Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold404
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: 638648
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 4 of 4
Found at i:509075 original size:21 final size:22
Alignment explanation
Indices: 509050--509091 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
509040 TCAAATTCTT
509050 ATACATTTGAT-AAATTGCAAG
1 ATACATTTGATGAAATTGCAAG
*
509071 ATACATTTGATGAACTTGCAA
1 ATACATTTGATGAAATTGCAA
509092 TTGAGTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (22 bp):
ATACATTTGATGAAATTGCAAG
Found at i:512136 original size:2 final size:2
Alignment explanation
Indices: 512129--512163 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
512119 TTTTTATTGA
512129 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 A
512164 GTAAAGCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:518408 original size:24 final size:24
Alignment explanation
Indices: 518345--518408 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
518335 AAATTATATT
*
518345 TATATCAAATAACATTTGTATCAA
1 TATATCAAATAACATTTATATCAA
* * *
518369 TAGAT-AAAAAAAATTTATAAT-AA
1 TATATCAAATAACATTTAT-ATCAA
518392 TATATCAAATAACATTT
1 TATATCAAATAACATTT
518409 TAAATTTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
23 16 0.52
24 15 0.48
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (24 bp):
TATATCAAATAACATTTATATCAA
Found at i:519644 original size:20 final size:22
Alignment explanation
Indices: 519600--519647 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
519590 ATGATTCAAC
**
519600 AAGAATTTGCGAAGAATCAGTA
1 AAGAATTTGCGAAGAATCAAAA
519622 AAGAATTTGC-AA-AATCAAAA
1 AAGAATTTGCGAAGAATCAAAA
519642 AAGAAT
1 AAGAAT
519648 GAGTTTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.50
21 2 0.08
22 10 0.42
ACGTcount: A:0.54, C:0.08, G:0.17, T:0.21
Consensus pattern (22 bp):
AAGAATTTGCGAAGAATCAAAA
Found at i:531107 original size:20 final size:20
Alignment explanation
Indices: 531082--531153 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
531072 TACCCAGATG
531082 TATCGATACATTTTTCAATT
1 TATCGATACATTTTTCAATT
* * * *
531102 TATCGATACATGTATGAATG
1 TATCGATACATTTTTCAATT
* *
531122 TATTGATACATTCTTCAATT
1 TATCGATACATTTTTCAATT
*
531142 TATTGATACATT
1 TATCGATACATT
531154 CTGTCTTTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (20 bp):
TATCGATACATTTTTCAATT
Found at i:532158 original size:20 final size:20
Alignment explanation
Indices: 532130--532204 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
532120 TTTTACCTTG
532130 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
532150 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
532170 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
*
532190 ATGTATCAATACATT
1 ATGTATCGATACATT
532205 ATGTCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:532202 original size:40 final size:39
Alignment explanation
Indices: 532130--532207 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
532120 TTTTACCTTG
* * *
532130 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCAATACAT-TATGA
* *
532170 ATGTATCGATATATTCTACAATGTATCAATACATTATG
1 ATGTATCGATACATTCTACAATATATCAATACATTATG
532208 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCAATACATTATGA
Found at i:533139 original size:21 final size:21
Alignment explanation
Indices: 533113--533169 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 21
533103 AGCCTTTGAC
533113 CATGCATTTTTTATTATGTTT
1 CATGCATTTTTTATTATGTTT
533134 CATGCATTTTTTTTTATTATGTTT
1 CATGCA---TTTTTTATTATGTTT
*
533158 CATG-TTTTTTTA
1 CATGCATTTTTTA
533170 ACATGTCCAG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 7 0.22
21 6 0.19
24 19 0.59
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.65
Consensus pattern (21 bp):
CATGCATTTTTTATTATGTTT
Found at i:533151 original size:24 final size:22
Alignment explanation
Indices: 533119--533168 Score: 82
Period size: 24 Copynumber: 2.2 Consensus size: 22
533109 TGACCATGCA
533119 TTTTTTATTATGTTTCATGCATTT
1 TTTTTTATTATGTTTCATG--TTT
533143 TTTTTTATTATGTTTCATGTTT
1 TTTTTTATTATGTTTCATGTTT
533165 TTTT
1 TTTT
533169 AACATGTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 7 0.27
24 19 0.73
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (22 bp):
TTTTTTATTATGTTTCATGTTT
Found at i:540379 original size:13 final size:13
Alignment explanation
Indices: 540361--540386 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
540351 TACAGCAAGT
540361 ATGTATCGATACA
1 ATGTATCGATACA
540374 ATGTATCGATACA
1 ATGTATCGATACA
540387 CAAAAAATTG
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:542637 original size:21 final size:21
Alignment explanation
Indices: 542604--542648 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
542594 TTGCAAGTTG
*
542604 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
542626 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
542646 AAA
1 AAA
542649 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:544472 original size:15 final size:15
Alignment explanation
Indices: 544452--544482 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
544442 TAAAAATGTC
*
544452 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
544467 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
544482 C
1 C
544483 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:546575 original size:20 final size:20
Alignment explanation
Indices: 546496--546575 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
546486 AATGTCCAAA
*
546496 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
546516 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
546541 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
546561 TTGTATCGATACATT
1 ATGTATCGATACATT
546576 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:546579 original size:13 final size:13
Alignment explanation
Indices: 546561--546599 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
546551 ACATTTTTCT
546561 TTGTATCGATACA
1 TTGTATCGATACA
546574 TTGTATCGATACA
1 TTGTATCGATACA
*
546587 CTGTATCGATACA
1 TTGTATCGATACA
546600 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:546763 original size:20 final size:20
Alignment explanation
Indices: 546720--546765 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
546710 AAATCTTTTG
546720 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
546741 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
546761 CAAAA
1 CAAAA
546766 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:549159 original size:13 final size:13
Alignment explanation
Indices: 549141--549166 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
549131 TACAGCAAGT
549141 ATGTATCGATACA
1 ATGTATCGATACA
549154 ATGTATCGATACA
1 ATGTATCGATACA
549167 CAAAAAATTG
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:550625 original size:27 final size:27
Alignment explanation
Indices: 550588--551052 Score: 723
Period size: 27 Copynumber: 17.0 Consensus size: 27
550578 GTGGCATTTT
* *
550588 CTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
550616 TTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
550643 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
550670 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* * *
550698 CTTTTAAGTCTACAACTTCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
550726 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
550753 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
550780 CTTTTAAGTCCACAACTCTGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
550808 CTTTTAAGACCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* **
550835 CTTTTAAGTCCACAACTCTGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
550862 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
550889 TTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
550916 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
550944 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
550971 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
550998 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
551025 CTTTTAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
551052 C
1 C
551053 ATTCCAAAGC
Statistics
Matches: 406, Mismatches: 28, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
27 300 0.74
28 106 0.26
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:550907 original size:109 final size:109
Alignment explanation
Indices: 550588--551052 Score: 747
Period size: 109 Copynumber: 4.3 Consensus size: 109
550578 GTGGCATTTT
* *
550588 CTTTTAAAGTCCACAACTCTGTGGCATCTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTT-AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
550653 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
* *
550698 CTTTTAAGTCTACAACT-TCGTGGCATCTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT
1 CTTTTAAGTCCACAACTCT-GTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT
*
550762 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCATCC
64 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
* * **
550808 CTTTTAAGACCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCATTCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* *
550873 ACAACTCCGTGGCACCTTTTTAAGTCCACAACTCTGTGGCA-CC
66 ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
* *
550916 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTT-AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
550981 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCAT-C
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
*
551025 CTTTTAAATCCACAACTCTGTGGCACCC
1 CTTTTAAGTCCACAACTCTGTGGCACCC
551053 ATTCCAAAGC
Statistics
Matches: 328, Mismatches: 22, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
108 29 0.09
109 192 0.59
110 106 0.32
111 1 0.00
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (109 bp):
CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
Found at i:551086 original size:32 final size:32
Alignment explanation
Indices: 551035--551522 Score: 457
Period size: 32 Copynumber: 16.2 Consensus size: 32
551025 CTTTTAAATC
* * *
551035 CACAACTCTGTGGC-ACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
551066 CATAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
551098 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
551130 CACAAGTTGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
551162 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
551194 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
551226 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
551258 CACAAGTCAGTGGC-ACTCC-TTTCAAAGCCCA
1 CACAAGTCGGTGGCAAC-CCATTTCAAAGCCCA
* * *
551289 CGCAAGTCAGTGGC-A-CCTTTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
551317 CACGAGTCAGTGGC-ACTC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
551345 CACAAGTCAGTGGC-ACCC-TTTC-AAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * * *
551372 CACGAGTCAGTGG-TA-CCTTTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
551400 CACGAGTCAGTGGC-A-CC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
551427 CACAAGTCAGTGGC-ACTC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
551455 CACGAGTCAGTGGC-ATCC-TTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
551485 CGCAAGTCAGTGGC-ACCC-TTTTAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
551515 CGCAAGTC
1 CACAAGTC
551523 AGTAAAACTC
Statistics
Matches: 420, Mismatches: 26, Indels: 23
0.90 0.06 0.05
Matches are distributed among these distances:
26 2 0.00
27 46 0.11
28 98 0.23
29 7 0.02
30 42 0.10
31 39 0.09
32 186 0.44
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.18
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:551338 original size:28 final size:28
Alignment explanation
Indices: 551246--551575 Score: 364
Period size: 28 Copynumber: 11.4 Consensus size: 28
551236 TGGCAACCCA
*
551246 TTTCAAAGCCCACACAAGTCAGTGGCACTCC
1 TTTCAAAG-CC-CACGAGTCAGTGGCACT-C
551277 TTTCAAAGCCCACGCAAGTCAGTGGCAC-C
1 TTTCAAAGCCCACG--AGTCAGTGGCACTC
551306 TTTTCAAAGCCCACGAGTCAGTGGCACTC
1 -TTTCAAAGCCCACGAGTCAGTGGCACTC
* *
551335 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACGAGTCAGTGGCACTC
*
551363 TTTC-AAGCCCACGAGTCAGTGGTAC-C
1 TTTCAAAGCCCACGAGTCAGTGGCACTC
551389 TTTTCAAAGCCCACGAGTCAGTGGCAC-C
1 -TTTCAAAGCCCACGAGTCAGTGGCACTC
*
551417 TTTCAAAGCCCACAAGTCAGTGGCACTC
1 TTTCAAAGCCCACGAGTCAGTGGCACTC
551445 TTTCAAAGCCCACGAGTCAGTGGCA-TCC
1 TTTCAAAGCCCACGAGTCAGTGGCACT-C
*
551473 TTTCAAAGCCCACGCAAGTCAGTGGCACCC
1 TTTCAAAGCCCACG--AGTCAGTGGCACTC
* ***
551503 TTTTAAAGCCCACGCAAGTCAGTAAAACTC
1 TTTCAAAGCCCACG--AGTCAGTGGCACTC
* *
551533 TTTTCAAAGCCCACATGTGTCAGTGGCAACTTT
1 -TTTCAAAGCCCAC--GAGTCAGTGGC-AC-TC
551566 TTTCAAAGCC
1 TTTCAAAGCC
551576 TACACAAGCT
Statistics
Matches: 263, Mismatches: 20, Indels: 31
0.84 0.06 0.10
Matches are distributed among these distances:
26 1 0.00
27 49 0.19
28 103 0.39
29 5 0.02
30 53 0.20
31 38 0.14
32 12 0.05
33 2 0.01
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.22
Consensus pattern (28 bp):
TTTCAAAGCCCACGAGTCAGTGGCACTC
Found at i:551379 original size:27 final size:28
Alignment explanation
Indices: 550625--551525 Score: 540
Period size: 27 Copynumber: 31.4 Consensus size: 28
550615 CTTTTTAAGT
* * * *
550625 CCACAACTCCGTGGCACCCTTT-TAAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * * *
550652 CCACAACTCCGTGGCACCCTTT-TAAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * * *
550679 CCACAACTCCGTGGCATCCCTTT-TAAGT
1 CCACAAGTCAGTGGCA-CCCTTTCAAAGC
* * * * *
550707 CTACAACTTC-GTGGCATCTCTTT-TAAGT
1 CCACAA-GTCAGTGGCA-CCCTTTCAAAGC
* * * *
550735 CCACAACTCCGTGGCACCCTTT-TAAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * * *
550762 CCACAACTCCGTGGCACCCTTT-TAAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * * *
550789 CCACAACTCTGTGGCATCCCTTT-TAAGA
1 CCACAAGTCAGTGGCA-CCCTTTCAAAGC
* * * *
550817 CCACAACTCTGTGGCACCCTTT-TAAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * ** * *
550844 CCACAACTCTGTGGCATTCTTT-TAAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * ** *
550871 CCACAACTCCGTGGCA-CCTTTTTAAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * * *
550898 CCACAACTCTGTGGCACCCTTTTAAAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * * *
550926 CCACAACTCCGTGGCACCCTTT-TAAGA
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * * *
550953 CCACAACTCCGTGGCACCCTTT-TAAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * * *
550980 CCACAACTCCGTGGCACCCTTT-TAAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * * * *
551007 CCACAACTCCGTGGCATCCTTTTAAA-T
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * *
551034 CCACAACTCTGTGGCACCCATTCCAAAGC
1 CCACAAGTCAGTGGCACCC-TTTCAAAGC
* *
551063 CCACATAAGTCGGTGGCAACCCATTCCAAAGCC
1 CCAC--AAGTCAGTGGC-ACCC-TTTCAAAG-C
*
551096 CACACAAGTCGGTGGCAACCCATTTCAAAGCC
1 C-CACAAGTCAGTGGC-ACCC-TTTCAAAG-C
**
551128 CACACAAGTTGGTGGCAACCCATTTCAAAGCC
1 C-CACAAGTCAGTGGC-ACCC-TTTCAAAG-C
* *
551160 CACACAAGTCGGTGGCAACCCATTCCAAAGCC
1 C-CACAAGTCAGTGGC-ACCC-TTTCAAAG-C
* *
551192 CACACAAGTCGGTGGCAACCCATTCCAAAGCC
1 C-CACAAGTCAGTGGC-ACCC-TTTCAAAG-C
*
551224 CACACAAGTCGGTGGCAACCCATTTCAAAGCC
1 C-CACAAGTCAGTGGC-ACCC-TTTCAAAG-C
551256 CACACAAGTCAGTGGCACTCCTTTCAAAGC
1 C-CACAAGTCAGTGGCAC-CCTTTCAAAGC
*
551286 CCACGCAAGTCAGTGGCACCTTTTCAAAGC
1 CCA--CAAGTCAGTGGCACCCTTTCAAAGC
* *
551316 CCACGAGTCAGTGGCACTCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
551344 CCACAAGTCAGTGGCACCCTTTC-AAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * *
551371 CCACGAGTCAGTGGTACCTTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
551399 CCACGAGTCAGTGGCA-CCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
551426 CCACAAGTCAGTGGCACTCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* *
551454 CCACGAGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
551482 CCACGCAAGTCAGTGGCACCCTTTTAAAGC
1 CCA--CAAGTCAGTGGCACCCTTTCAAAGC
551512 CCACGCAAGTCAGT
1 CCA--CAAGTCAGT
551526 AAAACTCTTT
Statistics
Matches: 800, Mismatches: 53, Indels: 39
0.90 0.06 0.04
Matches are distributed among these distances:
26 4 0.00
27 311 0.39
28 208 0.26
29 8 0.01
30 51 0.06
31 33 0.04
32 180 0.22
33 2 0.00
34 3 0.00
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (28 bp):
CCACAAGTCAGTGGCACCCTTTCAAAGC
Found at i:551392 original size:83 final size:83
Alignment explanation
Indices: 550881--551575 Score: 425
Period size: 96 Copynumber: 7.9 Consensus size: 83
550871 CCACAACTCC
** * * * * * * * *
550881 GTGGCACCTTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCT
1 GTGGCACCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACGAGTCAGTGGCA-CCT
* * * *
550946 TTT--AAGACCACAACTCC
65 TTTCAAAGCCCACGAGTCA
* * * * * * * * *
550963 GTGGCACCCTTT-TAAGTCCACAACTCCGTGGCACCCTTT-TAAGTCCACAACTCCGTGGCATCC
1 GTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACGAGTCAGTGGCA-CC
* * * *
551026 TTTT-AAA-TCCACAACTCT
64 TTTTCAAAGCCCACGAGTCA
* * * * *
551044 GTGGCACCCATTCCAAAGCCCACATAAGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTCGGT
1 GTGGCA-CC-TTTCAAAGCCCAC--AAGTCAGTGGC-ACCC-TTTCAAAG-CC-CACGAGTCAGT
* * **
551109 GGCAACCCATTTCAAAGCCCACACAAGTTG
58 GGC-A-CCTTTTCAAAG-CC-CACGAGTCA
* * * *
551139 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTCGG
1 GTGGC-A-CC-TTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-TTTCAAAG-CC-CACGAGTCAG
* * * *
551204 TGGCAACCCATTCCAAAGCCCACACAAGTCG
57 TGGC-A-CCTTTTCAAAG-CC-CACGAGTCA
551235 GTGGCAACCCATTTCAAAGCCCACACAAGTCAGTGGCACTCCTTTCAAAGCCCACGCAAGTCAGT
1 GTGGC-A-CC-TTTCAAAG-CC-CACAAGTCAGTGGCAC-CCTTTCAAAGCCCACG--AGTCAGT
551300 GGCACCTTTTCAAAGCCCACGAGTCA
58 GGCACCTTTTCAAAGCCCACGAGTCA
*
551326 GTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC-AAGCCCACGAGTCAGTGGTACCT
1 GTGGCAC-CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACGAGTCAGTGGCACCT
551390 TTTCAAAGCCCACGAGTCA
65 TTTCAAAGCCCACGAGTCA
*
551409 GTGGCACCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACGAGTCAGTGGCATCC-
1 GTGGCACCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACGAGTCAGTGGCA-CCT
551473 TTTCAAAGCCCACGCAAGTCA
65 TTTCAAAGCCCACG--AGTCA
* *** * *
551494 GTGGCACCCTTTTAAAGCCCACGCAAGTCAGTAAAACTCTTTTCAAAGCCCACATGTGTCAGTGG
1 GTGGCA-CCTTTCAAAGCCCA--CAAGTCAGTGGCAC-CCTTTCAAAGCCCAC--GAGTCAGTGG
*
551559 CAACTTTTTTCAAAGCC
60 C-AC-CTTTTCAAAGCC
551576 TACACAAGCT
Statistics
Matches: 534, Mismatches: 43, Indels: 61
0.84 0.07 0.10
Matches are distributed among these distances:
81 44 0.08
82 68 0.13
83 84 0.16
84 2 0.00
85 29 0.05
86 23 0.04
87 18 0.03
88 16 0.03
89 23 0.04
90 14 0.03
91 29 0.05
92 6 0.01
93 22 0.04
94 4 0.01
95 29 0.05
96 118 0.22
97 2 0.00
98 3 0.01
ACGTcount: A:0.27, C:0.34, G:0.18, T:0.21
Consensus pattern (83 bp):
GTGGCACCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACGAGTCAGTGGCACCTT
TTCAAAGCCCACGAGTCA
Found at i:551394 original size:55 final size:56
Alignment explanation
Indices: 550908--551593 Score: 399
Period size: 64 Copynumber: 11.6 Consensus size: 56
550898 CCACAACTCT
* * * * * * * *
550908 GTGGCACCCTTTT-AAAGTCCACAACTCCGTGGCACCCTTT-TAAGACCACAACTCC
1 GTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACGAGTCA
* * * * * * * *
550963 GTGGCACCCTTTT--AAGTCCACAACTCCGTGGCACCCTTT-TAAGTCCACAACTCC
1 GTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACGAGTCA
* * * * * *
551017 GTGGCATCCTTTT-AAA-TCCACAACTCTGTGGCACCCATTCCAAAGCCCACATAAGTCG
1 GTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCACCC-TTTCAAAGCCCAC--GAGTCA
* * * * **
551075 GTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTTG
1 GTGGC-A-CCTTTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-TTTCAAAG-CC-CACGAGTCA
* * * * *
551139 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTCG
1 GTGGC-A-CCTTTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-TTTCAAAG-CC-CACGAGTCA
* * * *
551203 GTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCA
1 GTGGC-A-CCTTTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-TTTCAAAG-CC-CACGAGTCA
* *
551267 GTGGCACTCCTTTCAAAGCCCACGCAAGTCAGTGGCACCTTTTCAAAGCCCACGAGTCA
1 GTGGCAC-CTTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCACGAGTCA
551326 GTGGCA-CTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC-AAGCCCACGAGTCA
1 GTGGCACCT-TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACGAGTCA
* * *
551381 GTGGTACCTTTTCAAAGCCCACGAGTCAGTGGCA-CCTTTCAAAGCCCACAAGTCA
1 GTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACGAGTCA
* *
551436 GTGGCA-CTCTTTCAAAGCCCACGAGTCAGTGGCATCCTTTCAAAGCCCACGCAAGTCA
1 GTGGCACCT-TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACG--AGTCA
*** * *
551494 GTGGCACCCTTTT-AAAGCCCACGCAAGTCAGTAAAACTCTTTTCAAAGCCCACATGTGTCA
1 GTGGCA-CCTTTTCAAAGCCCA--CAAGTCAGTGGCAC-CCTTTCAAAGCCCAC--GAGTCA
*
551555 GTGGCAACTTTTTTCAAAGCCTACACAAG-CTAGTGGCAC
1 GTGGC-AC-CTTTTCAAAGCC--CACAAGTC-AGTGGCAC
551594 ATTTTTTTTA
Statistics
Matches: 550, Mismatches: 45, Indels: 64
0.83 0.07 0.10
Matches are distributed among these distances:
54 79 0.14
55 103 0.19
56 43 0.08
57 1 0.00
58 40 0.07
59 22 0.04
60 16 0.03
61 34 0.06
62 13 0.02
63 48 0.09
64 144 0.26
65 4 0.01
66 3 0.01
ACGTcount: A:0.28, C:0.34, G:0.18, T:0.21
Consensus pattern (56 bp):
GTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACGAGTCA
Found at i:552182 original size:20 final size:20
Alignment explanation
Indices: 552154--552228 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
552144 TTTTACCTTG
552154 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
552174 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
552194 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
552214 ATGTATCGATACATT
1 ATGTATCGATACATT
552229 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:552221 original size:40 final size:39
Alignment explanation
Indices: 552154--552231 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
552144 TTTTACCTTG
* *
552154 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
552194 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
552232 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:553163 original size:21 final size:21
Alignment explanation
Indices: 553137--553192 Score: 78
Period size: 23 Copynumber: 2.6 Consensus size: 21
553127 AGCCTTTGAC
553137 CATGCATTTTTTATTATGTTT
1 CATGCATTTTTTATTATGTTT
553158 CATGCATTTTTTTTATTATGTTT
1 CATGCA--TTTTTTATTATGTTT
*
553181 CATG-TTTTTTTA
1 CATGCATTTTTTA
553193 ACATGTCCAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 7 0.22
21 6 0.19
23 19 0.59
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.64
Consensus pattern (21 bp):
CATGCATTTTTTATTATGTTT
Found at i:553173 original size:23 final size:21
Alignment explanation
Indices: 553143--553191 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 21
553133 TGACCATGCA
553143 TTTTTTATTATGTTTCATGCATT
1 TTTTTTATTATGTTTCATG--TT
553166 TTTTTTATTATGTTTCATGTT
1 TTTTTTATTATGTTTCATGTT
553187 TTTTT
1 TTTTT
553192 AACATGTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 7 0.27
23 19 0.73
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.71
Consensus pattern (21 bp):
TTTTTTATTATGTTTCATGTT
Found at i:568678 original size:11 final size:11
Alignment explanation
Indices: 568662--568689 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
568652 CCTTCATACA
568662 AAAAAAAAAAC
1 AAAAAAAAAAC
568673 AAAAAAAAAAC
1 AAAAAAAAAAC
568684 AAAAAA
1 AAAAAA
568690 GCAAAAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:568709 original size:19 final size:19
Alignment explanation
Indices: 568661--568697 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
568651 TCCTTCATAC
568661 AAAAA-AAAAAA-CAAAAA
1 AAAAACAAAAAAGCAAAAA
568678 AAAAACAAAAAAGCAAAAA
1 AAAAACAAAAAAGCAAAAA
568697 A
1 A
568698 CCAAGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 6 0.33
19 7 0.39
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (19 bp):
AAAAACAAAAAAGCAAAAA
Found at i:569979 original size:28 final size:28
Alignment explanation
Indices: 569937--571101 Score: 1120
Period size: 28 Copynumber: 41.0 Consensus size: 28
569927 GAATGTTCAT
*
569937 CTTTTCAAAGCCCACAAGTCAATGGCACC
1 CTTTT-AAAGCCCACAAGTCAGTGGCACC
569966 CTTTTAAAGCCCACAAGTCAGTGGCACC
1 CTTTTAAAGCCCACAAGTCAGTGGCACC
* *
569994 CTTTCAAAGCCCACAAGTCAATGGCACC
1 CTTTTAAAGCCCACAAGTCAGTGGCACC
* *
570022 CTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTTAAAGCCCACAAGTCAGTGGCACC
* * * *
570050 CTTTCAAAGCCCACAAGTCAATGCCATC
1 CTTTTAAAGCCCACAAGTCAGTGGCACC
* * * *
570078 CTTTCAAAGCCCACGAGTCAATGGCAACT
1 CTTTTAAAGCCCACAAGTCAGTGGC-ACC
* *
570107 CTTTTCAAAGCCCATAAGTCAGTGGCA-T
1 CTTTT-AAAGCCCACAAGTCAGTGGCACC
* *
570135 CTTTTCAAAGCCCACAAGTTAGTGGCA-T
1 CTTTT-AAAGCCCACAAGTCAGTGGCACC
*
570163 CTTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTT-AAAGCCCACAAGTCAGTGGCACC
*
570192 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTTAAAGCCCACAAGTCAGTGGCACC
* *
570220 CTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CTTTTAAAGCCCACAAGTCAGTGGCACC
* * *
570247 CTTTTCGAAGCCTACAAGTCAGTGGCA-T
1 CTTTT-AAAGCCCACAAGTCAGTGGCACC
* * *
570275 TTTTTCAAAGCCCACAAGTTAGTGGCA-T
1 CTTTT-AAAGCCCACAAGTCAGTGGCACC
*
570303 CTTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CTTTT-AAAGCCCACAAGTCAGTGGCACC
*
570331 CTTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTT-AAAGCCCACAAGTCAGTGGCACC
*
570360 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTTAAAGCCCACAAGTCAGTGGCACC
* * *
570388 CTTTCAAAGCCCACAAGGCAGTGGCATC
1 CTTTTAAAGCCCACAAGTCAGTGGCACC
* * *
570416 CTTTCAAAGCCCACAAGTCAATGGCA-T
1 CTTTTAAAGCCCACAAGTCAGTGGCACC
* * *
570443 TTTTTCAAAGCCCACAAGTTAGTGGCAACT
1 CTTTT-AAAGCCCACAAGTCAGTGGC-ACC
*
570473 CTTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTT-AAAGCCCACAAGTCAGTGGCACC
* *
570502 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTTAAAGCCCACAAGTCAGTGGCACC
* * *
570530 CTTTCAAAGCCCACAAGTTAGTGGCATC
1 CTTTTAAAGCCCACAAGTCAGTGGCACC
* *
570558 CTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTTAAAGCCCACAAGTCAGTGGCACC
* * * *
570586 CTTTCAAAGCCCATGAA-TCAGTGGTAACT
1 CTTTTAAAGCCCA-CAAGTCAGTGG-CACC
* * *
570615 CTTTTCAAAGCCCACAAGTCAATTGCA-T
1 CTTTT-AAAGCCCACAAGTCAGTGGCACC
*
570643 CTTTTCAGAGCCCACAAGTCAGTGGCACC
1 CTTTT-AAAGCCCACAAGTCAGTGGCACC
* *
570672 CTTTCAAAG-CC-C-A-TAAGTGGCACC
1 CTTTTAAAGCCCACAAGTCAGTGGCACC
* * * *
570696 CTTTCAAAACCTATGCAAGTCAGTGGCAAC
1 CTTTTAAAGCCCA--CAAGTCAGTGGCACC
* *
570726 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTTAAAGCCCACAAGTCAGTGGCACC
*
570754 CTTTTCAAAGCCCACAAGTTAGTGGCACC
1 CTTTT-AAAGCCCACAAGTCAGTGGCACC
*
570783 CTTTTAAAGCCCACAAGTCAGTGGCACT
1 CTTTTAAAGCCCACAAGTCAGTGGCACC
* * *
570811 CTTTTCAAAGCCCATAAGTTAGTGGCA-T
1 CTTTT-AAAGCCCACAAGTCAGTGGCACC
*
570839 TTTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTT-AAAGCCCACAAGTCAGTGGCACC
* * *
570868 CTTTCAAAGCCCACAAGTCAGTGACACT
1 CTTTTAAAGCCCACAAGTCAGTGGCACC
* *
570896 CTTTTCAAAGCCCATAAGTTAGTGGCA-C
1 CTTTT-AAAGCCCACAAGTCAGTGGCACC
* * *
570924 CTTTTCAAAGCCCACAAGTCAATAGCACT
1 CTTTT-AAAGCCCACAAGTCAGTGGCACC
*
570953 CTTTTCAAAGCCCACAAGTTAGTGGCACC
1 CTTTT-AAAGCCCACAAGTCAGTGGCACC
* * *
570982 CTTTCAAAGCCCACAAGTTAGTGGCACT
1 CTTTTAAAGCCCACAAGTCAGTGGCACC
* * *
571010 CTTTTCGAAGCCCACAAG-CTAGTGGTAACT
1 CTTTT-AAAGCCCACAAGTC-AGTGG-CACC
* *
571040 CTTTTCAAAGCCCACACGAGTCGGTGGCAACT
1 CTTTT-AAAGCCCACA--AGTCAGTGGC-ACC
* *
571072 CTTTTCAAAGCCTACACAAGTTAATGGCAC
1 CTTTT-AAAGCC--CACAAGTCAGTGGCAC
571102 ATTTTTTTTA
Statistics
Matches: 984, Mismatches: 119, Indels: 64
0.84 0.10 0.05
Matches are distributed among these distances:
24 18 0.02
25 2 0.00
26 1 0.00
27 9 0.01
28 675 0.69
29 151 0.15
30 93 0.09
31 2 0.00
32 28 0.03
33 1 0.00
34 4 0.00
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (28 bp):
CTTTTAAAGCCCACAAGTCAGTGGCACC
Found at i:570006 original size:56 final size:56
Alignment explanation
Indices: 569937--571101 Score: 1371
Period size: 56 Copynumber: 20.5 Consensus size: 56
569927 GAATGTTCAT
* *
569937 CTTTTCAAAGCCCACAAGTCAATGGCACCCTTTTAAAGCCCACAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* *
569993 CCTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-C
* * * * *
570050 C-TTTCAAAGCCCACAAGTCAATGCCATCCTTTCAAAGCCCACGAGTCAATGGCAAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC-AC
* * * * *
570106 TCTTTTCAAAGCCCATAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCAT
1 -CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
*
570163 CTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * * * *
570219 CCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCGAAGCCTACAAGTCAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * * *
570275 TTTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
*
570331 CTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * * *
570387 CCTTTCAAAGCCCACAAGGCAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
570443 TTTTTCAAAGCCCACAAGTTAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGC-AC-CCTTTCAAAGCCCACAAGTCAGTGGCA-C
* *
570502 C-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTTAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-C
* * *
570558 C-TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCATGAA-TCAGTGGTAAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA-CAAGTCAGTGG-CAC
* * * * *
570614 TCTTTTCAAAGCCCACAAGTCAATTGCATCTTTTCAGAGCCCACAAGTCAGTGGCAC
1 -CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
570671 CCTTTCAAAG-CC-C-A-TAAGTGGCACCCTTTCAAAACCTATGCAAGTCAGTGGCAAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAGTCAGTGGC-AC
* *
570726 C-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCA-C
* * * *
570783 CTTTT-AAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCATAAGTTAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCAC
* *
570839 TTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGACAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * * *
570895 TCTTTTCAAAGCCCATAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTCAATAGCAC
1 -CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* *
570952 TCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCAC
1 -CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
571009 TCTTTTCGAAGCCCACAAG-CTAGTGGTAACTCTTTTCAAAGCCCACACGAGTCGGTGGCAAC
1 -CTTTTCAAAGCCCACAAGTC-AGTGG-CAC-CCTTTCAAAGCCCACA--AGTCAGTGGC-AC
* *
571071 TCTTTTCAAAGCCTACACAAGTTAATGGCAC
1 -CTTTTCAAAGCC--CACAAGTCAGTGGCAC
571102 ATTTTTTTTA
Statistics
Matches: 972, Mismatches: 104, Indels: 59
0.86 0.09 0.05
Matches are distributed among these distances:
52 16 0.02
53 1 0.00
54 21 0.02
55 7 0.01
56 492 0.51
57 225 0.23
58 150 0.15
59 26 0.03
61 8 0.01
62 14 0.01
63 2 0.00
64 10 0.01
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (56 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:571980 original size:20 final size:20
Alignment explanation
Indices: 571957--572081 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
571947 AAGTACCCAG
571957 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
571977 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
571997 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
572017 ATGTATCAATACATTCTATCCTTTTGCCCA
1 ATGTATCGAT--A--C-AT--TTTT---CA
572047 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
572068 ATGTATCGATACAT
1 ATGTATCGATACAT
572082 CTAGTTAAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
20 56 0.67
21 2 0.02
22 1 0.01
24 5 0.06
25 2 0.02
26 2 0.02
27 4 0.05
29 1 0.01
30 2 0.02
31 9 0.11
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:573003 original size:22 final size:23
Alignment explanation
Indices: 572978--573026 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
572968 ATTTTTAATA
572978 TATCCAACA-TATCATTGAATG-T
1 TATCCAACAGT-TCATTGAATGAT
*
573000 TATCCAACAGTTCATTGTATGAT
1 TATCCAACAGTTCATTGAATGAT
573023 TATC
1 TATC
573027 ACATTTTCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (23 bp):
TATCCAACAGTTCATTGAATGAT
Found at i:576470 original size:20 final size:21
Alignment explanation
Indices: 576442--576480 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
576432 AATTCAAACT
* *
576442 AAATGATTTCAAAT-CTTTGC
1 AAATCATTTAAAATACTTTGC
576462 AAATCATTTAAAATACTTT
1 AAATCATTTAAAATACTTT
576481 ATAAAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (21 bp):
AAATCATTTAAAATACTTTGC
Found at i:580615 original size:21 final size:21
Alignment explanation
Indices: 580591--580637 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
580581 TTTAATGCTG
580591 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
580611 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
580632 ATTTTG
1 ATTTTG
580638 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:580776 original size:13 final size:13
Alignment explanation
Indices: 580758--580796 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
580748 ATAATCACCC
*
580758 TGTATCGATACAG
1 TGTATCGATACAA
580771 TGTATCGATACAA
1 TGTATCGATACAA
580784 TGTATCGATACAA
1 TGTATCGATACAA
580797 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:580807 original size:20 final size:20
Alignment explanation
Indices: 580782--580860 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
580772 GTATCGATAC
580782 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
580802 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
580827 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
580847 CATGTATCGATACA
1 AATGTATCGATACA
580861 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:584724 original size:21 final size:21
Alignment explanation
Indices: 584695--584739 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
584685 AAGTTTTCAT
*
584695 TTTTCTTAGCTAA-TTCATTA
1 TTTTCTTAGCCAACTTCATTA
*
584715 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
584737 TTT
1 TTT
584740 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 7 0.33
22 9 0.43
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:586356 original size:10 final size:10
Alignment explanation
Indices: 586332--586361 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
586322 TAGTGATACG
586332 TGAACAGTG-
1 TGAACAGTGA
586341 TGAACAGTGA
1 TGAACAGTGA
586351 TGAACAGTGA
1 TGAACAGTGA
586361 T
1 T
586362 ACATGAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.10, G:0.30, T:0.23
Consensus pattern (10 bp):
TGAACAGTGA
Found at i:586405 original size:10 final size:10
Alignment explanation
Indices: 586386--586416 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
586376 GTATCGATAC
*
586386 ATGAACAGTG
1 ATGAATAGTG
586396 ATGAATAGTG
1 ATGAATAGTG
586406 ATGAATAGTG
1 ATGAATAGTG
586416 A
1 A
586417 AAATGAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.29, T:0.26
Consensus pattern (10 bp):
ATGAATAGTG
Found at i:586504 original size:53 final size:53
Alignment explanation
Indices: 586440--586576 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
586430 CTACTTCCAA
586440 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGGCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGGCC
* *
586493 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGGCC
586546 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
586577 TATGCAATTT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 67 0.84
54 13 0.16
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGGCC
Found at i:586612 original size:21 final size:20
Alignment explanation
Indices: 586564--586618 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
586554 TACATATTTG
**
586564 TGTGTATCGATACTATGCAA
1 TGTGTATCGATACTATAAAA
* *
586584 TTTGTATCGATACATTTAAAA
1 TGTGTATCGATAC-TATAAAA
586605 TGTGTATCGATACT
1 TGTGTATCGATACT
586619 TTTCAGGGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (20 bp):
TGTGTATCGATACTATAAAA
Found at i:586683 original size:21 final size:21
Alignment explanation
Indices: 586657--586697 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
586647 GTCAACCTTG
586657 TGTATTAATACCAATA-GTATC
1 TGTATTAATA-CAATACGTATC
*
586678 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
586698 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATC
Found at i:589924 original size:21 final size:21
Alignment explanation
Indices: 589900--589952 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
589890 GGAAAAATTG
*
589900 TATCGATACATGCTTGTAATA
1 TATCGATACATGCTTGCAATA
*
589921 TATCGATACATGCTTGCAATG
1 TATCGATACATGCTTGCAATA
*
589942 TATCAATACAT
1 TATCGATACAT
589953 CACTTATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (21 bp):
TATCGATACATGCTTGCAATA
Found at i:591339 original size:20 final size:20
Alignment explanation
Indices: 591311--591383 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
591301 TTTTACCCAG
591311 ATGTATCGATACAATTTTCA
1 ATGTATCGATACAATTTTCA
* * *
591331 ATATATCGATAC-ATGTATGA
1 ATGTATCGATACAAT-TTTCA
*
591351 ATGTATCGATA-TATTCTTCA
1 ATGTATCGATACAATT-TTCA
591371 ATGTATCGATACA
1 ATGTATCGATACA
591384 TTATGTCTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
19 3 0.07
20 39 0.93
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACAATTTTCA
Found at i:591371 original size:40 final size:39
Alignment explanation
Indices: 591311--591388 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 39
591301 TTTTACCCAG
591311 ATGTATCGATACAATTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACAATTTTCAATATATCGATACAT-TATGA
* *
591351 ATGTATCGATA-TATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACAATT-TTCAATATATCGATACATTATG
591389 TCTTTTTACC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
39 7 0.20
40 28 0.80
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACAATTTTCAATATATCGATACATTATGA
Found at i:598436 original size:16 final size:17
Alignment explanation
Indices: 598417--598470 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 17
598407 AAAAAAAGTC
*
598417 AAAA-GCAAAAGCACAA
1 AAAATGCAAAAGCAAAA
598433 AAAATG-AAAAG-AAAA
1 AAAATGCAAAAGCAAAA
598448 AAAAGTGCAAAAGCAAAA
1 AAAA-TGCAAAAGCAAAA
598466 TAAAA
1 -AAAA
598471 AGGGAACAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 7 0.22
16 11 0.34
17 6 0.19
18 4 0.12
19 4 0.12
ACGTcount: A:0.72, C:0.09, G:0.13, T:0.06
Consensus pattern (17 bp):
AAAATGCAAAAGCAAAA
Found at i:598804 original size:20 final size:21
Alignment explanation
Indices: 598776--598814 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
598766 TAAACACCTA
*
598776 AACAAGGGGTAA-CTTAAAGC
1 AACAAGGGGAAATCTTAAAGC
*
598796 AACATGGGGAAATCTTAAA
1 AACAAGGGGAAATCTTAAA
598815 AGCCTCCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.46, C:0.13, G:0.23, T:0.18
Consensus pattern (21 bp):
AACAAGGGGAAATCTTAAAGC
Found at i:599785 original size:27 final size:27
Alignment explanation
Indices: 599748--600384 Score: 889
Period size: 27 Copynumber: 23.3 Consensus size: 27
599738 ACTGTGACCT
* * **
599748 CTTTAAAGTCCACAATTCCGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
* **
599775 CTTTTCAGTCCACAACTCCGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
599802 CTTTTCAGTCCACAACTCCGTGGCA-C
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
599828 CTTTTAAAGTCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
599856 CTTTTAAAGTCCACAACTCCGTGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
599884 CTTTTAAGTCCACCACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
599911 CTTTTAAGTCCATAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
599938 CTTTTAAGTCCATAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
599965 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
599992 CTTTTAAGTCCACAATTCTGTGACACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
600019 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
600047 CTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
600074 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
600101 CTTTTAAAGTCCACAACTTCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
600129 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
600157 CTTTTAAAGTCCACAACTCCATGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
600185 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
600213 CTTTTAAAGTCCACAACTCTGTGGCACA
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
600241 CTTTTAAGTTCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
600268 CTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
600295 CTTTTAAAGTCCACAACTCCATGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
600323 CTTTTAAGTTCACAACTTCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* * * *
600351 TTTTTAAGCCCACAAGTCAGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
600378 CTTTTAA
1 CTTTTAA
600385 AGCCCACACA
Statistics
Matches: 558, Mismatches: 46, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
26 5 0.01
27 318 0.57
28 235 0.42
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.28
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:599894 original size:82 final size:82
Alignment explanation
Indices: 599748--600674 Score: 935
Period size: 82 Copynumber: 11.0 Consensus size: 82
599738 ACTGTGACCT
* * ** * ** *
599748 CTTTAAAGTCCACAATTCCGTGGCATTCTTTT-CAGTCCACAACTCCGTGGCATTCTTTTCAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
599812 CACAACTCCGTGGCA-C
66 CACAACTCCGTGGCACC
* *
599828 CTTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGTACCCTTTTAAGT
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGT
*
599893 CCACCACTCCGTGGCACC
65 CCACAACTCCGTGGCACC
* * *
599911 CTTTTAAGTCCATAACTCCGTGGCACCCTTTT-AAGTCCATAACTCCGTGGCATCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
599975 CACAACTCCGTGGCATC
66 CACAACTCCGTGGCACC
* * * *
599992 CTTTTAAGTCCACAATTCTGTGACACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTAAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
600057 CACAACTCCGTGGCACC
66 CACAACTCCGTGGCACC
*
600074 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTTCGTGGCACCCTTTTAAAGT
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
600139 CCACAACTCCGTGGCACC
65 CCACAACTCCGTGGCACC
*
600157 CTTTTAAAGTCCACAACTCCATGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAG
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAG
* *
600222 TCCACAACTCTGTGGCACA
64 TCCACAACTCCGTGGCACC
*
600241 CTTTTAAGTTCACAACTCCGTGGCACCC-TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGT
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
*
600305 CCACAACTCCATGGCACC
65 CCACAACTCCGTGGCACC
* * * * * * *
600323 CTTTTAAGTTCACAACTTCGTGGCATCCTTTTTAAGCCCACAAGTCAGTGGCACCCTTTTAAAGC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAG-
* * * *
600388 CCACACAAGTCGGTGGCAAC
64 TC-CACAACTCCGTGGCACC
* * * * * * *
600408 CTATTTCAAAGCCTACACAAGTCGGTGGCAACCCATTTGAAAGCCCACACAAGTCGGTGGCAACC
1 CT-TTT--AAG--TCCACAACTCCGTGGC-ACCC-TTTTAAAG-TC-CACAACTCCGTGGC-ACC
* * * * *
600473 CATTTCAAAGCCCATAAATCAGTGGCACC
56 C-TTT-TAAGTCCACAACTCCGTGGCACC
* * * * * * * * *
600502 CTTTCAAAGCCCATAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCGGTGGCAACCCATTTCAG
1 CTTT-TAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGC-ACCC-TTTTA-
* * *
600567 AGCCCACAAATCAGTGGCACC
62 AGTCCACAACTCCGTGGCACC
* ** * * * * * * * *
600588 CTTTCAAACCCAAAAGTCAGTGGCACCCTTTTAAAGCCCACAAATCAGTGGCACCCTTTCAAAGC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTT-TAAGT
* * *
600653 CCACAAGTCAGTGGCACT
65 CCACAACTCCGTGGCACC
600671 CTTT
1 CTTT
600675 GCAAAGCCCA
Statistics
Matches: 743, Mismatches: 80, Indels: 45
0.86 0.09 0.05
Matches are distributed among these distances:
80 4 0.01
81 95 0.13
82 243 0.33
83 111 0.15
84 85 0.11
85 59 0.08
86 50 0.07
87 2 0.00
88 10 0.01
89 4 0.01
90 24 0.03
91 3 0.00
92 9 0.01
93 4 0.01
94 28 0.04
95 6 0.01
96 6 0.01
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (82 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
CACAACTCCGTGGCACC
Found at i:600599 original size:27 final size:28
Alignment explanation
Indices: 599811--601204 Score: 1105
Period size: 28 Copynumber: 48.8 Consensus size: 28
599801 TCTTTTCAGT
* * *
599811 CCACAACTCCGTGGCA-CCTTTTAAAGT
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* * *
599838 CCACAACTCTGTGGCACCCTTTTAAAGT
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* * * *
599866 CCACAACTCCGTGGTACCCTTTT-AAGT
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* * * *
599893 CCACCACTCCGTGGCACCCTTTT-AAGT
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* * * *
599920 CCATAACTCCGTGGCACCCTTTT-AAGT
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* * * * *
599947 CCATAACTCCGTGGCATCCTTTT-AAGT
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* * * *
599974 CCACAACTCCGTGGCATCCTTTT-AAGT
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* * * *
600001 CCACAATTCTGTGACACCCTTTTAAAGT
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* * *
600029 CCACAACTCCGTGGCACCC-TTTAAAGT
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* * *
600056 CCACAACTCCGTGGCACCCTTTT-AAGT
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* * *
600083 CCACAACTCCGTGGCACCCTTTTAAAGT
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* *
600111 CCACAACTTC-GTGGCACCCTTTTAAAGT
1 CCACAA-GTCAGTGGCACCCTTTTAAAGC
* * *
600139 CCACAACTCCGTGGCACCCTTTTAAAGT
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* *
600167 CCACAACTCCA-TGGCACCCTTTTAAAGT
1 CCACAAGT-CAGTGGCACCCTTTTAAAGC
* * *
600195 CCACAACTCCGTGGCACCCTTTTAAAGT
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* * * *
600223 CCACAACTCTGTGGCACACTTTT-AAGT
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* * * *
600250 TCACAACTCCGTGGCACCC-TTTAAAGT
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* * *
600277 CCACAACTCCGTGGCACCCTTTTAAAGT
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* *
600305 CCACAACTCCA-TGGCACCCTTTT-AAGT
1 CCACAAGT-CAGTGGCACCCTTTTAAAGC
* * * *
600332 TCACAACTTC-GTGGCATCCTTTTTAAGC
1 CCACAA-GTCAGTGGCACCCTTTTAAAGC
600360 CCACAAGTCAGTGGCACCCTTTTAAAGCC
1 CCACAAGTCAGTGGCACCCTTTTAAAG-C
* *
600389 CACACAAGTCGGTGGCAACCTATTTCAAAGC
1 C-CACAAGTCAGTGGCACCCT-TTT-AAAGC
* *
600420 CTACACAAGTCGGTGGCAACCCATTTGAAAGCC
1 C--CACAAGTCAGTGGC-ACCC-TTTTAAAG-C
* *
600453 CACACAAGTCGGTGGCAACCCATTTCAAAGC
1 C-CACAAGTCAGTGGC-ACCC-TTTTAAAGC
* * *
600484 CCATAAATCAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
*
600512 CCATAAGTCAGTGGCACCCTTTTAAAGC
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* * *
600540 CCACAAGTCGGTGGCAACCCATTTCAGAGC
1 CCACAAGTCAGTGGC-ACCC-TTTTAAAGC
* *
600570 CCACAAATCAGTGGCACCCTTTCAAA-C
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
*
600597 CCAAAAGTCAGTGGCACCCTTTTAAAGC
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* *
600625 CCACAAATCAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* *
600653 CCACAAGTCAGTGGCACTCTTTGCAAAGC
1 CCACAAGTCAGTGGCACCCTTT-TAAAGC
*
600682 CCACATGAGTCGGTGGCAACCCTTTTCAAAGC
1 CCACA--AGTCAGTGGC-ACCCTTTT-AAAGC
* * *
600714 CCACAAGTTAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* * *
600742 CCACGAGTCGGTGGCAACACTTTTCAAAGC
1 CCACAAGTCAGTGGC-ACCCTTTT-AAAGC
* *
600772 CCACAAGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* *
600800 CCATAAGTCAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* *
600828 CCATAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTT-AAAGC
* *
600857 CTACACGAGTCGGTGGCAACCCTTTTCAAAGC
1 C--CACAAGTCAGTGGC-ACCCTTTT-AAAGC
*
600889 CCACAAGTCAGTGGCATCCTTTTAAAGC
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* ** *
600917 CCACGAGTTGGTGGCAACACTTTTCAAAGC
1 CCACAAGTCAGTGGC-ACCCTTTT-AAAGC
* *
600947 CCACAAGTCAGTGGTACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* *
600975 CCACAAGTCAGTGGCATCCTTTCAAAGCC
1 CCACAAGTCAGTGGCACCCTTTTAAAG-C
*
601004 TCCACGAA-TCGGTGGCAACCCTTTTTAAAGC
1 -CCAC-AAGTCAGTGGC-ACCC-TTTTAAAGC
* * *
601035 CCACAAGTTAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
* * * * *
601063 CCACGAGTCGGTGGTAACATTTTCAAA-C
1 CCACAAGTCAGTGGCACCCTTTT-AAAGC
* *
601091 CCACAAGTTAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTTAAAGC
*
601119 CCACAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTT-AAAGC
** *
601148 CCACACGAGTTGGTGGCAACTCTTTTCAAAGCC
1 CCACA--AGTCAGTGGC-ACCCTTTT-AAAG-C
* *
601181 CACACAAGTTAGTGGCACCATTTT
1 C-CACAAGTCAGTGGCACCCTTTT
601205 TTTAAAAAAA
Statistics
Matches: 1183, Mismatches: 131, Indels: 102
0.84 0.09 0.07
Matches are distributed among these distances:
26 3 0.00
27 289 0.24
28 508 0.43
29 89 0.08
30 123 0.10
31 47 0.04
32 110 0.09
33 9 0.01
34 5 0.00
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (28 bp):
CCACAAGTCAGTGGCACCCTTTTAAAGC
Found at i:600813 original size:175 final size:173
Alignment explanation
Indices: 599811--601204 Score: 1010
Period size: 175 Copynumber: 8.1 Consensus size: 173
599801 TCTTTTCAGT
* * * * * *
599811 CCACAACTCCGTGGCA-CCTTTT-AAAGTCCACA--ACTCTGTGGCACCCTTTT-AAAGTCCACA
1 CCACAAGTCAGTGGCACCCTTTTCAAAGCCCACATGAGTCAGTGGCACCCTTTTCAAAGCCCACA
* * * * * * * * * * * * *
599871 ACTCCGTGGTACCCTTT-TAAGTCCACCACTCCGTGGCACCCTTTT--AAGTCCATAACTCCGTG
66 AGTCAGTGGCACCCTTTCAAAGCCCACAAGTCGGTGGCAACCTTTTCAAAGCCCACAAGTCAGTG
* * * * * * * *
599933 GCACCCTTT-TAAGTCCATAACTCCGTGGCATCCTTT-TAAGT
131 GCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
* * * * * * * *
599974 CCACAACTCCGTGGCATCCTTTT--AAGTCCACA--ATTCTGTGACACCCTTTT-AAAGTCCACA
1 CCACAAGTCAGTGGCACCCTTTTCAAAGCCCACATGAGTCAGTGGCACCCTTTTCAAAGCCCACA
* * * * * * * * *
600034 ACTCCGTGGCACCCTTT-AAAGTCCACAACTCCGTGGCACCCTTTT--AAGTCCACAACTCCGTG
66 AGTCAGTGGCACCCTTTCAAAGCCCACAAGTCGGTGGCAACCTTTTCAAAGCCCACAAGTCAGTG
* * * * *
600096 GCACCCTTTTAAAGTCCACAACTTC-GTGGCACCCTTTTAAAGT
131 GCACCCTTTCAAAGCCCACAA-GTCAGTGGCACCCTTTCAAAGC
* * * * *
600139 CCACAACTCCGTGGCACCCTTTT-AAAGTCCACA--ACTCCA-TGGCACCCTTTT-AAAGTCCAC
1 CCACAAGTCAGTGGCACCCTTTTCAAAGCCCACATGAGT-CAGTGGCACCCTTTTCAAAGCCCAC
* * * * * * ** * *
600199 AACTCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGC-ACACTTTT--AAGTTCACAACTCCG
65 AAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCGGTGGCAAC-CTTTTCAAAGCCCACAAGTCAG
* * * * *
600261 TGGCACCCTTT-AAAGTCCACAACTCCGTGGCACCCTTTTAAAGT
129 TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
* ** * * *
600305 CCACAACTCCA-TGGCACCCTTTT--AAGTTCACA--ACTTC-GTGGCATCCTTTT-TAAGCCCA
1 CCACAAGT-CAGTGGCACCCTTTTCAAAGCCCACATGA-GTCAGTGGCACCCTTTTCAAAGCCCA
*
600363 CAAGTCAGTGGCACCCTTTTAAAGCCCACACAAGTCGGTGGCAACCTATTTCAAAGCCTACACAA
64 CAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCGGTGGCAACCT-TTTCAAAGCC--CACAA
* * *
600428 GTCGGTGGCAACCCATTTGAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGC
124 GTCAGTGGC-ACCC-TTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-TTTCAAAGC
* * *
600484 CCATAAATCAGTGGCACCC-TTTCAAAG-CC-CATAAGTCAGTGGCACCCTTTT-AAAGCCCACA
1 CCACAAGTCAGTGGCACCCTTTTCAAAGCCCACATGAGTCAGTGGCACCCTTTTCAAAGCCCACA
* * * * * *
600545 AGTCGGTGGCAACCCATTTCAGAGCCCACAAATCAGTGGC-ACCCTTTCAAA-CCCAAAAGTCAG
66 AGTCAGTGGC-ACCC-TTTCAAAGCCCACAAGTCGGTGGCAACCTTTTCAAAGCCCACAAGTCAG
* *
600608 TGGCACCCTTTTAAAGCCCACAAATCAGTGGCACCCTTTCAAAGC
129 TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
* * *
600653 CCACAAGTCAGTGGCACTCTTTGCAAAGCCCACATGAGTCGGTGGCAACCCTTTTCAAAGCCCAC
1 CCACAAGTCAGTGGCACCCTTTTCAAAGCCCACATGAGTCAGTGGC-ACCCTTTTCAAAGCCCAC
* * *
600718 AAGTTAGTGGCATCCTTTCAAAGCCCACGAGTCGGTGGCAACACTTTTCAAAGCCCACAAGTCAG
65 AAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCGGTGGCAAC-CTTTTCAAAGCCCACAAGTCAG
* *
600783 TGGCATCCTTTCAAAGCCCATAAGTCAGTGGCACCCTTTCAAAGC
129 TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
* * * * *
600828 CCATAAGTCAGTGGCACTCTTTTCAAAGCCTACACGAGTCGGTGGCAACCCTTTTCAAAGCCCAC
1 CCACAAGTCAGTGGCACCCTTTTCAAAGCCCACATGAGTCAGTGGC-ACCCTTTTCAAAGCCCAC
* * * *
600893 AAGTCAGTGGCATCCTTTTAAAGCCCACGAGTTGGTGGCAACACTTTTCAAAGCCCACAAGTCAG
65 AAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCGGTGGCAAC-CTTTTCAAAGCCCACAAGTCAG
* *
600958 TGGTACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
129 TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG-C
* * * *
601004 TCCACGAA-TCGGTGGCAACCCTTTTTAAAGCCCACA--AGTTAGTGGCATCC-TTTCAAAGCCC
1 -CCAC-AAGTCAGTGGC-ACCCTTTTCAAAGCCCACATGAGTCAGTGGCACCCTTTTCAAAGCCC
* * * ** ** *
601065 ACGAGTCGGTGGTAACATTTTCAAA-CCCACAAGTTAGTGGC-ACCCTTTCAAAGCCCACAAGTC
63 ACAAGTCAGTGG-CACCCTTTCAAAGCCCACAAGTCGGTGGCAACCTTTTCAAAGCCCACAAGTC
* ** *
601128 AGTGGCACTCTTTTCAAAGCCCACACGAGTTGGTGGCAACTCTTTTCAAAGCC
127 AGTGGCAC-CCTTTCAAAGCCCACA--AGTCAGTGGC-AC-CCTTTCAAAG-C
* *
601181 CACACAAGTTAGTGGCACCATTTT
1 C-CACAAGTCAGTGGCACCCTTTT
601205 TTTAAAAAAA
Statistics
Matches: 1063, Mismatches: 113, Indels: 97
0.84 0.09 0.08
Matches are distributed among these distances:
163 118 0.11
164 26 0.02
165 79 0.07
166 101 0.10
167 65 0.06
168 5 0.00
169 25 0.02
170 14 0.01
171 14 0.01
172 72 0.07
173 41 0.04
174 68 0.06
175 249 0.23
176 21 0.02
177 44 0.04
178 36 0.03
179 27 0.03
180 46 0.04
181 6 0.01
182 6 0.01
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (173 bp):
CCACAAGTCAGTGGCACCCTTTTCAAAGCCCACATGAGTCAGTGGCACCCTTTTCAAAGCCCACA
AGTCAGTGGCACCCTTTCAAAGCCCACAAGTCGGTGGCAACCTTTTCAAAGCCCACAAGTCAGTG
GCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
Found at i:601808 original size:20 final size:19
Alignment explanation
Indices: 601764--601834 Score: 88
Period size: 20 Copynumber: 3.6 Consensus size: 19
601754 TACCCAGATA
*
601764 TATCGATACATTTTCAATT
1 TATCGATACATTTTCAATG
* *
601783 TATCGATACATGTATAAATG
1 TATCGATACAT-TTTCAATG
*
601803 TATCGATATATTCTTCAATG
1 TATCGATACATT-TTCAATG
601823 TATCGATACATT
1 TATCGATACATT
601835 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 12 0.28
20 31 0.72
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (19 bp):
TATCGATACATTTTCAATG
Found at i:606298 original size:53 final size:52
Alignment explanation
Indices: 606211--606319 Score: 157
Period size: 52 Copynumber: 2.1 Consensus size: 52
606201 GAGGTATTCC
*
606211 AACCTCGTTTTCACTTTTAAAAACACCAAATTTTTTATCTCTGGGGATACTCT
1 AACCCCGTTTTCACTTTTAAAAACACCAAATTTTTTATCT-TGGGGATACTCT
* ** *
606264 AACCCCGTTTTTACTTTT-AAAACATTAAATTTTTTATCTTTGGGATACTCT
1 AACCCCGTTTTCACTTTTAAAAACACCAAATTTTTTATCTTGGGGATACTCT
606315 AACCC
1 AACCC
606320 TACAATCTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 16 0.31
52 19 0.37
53 16 0.31
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.41
Consensus pattern (52 bp):
AACCCCGTTTTCACTTTTAAAAACACCAAATTTTTTATCTTGGGGATACTCT
Found at i:609694 original size:20 final size:20
Alignment explanation
Indices: 609647--609721 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
609637 AAAAAGACAT
*
609647 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
609666 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
609687 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
609707 AATGTATCGATACAT
1 AATGTATCGATACAT
609722 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:609715 original size:40 final size:39
Alignment explanation
Indices: 609644--609721 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
609634 GGTAAAAAGA
* *
609644 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
609683 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
609722 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:610329 original size:28 final size:28
Alignment explanation
Indices: 610247--611419 Score: 1544
Period size: 28 Copynumber: 40.9 Consensus size: 28
610237 TGAAAAGGGT
* * *
610247 TGCCATTGACTTGCATGGGCTTTAAAAGGG
1 TGCCACTGACTTG--TGGGCTTTGAAAGAG
* *
610277 TGCCACTGACTTGCGTGAGCTTTGAAAGAA
1 TGCCACTGACTT--GTGGGCTTTGAAAGAG
* *
610307 TGCCACTAACTCGTGGGCTTTGAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
610334 ATGCCACTGACTTGTGGGCTTTGAAAGAG
1 -TGCCACTGACTTGTGGGCTTTGAAAGAG
610363 TGCCACTGACTTGTGGGCTTTGAAA-AGG
1 TGCCACTGACTTGTGGGCTTTGAAAGA-G
* * * *
610391 TACCACTAACTTGCGTGAGCTTTAAAAGGAG
1 TGCCACTGACTT--GTGGGCTTTGAAA-GAG
* * *
610422 TGCCACTAACTTGTGTGGGCTTTAAAAGGG
1 TGCCACTGAC-T-TGTGGGCTTTGAAAGAG
*
610452 TGCCACTGACTTGTGGGCTTTAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * *
610480 TGCCACTGAATTGTGGGCTTCGCAATG-G
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
* *
610508 TGCCACTGACTTGTGGGCTTCGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * *
610536 TGCCATTGACTTGTGGGCTCTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* *
610564 TGCCACTAACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
610592 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
*
610621 TGCCACTGATTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
610650 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
610679 TGCCACTGACTTGTGGGCTTTGAAA-AGG
1 TGCCACTGACTTGTGGGCTTTGAAAGA-G
*
610707 TGCCACTAACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
* *
610736 TGCCACTGACTTGTAGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
*
610764 TGCCACTGACTTGTGGGCTTTGAAAAGAA
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
* *
610793 TGCCACTGATTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
610821 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
*
610850 TGCCACTGATTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
* *
610879 TGCCACTGATTTGTGGGCTTTGAAAAGAA
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
610908 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
*
610937 TGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* *
610965 TGCCACTAACTTGTGGACTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
*
610994 TGCCACTGATTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
*
611023 TGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* *
611051 TGCCACTGAGTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
611079 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
* *
611108 TGCCACTGATTTGTGGGATTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
611137 TGCCACTGACTTGTGGGCTTTGAAATGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
*
611166 TGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
*
611194 TGCCACTAACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
*
611223 TGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
*
611251 TGCCACTGACTTGTGGGCTTTGAAAAGAA
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
* *
611280 TGCCACTGATTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
*
611308 TGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
*
611336 TGCCATTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
* *
611365 TGCTACTGATTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
*
611394 TGCCGCTGACTTGTGGGCTTTGAAAG
1 TGCCACTGACTTGTGGGCTTTGAAAG
611420 GGATGAACAT
Statistics
Matches: 1025, Mismatches: 88, Indels: 62
0.87 0.07 0.05
Matches are distributed among these distances:
27 5 0.00
28 468 0.46
29 468 0.46
30 58 0.06
31 22 0.02
32 3 0.00
33 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTTGAAAGAG
Found at i:610737 original size:57 final size:57
Alignment explanation
Indices: 610247--611421 Score: 1632
Period size: 57 Copynumber: 20.5 Consensus size: 57
610237 TGAAAAGGGT
* * * *
610247 TGCCATTGACTTGCATGGGCTTTAAAAGGGTGCCACTGACTTGCGTGAGCTTTGAAA-GAA
1 TGCCACTGACTTG--TGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTTGAAAGGAG
* * *
610307 TGCCACTAACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAA-GAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAG
* * * * *
610363 TGCCACTGACTTGTGGGCTTTGAAAAGGTACCACTAACTTGCGTGAGCTTTAAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTTGAAAGGAG
* * *
610422 TGCCACTAACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTT-AAAAGAG
1 TGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAG
* * * * *
610480 TGCCACTGAATTGTGGGCTTCGCAATGGTGCCACTGACTTGTGGGCTTCGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
610536 TGCCATTGACTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
610592 TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAG
*
610650 TGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
610707 TGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTAGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGAG
** *
610764 TGCCACTGACTTGTGGGCTTTGAAAAGAATGCCACTGATTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
610821 TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAG
* **
610879 TGCCACTGATTTGTGGGCTTTGAAAAGAATGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
610937 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGACTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
610994 TGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
611051 TGCCACTGAGTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
611108 TGCCACTGATTTGTGGGATTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAATGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGAG
*
611166 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
611223 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAA
1 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAG
*
611280 TGCCACTGATTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAG
* * * *
611336 TGCCATTGACTTGTGGGCTTTGAAAAGAGTGCTACTGATTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAG
*
611394 TGCCGCTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGG
611422 ATGAACATTC
Statistics
Matches: 1006, Mismatches: 93, Indels: 35
0.89 0.08 0.03
Matches are distributed among these distances:
56 201 0.20
57 465 0.46
58 284 0.28
59 20 0.02
60 11 0.01
61 25 0.02
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (57 bp):
TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAG
Found at i:611419 original size:29 final size:29
Alignment explanation
Indices: 610247--611420 Score: 1643
Period size: 29 Copynumber: 40.9 Consensus size: 29
610237 TGAAAAGGGT
* *
610247 TGCCATTGACTTGCATGGGCTTTAAAAGG-G
1 TGCCACTGACTTG--TGGGCTTTGAAAGGAG
* *
610277 TGCCACTGACTTGCGTGAGCTTTGAAA-GAA
1 TGCCACTGACTT--GTGGGCTTTGAAAGGAG
* *
610307 TGCCACTAACTCGTGGGCTTTGAAAGGA-
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
610335 TGCCACTGACTTGTGGGCTTTGAAA-GAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
610363 TGCCACTGACTTGTGGGCTTTGAAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * * *
610391 TACCACTAACTTGCGTGAGCTTTAAAAGGAG
1 TGCCACTGACTT--GTGGGCTTTGAAAGGAG
* *
610422 TGCCACTAACTTGTGTGGGCTTTAAAAGG-G
1 TGCCACTGAC-T-TGTGGGCTTTGAAAGGAG
*
610452 TGCCACTGACTTGTGGGCTTT-AAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * * *
610480 TGCCACTGAATTGTGGGCTTCGCAATG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
610508 TGCCACTGACTTGTGGGCTTCGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
610536 TGCCATTGACTTGTGGGCTCTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
610564 TGCCACTAACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
610592 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
610621 TGCCACTGATTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
610650 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
610679 TGCCACTGACTTGTGGGCTTTGAAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
610707 TGCCACTAACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
610736 TGCCACTGACTTGTAGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
610764 TGCCACTGACTTGTGGGCTTTGAAAAGAA
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
610793 TGCCACTGATTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
610821 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
610850 TGCCACTGATTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
610879 TGCCACTGATTTGTGGGCTTTGAAAAGAA
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
610908 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
610937 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
610965 TGCCACTAACTTGTGGACTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
610994 TGCCACTGATTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
611023 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
611051 TGCCACTGAGTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
611079 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
611108 TGCCACTGATTTGTGGGATTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
611137 TGCCACTGACTTGTGGGCTTTGAAATGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
611166 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
611194 TGCCACTAACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
611223 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
611251 TGCCACTGACTTGTGGGCTTTGAAAAGAA
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
611280 TGCCACTGATTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
611308 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
611336 TGCCATTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
611365 TGCTACTGATTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
611394 TGCCGCTGACTTGTGGGCTTTGAAAGG
1 TGCCACTGACTTGTGGGCTTTGAAAGG
611421 GATGAACATT
Statistics
Matches: 1031, Mismatches: 91, Indels: 45
0.88 0.08 0.04
Matches are distributed among these distances:
27 6 0.01
28 463 0.45
29 482 0.47
30 53 0.05
31 24 0.02
32 2 0.00
33 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (29 bp):
TGCCACTGACTTGTGGGCTTTGAAAGGAG
Found at i:612652 original size:1 final size:1
Alignment explanation
Indices: 612648--612693 Score: 56
Period size: 1 Copynumber: 46.0 Consensus size: 1
612638 TTTTTTGCTA
* * * *
612648 TTTTTTTCTTTTTTTTTTTGTTTTTTTTTGTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
612694 GGGTGTAAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.02, G:0.07, T:0.91
Consensus pattern (1 bp):
T
Found at i:612663 original size:22 final size:22
Alignment explanation
Indices: 612638--612689 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
612628 GACCCTTCTA
612638 TTTTTTGCTATTTTTTTCTTTTT
1 TTTTTTG-TATTTTTTTCTTTTT
* *
612661 TTTTTTGTTTTTTTTTGTTTTT
1 TTTTTTGTATTTTTTTCTTTTT
612683 GTTTTTT
1 -TTTTTT
612690 TTTTGGGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.87
Consensus pattern (22 bp):
TTTTTTGTATTTTTTTCTTTTT
Found at i:612675 original size:16 final size:16
Alignment explanation
Indices: 612651--612693 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
612641 TTTGCTATTT
612651 TTTTCTTTTTTTTTTTG
1 TTTT-TTTTTTTTTTTG
*
612668 TTTTTTTTTGTTTTTG
1 TTTTTTTTTTTTTTTG
612684 TTTTTTTTTT
1 TTTTTTTTTT
612694 GGGTGTAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.00, C:0.02, G:0.07, T:0.91
Consensus pattern (16 bp):
TTTTTTTTTTTTTTTG
Found at i:612694 original size:11 final size:11
Alignment explanation
Indices: 612638--612693 Score: 55
Period size: 10 Copynumber: 5.1 Consensus size: 11
612628 GACCCTTCTA
612638 TTTTTTGCTATTT
1 TTTTTTG-T-TTT
*
612651 TTTTCT-TTTT
1 TTTTTTGTTTT
612661 TTTTTTG-TTT
1 TTTTTTGTTTT
612671 TTTTTTGTTTT
1 TTTTTTGTTTT
612682 TGTTTTT-TTTT
1 T-TTTTTGTTTT
612693 T
1 T
612694 GGGTGTAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
10 18 0.47
11 10 0.26
12 5 0.13
13 5 0.13
ACGTcount: A:0.02, C:0.04, G:0.07, T:0.88
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:626742 original size:20 final size:20
Alignment explanation
Indices: 626695--626769 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
626685 AAAAAGACAT
*
626695 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
626714 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
626735 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
626755 AATGTATCGATACAT
1 AATGTATCGATACAT
626770 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:626763 original size:40 final size:39
Alignment explanation
Indices: 626692--626769 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
626682 GGTAAAAAGA
* *
626692 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
626731 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
626770 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:629366 original size:13 final size:13
Alignment explanation
Indices: 629348--629372 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
629338 CAATTTTTTG
629348 TGTATCGATACAC
1 TGTATCGATACAC
629361 TGTATCGATACA
1 TGTATCGATACA
629373 TACTTTGTGT
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:629385 original size:32 final size:33
Alignment explanation
Indices: 629328--629391 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
629318 ACAAAGCCAA
**
629328 TGTATCGATACAATTTTTTGTGTATCGATACAC
1 TGTATCGATACAATACTTTGTGTATCGATACAC
629361 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
629392 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAC
Found at i:634594 original size:17 final size:16
Alignment explanation
Indices: 634559--634615 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
634549 AAAGGGAAGG
634559 AAGG-AAAGAAGAAAGGA
1 AAGGAAAAGAA-AAA-GA
*
634576 AAGGACAAGAAAGAAGA
1 AAGGAAAAGAAA-AAGA
*
634593 AAGAAAAAAGAAAAAGA
1 AAG-GAAAAGAAAAAGA
634610 AAGGAA
1 AAGGAA
634616 GCACCTCACC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
16 2 0.06
17 17 0.52
18 14 0.42
ACGTcount: A:0.70, C:0.02, G:0.28, T:0.00
Consensus pattern (16 bp):
AAGGAAAAGAAAAAGA
Found at i:637228 original size:18 final size:19
Alignment explanation
Indices: 637195--637231 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
637185 TGGGGGGAAC
637195 GGGGAAAAGGGGGGGAGGGG
1 GGGGAAAA-GGGGGGAGGGG
637215 GGGGAAAA-GGGGGAGGG
1 GGGGAAAAGGGGGGAGGG
637232 CAGGGCAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.27, C:0.00, G:0.73, T:0.00
Consensus pattern (19 bp):
GGGGAAAAGGGGGGAGGGG
Found at i:637913 original size:30 final size:31
Alignment explanation
Indices: 637878--637947 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
637868 AAAAATTCAA
* * *
637878 TTTATTTTTAT-GAGTTTTTTTTTTTTATTT
1 TTTATTTTTATAAAATTTTTTTTTTGTATTT
*
637908 TTTA-TTTCATAAAATTTTTTTTTTGTATTT
1 TTTATTTTTATAAAATTTTTTTTTTGTATTT
637938 TTTATATTTT
1 TTTAT-TTTT
637948 TTTGTAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
29 5 0.16
30 24 0.75
32 3 0.09
ACGTcount: A:0.19, C:0.01, G:0.04, T:0.76
Consensus pattern (31 bp):
TTTATTTTTATAAAATTTTTTTTTTGTATTT
Found at i:638382 original size:1 final size:1
Alignment explanation
Indices: 638378--638487 Score: 193
Period size: 1 Copynumber: 110.0 Consensus size: 1
638368 AAAATCAAGG
* *
638378 AAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
638443 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
638488 CAATGTATAA
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 103 1.00
ACGTcount: A:0.97, C:0.02, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Done.