Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold122
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: 766530
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.29
Warning! 93190 characters in sequence are not A, C, G, or T
File 4 of 5
Found at i:563786 original size:33 final size:33
Alignment explanation
Indices: 563749--563813 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
563739 TACCACTGTT
*
563749 TGTATCGATACATGGT-ACATTGTATCGATACAA
1 TGTATCGATACATGATGA-ATTGTATCGATACAA
563782 TGTATCGATACATGATGAATTGTATCGATACA
1 TGTATCGATACATGATGAATTGTATCGATACA
563814 TTACTTCTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATGATGAATTGTATCGATACAA
Found at i:564518 original size:20 final size:21
Alignment explanation
Indices: 564493--564531 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
564483 TTCCCGTGTA
564493 GATGTATCGATACA-ATTTTT
1 GATGTATCGATACATATTTTT
564513 GATGTATCGATACATATTT
1 GATGTATCGATACATATTT
564532 GAAAATATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (21 bp):
GATGTATCGATACATATTTTT
Found at i:564604 original size:13 final size:13
Alignment explanation
Indices: 564586--564611 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
564576 CAATTTTTTG
564586 TGTATCGATACAT
1 TGTATCGATACAT
564599 TGTATCGATACAT
1 TGTATCGATACAT
564612 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:565359 original size:21 final size:21
Alignment explanation
Indices: 565318--565361 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
565308 CTCCCCTTTA
* *
565318 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
565339 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
565360 TC
1 TC
565362 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:567182 original size:13 final size:13
Alignment explanation
Indices: 567164--567202 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
567154 ATAATCACCC
567164 TGTATCGATACAA
1 TGTATCGATACAA
567177 TGTATCGATACAA
1 TGTATCGATACAA
*
567190 TGTATCAATACAA
1 TGTATCGATACAA
567203 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:571147 original size:21 final size:21
Alignment explanation
Indices: 571118--571162 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
571108 AAGTTTTCAT
*
571118 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
571138 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
571160 TTT
1 TTT
571163 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:573396 original size:13 final size:13
Alignment explanation
Indices: 573378--573403 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
573368 CAATTTTTTG
573378 TGTATCGATACAT
1 TGTATCGATACAT
573391 TGTATCGATACAT
1 TGTATCGATACAT
573404 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:574088 original size:29 final size:29
Alignment explanation
Indices: 574055--574112 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
574045 GTTATTTTTC
574055 GAAAGCTCCTTTGTATTTGTTTTGAGCTT
1 GAAAGCTCCTTTGTATTTGTTTTGAGCTT
574084 GAAAGCTCCTTTGTATTTGTTTTGAGCTT
1 GAAAGCTCCTTTGTATTTGTTTTGAGCTT
574113 ACCTTTCCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (29 bp):
GAAAGCTCCTTTGTATTTGTTTTGAGCTT
Found at i:574108 original size:23 final size:24
Alignment explanation
Indices: 574049--574106 Score: 62
Period size: 29 Copynumber: 2.2 Consensus size: 24
574039 ATTGTTGTTA
574049 TTTTTCGAAAGCTCCTTTGTATTTG
1 TTTTT-GAAAGCTCCTTTGTATTTG
574074 TTTTGAGCTTGAAAGCTCCTTTGTATTTG
1 -TTT----TTGAAAGCTCCTTTGTATTTG
574103 TTTT
1 TTTT
574107 GAGCTTACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
24 1 0.04
26 3 0.11
28 3 0.11
29 19 0.68
30 2 0.07
ACGTcount: A:0.16, C:0.14, G:0.17, T:0.53
Consensus pattern (24 bp):
TTTTTGAAAGCTCCTTTGTATTTG
Found at i:576664 original size:13 final size:13
Alignment explanation
Indices: 576646--576673 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
576636 GCCAAGGAAA
576646 TGTATCGATACAT
1 TGTATCGATACAT
576659 TGTATCGATACAT
1 TGTATCGATACAT
576672 TG
1 TG
576674 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:580562 original size:34 final size:32
Alignment explanation
Indices: 580522--580589 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
580512 AGGTCAGATC
580522 AAATGTTTAACTATGTTT-AAAAATTATATGCCCA
1 AAATGTTTAA-T-T-TTTGAAAAATTATATGCCCA
* *
580556 AAATGTTTAATTTTTGAATAATTATATGCTCA
1 AAATGTTTAATTTTTGAAAAATTATATGCCCA
580588 AA
1 AA
580590 TGAGTCATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 3 0.10
32 17 0.55
33 1 0.03
34 10 0.32
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (32 bp):
AAATGTTTAATTTTTGAAAAATTATATGCCCA
Found at i:586223 original size:73 final size:74
Alignment explanation
Indices: 586141--586279 Score: 185
Period size: 74 Copynumber: 1.9 Consensus size: 74
586131 TTATAAAATA
* * *
586141 AATTTCATTT-ACCAAAAT-TTTTCAATAGAGTT-AAAATTCTTATTTATAAGTGTGATAAATCT
1 AATTTCATTTGACC-AAATCTTTT-AATAGAATTAAAAATTCTTATTAATAAGTATGATAAATCT
586203 TATTTTCTAAT
64 TATTTTCTAAT
* * *
586214 AATTTCATTTGACCAAATCTTTTAATATAATTAAAAATTTTTATTAATAATTATGATAAATCTTA
1 AATTTCATTTGACCAAATCTTTTAATAGAATTAAAAATTCTTATTAATAAGTATGATAAATCTTA
586279 T
66 T
586280 ATTAAGAATA
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
73 21 0.37
74 36 0.63
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (74 bp):
AATTTCATTTGACCAAATCTTTTAATAGAATTAAAAATTCTTATTAATAAGTATGATAAATCTTA
TTTTCTAAT
Found at i:586402 original size:2 final size:2
Alignment explanation
Indices: 586390--586443 Score: 78
Period size: 2 Copynumber: 28.5 Consensus size: 2
586380 GATATAGCTA
*
586390 AT AT A- AT AT AT AT -T AT AG AT A- 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 AT AT AT AT
586429 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
586444 AATGGAAATG
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
1 3 0.06
2 44 0.94
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:586603 original size:18 final size:18
Alignment explanation
Indices: 586582--586630 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
586572 ATTTTTATAT
586582 AAATTTATTTAATTGATA
1 AAATTTATTTAATTGATA
* *
586600 AAATTTATCTAATTTATA
1 AAATTTATTTAATTGATA
*
586618 AAA-ATATTTAATT
1 AAATTTATTTAATT
586631 CAATATAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 8 0.30
18 19 0.70
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
AAATTTATTTAATTGATA
Found at i:594777 original size:22 final size:25
Alignment explanation
Indices: 594749--594796 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 25
594739 TTTTGATTTG
594749 AATTTAAA-A-AATTTGA-TTAATT
1 AATTTAAATAGAATTTGATTTAATT
594771 AATTTAAATATGAATTTGATTTAATT
1 AATTTAAATA-GAATTTGATTTAATT
594797 TAAATTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 1 0.05
25 7 0.32
26 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (25 bp):
AATTTAAATAGAATTTGATTTAATT
Found at i:594797 original size:22 final size:20
Alignment explanation
Indices: 594740--594801 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 20
594730 GTTTGTCAAT
594740 TTTGATTTGAATTTAAA-AAA
1 TTTGATTT-AATTTAAATAAA
594760 TTTGATTAATTAATTTAAATATGAA
1 TTTGA-T--TTAATTTAAATA--AA
594785 TTTGATTTAATTTAAAT
1 TTTGATTTAATTTAAAT
594802 TAATAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
20 5 0.14
21 1 0.03
22 19 0.53
23 3 0.08
24 1 0.03
25 7 0.19
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (20 bp):
TTTGATTTAATTTAAATAAA
Found at i:594866 original size:16 final size:16
Alignment explanation
Indices: 594832--594933 Score: 105
Period size: 16 Copynumber: 6.3 Consensus size: 16
594822 CAAAATTGAT
594832 TAATTTGAATTTAAAAA
1 TAATTTGAATTT-AAAA
*
594849 TAATTTAAATTTAAAA
1 TAATTTGAATTTAAAA
*
594865 TAATTTAAATTTAAAA
1 TAATTTGAATTTAAAA
* * *
594881 TGATTCGAATTTTAAA
1 TAATTTGAATTTAAAA
*
594897 TTATTTGAATTTAAAA
1 TAATTTGAATTTAAAA
* * * *
594913 TGATTCGAATCTGAAA
1 TAATTTGAATTTAAAA
594929 TAATT
1 TAATT
594934 AAAATAATTA
Statistics
Matches: 72, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
16 61 0.85
17 11 0.15
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (16 bp):
TAATTTGAATTTAAAA
Found at i:595764 original size:16 final size:17
Alignment explanation
Indices: 595730--595785 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 17
595720 CTGAATTCAG
* *
595730 AATAACTCAAAC-CTAA
1 AATAATTCAAACTCGAA
*
595746 AATAATTCGAACTCG-A
1 AATAATTCAAACTCGAA
*
595762 AATGATTCAAACTCGAA
1 AATAATTCAAACTCGAA
595779 AATAATT
1 AATAATT
595786 AAAAAATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
16 24 0.75
17 8 0.25
ACGTcount: A:0.50, C:0.18, G:0.07, T:0.25
Consensus pattern (17 bp):
AATAATTCAAACTCGAA
Found at i:596803 original size:5 final size:5
Alignment explanation
Indices: 596757--596793 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
596747 CCTGCTTCGG
*
596757 AGAAA AGAAA AGAAC AGAAA AGAAA AGAAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AG-AAA AGAAA A
596794 TAGAAGAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:597191 original size:14 final size:14
Alignment explanation
Indices: 597151--597192 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
597141 TTTAAATTAG
*
597151 ATAAAATTTAAAAA
1 ATAAAATATAAAAA
597165 ATAAAATA-AAAAA
1 ATAAAATATAAAAA
*
597178 TATAAAAGATAAAAA
1 -ATAAAATATAAAAA
597193 GTAGTTAGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 5 0.21
14 14 0.58
15 5 0.21
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (14 bp):
ATAAAATATAAAAA
Found at i:597686 original size:80 final size:81
Alignment explanation
Indices: 597551--597707 Score: 237
Period size: 80 Copynumber: 2.0 Consensus size: 81
597541 ATCAAGGATA
* *
597551 TAATAATTGTCCCTTAATTTAAAAATATTATAAAGTGATCGGACTTAAATAGAGTGAAATTAATT
1 TAATAATTGTCCCTTAATCTAAAAAGATTATAAAGTGATCGGACTTAAATAGAGTGAAATTAATT
597616 ACGCGATGATCGGGTT
66 ACGCGATGATCGGGTT
* * * *
597632 TAATAATTGTTCCTTAATCT-AAAGGATTATAAAGTGATCAGG-CTTAGATCGAGTGAAATTAAT
1 TAATAATTGTCCCTTAATCTAAAAAGATTATAAAGTGATC-GGACTTAAATAGAGTGAAATTAAT
597695 TACGCGATGATCG
65 TACGCGATGATCG
597708 CCAAAGGTGA
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
80 49 0.71
81 20 0.29
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (81 bp):
TAATAATTGTCCCTTAATCTAAAAAGATTATAAAGTGATCGGACTTAAATAGAGTGAAATTAATT
ACGCGATGATCGGGTT
Found at i:601400 original size:54 final size:54
Alignment explanation
Indices: 601340--601450 Score: 159
Period size: 54 Copynumber: 2.1 Consensus size: 54
601330 CTATAAGTGG
* * * * *
601340 CTTGGTGTCATAAATAGTGATGCCAAGGTGGCGATCAGAAGTTGCTAAGAATGA
1 CTTGGTGTCATAAATAATAATGCCAAGGTGGCAATCAAAAGTTGCTAACAATGA
* *
601394 CTTGGTGTCATAGATAATAATGCCAAGGTGGCAATCAAAAGTTGCTACCAATGA
1 CTTGGTGTCATAAATAATAATGCCAAGGTGGCAATCAAAAGTTGCTAACAATGA
601448 CTT
1 CTT
601451 ATTATCATAG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.27
Consensus pattern (54 bp):
CTTGGTGTCATAAATAATAATGCCAAGGTGGCAATCAAAAGTTGCTAACAATGA
Found at i:601459 original size:54 final size:54
Alignment explanation
Indices: 601359--601463 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 54
601349 ATAAATAGTG
* * * * *
601359 ATGCCAAGGTGGCGATCAGAAGTTGCTAAGAATGACTTGGTGTCATAGATAATA
1 ATGCCAAGGTGGCAATCAAAAGTTGCTAACAATGACTTAGTATCATAGATAATA
* *
601413 ATGCCAAGGTGGCAATCAAAAGTTGCTACCAATGACTTATTATCATAGATA
1 ATGCCAAGGTGGCAATCAAAAGTTGCTAACAATGACTTAGTATCATAGATA
601464 GTATGTACGG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (54 bp):
ATGCCAAGGTGGCAATCAAAAGTTGCTAACAATGACTTAGTATCATAGATAATA
Found at i:608141 original size:3 final size:3
Alignment explanation
Indices: 608133--608162 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
608123 ATTTAGTGGA
608133 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
608163 TTCATTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:613286 original size:20 final size:20
Alignment explanation
Indices: 613261--613315 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
613251 ATTTTAACTA
613261 GATGTATCGATACATTATTC
1 GATGTATCGATACATTATTC
613281 GATGTATCGATACATTATTC
1 GATGTATCGATACATTATTC
*
613301 AATGTATCGATACAT
1 GATGTATCGATACAT
613316 CTAGGTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
GATGTATCGATACATTATTC
Found at i:613361 original size:20 final size:20
Alignment explanation
Indices: 613336--613386 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
613326 AGACAGAATA
613336 TATCGATACATTAAAAAATG
1 TATCGATACATTAAAAAATG
* * *
613356 TATCGATACATTCATACATG
1 TATCGATACATTAAAAAATG
613376 TATCGATACAT
1 TATCGATACAT
613387 CTGGGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (20 bp):
TATCGATACATTAAAAAATG
Found at i:615877 original size:65 final size:64
Alignment explanation
Indices: 615585--616122 Score: 487
Period size: 61 Copynumber: 8.5 Consensus size: 64
615575 AAGAGCAGGA
* * * * * *
615585 TGCCTTTTTCTTTTAAAGCCCACACGAGTTAGTGACACCTTTTAGTCCTCAAAGAGC-AG-GA-
1 TGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAAGACAC
* * ** * * * * *
615646 TGTCTTTTTCCTTTTAAAGCCCATATGAGTTGGTGACACCTTTTAGTCTTCAAAAAGCATG--AC
1 TG-CCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAAGACAC
* * * * * *
615709 T-CTTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTAAATCCTCAAAGAGCAAG--A-
1 TGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAAGACAC
* * *
615769 TGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTATTCCTCAAATAGCAAGACAC
1 TGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAAGACAC
* * ** * * * *
615833 TTTCCTTTTTCTTTTAAAATCTACATAAGTTGGTAGCACTTTTTAGTCCTCAAAGAGCAGGACAC
1 -TGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAAGACAC
* ** * *
615898 TCGCCTTTTCCTTTTAAAGCCCACACAAGCTGAAGGCACCTTTTAGTCCTTAAAGAGCAAG--A-
1 T-GCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAAGACAC
*
615960 TGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGACAC
1 TGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAAGACAC
* * *
616024 T-CACTTTTTCCTTTTAAAGCCTACACAAGTTGGTGGCACTCCTTCTCAGTCCTCAAAGAGTAAG
1 TGC-C-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACT--TT-TTAGTCCTCAAAGAGCAAG
616088 ACA-
61 ACAC
* * * *
616091 T--TTTTTCCTTTTAAACCCCACATAAGGTGGTG
1 TGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTG
616123 ACACCTCTTA
Statistics
Matches: 398, Mismatches: 62, Indels: 31
0.81 0.13 0.06
Matches are distributed among these distances:
60 1 0.00
61 157 0.39
62 50 0.13
63 6 0.02
64 29 0.07
65 133 0.33
67 3 0.01
68 19 0.05
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.33
Consensus pattern (64 bp):
TGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAAGACAC
Found at i:615960 original size:191 final size:186
Alignment explanation
Indices: 615572--616112 Score: 601
Period size: 191 Copynumber: 2.9 Consensus size: 186
615562 ACCTTTTTTT
* * * * *
615572 TTAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACGAGTTAGTGACACCTTTTAGTCCTCAA
1 TTAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAA
* * * * * *
615637 AGAGC-AG-GA-TGT-CTTTTTCCTTTTAAAGCCCATATGAGTTGGTGACACCTTTTAGTCTTCA
66 AGAGCAAGACACT-TCCTTTTTCCTTTTAAAGCCTACATAAGTTGGTG-CACTTTTTAGTCCTCA
* * * * * * **
615698 AAAAGCATGACTCTTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTAAATCC
129 AAGAGCAGGACTCCTTTTCCTTTTAAAGCCCACACAAGCTGAAGGCACCTTTAAATCC
* *
615756 TCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTATTCCTCAA
1 TTAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAA
* **
615821 ATAGCAAGACACTTTCCTTTTT-CTTTTAAAATCTACATAAGTTGGTAGCACTTTTTAGTCCTCA
66 AGAGCAAGACAC-TTCCTTTTTCCTTTTAAAGCCTACATAAGTTGGT-GCACTTTTTAGTCCTCA
* *
615885 AAGAGCAGGACACTCGCCTTTTCCTTTTAAAGCCCACACAAGCTGAAGGCACCTTTTAGTCC
129 AAGAGCAGG--ACT--CCTTTTCCTTTTAAAGCCCACACAAGCTGAAGGCACCTTTAAATCC
*
615947 TTAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAA
1 TTAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAA
* * *
616012 AGAGCAGGACAC-TCACTTTTTCCTTTTAAAGCCTACACAAGTTGGTGGCACTCCTTCTCAGTCC
66 AGAGCAAGACACTTC-CTTTTTCCTTTTAAAGCCTACATAAGTTGGT-GCACT--TT-TTAGTCC
* * * *
616076 TCAAAGAGTAAGACAT-TTTTTCCTTTTAAACCCCACA
126 TCAAAGAGCAGGAC-TCCTTTTCCTTTTAAAGCCCACA
616113 TAAGGTGGTG
Statistics
Matches: 301, Mismatches: 40, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
184 62 0.21
185 2 0.01
186 1 0.00
187 41 0.14
188 8 0.03
189 5 0.02
190 25 0.08
191 136 0.45
192 2 0.01
193 3 0.01
194 16 0.05
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.33
Consensus pattern (186 bp):
TTAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAA
AGAGCAAGACACTTCCTTTTTCCTTTTAAAGCCTACATAAGTTGGTGCACTTTTTAGTCCTCAAA
GAGCAGGACTCCTTTTCCTTTTAAAGCCCACACAAGCTGAAGGCACCTTTAAATCC
Found at i:615974 original size:126 final size:125
Alignment explanation
Indices: 615552--616136 Score: 552
Period size: 126 Copynumber: 4.7 Consensus size: 125
615542 GTTCAATTCG
** * *
615552 AGTTGGTGGCACCTTTT--TTTTTAAAGAGCAGGA-TGCCTTTTTCTTTTAAAGCCCACACGAGT
1 AGTTGGTGGCACCTTTTAGTCCTTAAAGAGCAAGACTGCCTTTTTCTTTTAAAGCCCACACAAGT
* * * * **
615614 TAGTGACACCTTTTAGTCCTCAAAGAGCAGG--ATGTCTTTTTCCTTTTAAAGCCCATATG
66 TGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACATG-CCTTTTCCTTTTAAAGCCCACACA
* * * * *
615673 AGTTGGTGACACCTTTTAGT-CTTCAAAAAGCATGACT-CTTTTTTCTTTTAAAGCCCACACGAG
1 AGTTGGTGGCACCTTTTAGTCCTT-AAAGAGCAAGACTGCCTTTTTCTTTTAAAGCCCACACAAG
* * *
615736 TTGGTGGCACCTTTAAATCCTCAAAGAGCA--AGATGCCTTTTCCTTTTAAAGCCCACACA
65 TTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACATGCCTTTTCCTTTTAAAGCCCACACA
* * * * ** * *
615795 AGTTGGTGGCACCTTTTATTCCTCAAATAGCAAGACACTTTCCTTTTTCTTTTAAAATCTACATA
1 AGTTGGTGGCACCTTTTAGTCCTTAAAGAGCAAG--AC-TGCCTTTTTCTTTTAAAGCCCACACA
* *
615860 AGTTGGTAGCACTTTTTAGTCCTCAAAGAGCAGGACACTCGCCTTTTCCTTTTAAAGCCCACACA
63 AGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACA-T-GCCTTTTCCTTTTAAAGCCCACACA
* ** *
615925 AGCTGAAGGCACCTTTTAGTCCTTAAAGAGCAAGA-TGCCTTTTCCTTTTAAAGCCCACACAAGT
1 AGTTGGTGGCACCTTTTAGTCCTTAAAGAGCAAGACTGCCTTTTTCTTTTAAAGCCCACACAAGT
* *
615989 TGGTGGCACTTTTTAGTCCTCAAAGAGCAGGACACT-CACTTTTTCCTTTTAAAGCCTACACA
66 TGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACA-TGC-C-TTTTCCTTTTAAAGCCCACACA
* * * *
616051 AGTTGGTGGCACTCCTTCTCAGTCCTCAAAGAGTAAGACAT---TTTTTCCTTTTAAACCCCACA
1 AGTTGGTGGCA--CCTT-TTAGTCCTTAAAGAGCAAGAC-TGCCTTTTT-CTTTTAAAGCCCACA
* * * *
616113 TAAGGTGGTGACACCTCTTA-TCCT
61 CAAGTTGGTGGCACCTTTTAGTCCT
616137 TTCAATTCTC
Statistics
Matches: 385, Mismatches: 56, Indels: 39
0.80 0.12 0.08
Matches are distributed among these distances:
121 16 0.04
122 48 0.12
123 66 0.17
124 4 0.01
125 2 0.01
126 133 0.35
128 15 0.04
129 47 0.12
130 53 0.14
131 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.33
Consensus pattern (125 bp):
AGTTGGTGGCACCTTTTAGTCCTTAAAGAGCAAGACTGCCTTTTTCTTTTAAAGCCCACACAAGT
TGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACATGCCTTTTCCTTTTAAAGCCCACACA
Found at i:616221 original size:67 final size:68
Alignment explanation
Indices: 616025--616310 Score: 271
Period size: 69 Copynumber: 4.2 Consensus size: 68
616015 GCAGGACACT
* * * * *
616025 CACTTTTTCCTTTTAAAGCCTACACAAGTTGGTGGCACTCCT-T-C--TCAGTCCTCAAAGAGTA
1 CACTTTTTCTTTTTAAAGCCTACACAAGCTGGTGACACTCTTATCCTTTCAGTCCTCAAAGAGCA
616086 AGA
66 AGA
* * * * * * * *
616089 CATTTTTTCCTTTTAAACCCCACATAAGGTGGTGACACCTCTTATCCTTTCAATTCTCAAAGAGC
1 CACTTTTTCTTTTTAAAGCCTACACAAGCTGGTGACA-CTCTTATCCTTTCAGTCCTCAAAGAGC
*
616154 ATGA
65 AAGA
* * *
616158 CACTTTTTCTTTTTAAAGCC-ACACGAGCTGGTGGCACAT-TTATCCTTTCAGTCATCAAAGAGC
1 CACTTTTTCTTTTTAAAGCCTACACAAGCTGGTGACAC-TCTTATCCTTTCAGTCCTCAAAGAGC
616221 AAGA
65 AAGA
** * * *
616225 TGCTTTTTCTTTTTAAAGCCTACACAAGCTGGCGACATCTCTTATCTTTTCATTCCTCAAAGAG-
1 CACTTTTTCTTTTTAAAGCCTACACAAGCTGGTGACA-CTCTTATCCTTTCAGTCCTCAAAGAGC
*
616289 AATGG
65 AA-GA
*
616294 CATTTTTTCTTTTTAAA
1 CACTTTTTCTTTTTAAA
616311 ACTTGCACGA
Statistics
Matches: 178, Mismatches: 34, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
64 31 0.17
65 4 0.02
66 1 0.01
67 44 0.25
68 29 0.16
69 69 0.39
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.36
Consensus pattern (68 bp):
CACTTTTTCTTTTTAAAGCCTACACAAGCTGGTGACACTCTTATCCTTTCAGTCCTCAAAGAGCA
AGA
Found at i:616241 original size:136 final size:133
Alignment explanation
Indices: 616025--616310 Score: 326
Period size: 136 Copynumber: 2.1 Consensus size: 133
616015 GCAGGACACT
* * * *
616025 CACTTTTTCCTTTTAAAGCCTACACAAGTTGGTGGCACTCCTTCTCAGTCCTCAAAGAGTAAGAC
1 CACTTTTTCTTTTTAAAGCCTACACAAGCTGGTGGCACTCCTTCTCAGTCATCAAAGAGCAAGAC
* * * * *
616090 ATTTTTTCCTTTTAAACCCCACATAAGGTGGTGACACCTCTTATCCTTTCAATT-CTCAAAGAGC
66 ACTTTTTCCTTTTAAACCCCACACAAGCTGGCGACACCTCTTATCCTTTC-ATTCCTCAAAGAGA
616154 ATGA
130 ATGA
*
616158 CACTTTTTCTTTTTAAAGCC-ACACGAGCTGGTGGCACATTTATCCTT-TCAGTCATCAAAGAGC
1 CACTTTTTCTTTTTAAAGCCTACACAAGCTGGTGGCAC-----TCCTTCTCAGTCATCAAAGAGC
** * * * * *
616221 AAGATGCTTTTTCTTTTTAAAGCCTACACAAGCTGGCGACATCTCTTATCTTTTCATTCCTCAAA
61 AAGACACTTTTTCCTTTTAAACCCCACACAAGCTGGCGACACCTCTTATCCTTTCATTCCTCAAA
*
616286 GAGAATGG
126 GAGAATGA
*
616294 CATTTTTTCTTTTTAAA
1 CACTTTTTCTTTTTAAA
616311 ACTTGCACGA
Statistics
Matches: 128, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
132 15 0.12
133 19 0.15
135 3 0.02
136 86 0.67
137 5 0.04
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.36
Consensus pattern (133 bp):
CACTTTTTCTTTTTAAAGCCTACACAAGCTGGTGGCACTCCTTCTCAGTCATCAAAGAGCAAGAC
ACTTTTTCCTTTTAAACCCCACACAAGCTGGCGACACCTCTTATCCTTTCATTCCTCAAAGAGAA
TGA
Found at i:618029 original size:37 final size:37
Alignment explanation
Indices: 617979--618053 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
617969 GGCTGGGTCA
*
617979 CGCAATGTTGTTGGAAAGATACGACACCACACCACGT
1 CGCAATATTGTTGGAAAGATACGACACCACACCACGT
618016 CGCAATATTGTTGGAAAGATACGACACCACACCACGT
1 CGCAATATTGTTGGAAAGATACGACACCACACCACGT
618053 C
1 C
618054 TGGAATGTCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.19
Consensus pattern (37 bp):
CGCAATATTGTTGGAAAGATACGACACCACACCACGT
Found at i:619669 original size:3 final size:3
Alignment explanation
Indices: 619661--619688 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
619651 AAAACCATCT
619661 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
619689 TACAATTCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:619924 original size:14 final size:15
Alignment explanation
Indices: 619905--619933 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
619895 ACTTTTATAT
619905 AAAAAA-TATAAATA
1 AAAAAATTATAAATA
619919 AAAAAATTATAAATA
1 AAAAAATTATAAATA
619934 TTAAATTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAAATTATAAATA
Found at i:623247 original size:17 final size:18
Alignment explanation
Indices: 623214--623252 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
623204 AAACTTTGAT
*
623214 TATTAAATAGTAAAAAAA
1 TATTAAAAAGTAAAAAAA
623232 TATTAAAAAG-AAAAAAA
1 TATTAAAAAGTAAAAAAA
623249 TATT
1 TATT
623253 GACTTAACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (18 bp):
TATTAAAAAGTAAAAAAA
Found at i:625528 original size:16 final size:16
Alignment explanation
Indices: 625494--625528 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
625484 TCCAGTTCGG
**
625494 TTTGGTTTTTTTTTTT
1 TTTGGTTTTTTTTCAT
625510 TTTGGTTTTTTTTCAT
1 TTTGGTTTTTTTTCAT
625526 TTT
1 TTT
625529 TTTCAATGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.03, G:0.11, T:0.83
Consensus pattern (16 bp):
TTTGGTTTTTTTTCAT
Found at i:626597 original size:13 final size:13
Alignment explanation
Indices: 626579--626605 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
626569 ACATTATGCT
626579 TTGTATCGATACA
1 TTGTATCGATACA
626592 TTGTATCGATACA
1 TTGTATCGATACA
626605 T
1 T
626606 ATTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:626602 original size:33 final size:32
Alignment explanation
Indices: 626560--626624 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
626550 CACACCCAGA
* *
626560 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCGATACA-TATGCATTGTATCAATACAT
*
626593 TGTATCGATACATATTCATTGTATCAATACAT
1 TGTATCGATACATATGCATTGTATCAATACAT
626625 GGACAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATATGCATTGTATCAATACAT
Found at i:626614 original size:19 final size:19
Alignment explanation
Indices: 626589--626644 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
626579 TTGTATCGAT
*
626589 ACATTGTATCGATACATAT
1 ACATTGTATCGATACATAG
* * *
626608 TCATTGTATCAATACATGG
1 ACATTGTATCGATACATAG
626627 ACAATTGTATCGATACAT
1 AC-ATTGTATCGATACAT
626645 GAAACTGGCA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (19 bp):
ACATTGTATCGATACATAG
Found at i:628980 original size:20 final size:21
Alignment explanation
Indices: 628939--628980 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
628929 TATTAAAAAG
*
628939 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAATAAAGAA
628960 TTAGCTAA-GAAAA-ACAAGAA
1 TTAGCTAATGAAAATA-AAGAA
628980 T
1 T
628981 ACGCATGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 1 0.05
20 10 0.53
21 8 0.42
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (21 bp):
TTAGCTAATGAAAATAAAGAA
Found at i:636287 original size:31 final size:30
Alignment explanation
Indices: 636218--636287 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
636208 TTGGTGATTA
* * *
636218 AGAAATTCAATTTGGATTTAGTTGGTTGCT
1 AGAAATTCAATTTAGATTTAGCTGGTGGCT
636248 AGAGAATTCAATTTAGATTT-GACTGGTGGCT
1 AGA-AATTCAATTTAGATTTAG-CTGGTGGCT
636279 AGGAAATTC
1 A-GAAATTC
636288 TAAATTGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 4 0.12
31 28 0.82
32 2 0.06
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.37
Consensus pattern (30 bp):
AGAAATTCAATTTAGATTTAGCTGGTGGCT
Found at i:637001 original size:31 final size:31
Alignment explanation
Indices: 636960--637029 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
636950 TTGATTTGGA
* *
636960 AATTTCCTAACCGCCAGCCAAATCTAAATTG
1 AATTTGCTAACCGCCAGCCAAATCCAAATTG
* * * *
636991 AATTTGCTAACTGCTAGCCAAATCCAATTTT
1 AATTTGCTAACCGCCAGCCAAATCCAAATTG
637022 AATTTGCT
1 AATTTGCT
637030 GGCGGCTAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (31 bp):
AATTTGCTAACCGCCAGCCAAATCCAAATTG
Found at i:637038 original size:31 final size:31
Alignment explanation
Indices: 636960--637048 Score: 81
Period size: 31 Copynumber: 2.9 Consensus size: 31
636950 TTGATTTGGA
* * * * *
636960 AATTTCCTAACCGCCAGCCAAATCTAAATTG
1 AATTTGCTAACGGCTAGCCAAATCCAATTTG
* *
636991 AATTTGCTAACTGCTAGCCAAATCCAATTTT
1 AATTTGCTAACGGCTAGCCAAATCCAATTTG
** *
637022 AATTTGCTGGCGGCTAG-CAAATTCAAT
1 AATTTGCTAACGGCTAGCCAAATCCAAT
637049 ATTTTGGAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 9 0.19
31 39 0.81
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (31 bp):
AATTTGCTAACGGCTAGCCAAATCCAATTTG
Found at i:637929 original size:13 final size:13
Alignment explanation
Indices: 637911--637941 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
637901 ACATTTCTTC
637911 ATGTATCGATACA
1 ATGTATCGATACA
637924 ATGTATCGATACA
1 ATGTATCGATACA
*
637937 TTGTA
1 ATGTA
637942 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:637929 original size:33 final size:33
Alignment explanation
Indices: 637891--637957 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 33
637881 GTTACAAGCT
637891 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
637924 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
637957 A
1 A
637958 ATAGTGATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:638044 original size:13 final size:13
Alignment explanation
Indices: 638026--638053 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
638016 ATACAATGAA
638026 AATGTATCGATAC
1 AATGTATCGATAC
638039 AATGTATCGATAC
1 AATGTATCGATAC
638052 AA
1 AA
638054 AGCAGCATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:638653 original size:22 final size:20
Alignment explanation
Indices: 638604--638657 Score: 74
Period size: 19 Copynumber: 2.6 Consensus size: 20
638594 CCTTTAAAAA
638604 ATTCTCCCCCTTAAACAATT
1 ATTCTCCCCCTTAAACAATT
*
638624 A-TCTCCCCCTTAAACAGTT
1 ATTCTCCCCCTTAAACAATT
638643 ATCTTCTCCCCCTTA
1 A--TTCTCCCCCTTA
638658 TGTAAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 18 0.60
20 1 0.03
22 11 0.37
ACGTcount: A:0.24, C:0.39, G:0.02, T:0.35
Consensus pattern (20 bp):
ATTCTCCCCCTTAAACAATT
Found at i:640519 original size:13 final size:13
Alignment explanation
Indices: 640501--640529 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
640491 AAATAGTACC
640501 CAATGTATCGATA
1 CAATGTATCGATA
640514 CAATGTATCGATA
1 CAATGTATCGATA
640527 CAA
1 CAA
640530 GGAATGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:646693 original size:33 final size:33
Alignment explanation
Indices: 646651--646714 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 33
646641 GTTACAAGCT
646651 ATGTATCGATACATT-T-CTTCATGTATCGATATA
1 ATGTATCGATACATTGTAC--CATGTATCGATATA
646684 ATGTATCGATACATTGTACCATGTATCGATA
1 ATGTATCGATACATTGTACCATGTATCGATA
646715 CAAATAGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATATA
Found at i:646805 original size:13 final size:13
Alignment explanation
Indices: 646787--646813 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
646777 TACAATGAAT
646787 ATGTATCGATACA
1 ATGTATCGATACA
646800 ATGTATCGATACA
1 ATGTATCGATACA
646813 A
1 A
646814 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:648937 original size:146 final size:146
Alignment explanation
Indices: 648772--649037 Score: 351
Period size: 146 Copynumber: 1.8 Consensus size: 146
648762 TAAACTAATT
*
648772 TACAAATAAAAATAAATCATATC-TTAAAAATTTAAAATCGTATAATCAAACTAAAAAAATAAAT
1 TACAAATAAAAATAAATCAT-TCTTTAAAAATTTAAAATCATATAATCAAACT-AAAAAATAAAT
* * *
648836 TTATACTTCTACCAATAAAAAAAAC-T-ATACCTTAAAAAAATTTAAACT-TATATAATAAAACT
64 TTAAACTTCTACAAATAAAAAAAACTTCATACATTAAAAAAA-TTAAACTCT-TATAATAAAACT
648898 AAAAAATAAATTTAAACTTA
127 AAAAAATAAATTTAAACTTA
* * * * **
648918 TACAAATAAAAATTAATCATTCTTTAAAAATTTAAACTCATATAATTATACTTTAAAATAAATTT
1 TACAAATAAAAATAAATCATTCTTTAAAAATTTAAAATCATATAATCAAACTAAAAAATAAATTT
* * *
648983 AAACTTTTACAAATAAAAATAACTTCATATATTAAAAAAATTAAACTCTTATAAT
66 AAACTTCTACAAATAAAAAAAACTTCATACATTAAAAAAATTAAACTCTTATAAT
649038 CTTTTAAAAA
Statistics
Matches: 103, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
145 32 0.31
146 58 0.56
147 13 0.13
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (146 bp):
TACAAATAAAAATAAATCATTCTTTAAAAATTTAAAATCATATAATCAAACTAAAAAATAAATTT
AAACTTCTACAAATAAAAAAAACTTCATACATTAAAAAAATTAAACTCTTATAATAAAACTAAAA
AATAAATTTAAACTTA
Found at i:648961 original size:72 final size:72
Alignment explanation
Indices: 648772--649037 Score: 286
Period size: 72 Copynumber: 3.6 Consensus size: 72
648762 TAAACTAATT
* * *
648772 TACAAATAAAAATAAATCATATCTT-AAAAATTTAAAATCGTATAATCAAACTAAAAAAATAAAT
1 TACAAATAAAAAT-AATCATATCTTAAAAAATTTAAACTCATATAATAAAACT-AAAAAATAAAT
* *
648836 TTATACTTC
64 TTAAACTTA
* * * *
648845 TACCAATAAAAA-AAACTATACCTTAAAAAAATTTAAACTTATATAATAAAACTAAAAAATAAAT
1 TACAAATAAAAATAATC-ATATCTT-AAAAAATTTAAACTCATATAATAAAACTAAAAAATAAAT
648909 TTAAACTTA
64 TTAAACTTA
* * * **
648918 TACAAATAAAAATTAATCAT-TCTTTAAAAATTTAAACTCATATAATTATACTTTAAAATAAATT
1 TACAAATAAAAA-TAATCATATCTTAAAAAATTTAAACTCATATAATAAAACTAAAAAATAAATT
*
648982 TAAACTTT
65 TAAACTTA
* * *
648990 TACAAATAAAAATAACTTCATATATTAAAAAAATTAAACTCTTATAAT
1 TACAAATAAAAATAA--TCATATCTTAAAAAATTTAAACTCATATAAT
649038 CTTTTAAAAA
Statistics
Matches: 162, Mismatches: 23, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
71 6 0.04
72 59 0.36
73 47 0.29
74 47 0.29
75 3 0.02
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (72 bp):
TACAAATAAAAATAATCATATCTTAAAAAATTTAAACTCATATAATAAAACTAAAAAATAAATTT
AAACTTA
Found at i:649048 original size:72 final size:71
Alignment explanation
Indices: 648772--649058 Score: 201
Period size: 73 Copynumber: 3.9 Consensus size: 71
648762 TAAACTAATT
* * * * * * * *
648772 TACAAATAAAAATAAATCA-TATCTTAAAAATTTAAAATCGTATAATCAAACTAAAAAAATAAAT
1 TACAAATAAAAATTAATCATTAT-TAAAAAAATTAAACTCATATAATTATA-T-TAAAAATAAAT
* *
648836 TTATACTTC
63 TTAAACTTA
* * * * * *
648845 TACCAATAAAAA--AAAC-TATACCTTAAAAAAATTTAAACTTATATAATAAAACTAAAAAATAA
1 TACAAATAAAAATTAATCAT-TA--TTAAAAAAA-TTAAACTCATATAATTATA-TTAAAAATAA
648907 ATTTAAACTTA
61 ATTTAAACTTA
* * * *
648918 TACAAATAAAAATTAATCATTCTTTAAAAATTTAAACTCATATAATTATACTTTAAAATAAATTT
1 TACAAATAAAAATTAATCATTATTAAAAAAATTAAACTCATATAATTATA-TTAAAAATAAATTT
*
648983 AAACTTT
65 AAACTTA
*
648990 TACAAATAAAAA-TAACTTCATATATTAAAAAAATTAAACTCTTATAATCT-T-TTAAAAATAAA
1 TACAAATAAAAATTAA--TCAT-TATTAAAAAAATTAAACTCATATAAT-TATATTAAAAATAAA
649052 TATTAAA
62 T-TTAAA
649059 ACAATTCTCG
Statistics
Matches: 175, Mismatches: 26, Indels: 26
0.77 0.11 0.11
Matches are distributed among these distances:
71 6 0.03
72 60 0.34
73 62 0.35
74 41 0.23
75 5 0.03
76 1 0.01
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (71 bp):
TACAAATAAAAATTAATCATTATTAAAAAAATTAAACTCATATAATTATATTAAAAATAAATTTA
AACTTA
Found at i:649376 original size:13 final size:13
Alignment explanation
Indices: 649358--649405 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 13
649348 CTCAAATAAA
649358 AAAAAATTATTTT
1 AAAAAATTATTTT
*
649371 AAAAAATGTTTTTT
1 AAAAAAT-TATTTT
*
649385 AAAAAATTTATTTA
1 AAAAAA-TTATTTT
649399 AAAAAAT
1 AAAAAAT
649406 AAAAAATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 8 0.27
14 21 0.70
15 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
AAAAAATTATTTT
Found at i:649376 original size:14 final size:14
Alignment explanation
Indices: 649357--649405 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
649347 ACTCAAATAA
649357 AAAAAAATTATTTT
1 AAAAAAATTATTTT
*
649371 -AAAAAATGTTTTTT
1 AAAAAAAT-TATTTT
*
649385 AAAAAATTTA-TTT
1 AAAAAAATTATTTT
649398 AAAAAAAT
1 AAAAAAAT
649406 AAAAAATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
13 17 0.59
14 6 0.21
15 6 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (14 bp):
AAAAAAATTATTTT
Found at i:651942 original size:24 final size:24
Alignment explanation
Indices: 651876--651946 Score: 74
Period size: 24 Copynumber: 2.9 Consensus size: 24
651866 GATTAAATTG
*
651876 TATAATATTAAATATAATTATATAAA
1 TATAATA-TAAA-ATAAATATATAAA
*
651902 TATAATAT-AGATAAA-ATATCAAAA
1 TATAATATAAAATAAATATAT--AAA
651926 TATAATATAAAATAAATATAT
1 TATAATATAAAATAAATATAT
651947 TTTAAAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 4 0.11
23 4 0.11
24 12 0.32
25 7 0.18
26 11 0.29
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (24 bp):
TATAATATAAAATAAATATATAAA
Found at i:651944 original size:16 final size:16
Alignment explanation
Indices: 651884--651968 Score: 64
Period size: 16 Copynumber: 4.9 Consensus size: 16
651874 TGTATAATAT
651884 TAAATATAATTATATAAA
1 TAAATATAA-TATA-AAA
651902 TATAATATAGATA-AAATA
1 TA-AATATA-ATATAAA-A
651920 TCAAAATATAATATAAAA
1 T--AAATATAATATAAAA
* *
651938 TAAATATATTTTAAAA
1 TAAATATAATATAAAA
**
651954 TTTATATAATATAAA
1 TAAATATAATATAAA
651969 TGATTAATAT
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
16 24 0.44
17 2 0.04
18 10 0.18
19 17 0.31
20 2 0.04
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (16 bp):
TAAATATAATATAAAA
Found at i:651999 original size:22 final size:22
Alignment explanation
Indices: 651974--652047 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
651964 ATAAATGATT
*
651974 AATATATAAAT-TTTTTTATATA
1 AATATA-AAATATTTTATATATA
651996 AATATAAAATATTTTATATATA
1 AATATAAAATATTTTATATATA
* * ***
652018 ATTTTAAAATAATAAAATATATA
1 AATATAAAAT-ATTTTATATATA
652041 AATATAA
1 AATATAA
652048 TATAAATATA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
21 4 0.10
22 24 0.57
23 14 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATATAAAATATTTTATATATA
Found at i:652000 original size:20 final size:20
Alignment explanation
Indices: 651977--652015 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
651967 AATGATTAAT
* *
651977 ATATAAATTTTTTTATATAA
1 ATATAAAATATTTTATATAA
651997 ATATAAAATATTTTATATA
1 ATATAAAATATTTTATATA
652016 TAATTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATAAAATATTTTATATAA
Found at i:652014 original size:34 final size:35
Alignment explanation
Indices: 651954--652022 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
651944 TATTTTAAAA
651954 TTTATATAATATAAATGATTAATATATA-AATTTT
1 TTTATATAATATAAATGATTAATATATATAATTTT
*
651988 TTTATATAAATATAAAAT-ATT-TTATATATAATTTT
1 TTTATAT-AATAT-AAATGATTAATATATATAATTTT
652023 AAAATAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
34 13 0.42
35 14 0.45
36 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (35 bp):
TTTATATAATATAAATGATTAATATATATAATTTT
Found at i:652561 original size:29 final size:28
Alignment explanation
Indices: 652513--652569 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
652503 TTAATAATTT
* *
652513 TTATATTTATATTATATTATATTATATAA
1 TTATATTTAAAATATATTATATT-TATAA
*
652542 TTATATTTAAAATATTTTATATTTATAA
1 TTATATTTAAAATATATTATATTTATAA
652570 AATTTTTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
TTATATTTAAAATATATTATATTTATAA
Found at i:652574 original size:16 final size:16
Alignment explanation
Indices: 652511--652575 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 16
652501 ATTTAATAAT
**
652511 TTTTATATTTATATTA
1 TTTTATATTTATAAAA
* *
652527 TATTATA-TTATATAA
1 TTTTATATTTATAAAA
652542 --TTATATTTA-AAATA
1 TTTTATATTTATAAA-A
652556 TTTTATATTTATAAAA
1 TTTTATATTTATAAAA
652572 TTTT
1 TTTT
652576 TATGAATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
13 7 0.17
14 4 0.10
15 7 0.17
16 20 0.49
17 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTATATTTATAAAA
Found at i:657138 original size:13 final size:13
Alignment explanation
Indices: 657120--657144 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
657110 ATTTGTAGAA
657120 TGTATCGATACAG
1 TGTATCGATACAG
657133 TGTATCGATACA
1 TGTATCGATACA
657145 TCGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:659567 original size:51 final size:51
Alignment explanation
Indices: 659496--659784 Score: 380
Period size: 51 Copynumber: 5.6 Consensus size: 51
659486 TTAAGTTTCT
* * * * *
659496 CAATTTTTCAAAATCAGGGATACTCCAACCCCGGTTTTATTTTTAAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACAC
* * * *
659547 TAATTTTCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCGAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACAC
* *
659598 CAATTTTCCATAACCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACAC
* * * *
659649 CAATTTTCTATAATCGGGGATACTCCAACTCCAATTTTATTTCCAAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACAC
* * * * *
659700 CAATTTTCTATAATCGGGGATACTCCAACTCCAACTTTATTTCCAAAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACAC
*
659752 CAATTTTTCATAATCGGGGATACTCCAACCCCG
1 CAATTTTCCATAATCGGGGATACTCCAACCCCG
659785 TTAATCATCG
Statistics
Matches: 212, Mismatches: 25, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
51 176 0.83
52 36 0.17
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.31
Consensus pattern (51 bp):
CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACAC
Found at i:659877 original size:79 final size:79
Alignment explanation
Indices: 659754--659966 Score: 302
Period size: 79 Copynumber: 2.7 Consensus size: 79
659744 AAAAACACCA
* * *** *
659754 ATTTTTCATAATCGGGGATACTCCAACCCCGTTA-ATCATCGGGGATACTCCAACCCTGGCTTTA
1 ATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTA
659818 TTCCTAAAATATTG
66 TTCCTAAAATATTG
*
659832 ATTTCTCATAATCGGGGATACTCTAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTA
1 ATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTA
659897 TTCCTAAAATATTG
66 TTCCTAAAATATTG
* * * * * *
659911 ATTTCTCACAATCGAGGATACTCCAACCCCGTTATTTTCGTGAGAATACTCCAACC
1 ATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACC
659967 TCGCTATTTT
Statistics
Matches: 120, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
78 32 0.27
79 88 0.73
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (79 bp):
ATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTA
TTCCTAAAATATTG
Found at i:659974 original size:28 final size:28
Alignment explanation
Indices: 659923--659996 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
659913 TTCTCACAAT
* * *
659923 CGAGGATACTCCAACCCCGTTATTTTCG
1 CGAGAATACTCCAACCTCGCTATTTTCG
*
659951 TGAGAATACTCCAACCTCGCTATTTTCG
1 CGAGAATACTCCAACCTCGCTATTTTCG
* *
659979 CGGGGATACTCCAACCTC
1 CGAGAATACTCCAACCTC
659997 AATTTTATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27
Consensus pattern (28 bp):
CGAGAATACTCCAACCTCGCTATTTTCG
Found at i:664464 original size:19 final size:19
Alignment explanation
Indices: 664436--664485 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
664426 TAATTCGCTG
* *
664436 TGTATAGATACCAAG-ATCA
1 TGTATCGATACAAAGAAT-A
664455 TGTATCGATACAAAGTAATA
1 TGTATCGATACAAAG-AATA
664475 TGTATCGATAC
1 TGTATCGATAC
664486 TTCTGGGCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 13 0.48
20 12 0.44
21 2 0.07
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
TGTATCGATACAAAGAATA
Found at i:665064 original size:23 final size:23
Alignment explanation
Indices: 665038--665085 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
665028 TTTGTTTAAA
665038 AACAAATTTTTACTAAGAGGTTT
1 AACAAATTTTTACTAAGAGGTTT
665061 AACAAATTTTTACTAAGAGGTTT
1 AACAAATTTTTACTAAGAGGTTT
665084 AA
1 AA
665086 GGTAGATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (23 bp):
AACAAATTTTTACTAAGAGGTTT
Found at i:665162 original size:20 final size:19
Alignment explanation
Indices: 665124--665162 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
665114 TAAAAAACGT
*
665124 TTTCTCCCTCTTAATAAAA
1 TTTCTCCCTCTTAAAAAAA
*
665143 TTTCTTCCCTTTTAAAAAAA
1 TTTC-TCCCTCTTAAAAAAA
665163 ATATGTCTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTCTCCCTCTTAAAAAAA
Found at i:673381 original size:47 final size:47
Alignment explanation
Indices: 673307--673400 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
673297 TCGATAAATA
* *
673307 TATCAATACAATGTCTCATGTATCGATACAAACAGTGGTAGGGTAGC
1 TATCAATACAATATCCCATGTATCGATACAAACAGTGGTAGGGTAGC
* *
673354 TATCGATACAATATCCCATGTATCGATACAAATAGTGGTAGGGTAGC
1 TATCAATACAATATCCCATGTATCGATACAAACAGTGGTAGGGTAGC
673401 AACTACCAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (47 bp):
TATCAATACAATATCCCATGTATCGATACAAACAGTGGTAGGGTAGC
Found at i:673472 original size:13 final size:13
Alignment explanation
Indices: 673454--673478 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
673444 ACCAAGATCA
673454 TGTATCGATACAG
1 TGTATCGATACAG
673467 TGTATCGATACA
1 TGTATCGATACA
673479 AAGCAATATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:673477 original size:32 final size:32
Alignment explanation
Indices: 673434--673497 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
673424 ACAATTCGCT
*
673434 GTGTATAGATACCAAG-ATCATGTATCGATACA
1 GTGTATAGATACAAAGAAT-ATGTATCGATACA
*
673466 GTGTATCGATACAAAGCAATATGTATCGATAC
1 GTGTATAGATACAAAG-AATATGTATCGATAC
673498 TTCTGGGCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 14 0.50
33 12 0.43
34 2 0.07
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (32 bp):
GTGTATAGATACAAAGAATATGTATCGATACA
Found at i:673889 original size:20 final size:21
Alignment explanation
Indices: 673852--673903 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
673842 GACAGGTCCA
* * *
673852 GTATCGATAAATTCACTTA-T
1 GTATCAATACATTAACTTATT
673872 GTATCAATACATTAACTTATT
1 GTATCAATACATTAACTTATT
673893 GTATCAATACA
1 GTATCAATACA
673904 AATTATAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (21 bp):
GTATCAATACATTAACTTATT
Found at i:677063 original size:13 final size:13
Alignment explanation
Indices: 677045--677071 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
677035 ACATTATGCT
677045 TTGTATCGATACA
1 TTGTATCGATACA
677058 TTGTATCGATACA
1 TTGTATCGATACA
677071 T
1 T
677072 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:677157 original size:13 final size:13
Alignment explanation
Indices: 677136--677188 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
677126 CGATACATGG
*
677136 TACAATGTATCGA
1 TACATTGTATCGA
677149 TACATTGTATCGA
1 TACATTGTATCGA
677162 TACA-TG-AT-G-
1 TACATTGTATCGA
677171 -A-ATTGTATCGA
1 TACATTGTATCGA
677182 TACATTG
1 TACATTG
677189 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 20 0.61
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:677162 original size:33 final size:33
Alignment explanation
Indices: 677120--677188 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
677110 CTACCACTGT
*
677120 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
*
677153 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
677186 TTG
1 TTG
677189 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:679437 original size:21 final size:20
Alignment explanation
Indices: 679403--679445 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
679393 TATTAAAAAG
*
679403 TTAGCTAACGAAAATAATGAA
1 TTAGCTAACGAAAACAA-GAA
679424 TTAGCTAA-GAAAAACAAGAA
1 TTAGCTAACG-AAAACAAGAA
679444 TT
1 TT
679446 TGCATGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.23
Consensus pattern (20 bp):
TTAGCTAACGAAAACAAGAA
Found at i:679444 original size:20 final size:21
Alignment explanation
Indices: 679403--679445 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
679393 TATTAAAAAG
*
679403 TTAGCTAACGAAAATAATGAA
1 TTAGCTAACGAAAATAAAGAA
679424 TTAGCTAA-GAAAA-ACAAGAA
1 TTAGCTAACGAAAATA-AAGAA
679444 TT
1 TT
679446 TGCATGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 11 0.55
21 8 0.40
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.23
Consensus pattern (21 bp):
TTAGCTAACGAAAATAAAGAA
Found at i:684595 original size:22 final size:22
Alignment explanation
Indices: 684570--684625 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
684560 AGATTTGACA
*
684570 AAGGGGGAGAAATGCCTTGATT
1 AAGGGGGAGAAATGCCTTAATT
* *
684592 AAGGGGGAGAAATTCTTTAATT
1 AAGGGGGAGAAATGCCTTAATT
*
684614 AACGGGGAGAAA
1 AAGGGGGAGAAA
684626 AATGAAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.07, G:0.34, T:0.21
Consensus pattern (22 bp):
AAGGGGGAGAAATGCCTTAATT
Found at i:685193 original size:19 final size:21
Alignment explanation
Indices: 685150--685202 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 21
685140 TTCACCCAGA
*
685150 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGTATGCAT
685170 TGTATCGATACATGT-T-CAT
1 TGTATCGATACATGTATGCAT
685189 TGTATCGATACATG
1 TGTATCGATACATG
685203 AAATTGGTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 16 0.52
20 14 0.45
21 1 0.03
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATGTATGCAT
Found at i:685265 original size:13 final size:13
Alignment explanation
Indices: 685247--685278 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
685237 CGATACATGG
685247 TACATTGTATCAA
1 TACATTGTATCAA
*
685260 TACATTGTATCGA
1 TACATTGTATCAA
685273 TACATT
1 TACATT
685279 ACTTGTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (13 bp):
TACATTGTATCAA
Found at i:690410 original size:16 final size:16
Alignment explanation
Indices: 690378--690423 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 16
690368 ATTAAGATAA
*
690378 AAAATAA-TAATAAAAT
1 AAAATAATTAAT-TAAT
690394 AAAATAATTAATTAAT
1 AAAATAATTAATTAAT
690410 -AAA-AATTAATTAAT
1 AAAATAATTAATTAAT
690424 TTTATATATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 11 0.39
15 3 0.11
16 10 0.36
17 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATAATTAATTAAT
Found at i:690574 original size:45 final size:45
Alignment explanation
Indices: 690522--690609 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
690512 CCAAACTCAC
*
690522 ATATATTCTATTTAATATGAATATATACTT-TATTATATTTAAATA
1 ATATATTCTATTTAATATGAATATACA-TTGTATTATATTTAAATA
690567 ATATATTCTATTTAATATGAATATACATTGTATTATATTTAAA
1 ATATATTCTATTTAATATGAATATACATTGTATTATATTTAAA
690610 CAATTTAACA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 2 0.05
45 39 0.95
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (45 bp):
ATATATTCTATTTAATATGAATATACATTGTATTATATTTAAATA
Found at i:690578 original size:18 final size:20
Alignment explanation
Indices: 690552--690591 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
690542 ATATATACTT
690552 TATTATATTTAA-AT-AATA
1 TATTATATTTAATATGAATA
*
690570 TATTCTATTTAATATGAATA
1 TATTATATTTAATATGAATA
690590 TA
1 TA
690592 CATTGTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 2 0.11
20 6 0.32
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
TATTATATTTAATATGAATA
Found at i:693974 original size:21 final size:21
Alignment explanation
Indices: 693948--693987 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
693938 TTTGATTATT
*
693948 AAAAATTATA-TTTTTCATTC
1 AAAAAATATATTTTTTCATTC
693968 AAAAAATATATTTTTTCATT
1 AAAAAATATATTTTTTCATT
693988 TATTCAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
AAAAAATATATTTTTTCATTC
Found at i:694125 original size:2 final size:2
Alignment explanation
Indices: 694118--694152 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
694108 AACAATTTTC
694118 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
694153 GCTTCATTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:694589 original size:16 final size:16
Alignment explanation
Indices: 694564--694601 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
694554 TAAAATTTTA
694564 ATTATA-TTTTATTAT
1 ATTATATTTTTATTAT
694579 ATTATATTTTTATTAT
1 ATTATATTTTTATTAT
*
694595 TTTATAT
1 ATTATAT
694602 ATATTATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTATATTTTTATTAT
Found at i:694886 original size:11 final size:11
Alignment explanation
Indices: 694867--694903 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
694857 ATTACGTTGA
*
694867 ATTTTATTTTT
1 ATTTAATTTTT
694878 ATTTAATTTTT
1 ATTTAATTTTT
694889 ATTTAATTTTT
1 ATTTAATTTTT
694900 ATTT
1 ATTT
694904 TTTATAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
ATTTAATTTTT
Found at i:695338 original size:19 final size:19
Alignment explanation
Indices: 695314--695368 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
695304 TGTATGAATA
*
695314 CATTGTATCAATACAT-CC
1 CATTGTATCGATACATACC
*
695332 TCATTGTATCGATATATACC
1 -CATTGTATCGATACATACC
695352 CAATTGTATCGATACAT
1 C-ATTGTATCGATACAT
695369 GAAACTGGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (19 bp):
CATTGTATCGATACATACC
Found at i:695436 original size:13 final size:13
Alignment explanation
Indices: 695418--695443 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
695408 CATAGGATAA
695418 TGTATCGATACAT
1 TGTATCGATACAT
695431 TGTATCGATACAT
1 TGTATCGATACAT
695444 AAAGAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:695442 original size:33 final size:33
Alignment explanation
Indices: 695400--695464 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
695390 AAGTGAAATT
*
695400 TATCGATACAT-AGGATAATGTATCGATACATTG
1 TATCGATACATAAAGA-AATGTATCGATACATTG
*
695433 TATCGATACATAAAGAATTGTATCGATACATT
1 TATCGATACATAAAGAAATGTATCGATACATT
695465 ATGTCCAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 26 0.90
34 3 0.10
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (33 bp):
TATCGATACATAAAGAAATGTATCGATACATTG
Found at i:697071 original size:9 final size:9
Alignment explanation
Indices: 697057--697087 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
697047 TCAACCGTCA
697057 AAGATGATG
1 AAGATGATG
697066 AAGATGATG
1 AAGATGATG
*
697075 ATGATGATG
1 AAGATGATG
697084 AAGA
1 AAGA
697088 AGTTGACTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.23
Consensus pattern (9 bp):
AAGATGATG
Found at i:697567 original size:20 final size:20
Alignment explanation
Indices: 697544--697605 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
697534 TGCTTTGTAT
*
697544 TGATACAATGTATCGATACA
1 TGATACATTGTATCGATACA
*
697564 TGAT-CATTGTATCGATTCA
1 TGATACATTGTATCGATACA
697583 TGGATA-ATTGTATCGATACA
1 T-GATACATTGTATCGATACA
697603 TGA
1 TGA
697606 AACTAGTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 16 0.43
20 21 0.57
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (20 bp):
TGATACATTGTATCGATACA
Found at i:697689 original size:33 final size:33
Alignment explanation
Indices: 697633--697696 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
697623 CTACCACTGT
* *
697633 TTGTATCGATACATGGTACATTGTGTCGATATA
1 TTGTATCGATACATGATACATTGTATCGATATA
697666 TTGTATCGATACATGATGA-ATTGTATCGATA
1 TTGTATCGATACATGAT-ACATTGTATCGATA
697697 CATTACTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (33 bp):
TTGTATCGATACATGATACATTGTATCGATATA
Found at i:706253 original size:13 final size:13
Alignment explanation
Indices: 706235--706261 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
706225 ACATTATGCT
706235 TTGTATCGATACA
1 TTGTATCGATACA
706248 TTGTATCGATACA
1 TTGTATCGATACA
706261 T
1 T
706262 GGACAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:711085 original size:52 final size:52
Alignment explanation
Indices: 710937--711065 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
710927 CGAAATATGA
*
710937 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
*
710989 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGT
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
711041 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
711066 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
Found at i:711092 original size:13 final size:13
Alignment explanation
Indices: 711074--711098 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
711064 CAAAGATCAG
711074 TGTATCGATACAA
1 TGTATCGATACAA
711087 TGTATCGATACA
1 TGTATCGATACA
711099 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:711165 original size:19 final size:18
Alignment explanation
Indices: 711141--711238 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
711131 TAGCTTACAT
711141 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
711160 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
711173 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
711192 TGTATCGATAC--AC---
1 TGTATCGATACAAACTTA
*
711205 TGTATTGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
711225 TGTATCGATACAAA
1 TGTATCGATACAAA
711239 TCGTTGAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
13 21 0.33
14 1 0.02
16 6 0.09
18 1 0.02
19 23 0.36
20 12 0.19
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:711177 original size:32 final size:32
Alignment explanation
Indices: 711136--711236 Score: 166
Period size: 32 Copynumber: 3.1 Consensus size: 32
711126 GGCCGTAGCT
*
711136 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
711168 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
* *
711200 TACACTGTATTGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
711233 TACA
1 TACA
711237 AATCGTTGAA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 50 0.77
33 15 0.23
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.35
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:711178 original size:13 final size:13
Alignment explanation
Indices: 711160--711184 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
711150 ACAAAACTTA
711160 TGTATCGATACAT
1 TGTATCGATACAT
711173 TGTATCGATACA
1 TGTATCGATACA
711185 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:711315 original size:21 final size:22
Alignment explanation
Indices: 711268--711315 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
711258 TTAACCGTTG
*
711268 GGACATTGTATCGATACATTCT
1 GGACAATGTATCGATACATTCT
* *
711290 -AACAATGTATCGATATATT-T
1 GGACAATGTATCGATACATTCT
711310 GGACAA
1 GGACAA
711316 AAATATAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (22 bp):
GGACAATGTATCGATACATTCT
Found at i:712094 original size:58 final size:55
Alignment explanation
Indices: 712038--712188 Score: 224
Period size: 52 Copynumber: 2.9 Consensus size: 55
712028 TGTTAAAGAT
* *
712038 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAA
1 GAAGGCGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAA
*
712093 G-A--CGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAC--A
1 GAAGGCGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAA
*
712143 -AAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 GAAGGCGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
712189 GTACCAATGT
Statistics
Matches: 90, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
50 2 0.02
52 86 0.96
54 1 0.01
55 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (55 bp):
GAAGGCGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAA
Found at i:712272 original size:92 final size:92
Alignment explanation
Indices: 712096--712828 Score: 1013
Period size: 92 Copynumber: 8.0 Consensus size: 92
712086 TGACAAAGAC
* * * * *
712096 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGA
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA--A-GAAGGTGCCAATATGCTGA
*
712161 TTCAAGGCCAGCGATATTGGACTTAAAGGT
63 TTCAAGGCCAGCTATATTGGACTTAAAGGT
* *
712191 ACCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAAGAAGGTGCCAATATGCTGATTC
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTC
712256 AAGGCCAGCTATATTGGACTTAAAGGT
66 AAGGCCAGCTATATTGGACTTAAAGGT
*
712283 GCCAATGTGCGGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTC
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTC
*
712348 GAGGCCAGCTATATTGGACTTAAAGGT
66 AAGGCCAGCTATATTGGACTTAAAGGT
* * * *
712375 GCCAATGTGTTGATTCAAGGCCAGCTACGTTGGACTT-----A-AAGGTGACAATGTGCTGATTC
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTC
*
712434 AAGGCCAGCTACATTGGACTTAAAGAAGAAGGT
66 AAGGCCAGCTATATTGGACTT-----A-AAGGT
* * * *
712467 GCCAATATGCTGATTCAAGGCCAGCTATATTAGACTT-----A-AAGGTGCCAATGTGCTGATTC
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTC
** *
712526 AAGGCCAGCTACGTTGGACTTTAAGGT
66 AAGGCCAGCTATATTGGACTTAAAGGT
* *
712553 GCCAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAATAAGAAGGTGCCAATATGCTGATTC
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTC
712618 AAGGCCAGCTATATTGGACTTAAAGGT
66 AAGGCCAGCTATATTGGACTTAAAGGT
* * *
712645 GCCAATGTGCTGATTCAAGGCTAGCTACCTTGGACTTAAAGAAGAAGGTGCCAATATACTGATTC
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTC
712710 AAGGCCAGCTATATTGGACTTAAAGGT
66 AAGGCCAGCTATATTGGACTTAAAGGT
* *
712737 GCCAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAGATGAAGGTGCCAATATGCTGATTC
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTC
* *
712802 AAGGCCAGCGATATTGGGCTTAGAAGG
66 AAGGCCAGCTATATTGGACTTA-AAGG
712829 GTTGCCACCG
Statistics
Matches: 579, Mismatches: 46, Indels: 28
0.89 0.07 0.04
Matches are distributed among these distances:
86 76 0.13
87 1 0.00
91 2 0.00
92 458 0.79
93 5 0.01
95 37 0.06
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (92 bp):
GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTC
AAGGCCAGCTATATTGGACTTAAAGGT
Found at i:712389 original size:135 final size:134
Alignment explanation
Indices: 712142--712828 Score: 827
Period size: 135 Copynumber: 5.0 Consensus size: 134
712132 TAAAGATGAC
* * * * * *
712142 AAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-AAGGTACCAATGTGCT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAAAGAAGGTGCCAATATGCT
* * *
712202 GATTCAAGGCCAGCTACATTGAACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
66 GATTCAAGGCCAGCTATATTGGACTT-----A-AAGGTGCCAATGTGCTGATTCAAGGCCAGCTA
*
712267 TATTGGACTT
125 CATTGGACTT
*
712277 AAAGGTGCCAATGTGCGGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA-AAGAAGGTGCCAATATGC
* * *
712342 TGATTCGAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGTTGATTCAAGGCCAGCTACGTTG
65 TGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
712407 GACTT
130 GACTT
*
712412 AAAGGTGACAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA-AAGAAGGTGCCAATATGC
* *
712477 TGATTCAAGGCCAGCTATATTAGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACGTTG
65 TGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
712542 GACTT
130 GACTT
* *
712547 TAAGGTGCCAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAATAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA-AAGAAGGTGCCAATATGC
* *
712612 TGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCTAGCTACCTTG
65 TGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
712677 GACTT
130 GACTT
* * *
712682 AAAGAAGAAGGTGCCAATATACTGATTCAAGGCCAGCTATATTGGACTT----A-AAGGTGCCAA
1 -----A-AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAAAGAAGGTGCCAA
* ** *
712742 TGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGC
60 TATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAAGGC
* * *
712807 CAGCGATATTGGGCTT
119 CAGCTACATTGGACTT
712823 AGAAGG
1 A-AAGG
712829 GTTGCCACCG
Statistics
Matches: 494, Mismatches: 40, Indels: 35
0.87 0.07 0.06
Matches are distributed among these distances:
135 373 0.76
136 8 0.02
139 1 0.00
140 1 0.00
141 111 0.22
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (134 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAAAGAAGGTGCCAATATGCT
GATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGG
ACTT
Found at i:712505 original size:227 final size:231
Alignment explanation
Indices: 712039--712823 Score: 1133
Period size: 227 Copynumber: 3.4 Consensus size: 231
712029 GTTAAAGATG
* * **
712039 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGACGCCAATAT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA--A-GAAGGTGCCAATAT
* *
712104 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGC
63 GCTGATTCAAGGCCAGCGATATTGGACTTATA-A-G---AAGGTGCCAATATGCTGATTCAAGGC
* *
712169 CAGCGATATTGGACTTAAAGGT-ACCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGA
123 CAGCTATATTGGACTTAAAGGTGA-CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA
712233 AGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
187 AGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
*
712278 AAGGTGCCAATGTGCGGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCT
* * * * **
712343 GATTCGAGGCCAGCTATATTGGAC-T-T-A-AAGGTGCCAATGTGTTGATTCAAGGCCAGCTACG
66 GATTCAAGGCCAGCGATATTGGACTTATAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATA
712404 TTGGACTTAAAGGTGACAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
131 TTGGACTTAAAGGTGACAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
*
712469 CAATATGCTGATTCAAGGCCAGCTATATTAGACTTA
196 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
* * *
712505 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACGTTGGACTT------TAAGGTGCCAATGTGCT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCT
* * *
712564 AATTCAAGGCCAGCTACATTGGACTTAAATAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
66 GATTCAAGGCCAGCGATATTGGACTT--ATAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
* * *
712629 TATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCTAGCTACCTTGGACTTAAAGAAGAAGGT
129 TATTGGACTTAAAGGTGACAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGT
*
712694 GCCAATATACTGATTCAAGGCCAGCTATATTGGACTTA
194 GCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
* *
712732 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAGATGAAGGTGCCAATATGCT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCT
*
712797 GATTCAAGGCCAGCGATATTGGGCTTA
66 GATTCAAGGCCAGCGATATTGGACTTA
712824 GAAGGGTTGC
Statistics
Matches: 495, Mismatches: 38, Indels: 34
0.87 0.07 0.06
Matches are distributed among these distances:
221 36 0.07
222 1 0.00
225 1 0.00
226 1 0.00
227 333 0.67
228 1 0.00
231 1 0.00
232 1 0.00
233 37 0.07
235 1 0.00
236 36 0.07
237 1 0.00
239 45 0.09
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (231 bp):
AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCT
GATTCAAGGCCAGCGATATTGGACTTATAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATA
TTGGACTTAAAGGTGACAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
CAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
Found at i:712911 original size:32 final size:33
Alignment explanation
Indices: 712823--713010 Score: 276
Period size: 32 Copynumber: 5.8 Consensus size: 33
712813 TATTGGGCTT
712823 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* * *
712856 AGAATGGTTGCCACCAACCTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* * * *
712889 AG-AGAGTTGCTACTGACTTGTGTGGGCTTTTG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
712921 -GAAGGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
712952 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
712984 AGAAGGGTTGCCATCGACTTGTGTGGG
1 AGAAGGGTTGCCACCGACTTGTGTGGG
713011 ATTTCAAAAG
Statistics
Matches: 139, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
31 2 0.01
32 105 0.76
33 32 0.23
ACGTcount: A:0.17, C:0.18, G:0.36, T:0.29
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:713180 original size:131 final size:129
Alignment explanation
Indices: 713025--713658 Score: 674
Period size: 131 Copynumber: 4.9 Consensus size: 129
713015 CAAAAGGGTG
* * * *
713025 AAAGA-TGCCACGAAGTTGTGGACTTAAAAGGAACAAG-GTGCCACGGAGTTGTGGACTTAGAAG
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT-----
* * * * * *
713088 GAAAAAGAGTGTCACAGAGTTGTGGGCTTTGAA-AAGAAG-GTGCCACGGAGTCGTGGACTTAAA
61 -AAAAAGAGTGCCACAGAGTTGTGGACTTAGAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAA
713151 AGGAA
125 AGGAA
* * * *
713156 CAAG-GTGCCATGGAGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGTTTTGA
1 AAAGAGTGCCACGGAGTTGTGGAC-TTAGAA-GGAAAAAGAGTGCCACGGAGTTGTGGG-CTT-A
*
713220 AAAAAAGGTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
62 AAAAGA-GTGCCACAGAGTTGTGGACTTAGAA-GAAAAAGAGTGCCACGGAGTTGTGGGC-TTAA
713285 AAGGGAA
124 AA-GGAA
* * * * *
713292 AAAGAATGCCACGGAGTTGTGGGCTTTGAA--AAGAAG-GTGCCACAGAGTTGTGGGCTT-AAAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAA
* * *
713353 GGGTGCCACGGAGTTGTGGACCTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT---A-G--
66 GAGTGCCACAGAGTTGTGGACTTAGAA-GAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
713412 -AAGGGTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT-AAAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAA
* * *
713475 GGGTGCCACAGAGTTGTGGACCTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
66 GAGTGCCACAGAGTTGTGGACTTAGAA-GAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
713540 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCAGGGAGTTGTGGGCTTTAAAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TTAAAA
* * *
713605 AGAGTGCCACGGAGTTGTGGACTTTGAAAAGAAAAAG-GTGCCACGGAGTCGTGG
65 AGAGTGCCACAGAGTTGTGGAC-TT-AGAAGAAAAAGAGTGCCACGGAGTTGTGG
713659 ACTTTGGAAA
Statistics
Matches: 434, Mismatches: 43, Indels: 52
0.82 0.08 0.10
Matches are distributed among these distances:
119 24 0.06
121 5 0.01
122 81 0.19
124 1 0.00
125 1 0.00
126 1 0.00
127 2 0.00
128 51 0.12
129 57 0.13
130 9 0.02
131 82 0.19
132 31 0.07
133 20 0.05
134 34 0.08
135 8 0.02
136 11 0.03
137 16 0.04
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.20
Consensus pattern (129 bp):
AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAA
GAGTGCCACAGAGTTGTGGACTTAGAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
Found at i:713265 original size:34 final size:34
Alignment explanation
Indices: 713025--713662 Score: 589
Period size: 34 Copynumber: 19.8 Consensus size: 34
713015 CAAAAGGGTG
* *
713025 AAAGA-TGCCACGAAGTTGTGGACTTAAAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
*
713058 CAAG-GTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* * * *
713091 AAAGAGTGTCACAGAGTTGTGGGCTTTGAA--AA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* * *
713123 GAAG-GTGCCACGGAGTCGTGGACTTAAAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* * *
713156 CAAG-GTGCCATGGAGTTGTGGACTTTAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGAC-TTAGAA-GGAA
** *
713191 AAAGAGTGCCACGGAGTTGTGGGTTTTGAA--AA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
*
713223 AAAG-GTGCCACAGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* *
713256 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGAC-TTAGAA-GGAA
* * *
713292 AAAGAATGCCACGGAGTTGTGGGCTTTGAA--AA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* * *
713324 GAAG-GTGCCACAGAGTTGTGGGCTT-------A
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* *
713350 AAAGGGTGCCACGGAGTTGTGGACCTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
*
713384 AAAGAGTGCCACGGAGTTGTGGGCTTAGAA-G--
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
*
713415 ---G-GTGCCACAGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
*
713445 AAAGAGTGCCACGGAGTTGTGGGCTT-------A
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* * *
713472 AAAGGGTGCCACAGAGTTGTGGACCTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
*
713506 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
*
713540 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* * *
713574 AAAGAGTGCCAGGGAGTTGTGGGCTT-----TAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* *
713603 AAAGAGTGCCACGGAGTTGTGGACTTTGAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAG-AAGGAA
*
713638 AAAG-GTGCCACGGAGTCGTGGACTT
1 AAAGAGTGCCACGGAGTTGTGGACTT
713663 TGGAAAGAGA
Statistics
Matches: 503, Mismatches: 62, Indels: 79
0.78 0.10 0.12
Matches are distributed among these distances:
26 4 0.01
27 64 0.13
28 2 0.00
29 26 0.05
31 59 0.12
32 16 0.03
33 62 0.12
34 201 0.40
35 26 0.05
36 43 0.09
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.20
Consensus pattern (34 bp):
AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
Found at i:713366 original size:27 final size:27
Alignment explanation
Indices: 713298--713493 Score: 149
Period size: 27 Copynumber: 6.6 Consensus size: 27
713288 GGAAAAAGAA
713298 TGCCACGGAGTTGTGGGCTTTGAAAAGAAGG
1 TGCCACGGAGTTGTGGGC-TT-AAAAG--GG
*
713329 TGCCACAGAGTTGTGGGCTTAAAAGGG
1 TGCCACGGAGTTGTGGGCTTAAAAGGG
* * *
713356 TGCCACGGAGTTGTGGACCTAGAAGGAAAAAGAG
1 TGCCACGGAGTTGTGG-GCT------TAAAAGGG
*
713390 TGCCACGGAGTTGTGGGCTTAGAAGGG
1 TGCCACGGAGTTGTGGGCTTAAAAGGG
* * *
713417 TGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAG
1 TGCCACGGAGTTGTGGGCTT-------AAAAGGG
713451 TGCCACGGAGTTGTGGGCTTAAAAGGG
1 TGCCACGGAGTTGTGGGCTTAAAAGGG
*
713478 TGCCACAGAGTTGTGG
1 TGCCACGGAGTTGTGG
713494 ACCTAGAAGG
Statistics
Matches: 134, Mismatches: 17, Indels: 32
0.73 0.09 0.17
Matches are distributed among these distances:
27 61 0.46
28 2 0.01
29 5 0.04
30 2 0.01
31 17 0.13
33 2 0.01
34 45 0.34
ACGTcount: A:0.28, C:0.14, G:0.38, T:0.20
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGGCTTAAAAGGG
Found at i:713410 original size:61 final size:61
Alignment explanation
Indices: 713298--713658 Score: 460
Period size: 61 Copynumber: 5.8 Consensus size: 61
713288 GGAAAAAGAA
* * * *
713298 TGCCACGGAGTTGTGGGCTTTGAA--AAGAAG-GTGCCACAGAGTTGTGGGCTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGG
* *
713356 TGCCACGGAGTTGTGGACCTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGG
1 TGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGG
*
713417 TGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGG
* *
713478 TGCCACAGAGTTGTGGACCTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAA
1 TGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT-------AAAA
*
713543 GAG
59 GGG
* * *
713546 TGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCAGGGAGTTGTGGGCTTTAAAAAGAG
1 TGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT-AAAAGGG
* * *
713609 TGCCACGGAGTTGTGGACTTTGAAAAGAAAAAG-GTGCCACGGAGTCGTGG
1 TGCCACGGAGTTGTGGACTTAG-AAGGAAAAAGAGTGCCACGGAGTTGTGG
713659 ACTTTGGAAA
Statistics
Matches: 271, Mismatches: 20, Indels: 19
0.87 0.06 0.06
Matches are distributed among these distances:
58 21 0.08
60 5 0.02
61 137 0.51
63 43 0.16
64 9 0.03
68 54 0.20
69 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.37, T:0.19
Consensus pattern (61 bp):
TGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGG
Found at i:713497 original size:122 final size:125
Alignment explanation
Indices: 713127--713658 Score: 592
Period size: 122 Copynumber: 4.1 Consensus size: 125
713117 TGAAAAGAAG
* * * * * * *
713127 GTGCCACGGAGTCGTGGACTTAAAAGGAACAAGGTGCCATGGAGTTGTGGACTTTAAAAGGGAAA
1 GTGCCACGGAGTTGTGGGCTTAGAAGG-A-GA-GTGCCACGGAGTTGTGGGC-TTAGAA-GGAAA
* * * *
713192 AAGAGTGCCACGGAGTTGTGGGTTTTGAAAAAAAGGTGCCACAGAGTTGTGGACTTAGAAGGAAA
61 AAGAGTGCCACGGAGTTGTGGG-CTT---AAAAGGGTGCCACGGAGTTGTGGACCTAGAAGGAAA
713257 AAGA
122 AAGA
* * *
713261 GTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAATGCCACGGAGTTGTGGGCTTTGAA--AA
1 GTGCCACGGAGTTGTGGGC-TTAGAA-GG----AGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* *
713324 GAAG-GTGCCACAGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACCTAGAAGGAAAAAG
60 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACCTAGAAGGAAAAAG
713388 A
125 A
* *
713389 GTGCCACGGAGTTGTGGGCTTAGAA-G-G-GTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAG
1 GTGCCACGGAGTTGTGGGCTTAGAAGGAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAG
*
713451 TGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACAGAGTTGTGGACCTAGAAGGAAAAAGA
66 TGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACCTAGAAGGAAAAAGA
713511 GTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAA
1 GTGCCACGGAGTTGTGGGCTTAGAAGG----AGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAA
* * * * *
713576 AGAGTGCCAGGGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTTGTGGACTTTGAAAAGAAAAA
62 AGAGTGCCACGGAGTTGTGGGC-TT-AAAAGGGTGCCACGGAGTTGTGGACCTAG-AAGGAAAAA
713641 G-
124 GA
*
713642 GTGCCACGGAGTCGTGG
1 GTGCCACGGAGTTGTGG
713659 ACTTTGGAAA
Statistics
Matches: 349, Mismatches: 31, Indels: 39
0.83 0.07 0.09
Matches are distributed among these distances:
119 21 0.06
120 1 0.00
121 5 0.01
122 84 0.24
123 1 0.00
125 1 0.00
127 5 0.01
128 57 0.16
129 50 0.14
130 2 0.01
131 43 0.12
132 26 0.07
133 5 0.01
134 17 0.05
135 6 0.02
136 6 0.02
137 16 0.05
138 1 0.00
139 2 0.01
ACGTcount: A:0.31, C:0.13, G:0.36, T:0.20
Consensus pattern (125 bp):
GTGCCACGGAGTTGTGGGCTTAGAAGGAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAG
TGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACCTAGAAGGAAAAAGA
Found at i:713503 original size:27 final size:27
Alignment explanation
Indices: 713444--713503 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
713434 CTTAGAAGGA
* * * *
713444 AAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACAGAGTTGTGGACCT
713471 AAAAGGGTGCCACAGAGTTGTGGACCT
1 AAAAGGGTGCCACAGAGTTGTGGACCT
*
713498 AGAAGG
1 AAAAGG
713504 AAAAAGAGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.15, G:0.37, T:0.18
Consensus pattern (27 bp):
AAAAGGGTGCCACAGAGTTGTGGACCT
Found at i:713580 original size:68 final size:63
Alignment explanation
Indices: 713289--713829 Score: 463
Period size: 63 Copynumber: 8.6 Consensus size: 63
713279 CTTTAAAAGG
* * * * *
713289 GAAAAAGAATGCCACGGAGTTGTGGGCTTTGAA--AAGAAG-GTGCCACAGAGTTGTGGGCTT
1 GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* *
713349 --AAAAGGGTGCCACGGAGTTGTGGACCTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* * *
713410 --AGAAGGGTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* * *
713471 --AAAAGGGTGCCACAGAGTTGTGGACCTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* *
713532 AGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCAGGGAGTTGTGGG
1 -----GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGG
713597 CTT
61 CTT
* * * * *
713600 TAAAAAGAGTGCCACGGAGTTGTGGACTTTGAAAAGAAAAAG-GTGCCACGGAGTCGTGGACTTT
1 GAAAAAGAGTGCCACGGAGTTGTGGACTTAG-AAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT
* ** * * **
713664 G-GAAAGAGATGCCACTAAATTGTGGACTTTAAGAAGG--AAAGA-TGCCACTGAGCCGTGGGCT
1 GAAAAAGAG-TGCCACGGAGTTGTGGAC-TT-AGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-
713725 TT
62 TT
* ** * * *
713727 G-GAAAGAGATGCCACTAAATTGTGGACTTTAAGAAGG--AAAGA-TGCCACTGAGCTGTGGGCT
1 GAAAAAGAG-TGCCACGGAGTTGTGGAC-TT-AGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-
713788 TT
62 TT
** *
713790 GGAAAAAGA-TGCCACTAAATTGTGGACTTTAAGAAGGAAA
1 -GAAAAAGAGTGCCACGGAGTTGTGGAC-TT-AGAAGGAAA
713830 GATGCCACTG
Statistics
Matches: 425, Mismatches: 36, Indels: 35
0.86 0.07 0.07
Matches are distributed among these distances:
58 26 0.06
60 5 0.01
61 137 0.32
63 162 0.38
64 27 0.06
65 11 0.03
66 1 0.00
68 56 0.13
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.20
Consensus pattern (63 bp):
GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
Found at i:713677 original size:30 final size:30
Alignment explanation
Indices: 713025--713841 Score: 256
Period size: 34 Copynumber: 25.5 Consensus size: 30
713015 CAAAAGGGTG
*
713025 AAAGATGCCAC-GAAGTTGTGGACTTAAAAGGAA
1 AAAGATGCCACTG-AGTTGTGGACTT---TGGAA
* * * *
713058 CAAGGTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGATGCCACTGAGTTGTGGACTT---TGGAA
* * * *
713091 AAAGAGTGTCACAGAGTTGTGGGCTTTGAAA
1 AAAGA-TGCCACTGAGTTGTGGACTTTGGAA
* * * *
713122 AGAAGGTGCCACGGAGTCGTGGACTTAAAAGGAA
1 A-AAGATGCCACTGAGTTGTGGACTT---TGGAA
* *
713156 CAAGGTGCCA-TGGAGTTGTGGACTTTAAAAGGGAA
1 AAAGATGCCACT-GAGTTGTGGACTTT-----GGAA
* ** *
713191 AAAGAGTGCCACGGAGTTGTGGGTTTTGAAAA
1 AAAGA-TGCCACTGAGTTGTGGACTTTG-GAA
* * *
713223 AAAGGTGCCACAGAGTTGTGGACTTAGAAGGAA
1 AAAGATGCCACTGAGTTGTGGACTT---TGGAA
* *
713256 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGGAA
1 AAAGA-TGCCACTGAGTTGTGGACTTT-----GGAA
* * *
713292 AAAGAATGCCACGGAGTTGTGGGCTTTGAAA
1 AAAG-ATGCCACTGAGTTGTGGACTTTGGAA
* * *
713323 AGAAGGTGCCACAGAGTTGTGGGC-TT--AA
1 A-AAGATGCCACTGAGTTGTGGACTTTGGAA
* * * **
713351 AAGGGTGCCACGGAGTTGTGGACCTAGAAGGAA
1 AAAGATGCCACTGAGTTGTGGA-CT--TTGGAA
* * *
713384 AAAGAGTGCCACGGAGTTGTGGGC-TT--AG
1 AAAGA-TGCCACTGAGTTGTGGACTTTGGAA
* * * *
713412 AAGGGTGCCACAGAGTTGTGGACTTAGAAGGAA
1 AAAGATGCCACTGAGTTGTGGACTT---TGGAA
* *
713445 AAAGAGTGCCACGGAGTTGTGGGC-TT--AA
1 AAAGA-TGCCACTGAGTTGTGGACTTTGGAA
* * * **
713473 AAGGGTGCCACAGAGTTGTGGACCTAGAAGGAA
1 AAAGATGCCACTGAGTTGTGGA-CT--TTGGAA
* * *
713506 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGA-TGCCACTGAGTTGTGGACTT---TGGAA
* * *
713540 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGA-TGCCACTGAGTTGTGGACTT---TGGAA
** *
713574 AAAGAGTGCCAGGGAGTTGTGGGCTTT--AA
1 AAAGA-TGCCACTGAGTTGTGGACTTTGGAA
*
713603 AAAGAGTGCCACGGAGTTGTGGACTTTGAAAAGAA
1 AAAGA-TGCCACTGAGTTGTGGACTTTG----GAA
* * *
713638 AAAGGTGCCACGGAGTCGTGGACTTTGGAA
1 AAAGATGCCACTGAGTTGTGGACTTTGGAA
* * * *
713668 AGAGATGCCACTAAATTGTGGACTTTAAGAA
1 AAAGATGCCACTGAGTTGTGGACTTT-GGAA
** *
713699 GGAAAGATGCCACTGAGCCGTGGGCTTTGGAA
1 --AAAGATGCCACTGAGTTGTGGACTTTGGAA
* * * *
713731 AGAGATGCCACTAAATTGTGGACTTTAAGAA
1 AAAGATGCCACTGAGTTGTGGACTTT-GGAA
* *
713762 GGAAAGATGCCACTGAGCTGTGGGCTTTGGAA
1 --AAAGATGCCACTGAGTTGTGGACTTTGGAA
* * *
713794 AAAGATGCCACTAAATTGTGGACTTTAAGAA
1 AAAGATGCCACTGAGTTGTGGACTTT-GGAA
713825 GGAAAGATGCCACTGAG
1 --AAAGATGCCACTGAG
713842 CCGTGGGCTT
Statistics
Matches: 606, Mismatches: 113, Indels: 130
0.71 0.13 0.15
Matches are distributed among these distances:
27 49 0.08
28 15 0.02
29 27 0.04
30 67 0.11
31 68 0.11
32 18 0.03
33 130 0.21
34 172 0.28
35 13 0.02
36 46 0.08
37 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (30 bp):
AAAGATGCCACTGAGTTGTGGACTTTGGAA
Found at i:713711 original size:33 final size:33
Alignment explanation
Indices: 713670--713838 Score: 188
Period size: 33 Copynumber: 5.3 Consensus size: 33
713660 CTTTGGAAAG
713670 AGATGCCACTAAATTGTGGACTTTAAGAAGGAA
1 AGATGCCACTAAATTGTGGACTTTAAGAAGGAA
* *** * * *
713703 AGATGCCACTGAGCCGTGGGCTTT-GGAA--AG
1 AGATGCCACTAAATTGTGGACTTTAAGAAGGAA
713733 AGATGCCACTAAATTGTGGACTTTAAGAAGGAA
1 AGATGCCACTAAATTGTGGACTTTAAGAAGGAA
* ** * *
713766 AGATGCCACTGAGCTGTGGGCTTT-GGAA--AA
1 AGATGCCACTAAATTGTGGACTTTAAGAAGGAA
713796 AGATGCCACTAAATTGTGGACTTTAAGAAGGAA
1 AGATGCCACTAAATTGTGGACTTTAAGAAGGAA
713829 AGATGCCACT
1 AGATGCCACT
713839 GAGCCGTGGG
Statistics
Matches: 106, Mismatches: 24, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
30 42 0.40
31 6 0.06
32 6 0.06
33 52 0.49
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (33 bp):
AGATGCCACTAAATTGTGGACTTTAAGAAGGAA
Found at i:713790 original size:126 final size:126
Alignment explanation
Indices: 713592--713862 Score: 388
Period size: 126 Copynumber: 2.1 Consensus size: 126
713582 CCAGGGAGTT
* * * *
713592 GTGGGCTTT-AAAAAGAGTGCCACGGAGTTGTGGACTTTGAAAAGAAAAAGGTGCCACGGAGTCG
1 GTGGGCTTTGAAAGAGA-TGCCACGAAATTGTGGACTTTGAAAAGAAAAAGATGCCACGGAGTCG
*
713656 TGGACTTTGGAAAGAGATGCCACTAAATTGTGGACTTTAAGAAGGAAAGATGCCACTGAGCC
65 TGGACTTTGGAAAAAGATGCCACTAAATTGTGGACTTTAAGAAGGAAAGATGCCACTGAGCC
* * *
713718 GTGGGCTTTGGAAAGAGATGCCACTAAATTGTGGACTTT-AAGAAG-GAAAGATGCCACTGAG-C
1 GTGGGCTTT-GAAAGAGATGCCACGAAATTGTGGACTTTGAA-AAGAAAAAGATGCCACGGAGTC
*
713780 TGTGGGCTTTGGAAAAAGATGCCACTAAATTGTGGACTTTAAGAAGGAAAGATGCCACTGAGCC
64 -GTGGACTTTGGAAAAAGATGCCACTAAATTGTGGACTTTAAGAAGGAAAGATGCCACTGAGCC
713844 GTGGGCTTTGAGAAGAGAT
1 GTGGGCTTTGA-AAGAGAT
713863 TTGAAGAATT
Statistics
Matches: 131, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
125 3 0.02
126 101 0.77
127 21 0.16
128 6 0.05
ACGTcount: A:0.32, C:0.14, G:0.31, T:0.23
Consensus pattern (126 bp):
GTGGGCTTTGAAAGAGATGCCACGAAATTGTGGACTTTGAAAAGAAAAAGATGCCACGGAGTCGT
GGACTTTGGAAAAAGATGCCACTAAATTGTGGACTTTAAGAAGGAAAGATGCCACTGAGCC
Found at i:713858 original size:33 final size:33
Alignment explanation
Indices: 713603--713858 Score: 174
Period size: 33 Copynumber: 8.0 Consensus size: 33
713593 TGGGCTTTAA
* * *
713603 AAAGAGTGCCACGGAGTTGTGGACTTTGAA-AAGAA
1 AAAGA-TGCCACTGAGCTGTGGACTTT-AAGAAG-G
* * *
713638 AAAGGTGCCACGGAG-TCGTGGACTTT-GGAA--
1 AAAGATGCCACTGAGCT-GTGGACTTTAAGAAGG
* * **
713668 AGAGATGCCACTAAATTGTGGACTTTAAGAAGG
1 AAAGATGCCACTGAGCTGTGGACTTTAAGAAGG
* * *
713701 AAAGATGCCACTGAGCCGTGGGCTTT-GGAA--
1 AAAGATGCCACTGAGCTGTGGACTTTAAGAAGG
* * **
713731 AGAGATGCCACTAAATTGTGGACTTTAAGAAGG
1 AAAGATGCCACTGAGCTGTGGACTTTAAGAAGG
* *
713764 AAAGATGCCACTGAGCTGTGGGCTTT-GGAA--
1 AAAGATGCCACTGAGCTGTGGACTTTAAGAAGG
* **
713794 AAAGATGCCACTAAATTGTGGACTTTAAGAAGG
1 AAAGATGCCACTGAGCTGTGGACTTTAAGAAGG
* * *
713827 AAAGATGCCACTGAGCCGTGGGCTTTGAGAAG
1 AAAGATGCCACTGAGCTGTGGACTTTAAGAAG
713859 AGATTTGAAG
Statistics
Matches: 170, Mismatches: 39, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
30 61 0.36
31 10 0.06
32 6 0.04
33 70 0.41
34 19 0.11
35 4 0.02
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.22
Consensus pattern (33 bp):
AAAGATGCCACTGAGCTGTGGACTTTAAGAAGG
Found at i:714845 original size:17 final size:17
Alignment explanation
Indices: 714805--714858 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 17
714795 CTTTCTTCTT
*
714805 TTTTTTG-TTTGTTT-G
1 TTTTTTGTTTTGTTTCC
*
714820 TTTCTT-TTTT-TTTCC
1 TTTTTTGTTTTGTTTCC
*
714835 TTTTTTGTTTTGTTTCT
1 TTTTTTGTTTTGTTTCC
714852 TTTTTTG
1 TTTTTTG
714859 GAAAAGAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 3 0.10
15 13 0.42
16 4 0.13
17 11 0.35
ACGTcount: A:0.00, C:0.07, G:0.11, T:0.81
Consensus pattern (17 bp):
TTTTTTGTTTTGTTTCC
Found at i:714853 original size:27 final size:24
Alignment explanation
Indices: 714796--714857 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 24
714786 GGGTTTTTCC
*
714796 TTTCTTCTTTTTTTTGTTTGTTTG
1 TTTCTTTTTTTTTTTGTTTGTTTG
*
714820 TTTCTTTTTTTTTCCTTTTTTGTTTTG
1 TTTCTTTTTTTTT--TTGTTTG-TTTG
714847 TTTCTTTTTTT
1 TTTCTTTTTTT
714858 GGAAAAGAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 12 0.36
26 6 0.18
27 15 0.45
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.82
Consensus pattern (24 bp):
TTTCTTTTTTTTTTTGTTTGTTTG
Found at i:715130 original size:14 final size:14
Alignment explanation
Indices: 715105--715139 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
715095 CTTTTTTCTG
*
715105 TGTTTTTTTTTGTT
1 TGTTTTGTTTTGTT
715119 TGTTTTGTTTTGTT
1 TGTTTTGTTTTGTT
715133 T-TTTTGT
1 TGTTTTGT
715140 GTTTACTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (14 bp):
TGTTTTGTTTTGTT
Done.