATATAATTACATTCAAAC
* *
503412 AATATAATTACATTTAACC
1 AATATAATTACATTCAAAC
* *
503431 TACTATGATTACATTCAAAC
1 -AATATAATTACATTCAAAC
* * * *
503451 TATATGATGACATTCAAAT
1 AATATAATTACATTCAAAC
503470 AATAT
1 AATAT
503475 GGTTATTCAA
Statistics
Matches: 64, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
18 14 0.22
19 35 0.55
20 15 0.23
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (19 bp):
AATATAATTACATTCAAAC
Found at i:503464 original size:39 final size:37
Alignment explanation
Indices: 503375--503467 Score: 114
Period size: 39 Copynumber: 2.5 Consensus size: 37
503365 AGGGTCACAT
*
503375 AATATGATTACATTCAACCTAATAATTACATTTAAAC
1 AATATGATTACATTCAACCTAATAATTACATTCAAAC
* * *
503412 AATATAATTACATTTAACCTACTATGATTACATTCAAAC
1 AATATGATTACATTCAACCTA--ATAATTACATTCAAAC
* *
503451 TATATGATGACATTCAA
1 AATATGATTACATTCAA
503468 ATAATATGGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
37 19 0.41
39 27 0.59
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.35
Consensus pattern (37 bp):
AATATGATTACATTCAACCTAATAATTACATTCAAAC
Found at i:503495 original size:20 final size:20
Alignment explanation
Indices: 503470--503507 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
503460 ACATTCAAAT
*
503470 AATATGGTTATTCAAACAAC
1 AATATGATTATTCAAACAAC
503490 AATATGATTATTCAAACA
1 AATATGATTATTCAAACA
503508 TTCAAACATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (20 bp):
AATATGATTATTCAAACAAC
Found at i:504517 original size:13 final size:13
Alignment explanation
Indices: 504499--504523 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
504489 CATATTGCTT
504499 TGTATCGATACAC
1 TGTATCGATACAC
504512 TGTATCGATACA
1 TGTATCGATACA
504524 TGATCTTGGT
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:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:504537 original size:19 final size:19
Alignment explanation
Indices: 504512--504565 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
504502 ATCGATACAC
*
504512 TGTATCGATACATGAT-CT
1 TGTATCGATACATGATAAT
*
504530 TGGTATCGATACATAATGAAT
1 T-GTATCGATACATGAT-AAT
504551 TGTATCGATACATGA
1 TGTATCGATACATGA
504566 AACTAACAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 1 0.03
19 14 0.47
20 13 0.43
21 2 0.07
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATGATAAT
Found at i:504541 original size:32 final size:33
Alignment explanation
Indices: 504481--504542 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
504471 GACCTAAAAA
*
504481 TATCGATACATATTGCTTTGTATCGATACACTG
1 TATCGATACATATTGCTTGGTATCGATACACTG
504514 TATCGATACATGA-T-CTTGGTATCGATACA
1 TATCGATACAT-ATTGCTTGGTATCGATACA
504543 TAATGAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 14 0.52
33 12 0.44
34 1 0.04
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (33 bp):
TATCGATACATATTGCTTGGTATCGATACACTG
Found at i:514926 original size:22 final size:21
Alignment explanation
Indices: 514901--514960 Score: 59
Period size: 23 Copynumber: 2.8 Consensus size: 21
514891 ATTATTATTT
514901 TTTAATAAAATTAAAAATAATA
1 TTTAATAAAATTAAAAA-AATA
**
514923 TTTAATTAAGTTTAAAAAAATA
1 TTTAA-TAAAATTAAAAAAATA
*
514945 TATTAA-CAAATTAAAA
1 T-TTAATAAAATTAAAA
514961 TATTAATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
21 7 0.23
22 10 0.32
23 14 0.45
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
TTTAATAAAATTAAAAAAATA
Found at i:515556 original size:125 final size:123
Alignment explanation
Indices: 515363--515721 Score: 466
Period size: 125 Copynumber: 2.9 Consensus size: 123
515353 AAAAAAATAT
* *
515363 AATTATAATAAAAAACTTTTTTTAATTTAAAA-TTTTTATTTTAAAAATATAATAATTAATATTT
1 AATTATAATAAAAAACCTTTTTTATTTTAAAATTTTTTATTTTAAAAA-ATAATAATTAATATTT
* *
515427 TAATTTGTTAATTTAAAATTTTTAAACTTAATTAAATATTATTTTTTATTTAATT-AAA
65 TAATTTGTTAATATAAATTTTTTAAACTTAATTAAATATTATTTTTTATTTAATTAAAA
*
515485 AATTTTAA-AAAAAACCTTTTTTATTTTAAAATTTTTTATTTTTATAAAAACATAATAATTAATA
1 AATTATAATAAAAAACCTTTTTTATTTTAAAATTTTTTA--TTT-TAAAAA-ATAATAATTAATA
* * *
515549 TTTTAATTTGTTAATGT-AATTTTTTAAACTTAATTAAATA-T-TTTTTAATTTTATTAAAA
62 TTTTAATTTGTTAATATAAATTTTTTAAACTTAATTAAATATTATTTTTTATTTAATTAAAA
* * * *
515608 AATAATAATAATAAACCCTTTTTTTTTATTTAAATTTTTTA-TTTAAAAAA-AAT-ATTAATATT
1 AATTATAATAA-AAAACCTTTTTTATT-TTAAAATTTTTTATTTTAAAAAATAATAATTAATATT
*
515670 TTAATTTGTTAATATAAATTTTTTTAAAGTTAATTAAATATTATTTTTTATT
64 TTAATTTGTTAATATAAA-TTTTTTAAACTTAATTAAATATTATTTTTTATT
515722 CAAAATAATA
Statistics
Matches: 209, Mismatches: 16, Indels: 23
0.84 0.06 0.09
Matches are distributed among these distances:
119 23 0.11
120 5 0.02
121 42 0.20
122 32 0.15
123 20 0.10
124 27 0.13
125 48 0.23
126 12 0.06
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (123 bp):
AATTATAATAAAAAACCTTTTTTATTTTAAAATTTTTTATTTTAAAAAATAATAATTAATATTTT
AATTTGTTAATATAAATTTTTTAAACTTAATTAAATATTATTTTTTATTTAATTAAAA
Found at i:515647 original size:14 final size:13
Alignment explanation
Indices: 515629--515654 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
515619 TAAACCCTTT
515629 TTTTTTATTTAAA
1 TTTTTTATTTAAA
515642 TTTTTTATTTAAA
1 TTTTTTATTTAAA
515655 AAAAATATTA
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:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTTATTTAAA
Found at i:516564 original size:183 final size:186
Alignment explanation
Indices: 516324--516718 Score: 500
Period size: 183 Copynumber: 2.1 Consensus size: 186
516314 AAAATAAATG
* * * * *
516324 TGATTATATCTGAGAATCGGATT-TTTTTTAT-G--GAAAAAAAGAAAAGTTAATTGATTGTAAA
1 TGATTATATATAAGAATCAGATTCTTTTTTATAGAAAAAAAAAAGAAAAGTTAACTGATTGTAAA
** * * *
516385 TGTCAGACTGTAAGGATTAGACTAATGCATAAATTATATCTGATAATCGGATT-ATTTTTATAG-
66 TGTCAGACTACAAGAATTAGACTAATGCATAAATTATATCTGAGAATCAGATTCATTTTTATAGT
* * *
516448 AAAAA-AAAG-ACTGATTGATTGTAAATGTCAAACTGTAAGGATTAAACTAATGCA
131 AAAAAGAAAGAACTAATTGATTGCAAATGTCAAACTGCAAGGATTAAACTAATGCA
*
516502 TGAATTATATATAAGAATCAGATTCTTTTTTATAGAAAAAAAAAAGAAAAGTTGACTGATTGTAA
1 TG-ATTATATATAAGAATCAGATTCTTTTTTATAGAAAAAAAAAAGAAAAGTTAACTGATTGTAA
* *
516567 ATGTCAGACTACAAGAATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAG
65 ATGTCAGACTACAAGAATTAGACTAATGCATAAATTATATCTGAGAATCAGATTCATTTTTATAG
* *
516632 TAAAAAGAAAGAAATACTAATTGATTGCAAATGTCAGACTGCAAGGATTAGACTAATGCA
130 TAAAAAGAAAG--A-ACTAATTGATTGCAAATGTCAAACTGCAAGGATTAAACTAATGCA
* * **
516692 TGATTATCTCTAAGAATTGGATTCTTT
1 TGATTATATATAAGAATCAGATTCTTT
516719 AAACTCAAAG
Statistics
Matches: 183, Mismatches: 22, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
178 2 0.01
179 18 0.10
180 8 0.04
181 1 0.01
183 73 0.40
184 9 0.05
185 5 0.03
186 4 0.02
189 21 0.11
190 42 0.23
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (186 bp):
TGATTATATATAAGAATCAGATTCTTTTTTATAGAAAAAAAAAAGAAAAGTTAACTGATTGTAAA
TGTCAGACTACAAGAATTAGACTAATGCATAAATTATATCTGAGAATCAGATTCATTTTTATAGT
AAAAAGAAAGAACTAATTGATTGCAAATGTCAAACTGCAAGGATTAAACTAATGCA
Found at i:516592 original size:95 final size:93
Alignment explanation
Indices: 516326--516718 Score: 444
Period size: 95 Copynumber: 4.3 Consensus size: 93
516316 AATAAATGTG
* * * *
516326 ATTATATCTGAGAATCGGATT-TTTTTTAT-G-GAAAAAAAGAAAAGTTAATTGATTGTAAATGT
1 ATTATATCTAAGAATCAGATTCTTTTTTATAGAAAAAAAAAGAAAA-CTAATTGATTGTAAATGT
* *
516388 CAGACTGTAAGGATTAGACTAATGCATAA
65 CAGACTGCAAGGATTAGACTAATGCATGA
* * * * *
516417 ATTATATCTGATAATCGGATT-ATTTTTATAG-AAAAAAAAG---ACTGATTGATTGTAAATGTC
1 ATTATATCTAAGAATCAGATTCTTTTTTATAGAAAAAAAAAGAAAACTAATTGATTGTAAATGTC
* * *
516477 AAACTGTAAGGATTAAACTAATGCATGA
66 AGACTGCAAGGATTAGACTAATGCATGA
* * * *
516505 ATTATATATAAGAATCAGATTCTTTTTTATAGAAAAAAAAAAGAAAAGTTGACTGATTGTAAATG
1 ATTATATCTAAGAATCAGATTCTTTTTTATAG-AAAAAAAAAGAAAA-CTAATTGATTGTAAATG
* *
516570 TCAGACTACAAGAATTAGACTAATGCATGA
64 TCAGACTGCAAGGATTAGACTAATGCATGA
* * *
516600 ATTATATCTGAGAATCAGATTCTTTTTTATAGTAAAAAGAAAGAAATACTAATTGATTGCAAATG
1 ATTATATCTAAGAATCAGATTCTTTTTTATAG-AAAAAAAAAGAAA-ACTAATTGATTGTAAATG
516665 TCAGACTGCAAGGATTAGACTAATGCATG-
64 TCAGACTGCAAGGATTAGACTAATGCATGA
* **
516694 ATTATCTCTAAGAATTGGATTCTTT
1 ATTATATCTAAGAATCAGATTCTTT
516719 AAACTCAAAG
Statistics
Matches: 259, Mismatches: 34, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
88 59 0.23
89 10 0.04
91 36 0.14
92 9 0.03
94 22 0.08
95 122 0.47
96 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (93 bp):
ATTATATCTAAGAATCAGATTCTTTTTTATAGAAAAAAAAAGAAAACTAATTGATTGTAAATGTC
AGACTGCAAGGATTAGACTAATGCATGA
Found at i:517560 original size:20 final size:20
Alignment explanation
Indices: 517533--517588 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
517523 CTACTAGTTT
517533 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAG
**
517553 TTTGTATCGATACAA-TGAG
1 CATGTATCGATACAATTGAG
*
517572 CATGTCTCGATACAATT
1 CATGTATCGATACAATT
517589 ATTGATACAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:517616 original size:32 final size:32
Alignment explanation
Indices: 517573--517688 Score: 99
Period size: 32 Copynumber: 3.4 Consensus size: 32
517563 TACAATGAGC
*
517573 ATGTCTCGATACAATTATTGATACAAAGCATA
1 ATGTATCGATACAATTATTGATACAAAGCATA
* * **
517605 ATGTATCGATACATCTGGATGTGTATCGATACAATG-AGC
1 ATGTATCGATACA-----A--T-TATTGATACAAAGCATA
*
517644 ATGTCTCGATACAATTATTGATACAAAGCATA
1 ATGTATCGATACAATTATTGATACAAAGCATA
517676 ATGTATCGATACA
1 ATGTATCGATACA
517689 TCTGGATGTG
Statistics
Matches: 64, Mismatches: 11, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
31 11 0.17
32 26 0.41
34 1 0.02
37 1 0.02
39 14 0.22
40 11 0.17
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (32 bp):
ATGTATCGATACAATTATTGATACAAAGCATA
Found at i:517650 original size:71 final size:71
Alignment explanation
Indices: 517534--517707 Score: 307
Period size: 71 Copynumber: 2.5 Consensus size: 71
517524 TACTAGTTTC
*
517534 ATGTATCGATACAAT-T-GAGTTTGTATCGATACAATGAGCATGTCTCGATACAATTATTGATAC
1 ATGTATCGATAC-ATCTGGA-TGTGTATCGATACAATGAGCATGTCTCGATACAATTATTGATAC
517597 AAAGCATA
64 AAAGCATA
517605 ATGTATCGATACATCTGGATGTGTATCGATACAATGAGCATGTCTCGATACAATTATTGATACAA
1 ATGTATCGATACATCTGGATGTGTATCGATACAATGAGCATGTCTCGATACAATTATTGATACAA
517670 AGCATA
66 AGCATA
517676 ATGTATCGATACATCTGGATGTGTATCGATAC
1 ATGTATCGATACATCTGGATGTGTATCGATAC
517708 TTTCTAGGGT
Statistics
Matches: 100, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
70 2 0.02
71 96 0.96
72 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (71 bp):
ATGTATCGATACATCTGGATGTGTATCGATACAATGAGCATGTCTCGATACAATTATTGATACAA
AGCATA
Found at i:521286 original size:16 final size:16
Alignment explanation
Indices: 521265--521295 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
521255 CAACATTTCC
*
521265 TCTATTAAAACTTTTT
1 TCTATTAAAAATTTTT
521281 TCTATTAAAAATTTT
1 TCTATTAAAAATTTT
521296 GAAAGCCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TCTATTAAAAATTTTT
Found at i:526057 original size:13 final size:13
Alignment explanation
Indices: 526039--526064 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
526029 ACAATTCTTT
526039 ATGTATCGATACA
1 ATGTATCGATACA
526052 ATGTATCGATACA
1 ATGTATCGATACA
526065 TTGTCCTATG
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:526061 original size:33 final size:33
Alignment explanation
Indices: 526019--526084 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
526009 GTTGGGCATG
*
526019 ATGTATCGATACAATTCT-TTATGTATCGATACA
1 ATGTATCGATAC-ATTCTCCTATGTATCGATACA
*
526052 ATGTATCGATACATTGTCCTATGTATCGATACA
1 ATGTATCGATACATTCTCCTATGTATCGATACA
526085 TTTCACTTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 4 0.13
33 26 0.87
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.38
Consensus pattern (33 bp):
ATGTATCGATACATTCTCCTATGTATCGATACA
Found at i:526156 original size:19 final size:20
Alignment explanation
Indices: 526113--526159 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
526103 CTACCAGTTT
526113 CATGTATCGATAAAATTGAG
1 CATGTATCGATAAAATTGAG
* *
526133 TATGTATCGATACAA-TGAG
1 CATGTATCGATAAAATTGAG
526152 CATGTATC
1 CATGTATC
526160 AATATAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (20 bp):
CATGTATCGATAAAATTGAG
Found at i:526693 original size:25 final size:25
Alignment explanation
Indices: 526659--526711 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
526649 TGAAATATTT
*
526659 ATTTATTTATATTTTTGGTAACACA
1 ATTTATTTATATTTTTGATAACACA
* *
526684 ATTTGTTTATATTTTTGATAACGCA
1 ATTTATTTATATTTTTGATAACACA
526709 ATT
1 ATT
526712 AAGGTTTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.09, T:0.53
Consensus pattern (25 bp):
ATTTATTTATATTTTTGATAACACA
Found at i:528198 original size:14 final size:16
Alignment explanation
Indices: 528179--528216 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
528169 AATTATTTAT
528179 TTAATTTT-AA-TAAA
1 TTAATTTTAAATTAAA
528193 TTAATTTTAAATTAAA
1 TTAATTTTAAATTAAA
*
528209 TCAATTTT
1 TTAATTTT
528217 TTTAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 2 0.10
16 11 0.52
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATTTTAAATTAAA
Found at i:528250 original size:27 final size:28
Alignment explanation
Indices: 528220--528277 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
528210 CAATTTTTTT
528220 AAAATT-TTTATTA-TT-ATTTAATAAATA
1 AAAATTATTT-TTACTTCATTTAAT-AATA
528247 AAAATTATTTTTACTTGCATTTAATAATA
1 AAAATTATTTTTACTT-CATTTAATAATA
528276 AA
1 AA
528278 TATAAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
27 9 0.33
28 5 0.19
29 6 0.22
30 7 0.26
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (28 bp):
AAAATTATTTTTACTTCATTTAATAATA
Found at i:529178 original size:22 final size:19
Alignment explanation
Indices: 529148--529203 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
529138 TTCAATTTCA
529148 AATT-TTATATTTTAGAATAT
1 AATTATTATATTTTA-AA-AT
*
529168 AATTATATATATTTTATAAT
1 AATTAT-TATATTTTAAAAT
529188 AATTATTATAATTTTA
1 AATTATTAT-ATTTTA
529204 TTTTATTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 3 0.09
20 18 0.56
21 2 0.06
22 9 0.28
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
AATTATTATATTTTAAAAT
Found at i:529189 original size:20 final size:20
Alignment explanation
Indices: 529166--529204 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
529156 ATTTTAGAAT
529166 ATAATTA-TATATATTTTATA
1 ATAATTATTATA-ATTTTATA
529186 ATAATTATTATAATTTTAT
1 ATAATTATTATAATTTTAT
529205 TTTATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATAATTATTATAATTTTATA
Found at i:529304 original size:16 final size:15
Alignment explanation
Indices: 529265--529334 Score: 60
Period size: 15 Copynumber: 4.9 Consensus size: 15
529255 TATATTTTTA
*
529265 AAAAAATA-TTAA-C
1 AAAAAATATTTAATT
529278 AAAAAA-A-TTAATT
1 AAAAAATATTTAATT
529291 AAAAATATATTTAATT
1 AAAAA-ATATTTAATT
* *
529307 ATTAAAAT-TTAAATT
1 A-AAAAATATTTAATT
529322 AAAAAATATTTAA
1 AAAAAATATTTAA
529335 AAATAAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
12 5 0.11
13 11 0.24
14 6 0.13
15 12 0.26
16 9 0.20
17 3 0.07
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAAAATATTTAATT
Found at i:529335 original size:16 final size:16
Alignment explanation
Indices: 529287--529335 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
529277 CAAAAAAATT
529287 AATTAAAAATATATTT-
1 AATTAAAAA-ATATTTA
**
529303 AATTATTAAA-ATTTA
1 AATTAAAAAATATTTA
529318 AATTAAAAAATATTTA
1 AATTAAAAAATATTTA
529334 AA
1 AA
529336 AATAAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 4 0.15
15 9 0.33
16 14 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTAAAAAATATTTA
Found at i:529344 original size:30 final size:29
Alignment explanation
Indices: 529265--529344 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 29
529255 TATATTTTTA
*
529265 AAAAAATA-TTAACAA-AAAAA-TTAATT
1 AAAAAATATTTAAAAATAAAAATTTAATT
** *
529291 AAAAATATATTTAATTATTAAAATTTAAATT
1 AAAAA-ATATTTAAAAATAAAAATTT-AATT
529322 AAAAAATATTTAAAAATAAAAAT
1 AAAAAATATTTAAAAATAAAAAT
529345 ATAACATAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.12
27 3 0.07
28 5 0.12
29 4 0.09
30 17 0.40
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (29 bp):
AAAAAATATTTAAAAATAAAAATTTAATT
Found at i:529355 original size:30 final size:28
Alignment explanation
Indices: 529265--529355 Score: 78
Period size: 30 Copynumber: 3.1 Consensus size: 28
529255 TATATTTTTA
* *
529265 AAAAAATA-TTAACAA-AAAAATTAATT
1 AAAAAATATTTAAAAATAAAAATTAAAT
* * *
529291 AAAAATATATTTAATTATTAAAATTTAAATT
1 AAAAA-ATATTTAA-AAATAAAAATTAAA-T
529322 AAAAAATATTTAAAAATAAAAATATAACAT
1 AAAAAATATTTAAAAATAAAAAT-TAA-AT
529352 AAAA
1 AAAA
529356 TAATCTAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
26 5 0.10
27 3 0.06
28 4 0.08
29 8 0.16
30 24 0.47
31 7 0.14
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (28 bp):
AAAAAATATTTAAAAATAAAAATTAAAT
Found at i:533902 original size:23 final size:20
Alignment explanation
Indices: 533873--533936 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 20
533863 TTATATTCGT
533873 ATAAAAATATATTTAAATATAA
1 ATAAAAATAT-TTTAAATAT-A
533895 ATATAAAATAAATTTTTAAATAT-
1 ATA-AAAAT--A-TTTTAAATATA
533918 ATAAAAA-ATTTTAAATATA
1 ATAAAAATATTTTAAATATA
533937 TATTAGACAC
Statistics
Matches: 37, Mismatches: 0, Indels: 13
0.74 0.00 0.26
Matches are distributed among these distances:
18 10 0.27
19 1 0.03
22 7 0.19
23 8 0.22
25 10 0.27
26 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAAAAATATTTTAAATATA
Found at i:533931 original size:18 final size:20
Alignment explanation
Indices: 533892--533938 Score: 73
Period size: 18 Copynumber: 2.5 Consensus size: 20
533882 TATTTAAATA
533892 TAAATATA-AAATAAATTTT
1 TAAATATATAAATAAATTTT
533911 TAAATATATAAA-AAA-TTT
1 TAAATATATAAATAAATTTT
533929 TAAATATATA
1 TAAATATATA
533939 TTAGACACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.48
19 11 0.41
20 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATATATAAATAAATTTT
Found at i:534885 original size:57 final size:57
Alignment explanation
Indices: 534797--534914 Score: 155
Period size: 57 Copynumber: 2.1 Consensus size: 57
534787 CAGTTTTTTT
* * * *
534797 ATAATGAATTAAATGTATTATAATTATTATCAAACTAACATTGCAATAAAAAGATTA
1 ATAATAAATCAAATGTACTATAATTATTATCAAACTAACATTGAAATAAAAAGATTA
* * ** *
534854 ATAATAAATCAAATGTACTGTAATTATTATCAAACTAGCATTGAAATCGAAGGATTA
1 ATAATAAATCAAATGTACTATAATTATTATCAAACTAACATTGAAATAAAAAGATTA
534911 ATAA
1 ATAA
534915 ACCACAACTG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.33
Consensus pattern (57 bp):
ATAATAAATCAAATGTACTATAATTATTATCAAACTAACATTGAAATAAAAAGATTA
Found at i:535936 original size:31 final size:31
Alignment explanation
Indices: 535891--535966 Score: 134
Period size: 31 Copynumber: 2.4 Consensus size: 31
535881 AGAATTTGAT
*
535891 TTGAAATTTGCTAGTCGCCAGTCAAGTTCAAA
1 TTGAAA-TTGCTAGTCGCCAGCCAAGTTCAAA
535923 TTGAAATTGCTAGTCGCCAGCCAAGTTCAAA
1 TTGAAATTGCTAGTCGCCAGCCAAGTTCAAA
535954 TTGAAATTGCTAG
1 TTGAAATTGCTAG
535967 CCGTCAACCG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 37 0.86
32 6 0.14
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (31 bp):
TTGAAATTGCTAGTCGCCAGCCAAGTTCAAA
Found at i:539412 original size:51 final size:52
Alignment explanation
Indices: 539351--539469 Score: 138
Period size: 51 Copynumber: 2.3 Consensus size: 52
539341 AAATAACAGG
* * *
539351 GTTGGAGTATCCCT-GATTATAGAAAA-TTGGTGTTTT-GAAAATAAAATTGGA
1 GTTGGAGTATCCCTCGACTAT-GAAAATTTGGTATTTTAG-AAATAAAATCGGA
* *
539402 GTTGGAGTAT-CCTCGACTGTGAAAATTTGGTATTTTAGAAATAAAATCGGG
1 GTTGGAGTATCCCTCGACTATGAAAATTTGGTATTTTAGAAATAAAATCGGA
539453 GTTGGAGTATCCTCTCG
1 GTTGGAGTATCC-CTCG
539470 GAAATAACGG
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
50 8 0.14
51 44 0.76
52 2 0.03
53 4 0.07
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.34
Consensus pattern (52 bp):
GTTGGAGTATCCCTCGACTATGAAAATTTGGTATTTTAGAAATAAAATCGGA
Found at i:539414 original size:79 final size:79
Alignment explanation
Indices: 539195--539415 Score: 322
Period size: 79 Copynumber: 2.8 Consensus size: 79
539185 AAAACGGGGC
* * *
539195 TGGAGTATCCCCGATTAT-GAAAAATCGGTGTTTT-AGAAGTAAAATCGGGGTTGGAGTATCCCC
1 TGGAGTATCCCTGATTATAG-AAAATCGGTGTTTTGA-AAATAAAATCGGGGTTGGAGTATCCTC
539258 TCAGAAATAACAGGGT
64 TCAGAAATAACAGGGT
* *
539274 TGGAGTATCCCTGATTATAGAAAATCGGTATTTTGAAACTAAAATCGGGGTTGGAGTATCCTCTC
1 TGGAGTATCCCTGATTATAGAAAATCGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCTCTC
539339 -GAAAATAACAGGGT
66 AG-AAATAACAGGGT
* * *
539353 TGGAGTATCCCTGATTATAGAAAATTGGTGTTTTGAAAATAAAATTGGAGTTGGAGTATCCTC
1 TGGAGTATCCCTGATTATAGAAAATCGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCTC
539416 GACTGTGAAA
Statistics
Matches: 130, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
78 1 0.01
79 127 0.98
80 2 0.02
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (79 bp):
TGGAGTATCCCTGATTATAGAAAATCGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCTCTC
AGAAATAACAGGGT
Found at i:539486 original size:79 final size:79
Alignment explanation
Indices: 539403--539622 Score: 266
Period size: 78 Copynumber: 2.8 Consensus size: 79
539393 AAAATTGGAG
* * *
539403 TTGGAGTATCCTCGACTGTGAAAATTTGGTATTTTAGAAATAAAATCGGGGTTGGAGTAT-CCTC
1 TTGGAGTATCCCCAATTGTGAAAATTTGGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCT-
539467 TCGGAAATAACGGGA
65 TCGGAAATAACGGGA
* * *** * *
539482 TTGGAGTA-CCCCAATTATGAAAAATCAATATTTTAGATATAAAACCGGGGTTGGAGTATCCCTT
1 TTGGAGTATCCCCAATTGTGAAAATTTGGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCTT
*
539546 CGGAAATAACGGGG
66 CGGAAATAACGGGA
* ***
539560 TTGGAGTATCCCCAATTGT-AAAATATTGGTGTTTTAGAAATAAAATCAAAGTTGGAGTATCCC
1 TTGGAGTATCCCCAATTGTGAAAAT-TTGGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCC
539623 CGATTGCAGT
Statistics
Matches: 116, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
78 67 0.58
79 49 0.42
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (79 bp):
TTGGAGTATCCCCAATTGTGAAAATTTGGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCTT
CGGAAATAACGGGA
Found at i:539594 original size:208 final size:209
Alignment explanation
Indices: 539195--539625 Score: 552
Period size: 208 Copynumber: 2.1 Consensus size: 209
539185 AAAACGGGGC
* * *
539195 TGGAGTATCCCCGATTATGAAAAATCGGTGTTTTAGAAGTAAAATCGGGGTTGGAGTATCCCCTC
1 TGGAGTATCCCCGACTATGAAAAATCGGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTC
** ** *
539260 AGAAATAACAGGGTTGGAGTATCCCTGATTATAGAAAATCGGTATTTTGAAACTAAAATCGGGGT
66 AGAAATAACAGGGTTGGAGTATCCCCAATTATAGAAAATCAATATTTTGAAACTAAAACCGGGGT
**
539325 TGGAGTATCCTCTCGAAAATAACAGGGTTGGAGTATCCCTGATTATAGAAAATTGGTGTTTT-GA
131 TGGAGTATCCTCTCGAAAATAACAGGGTTGGAGTATCCCCAATTATAGAAAATTGGTGTTTTAG-
***
539389 AAATAAAATTGGAGT
195 AAATAAAATCAAAGT
* * * * *
539404 TGGAGTATCCTCGACTGTGAAAATTTGGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCTCTC
1 TGGAGTATCCCCGACTATGAAAAATCGGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTC
* *
539469 GGAAATAAC-GGGATTGGAGTA-CCCCAATTAT-GAAAAATCAATATTTTAGATA-TAAAACCGG
66 AGAAATAACAGGG-TTGGAGTATCCCCAATTATAG-AAAATCAATATTTT-GAAACTAAAACCGG
* * *
539530 GGTTGGAGTATCC-CTTCGGAAATAACGGGGTTGGAGTATCCCCAATTGTA-AAATATTGGTGTT
128 GGTTGGAGTATCCTC-TCGAAAATAACAGGGTTGGAGTATCCCCAATTATAGAAA-ATTGGTGTT
539593 TTAGAAATAAAATCAAAGT
191 TTAGAAATAAAATCAAAGT
539612 TGGAGTATCCCCGA
1 TGGAGTATCCCCGA
539626 TTGCAGTAAA
Statistics
Matches: 192, Mismatches: 24, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
207 5 0.03
208 110 0.57
209 77 0.40
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.29
Consensus pattern (209 bp):
TGGAGTATCCCCGACTATGAAAAATCGGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTC
AGAAATAACAGGGTTGGAGTATCCCCAATTATAGAAAATCAATATTTTGAAACTAAAACCGGGGT
TGGAGTATCCTCTCGAAAATAACAGGGTTGGAGTATCCCCAATTATAGAAAATTGGTGTTTTAGA
AATAAAATCAAAGT
Found at i:542046 original size:20 final size:20
Alignment explanation
Indices: 542021--542072 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
542011 GAAATACTTG
* **
542021 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATACAA
542041 AATGTATCGATACAATACAA
1 AATGTATCGATACAATACAA
542061 AATGTATCGATA
1 AATGTATCGATA
542073 TATCTGGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACAATACAA
Found at i:542137 original size:13 final size:13
Alignment explanation
Indices: 542090--542119 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
542080 GTAAACCGAG
*
542090 AATGTATTGATAC
1 AATGTATCGATAC
542103 AATGTATCGATAC
1 AATGTATCGATAC
542116 AATG
1 AATG
542120 AACAATGTAT
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:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:542198 original size:21 final size:21
Alignment explanation
Indices: 542174--542229 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
542164 ATTGGGGCCT
542174 TGTATCGATACATTAAAGGCA
1 TGTATCGATACATTAAAGGCA
542195 TGTATCGATACATTAAAGGCA
1 TGTATCGATACATTAAAGGCA
542216 TGTATCGATACATT
1 TGTATCGATACATT
542230 TTGGCAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (21 bp):
TGTATCGATACATTAAAGGCA
Found at i:550062 original size:14 final size:14
Alignment explanation
Indices: 550043--550071 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
550033 AGCCGTTCGC
550043 TACTCAAATTCAAA
1 TACTCAAATTCAAA
550057 TACTCAAATTCAAA
1 TACTCAAATTCAAA
550071 T
1 T
550072 TGAATTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (14 bp):
TACTCAAATTCAAA
Found at i:550154 original size:2 final size:2
Alignment explanation
Indices: 550149--550173 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
550139 ACACTTACTC
550149 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 T
550174 GCTTGCTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:551854 original size:15 final size:15
Alignment explanation
Indices: 551829--551864 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
551819 TTCTTGGAAA
551829 TTTTAATGGGTTTTCT
1 TTTTAATGGGTTTT-T
551845 TTTTAA-GGGTTTTT
1 TTTTAATGGGTTTTT
551859 TTTTAA
1 TTTTAA
551865 AAAAATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.35
15 7 0.35
16 6 0.30
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.64
Consensus pattern (15 bp):
TTTTAATGGGTTTTT
Found at i:554490 original size:14 final size:15
Alignment explanation
Indices: 554435--554493 Score: 59
Period size: 15 Copynumber: 4.0 Consensus size: 15
554425 CTCGTACTAG
* *
554435 AGTACCTGTGTTAAG
1 AGTACCTGTGTCAAA
*
554450 AGTACC-GATGCCAAA
1 AGTACCTG-TGTCAAA
554465 AGTACCTGTGTCAAA
1 AGTACCTGTGTCAAA
*
554480 A-TACTTGTGTCAAA
1 AGTACCTGTGTCAAA
554494 CGAGAGCTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
14 13 0.35
15 23 0.62
16 1 0.03
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (15 bp):
AGTACCTGTGTCAAA
Found at i:555606 original size:84 final size:82
Alignment explanation
Indices: 555461--555783 Score: 352
Period size: 81 Copynumber: 3.9 Consensus size: 82
555451 CCTGTTAGTG
* * * * *
555461 TCACCTTCAATATTTTGGATATCACCAGTTT-TGTTGTCATCAAGCACTCTTCGCCTCAACTTAA
1 TCACC-TCTATATTTTGGTTATCACCA-TTTCTGTTGTCAACAAGCACTCTTCGCCTGAACTTGA
*
555525 GTTTACTTGGAGT-ACAATCC
64 GTTT-CTTGGAGTGA-ACTCC
* * * * * * *
555545 TCACCTCTATCATTTTGTTTATCAGCATTTATGTTATCAACAAGAACTCTTTGCCGGAACTTGAG
1 TCACCTCTAT-ATTTTGGTTATCACCATTTCTGTTGTCAACAAGCACTCTTCGCCTGAACTTGAG
*
555610 CCTTCTTGGAGTGAACTCC
65 -TTTCTTGGAGTGAACTCC
* *
555629 TCACCTCTA-A-TTTGGTTATCACCATTTCTGTTGTGAACAAGCAGTCTTCGCCTGAACTTGAGT
1 TCACCTCTATATTTTGGTTATCACCATTTCTGTTGTCAACAAGCACTCTTCGCCTGAACTTGAGT
**
555692 AGCCTTGGAGTGAACTCC
66 -TTCTTGGAGTGAACTCC
*
555710 TCACCTC--TATTTTGGTTATCACCATTTCTGCTGTCAACAAGCACTCTTCGCCTGAACTTGAGT
1 TCACCTCTATATTTTGGTTATCACCATTTCTGTTGTCAACAAGCACTCTTCGCCTGAACTTGAGT
*
555773 CTCTTTGGAGT
66 TTC-TTGGAGT
555784 ACAGTCAAAT
Statistics
Matches: 201, Mismatches: 30, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
80 2 0.01
81 122 0.61
82 1 0.00
83 7 0.03
84 66 0.33
85 3 0.01
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (82 bp):
TCACCTCTATATTTTGGTTATCACCATTTCTGTTGTCAACAAGCACTCTTCGCCTGAACTTGAGT
TTCTTGGAGTGAACTCC
Found at i:556737 original size:231 final size:231
Alignment explanation
Indices: 556277--556720 Score: 656
Period size: 231 Copynumber: 1.9 Consensus size: 231
556267 CATGCTCTTC
* * * * *
556277 TCCTTAGAGGATGAAGATGGCATTCTTGTAAAATCACTGGCATGAACCCTATTTTGAATTGATTC
1 TCCTTAGAGGATGAAGATGGCATTCTGGCAAAATCACTGGCATGAACACTATTTCGAATGGATTC
* *
556342 TGCAGGCTTGTTCTCAGGATTTGGCTCAATTACGTACAAAGTCTTATCAGGAATATCAGCAAAGC
66 TGCAGGCTGGTTCTCAGGATTTGGCTCAATTACGTACAAAGTCTTATCAGGAACATCAGCAAAGC
* * * * * *
556407 TGGCTCTTTCAGAATTATGTTTCTTAATATTCTCTTGATCCATCAAATGAGAAACTTCCTTTTGG
131 TGGCTCTCTCAGAATTATGTTCCTTAACATTCTCTTGATCCATCAAACGAGAAACTCCCGTTTGG
*
556472 TTCTCGGACCCTCTGGCACTCTTACCACAGGACTTT
196 TTCTCGGACACTCTGGCACTCTTACCACAGGACTTT
* * *
556508 TCCTTAGAGGATGAAGATGGCATTGTGGCAAAATCACTGGCATGGACACTGTTTCGAATGGATTC
1 TCCTTAGAGGATGAAGATGGCATTCTGGCAAAATCACTGGCATGAACACTATTTCGAATGGATTC
* * * *
556573 TGCAGGCTGGTTCTCGGGATTTGGCTCAATTATGTACAAAGTCTTATCAGGAACATCTGTAAAGC
66 TGCAGGCTGGTTCTCAGGATTTGGCTCAATTACGTACAAAGTCTTATCAGGAACATCAGCAAAGC
*
556638 TGGCT-TCCTCAGAATTATGTTCCTTAACATTCTCTTGATCCATTAAACGAGAAACTCCCGTTTG
131 TGGCTCT-CTCAGAATTATGTTCCTTAACATTCTCTTGATCCATCAAACGAGAAACTCCCGTTTG
* *
556702 GTTCTTGGACACTTTGGCA
195 GTTCTCGGACACTCTGGCA
556721 TTACTACTGC
Statistics
Matches: 188, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
230 1 0.01
231 187 0.99
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (231 bp):
TCCTTAGAGGATGAAGATGGCATTCTGGCAAAATCACTGGCATGAACACTATTTCGAATGGATTC
TGCAGGCTGGTTCTCAGGATTTGGCTCAATTACGTACAAAGTCTTATCAGGAACATCAGCAAAGC
TGGCTCTCTCAGAATTATGTTCCTTAACATTCTCTTGATCCATCAAACGAGAAACTCCCGTTTGG
TTCTCGGACACTCTGGCACTCTTACCACAGGACTTT
Found at i:559440 original size:21 final size:22
Alignment explanation
Indices: 559414--559457 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
559404 TAATTTTTTT
*
559414 ATAAAAAATTAT-AAT-TTAAA
1 ATAAAAAAATATAAATATTAAA
559434 ATAAAAAAATATAAATATTAAA
1 ATAAAAAAATATAAATATTAAA
559456 AT
1 AT
559458 TTATATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.52
21 3 0.14
22 7 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
ATAAAAAAATATAAATATTAAA
Found at i:560074 original size:3 final size:3
Alignment explanation
Indices: 560068--560110 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
560058 TAAGATTAAT
560068 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
560111 GCATTGTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:563618 original size:51 final size:51
Alignment explanation
Indices: 563543--563652 Score: 113
Period size: 51 Copynumber: 2.2 Consensus size: 51
563533 ATATTATTAA
*
563543 AATA-TTTATTTTAAAAGTTAAATAATAATTAAATATGTAAA-T-AAATATTT
1 AATATTTTATTTTAAAAGTTAAATAA-AATTAAAT-TATAAATTAAAATATTT
* *
563593 AATTTTTTATTTATATAAA-TT-AATAAATTTAAATTATAAATTAAAATATTT
1 AATATTTTATTT-TA-AAAGTTAAATAAAATTAAATTATAAATTAAAATATTT
*
563644 GATATTTTA
1 AATATTTTA
563653 CAAATTAAGT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
49 5 0.10
50 11 0.22
51 27 0.54
52 4 0.08
53 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (51 bp):
AATATTTTATTTTAAAAGTTAAATAAAATTAAATTATAAATTAAAATATTT
Found at i:563706 original size:22 final size:22
Alignment explanation
Indices: 563680--563740 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
563670 GATTGAATAA
* * *
563680 TAAATTTTTAAAAATTTATTTT
1 TAAATTTATAAAAATTAATATT
563702 TAAATTTAATAAAAA-TAATATT
1 TAAATTT-ATAAAAATTAATATT
563724 TAAA-TTATAAAAATTAA
1 TAAATTTATAAAAATTAA
563741 ATAATATCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 7 0.21
21 5 0.15
22 16 0.47
23 6 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TAAATTTATAAAAATTAATATT
Found at i:563891 original size:7 final size:7
Alignment explanation
Indices: 563879--563908 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
563869 TAACTTAAAA
563879 AAATTTT
1 AAATTTT
563886 AAATTTT
1 AAATTTT
563893 AAATTTT
1 AAATTTT
563900 AAATTTT
1 AAATTTT
563907 AA
1 AA
563909 TTTAATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
AAATTTT
Found at i:563928 original size:27 final size:26
Alignment explanation
Indices: 563898--563949 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
563888 ATTTTAAATT
563898 TTAAATT-TTAATTTAATTTATATAAAG
1 TTAAATTATT-ATTTAATTTAT-TAAAG
*
563925 TTAAATTATTATTTATTTTATTAAA
1 TTAAATTATTATTTAATTTATTAAA
563950 AATTATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 17 0.74
28 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (26 bp):
TTAAATTATTATTTAATTTATTAAAG
Found at i:563985 original size:18 final size:19
Alignment explanation
Indices: 563932--563982 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
563922 AAGTTAAATT
*
563932 ATTATTTATTTTATTAAAA
1 ATTATTTATTTTATTAATA
*
563951 ATTATTT-TTATATTAATA
1 ATTATTTATTTTATTAATA
*
563969 TTTATTTATTTTAT
1 ATTATTTATTTTAT
563983 AATTAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTATTTATTTTATTAATA
Found at i:564017 original size:19 final size:18
Alignment explanation
Indices: 563990--564029 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
563980 TATAATTAAA
* *
563990 TTTAAATAAATATATTAT
1 TTTAAATAAAAATAATAT
564008 TTTAATATAAAAATAATAT
1 TTTAA-ATAAAAATAATAT
564027 TTT
1 TTT
564030 GACCAAACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATAAAAATAATAT
Found at i:568201 original size:56 final size:56
Alignment explanation
Indices: 568117--568230 Score: 201
Period size: 56 Copynumber: 2.0 Consensus size: 56
568107 ATTCATTTAA
*
568117 TTAAATGAATATATTTATAAATATATAATCAAACATGTTCATGAATAATTAAAAAT
1 TTAAACGAATATATTTATAAATATATAATCAAACATGTTCATGAATAATTAAAAAT
* *
568173 TTAAACGAATATATTTATAAATATATAATTAAATATGTTCATGAATAATTAAAAAT
1 TTAAACGAATATATTTATAAATATATAATCAAACATGTTCATGAATAATTAAAAAT
568229 TT
1 TT
568231 GTTCATGACA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.39
Consensus pattern (56 bp):
TTAAACGAATATATTTATAAATATATAATCAAACATGTTCATGAATAATTAAAAAT
Found at i:568322 original size:29 final size:31
Alignment explanation
Indices: 568259--568322 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
568249 AATTTAAGTT
*
568259 ATTATTAAATATAAAAGAATAAAATAAAATT
1 ATTATTAAATATAAAAGAATAAAATAAAATA
**
568290 ATTATTAAATA-AAAA-AATAATGTAAAATA
1 ATTATTAAATATAAAAGAATAAAATAAAATA
568319 ATTA
1 ATTA
568323 AATACAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 15 0.50
30 4 0.13
31 11 0.37
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (31 bp):
ATTATTAAATATAAAAGAATAAAATAAAATA
Found at i:568500 original size:22 final size:23
Alignment explanation
Indices: 568455--568504 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
568445 ATAATAAATT
* *
568455 AATTTTAAATAATTTATTAAACA
1 AATTTTAAACAATTCATTAAACA
568478 AATTTTAAACAATTCA-TAAACA
1 AATTTTAAACAATTCATTAAACA
568500 AATTT
1 AATTT
568505 ATTTAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (23 bp):
AATTTTAAACAATTCATTAAACA
Found at i:569173 original size:3 final size:3
Alignment explanation
Indices: 569165--569202 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
569155 TTAATTCAAG
*
569165 TAA TAA TAA TAA TAA TAA TAA TAC TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
569203 TTTTTTCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:570702 original size:19 final size:20
Alignment explanation
Indices: 570648--570704 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 20
570638 GAATAATTTA
* *
570648 ATTAAA-AAATAATTAAAAT
1 ATTAAATAAGTAATAAAAAT
*
570667 ATTAAATAAGTATTAAAAAT
1 ATTAAATAAGTAATAAAAAT
**
570687 A-TAAATACTTAATAAAAA
1 ATTAAATAAGTAATAAAAA
570705 ATACATTTAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 20 0.65
20 11 0.35
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
ATTAAATAAGTAATAAAAAT
Found at i:570802 original size:19 final size:19
Alignment explanation
Indices: 570778--570815 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
570768 AAATTTAAAA
*
570778 ATTGATTTAATTAATTTTT
1 ATTGATTTAATAAATTTTT
570797 ATTGATTTAATAAATTTTT
1 ATTGATTTAATAAATTTTT
570816 TAATTTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
ATTGATTTAATAAATTTTT
Found at i:571484 original size:25 final size:26
Alignment explanation
Indices: 571436--571508 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 26
571426 ATTATAATTA
*
571436 TAAA-TATAATAAATATT-ATTAAAAT
1 TAAATTATAAT-AATATTAATAAAAAT
571461 T-AATTATAATAATATTAATAAAAAAT
1 TAAATTATAATAATATTAAT-AAAAAT
*
571487 TAAAATTATAA-AATAATAATAA
1 T-AAATTATAATAATATTAATAA
571509 TATGTATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
24 8 0.20
25 9 0.22
26 8 0.20
27 8 0.20
28 8 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
TAAATTATAATAATATTAATAAAAAT
Found at i:573927 original size:13 final size:13
Alignment explanation
Indices: 573911--573938 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
573901 TATTTTTTTC
573911 AATATTTATATTT
1 AATATTTATATTT
573924 AATATTTATATTT
1 AATATTTATATTT
573937 AA
1 AA
573939 CATATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:577175 original size:9 final size:10
Alignment explanation
Indices: 577155--577184 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
577145 AATTAATTAT
577155 TTTAAAATAA
1 TTTAAAATAA
577165 TTTAAAA-AA
1 TTTAAAATAA
577174 TTTAAAATAA
1 TTTAAAATAA
577184 T
1 T
577185 CGACTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
TTTAAAATAA
Found at i:578600 original size:14 final size:14
Alignment explanation
Indices: 578577--578629 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
578567 ATGATAAAAA
*
578577 AAATTATAAATATT
1 AAATTTTAAATATT
578591 AAATTTTAAA-ATTT
1 AAATTTTAAATA-TT
578605 AAATTTATTAAATATT
1 AAA-TT-TTAAATATT
578621 -AATTTTAAA
1 AAATTTTAAA
578630 AATAATTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
13 6 0.18
14 16 0.47
15 4 0.12
16 7 0.21
17 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATTTTAAATATT
Found at i:578632 original size:15 final size:15
Alignment explanation
Indices: 578584--578633 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
578574 AAAAAATTAT
578584 AAATATTAAATTTT-A
1 AAATATT-AATTTTAA
* *
578599 AAAT-TTAAATTTATT
1 AAATATTAATTTTA-A
578614 AAATATTAATTTTAA
1 AAATATTAATTTTAA
578629 AAATA
1 AAATA
578634 ATTATGTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 5 0.18
14 2 0.07
15 13 0.46
16 8 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AAATATTAATTTTAA
Found at i:578930 original size:25 final size:25
Alignment explanation
Indices: 578857--578932 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
578847 TAGAGTATTA
*
578857 TATATTTATA-TATATTTTAATACATTA
1 TATATTTATATTATA-TTT-ATA-TTTA
* **
578884 -ATAATTTATTTTATATAAATATTTA
1 TAT-ATTTATATTATATTTATATTTA
578909 TATATTTATATTATATTTATATTT
1 TATATTTATATTATATTTATATTT
578933 TATTTTCAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
25 21 0.54
26 7 0.18
27 7 0.18
28 4 0.10
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (25 bp):
TATATTTATATTATATTTATATTTA
Found at i:578946 original size:44 final size:44
Alignment explanation
Indices: 578858--578946 Score: 108
Period size: 43 Copynumber: 2.0 Consensus size: 44
578848 AGAGTATTAT
* *
578858 ATATTTATATATATTTTAATACATTAATAATTTATTTTATATAA
1 ATATTTATATATATTATAATACATTAATAATTTATTTTAAATAA
* * * *
578902 ATATTTATATAT-TTATATTATATTTATATTTTATTTTCAAATAA
1 ATATTTATATATATTATAATACATTAATAATTTATTTT-AAATAA
578946 A
1 A
578947 ATAAATTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 20 0.53
44 18 0.47
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (44 bp):
ATATTTATATATATTATAATACATTAATAATTTATTTTAAATAA
Found at i:579099 original size:27 final size:28
Alignment explanation
Indices: 579062--579116 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
579052 ATCAAAATCT
579062 ATATAATATAAAT-TATTAACATATTAAA
1 ATATAATATAAATGTA-TAACATATTAAA
*
579090 ATAT-ATATAAATGTATAATATATTAAA
1 ATATAATATAAATGTATAACATATTAAA
579117 TATGATCATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (28 bp):
ATATAATATAAATGTATAACATATTAAA
Found at i:581179 original size:17 final size:17
Alignment explanation
Indices: 581134--581233 Score: 68
Period size: 16 Copynumber: 6.0 Consensus size: 17
581124 ATATATTAAT
*
581134 TTTATATTAAAAATTATA
1 TTTATATTAAATATT-TA
* *
581152 GTATTAAATTAAATATATA
1 -T-TTATATTAAATATTTA
* *
581171 TTTTTATTAATTATTTA
1 TTTATATTAAATATTTA
*
581188 -TTATATTTAATATTTA
1 TTTATATTAAATATTTA
581204 TTTAATATTAAA-A-TTA
1 TTT-ATATTAAATATTTA
581220 -TT-T-TTAAATATTTA
1 TTTATATTAAATATTTA
581234 AAAAAATTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 15
0.71 0.12 0.16
Matches are distributed among these distances:
12 5 0.08
13 2 0.03
14 3 0.05
15 2 0.03
16 16 0.25
17 15 0.23
18 8 0.12
19 3 0.05
20 11 0.17
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (17 bp):
TTTATATTAAATATTTA
Found at i:581221 original size:20 final size:20
Alignment explanation
Indices: 581179--581236 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
581169 TATTTTTATT
*
581179 AATTATTTA-TT-ATATT-T
1 AATTATTTATTTAATATTAA
581196 AA-TATTTATTTAATATTAA
1 AATTATTTATTTAATATTAA
*
581215 AATTATTT-TTAAATATTTAA
1 AATTATTTATTTAATA-TTAA
581235 AA
1 AA
581237 AAATTTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 6 0.18
17 4 0.12
18 5 0.15
19 8 0.24
20 11 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTATTTATTTAATATTAA
Found at i:587484 original size:2 final size:2
Alignment explanation
Indices: 587477--587503 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
587467 AAAGTCCCCA
587477 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
587504 ATTGTTAGTT
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:588254 original size:2 final size:2
Alignment explanation
Indices: 588247--588289 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
588237 AGACAATAGA
* * *
588247 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
588289 A
1 A
588290 AAACTGAAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (2 bp):
AT
Found at i:589960 original size:27 final size:27
Alignment explanation
Indices: 589930--589981 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
589920 TTTTTATATA
* * *
589930 AAATTAAATTTATTCAATAAATTTTTT
1 AAATTAAATTAATTAAAAAAATTTTTT
*
589957 AAATTTAATTAATTAAAAAAATTTT
1 AAATTAAATTAATTAAAAAAATTTT
589982 AAAATCCAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
AAATTAAATTAATTAAAAAAATTTTTT
Found at i:590745 original size:21 final size:21
Alignment explanation
Indices: 590694--590747 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
590684 ATTAAGTTAA
* *
590694 TTTTAATATTAAATAAATAAT
1 TTTTAAAATAAAATAAATAAT
* * * *
590715 TATTATAATAAAATATATGAT
1 TTTTAAAATAAAATAAATAAT
590736 TTTTAAAATAAA
1 TTTTAAAATAAA
590748 TTTAAATATT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TTTTAAAATAAAATAAATAAT
Found at i:591493 original size:22 final size:24
Alignment explanation
Indices: 591468--591517 Score: 70
Period size: 22 Copynumber: 2.2 Consensus size: 24
591458 TATTATTTAA
591468 AAATATT-AATATTTTTA-TAATT
1 AAATATTAAATATTTTTATTAATT
*
591490 AAAT-TTAAATATTTTTATTGATT
1 AAATATTAAATATTTTTATTAATT
591513 AAATA
1 AAATA
591518 GTATTTATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 2 0.08
22 14 0.58
23 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
AAATATTAAATATTTTTATTAATT
Found at i:595736 original size:2 final size:2
Alignment explanation
Indices: 595729--595770 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
595719 TGAATATAAC
*
595729 AT AT AT AT AT AT AT AT AT AT AA AT AT AT CAT AT A- AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
595770 A
1 A
595771 ATTATTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 31 0.89
3 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:595753 original size:29 final size:27
Alignment explanation
Indices: 595716--595770 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
595706 TAAATTTTAA
*
595716 ATATGAATATAACATATATATATATATAT
1 ATATAAATATAACATATA-ATAT-TATAT
*
595745 ATATAAATATATCATATAATATTATA
1 ATATAAATATAACATATAATATTATA
595771 ATTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 4 0.17
29 16 0.67
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (27 bp):
ATATAAATATAACATATAATATTATAT
Found at i:596684 original size:17 final size:17
Alignment explanation
Indices: 596662--596706 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
596652 CAAGTGGGTG
*
596662 AAAAAATATT-TTTTTT
1 AAAAAATATTATATTTT
596678 AAAAAAATATTATATTTT
1 -AAAAAATATTATATTTT
596696 AAAAAATATTA
1 AAAAAATATTA
596707 AAATATAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 21 0.81
18 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAAAATATTATATTTT
Found at i:597019 original size:15 final size:16
Alignment explanation
Indices: 596999--597032 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
596989 GTATTAATAA
596999 AATGAATAG-ATTTTT
1 AATGAATAGTATTTTT
597014 AATGAATAGTTATTTTT
1 AATGAATAG-TATTTTT
597031 AA
1 AA
597033 AAAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (16 bp):
AATGAATAGTATTTTT
Found at i:598128 original size:18 final size:19
Alignment explanation
Indices: 598105--598143 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
598095 TGATCAAATT
*
598105 ATTTATTTAA-ATTTAAAA
1 ATTTATATAATATTTAAAA
598123 ATTTATATAATATTTAAAA
1 ATTTATATAATATTTAAAA
598142 AT
1 AT
598144 ATTTGAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTATATAATATTTAAAA
Found at i:598938 original size:2 final size:2
Alignment explanation
Indices: 598931--598967 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
598921 CCTTTCAATC
598931 AT AT AT AT AT 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 AT AT AT AT AT A
598968 GAATAGGGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:599080 original size:22 final size:23
Alignment explanation
Indices: 599055--599110 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
599045 TATCAAGAAT
*
599055 TTAAATTTTT-TTAAATTTTA-TA
1 TTAAATTTTTATT-AATTTAAGTA
599077 TTAAATTTATTATTAATTTAAGTA
1 TTAAATTT-TTATTAATTTAAGTA
599101 -TAAATTTTTA
1 TTAAATTTTTA
599111 AATATTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 11 0.37
23 15 0.50
24 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TTAAATTTTTATTAATTTAAGTA
Found at i:599090 original size:12 final size:11
Alignment explanation
Indices: 599055--599092 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
599045 TATCAAGAAT
599055 TTAAATTTTT-
1 TTAAATTTTTA
599065 TTAAATTTTATA
1 TTAAATTTT-TA
599077 TTAAATTTATTA
1 TTAAATTT-TTA
599089 TTAA
1 TTAA
599093 TTTAAGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.36
11 1 0.04
12 14 0.56
13 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTAAATTTTTA
Found at i:599698 original size:10 final size:9
Alignment explanation
Indices: 599667--599697 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
599657 TCCCACCATC
*
599667 AAAAGAAAA
1 AAAATAAAA
599676 AAAATAAAA
1 AAAATAAAA
599685 AAAATAAAA
1 AAAATAAAA
599694 AAAA
1 AAAA
599698 AAGATAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.03, T:0.06
Consensus pattern (9 bp):
AAAATAAAA
Found at i:600343 original size:13 final size:13
Alignment explanation
Indices: 600295--600348 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
600285 TTTAACTCAA
600295 TATTAAATTTTAT
1 TATTAAATTTTAT
* * *
600308 CAATATATTTTCATT
1 TATTAAATTTT-A-T
600323 TAATTAAATTTTAT
1 T-ATTAAATTTTAT
600337 TATTAAATTTTA
1 TATTAAATTTTA
600349 ATTTTTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
13 19 0.59
14 3 0.09
15 2 0.06
16 8 0.25
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (13 bp):
TATTAAATTTTAT
Found at i:600357 original size:18 final size:19
Alignment explanation
Indices: 600329--600365 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
600319 CATTTAATTA
600329 AATTTTATTATTAAATTTT
1 AATTTTATTATTAAATTTT
600348 AATTTT-TTATTAAATTTT
1 AATTTTATTATTAAATTTT
600366 TTCTCTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
AATTTTATTATTAAATTTT
Found at i:600378 original size:31 final size:31
Alignment explanation
Indices: 600295--600365 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 31
600285 TTTAACTCAA
* * * *
600295 TATTAAATTTTATCAATATATTTTCA--TTT
1 TATTAAATTTTATTATTAAATTTTAATTTTT
*
600324 AATTAAATTTTATTATTAAATTTTAATTTTT
1 TATTAAATTTTATTATTAAATTTTAATTTTT
600355 TATTAAATTTT
1 TATTAAATTTT
600366 TTCTCTTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 21 0.62
31 13 0.38
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (31 bp):
TATTAAATTTTATTATTAAATTTTAATTTTT
Found at i:600532 original size:17 final size:18
Alignment explanation
Indices: 600510--600544 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
600500 CCTTTAACCC
600510 TATTTAATAT-AATAATA
1 TATTTAATATAAATAATA
*
600527 TATTTATTATAAATAATA
1 TATTTAATATAAATAATA
600545 AATATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTTAATATAAATAATA
Found at i:600542 original size:21 final size:22
Alignment explanation
Indices: 600510--600552 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
600500 CCTTTAACCC
600510 TATTTAATATAAT-AATATATT
1 TATTTAATATAATAAATATATT
600531 TATTATAA-ATAATAAATATATT
1 TATT-TAATATAATAAATATATT
600553 AACTAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTTAATATAATAAATATATT
Found at i:606722 original size:7 final size:7
Alignment explanation
Indices: 606710--606745 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
606700 AGATAGATTT
606710 CTGGAAC
1 CTGGAAC
606717 CTGGAAC
1 CTGGAAC
606724 CTGGAAC
1 CTGGAAC
*
606731 CAGGAAC
1 CTGGAAC
*
606738 CAGGAAC
1 CTGGAAC
606745 C
1 C
606746 ATGTCAAGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.33, C:0.31, G:0.28, T:0.08
Consensus pattern (7 bp):
CTGGAAC
Found at i:607311 original size:2 final size:2
Alignment explanation
Indices: 607304--607336 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
607294 AGGTCTGTTA
607304 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
607337 TACTCAGCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:610565 original size:15 final size:15
Alignment explanation
Indices: 610545--610594 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
610535 TTACTATAAT
*
610545 TTAAAAACATAAAAA
1 TTAAAAATATAAAAA
* *
610560 TT-AAAATATTAAAT
1 TTAAAAATATAAAAA
610574 TTAAAAATATAAAAA
1 TTAAAAATATAAAAA
610589 TTAAAA
1 TTAAAA
610595 TATTTTATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
TTAAAAATATAAAAA
Found at i:610579 original size:21 final size:21
Alignment explanation
Indices: 610554--610593 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
610544 TTTAAAAACA
610554 TAAAAAT-TAAAATATTAAATT
1 TAAAAATATAAAA-ATTAAATT
610575 TAAAAATATAAAAATTAAA
1 TAAAAATATAAAAATTAAA
610594 ATATTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAATATAAAAATTAAATT
Found at i:610585 original size:29 final size:29
Alignment explanation
Indices: 610542--610621 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
610532 TATTTACTAT
*
610542 AATTTAAAAACATAAAAATTAAAATATTA
1 AATTTAAAAATATAAAAATTAAAATATTA
*
610571 AATTTAAAAATATAAAAATTAAAATATTT
1 AATTTAAAAATATAAAAATTAAAATATTA
* *
610600 TATTTATTATAATATAAAAATT
1 AATTTA--AAAATATAAAAATT
610622 TTTAATAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 32 0.71
31 13 0.29
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (29 bp):
AATTTAAAAATATAAAAATTAAAATATTA
Found at i:610595 original size:14 final size:14
Alignment explanation
Indices: 610548--610597 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
610538 CTATAATTTA
*
610548 AAAACATAAAAATT
1 AAAATATAAAAATT
* *
610562 AAAATATTAAATTT
1 AAAATATAAAAATT
610576 AAAAATATAAAAATT
1 -AAAATATAAAAATT
610591 AAAATAT
1 AAAATAT
610598 TTTATTTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:613094 original size:17 final size:17
Alignment explanation
Indices: 613074--613108 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
613064 TATATTGTTA
613074 ATATTTATATATTATAT
1 ATATTTATATATTATAT
* *
613091 ATATTTATTTTTTATAT
1 ATATTTATATATTATAT
613108 A
1 A
613109 ATAAAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATATTTATATATTATAT
Found at i:613158 original size:18 final size:17
Alignment explanation
Indices: 613107--613164 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 17
613097 ATTTTTTATA
*
613107 TAATAAAAATTACATAAT
1 TAATAAATATTA-ATAAT
*
613125 AAATAAATA-TAA-AAT
1 TAATAAATATTAATAAT
613140 TAATAAATATTATATAAT
1 TAATAAATATTA-ATAAT
613158 TAA-AAAT
1 TAATAAAT
613165 GGATTAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 11 0.32
16 3 0.09
17 7 0.21
18 13 0.38
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
TAATAAATATTAATAAT
Found at i:617423 original size:30 final size:32
Alignment explanation
Indices: 617389--617456 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 32
617379 TATCAAAAAC
617389 ATAATTA-AAATATAATAAAAAAATA-TAATT
1 ATAATTATAAATATAATAAAAAAATATTAATT
* *
617419 ATAA-TATAAATATATTAAAAATATATTAATT
1 ATAATTATAAATATAATAAAAAAATATTAATT
617450 ATTAATT
1 A-TAATT
617457 TATTAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 2 0.06
30 20 0.62
31 6 0.19
32 3 0.09
33 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (32 bp):
ATAATTATAAATATAATAAAAAAATATTAATT
Found at i:617474 original size:26 final size:25
Alignment explanation
Indices: 617418--617474 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
617408 AAAATATAAT
617418 TATAA-TATAAATATATTAAAAATA
1 TATAATTATAAATATATTAAAAATA
* * *
617442 TATTAATTATTAATTTATTAAAATTTA
1 TA-TAATTATAAATATATTAAAA-ATA
617469 TATAAT
1 TATAAT
617475 ATTTTAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 2 0.07
25 3 0.11
26 18 0.67
27 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TATAATTATAAATATATTAAAAATA
Found at i:618204 original size:28 final size:30
Alignment explanation
Indices: 618141--618206 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
618131 CATTTGTATC
*
618141 TAAATAAATTTTTAACTTTTAACTTATATC
1 TAAATAAATTTTTAACTTTTAACTTATATA
* *
618171 TAAATAAATTTTTAA-TTTTTA-TTATTTA
1 TAAATAAATTTTTAACTTTTAACTTATATA
618199 TAAATAAA
1 TAAATAAA
618207 ATCTTAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 13 0.39
29 5 0.15
30 15 0.45
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (30 bp):
TAAATAAATTTTTAACTTTTAACTTATATA
Found at i:619235 original size:2 final size:2
Alignment explanation
Indices: 619187--619219 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
619177 CAGAAGTATT
619187 TA 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 TA T
619220 TGGTTTACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:619837 original size:15 final size:17
Alignment explanation
Indices: 619810--619845 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
619800 AAAAAGTTCG
619810 TAAAATCAAAATATTT-
1 TAAAATCAAAATATTTA
619826 TAAAAT-AAAATATTTA
1 TAAAATCAAAATATTTA
619842 TAAA
1 TAAA
619846 GTTAAAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAATCAAAATATTTA
Found at i:619966 original size:24 final size:24
Alignment explanation
Indices: 619939--619988 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
619929 GCAAAATTAC
619939 AAACTTTTAAGA-TGAAAAGTTTGT
1 AAACTTTT-AGATTGAAAAGTTTGT
* *
619963 AAACTTTTGGATTGAAAATTTTGT
1 AAACTTTTAGATTGAAAAGTTTGT
619987 AA
1 AA
619989 TGTTTTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (24 bp):
AAACTTTTAGATTGAAAAGTTTGT
Found at i:620442 original size:17 final size:16
Alignment explanation
Indices: 620420--620453 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
620410 ATTGTTATGA
620420 ATATATAGTAAACATAT
1 ATATATAGTAAA-ATAT
*
620437 ATATATATTAAAATAT
1 ATATATAGTAAAATAT
620453 A
1 A
620454 ATTTATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (16 bp):
ATATATAGTAAAATAT
Found at i:621062 original size:15 final size:16
Alignment explanation
Indices: 621025--621070 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
621015 TTATTATTTT
621025 TAAAATATATTTAAAA
1 TAAAATATATTTAAAA
621041 -AATAATA-ATTTAAAA
1 TAA-AATATATTTAAAA
621056 TAAAATATATATTAA
1 TAAAATATAT-TTAA
621071 TATTTTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 14 0.54
16 8 0.31
17 4 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAATATATTTAAAA
Found at i:621570 original size:29 final size:29
Alignment explanation
Indices: 621530--621595 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
621520 TTTGATTAAC
* *
621530 ATATAATATTTAATATTTA-ATATATATAT
1 ATATATTATTTAATAATTATAT-TATATAT
*
621559 ATATATTATTTAATAATTATATTATATTT
1 ATATATTATTTAATAATTATATTATATAT
621588 ATATATTA
1 ATATATTA
621596 ATAATTGATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 31 0.94
30 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
ATATATTATTTAATAATTATATTATATAT
Found at i:621597 original size:22 final size:23
Alignment explanation
Indices: 621530--621598 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 23
621520 TTTGATTAAC
*
621530 ATATAATATTTA-ATATTTAATAT
1 ATATTATATTTATATA-TTAATAT
* *
621553 ATATATATATATTATTTAATAAT-T
1 ATAT-TATAT-TTATATATTAATAT
621577 ATATTATATTTATATATTAATA
1 ATATTATATTTATATATTAATA
621599 ATTGATAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
22 10 0.27
23 9 0.24
24 9 0.24
25 7 0.19
26 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
ATATTATATTTATATATTAATAT
Found at i:621599 original size:25 final size:27
Alignment explanation
Indices: 621530--621601 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 27
621520 TTTGATTAAC
*
621530 ATATA-ATAT-TTAATATTTAATATAT
1 ATATATATATATTAATAATTAATATAT
621555 ATATATATATTATTTAATAATT-ATAT-T
1 ATATATATA-TA-TTAATAATTAATATAT
*
621582 ATATTTATATATTAATAATT
1 ATATATATATATTAATAATT
621602 GATAAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
25 14 0.34
26 5 0.12
27 10 0.24
28 4 0.10
29 8 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
ATATATATATATTAATAATTAATATAT
Found at i:622260 original size:2 final size:2
Alignment explanation
Indices: 622248--622279 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
622238 AATTTTTCTC
622248 AT AT CAT 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 AT AT A
622280 ATTTTATGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:623002 original size:17 final size:17
Alignment explanation
Indices: 622967--623015 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
622957 CCAAACTATG
*
622967 AAATAATTAGTTTTGA-A
1 AAATAATTA-TTTTTATA
*
622984 AAAT-TTTATTTTTATA
1 AAATAATTATTTTTATA
623000 AAATAATTATTTTTAT
1 AAATAATTATTTTTAT
623016 TTTATAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 5 0.19
16 8 0.30
17 14 0.52
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
AAATAATTATTTTTATA
Found at i:623015 original size:23 final size:22
Alignment explanation
Indices: 622987--623033 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
622977 TTTTGAAAAA
*
622987 TTTTATTTTTATAAAATAATTAT
1 TTTTA-TTTTATAAAATAATCAT
623010 TTTTATTTTATAAAATAATCAT
1 TTTTATTTTATAAAATAATCAT
623032 TT
1 TT
623034 CGTTAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTATTTTATAAAATAATCAT
Found at i:623185 original size:17 final size:17
Alignment explanation
Indices: 623165--623230 Score: 73
Period size: 16 Copynumber: 4.0 Consensus size: 17
623155 TTTTTGTTAA
623165 AATATAAAATAAAATAT
1 AATATAAAATAAAATAT
* * *
623182 AATATGATATAAAAAAT
1 AATATAAAATAAAATAT
*
623199 AATAT-AAATATAATAT
1 AATATAAAATAAAATAT
*
623215 AA-ATAAAATAATATAT
1 AATATAAAATAAAATAT
623231 TAAAATTTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
15 2 0.05
16 19 0.47
17 19 0.47
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
AATATAAAATAAAATAT
Found at i:623191 original size:22 final size:23
Alignment explanation
Indices: 623165--623224 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
623155 TTTTTGTTAA
623165 AATATAAAATAAAATAT-AATAT
1 AATATAAAATAAAATATAAATAT
*
623187 GATATAAAA-AATAATATAAATAT
1 AATATAAAATAA-AATATAAATAT
623210 AATAT-AAATAAAATA
1 AATATAAAATAAAATA
623225 ATATATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 2 0.06
22 20 0.61
23 11 0.33
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (23 bp):
AATATAAAATAAAATATAAATAT
Found at i:623227 original size:28 final size:28
Alignment explanation
Indices: 623162--623261 Score: 82
Period size: 28 Copynumber: 3.5 Consensus size: 28
623152 TAGTTTTTGT
* *
623162 TAAAAT-ATAAAATAAAATATAATATGATA
1 TAAAATAATAATAT-AAATATAATAT-AAA
623191 TAAAA-AATAATATAAATATAATATAAA
1 TAAAATAATAATATAAATATAATATAAA
*
623218 TAAAATAAT-ATATTAAA-ATTTATATAATA
1 TAAAATAATAATA-TAAATA-TAATATAA-A
* *
623247 TAAATTATTAATATA
1 TAAAATAATAATATA
623262 TTAAAAATTA
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
27 11 0.18
28 25 0.42
29 21 0.35
30 3 0.05
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (28 bp):
TAAAATAATAATATAAATATAATATAAA
Found at i:623243 original size:33 final size:32
Alignment explanation
Indices: 623206--623273 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
623196 AATAATATAA
*
623206 ATATAATATAAATAAAATAATATATTAAAATTT
1 ATATAATATAAAT-AAATAATATATTAAAAATT
* *
623239 ATATAATATAAATTATTAATATATTAAAAATT
1 ATATAATATAAATAAATAATATATTAAAAATT
623271 ATA
1 ATA
623274 AAAATATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (32 bp):
ATATAATATAAATAAATAATATATTAAAAATT
Found at i:623249 original size:5 final size:5
Alignment explanation
Indices: 623172--623261 Score: 59
Period size: 5 Copynumber: 19.2 Consensus size: 5
623162 TAAAATATAA
* *
623172 AATAA AATAT AATAT GATAT AA-A- AA-AT AATAT AAATAT AATAT AA-AT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT
* * * * *
623219 AAAAT AATAT ATTAA AAT-T TATAT AATAT AA-AT TAT-T AATAT A
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT A
623262 TTAAAAATTA
Statistics
Matches: 66, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
3 3 0.05
4 15 0.23
5 43 0.65
6 5 0.08
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:623269 original size:18 final size:18
Alignment explanation
Indices: 623223--623300 Score: 74
Period size: 18 Copynumber: 4.6 Consensus size: 18
623213 ATAAATAAAA
623223 TAATATATT-AAAA-T-T
1 TAATATATTAAAAATTAT
* *
623238 T-ATATAATATAAATTAT
1 TAATATATTAAAAATTAT
623255 TAATATATTAAAAATTAT
1 TAATATATTAAAAATTAT
* * * *
623273 AAAAATATTAAATATTTT
1 TAATATATTAAAAATTAT
623291 TAATATATTA
1 TAATATATTA
623301 TAATATATAA
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
14 6 0.12
15 4 0.08
16 1 0.02
17 2 0.04
18 36 0.73
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATATATTAAAAATTAT
Found at i:623305 original size:26 final size:24
Alignment explanation
Indices: 623220--623335 Score: 84
Period size: 26 Copynumber: 4.8 Consensus size: 24
623210 AATATAAATA
623220 AAATA-AT-ATATTAAA-ATTTAT
1 AAATATATAATATTAAATATTTAT
*
623241 ATAATATA-AATTATT-AATATATTAA
1 A-AATATATAA-TATTAAATAT-TTAT
* *
623266 AAATTATAAAAATATTAAATATTTTT
1 AAA-TAT-ATAATATTAAATATTTAT
623292 AATATATTATAATATATAAA-ATTTAT
1 AA-ATA-TATAATAT-TAAATATTTAT
623318 AAATATATAATA-TAAATA
1 AAATATATAATATTAAATA
623336 CATAAATTAA
Statistics
Matches: 76, Mismatches: 5, Indels: 26
0.71 0.05 0.24
Matches are distributed among these distances:
21 1 0.01
22 8 0.11
23 5 0.07
24 15 0.20
25 10 0.13
26 24 0.32
27 13 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAATATATAATATTAAATATTTAT
Found at i:623321 original size:36 final size:38
Alignment explanation
Indices: 623177--623325 Score: 112
Period size: 36 Copynumber: 3.9 Consensus size: 38
623167 TATAAAATAA
* * * * *
623177 AATATAATATGATATAAAAAATAATATAAATATAATA-T
1 AATATATTATAATATATAAAAT-TTATAAATATATTATT
**
623215 AA-ATAAAATAATATATTAAAATTTATATAATATAAATTATT
1 AATATATTATAATATA-TAAAATTTATA-AATAT--ATTATT
* *
623256 AATATATTA-AAAATTATAAAA-ATATTAAATAT-TT-TT
1 AATATATTATAATA-TATAAAATTTA-TAAATATATTATT
623292 AATATATTATAATATATAAAATTTATAAATATAT
1 AATATATTATAATATATAAAATTTATAAATATAT
623326 AATATAAATA
Statistics
Matches: 89, Mismatches: 11, Indels: 23
0.72 0.09 0.19
Matches are distributed among these distances:
36 25 0.28
37 23 0.26
38 12 0.13
40 10 0.11
41 13 0.15
42 6 0.07
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (38 bp):
AATATATTATAATATATAAAATTTATAAATATATTATT
Found at i:623325 original size:29 final size:29
Alignment explanation
Indices: 623293--623350 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
623283 AATATTTTTA
* * *
623293 ATATATTAT-AATATATAAAATTTATAAAT
1 ATATAATATAAATACAT-AAATTAATAAAT
623322 ATATAATATAAATACATAAATTAATAAAT
1 ATATAATATAAATACATAAATTAATAAAT
623351 TTATGAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (29 bp):
ATATAATATAAATACATAAATTAATAAAT
Found at i:624111 original size:18 final size:18
Alignment explanation
Indices: 624090--624142 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
624080 ATATAATTTT
*
624090 TTTTAAAAAACTAATCAA
1 TTTTAAAAAAATAATCAA
* *
624108 TTTTAAGAAAAATCAATTAT
1 TTTTAA-AAAAAT-AATCAA
*
624128 TTTTAAAAAATTAAT
1 TTTTAAAAAAATAAT
624143 TTTCAAGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 9 0.31
19 10 0.34
20 10 0.34
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.40
Consensus pattern (18 bp):
TTTTAAAAAAATAATCAA
Found at i:624143 original size:18 final size:18
Alignment explanation
Indices: 624083--624143 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
624073 ATTAGTTATA
* *
624083 TAATTTTTTTTAAAAAAC
1 TAATTATTTTTAAAAAAT
* *
624101 TAATCAATTTTAAGAAAAAT
1 TAAT-TATTTTTA-AAAAAT
*
624121 CAATTATTTTTAAAAAAT
1 TAATTATTTTTAAAAAAT
624139 TAATT
1 TAATT
624144 TTCAAGAATA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
18 14 0.42
19 11 0.33
20 8 0.24
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (18 bp):
TAATTATTTTTAAAAAAT
Done.