Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008530.1 Hibiscus syriacus cultivar Beakdansim tig00111408_pilon, whole genome shotgun sequence
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: 724678
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:272418 original size:16 final size:16
Alignment explanation
Indices: 272397--272427 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
272387 ATAAATAAAT
272397 GAACATAAACGAACAC
1 GAACATAAACGAACAC
272413 GAACATAAACGAACA
1 GAACATAAACGAACA
272428 AATTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:272522 original size:24 final size:20
Alignment explanation
Indices: 272483--272540 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
272473 ATTTAAATGA
272483 TAAACGAACACAAACGAACG
1 TAAACGAACACAAACGAACG
*
272503 TAAACGAATACAAACGAACG
1 TAAACGAACACAAACGAACG
272523 TAAACGAACACAAACGAA
1 TAAACGAACACAAACGAA
272541 TGAACATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.57, C:0.22, G:0.14, T:0.07
Consensus pattern (20 bp):
TAAACGAACACAAACGAACG
Found at i:272555 original size:10 final size:10
Alignment explanation
Indices: 272482--272569 Score: 77
Period size: 10 Copynumber: 8.4 Consensus size: 10
272472 CATTTAAATG
272482 ATAAACGAAC
1 ATAAACGAAC
*
272492 ACAAACGAAC
1 ATAAACGAAC
* *
272502 GTAAACGAAT
1 ATAAACGAAC
*
272512 ACAAACGAAC
1 ATAAACGAAC
*
272522 GTAAACGAAC
1 ATAAACGAAC
*
272532 ACAAACGAATGAAC
1 ATAAAC----GAAC
272546 ATAAACGAAC
1 ATAAACGAAC
*
272556 ATAAATGAAC
1 ATAAACGAAC
272566 ATAA
1 ATAA
272570 TAAATGAATA
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
10 52 0.85
14 9 0.15
ACGTcount: A:0.58, C:0.19, G:0.12, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:272564 original size:20 final size:20
Alignment explanation
Indices: 272482--272569 Score: 95
Period size: 20 Copynumber: 4.2 Consensus size: 20
272472 CATTTAAATG
272482 ATAAACGAACACAAACGAAC
1 ATAAACGAACACAAACGAAC
* *
272502 GTAAACGAATACAAACGAAC
1 ATAAACGAACACAAACGAAC
*
272522 GTAAACGAACACAAACGAATGAAC
1 ATAAACGAACACAAAC----GAAC
* *
272546 ATAAACGAACATAAATGAAC
1 ATAAACGAACACAAACGAAC
272566 ATAA
1 ATAA
272570 TAAATGAATA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
20 41 0.71
24 17 0.29
ACGTcount: A:0.58, C:0.19, G:0.12, T:0.10
Consensus pattern (20 bp):
ATAAACGAACACAAACGAAC
Found at i:272582 original size:23 final size:23
Alignment explanation
Indices: 272546--272592 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
272536 ACGAATGAAC
**
272546 ATAAACGAACATAAATGAACATA
1 ATAAACGAACATAAACAAACATA
* *
272569 ATAAATGAATATAAACAAACATA
1 ATAAACGAACATAAACAAACATA
272592 A
1 A
272593 ACAAACACAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.64, C:0.11, G:0.06, T:0.19
Consensus pattern (23 bp):
ATAAACGAACATAAACAAACATA
Found at i:272583 original size:33 final size:33
Alignment explanation
Indices: 272514--272622 Score: 130
Period size: 33 Copynumber: 3.3 Consensus size: 33
272504 AAACGAATAC
* *
272514 AAACGAACGTAAACGAACACAA-ACGAATGAACAT
1 AAACAAACATAAACGAACACAATA--AATGAACAT
* * * *
272548 AAACGAACATAAATGAACATAATAAATGAATAT
1 AAACAAACATAAACGAACACAATAAATGAACAT
*
272581 AAACAAACATAAACAAACACAATAAATGAACAT
1 AAACAAACATAAACGAACACAATAAATGAACAT
272614 AAACAAACA
1 AAACAAACA
272623 ACACAAACAC
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
33 45 0.69
34 19 0.29
35 1 0.02
ACGTcount: A:0.62, C:0.17, G:0.08, T:0.13
Consensus pattern (33 bp):
AAACAAACATAAACGAACACAATAAATGAACAT
Found at i:272605 original size:23 final size:23
Alignment explanation
Indices: 272579--272622 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
272569 ATAAATGAAT
272579 ATAAACAAACATAAACAAACACA
1 ATAAACAAACATAAACAAACACA
**
272602 ATAAATGAACATAAACAAACA
1 ATAAACAAACATAAACAAACA
272623 ACACAAACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.68, C:0.18, G:0.02, T:0.11
Consensus pattern (23 bp):
ATAAACAAACATAAACAAACACA
Found at i:274737 original size:19 final size:21
Alignment explanation
Indices: 274704--274744 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
274694 ATTAGTATTA
*
274704 TTTATAACTTTAAAG-ACATT
1 TTTATAACTTAAAAGCACATT
274724 TTTAT-ACTTAAAAGCACATT
1 TTTATAACTTAAAAGCACATT
274744 T
1 T
274745 AAAAAGCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (21 bp):
TTTATAACTTAAAAGCACATT
Found at i:278447 original size:6 final size:6
Alignment explanation
Indices: 278436--278473 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
278426 TAAAATAGAC
278436 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AA
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AA
278474 AATATATCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
AATTTT
Found at i:280514 original size:92 final size:92
Alignment explanation
Indices: 280399--280668 Score: 416
Period size: 93 Copynumber: 2.9 Consensus size: 92
280389 TTTGAAAATT
*
280399 ATTAACCGAATTTTATTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCAA
1 ATTAACC-AATTTT-TTTCTTTAACATTAATTGAACCGAAATTATTTGACCGTTAATCGAACCAA
280464 AATTATTTGAAAATTATTAACCAAACCAA
64 AATTATTTGAAAATTATTAACCAAACCAA
280493 ATTAACCAATTTTTTTCTTTAACATTAATTGAACCGAAATTATTTGACCGTTAATCGAACCAAAA
1 ATTAACCAATTTTTTTCTTTAACATTAATTGAACCGAAATTATTTGACCGTTAATCGAACCAAAA
*
280558 TTCATTTGAAAATTATTAACCGAACCAA
66 TT-ATTTGAAAATTATTAACCAAACCAA
* * * *
280586 ATCAACCGATTTATTT-TTTAACCATTAATTGAACCGAAATTATTTGACCGTTAATCGAATCGAA
1 ATTAACCAATTTTTTTCTTTAA-CATTAATTGAACCGAAATTATTTGACCGTTAATCGAA-CCAA
* *
280650 ATTTATTTGAAATTTATTA
64 AATTATTTGAAAATTATTA
280669 GCCGAATAAA
Statistics
Matches: 165, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
92 58 0.35
93 94 0.57
94 13 0.08
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (92 bp):
ATTAACCAATTTTTTTCTTTAACATTAATTGAACCGAAATTATTTGACCGTTAATCGAACCAAAA
TTATTTGAAAATTATTAACCAAACCAA
Found at i:281852 original size:2 final size:2
Alignment explanation
Indices: 281845--281869 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
281835 ACCCCTCCCC
281845 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 A
281870 AATTATTAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:284426 original size:59 final size:60
Alignment explanation
Indices: 284288--284467 Score: 172
Period size: 60 Copynumber: 3.0 Consensus size: 60
284278 ATTTGGGGGA
** * * * *
284288 AAAATTAGAATATTCAAAAGTTTGGGGACCAATTTTGAAA-GAGGATC-ATAGTCT-AGGAAT
1 AAAATTAGAATATTCAAAAGTTTAAGGATCAA-TTTAAAATGA-GACCTATAGTTTGAGG-AT
* * * **
284348 GAAATTAGAATGTTCAAAAGTTTAAGGA-CTAA-TTAGAATGAGAGTTATAGTTTGAGGAT
1 AAAATTAGAATATTCAAAAGTTTAAGGATC-AATTTAAAATGAGACCTATAGTTTGAGGAT
* *
284407 AAAATTGGAATATTTAAAAGTTTAAGGATCAATTTAAAATGAGACCTATAGTTTGAGGAT
1 AAAATTAGAATATTCAAAAGTTTAAGGATCAATTTAAAATGAGACCTATAGTTTGAGGAT
284467 A
1 A
284468 TATGATGTAA
Statistics
Matches: 98, Mismatches: 16, Indels: 12
0.78 0.13 0.10
Matches are distributed among these distances:
58 6 0.06
59 37 0.38
60 55 0.56
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (60 bp):
AAAATTAGAATATTCAAAAGTTTAAGGATCAATTTAAAATGAGACCTATAGTTTGAGGAT
Found at i:284747 original size:20 final size:20
Alignment explanation
Indices: 284722--284912 Score: 125
Period size: 20 Copynumber: 9.4 Consensus size: 20
284712 GATTCACAAC
*
284722 GCGATTTTGACTATCGCATT
1 GCGATTTTGACTATCGCAAT
* * **
284742 GCGATTTT-CCAAATTCGCGTT
1 GCGATTTTGAC-TA-TCGCAAT
284763 GCGATTTTCCGACTATCGCAAT
1 GCGATTTT--GACTATCGCAAT
* * *
284785 GCGAATATGTA-AATCGCAAT
1 GCGATTTTG-ACTATCGCAAT
* * *
284805 GCGAGTATGACTATCGCAAC
1 GCGATTTTGACTATCGCAAT
* *
284825 GCGATTCTGACTATCGCAAC
1 GCGATTTTGACTATCGCAAT
** *
284845 GAAATTTTGACTATCGCAAC
1 GCGATTTTGACTATCGCAAT
* * * *
284865 GCGATTCTGACTGTCACAAC
1 GCGATTTTGACTATCGCAAT
**
284885 GCGATGCTGACTATCGCAAT
1 GCGATTTTGACTATCGCAAT
284905 GCGATTTT
1 GCGATTTT
284913 CAAAGCGCCA
Statistics
Matches: 135, Mismatches: 29, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
19 2 0.01
20 105 0.78
21 15 0.11
22 11 0.08
23 1 0.01
24 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (20 bp):
GCGATTTTGACTATCGCAAT
Found at i:284912 original size:60 final size:60
Alignment explanation
Indices: 284773--284912 Score: 156
Period size: 60 Copynumber: 2.3 Consensus size: 60
284763 GCGATTTTCC
* * * * *
284773 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTATGACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGATTTTGTAAATCGCAACGCGAGTATGACTATCACAACGCGATGCT
* ** * * * *
284833 GACTATCGCAACGAAATTTTG-ACTATCGCAACGCGATTCTGACTGTCACAACGCGATGCT
1 GACTATCGCAATGCGATTTTGTA-AATCGCAACGCGAGTATGACTATCACAACGCGATGCT
284893 GACTATCGCAATGCGATTTT
1 GACTATCGCAATGCGATTTT
284913 CAAAGCGCCA
Statistics
Matches: 64, Mismatches: 15, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
59 1 0.02
60 63 0.98
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (60 bp):
GACTATCGCAATGCGATTTTGTAAATCGCAACGCGAGTATGACTATCACAACGCGATGCT
Found at i:285506 original size:19 final size:19
Alignment explanation
Indices: 285484--285567 Score: 80
Period size: 20 Copynumber: 4.3 Consensus size: 19
285474 AGAATCGCAA
285484 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCA-TTTCGCGT
285503 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
** *
285522 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTC-ATTTCGCGT
** *
285542 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCA-TTTCGCGT
285562 TGCGAT
1 TGCGAT
285568 AATAATGGCG
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
19 26 0.46
20 31 0.54
ACGTcount: A:0.15, C:0.18, G:0.25, T:0.42
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:285540 original size:20 final size:19
Alignment explanation
Indices: 285497--285685 Score: 139
Period size: 20 Copynumber: 9.6 Consensus size: 19
285487 GATTTTAGTT
** **
285497 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATAGTCAAA
285516 TCGCGTTGCGATAGTCAAA
1 TCGCGTTGCGATAGTCAAA
**
285535 TTCGCGTTGCGATAGTCATTT
1 -TCGCGTTGCGATAGTCA-AA
* *
285556 TCGTGTTGCGATAAT--AA
1 TCGCGTTGCGATAGTCAAA
* *
285573 TGGCGCTTGCGATAGTCAGCA
1 TCGCG-TTGCGATAGTCA-AA
**
285594 TCGCGTTGCGGCAGTCAGAA
1 TCGCGTTGCGATAGTCA-AA
285614 TCGCGTTGCGATAGTCAGAA
1 TCGCGTTGCGATAGTCA-AA
* *
285634 TCTCGTTGTGATAGTCAGAA
1 TCGCGTTGCGATAGTCA-AA
* *
285654 TCGCGTTACGATAGTCATAC
1 TCGCGTTGCGATAGTCA-AA
*
285674 TCGCATTGCGAT
1 TCGCGTTGCGAT
285686 TTACATATTC
Statistics
Matches: 135, Mismatches: 29, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
17 3 0.02
18 9 0.07
19 15 0.11
20 103 0.76
21 5 0.04
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (19 bp):
TCGCGTTGCGATAGTCAAA
Found at i:285707 original size:60 final size:60
Alignment explanation
Indices: 285497--285709 Score: 186
Period size: 60 Copynumber: 3.6 Consensus size: 60
285487 GATTTTAGTT
* **
285497 TCGCGTTGCGATTTTCAT-TTCGCGTTGCGATAGTCA-AATTCGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTACATATTCGCGTTGCGATAGTCAGAA-TCGCGTTGCGATAGTCATAA
* * * * ** *
285556 TCGTGTTGCGA--TA-ATAATGGCGCTTGCGATAGTCAGCATCGCGTTGCGGCAGTCAGAA
1 TCGCGTTGCGATTTACATATTCGCG-TTGCGATAGTCAGAATCGCGTTGCGATAGTCATAA
* * * * * * *
285614 TCGCGTTGCGATAGT-CAGAATCTCGTTGTGATAGTCAGAATCGCGTTACGATAGTCATAC
1 TCGCGTTGCGAT-TTACATATTCGCGTTGCGATAGTCAGAATCGCGTTGCGATAGTCATAA
* *
285674 TCGCATTGCGATTTACATATTCGCATTGCGATAGTC
1 TCGCGTTGCGATTTACATATTCGCGTTGCGATAGTC
285710 GGAAAATCGC
Statistics
Matches: 118, Mismatches: 28, Indels: 15
0.73 0.17 0.09
Matches are distributed among these distances:
56 2 0.02
57 5 0.04
58 37 0.31
59 12 0.10
60 55 0.47
61 7 0.06
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (60 bp):
TCGCGTTGCGATTTACATATTCGCGTTGCGATAGTCAGAATCGCGTTGCGATAGTCATAA
Found at i:286173 original size:24 final size:24
Alignment explanation
Indices: 286156--286202 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
286146 AATTGATAGT
286156 TTAATTAAAAATAAAATTAAAATC
1 TTAATTAAAAATAAAATTAAAATC
* *
286180 TTAATTAAAGATAAAAATAAAAT
1 TTAATTAAAAATAAAATTAAAAT
286203 TACTTTTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (24 bp):
TTAATTAAAAATAAAATTAAAATC
Found at i:286475 original size:151 final size:153
Alignment explanation
Indices: 286191--286492 Score: 518
Period size: 151 Copynumber: 2.0 Consensus size: 153
286181 TAATTAAAGA
286191 TAAAAATAAAATTACTTTTTACGAATTGTATACTTAACGGAGATTTAGTATGTTTGGTTTTTTTT
1 TAAAAATAAAATTACTTTTTACGAATTGTATACTTAACGGAGATTTAGTATGTTTGGTTTTTTTT
* * * * *
286256 TTAACTGATCGGATCGATTTTGGTTTTAAAATCCGGAACCGATCCAAACCGAACTGAACCGATGA
66 TAAACCGATCGGATCGATTTTGGTTTGAAAATCCAGAACCGATCCAAACCGAACCGAACCGATGA
286321 AATGAAATATTGAATTTACAAAC
131 AATGAAATATTGAATTTACAAAC
286344 TAAAAATAAAATTACTTTTTACGAATTGTATACTTAACGGAGATTTAGTATGTTT-G-TTTTTTT
1 TAAAAATAAAATTACTTTTTACGAATTGTATACTTAACGGAGATTTAGTATGTTTGGTTTTTTTT
* *
286407 TAAACCGATCGGTTCGGTTTTGGTTTGAAAATCCAGAACCGATCCAAACCGAACCGAACCGATGA
66 TAAACCGATCGGATCGATTTTGGTTTGAAAATCCAGAACCGATCCAAACCGAACCGAACCGATGA
*
286472 AATGAAATATTGAGTTTACAA
131 AATGAAATATTGAATTTACAA
286493 GCTTGAAACA
Statistics
Matches: 141, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
151 85 0.60
152 1 0.01
153 55 0.39
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (153 bp):
TAAAAATAAAATTACTTTTTACGAATTGTATACTTAACGGAGATTTAGTATGTTTGGTTTTTTTT
TAAACCGATCGGATCGATTTTGGTTTGAAAATCCAGAACCGATCCAAACCGAACCGAACCGATGA
AATGAAATATTGAATTTACAAAC
Found at i:287677 original size:60 final size:59
Alignment explanation
Indices: 287554--287677 Score: 135
Period size: 59 Copynumber: 2.1 Consensus size: 59
287544 ATTGTGTGAT
* * * *
287554 TATTTTGTAACTTTTAATAGTTGGGGTATCAACAAAACAATATCCTATAGTCGAAGAAT
1 TATTTTATAACTTTTAATAGTCGGGGTATCAACAAAACAATACCCTATAGTCGAAGAAC
** * *
287613 TATTTTATAACTTTTAATAGTCGAGGG-ACTCAAC-AAAGTATCACCCTATAGTCGAGGGAC
1 TATTTTATAACTTTTAATAGTCG-GGGTA-TCAACAAAACAAT-ACCCTATAGTCGAAGAAC
287673 TATTT
1 TATTT
287678 ATGCACTTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
59 27 0.50
60 27 0.50
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (59 bp):
TATTTTATAACTTTTAATAGTCGGGGTATCAACAAAACAATACCCTATAGTCGAAGAAC
Found at i:292452 original size:24 final size:24
Alignment explanation
Indices: 292405--292452 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
292395 TGTTAACCAA
* *
292405 AAACGCCACAGTAGGTAACGATAT
1 AAACGCCACAATAGGTAACAATAT
* *
292429 AAACGCCGCAATAGGTACCAATAT
1 AAACGCCACAATAGGTAACAATAT
292453 TTAGTGGCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.17
Consensus pattern (24 bp):
AAACGCCACAATAGGTAACAATAT
Found at i:295160 original size:85 final size:83
Alignment explanation
Indices: 295031--295231 Score: 219
Period size: 83 Copynumber: 2.4 Consensus size: 83
295021 GTTTTAATAT
* * * *
295031 AAACGCCACGATAAACAACA-TATTGCGACGTTTGTAGGACAAATGCCGCTATATTA-TTACTCT
1 AAACGCCACTATAAACAACACTATTGCGGCGTTTGTAGGACAAATGCCGCGAAATTACTT-CTCT
* * * * *
295094 ATTGCGGTGT-TTTTTTTGCAC
65 A-T--AGTGTCGTTTGTTGAAA
* ** *
295115 AAACGCCACTATAAACAATACTATTGCGGCGTTTGTTTGATAAATGCCGCGAAATTACTTCTCTA
1 AAACGCCACTATAAACAACACTATTGCGGCGTTTGTAGGACAAATGCCGCGAAATTACTTCTCTA
295180 TAGTGTCGTTTGTTGAAA
66 TAGTGTCGTTTGTTGAAA
*
295198 AAACGCCACTATAAACAACACTATCGCGGCGTTT
1 AAACGCCACTATAAACAACACTATTGCGGCGTTT
295232 CTAAATTTCC
Statistics
Matches: 99, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
82 4 0.04
83 39 0.39
84 19 0.19
85 35 0.35
86 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (83 bp):
AAACGCCACTATAAACAACACTATTGCGGCGTTTGTAGGACAAATGCCGCGAAATTACTTCTCTA
TAGTGTCGTTTGTTGAAA
Found at i:295352 original size:42 final size:41
Alignment explanation
Indices: 295232--295360 Score: 120
Period size: 42 Copynumber: 3.1 Consensus size: 41
295222 CGCGGCGTTT
* * * * *
295232 CTAAATTTCCACTCTATTGCGGCGTTTGTTGAAAAACGCCA
1 CTAAATTACCTCTCTATTGCGGCATTTGTTTAAAAACGCCG
* * * *
295273 CTATAA--ACATCTCTATTGCGACATTT-TAGCTATAAACGCCG
1 CTA-AATTACCTCTCTATTGCGGCATTTGT--TTAAAAACGCCG
295314 CTAAATTACCTCTCTATTGCGGCATTTGTTTAAAAAACGCCG
1 CTAAATTACCTCTCTATTGCGGCATTTGTTT-AAAAACGCCG
295356 CTAAA
1 CTAAA
295361 GTATCATTTT
Statistics
Matches: 68, Mismatches: 13, Indels: 13
0.72 0.14 0.14
Matches are distributed among these distances:
39 1 0.01
40 17 0.25
41 15 0.22
42 34 0.50
43 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (41 bp):
CTAAATTACCTCTCTATTGCGGCATTTGTTTAAAAACGCCG
Found at i:298023 original size:6 final size:6
Alignment explanation
Indices: 298012--298036 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
298002 TTGAATAAAC
298012 AAGGGA AAGGGA AAGGGA AAGGGA A
1 AAGGGA AAGGGA AAGGGA AAGGGA A
298037 GGAGATGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
AAGGGA
Found at i:298721 original size:20 final size:20
Alignment explanation
Indices: 298685--298729 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
298675 TTGGTGATAG
*
298685 AATTTGAGAGACAAACTTCA
1 AATTTGAGAGACAAACTTAA
*
298705 AATTTGAGATAGC-AACTTAA
1 AATTTGAGAGA-CAAACTTAA
298725 AATTT
1 AATTT
298730 TAAAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (20 bp):
AATTTGAGAGACAAACTTAA
Found at i:306444 original size:20 final size:22
Alignment explanation
Indices: 306407--306447 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
306397 TTGGTTGATT
306407 TTTTTTAAACAAATTTAATATA
1 TTTTTTAAACAAATTTAATATA
*
306429 TTTTTTGAA-AAA-TTAATAT
1 TTTTTTAAACAAATTTAATAT
306448 TAATCATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTTTTAAACAAATTTAATATA
Found at i:309720 original size:39 final size:41
Alignment explanation
Indices: 309677--309761 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 41
309667 ATAATAAAAT
*
309677 AATATATTATCGAT-CA-TTT-ATATAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTGATATAAAT-ATTTTTATTTA
309716 AATATATTATCGATGAATTTTGATATAAATATTTTTATTTA
1 AATATATTATCGATGAATTTTGATATAAATATTTTTATTTA
309757 AATAT
1 AATAT
309762 TTAAAATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
39 14 0.33
40 1 0.02
41 19 0.45
42 8 0.19
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.51
Consensus pattern (41 bp):
AATATATTATCGATGAATTTTGATATAAATATTTTTATTTA
Found at i:310325 original size:60 final size:59
Alignment explanation
Indices: 310212--310361 Score: 160
Period size: 60 Copynumber: 2.5 Consensus size: 59
310202 TTAATTTTTT
* * * * *
310212 TTAAATTTTTAAATATTTTAATTTCATCCTTAAATTATATCTATCTTTATAAATTAGTTC
1 TTAAACTTTTAAATATTTTAATTTCATCCCTAAATTAAATCTATCATTATAAATT-GATC
*
310272 TTAAACTTTTAAATATTTTAATTTCATCCCTAAACTATAAATCT-T-ATTCTAAATTGATC
1 TTAAACTTTTAAATATTTTAATTTCATCCCTAAA-T-TAAATCTATCATTATAAATTGATC
* * **
310331 TTCAAACTTTTGAATCTTCCAATTTCATCCC
1 TT-AAACTTTTAAATATTTTAATTTCATCCC
310362 CCAAATTCAT
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
59 5 0.06
60 64 0.83
61 2 0.03
62 6 0.08
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.48
Consensus pattern (59 bp):
TTAAACTTTTAAATATTTTAATTTCATCCCTAAATTAAATCTATCATTATAAATTGATC
Found at i:310622 original size:60 final size:62
Alignment explanation
Indices: 310499--310636 Score: 176
Period size: 60 Copynumber: 2.3 Consensus size: 62
310489 ATAATTTGGA
* **
310499 ATGAAATTGAAATGTTCAAAAAGTTTTGGGGACCAATTTAGAATGAAGATCATAGTTTGAGG
1 ATGAAATTGAAATGTTCAAAAAGTTTTGAGGACCAATTTAGAATGAAGATCATAGTTCAAGG
*
310561 ATGAAATTGAAATGTTC-AAAAG-TTTGAGGACTAATTTAGAAT-AATTG-TCATAGTTCAAGG
1 ATGAAATTGAAATGTTCAAAAAGTTTTGAGGACCAATTTAGAATGAA--GATCATAGTTCAAGG
* *
310621 ATAAAATTAAAATGTT
1 ATGAAATTGAAATGTT
310637 TATACGTTTA
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
59 2 0.03
60 43 0.63
61 6 0.09
62 17 0.25
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (62 bp):
ATGAAATTGAAATGTTCAAAAAGTTTTGAGGACCAATTTAGAATGAAGATCATAGTTCAAGG
Found at i:316794 original size:21 final size:21
Alignment explanation
Indices: 316768--316810 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
316758 AGAATGATGA
316768 GCGTCAATTAATTGTGCGCAT
1 GCGTCAATTAATTGTGCGCAT
316789 GCGTCAATTAATTGTGCGCAT
1 GCGTCAATTAATTGTGCGCAT
316810 G
1 G
316811 GGTAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (21 bp):
GCGTCAATTAATTGTGCGCAT
Found at i:317694 original size:17 final size:17
Alignment explanation
Indices: 317649--317699 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
317639 TTTATATCTG
* *
317649 TAAAAAAATTAATTAAA
1 TAAAATAATTAAATAAA
*
317666 TAAAAT-ATTAAATAAT
1 TAAAATAATTAAATAAA
317682 TAAAATAATTAAATAAA
1 TAAAATAATTAAATAAA
317699 T
1 T
317700 TACTAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 14 0.48
17 15 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAATAATTAAATAAA
Found at i:323600 original size:22 final size:23
Alignment explanation
Indices: 323565--323610 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
323555 ATAATATGTT
323565 AAAAGTATCCATACTTTTTATAA
1 AAAAGTATCCATACTTTTTATAA
* *
323588 AAAAG-ATCGATACTTTTTTTAA
1 AAAAGTATCCATACTTTTTATAA
323610 A
1 A
323611 GTTATGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (23 bp):
AAAAGTATCCATACTTTTTATAA
Found at i:323990 original size:23 final size:23
Alignment explanation
Indices: 323960--324032 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
323950 ATAATTTACA
*
323960 ATATAAGCGCTATCTATTACATT
1 ATATAAGCGCTACCTATTACATT
323983 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
324006 ATATATGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
324029 ATAT
1 ATAT
324033 TTTTACCTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:324505 original size:23 final size:23
Alignment explanation
Indices: 324440--324507 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
324430 ATACTTTACA
*
324440 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
324463 ATATAAACGTTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
324486 ATATAAGCGCTACTTCTTACAT
1 ATATAAGCGCTACCTATTACAT
324508 CATACCTATT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.37
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:324942 original size:23 final size:23
Alignment explanation
Indices: 324907--324979 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
324897 ATACTTTACA
* *
324907 ATATAAGCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
324930 ATATAAATGCTACCTATTACTTT
1 ATATAAACGCTACCTATTACATT
* *
324953 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
324976 ATAT
1 ATAT
324980 TTTTACCTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:325420 original size:23 final size:23
Alignment explanation
Indices: 325385--325457 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
325375 ATACTTTACA
*
325385 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
325408 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
325431 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
325454 ATAT
1 ATAT
325458 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:325702 original size:477 final size:477
Alignment explanation
Indices: 323566--327240 Score: 5869
Period size: 477 Copynumber: 7.7 Consensus size: 477
323556 TAATATGTTA
* *
323566 AAAGTATCCATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
1 AAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
* * *
323631 A-TTTTTTAATAGTGTTTCATGTTTTCCCCCTATAATATTAATTTAATAATTTCATTTGCACAAA
66 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAA
* *
323695 AAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTATAATTTAAATTTAACAATATTAAC
131 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
* * *
323760 CAAAGATAAAAATAAATATGTAATATATATGCTTATT-TTTTTAATTTAATGATAATATATACCG
196 CAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCG
* **** * *
323824 TAACATAAAAAATAAATCATTAGATAAATATAATTACTAAATTGATATCTTAAAATTCACTTAAA
261 TAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT-TTTAAA---AC-T---
* * *
323889 ATAACTTAAATTAATATTTTCCACAGT-AAAATAAGTATAGG-CACTTCTATAAAAAAGATAGAT
318 A-ACCTTAAATTAATATTTTCCACAGTGAAAA-AAGTAT-GGACACTTTTATAAAAAGGATAGAT
* * * * *
323952 AATTTACAATATAAGCGCTATCTATTACATTATATAAGCGCTACCTATTACATTATATATGCGCT
380 ACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCT
324017 ACCTATTACATCATATTTTTACCTGA-TATATTG
445 ACCTATTACATCATATTTTTACCT-ATTATATTG
* * *
324050 TAAAGTATCGAT-CATTTTTATAAAAATGATCGATATTTTTTTTAAAGTTATGTAATTTATGTTT
1 -AAAGTGTCCATAC-TTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTT
324114 CAATTTATTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
64 CAATTT-TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
*
324179 AAAAAATTATTTGATTGTTTTAATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
128 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
*
324244 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATAAATA
193 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
* *
324309 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTAACAT
258 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATTTTAAAACTAACCT
*
324374 TAAATTAATATTTTCCACAGTGAAAAACGTATGGACACTTTTATAAAAATGGATAGATACTTTAC
323 TAAATTAATATTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAA-GGATAGATACTTTAC
* * *
324439 AATATAAGCACTACCTATTACATTATATAAACGTTACCTATTACATTATATAAGCGCTACTTCTT
387 AATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATT
324504 ACATC--A----TACCTATTATATTG
452 ACATCATATTTTTACCTATTATATTG
* *
324524 AAAGTGTCCATATTTTTTATAAAAATGATCGATA-TTTTTTTAAAAAGTTATGTAATTTATATTT
1 AAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTT--AAAGTTATGTAATTTATGTTT
324588 CAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC-
64 CAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACA
324652 AAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTA
129 AAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTA
324717 ACCAAAGATAATAAT-AATATGT-A-ATATATGTTTATTG-TTTTAATTTAATAATAATATATAC
194 ACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATAC
*
324778 CGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATATTAAAACTAACCTT
259 CGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATTTTAAAACTAACCTT
* * * *
324843 AAATTAATGTTTTCTACAGTGAAAAAAGTATGGATACTTTTATAAAAATGATAGATACTTTACAA
324 AAATTAATATTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAA
* *
324908 TATAAGCACTACCTATTACATTATATAAATGCTACCTATTACTTTATATAAGCGCTACCTATTAC
389 TATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTAC
324973 ATCATATTTTTACCTATTATATTG
454 ATCATATTTTTACCTATTATATTG
324997 AAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
1 AAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
*
325062 ATTTTTTTTAATAGTGTTTCATGTTTTCCACTTACAATATTAATTTAATAATTTCATTTACACAA
66 A-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAA
325127 AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
130 AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
*
325192 CTAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACC
195 CCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACC
*
325257 GTAACGTAAAAAATAAATCATTAGACGTCTATAATTACTAAATTAATATTTTAAAACTAACCTTA
260 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATTTTAAAACTAACCTTA
* *
325322 AATTAATGTTTTCCACAGTGAAAAAAGTATGTACACTTTTATAAAAAGGATAGATACTTTACAAT
325 AATTAATATTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAAT
325387 ATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACA
390 ATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACA
325452 TCATATTTTTACCTATTATATTG
455 TCATATTTTTACCTATTATATTG
325475 AAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
1 AAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
* *
325540 ATTTTTTTAATAGTGTTTCATG-TTTCCAACCTACAATATTAATTTAATAATTTCATTTGCATAA
66 ATTTTTTTAATAGTGTTTCATGTTTTCC-ACCTACAATATTAATTTAATAATTTCATTTACACAA
*
325604 AAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAA
130 AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
325669 CCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACC
195 CCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACC
* *
325734 TTAACGTAAAAAATAAATCATTAGACGTCTATAATTACTAAATTAATATTTTAAAACTAACCTTA
260 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATTTTAAAACTAACCTTA
* * * * *
325799 AATTAATGTTTTCCACAGTAAAAAAAGTATGGAAACTTTTATAAAAATGATAAATACTTTACAAT
325 AATTAATATTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAAT
325864 ATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACA
390 ATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACA
325929 TCATATTTTTACCTATTATATTG
455 TCATATTTTTACCTATTATATTG
325952 AAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
1 AAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
* *
326017 A-TTTTTTAATAGTGTTTCATGTTTTCCACCTATAATATTAATTTAATAATTTCATTTGCACAAA
66 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAA
*
326081 AAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAAC
131 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
* *
326146 CAAAGATAAAAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATATACCG
196 CAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCG
** * * *
326211 TAACGTAAAAAATAAATCATTAGATACATATAATTATTAAATTGATATCTTAAAACTCACTCAAA
261 TAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT-A-ATATT-----T---T-AAA
* * *
326276 AGATAACCTTAAATTAATATTTTCCACAGTGAAATAAGTATGGACACTTCTATAAAAAGGATAG-
315 A-CTAACCTTAAATTAATATTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGA
*
326340 -----------AT----A--A--T-TTACA--ATATAAGCGCTACCTATTACATTATATAAGCGC
379 TACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGC
326383 TACCTATTACATCATATTTTTACCTGA-TATATTG
444 TACCTATTACATCATATTTTTACCT-ATTATATTG
* * * *
326417 TAAAGTATCGATCCTTTTTATAAAAA-GATCGATATTTTTTTTAAAGTTATGTAATTTATGTTTC
1 -AAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTC
326481 AATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAA
65 AATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAA
*
326546 AAAATTATTTGATTGTTTTAATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
130 AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
* * *
326611 CCAAAGATAATAATAAATATGTACTATATATGTTTATTGTTTTTAATTTAATAATAATAAATAAC
195 CCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACC
* *
326676 GTAACGTAAAAAATAAATCATTAGATGCCTATAATTACTAAATTAATATCTTAAAACTAACCTTA
260 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATTTTAAAACTAACCTTA
326741 AATTAATATTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAAT
325 AATTAATATTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAAT
326806 ATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACA
390 ATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACA
326871 TCATATTTTTACCTATTATATTG
455 TCATATTTTTACCTATTATATTG
*
326894 AAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
1 AAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
*
326959 ATTTTTTTAATAGTGTTTCATGTTTTCCACTTACAATATTAATTTAATAATTTCATTTACACAAA
66 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAA
*
327024 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTATC
131 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
*
327089 CAAAGATAATAATAAATACGTAATATATATGTTTATTGTTTTTAATTTAATAAT-A-ATATACCG
196 CAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCG
* * * *
327152 CAACGTAAAAAATAAATCATTTGACGCCTATAATTACTAAATTAATATCTTAAATCTAACCTTAA
261 TAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATTTTAAAACTAACCTTAA
* *
327217 ATTAATGTTTTCCACAGTTAAAAA
326 ATTAATATTTTCCACAGTGAAAAA
327241 CATATACCGC
Statistics
Matches: 2990, Mismatches: 134, Indels: 142
0.92 0.04 0.04
Matches are distributed among these distances:
454 59 0.02
455 4 0.00
456 1 0.00
459 1 0.00
464 3 0.00
465 104 0.03
466 249 0.08
467 84 0.03
468 131 0.04
469 15 0.01
470 3 0.00
471 7 0.00
472 111 0.04
473 196 0.07
474 125 0.04
475 101 0.03
476 252 0.08
477 761 0.25
478 308 0.10
479 41 0.01
480 81 0.03
483 2 0.00
484 3 0.00
485 61 0.02
486 3 0.00
487 163 0.05
488 121 0.04
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (477 bp):
AAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAA
AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
CAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCG
TAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATTTTAAAACTAACCTTAA
ATTAATATTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATA
TAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACAT
CATATTTTTACCTATTATATTG
Found at i:325897 original size:23 final size:23
Alignment explanation
Indices: 325862--325934 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
325852 ATACTTTACA
*
325862 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
325885 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
325908 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
325931 ATAT
1 ATAT
325935 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:326380 original size:23 final size:23
Alignment explanation
Indices: 326350--326399 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
326340 ATAATTTACA
*
326350 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATC
326373 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATC
326396 ATAT
1 ATAT
326400 TTTTACCTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATC
Found at i:326688 original size:942 final size:936
Alignment explanation
Indices: 323566--327240 Score: 5647
Period size: 942 Copynumber: 3.9 Consensus size: 936
323556 TAATATGTTA
*
323566 AAAGTATCCATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
1 AAAGTATCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
* * *
323631 A-TTTTTTAATAGTGTTTCATGTTTTCCCCCTATAATATTAATTTAATAATTTCATTTGCACAAA
66 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAA
*
323695 AAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTATAATTTAAATTTAACAATATTAAC
131 AAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAAC
* * *
323760 CAAAGATAAAAATAAATATGTAATATATATGCTTATT-TTTTTAATTTAATGATAATATATACCG
196 CAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCG
* **** * *
323824 TAACATAAAAAATAAATCATTAGATAAATATAATTACTAAATTGATATCTTAAAATTCACTTAAA
261 TAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT-TTTAAA---AC-T---
* * * *
323889 ATAACTTAAATTAATATTTTCCACAGTAAAATAAGTATAGG-CACTTCTATAAAAAAGATAGATA
318 A-ACCTTAAATTAATATTTTCCACAGTAAAAAAAGTAT-GGACACTTTTATAAAAATGATAGATA
* * * * *
323953 ATTTACAATATAAGCGCTATCTATTACATTATATAAGCGCTACCTATTACATTATATATGCGCTA
381 CTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTA
* *
324018 CCTATTACATCATATTTTTACCTGA-TATATTGTAAAGTATCGAT-CATTTTTATAAAAATGATC
446 CCTATTACATCATATTTTTACCT-ATTATATTG-AAAGTGTCCATAC-TTTTTATAAAAATGATC
*
324081 GATATTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTATTTTAATAGTGTTTCATGTTTTCCA
508 GATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT-TTTTAATAGTGTTTCATGTTTTCCA
*
324146 CCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTAATATTTTATA
572 CCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATA
324211 AAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATATA
637 AAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATATA
*
324276 TGTTTATTGTTTTTAATTTAATAATAATAAATACCGTAACGTAAAAAATAAATCATTAGACGCCT
702 TGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCT
*
324341 ATAATTACTAAATTAATATCTTAAA-A-C----TAACATTAAATTAATATTTTCCACAGTGAAAA
767 ATAATTACTAAATTAATATCTTAAATATCAAAATAACCTTAAATTAATATTTTCCACAGTGAAAA
* *
324400 ACGTATGGACACTTTTATAAAAATGGATAGATACTTTACAATATAAGCACTACCTATTACATTAT
832 A-GTATGGACACTTTTATAAAAA-GGATAGATAATTTACAATATAAGCGCTACCTATTACATTAT
* * *
324465 ATAAACGTTACCTATTACATTATATAAGCGCTACTTCTTACATCATACCTATTATATTG
895 ATAAGCGCTACCTATTAC-----AT---C-ATA--T-TT---T--TACCTATTATATTG
* * *
324524 AAAGTGTCCATATTTTTTATAAAAATGATCGATA-TTTTTTTAAAAAGTTATGTAATTTATATTT
1 AAAGTATCCATACTTTTTATAAAAATGATCGATACTTTTTTT--AAAGTTATGTAATTTATGTTT
324588 CAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC-
64 CAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACA
*
324652 AAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTA
129 AAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTA
324717 ACCAAAGATAATAAT-AATATGT-A-ATATATGTTTATTG-TTTTAATTTAATAATAATATATAC
194 ACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATAC
*
324778 CGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATATTAAAACTAACCTT
259 CGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATTTTAAAACTAACCTT
* * * *
324843 AAATTAATGTTTTCTACAGTGAAAAAAGTATGGATACTTTTATAAAAATGATAGATACTTTACAA
324 AAATTAATATTTTCCACAGTAAAAAAAGTATGGACACTTTTATAAAAATGATAGATACTTTACAA
* *
324908 TATAAGCACTACCTATTACATTATATAAATGCTACCTATTACTTTATATAAGCGCTACCTATTAC
389 TATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTAC
324973 ATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTT
454 ATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTT
*
325038 TAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACTTACAATATT
519 TAAAGTTATGTAATTTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATT
325103 AATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTT
583 AATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTT
*
325168 AGAATTTAAATTTAACAATATTAACTAAAGATAATAATAAATATGTAATATATATGTTTATTGTT
648 AGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTT
*
325233 TTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGTCTATAATTACTAA
713 TTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAA
* * *
325298 ATTAATAT-TT---TA--AAACTAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGTACA
778 ATTAATATCTTAAATATCAAAATAACCTTAAATTAATATTTTCCACAGTG-AAAAAGTATGGACA
*
325357 CTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACC
842 CTTTTATAAAAAGGATAG------------AT----A--A--T-TTACA--ATATAAGCGCTACC
325422 TATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTG
884 TATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTG
*
325475 AAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
1 AAAGTATCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
* *
325540 ATTTTTTTAATAGTGTTTCATG-TTTCCAACCTACAATATTAATTTAATAATTTCATTTGCATAA
66 ATTTTTTTAATAGTGTTTCATGTTTTCC-ACCTACAATATTAATTTAATAATTTCATTTACACAA
325604 AAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAA
130 AAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAA
325669 CCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACC
195 CCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACC
* *
325734 TTAACGTAAAAAATAAATCATTAGACGTCTATAATTACTAAATTAATATTTTAAAACTAACCTTA
260 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATTTTAAAACTAACCTTA
* * *
325799 AATTAATGTTTTCCACAGTAAAAAAAGTATGGAAACTTTTATAAAAATGATAAATACTTTACAAT
325 AATTAATATTTTCCACAGTAAAAAAAGTATGGACACTTTTATAAAAATGATAGATACTTTACAAT
325864 ATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACA
390 ATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACA
325929 TCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTT
455 TCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTT
*
325994 AAAGTTATGTAATTTATGTTTCAA-TTTTTTAATAGTGTTTCATGTTTTCCACCTATAATATTAA
520 AAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAA
* *
326058 TTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAG
585 TTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAG
*
326123 AATTTAAATTTAACAATATTAACCAAAGATAAAAATAAATATGTAATATATATGTTTATTGTTTT
650 AATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTT
* ** * *
326188 TAATTTAATGATAATATATACCGTAACGTAAAAAATAAATCATTAGATACATATAATTATTAAAT
715 TAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAAT
*
326253 TGATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATATTTTCCACAGTGAAATAAGTATG
780 TAATATCTT-AAA-T-A-TC-AAA-ATAACCTTAAATTAATATTTTCCACAGTGAAA-AAGTATG
*
326318 GACACTTCTATAAAAAGGATAGATAATTTACAATATAAGCGCTACCTATTACATTATATAAGCGC
838 GACACTTTTATAAAAAGGATAGATAATTTACAATATAAGCGCTACCTATTACATTATATAAGCGC
326383 TACCTATTACATCATATTTTTACCTGA-TATATTG
903 TACCTATTACATCATATTTTTACCT-ATTATATTG
* * *
326417 TAAAGTATCGATCCTTTTTATAAAAA-GATCGATATTTTTTTTAAAGTTATGTAATTTATGTTTC
1 -AAAGTATCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTC
326481 AATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAA
65 AATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAA
* *
326546 AAAATTATTTGATTGTTTTAATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
130 AAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAA
* * *
326611 CCAAAGATAATAATAAATATGTACTATATATGTTTATTGTTTTTAATTTAATAATAATAAATAAC
195 CCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACC
* *
326676 GTAACGTAAAAAATAAATCATTAGATGCCTATAATTACTAAATTAATATCTTAAAACTAACCTTA
260 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATTTTAAAACTAACCTTA
* *
326741 AATTAATATTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAAT
325 AATTAATATTTTCCACAGTAAAAAAAGTATGGACACTTTTATAAAAATGATAGATACTTTACAAT
326806 ATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACA
390 ATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACA
*
326871 TCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTT
455 TCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTT
*
326936 AAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACTTACAATATTAA
520 AAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAA
327001 TTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAG
585 TTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAG
* *
327066 AATTTAAATTTAACAATATTATCCAAAGATAATAATAAATACGTAATATATATGTTTATTGTTTT
650 AATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTT
* *
327131 TAATTTAATAAT-A-ATATACCGCAACGTAAAAAATAAATCATTTGACGCCTATAATTACTAAAT
715 TAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAAT
* *
327194 TAATATCTT-AA-ATC----TAACCTTAAATTAATGTTTTCCACAGTTAAAAA
780 TAATATCTTAAATATCAAAATAACCTTAAATTAATATTTTCCACAGTGAAAAA
327241 CATATACCGC
Statistics
Matches: 2534, Mismatches: 122, Indels: 152
0.90 0.04 0.05
Matches are distributed among these distances:
928 2 0.00
929 29 0.01
935 2 0.00
936 1 0.00
939 2 0.00
941 52 0.02
942 558 0.22
943 203 0.08
944 5 0.00
945 9 0.00
946 344 0.14
947 149 0.06
948 1 0.00
949 6 0.00
950 76 0.03
951 127 0.05
952 16 0.01
953 232 0.09
954 16 0.01
955 304 0.12
956 81 0.03
957 11 0.00
958 38 0.01
959 103 0.04
960 59 0.02
961 1 0.00
963 2 0.00
964 6 0.00
965 55 0.02
966 5 0.00
968 39 0.02
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (936 bp):
AAAGTATCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAA
AAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAAC
CAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCG
TAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATTTTAAAACTAACCTTAA
ATTAATATTTTCCACAGTAAAAAAAGTATGGACACTTTTATAAAAATGATAGATACTTTACAATA
TAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACAT
CATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTA
AAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAAT
TTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGA
ATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTT
AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
AATATCTTAAATATCAAAATAACCTTAAATTAATATTTTCCACAGTGAAAAAGTATGGACACTTT
TATAAAAAGGATAGATAATTTACAATATAAGCGCTACCTATTACATTATATAAGCGCTACCTATT
ACATCATATTTTTACCTATTATATTG
Found at i:326839 original size:23 final size:23
Alignment explanation
Indices: 326804--326876 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
326794 ATACTTTACA
*
326804 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
326827 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
326850 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
326873 ATAT
1 ATAT
326877 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:328895 original size:120 final size:120
Alignment explanation
Indices: 328682--328928 Score: 422
Period size: 120 Copynumber: 2.1 Consensus size: 120
328672 TTTTTCTTCC
*
328682 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGACATAGGTTATAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTATAGACCTATTCGCT
328747 AATAAAACAGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
66 AATAAAACAGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
* *
328802 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTATAGACCTATTCGCT
* * * * *
328867 CATAAAACCGGTATATTTATACCGGTTATATTATAAAATTATCTATTACATTATA
66 AATAAAACAGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
328922 ATTCTGG
1 ATTCTGG
328929 GTTCCGATGT
Statistics
Matches: 119, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 119 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32
Consensus pattern (120 bp):
ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTATAGACCTATTCGCT
AATAAAACAGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
Found at i:329072 original size:303 final size:303
Alignment explanation
Indices: 328517--329111 Score: 1073
Period size: 303 Copynumber: 2.0 Consensus size: 303
328507 TTAAAATTAG
* * *
328517 CGACACAATATTAAAAAGTGTTGATATAGGTTGTAGACCTATTCGCTCATAAAACTGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
328582 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTATAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTATAAATGTCGA
*
328647 CACTTTTTGACAAGGTATCGACATATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
328712 AAAAAGTGTCGACATAGGTTATAGACCTATTCGCTAATAAAACAGGTATACTTATACCGGTTATA
196 AAAAAGTGTCGACATAGGTTATAGACCTATTCGCTAATAAAACAGGTATACTTATACCGGTTATA
328777 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
261 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
328820 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
* * *
328885 ATACCGGTTATATTATAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTTGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTATAAATGTCGA
328950 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
* * * * *
329015 AAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTATA
196 AAAAAGTGTCGACATAGGTTATAGACCTATTCGCTAATAAAACAGGTATACTTATACCGGTTATA
*
329080 TTACAAAATTATCTATTACATTATAATTCTGG
261 TTACAAAATTATCTAGTACATTATAATTCTGG
329112 GTTCCGATGT
Statistics
Matches: 279, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
303 279 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (303 bp):
CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTATAAATGTCGA
CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
AAAAAGTGTCGACATAGGTTATAGACCTATTCGCTAATAAAACAGGTATACTTATACCGGTTATA
TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
Found at i:329110 original size:183 final size:183
Alignment explanation
Indices: 328802--329389 Score: 1002
Period size: 183 Copynumber: 3.2 Consensus size: 183
328792 GTACATTATA
*
328802 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
*
328867 CATAAAACCGGTATATTTATACCGGTTATATTATAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
*
328932 CCGATGTGTAAATGTTGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
328985 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
329050 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
*
329115 CCGATGTGTAAATGTCGACACGTTTTGACAAGGTATCGACACATTTTTCTTCC
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
* *
329168 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATATGTTGTAGATCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* *
329233 CATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACA-TATAATTATGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
* * * * * *
329297 TCGATGTTTTTTCAA--TCGACACTTTTTGAAAAGGTATCAACATATTTTTCTTCC
131 CCGATG---TGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
329351 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
329390 GAAAACTTTG
Statistics
Matches: 387, Mismatches: 15, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
182 18 0.05
183 365 0.94
185 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (183 bp):
ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
Found at i:330621 original size:12 final size:12
Alignment explanation
Indices: 330600--330645 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
330590 CTTGTTTGGA
*
330600 TCATCATCATCT
1 TCATCGTCATCT
330612 TCATCGTCATCT
1 TCATCGTCATCT
*
330624 TCATCGTCAGCT
1 TCATCGTCATCT
*
330636 TCATCTTCAT
1 TCATCGTCAT
330646 TGACCGCTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.20, C:0.33, G:0.07, T:0.41
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:330643 original size:6 final size:6
Alignment explanation
Indices: 330600--330645 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
330590 CTTGTTTGGA
* * * *
330600 TCATCA TCATCT TCATCG TCATCT TCATCG TCAGCT TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
330646 TGACCGCTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.20, C:0.33, G:0.07, T:0.41
Consensus pattern (6 bp):
TCATCT
Found at i:333480 original size:15 final size:16
Alignment explanation
Indices: 333460--333489 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
333450 TGATTTACGT
333460 TAATACATGT-ATATA
1 TAATACATGTGATATA
333475 TAATACATGTGATAT
1 TAATACATGTGATAT
333490 GATATGAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (16 bp):
TAATACATGTGATATA
Found at i:333687 original size:30 final size:30
Alignment explanation
Indices: 333651--333714 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
333641 AAGGAACATA
* *
333651 TGGATAGTTATCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
333681 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
333711 TGGA
1 TGGA
333715 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.36
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:334820 original size:200 final size:200
Alignment explanation
Indices: 334470--335209 Score: 1309
Period size: 200 Copynumber: 3.7 Consensus size: 200
334460 TTATATACCA
* * *
334470 ATTCTCCCATAAAACCGGTATACTTATACCGGTTAGATTGAAAAATTACCTAATACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
* *
334535 TTGGGTTTTGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
* * *
334600 TGTTTGCCATTCATTCTGGACCAAAAATAACGACGCAAACTACAAAAGTGTCGACACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTA
334665 GACCT
196 GACCT
*
334670 ATTCTCTCATAAAACCAGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
*
334735 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
*
334800 TGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTA
334865 GACCT
196 GACCT
334870 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
* *
334935 ATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
335000 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTA
335065 GACCT
196 GACCT
* * *
335070 ATTCTCTCATAAAACTGGTATACTTGTACCGATTAGATTGAAAAATTACTTATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
* * *
335135 TTGGGTTTCGATGTGTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCT
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
335200 TGTTTGCCAT
131 TGTTTGCCAT
335210 ATTGTAAATT
Statistics
Matches: 518, Mismatches: 22, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
200 518 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (200 bp):
ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTA
GACCT
Found at i:335452 original size:18 final size:18
Alignment explanation
Indices: 335431--335491 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
335421 TCTCATTCAT
*
335431 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
335449 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
335468 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
335487 AATTA
1 AATTA
335492 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:335467 original size:19 final size:19
Alignment explanation
Indices: 335443--335491 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
335433 TTATATTCAC
335443 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
335462 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
335481 ATACAAAATTA
1 ATACAAAATTA
335492 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:337320 original size:33 final size:33
Alignment explanation
Indices: 337283--337348 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
337273 CATCTTAATA
* *
337283 TCACCCCTTAACACCCCAACTTCTTTTACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
337316 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
337349 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:337407 original size:21 final size:21
Alignment explanation
Indices: 337382--337446 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
337372 CCCCTTATGC
* * *
337382 CTCTCAAGTGTATCTTAGACT
1 CTCTCAAGTTTCTCTTCGACT
337403 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
337424 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
337445 CT
1 CT
337447 TGATTGTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.18, C:0.29, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:339921 original size:20 final size:19
Alignment explanation
Indices: 339875--339921 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
339865 TCTGGTAACG
339875 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
339894 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
339915 TTTTACC
1 TTTTACC
339922 TGGTACATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:340087 original size:182 final size:181
Alignment explanation
Indices: 339662--340133 Score: 712
Period size: 182 Copynumber: 2.6 Consensus size: 181
339652 CGTACTTACG
* * *
339662 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTATCGGTTTTATCATTTTGATATCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
339727 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATA-TTTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
*
339791 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
*
339842 AAAGTATCGACACTTTCAATATATCTGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
339907 TATCATATTTTTACCTGGTACATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** * *
339972 AGGATTTAAAACTGTTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * **
340024 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
340089 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
340134 AATTTGGATC
Statistics
Matches: 263, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
180 96 0.37
181 68 0.26
182 99 0.38
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:340148 original size:182 final size:179
Alignment explanation
Indices: 339662--340135 Score: 696
Period size: 180 Copynumber: 2.6 Consensus size: 179
339652 CGTACTTACG
* * *
339662 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTATCGGTTTTATCATTTTGATATCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* **
339727 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATTTTTTTTAAAGTATCGACACATTATA
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATA-CATTTTTAAAGTATCGACACATTATA
*
339792 GGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
130 GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
*
339842 AAAGTATCGACACTTTCAATATATCTGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
339907 TATCATATTTTTACCTGGTACATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACA-TTTTT-AAAGTATCGACACATTAT
** * *
339972 AGGATTTAAAACTGTTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
129 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * **
340024 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
340089 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAA
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAA
340136 TTTGGATCGA
Statistics
Matches: 264, Mismatches: 27, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
180 103 0.39
181 67 0.25
182 94 0.36
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (179 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAAAGTATCGACACATTATAG
GAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:342451 original size:33 final size:33
Alignment explanation
Indices: 342414--342490 Score: 129
Period size: 33 Copynumber: 2.4 Consensus size: 33
342404 CTGCATGGAA
*
342414 CATGCACGTCCCCAACACCCCAACACAGGTCGT
1 CATGCACGTCCCCAACACCCCAACACAGGTCGC
*
342447 CATGCACGTCCCCAACACCCCAACATAGGTCGC
1 CATGCACGTCCCCAACACCCCAACACAGGTCGC
342480 CATGCAC-TCCC
1 CATGCACGTCCC
342491 AGCGACCTAC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
32 4 0.10
33 38 0.90
ACGTcount: A:0.26, C:0.47, G:0.14, T:0.13
Consensus pattern (33 bp):
CATGCACGTCCCCAACACCCCAACACAGGTCGC
Found at i:342515 original size:29 final size:29
Alignment explanation
Indices: 342473--342555 Score: 121
Period size: 29 Copynumber: 2.9 Consensus size: 29
342463 ACCCCAACAT
342473 AGGTCGCCATGCACTCCCAGCGACCTACA
1 AGGTCGCCATGCACTCCCAGCGACCTACA
***
342502 AGGTCGCCATGCACTCCCAGCGACCTTGT
1 AGGTCGCCATGCACTCCCAGCGACCTACA
* *
342531 AGGTCGCCAAGCAGTCCCAGCGACC
1 AGGTCGCCATGCACTCCCAGCGACC
342556 AAGCTTAGGA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.22, C:0.40, G:0.24, T:0.14
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCAGCGACCTACA
Found at i:342592 original size:22 final size:22
Alignment explanation
Indices: 342564--342626 Score: 117
Period size: 22 Copynumber: 2.9 Consensus size: 22
342554 CCAAGCTTAG
342564 GACCAAACTTATCCCTGCTGGC
1 GACCAAACTTATCCCTGCTGGC
342586 GACCAAACTTATCCCTGCTGGC
1 GACCAAACTTATCCCTGCTGGC
*
342608 GACCAAACTTAACCCTGCT
1 GACCAAACTTATCCCTGCT
342627 CCCTCGTGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.25, C:0.37, G:0.16, T:0.22
Consensus pattern (22 bp):
GACCAAACTTATCCCTGCTGGC
Found at i:343126 original size:28 final size:30
Alignment explanation
Indices: 343086--343147 Score: 110
Period size: 28 Copynumber: 2.1 Consensus size: 30
343076 AATTTAGTTA
343086 ATTAGTTTGTTAGTTTAAG-T-TATATTAT
1 ATTAGTTTGTTAGTTTAAGTTATATATTAT
343114 ATTAGTTTGTTAGTTTAAGTTATATATTAT
1 ATTAGTTTGTTAGTTTAAGTTATATATTAT
343144 ATTA
1 ATTA
343148 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (30 bp):
ATTAGTTTGTTAGTTTAAGTTATATATTAT
Found at i:343485 original size:20 final size:21
Alignment explanation
Indices: 343441--343485 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
343431 AAATATTGTG
**
343441 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
343462 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
343482 TTTA
1 TTTA
343486 TATTATATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:346715 original size:60 final size:60
Alignment explanation
Indices: 346640--346885 Score: 347
Period size: 60 Copynumber: 4.3 Consensus size: 60
346630 TATGTATTTA
* *
346640 TAAT-ATTTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGGTTTGATAG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
*
346699 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
* *
346759 TAATGATTTATTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
*
346819 TAATGA-TTAG---T-A--A-TAATAAT----TTATTATTAATATTTAATGATTTGATAT
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
346867 TAATGATTTAGTAATGATT
1 TAATGATTTAGTAATGATT
346886 TGATAGTAAT
Statistics
Matches: 170, Mismatches: 9, Indels: 20
0.85 0.05 0.10
Matches are distributed among these distances:
48 32 0.19
49 4 0.02
52 8 0.05
53 2 0.01
55 1 0.01
56 1 0.01
59 7 0.04
60 115 0.68
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (60 bp):
TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
Found at i:346794 original size:25 final size:25
Alignment explanation
Indices: 346744--346796 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
346734 TTATTAATAT
* * *
346744 TTAATGATTTGATATTAATGATTTA
1 TTAATGATTAGATAATAATGAATTA
346769 TTAATGATTAG-TAATAATGAAATTA
1 TTAATGATTAGATAATAATG-AATTA
346794 TTA
1 TTA
346797 TTAATTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (25 bp):
TTAATGATTAGATAATAATGAATTA
Found at i:346856 original size:48 final size:48
Alignment explanation
Indices: 346758--346881 Score: 182
Period size: 48 Copynumber: 2.6 Consensus size: 48
346748 TGATTTGATA
*
346758 TTAATGATTT-AT-TAATGATTAGTAATAATGAAATTATTATTAATTT
1 TTAATGATTTGATATAATGATTAGTAATAATGAAATTATTATTAATAT
*
346804 TTAATGATTTGATAGTAATGATTAGTAATAAT-AATTTATTATTAATAT
1 TTAATGATTTGATA-TAATGATTAGTAATAATGAAATTATTATTAATAT
346852 TTAATGATTTGATATTAATGATTTAGTAAT
1 TTAATGATTTGATA-TAATGA-TTAGTAAT
346882 GATTTGATAG
Statistics
Matches: 71, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
46 10 0.14
47 2 0.03
48 34 0.48
49 25 0.35
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.49
Consensus pattern (48 bp):
TTAATGATTTGATATAATGATTAGTAATAATGAAATTATTATTAATAT
Found at i:346869 original size:14 final size:14
Alignment explanation
Indices: 346853--346900 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
346843 TATTAATATT
*
346853 TAATGATTTGATAT
1 TAATGATTTGATAG
346867 TAATGA-TT--TAG
1 TAATGATTTGATAG
346878 TAATGATTTGATAG
1 TAATGATTTGATAG
346892 TAATGATTT
1 TAATGATTT
346901 AGTAATGAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:346882 original size:25 final size:24
Alignment explanation
Indices: 346805--346908 Score: 106
Period size: 25 Copynumber: 4.2 Consensus size: 24
346795 TATTAATTTT
346805 TAATGATTTGATAGTAATGATTAG
1 TAATGATTTGATAGTAATGATTAG
* * *
346829 TAATAATAATTTATTATTAAT-ATT--
1 TAATGAT--TTGA-TAGTAATGATTAG
*
346853 TAATGATTTGATATTAATGATTTAG
1 TAATGATTTGATAGTAATGA-TTAG
346878 TAATGATTTGATAGTAATGATTTAG
1 TAATGATTTGATAGTAATGA-TTAG
346903 TAATGA
1 TAATGA
346909 GTAGATGGAT
Statistics
Matches: 67, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
21 7 0.10
22 4 0.06
23 2 0.03
24 12 0.18
25 30 0.45
26 6 0.09
27 6 0.09
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.46
Consensus pattern (24 bp):
TAATGATTTGATAGTAATGATTAG
Found at i:348794 original size:15 final size:14
Alignment explanation
Indices: 348771--348801 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
348761 TACAACACTA
348771 AACTTTAATATAAT
1 AACTTTAATATAAT
348785 AACTTATAATATAAT
1 AACTT-TAATATAAT
348800 AA
1 AA
348802 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:348809 original size:16 final size:16
Alignment explanation
Indices: 348776--348822 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
348766 CACTAAACTT
*
348776 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
348791 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
348807 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
348823 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:349076 original size:39 final size:40
Alignment explanation
Indices: 349005--349112 Score: 103
Period size: 40 Copynumber: 2.6 Consensus size: 40
348995 TTTAACTACC
*
349005 ACAAACTAATTAAATAATTTGTTTATA-TAACTAACAATTAACAAA
1 ACAAACTAATTAAATAATTT-TTTA-ACT-A-T-ACAACTAAC-AA
* * *
349050 ACAAACTAATT-AATTATTTTTTAACTATATAACTATCAA
1 ACAAACTAATTAAATAATTTTTTAACTATACAACTAACAA
*
349089 ACATACTAATTAAATAATTTTTTA
1 ACAAACTAATTAAATAATTTTTTA
349113 TTTATGTATA
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
39 12 0.22
40 17 0.31
41 1 0.02
42 2 0.04
43 5 0.09
44 7 0.13
45 11 0.20
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (40 bp):
ACAAACTAATTAAATAATTTTTTAACTATACAACTAACAA
Found at i:349161 original size:22 final size:21
Alignment explanation
Indices: 349123--349163 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
349113 TTTATGTATA
*
349123 ATATAACTTAAACTAACAATC
1 ATATAACCTAAACTAACAATC
*
349144 ATATAACCCTAAATTAACAA
1 ATATAA-CCTAAACTAACAA
349164 ACTAATTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.27
Consensus pattern (21 bp):
ATATAACCTAAACTAACAATC
Found at i:349318 original size:28 final size:28
Alignment explanation
Indices: 349265--349328 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 28
349255 CTCACAAGAG
*
349265 CCTTATCTCCCTTTCTTCTTCTTCTT-TT
1 CCTT-TCTCCCTTTCTTCTTCTTCTTCTC
349293 CCTTTCTCCCTTTCTTTCTT-TATCTTCTC
1 CCTTTCTCCCTTTC-TTCTTCT-TCTTCTC
349322 CCTTTCT
1 CCTTTCT
349329 TCTTCTACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 11 0.34
28 13 0.41
29 8 0.25
ACGTcount: A:0.03, C:0.38, G:0.00, T:0.59
Consensus pattern (28 bp):
CCTTTCTCCCTTTCTTCTTCTTCTTCTC
Found at i:349685 original size:33 final size:33
Alignment explanation
Indices: 349635--349711 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 33
349625 CAAGGTCGCT
349635 GGGA-GTGCATGGCGACCTGTGTTGGGGTGTTG
1 GGGACGTGCATGGCGACCTGTGTTGGGGTGTTG
*
349667 GGGACGTGCATGGTGACCTGTGTTGGGGTGTTG
1 GGGACGTGCATGGCGACCTGTGTTGGGGTGTTG
349700 GGGACGTGCATG
1 GGGACGTGCATG
349712 TGCCATGCAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 4 0.09
33 39 0.91
ACGTcount: A:0.10, C:0.13, G:0.49, T:0.27
Consensus pattern (33 bp):
GGGACGTGCATGGCGACCTGTGTTGGGGTGTTG
Found at i:356235 original size:17 final size:19
Alignment explanation
Indices: 356215--356260 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
356205 CATTAAACAT
356215 TATTTAGTCAT-AAATA-A
1 TATTTAGTCATGAAATACA
* *
356232 TATTTAG-GATGAACTACA
1 TATTTAGTCATGAAATACA
356250 TATTTAGTCAT
1 TATTTAGTCAT
356261 TCAATTATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 2 0.09
17 11 0.48
18 8 0.35
19 2 0.09
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (19 bp):
TATTTAGTCATGAAATACA
Found at i:359836 original size:19 final size:19
Alignment explanation
Indices: 359812--359859 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
359802 AAACTTTAAG
*
359812 AAAGAATTAATGCAAAGAT
1 AAAGAATTAACGCAAAGAT
* *
359831 AAAGAACTAACGCAAAGGT
1 AAAGAATTAACGCAAAGAT
*
359850 AAATAATTAA
1 AAAGAATTAA
359860 AGGAAATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.58, C:0.08, G:0.15, T:0.19
Consensus pattern (19 bp):
AAAGAATTAACGCAAAGAT
Found at i:366029 original size:37 final size:37
Alignment explanation
Indices: 365959--366030 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 37
365949 ATAAGATATT
* *
365959 TATATATTTTCTTTAAAAAATTTAAATTCATAAAATG
1 TATATATTTTCTTTAAAAAATTAAAAATCATAAAATG
* *
365996 TATATAATTTTTTTTACAAAATTAAAAAT-ATAAAA
1 TATAT-ATTTTCTTTAAAAAATTAAAAATCATAAAA
366031 AAGTTTAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 11 0.37
38 19 0.63
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.44
Consensus pattern (37 bp):
TATATATTTTCTTTAAAAAATTAAAAATCATAAAATG
Found at i:384183 original size:22 final size:22
Alignment explanation
Indices: 384153--384201 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
384143 TGTCAAAAAG
*
384153 AAGGCAAATAATGGCACAGTAA
1 AAGGTAAATAATGGCACAGTAA
*
384175 AAGGTAAATAATGGTACAGTAA
1 AAGGTAAATAATGGCACAGTAA
384197 AAGGT
1 AAGGT
384202 TCTTTCAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.49, C:0.08, G:0.24, T:0.18
Consensus pattern (22 bp):
AAGGTAAATAATGGCACAGTAA
Found at i:384527 original size:2 final size:2
Alignment explanation
Indices: 384522--384549 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
384512 GCGCACACAC
384522 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
384550 TCCAAATTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:400973 original size:18 final size:19
Alignment explanation
Indices: 400952--400995 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
400942 AGGTTTTGAT
400952 AAAAATGA-TTAAA-TAATA
1 AAAAATGATTTAAAGTAA-A
400970 AAAAATGATTTAAAGTAAA
1 AAAAATGATTTAAAGTAAA
400989 AAAAATG
1 AAAAATG
400996 TAAAGTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.33
19 13 0.54
20 3 0.12
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (19 bp):
AAAAATGATTTAAAGTAAA
Found at i:418921 original size:24 final size:24
Alignment explanation
Indices: 418851--418921 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
418841 CAATATTATA
*
418851 TGGCACTACGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
* *
418874 CGGCACTTCGGTGCAAATTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
*
418898 TGGCACTTCGGTGCAATTTATACG
1 TGGCACTTCGGTGCAATTTCTACG
418922 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
23 12 0.29
24 29 0.71
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTACG
Found at i:419022 original size:2 final size:2
Alignment explanation
Indices: 419010--419042 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
419000 AAGAGATTAA
419010 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
419043 GATGCATATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:419149 original size:20 final size:20
Alignment explanation
Indices: 419113--419150 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
419103 TTGTATCTGT
*
419113 TATATGAATGAGACATAATA
1 TATATGAAAGAGACATAATA
419133 TATATGATAAGAG-CATAA
1 TATATGA-AAGAGACATAA
419151 GAGATTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (20 bp):
TATATGAAAGAGACATAATA
Found at i:420962 original size:22 final size:22
Alignment explanation
Indices: 420912--420962 Score: 88
Period size: 20 Copynumber: 2.4 Consensus size: 22
420902 TTTAAATGTA
420912 ATACCTTATAATCAACCCATGC
1 ATACCTTATAATCAACCCATGC
420934 --ACCTTATAATCAACCCATGC
1 ATACCTTATAATCAACCCATGC
420954 ATACCTTAT
1 ATACCTTAT
420963 TTATGATGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 20 0.74
22 7 0.26
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.29
Consensus pattern (22 bp):
ATACCTTATAATCAACCCATGC
Found at i:426130 original size:17 final size:18
Alignment explanation
Indices: 426097--426131 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
426087 ATTAAATTAT
426097 CTATAAAAAATATTTAAA
1 CTATAAAAAATATTTAAA
*
426115 CTATATAAAA-ATTTAAA
1 CTATAAAAAATATTTAAA
426132 ATTTTCAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (18 bp):
CTATAAAAAATATTTAAA
Found at i:427413 original size:10 final size:10
Alignment explanation
Indices: 427400--427443 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
427390 TGTTTATTTA
427400 TTATGTTCGT
1 TTATGTTCGT
*
427410 TTATGTTAGT
1 TTATGTTCGT
* *
427420 TTACGTTCAT
1 TTATGTTCGT
*
427430 TTATATTCGT
1 TTATGTTCGT
427440 TTAT
1 TTAT
427444 CATTTAAATG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.18, C:0.09, G:0.14, T:0.59
Consensus pattern (10 bp):
TTATGTTCGT
Found at i:434394 original size:20 final size:20
Alignment explanation
Indices: 434369--434435 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
434359 TTGTTTAATC
434369 TAAAATGTTATATAAGTTTA
1 TAAAATGTTATATAAGTTTA
* **
434389 TAAAATATTAT-TTTGTTTAA
1 TAAAATGTTATATAAGTTT-A
* *
434409 TCTAAAAAGTTATATAAGTTTG
1 --TAAAATGTTATATAAGTTTA
434431 TAAAA
1 TAAAA
434436 ATTTTCGGTT
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
19 5 0.14
20 16 0.46
22 9 0.26
23 5 0.14
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.45
Consensus pattern (20 bp):
TAAAATGTTATATAAGTTTA
Found at i:434394 original size:42 final size:42
Alignment explanation
Indices: 434347--434435 Score: 160
Period size: 42 Copynumber: 2.1 Consensus size: 42
434337 ATTTTTAATT
*
434347 TAAAATATTATTTTGTTTAATCTAAAATGTTATATAAGTTTA
1 TAAAATATTATTTTGTTTAATCTAAAAAGTTATATAAGTTTA
*
434389 TAAAATATTATTTTGTTTAATCTAAAAAGTTATATAAGTTTG
1 TAAAATATTATTTTGTTTAATCTAAAAAGTTATATAAGTTTA
434431 TAAAA
1 TAAAA
434436 ATTTTCGGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (42 bp):
TAAAATATTATTTTGTTTAATCTAAAAAGTTATATAAGTTTA
Found at i:434421 original size:22 final size:22
Alignment explanation
Indices: 434340--434415 Score: 86
Period size: 22 Copynumber: 3.5 Consensus size: 22
434330 TAAGATGATT
*
434340 TTTAATTTAAAATATTATTTTG
1 TTTAATCTAAAATATTATTTTG
* **
434362 TTTAATCTAAAATGTTATATAAG
1 TTTAATCTAAAATATTAT-TTTG
434385 TTT-A--TAAAATATTATTTTG
1 TTTAATCTAAAATATTATTTTG
434404 TTTAATCTAAAA
1 TTTAATCTAAAA
434416 AGTTATATAA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
19 5 0.12
20 11 0.26
22 22 0.51
23 5 0.12
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTAATCTAAAATATTATTTTG
Found at i:436062 original size:39 final size:40
Alignment explanation
Indices: 435997--436076 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
435987 GAAACTCTAA
435997 GGTTCTAAGTTTTTTCAAATATTTTGGAGGATCACCTCAT
1 GGTTCTAAGTTTTTTCAAATATTTTGGAGGATCACCTCAT
436037 GGTTCTAAGTTTTTTCAAATA-TTTGGAGGATCACCTCAT
1 GGTTCTAAGTTTTTTCAAATATTTTGGAGGATCACCTCAT
436076 G
1 G
436077 CCCGAATGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 19 0.47
40 21 0.52
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (40 bp):
GGTTCTAAGTTTTTTCAAATATTTTGGAGGATCACCTCAT
Found at i:438020 original size:14 final size:14
Alignment explanation
Indices: 437985--438030 Score: 74
Period size: 14 Copynumber: 3.1 Consensus size: 14
437975 TCATGTATTA
437985 ACTGTAGAAAACAG
1 ACTGTAGAAAACAG
437999 ACTGTGTAGAAAACAG
1 AC--TGTAGAAAACAG
438015 ACTGTAGAAAACAG
1 ACTGTAGAAAACAG
438029 AC
1 AC
438031 AAGTCTGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 16 0.53
16 14 0.47
ACGTcount: A:0.48, C:0.15, G:0.22, T:0.15
Consensus pattern (14 bp):
ACTGTAGAAAACAG
Found at i:440327 original size:51 final size:51
Alignment explanation
Indices: 440251--440351 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
440241 TAAGGAAATG
*
440251 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGTTGAAATTCCTTGTAACTA
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
440302 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
440352 CTCCCCCTGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.31
Consensus pattern (51 bp):
ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
Found at i:448218 original size:4 final size:4
Alignment explanation
Indices: 448211--448241 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
448201 ACTGCAATGA
448211 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATG
448242 AGAGTACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.48, T:0.26
Consensus pattern (4 bp):
ATGG
Found at i:451603 original size:19 final size:19
Alignment explanation
Indices: 451571--451633 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
451561 TGACTTAAAA
**
451571 ATTTAAAATTATTATATAT
1 ATTTAAAAAAATTATATAT
*
451590 ATTTAAAAAAATTAGATAT
1 ATTTAAAAAAATTATATAT
* * *
451609 TTTTATTAAAACATTATTTAT
1 ATTTA--AAAAAATTATATAT
451630 ATTT
1 ATTT
451634 TATTAAAATT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
19 20 0.59
21 14 0.41
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
ATTTAAAAAAATTATATAT
Found at i:451619 original size:21 final size:22
Alignment explanation
Indices: 451595--451641 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
451585 TATATATTTA
451595 AAAAAATTAGATAT-TTTTATT
1 AAAAAATTAGATATATTTTATT
* **
451616 AAAACATTATTTATATTTTATT
1 AAAAAATTAGATATATTTTATT
451638 AAAA
1 AAAA
451642 TTTCATAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
AAAAAATTAGATATATTTTATT
Found at i:451858 original size:20 final size:20
Alignment explanation
Indices: 451821--451859 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
451811 AAAAGACATA
* * *
451821 TAATATTAATAATTTTTAAT
1 TAATATCAACAATATTTAAT
451841 TAATATCAACAATATTTAA
1 TAATATCAACAATATTTAA
451860 AATAGATAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATATCAACAATATTTAAT
Found at i:454676 original size:22 final size:22
Alignment explanation
Indices: 454651--454700 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
454641 CTACGACGAC
* *
454651 ATCCGTCCCCATCTCCGGTGAA
1 ATCCGTCCCCATCTCCAGCGAA
454673 ATCCGTCCCCATCTCCAGCGAA
1 ATCCGTCCCCATCTCCAGCGAA
454695 ATCCGT
1 ATCCGT
454701 ATATCTCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.42, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCAGCGAA
Found at i:455098 original size:20 final size:19
Alignment explanation
Indices: 455060--455114 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
455050 AAATCGCAAC
*
455060 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCACGTT
*
455079 GCGATTTTCATTTTCACGTT
1 GCGATTTT-AGTTTCACGTT
*
455099 GCGAATTTAAGTTTCA
1 GCG-ATTTTAGTTTCA
455115 GAAACTACTC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 8 0.27
20 18 0.60
21 4 0.13
ACGTcount: A:0.18, C:0.16, G:0.20, T:0.45
Consensus pattern (19 bp):
GCGATTTTAGTTTCACGTT
Found at i:456647 original size:21 final size:21
Alignment explanation
Indices: 456604--456653 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
456594 GTTAAGGGAG
*
456604 TTACGTGATGAGGTAAGTGCT
1 TTACGTGATGAGGTAAGTACT
* **
456625 TTGCGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTAAGTACT
456646 TTACGTGA
1 TTACGTGA
456654 CGACAATGTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.12, G:0.34, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTAAGTACT
Found at i:457090 original size:21 final size:21
Alignment explanation
Indices: 457064--457134 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
457054 CCTATCATCG
457064 TTCAAGAGGCCCCTCCCACCA
1 TTCAAGAGGCCCCTCCCACCA
** * *
457085 TTCAAGAGGCCCCTGTCATCG
1 TTCAAGAGGCCCCTCCCACCA
* *
457106 TTCAAGAAGTCCCTCCCACCA
1 TTCAAGAGGCCCCTCCCACCA
457127 TTCAAGAG
1 TTCAAGAG
457135 CCCGATTCAC
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.25, C:0.38, G:0.17, T:0.20
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCCACCA
Found at i:458883 original size:6 final size:6
Alignment explanation
Indices: 458864--458902 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
458854 GTGAAGCTGG
**
458864 TTTTGA TTGGGA TTTTGA TTTTGA TTTTGA TTTTGA TTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTT
458903 CCTTTTGCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.15, C:0.00, G:0.21, T:0.64
Consensus pattern (6 bp):
TTTTGA
Found at i:461228 original size:24 final size:24
Alignment explanation
Indices: 461177--461228 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
461167 ATCTGAGTAT
** *
461177 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
461201 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
461225 TGAC
1 TGAC
461229 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:461989 original size:14 final size:16
Alignment explanation
Indices: 461954--461990 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
461944 GAAATCATTG
461954 AAAATTATATAGAAAT
1 AAAATTATATAGAAAT
*
461970 AAAATTATGTA-AAA-
1 AAAATTATATAGAAAT
461984 AAAATTA
1 AAAATTA
461991 GAGATTGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (16 bp):
AAAATTATATAGAAAT
Found at i:462235 original size:21 final size:20
Alignment explanation
Indices: 462168--462298 Score: 97
Period size: 20 Copynumber: 6.5 Consensus size: 20
462158 AATTTCGTGA
* * *
462168 TGCGAATTCGAAAATCGAGT
1 TGCGAATTTGAAATTCGCGT
* * *
462188 TTCGAATTCAGAAA-TCGAGT
1 TGCGAATT-TGAAATTCGCGT
* *
462208 TGTGAATTTGAAATTCAGTGT
1 TGCGAATTTGAAATTC-GCGT
462229 TGCGAATTTGGAAA-TCGCGT
1 TGCGAATTT-GAAATTCGCGT
* *
462249 TGCGAATTT-AACTTCTGTGT
1 TGCGAATTTGAAATTC-GCGT
* *
462269 TGCGAAATTGTAATTCGCGT
1 TGCGAATTTGAAATTCGCGT
462289 TGCGAATTTG
1 TGCGAATTTG
462299 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 15, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
18 2 0.02
19 6 0.07
20 56 0.63
21 21 0.24
22 4 0.04
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.35
Consensus pattern (20 bp):
TGCGAATTTGAAATTCGCGT
Found at i:462235 original size:41 final size:40
Alignment explanation
Indices: 462190--462274 Score: 107
Period size: 41 Copynumber: 2.1 Consensus size: 40
462180 AATCGAGTTT
*
462190 CGAATTCAGAAATCGAGTTGTGAATTTGAAATTCAGTGTTG
1 CGAATTCAGAAATCGAGTTGCGAATTT-AAATTCAGTGTTG
** * * *
462231 CGAATTTGGAAATCGCGTTGCGAATTTAACTTCTGTGTTG
1 CGAATTCAGAAATCGAGTTGCGAATTTAAATTCAGTGTTG
462271 CGAA
1 CGAA
462275 ATTGTAATTC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
40 15 0.39
41 23 0.61
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (40 bp):
CGAATTCAGAAATCGAGTTGCGAATTTAAATTCAGTGTTG
Found at i:462287 original size:40 final size:41
Alignment explanation
Indices: 462198--462298 Score: 132
Period size: 40 Copynumber: 2.5 Consensus size: 41
462188 TTCGAATTCA
* * *
462198 GAAATCGAGTTGTGAATTTGAAATTCAGTGTTGCGAATTTG
1 GAAATCGCGTTGCGAATTTGAAATTCAGTGTTGCGAAATTG
* *
462239 GAAATCGCGTTGCGAATTT-AACTTCTGTGTTGCGAAATTG
1 GAAATCGCGTTGCGAATTTGAAATTCAGTGTTGCGAAATTG
* *
462279 TAATTCGCGTTGCGAATTTG
1 GAAATCGCGTTGCGAATTTG
462299 TTGGTCATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
40 35 0.67
41 17 0.33
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.37
Consensus pattern (41 bp):
GAAATCGCGTTGCGAATTTGAAATTCAGTGTTGCGAAATTG
Found at i:465219 original size:72 final size:74
Alignment explanation
Indices: 465076--465227 Score: 193
Period size: 72 Copynumber: 2.1 Consensus size: 74
465066 TAGATATTCA
* * * **
465076 ATGTTTTCAACATTAGTTTTTTAAAATATTTGTATTATAATAATTATTTAAAAAATTATTATTTG
1 ATGTTTTCAACATTAGTTTTTTAAAATATCTATATTATAAAAATTATTTAAAAAATTATTATAGG
*
465141 ATATGAGTT
66 ACATGAGTT
* * *
465150 ATGTTTTCAATATTA-TTTTTT-AAGTATCTATTTTATAAAAATTA-TTAAAAATATTATTATAG
1 ATGTTTTCAACATTAGTTTTTTAAAATATCTATATTATAAAAATTATTTAAAAA-ATTATTATAG
465212 GACATGAGTT
65 GACATGAGTT
465222 ATGTTT
1 ATGTTT
465228 ATATATTTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
71 7 0.10
72 41 0.60
73 6 0.09
74 14 0.21
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.51
Consensus pattern (74 bp):
ATGTTTTCAACATTAGTTTTTTAAAATATCTATATTATAAAAATTATTTAAAAAATTATTATAGG
ACATGAGTT
Found at i:469816 original size:61 final size:60
Alignment explanation
Indices: 469706--469853 Score: 178
Period size: 61 Copynumber: 2.5 Consensus size: 60
469696 ATTAAAACAT
* * *
469706 TCAAAAGTTTA-GGAACTAATATAGAATGAGAGTCATAGTTTGGAGATGAAATT-GTAATGC
1 TCAAAAGTTTAGGGATC-AATTTAGAATGAGAGTCATAGTTTGGAGATGAAATTAG-AATAC
* *
469766 TCAAAAGTTTAGGGATCAATTTAAGAATGAGAGTCATAGTTTATGA-ATGAAATTAGAATAT
1 TCAAAAGTTTAGGGATCAATTT-AGAATGAGAGTCATAGTTT-GGAGATGAAATTAGAATAC
469827 TCAAAAGTTT-GAGGATCAATTTAGAAT
1 TCAAAAGTTTAG-GGATCAATTTAGAAT
469854 AAAAGCTATA
Statistics
Matches: 78, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
60 21 0.27
61 54 0.69
62 3 0.04
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (60 bp):
TCAAAAGTTTAGGGATCAATTTAGAATGAGAGTCATAGTTTGGAGATGAAATTAGAATAC
Found at i:470768 original size:3 final size:3
Alignment explanation
Indices: 470760--470814 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
470750 AATTATAGAC
470760 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
470807 ATT ATT AT
1 ATT ATT AT
470815 ATGTAAATCA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:471785 original size:12 final size:13
Alignment explanation
Indices: 471768--471798 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
471758 GAATTTATTT
471768 AAAAAATT-TTAA
1 AAAAAATTATTAA
471780 AAAAAATTATTAA
1 AAAAAATTATTAA
471793 AAAAAA
1 AAAAAA
471799 CCACAGCCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAAAATTATTAA
Found at i:473794 original size:137 final size:138
Alignment explanation
Indices: 473546--473795 Score: 412
Period size: 138 Copynumber: 1.8 Consensus size: 138
473536 AAAACTATTG
* *
473546 AGTGAGGGTTTTACGTACCACCTCAATTTTGCGTCATACCATTATCTCTTTCCTTACCATGCATC
1 AGTGAGGGTTTTACGTACCACCTCAATTTTGCATCATACCATTATCTCTTTCCTTACCATACATC
* *
473611 ATATCGAAGTTTGATGCTACAATTTAGTTCTCGAAGTATTGAGCTGCTGAAATATGACATGTGAG
66 ATATCGAAGTTTGATACTACAATTTAGGTCTCGAAGTATTGAGCTGCTGAAATATGACATGTGAG
473676 ATATGACA
131 ATATGACA
* * * *
473684 AGTGAGGGTTTTACGTACCACCTCGATTTTGCATCATACTATTGTCTTTTTCCTTACCA-ACATC
1 AGTGAGGGTTTTACGTACCACCTCAATTTTGCATCATACCATTATCTCTTTCCTTACCATACATC
*
473748 ATATCGAAGTTTGATACTACAATTTAGGTCTCGAAGTATTTAGCTGCT
66 ATATCGAAGTTTGATACTACAATTTAGGTCTCGAAGTATTGAGCTGCT
473796 TAGATACAAT
Statistics
Matches: 103, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
137 49 0.48
138 54 0.52
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.36
Consensus pattern (138 bp):
AGTGAGGGTTTTACGTACCACCTCAATTTTGCATCATACCATTATCTCTTTCCTTACCATACATC
ATATCGAAGTTTGATACTACAATTTAGGTCTCGAAGTATTGAGCTGCTGAAATATGACATGTGAG
ATATGACA
Found at i:473811 original size:137 final size:138
Alignment explanation
Indices: 473546--473804 Score: 394
Period size: 137 Copynumber: 1.9 Consensus size: 138
473536 AAAACTATTG
* *
473546 AGTGAGGGTTTTACGTACCACCTCAATTTTGCGTCATACCATTATCTCTTTCCTTACCATGCATC
1 AGTGAGGGTTTTACGTACCACCTCAATTTTGCATCATACCATTATCTCTTTCCTTACCATACATC
* * **
473611 ATATCGAAGTTTGATGCTACAATTTAGTTCTCGAAGTATTGAGCTGCTGAAATATGACATGTGAG
66 ATATCGAAGTTTGATACTACAATTTAGGTCTCGAAGTATTGAGCTGCTGAAATACAACATGTGAG
473676 ATATGACA
131 ATATGACA
* * * *
473684 AGTGAGGGTTTTACGTACCACCTCGATTTTGCATCATACTATTGTCTTTTTCCTTACCA-ACATC
1 AGTGAGGGTTTTACGTACCACCTCAATTTTGCATCATACCATTATCTCTTTCCTTACCATACATC
* * *
473748 ATATCGAAGTTTGATACTACAATTTAGGTCTCGAAGTATTTAGCTGCTTAGATACAA
66 ATATCGAAGTTTGATACTACAATTTAGGTCTCGAAGTATTGAGCTGCTGAAATACAA
473805 TGTGTGAAGT
Statistics
Matches: 108, Mismatches: 13, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
137 54 0.50
138 54 0.50
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (138 bp):
AGTGAGGGTTTTACGTACCACCTCAATTTTGCATCATACCATTATCTCTTTCCTTACCATACATC
ATATCGAAGTTTGATACTACAATTTAGGTCTCGAAGTATTGAGCTGCTGAAATACAACATGTGAG
ATATGACA
Found at i:474475 original size:20 final size:20
Alignment explanation
Indices: 474430--474475 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
474420 CTCTTTTTAC
*
474430 TGTTACCCTTTCCATGGAAG
1 TGTTATCCTTTCCATGGAAG
474450 TGTTATCCTTTCCATGGAAG
1 TGTTATCCTTTCCATGGAAG
474470 TGTTAT
1 TGTTAT
474476 TAGTTTATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (20 bp):
TGTTATCCTTTCCATGGAAG
Found at i:481147 original size:59 final size:59
Alignment explanation
Indices: 481023--481155 Score: 164
Period size: 59 Copynumber: 2.2 Consensus size: 59
481013 TAATATGACT
* * *
481023 ATTTTATAACTTTTAATAGTTGAAAGATTCAATAAAATAATGCCTTATAATCAGAGATT
1 ATTTTATAACTTTAAATAGTTGAAAGATTCAATAAAATAATACCTTATAATCAGAGATC
* *
481082 ATTTTATAACTTTAAATAGTTGAGAAG-TTCAATAAAATAATAACC-TATAGTCGGAGGATC
1 ATTTTATAACTTTAAATAGTTGA-AAGATTCAATAAAATAAT-ACCTTATAATCAGA-GATC
481142 A-TTTATATACTTTA
1 ATTTTATA-ACTTTA
481156 CTCAAAATTA
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
59 50 0.77
60 15 0.23
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.38
Consensus pattern (59 bp):
ATTTTATAACTTTAAATAGTTGAAAGATTCAATAAAATAATACCTTATAATCAGAGATC
Found at i:482696 original size:76 final size:76
Alignment explanation
Indices: 482611--482754 Score: 207
Period size: 76 Copynumber: 1.9 Consensus size: 76
482601 TAAAATAAAC
* * * * *
482611 GCAACTTATTACGTTAAACTAGCCACTGGTTTGTTTAAATATATAATAATAATGTAAACGATAAA
1 GCAACTTATTACGTTAAACTAACCACCGGTTTGTTTAAAGATATAATAATAATATAAACGACAAA
482676 ATAAAATGTGT
66 ATAAAATGTGT
* * * *
482687 GCAATTTATTACGTTAAATTAACTACCGGTTTGTTTAAAGGTATAATAATAATATAAACGACAAA
1 GCAACTTATTACGTTAAACTAACCACCGGTTTGTTTAAAGATATAATAATAATATAAACGACAAA
482752 ATA
66 ATA
482755 TTTACAACTT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
76 59 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.34
Consensus pattern (76 bp):
GCAACTTATTACGTTAAACTAACCACCGGTTTGTTTAAAGATATAATAATAATATAAACGACAAA
ATAAAATGTGT
Found at i:482739 original size:176 final size:176
Alignment explanation
Indices: 482534--482854 Score: 421
Period size: 176 Copynumber: 1.8 Consensus size: 176
482524 TGCAACCTAT
* * * * *
482534 TACCGATTTGTTTAAATATATAATAATAATGTAAACAATAAACTAATTACAACTTACCCT-ATTA
1 TACCGATTTGTTTAAAGATATAATAATAATATAAACAACAAAATAATTACAACTTA-ACTGATTA
* * * *
482598 AAATAAAATAAACGCAA-CTTATTACGTTAAACTAGCCACTGGTTTGTTTAAATATATAATAATA
65 AAATAAAATAAACGCAATC-TATAACATTAAACTAGCCAATGGTTTGTTTAAAGATATAATAATA
482662 ATGTAAACGATAAAATAAAATGTGTGCAATTTATTACGTTAAATTAAC
129 ATGTAAACGATAAAATAAAATGTGTGCAATTTATTACGTTAAATTAAC
* * * * *
482710 TACCGGTTTGTTTAAAGGTATAATAATAATATAAACGACAAAATATTTACAACTTAACTGGTTAA
1 TACCGATTTGTTTAAAGATATAATAATAATATAAACAACAAAATAATTACAACTTAACTGATTAA
* * * *
482775 AATAAAATAGACGCAATCTATAACATTAAATTAGCTAATGGTTTGTTTAAAGGTATAATAATAAT
66 AATAAAATAAACGCAATCTATAACATTAAACTAGCCAATGGTTTGTTTAAAGATATAATAATAAT
* * *
482840 TTAAATGGTAAAATA
131 GTAAACGATAAAATA
482855 TTTACCACTT
Statistics
Matches: 122, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
175 2 0.02
176 119 0.98
177 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.34
Consensus pattern (176 bp):
TACCGATTTGTTTAAAGATATAATAATAATATAAACAACAAAATAATTACAACTTAACTGATTAA
AATAAAATAAACGCAATCTATAACATTAAACTAGCCAATGGTTTGTTTAAAGATATAATAATAAT
GTAAACGATAAAATAAAATGTGTGCAATTTATTACGTTAAATTAAC
Found at i:482938 original size:99 final size:99
Alignment explanation
Indices: 482687--482965 Score: 364
Period size: 99 Copynumber: 2.8 Consensus size: 99
482677 TAAAATGTGT
* * **
482687 GCAATTTATTACGTTAAATTAACTACCGGTTTGTTTAAAGGTATAATAATAATATAAACGACAAA
1 GCAATCTATTACGTTAAATTAGCTACCGGTTTGTTTAAAGGTATAATAATAATATAAACGGTAAA
* *
482752 ATATTTACAACTTAACTGGTTAAAATAAAATAGAC
66 ATATTTACAACTTAACAGG-TAAAATAAAATAAAC
* * ** * *
482787 GCAATCTATAACATTAAATTAGCTAATGGTTTGTTTAAAGGTATAATAATAATTTAAATGGTAAA
1 GCAATCTATTACGTTAAATTAGCTACCGGTTTGTTTAAAGGTATAATAATAATATAAACGGTAAA
*
482852 ATATTTACCACTTAACCAGG-AAAATAAAATAAAC
66 ATATTTACAACTTAA-CAGGTAAAATAAAATAAAC
* * * *
482886 GCAA-CATATTACGTTAAACTAGCTACCGGTTAGTTTGAAGGTATAATAATAATGTAAACGGTAA
1 GCAATC-TATTACGTTAAATTAGCTACCGGTTTGTTTAAAGGTATAATAATAATATAAACGGTAA
482950 AATATTTACAACTTAA
65 AATATTTACAACTTAA
482966 TAATTTGAAA
Statistics
Matches: 154, Mismatches: 23, Indels: 5
0.85 0.13 0.03
Matches are distributed among these distances:
98 1 0.01
99 81 0.53
100 69 0.45
101 3 0.02
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.32
Consensus pattern (99 bp):
GCAATCTATTACGTTAAATTAGCTACCGGTTTGTTTAAAGGTATAATAATAATATAAACGGTAAA
ATATTTACAACTTAACAGGTAAAATAAAATAAAC
Found at i:490614 original size:21 final size:21
Alignment explanation
Indices: 490590--490651 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
490580 TCAACAATGC
490590 TTTTTATTTTTATAATTAAGA
1 TTTTTATTTTTATAATTAAGA
*
490611 TTTTTAATTTTT-TAATTTTA-A
1 TTTTT-ATTTTTATAA-TTAAGA
* *
490632 TTTTTCTTTTCATAATTAAG
1 TTTTTATTTTTATAATTAAG
490652 GCCCTTAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
20 7 0.21
21 17 0.52
22 9 0.27
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (21 bp):
TTTTTATTTTTATAATTAAGA
Found at i:490704 original size:43 final size:43
Alignment explanation
Indices: 490643--491252 Score: 439
Period size: 43 Copynumber: 14.1 Consensus size: 43
490633 TTTTCTTTTC
* * * *
490643 ATAATTAAGGCCCTTAATTTTTATAATCTCACTATTTACCTTT
1 ATAATTGAGACCCTTAATTTTTTTAATCTCACTTTTTACCTTT
* * * *
490686 ACAATTGAGACCCTTAATTTTTTCAATCTAAGTTTTTACCTTT
1 ATAATTGAGACCCTTAATTTTTTTAATCTCACTTTTTACCTTT
* * * *
490729 ATAATCGA-AGCCCCTAATTTTTTTTATTCTCACTTTTTAACTTT
1 ATAATTGAGA-CCCTTAA-TTTTTTTAATCTCACTTTTTACCTTT
* * * * *
490773 ATAATTGAGATCAC-TAGTTTTTCTAATC-CAACTGTTTACTTTT
1 ATAATTGAGA-CCCTTAATTTTTTTAATCTC-ACTTTTTACCTTT
* * * *
490816 ATAATTGAGGCCCCTAATTTTTTTCAATCTCACTTTCTAACTTT
1 ATAATTGAGACCCTTAATTTTTTT-AATCTCACTTTTTACCTTT
* * *
490860 ATAATTGA-AGCCTTTAATTTTTTTAATCTTATTTTTTACCTTT
1 ATAATTGAGA-CCCTTAATTTTTTTAATCTCACTTTTTACCTTT
* *** * * * *
490903 ATAATTAAGGTTCATAATTTTTTCAATCTCACTTTCTATCTTT
1 ATAATTGAGACCCTTAATTTTTTTAATCTCACTTTTTACCTTT
* *
490946 ATAATTGAAGTCCC-TAATTTTTTTAATCTCACTTTTTACTTTT
1 ATAATTG-AGACCCTTAATTTTTTTAATCTCACTTTTTACCTTT
* * * *
490989 ATAATTGATG--TCTTAATTTTTTACAAT-TCCACCTTTTATCTTT
1 ATAATTGA-GACCCTTAATTTTTT-TAATCT-CACTTTTTACCTTT
*
491032 ATAATTGAAGTCCC-TAATTTTTTTAATCTCATCTTTTATA--TTT
1 ATAATTG-AGACCCTTAATTTTTTTAATCTCA-CTTTT-TACCTTT
* *
491075 ATAATTGGGCCCCTTAAATTTTTTTAATCTCACTTTTTACCTTT
1 ATAATTGAGACCCTT-AATTTTTTTAATCTCACTTTTTACCTTT
* * * *
491119 ATAAGTAAGGTCCC-TAATTTTTTCAATCTCA-TTTTCTACCTTT
1 ATAATTGA-GACCCTTAATTTTTTTAATCTCACTTTT-TACCTTT
* * *
491162 ATAATTCA-AGCCCCTAA--TTTTTAATCTCACTTTTTAGCTTT
1 ATAATTGAGA-CCCTTAATTTTTTTAATCTCACTTTTTACCTTT
* * *
491203 ATAATTGA-AGCTCC-CAATTTTTATAATC-CAACTTTTTTACTTTT
1 ATAATTGAGA-C-CCTTAATTTTTTTAATCTC-AC-TTTTTACCTTT
491247 ATAATT
1 ATAATT
491253 TAGGCCCCTA
Statistics
Matches: 449, Mismatches: 84, Indels: 67
0.75 0.14 0.11
Matches are distributed among these distances:
41 30 0.07
42 35 0.08
43 252 0.56
44 121 0.27
45 11 0.02
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.50
Consensus pattern (43 bp):
ATAATTGAGACCCTTAATTTTTTTAATCTCACTTTTTACCTTT
Found at i:490780 original size:87 final size:84
Alignment explanation
Indices: 490643--491210 Score: 472
Period size: 87 Copynumber: 6.6 Consensus size: 84
490633 TTTTCTTTTC
* * * * *
490643 ATAATT-AAGGCCCTTAATTTTTATAATCTCACTATTTACCTTTACAATTGAGACCCTTAATTTT
1 ATAATTGAA-GCCCCTAATTTTTTTAATCTCACTTTTTAACTTTATAATTGAGACCC-TAATTTT
*
490707 TTCAATCTAAGTTTTTACCTTT
64 TTCAATCTCA-TTTTTACCTTT
* * * *
490729 ATAATCGAAGCCCCTAATTTTTTTTATTCTCACTTTTTAACTTTATAATTGAGATCACT-AGTTT
1 ATAATTGAAGCCCCTAA-TTTTTTTAATCTCACTTTTTAACTTTATAATTGAGA-CCCTAATTTT
* *
490793 TTCTAATC-CAACTGTTTACTTTT
64 TTC-AATCTC-A-TTTTTACCTTT
* * *
490816 ATAATTGAGGCCCCTAATTTTTTTCAATCTCACTTTCTAACTTTATAATTGA-AGCCTTTAATTT
1 ATAATTGAAGCCCCTAATTTTTTT-AATCTCACTTTTTAACTTTATAATTGAGA-CC-CTAATTT
* *
490880 TTTTAATCTTATTTTTTACCTTT
63 TTTCAATCTCA-TTTTTACCTTT
** * * * * *
490903 ATAATT-AAGGTTCATAATTTTTTCAATCTCACTTTCTATCTTTATAATTGAAGTCCCTAATTTT
1 ATAATTGAA-GCCCCTAATTTTTTTAATCTCACTTTTTAACTTTATAATTG-AGACCCTAATTTT
* *
490967 TTTAATCTCACTTTTTACTTTT
64 TTCAATCTCA-TTTTTACCTTT
* * * * * * *
490989 ATAATTGATG-TCTTAATTTTTTACAAT-TCCACCTTTTATCTTTATAATTGAAGTCCCTAATTT
1 ATAATTGAAGCCCCTAATTTTTT-TAATCT-CACTTTTTAACTTTATAATTG-AGACCCTAATTT
* **
491052 TTTTAATCTCATCTTTTATATTT
63 TTTCAATCTCAT-TTTTACCTTT
* * * * *
491075 ATAATTG-GGCCCCTTAAATTTTTTTAATCTCACTTTTTACCTTTATAAGTAAGGTCCCTAATTT
1 ATAATTGAAGCCCC-T-AATTTTTTTAATCTCACTTTTTAACTTTATAATTGA-GACCCTAATTT
491139 TTTCAATCTCATTTTCTACCTTT
63 TTTCAATCTCATTTT-TACCTTT
* *
491162 ATAATTCAAGCCCCTAA--TTTTTAATCTCACTTTTTAGCTTTATAATTGA
1 ATAATTGAAGCCCCTAATTTTTTTAATCTCACTTTTTAACTTTATAATTGA
491211 AGCTCCCAAT
Statistics
Matches: 400, Mismatches: 59, Indels: 48
0.79 0.12 0.09
Matches are distributed among these distances:
84 29 0.07
85 14 0.04
86 156 0.39
87 179 0.45
88 22 0.05
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.50
Consensus pattern (84 bp):
ATAATTGAAGCCCCTAATTTTTTTAATCTCACTTTTTAACTTTATAATTGAGACCCTAATTTTTT
CAATCTCATTTTTACCTTT
Found at i:492277 original size:17 final size:18
Alignment explanation
Indices: 492240--492280 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
492230 ATATTATGTA
*
492240 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
492258 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
492275 TTTACT
1 TTTACT
492281 AATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:498547 original size:26 final size:27
Alignment explanation
Indices: 498510--498562 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
498500 TTAAATATTA
498510 AACATTTAC-TTTATCAG-GAGAAAAC
1 AACATTTACTTTTATCAGAGAGAAAAC
*
498535 AACACTTTCCTTTTATCAGAAGAGAAAA
1 AACA-TTTACTTTTATCAG-AGAGAAAA
498563 TCGCCTTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 8 0.35
29 7 0.30
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.28
Consensus pattern (27 bp):
AACATTTACTTTTATCAGAGAGAAAAC
Done.