Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 7 of 135
Found at i:2923689 original size:32 final size:32
Alignment explanation
Indices: 2923653--2923730 Score: 156
Period size: 32 Copynumber: 2.4 Consensus size: 32
2923643 GATTAAGCTT
2923653 AATTTAATAATATATATAAAAAATAATAACAC
1 AATTTAATAATATATATAAAAAATAATAACAC
2923685 AATTTAATAATATATATAAAAAATAATAACAC
1 AATTTAATAATATATATAAAAAATAATAACAC
2923717 AATTTAATAATATA
1 AATTTAATAATATA
2923731 AAATATTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (32 bp):
AATTTAATAATATATATAAAAAATAATAACAC
Found at i:2923725 original size:16 final size:16
Alignment explanation
Indices: 2923674--2923728 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
2923664 ATATATAAAA
2923674 AATAATAACACAATTT
1 AATAATAACACAATTT
* * **
2923690 AATAATATATATAA-AA
1 AATAATA-ACACAATTT
2923706 AATAATAACACAATTT
1 AATAATAACACAATTT
2923722 AATAATA
1 AATAATA
2923729 TAAAATATTA
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
15 4 0.14
16 21 0.72
17 4 0.14
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (16 bp):
AATAATAACACAATTT
Found at i:2935164 original size:51 final size:51
Alignment explanation
Indices: 2935088--2935192 Score: 210
Period size: 51 Copynumber: 2.1 Consensus size: 51
2935078 TAAAAATAAA
2935088 ATAAAATAAAAGAGACAATAATGGGGATCTGTTAACGCTGACTTGGACGCC
1 ATAAAATAAAAGAGACAATAATGGGGATCTGTTAACGCTGACTTGGACGCC
2935139 ATAAAATAAAAGAGACAATAATGGGGATCTGTTAACGCTGACTTGGACGCC
1 ATAAAATAAAAGAGACAATAATGGGGATCTGTTAACGCTGACTTGGACGCC
2935190 ATA
1 ATA
2935193 TTTTTTATTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (51 bp):
ATAAAATAAAAGAGACAATAATGGGGATCTGTTAACGCTGACTTGGACGCC
Found at i:2935583 original size:4 final size:4
Alignment explanation
Indices: 2935570--2935600 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
2935560 TCTGAGAGGA
2935570 AAAT -AAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
2935601 GTCATCGTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:2940087 original size:18 final size:16
Alignment explanation
Indices: 2940050--2940087 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
2940040 TAGTTTTAAG
2940050 TAATATATAAAAAATA
1 TAATATATAAAAAATA
2940066 -AATATGATAAAAAATTA
1 TAATAT-ATAAAAAA-TA
2940083 TAATA
1 TAATA
2940088 AAATTAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.26
16 8 0.42
17 2 0.11
18 4 0.21
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
TAATATATAAAAAATA
Found at i:2948067 original size:3 final size:3
Alignment explanation
Indices: 2948059--2948084 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2948049 TGGTTCAGCA
2948059 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
2948085 ATCCATTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:2951111 original size:16 final size:16
Alignment explanation
Indices: 2951066--2951116 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2951056 CCTTAAAATA
2951066 ATAAAATTTT-AATTT
1 ATAAAATTTTAAATTT
**
2951081 A-AATCTTTTATAATTT
1 ATAAAATTTTA-AATTT
*
2951097 ATAAAATTTTAAATTA
1 ATAAAATTTTAAATTT
2951113 ATAA
1 ATAA
2951117 TAATAAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
14 6 0.21
15 1 0.04
16 14 0.50
17 7 0.25
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAAAATTTTAAATTT
Found at i:2959112 original size:8 final size:8
Alignment explanation
Indices: 2959094--2959126 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
2959084 TTAAATGAAT
2959094 ATAAT-TA
1 ATAATATA
*
2959101 ATAACATA
1 ATAATATA
2959109 ATAATATA
1 ATAATATA
2959117 ATAATATA
1 ATAATATA
2959125 AT
1 AT
2959127 CCTAGTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
7 4 0.17
8 19 0.83
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (8 bp):
ATAATATA
Found at i:2959359 original size:4 final size:4
Alignment explanation
Indices: 2959350--2959462 Score: 51
Period size: 4 Copynumber: 28.0 Consensus size: 4
2959340 CATAAAGAAT
*
2959350 AATA AATA AATAA AATA CATA AA-A TAATA AATAA AATTA AATA AA-A
1 AATA AATA AAT-A AATA AATA AATA -AATA AAT-A AA-TA AATA AATA
* * * * *
2959396 GCAAAA ATATA AAT- AACA AA-A AATG AAT- AATC GATA AATA AAT- AATA
1 --AATA A-ATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
2959443 AATA AATA AA-A TAATA AATA
1 AATA AATA AATA -AATA AATA
2959463 TATGAAATGC
Statistics
Matches: 86, Mismatches: 8, Indels: 30
0.69 0.06 0.24
Matches are distributed among these distances:
3 14 0.16
4 53 0.62
5 17 0.20
6 2 0.02
ACGTcount: A:0.71, C:0.04, G:0.03, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:2959385 original size:72 final size:78
Alignment explanation
Indices: 2959299--2959462 Score: 196
Period size: 72 Copynumber: 2.1 Consensus size: 78
2959289 TAAAAATATC
* * * * * *
2959299 AATAAGTAAATAAAATTAAATGAAGGTAAAAATGTAAATAGC-ATAAA-GAAT-A-ATAAATAAA
1 AATAA-TAAATAAAATTAAATAAAAGCAAAAATATAAATAACAAAAAATGAATAACATAAATAAA
*
2959360 T-A-AAATACATAA
65 TAATAAATAAATAA
2959372 AATAATAAATAAAATTAAATAAAAGCAAAAATATAAATAACAAAAAATGAATAATCGATAAATAA
1 AATAATAAATAAAATTAAATAAAAGCAAAAATATAAATAACAAAAAATGAATAA-C-ATAAATAA
2959437 ATAATAAATAAATAA
64 ATAATAAATAAATAA
2959452 AATAATAAATA
1 AATAATAAATA
2959463 TATGAAATGC
Statistics
Matches: 76, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
72 31 0.41
73 9 0.12
74 4 0.05
75 1 0.01
78 10 0.13
79 1 0.01
80 20 0.26
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.23
Consensus pattern (78 bp):
AATAATAAATAAAATTAAATAAAAGCAAAAATATAAATAACAAAAAATGAATAACATAAATAAAT
AATAAATAAATAA
Found at i:2959403 original size:22 final size:22
Alignment explanation
Indices: 2959354--2959409 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
2959344 AAGAATAATA
* *
2959354 AATAAATAAAA-TACATAAAAT
1 AATAAATAAAATTAAATAAAAC
2959375 AATAAATAAAATTAAATAAAAGC
1 AATAAATAAAATTAAATAAAA-C
2959398 AA-AAATATAAAT
1 AATAAATA-AAAT
2959410 AACAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 6 0.20
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (22 bp):
AATAAATAAAATTAAATAAAAC
Found at i:2959470 original size:16 final size:16
Alignment explanation
Indices: 2959347--2959462 Score: 81
Period size: 16 Copynumber: 7.7 Consensus size: 16
2959337 TAGCATAAAG
2959347 AATAATAAATAAATAA
1 AATAATAAATAAATAA
2959363 AATACATAAA-ATAAT-A
1 AATA-ATAAATA-AATAA
*
2959379 AATAA-AATTAAATAA
1 AATAATAAATAAATAA
*
2959394 AAGCAA-AAAT--AT-A
1 AA-TAATAAATAAATAA
* *
2959407 AATAACAAA-AAAT-G
1 AATAATAAATAAATAA
**
2959421 AATAATCGATAAAT-A
1 AATAATAAATAAATAA
2959436 AATAATAAATAAATAA
1 AATAATAAATAAATAA
2959452 AATAATAAATA
1 AATAATAAATA
2959463 TATGAAATGC
Statistics
Matches: 79, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
12 2 0.03
13 6 0.08
14 15 0.19
15 21 0.27
16 27 0.34
17 8 0.10
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (16 bp):
AATAATAAATAAATAA
Found at i:2959685 original size:13 final size:13
Alignment explanation
Indices: 2959532--2959716 Score: 51
Period size: 13 Copynumber: 13.5 Consensus size: 13
2959522 GTAATTAAAT
2959532 AAATAAA-AATAA
1 AAATAAATAATAA
* * *
2959544 AATTTAATGATAAA
1 AAATAAATAAT-AA
2959558 TAAATAATATAATAA
1 -AAATAA-ATAATAA
*
2959573 TAATAAATACA-AA
1 AAATAAATA-ATAA
2959586 TTAAATAAA-AATAA
1 --AAATAAATAATAA
* *
2959600 TAATAAAAGAGATAA
1 AAAT-AAATA-ATAA
* *
2959615 CAATAGAATGACATTA
1 AAATA-AAT-A-ATAA
*
2959631 AAATAAATAACAA
1 AAATAAATAATAA
*
2959644 CTAGATAAATAA-ACA
1 --AAATAAATAATA-A
2959659 AAATAAATAATAA
1 AAATAAATAATAA
2959672 AAATAAA-AATTAA
1 AAATAAATAA-TAA
** *
2959685 ATGTTAA-AATAA
1 AAATAAATAATAA
2959697 ACAATAAAT-ATAA
1 A-AATAAATAATAA
2959710 ATAATAA
1 A-AATAA
2959717 TAAAAAGAAT
Statistics
Matches: 128, Mismatches: 25, Indels: 39
0.67 0.13 0.20
Matches are distributed among these distances:
12 14 0.11
13 52 0.41
14 16 0.12
15 34 0.27
16 12 0.09
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (13 bp):
AAATAAATAATAA
Found at i:2962634 original size:13 final size:14
Alignment explanation
Indices: 2962613--2962646 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2962603 GAAAAAAATA
2962613 TTTTATATTAAATTT
1 TTTTAT-TTAAATTT
*
2962628 TTTTATTTAAAGTT
1 TTTTATTTAAATTT
2962642 TTTTA
1 TTTTA
2962647 ATAATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (14 bp):
TTTTATTTAAATTT
Found at i:2969292 original size:86 final size:85
Alignment explanation
Indices: 2969147--2969312 Score: 269
Period size: 86 Copynumber: 1.9 Consensus size: 85
2969137 GTATTATTCA
* * *
2969147 TTCAATTATGAAGTAAATTTGATTTACTGAAATAAAATATTTAGCTGATTAATAATTTTAGATAT
1 TTCAATTATAAAATAAATTTGATTTACTGAAATAAAATATTTAGCTGATCAATAATTTTAGATAT
2969212 TAAAAAAAATTCGAAGATAGG
66 T-AAAAAAATTCGAAGATAGG
* *
2969233 TTCAATTATAAAATAAATTTGATTTACTGAAATTAAATATTTAGTTGATCAATAATTTTAGATAT
1 TTCAATTATAAAATAAATTTGATTTACTGAAATAAAATATTTAGCTGATCAATAATTTTAGATAT
*
2969298 TAAAAAAGTTCGAAG
66 TAAAAAAATTCGAAG
2969313 TATTCTATCA
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
85 13 0.18
86 61 0.82
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (85 bp):
TTCAATTATAAAATAAATTTGATTTACTGAAATAAAATATTTAGCTGATCAATAATTTTAGATAT
TAAAAAAATTCGAAGATAGG
Found at i:2972133 original size:9 final size:9
Alignment explanation
Indices: 2972119--2972158 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
2972109 GTTTGCAGCT
2972119 ACAACACCA
1 ACAACACCA
2972128 ACAACACCA
1 ACAACACCA
* *
2972137 CCACCACCA
1 ACAACACCA
*
2972146 ACAACAACA
1 ACAACACCA
2972155 ACAA
1 ACAA
2972159 AAAAGACATC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.55, C:0.45, G:0.00, T:0.00
Consensus pattern (9 bp):
ACAACACCA
Found at i:2980219 original size:17 final size:18
Alignment explanation
Indices: 2980191--2980225 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
2980181 TCTTACCTTT
2980191 AAAAAGACAAAAAAAAGA
1 AAAAAGACAAAAAAAAGA
2980209 AAAAAGA-AAAAAAAAGA
1 AAAAAGACAAAAAAAAGA
2980226 GCAATGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (18 bp):
AAAAAGACAAAAAAAAGA
Found at i:2987416 original size:6 final size:6
Alignment explanation
Indices: 2987407--2987437 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2987397 TCTTCTTCTT
2987407 CTTCAA CTTCAA CTTCAA CTTCAA CTTCAA C
1 CTTCAA CTTCAA CTTCAA CTTCAA CTTCAA C
2987438 GATCAACGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (6 bp):
CTTCAA
Found at i:2989519 original size:38 final size:38
Alignment explanation
Indices: 2989468--2989543 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
2989458 TGCACAATGG
2989468 CATGACTTAATAGGGGGATAAGAAAGATGATTAGAATA
1 CATGACTTAATAGGGGGATAAGAAAGATGATTAGAATA
2989506 CATGACTTAATAGGGGGATAAGAAAGATGATTAGAATA
1 CATGACTTAATAGGGGGATAAGAAAGATGATTAGAATA
2989544 TTGTCAGGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.45, C:0.05, G:0.26, T:0.24
Consensus pattern (38 bp):
CATGACTTAATAGGGGGATAAGAAAGATGATTAGAATA
Found at i:2993379 original size:12 final size:12
Alignment explanation
Indices: 2993359--2993406 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
2993349 ATACATCATT
2993359 AACAACTAATAA
1 AACAACTAATAA
* *
2993371 AACAGCTAACAA
1 AACAACTAATAA
*
2993383 GAATAACTAATAA
1 -AACAACTAATAA
*
2993396 AACAGCTAATA
1 AACAACTAATA
2993407 TGAGCAGCTT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.60, C:0.17, G:0.06, T:0.17
Consensus pattern (12 bp):
AACAACTAATAA
Found at i:3006681 original size:6 final size:6
Alignment explanation
Indices: 3006670--3006699 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3006660 ATTACCTCCG
*
3006670 TATTTA TATTTA TATTTA TATGTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA
3006700 ATTGATGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (6 bp):
TATTTA
Found at i:3007621 original size:3 final size:3
Alignment explanation
Indices: 3007613--3007668 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
3007603 TATTATCAAC
3007613 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3007661 ATT ATT AT
1 ATT ATT AT
3007669 AACTTGTTAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3008673 original size:15 final size:16
Alignment explanation
Indices: 3008646--3008675 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3008636 TAAGGAAAAA
3008646 TAAAAGAAAATAGAAC
1 TAAAAGAAAATAGAAC
3008662 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
3008676 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.03, G:0.13, T:0.13
Consensus pattern (16 bp):
TAAAAGAAAATAGAAC
Found at i:3009477 original size:6 final size:6
Alignment explanation
Indices: 3009466--3009512 Score: 60
Period size: 6 Copynumber: 7.8 Consensus size: 6
3009456 ATAAATACAA
* *
3009466 AAATAT AAATAT AAATAT AAAT-T AAATAC AAATTT AAATAAT AAATA
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAAT-AT AAATA
3009513 ATATCTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 5 0.14
6 25 0.71
7 5 0.14
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:3009493 original size:17 final size:18
Alignment explanation
Indices: 3009466--3009512 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
3009456 ATAAATACAA
*
3009466 AAATATAAATATAAATAT
1 AAATATAAATACAAATAT
*
3009484 AAAT-TAAATACAAATTT
1 AAATATAAATACAAATAT
3009501 AAATAATAAATA
1 AAAT-ATAAATA
3009513 ATATCTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 15 0.60
18 4 0.16
19 6 0.24
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATATAAATACAAATAT
Found at i:3009498 original size:23 final size:24
Alignment explanation
Indices: 3009466--3009511 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
3009456 ATAAATACAA
*
3009466 AAATATAAATATAAAT-ATAAATT
1 AAATACAAATATAAATAATAAATT
*
3009489 AAATACAAATTTAAATAATAAAT
1 AAATACAAATATAAATAATAAAT
3009512 AATATCTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
AAATACAAATATAAATAATAAATT
Found at i:3010323 original size:107 final size:106
Alignment explanation
Indices: 3010128--3010326 Score: 231
Period size: 107 Copynumber: 1.9 Consensus size: 106
3010118 ATACATTGGA
* * * * *
3010128 CCTTTTGACACGAAATGAAATGACACCCAAGCACTCCATCCCGGTTACTCAGCCCAACATGCTCT
1 CCTTTTGACACGAAATGAAATGACAACCAAACACTCCACCCCGATTACTCAACCCAACA-GCTCT
* * *
3010193 CAATTTTTTTCTTCTCTTTTTTTTTTTGTAGAATGCATTAGC
65 CAATTTATTTATTATCTTTTTTTTTTTGTAGAATGCATTAGC
* * * * *
3010235 CCTTTTGACGCGAAATGAAATTACAACCAAACACTCCACCCCGATTACTCAATCTAACA-CATTT
1 CCTTTTGACACGAAATGAAATGACAACCAAACACTCCACCCCGATTACTCAACCCAACAGC-TCT
3010299 CAAATTTATTTATTAT-TTTCTTTTTTTT
65 C-AATTTATTTATTATCTTT-TTTTTTTT
3010327 ATTCGGGTTA
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
105 1 0.01
106 6 0.08
107 69 0.91
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.38
Consensus pattern (106 bp):
CCTTTTGACACGAAATGAAATGACAACCAAACACTCCACCCCGATTACTCAACCCAACAGCTCTC
AATTTATTTATTATCTTTTTTTTTTTGTAGAATGCATTAGC
Found at i:3015057 original size:21 final size:21
Alignment explanation
Indices: 3015031--3015070 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3015021 ATAGATGCCT
*
3015031 CAGTTTTCTTTTGAAAATCCA
1 CAGTTTGCTTTTGAAAATCCA
*
3015052 CAGTTTGCTTTTGGAAATC
1 CAGTTTGCTTTTGAAAATC
3015071 TATAGATTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.42
Consensus pattern (21 bp):
CAGTTTGCTTTTGAAAATCCA
Found at i:3015080 original size:21 final size:21
Alignment explanation
Indices: 3015038--3015081 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3015028 CCTCAGTTTT
*
3015038 CTTTTGAAAATCCACAGTTTG
1 CTTTTGAAAATCCACAGATTG
* * *
3015059 CTTTTGGAAATCTATAGATTG
1 CTTTTGAAAATCCACAGATTG
3015080 CT
1 CT
3015082 GCTGAAATTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (21 bp):
CTTTTGAAAATCCACAGATTG
Found at i:3016655 original size:22 final size:22
Alignment explanation
Indices: 3016610--3016670 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
3016600 TGATCTAAGG
* *
3016610 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAACT
*
3016631 AAAAATAAAAGAAAATATAACT
1 AAAAATAAAAGAAAATAGAACT
*
3016653 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
3016671 GGAAGTCGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 11 0.33
22 21 0.64
23 1 0.03
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAACT
Found at i:3018908 original size:25 final size:25
Alignment explanation
Indices: 3018877--3018926 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3018867 TTTTATTTAG
3018877 TTTCTTTTAATTATAAAATTTAAGC
1 TTTCTTTTAATTATAAAATTTAAGC
3018902 TTTCTTTTAATTATAAAATTTAAGC
1 TTTCTTTTAATTATAAAATTTAAGC
3018927 AAAATTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (25 bp):
TTTCTTTTAATTATAAAATTTAAGC
Found at i:3018934 original size:25 final size:25
Alignment explanation
Indices: 3018881--3018934 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
3018871 ATTTAGTTTC
****
3018881 TTTTAATTATAAAATTTAAGCTTTC
1 TTTTAATTATAAAATTTAAGCAAAA
3018906 TTTTAATTATAAAATTTAAGCAAAA
1 TTTTAATTATAAAATTTAAGCAAAA
3018931 TTTT
1 TTTT
3018935 GAAGCCACGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.50
Consensus pattern (25 bp):
TTTTAATTATAAAATTTAAGCAAAA
Found at i:3025535 original size:19 final size:20
Alignment explanation
Indices: 3025513--3025552 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3025503 GATATTTTAG
*
3025513 TTATTTT-AATGTTTTTATT
1 TTATTTTCAATGTTTTAATT
*
3025532 TTATTTTCCATGTTTTAATT
1 TTATTTTCAATGTTTTAATT
3025552 T
1 T
3025553 ATAGCATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (20 bp):
TTATTTTCAATGTTTTAATT
Found at i:3026203 original size:20 final size:20
Alignment explanation
Indices: 3026175--3026241 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
3026165 GCACGTCAAC
*
3026175 AAATAATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
3026195 AAATTATTTTTTAAAA-TA-TA
1 AAATTA--TTTTAAAATTATTA
3026215 AAATTA--TTAAAATTATTTTA
1 AAATTATTTTAAAATTA--TTA
3026235 AAATTAT
1 AAATTAT
3026242 AATCATCATC
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
16 6 0.15
17 2 0.05
20 21 0.54
21 2 0.05
22 8 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:3040845 original size:5 final size:5
Alignment explanation
Indices: 3040827--3040881 Score: 51
Period size: 5 Copynumber: 11.0 Consensus size: 5
3040817 GTTTTGAGCA
* * *
3040827 ATTTA ATTTT -TTTT ATTTT ATGTT ATTTT AATTTTT GTTTT ATTTT -TTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT -A-TTTT ATTTT ATTTT ATTTT
3040877 ATTTT
1 ATTTT
3040882 CCATTCTCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
4 8 0.20
5 28 0.68
6 1 0.02
7 4 0.10
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:3040867 original size:22 final size:20
Alignment explanation
Indices: 3040836--3040881 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
3040826 AATTTAATTT
3040836 TTTTTATTTTATGTTATTTTAA
1 TTTTTATTTTAT-TT-TTTTAA
* *
3040858 TTTTTGTTTTATTTTTTTTA
1 TTTTTATTTTATTTTTTTAA
3040878 TTTT
1 TTTT
3040882 CCATTCTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 2 0.09
22 11 0.50
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.80
Consensus pattern (20 bp):
TTTTTATTTTATTTTTTTAA
Found at i:3046365 original size:17 final size:17
Alignment explanation
Indices: 3046322--3046367 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
3046312 TTTTTTTTAT
3046322 AACATGCTTGTTAAAAC
1 AACATGCTTGTTAAAAC
*
3046339 -A-TTGGTCTTGTTAAAAC
1 AACAT-G-CTTGTTAAAAC
3046356 AACATGCTTGTT
1 AACATGCTTGTT
3046368 GCCGATTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 8
0.70 0.06 0.24
Matches are distributed among these distances:
15 1 0.04
16 2 0.09
17 17 0.74
18 2 0.09
19 1 0.04
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (17 bp):
AACATGCTTGTTAAAAC
Found at i:3050793 original size:28 final size:27
Alignment explanation
Indices: 3050737--3050791 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
3050727 CCGCATAGTA
3050737 TAAAATACAATGGAACAATCCAGGGTT
1 TAAAATACAATGGAACAATCCAGGGTT
*
3050764 TAAAATATATATGGAA-AA-CCGAGGGTT
1 TAAAATACA-ATGGAACAATCC-AGGGTT
3050791 T
1 T
3050792 TAGAGGAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 2 0.08
27 17 0.68
28 6 0.24
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (27 bp):
TAAAATACAATGGAACAATCCAGGGTT
Found at i:3053510 original size:269 final size:272
Alignment explanation
Indices: 3053024--3053531 Score: 835
Period size: 269 Copynumber: 1.9 Consensus size: 272
3053014 TAGATTACCT
3053024 TTTTTGGAAGTTATTGCCAAGTTGTAGTATTTTCTTTTTTTTTTTGGTGGAACAAGTTGTAGCGT
1 TTTTTGGAAGTTATTGCCAAGTTGTAGTA--TTCTTTTTTTTTTTGGTGGAACAA--TGTAGCGT
* *
3053089 TTTATTAAATAATACATCATATTTAAGTTTTAACTTTAAAATATGAACTCAACAAGCGATTCTAG
62 TTTATTAAATAATACATCATATTTAAGTTTTAACTTTAAAATATGAACTCAACAAGCGACTCTAA
* *
3053154 TGAAAAAAAAAGATATTATTCATTTTAAGGGTTTCAGGTTTGAGTACTTGTGTGTGCAAGGTATT
127 TGAAAAAAAAAGATATTATTCATTTTAAGGGTTTCAGGTTTGAGCACCTGTGTGTGCAAGGTATT
*
3053219 TGTGTCTTATTAAAAGGTTAAAAAAGTATGAACAGATATTACTATATAATCACACCAATATATTA
192 TGTGTCTTATCAAAAGGTTAAAAAAGTATGAACAGATATTACTATATAATCACACCAATATATTA
3053284 CTTTAAAATATAAATA
257 CTTTAAAATATAAATA
3053300 TTTTTGGAAGTTATTGCCAAGTTGTAGTA-T-TTTTTTTTTTTGGTGGAACAA-GTAGCGTTTTA
1 TTTTTGGAAGTTATTGCCAAGTTGTAGTATTCTTTTTTTTTTTGGTGGAACAATGTAGCGTTTTA
* * * *
3053362 TTAAATAATACATCATATTTAAGTTTTAATTTTAAAATATGAACTTAACAAGTGGCTCTAATG-A
66 TTAAATAATACATCATATTTAAGTTTTAACTTTAAAATATGAACTCAACAAGCGACTCTAATGAA
* *
3053426 AAAAAATGATAGTTATTCATTTTAAGGGTTTCAGGTTTGAGCACCTGTGTGTGCAAGGTGTTTGT
131 AAAAAAAGATA-TTATTCATTTTAAGGGTTTCAGGTTTGAGCACCTGTGTGTGCAAGGTATTTGT
*
3053491 GTCTTATCAAAAGGTTAAAAAAGTATGAATAGATATTACTA
195 GTCTTATCAAAAGGTTAAAAAAGTATGAACAGATATTACTA
3053532 ACAGATATTA
Statistics
Matches: 219, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
268 11 0.05
269 157 0.72
272 21 0.10
273 1 0.00
276 29 0.13
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (272 bp):
TTTTTGGAAGTTATTGCCAAGTTGTAGTATTCTTTTTTTTTTTGGTGGAACAATGTAGCGTTTTA
TTAAATAATACATCATATTTAAGTTTTAACTTTAAAATATGAACTCAACAAGCGACTCTAATGAA
AAAAAAAGATATTATTCATTTTAAGGGTTTCAGGTTTGAGCACCTGTGTGTGCAAGGTATTTGTG
TCTTATCAAAAGGTTAAAAAAGTATGAACAGATATTACTATATAATCACACCAATATATTACTTT
AAAATATAAATA
Found at i:3053752 original size:23 final size:24
Alignment explanation
Indices: 3053721--3053767 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
3053711 AATCATTATA
3053721 TTATAAATTAATTAAATTTAATTT
1 TTATAAATTAATTAAATTTAATTT
* *
3053745 TTAT-AATTAATTTATTTTAATTT
1 TTATAAATTAATTAAATTTAATTT
3053768 ATGTATCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTATAAATTAATTAAATTTAATTT
Found at i:3054414 original size:29 final size:31
Alignment explanation
Indices: 3054382--3054452 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 31
3054372 AAATAAAAAA
* *
3054382 TTCATATATAAAATTACA-A-AAAATCAAAG
1 TTCATGTATAAAATGACACATAAAATCAAAG
* * *
3054411 TTCATGTATATAATGACACATTAAATCATAG
1 TTCATGTATAAAATGACACATAAAATCAAAG
3054442 TTCATGTATAA
1 TTCATGTATAA
3054453 TTTTAAGATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 15 0.44
30 1 0.03
31 18 0.53
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.34
Consensus pattern (31 bp):
TTCATGTATAAAATGACACATAAAATCAAAG
Found at i:3057604 original size:43 final size:43
Alignment explanation
Indices: 3057556--3057641 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
3057546 AGTAAGCTAT
*
3057556 ATCTCTATGATAACCTATGTATCTTGCAAAAAGCATCAGTGAA
1 ATCTCTATGATAACCTATATATCTTGCAAAAAGCATCAGTGAA
3057599 ATCTCTATGATAACCTATATATCTTGCAAAAAGCATCAGTGAA
1 ATCTCTATGATAACCTATATATCTTGCAAAAAGCATCAGTGAA
3057642 TCAGATGATG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (43 bp):
ATCTCTATGATAACCTATATATCTTGCAAAAAGCATCAGTGAA
Found at i:3067100 original size:20 final size:22
Alignment explanation
Indices: 3067061--3067120 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
3067051 ATTTTTTAAA
3067061 ATTTTAAAAAAAGTATAAAATT
1 ATTTTAAAAAAAGTATAAAATT
3067083 ATTTTAAAAAAA-TA-AAAATT
1 ATTTTAAAAAAAGTATAAAATT
*
3067103 A--TTAAAATAAGTATAAAA
1 ATTTTAAAAAAAGTATAAAA
3067121 AATATATATT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
18 8 0.23
19 2 0.06
20 11 0.31
21 2 0.06
22 12 0.34
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (22 bp):
ATTTTAAAAAAAGTATAAAATT
Found at i:3067928 original size:39 final size:40
Alignment explanation
Indices: 3067885--3067960 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
3067875 ATAGTAACTT
*
3067885 TTTGTTTTGT-ACTTTT-AGAT-TTATTTTTACAAAATTAAC
1 TTTGTTTTATGACTTTTGA-ATATTA-TTTTACAAAATTAAC
3067924 TTTGTTTTATGACTTTTGAATATTATTTTACAAAATT
1 TTTGTTTTATGACTTTTGAATATTATTTTACAAAATT
3067961 TTGAGGGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
39 9 0.27
40 20 0.61
41 4 0.12
ACGTcount: A:0.29, C:0.07, G:0.08, T:0.57
Consensus pattern (40 bp):
TTTGTTTTATGACTTTTGAATATTATTTTACAAAATTAAC
Found at i:3068947 original size:50 final size:50
Alignment explanation
Indices: 3068887--3068992 Score: 167
Period size: 50 Copynumber: 2.1 Consensus size: 50
3068877 GGGCAGTTAG
* *
3068887 TTTGTGAGAAATCATTAACTGAAGAACATATTTCGAGAAGAATCAATTCA
1 TTTGTAAGAAATCATTAACTGAAGAACAAATTTCGAGAAGAATCAATTCA
* * *
3068937 TTTGTAAGAAATCATTATCTGACGACCAAATTTCGAGAAGAATCAATTCA
1 TTTGTAAGAAATCATTAACTGAAGAACAAATTTCGAGAAGAATCAATTCA
3068987 TTTGTA
1 TTTGTA
3068993 TTTGGTTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (50 bp):
TTTGTAAGAAATCATTAACTGAAGAACAAATTTCGAGAAGAATCAATTCA
Found at i:3073170 original size:16 final size:17
Alignment explanation
Indices: 3073149--3073182 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3073139 ATGACAAATG
3073149 ATAATAT-CTTATCAAA
1 ATAATATGCTTATCAAA
*
3073165 ATAATATGGTTATCAAA
1 ATAATATGCTTATCAAA
3073182 A
1 A
3073183 GTGATTTGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (17 bp):
ATAATATGCTTATCAAA
Found at i:3074229 original size:3 final size:3
Alignment explanation
Indices: 3074221--3074252 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3074211 ACATAGTAGG
3074221 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3074253 ATTAAGCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3082726 original size:15 final size:16
Alignment explanation
Indices: 3082697--3082729 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
3082687 TAAAAAATAG
3082697 AATATTTATAATATTA
1 AATATTTATAATATTA
3082713 AATATTTA-AATATTA
1 AATATTTATAATATTA
3082728 AA
1 AA
3082730 AAATAGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATATTTATAATATTA
Found at i:3086150 original size:15 final size:15
Alignment explanation
Indices: 3086104--3086155 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
3086094 AAATAAAAAA
*
3086104 AATATTAAATATTA-
1 AATATAAAATATTAT
*
3086118 AATATTAAAATATAAT
1 AATA-TAAAATATTAT
*
3086134 AATATAAAAAATTAT
1 AATATAAAATATTAT
*
3086149 AAAATAA
1 AATATAA
3086156 TATGAACGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 4 0.13
15 23 0.74
16 4 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATATAAAATATTAT
Found at i:3086155 original size:23 final size:22
Alignment explanation
Indices: 3086101--3086157 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
3086091 AATAAATAAA
* * *
3086101 AAAAATATTAAATATTAAATATT
1 AAAAATAAT-AATATAAAAAATT
3086124 AAAATATAATAATATAAAAAATT
1 AAAA-ATAATAATATAAAAAATT
3086147 ATAAAATAATA
1 A-AAAATAATA
3086158 TGAACGAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 22 0.76
24 7 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAAATAATAATATAAAAAATT
Found at i:3090261 original size:22 final size:22
Alignment explanation
Indices: 3090204--3090246 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
3090194 CGATCTGAGG
*
3090204 AAAAATAAAA-TAAACAGAATT
1 AAAAATAAAAGAAAACAGAATT
3090225 AAAAATAAAAGAAAACAGAATT
1 AAAAATAAAAGAAAACAGAATT
3090247 GAAAGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.72, C:0.05, G:0.07, T:0.16
Consensus pattern (22 bp):
AAAAATAAAAGAAAACAGAATT
Found at i:3092324 original size:24 final size:26
Alignment explanation
Indices: 3092297--3092344 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
3092287 AGAGAAATGT
3092297 AAATG-TG-ATATATGAAATTATGAG
1 AAATGATGAATATATGAAATTATGAG
* *
3092321 AAATGATGAATATGTGAGATTATG
1 AAATGATGAATATATGAAATTATG
3092345 CCCATGTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 2 0.10
26 13 0.65
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (26 bp):
AAATGATGAATATATGAAATTATGAG
Found at i:3092482 original size:20 final size:21
Alignment explanation
Indices: 3092428--3092494 Score: 82
Period size: 20 Copynumber: 3.1 Consensus size: 21
3092418 AGCACGTTTC
*
3092428 GTGCCCTCTGTTCAGCACTGTGT
1 GTGCCCTCTGTTCAACAC--TGT
3092451 GTGCCCTCTGTTCAACACTGT
1 GTGCCCTCTGTTCAACACTGT
* *
3092472 GTG-CTTCTGTTTAACACTGT
1 GTGCCCTCTGTTCAACACTGT
3092492 GTG
1 GTG
3092495 TGCTTCTGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
20 18 0.44
21 6 0.15
23 17 0.41
ACGTcount: A:0.12, C:0.27, G:0.24, T:0.37
Consensus pattern (21 bp):
GTGCCCTCTGTTCAACACTGT
Found at i:3092497 original size:22 final size:22
Alignment explanation
Indices: 3092434--3092519 Score: 88
Period size: 22 Copynumber: 4.0 Consensus size: 22
3092424 TTTCGTGCCC
* *
3092434 TCTGTTCAGCACTGTGTGTGCCC
1 TCTGTTCAACACTGTGTGTG-CT
3092457 TCTGTTCAACAC--TGTGTGCT
1 TCTGTTCAACACTGTGTGTGCT
*
3092477 TCTGTTTAACACTGTGTGTGCT
1 TCTGTTCAACACTGTGTGTGCT
* *
3092499 TCTGATT-AGCACTTTGTGTGC
1 TCTG-TTCAACACTGTGTGTGC
3092520 CTACTGTTGC
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
20 12 0.22
21 6 0.11
22 24 0.44
23 13 0.24
ACGTcount: A:0.13, C:0.23, G:0.23, T:0.41
Consensus pattern (22 bp):
TCTGTTCAACACTGTGTGTGCT
Found at i:3094836 original size:12 final size:14
Alignment explanation
Indices: 3094819--3094850 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3094809 TTACATTGAT
3094819 AATATAT-AA-TAA
1 AATATATGAATTAA
3094831 AATATATGAATTAA
1 AATATATGAATTAA
3094845 AATATA
1 AATATA
3094851 GGTAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 2 0.11
14 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (14 bp):
AATATATGAATTAA
Found at i:3101035 original size:34 final size:35
Alignment explanation
Indices: 3100997--3101065 Score: 81
Period size: 34 Copynumber: 2.0 Consensus size: 35
3100987 TTTACTATCT
* *
3100997 TTTTTATTG-TATTTTAA-ATTTTATAGTTATTAAG
1 TTTTT-TTGATATTTTAAGATATTATAGTTATGAAG
*
3101031 -TTTTTTGATATTTTAAGATATTGTAGTTATGAAG
1 TTTTTTTGATATTTTAAGATATTATAGTTATGAAG
3101065 T
1 T
3101066 CGGAAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
32 3 0.10
33 12 0.41
34 14 0.48
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (35 bp):
TTTTTTTGATATTTTAAGATATTATAGTTATGAAG
Found at i:3125981 original size:12 final size:12
Alignment explanation
Indices: 3125964--3125994 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3125954 AGAATTTTAT
*
3125964 ATAATTTGTAAC
1 ATAATTTATAAC
3125976 ATAATTTATAAC
1 ATAATTTATAAC
3125988 ATAATTT
1 ATAATTT
3125995 TTATTGCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (12 bp):
ATAATTTATAAC
Found at i:3128613 original size:19 final size:19
Alignment explanation
Indices: 3128589--3128628 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3128579 TTCTGTTCAA
*
3128589 TTTAAT-TTTTGTATTTATT
1 TTTAATATTTT-TAATTATT
3128608 TTTAATATTTTTAATTATT
1 TTTAATATTTTTAATTATT
3128627 TT
1 TT
3128629 AAAGTCAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTAATATTTTTAATTATT
Found at i:3132164 original size:13 final size:13
Alignment explanation
Indices: 3132146--3132175 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3132136 TATTATTTTT
*
3132146 ATTTTTAGTTATA
1 ATTTTTAATTATA
3132159 ATTTTTAATTATA
1 ATTTTTAATTATA
3132172 ATTT
1 ATTT
3132176 GAAATAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (13 bp):
ATTTTTAATTATA
Found at i:3132252 original size:19 final size:20
Alignment explanation
Indices: 3132204--3132253 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
3132194 ATTATAATTG
* *
3132204 TTTTAATTTTATTTTTTAAA
1 TTTTAATATTATATTTTAAA
*
3132224 TTTGAA-ATTATATTTT-AA
1 TTTTAATATTATATTTTAAA
3132242 TTTTAATATTAT
1 TTTTAATATTAT
3132254 CAGAATAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 7 0.28
19 13 0.52
20 5 0.20
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTAATATTATATTTTAAA
Found at i:3132432 original size:18 final size:18
Alignment explanation
Indices: 3132402--3132467 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
3132392 AAATTCTTAT
*
3132402 TAATTT-AATTTCAAATT
1 TAATTTAAATTTCAAATA
** *
3132419 TAATTTTCATTTCAACTA
1 TAATTTAAATTTCAAATA
3132437 TAATTTAAATTTCAAACTA
1 TAATTTAAATTTCAAA-TA
**
3132456 GCATTTAAATTT
1 TAATTTAAATTT
3132468 TAAACTAGTA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
17 6 0.15
18 21 0.54
19 12 0.31
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (18 bp):
TAATTTAAATTTCAAATA
Found at i:3132461 original size:19 final size:19
Alignment explanation
Indices: 3132439--3132480 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3132429 TTCAACTATA
3132439 ATTTAAATTTCAAACTAGC
1 ATTTAAATTTCAAACTAGC
* *
3132458 ATTTAAATTTTAAACTAGT
1 ATTTAAATTTCAAACTAGC
3132477 ATTT
1 ATTT
3132481 TATTTTGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (19 bp):
ATTTAAATTTCAAACTAGC
Found at i:3143739 original size:11 final size:12
Alignment explanation
Indices: 3143694--3143740 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
3143684 GTTCACGAAC
* *
3143694 AAGCTCGTCTAA
1 AAGCTCGTTTAT
3143706 AAGCTCGTTTAT
1 AAGCTCGTTTAT
*
3143718 AAGCTCATTTAT
1 AAGCTCGTTTAT
3143730 -AGCTCGTTTAT
1 AAGCTCGTTTAT
3143741 TTATTAATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
11 10 0.32
12 21 0.68
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (12 bp):
AAGCTCGTTTAT
Found at i:3151147 original size:3 final size:3
Alignment explanation
Indices: 3151141--3151167 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3151131 AATAATAACA
3151141 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
3151168 TCTTTGGCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3155116 original size:19 final size:18
Alignment explanation
Indices: 3155094--3155130 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
3155084 GTCACTCATC
*
3155094 GTAATCAAATTTGTCTATT
1 GTAATCAAAATTGT-TATT
3155113 GTAATCAAAATTGTTATT
1 GTAATCAAAATTGTTATT
3155131 AACTTTCATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (18 bp):
GTAATCAAAATTGTTATT
Found at i:3155890 original size:30 final size:30
Alignment explanation
Indices: 3155833--3155890 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
3155823 GGGAGAGAAG
* **
3155833 TAAAACTTTTGGAGAGAAAATGGAAAGGAA
1 TAAAAATTTTGGAGAGAAAATAAAAAGGAA
3155863 TAAAAATTTTGG-GAGAAAAGTAAAAAGG
1 TAAAAATTTTGGAGAGAAAA-TAAAAAGG
3155891 TTTGGGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.52, C:0.02, G:0.26, T:0.21
Consensus pattern (30 bp):
TAAAAATTTTGGAGAGAAAATAAAAAGGAA
Found at i:3155944 original size:9 final size:9
Alignment explanation
Indices: 3155930--3155966 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
3155920 TATAATTTGA
*
3155930 TATTCGATT
1 TATTCGAAT
3155939 TATTCGAAT
1 TATTCGAAT
*
3155948 TATTCGAGT
1 TATTCGAAT
3155957 TATTCGAAT
1 TATTCGAAT
3155966 T
1 T
3155967 CGAAAACCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:3155953 original size:18 final size:18
Alignment explanation
Indices: 3155930--3155966 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3155920 TATAATTTGA
*
3155930 TATTCGATTTATTCGAAT
1 TATTCGAGTTATTCGAAT
3155948 TATTCGAGTTATTCGAAT
1 TATTCGAGTTATTCGAAT
3155966 T
1 T
3155967 CGAAAACCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.49
Consensus pattern (18 bp):
TATTCGAGTTATTCGAAT
Found at i:3158172 original size:24 final size:24
Alignment explanation
Indices: 3158138--3158185 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
3158128 ATGGATGTTC
*
3158138 AACCTTTCATCTTCCTTAACCTTT
1 AACCTTCCATCTTCCTTAACCTTT
*
3158162 AACCTTCCATCTTCTTTAACCTTT
1 AACCTTCCATCTTCCTTAACCTTT
3158186 TATATTCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.33, G:0.00, T:0.46
Consensus pattern (24 bp):
AACCTTCCATCTTCCTTAACCTTT
Found at i:3164211 original size:2 final size:2
Alignment explanation
Indices: 3164120--3164195 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
3164110 AGACTGAAGC
3164120 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3164162 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3164196 CTGCTTGCCT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3172284 original size:3 final size:3
Alignment explanation
Indices: 3172278--3172310 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3172268 TCTCTAAGTT
3172278 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
3172311 GCAAGGAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:3175330 original size:31 final size:30
Alignment explanation
Indices: 3175276--3175334 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
3175266 TTTCAATCAT
*
3175276 TATATTTTTTGAATTGAACAATTTTAATCCA
1 TATACTTTTTGAATTGAACAA-TTTAATCCA
*
3175307 TATACTTTTTGAAATTTAA-AATTTAATC
1 TATACTTTTTG-AATTGAACAATTTAATC
3175335 TTGATCCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.28
31 12 0.48
32 6 0.24
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.49
Consensus pattern (30 bp):
TATACTTTTTGAATTGAACAATTTAATCCA
Found at i:3187659 original size:2 final size:2
Alignment explanation
Indices: 3187652--3187677 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3187642 CCATTGTACC
3187652 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3187678 TACTTTCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3189789 original size:21 final size:21
Alignment explanation
Indices: 3189765--3189812 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
3189755 TAAAAAAAAT
*
3189765 TAAAAATAT-TTTTTAAAATTC
1 TAAAAATATAATTTT-AAATTC
* *
3189786 TAAACATATAATTTTAAATTT
1 TAAAAATATAATTTTAAATTC
3189807 TAAAAA
1 TAAAAA
3189813 GTAAAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAAATATAATTTTAAATTC
Found at i:3189832 original size:20 final size:19
Alignment explanation
Indices: 3189807--3189865 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
3189797 TTTTAAATTT
3189807 TAAAAAGTAAAAATAATATA
1 TAAAAA-TAAAAATAATATA
*
3189827 TAAAAATTAAAA-AATGATA
1 TAAAAATAAAAATAAT-ATA
*
3189846 TTAAAATTAAAAAT-ATATA
1 -TAAAAATAAAAATAATATA
3189865 T
1 T
3189866 TTAATTTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
18 4 0.12
19 11 0.33
20 18 0.55
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (19 bp):
TAAAAATAAAAATAATATA
Found at i:3189865 original size:19 final size:19
Alignment explanation
Indices: 3189809--3189866 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
3189799 TTAAATTTTA
* *
3189809 AAAAGTAAAAATAATATATA
1 AAAATTAAAAAT-ATATATT
3189829 AAAATTAAAAA-ATGATATT
1 AAAATTAAAAATAT-ATATT
3189848 AAAATTAAAAATATATATT
1 AAAATTAAAAATATATATT
3189867 TAATTTTCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 2 0.06
19 20 0.59
20 12 0.35
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (19 bp):
AAAATTAAAAATATATATT
Found at i:3189953 original size:19 final size:19
Alignment explanation
Indices: 3189929--3189968 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3189919 TTTTATAAAA
3189929 AATTATTTTTAAACTTTTT
1 AATTATTTTTAAACTTTTT
* *
3189948 AATTATTTTTACATTTTTT
1 AATTATTTTTAAACTTTTT
3189967 AA
1 AA
3189969 ATAATAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
AATTATTTTTAAACTTTTT
Found at i:3190026 original size:16 final size:15
Alignment explanation
Indices: 3189990--3190024 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3189980 ATTTTTTATT
* *
3189990 ATTTTATTTTTGTAA
1 ATTTTAGTTTTATAA
3190005 ATTTTAGTTTTATAA
1 ATTTTAGTTTTATAA
3190020 ATTTT
1 ATTTT
3190025 TATACTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (15 bp):
ATTTTAGTTTTATAA
Found at i:3190097 original size:24 final size:24
Alignment explanation
Indices: 3190052--3190097 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3190042 TCTATGTTTA
* *
3190052 TATATTTTTTGAATTTTCTATATT
1 TATATTTTTTGAATTGTATATATT
3190076 TATATTTTTT-AATGTGTATATA
1 TATATTTTTTGAAT-TGTATATA
3190098 CATTTAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (24 bp):
TATATTTTTTGAATTGTATATATT
Found at i:3203213 original size:15 final size:14
Alignment explanation
Indices: 3203191--3203222 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
3203181 TTTTATGGAA
3203191 TTTAATTTTTAATT
1 TTTAATTTTTAATT
3203205 TTTATATTTTTAATT
1 TTTA-ATTTTTAATT
3203220 TTT
1 TTT
3203223 TTAATTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTAATTTTTAATT
Found at i:3203230 original size:7 final size:7
Alignment explanation
Indices: 3203191--3203222 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
3203181 TTTTATGGAA
3203191 TTTAATT
1 TTTAATT
3203198 TTTAATT
1 TTTAATT
3203205 TTTATATT
1 TTTA-ATT
3203213 TTTAATT
1 TTTAATT
3203220 TTT
1 TTT
3203223 TTAATTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTAATT
Found at i:3203230 original size:15 final size:15
Alignment explanation
Indices: 3203191--3203230 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
3203181 TTTTATGGAA
3203191 TTTAATTTTTAATTTT
1 TTTAA-TTTTAATTTT
* *
3203207 TATATTTTTAATTTT
1 TTTAATTTTAATTTT
3203222 TTTAATTTT
1 TTTAATTTT
3203231 CATACTTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTAATTTTAATTTT
Found at i:3203243 original size:24 final size:24
Alignment explanation
Indices: 3203196--3203244 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3203186 TGGAATTTAA
* * **
3203196 TTTTTAATTTTTATATTTTTAATT
1 TTTTTAATTTTCATACTTAAAATT
3203220 TTTTTAATTTTCATACTTAAAATT
1 TTTTTAATTTTCATACTTAAAATT
3203244 T
1 T
3203245 AAATTTAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTTTAATTTTCATACTTAAAATT
Found at i:3209809 original size:16 final size:17
Alignment explanation
Indices: 3209788--3209821 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3209778 CTAAGAGCTT
3209788 GGCTTG-TGTAGCTTAG
1 GGCTTGATGTAGCTTAG
3209804 GGCTTGACTGTAGCTTAG
1 GGCTTGA-TGTAGCTTAG
3209822 ATACGTGTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.15, C:0.15, G:0.35, T:0.35
Consensus pattern (17 bp):
GGCTTGATGTAGCTTAG
Found at i:3228214 original size:21 final size:21
Alignment explanation
Indices: 3228161--3228215 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
3228151 TTGAAACAAT
*
3228161 AAATAAATAAAACTCTTTGCA
1 AAATAAATAAAAATCTTTGCA
* * *
3228182 AAAAAAAAAAAAATCTTTTCA
1 AAATAAATAAAAATCTTTGCA
*
3228203 AAATAAGTAAAAA
1 AAATAAATAAAAA
3228216 GAATTTCTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.64, C:0.09, G:0.04, T:0.24
Consensus pattern (21 bp):
AAATAAATAAAAATCTTTGCA
Found at i:3232573 original size:13 final size:13
Alignment explanation
Indices: 3232553--3232586 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3232543 TTCTAGTGTT
*
3232553 AATTTTTTTT-TC
1 AATTTTTTTTGAC
3232565 AATTTTTTTTGAC
1 AATTTTTTTTGAC
3232578 AATTTTTTT
1 AATTTTTTT
3232587 AAATTAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.71
Consensus pattern (13 bp):
AATTTTTTTTGAC
Found at i:3236690 original size:44 final size:43
Alignment explanation
Indices: 3236664--3236753 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 43
3236654 ACAACATTGT
3236664 TAAGAGAAGTAACCACGAATTCCAAACATAAATCGAAAAACAAA
1 TAAGAGAAGTAACCACGAATTCCAAACATAAATC-AAAAACAAA
3236708 TAAGAGAAGTAACCACGAATTCCAAACATAAATCGAAAAACAAA
1 TAAGAGAAGTAACCACGAATTCCAAACATAAATC-AAAAACAAA
3236752 TA
1 TA
3236754 TGTAAGAAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.57, C:0.18, G:0.11, T:0.14
Consensus pattern (43 bp):
TAAGAGAAGTAACCACGAATTCCAAACATAAATCAAAAACAAA
Found at i:3241329 original size:20 final size:19
Alignment explanation
Indices: 3241291--3241330 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
3241281 TGTAAAAGTG
*
3241291 CAACATTGTGAGGAAAGCT
1 CAACATTGTGAGCAAAGCT
*
3241310 CAACATTGGTGAGCACAGCT
1 CAACATT-GTGAGCAAAGCT
3241330 C
1 C
3241331 GTGCACATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.20
Consensus pattern (19 bp):
CAACATTGTGAGCAAAGCT
Found at i:3258983 original size:23 final size:22
Alignment explanation
Indices: 3258955--3259082 Score: 89
Period size: 23 Copynumber: 5.5 Consensus size: 22
3258945 ACACTAGTGC
3258955 GCCCTCTGTTTAGCA-TGTTTCGT
1 GCCCTCTGTTTAGCACT-TTT-GT
* * *
3258978 GCCCTCTGTTCAGCACAGTGTGT
1 GCCCTCTGTTTAGCAC-TTTTGT
*
3259001 GCCCTCTGTTATTAGCAC-TTCGT
1 GCCCTCTG-T-TTAGCACTTTTGT
*
3259024 GTCCCTCTGCTTAGCACTTTGTGT
1 G-CCCTCTGTTTAGCACTTT-TGT
* *
3259048 GCCCTCTGTTACCCAGCACTTATGT
1 GCCCTCTGTT---TAGCACTTTTGT
3259073 GCCCTCTGTT
1 GCCCTCTGTT
3259083 AAGTATTCCG
Statistics
Matches: 84, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
22 7 0.08
23 38 0.45
24 13 0.15
25 19 0.23
26 7 0.08
ACGTcount: A:0.11, C:0.31, G:0.20, T:0.38
Consensus pattern (22 bp):
GCCCTCTGTTTAGCACTTTTGT
Found at i:3259025 original size:25 final size:24
Alignment explanation
Indices: 3258996--3259083 Score: 92
Period size: 25 Copynumber: 3.7 Consensus size: 24
3258986 TTCAGCACAG
3258996 TGTGTGCCCTCTGTTATTAGCACT
1 TGTGTGCCCTCTGTTATTAGCACT
*
3259020 TCGTGT-CCCTCTG--CTTAGCACTT
1 T-GTGTGCCCTCTGTTATTAGCAC-T
**
3259043 TGTGTGCCCTCTGTTACCCAGCACT
1 TGTGTGCCCTCTGTTA-TTAGCACT
*
3259068 TATGTGCCCTCTGTTA
1 TGTGTGCCCTCTGTTA
3259084 AGTATTCCGG
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
22 11 0.21
23 9 0.17
24 8 0.15
25 20 0.38
26 5 0.09
ACGTcount: A:0.11, C:0.31, G:0.19, T:0.39
Consensus pattern (24 bp):
TGTGTGCCCTCTGTTATTAGCACT
Found at i:3264999 original size:2 final size:2
Alignment explanation
Indices: 3264992--3265024 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3264982 CCGAATTCCC
*
3264992 TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3265025 GATGTTGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3270999 original size:4 final size:4
Alignment explanation
Indices: 3270992--3271026 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
3270982 CATATATATT
*
3270992 TATG TATG TATG TATG TATG TATG TATG CATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
3271027 ACATGGTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:3276602 original size:69 final size:69
Alignment explanation
Indices: 3276552--3276704 Score: 218
Period size: 69 Copynumber: 2.2 Consensus size: 69
3276542 AAAATTATAA
* * * *
3276552 ATAA-CAAATCCAAATAATTATAACTAAAATCAATAAACATTCTTTAAAAAAAACAATAAATACA
1 ATAATCAAATCCAAATAAGTAGAACTAAAATCAATAAACACTATTTAAAAAAAACAATAAATACA
3276616 AAAC
66 AAAC
* * *
3276620 ATAATTAAATTCAAATAAGTAGAACTAAAATCAATAAACACTATTTAAAAAAATCAATAAATACA
1 ATAATCAAATCCAAATAAGTAGAACTAAAATCAATAAACACTATTTAAAAAAAACAATAAATACA
3276685 AAAC
66 AAAC
* *
3276689 ATAATTAAATCAAAAT
1 ATAATCAAATCCAAAT
3276705 TCAAAATATA
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
68 4 0.05
69 71 0.95
ACGTcount: A:0.61, C:0.12, G:0.01, T:0.25
Consensus pattern (69 bp):
ATAATCAAATCCAAATAAGTAGAACTAAAATCAATAAACACTATTTAAAAAAAACAATAAATACA
AAAC
Found at i:3279516 original size:31 final size:32
Alignment explanation
Indices: 3279492--3279562 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 32
3279482 TTTATTTTTC
3279492 ATTTATCATTATATTAAATT-ATTTAAATATT
1 ATTTATCATTATATTAAATTCATTTAAATATT
*
3279523 ATTTATCATTATATTTAAAAT--TTTAATATATT
1 ATTTATCATTATA-TTAAATTCATTTAA-ATATT
3279555 ATTGTATC
1 ATT-TATC
3279563 TTTAAATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
31 18 0.50
32 14 0.39
33 4 0.11
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.55
Consensus pattern (32 bp):
ATTTATCATTATATTAAATTCATTTAAATATT
Found at i:3286312 original size:58 final size:57
Alignment explanation
Indices: 3286231--3286386 Score: 174
Period size: 58 Copynumber: 2.7 Consensus size: 57
3286221 ATTAGATCTA
* *
3286231 AAAAAAAGCTTAGGTACCAAATTAGAAAAAAATGTCAAGTTC-AGT-TACAAATTGGATCC
1 AAAAAAA-TTTAGATACCAAATTAG-AAAAAATGTCAAGTTCGAGTAT-CAAATTGGAT-C
* * * *
3286290 AAAAAAATTTA-AGTATCAAATTAGGAAAATATGTCAAATTCGAGTATCAAATTGGGTC
1 AAAAAAATTTAGA-TACCAAATTA-GAAAAAATGTCAAGTTCGAGTATCAAATTGGATC
*
3286348 AAAAAAATTTAGATACCAAATTAGAAAAAATTTCAAGTT
1 AAAAAAATTTAGATACCAAATTAGAAAAAATGTCAAGTT
3286387 TAAGTACCAA
Statistics
Matches: 82, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
57 13 0.16
58 47 0.57
59 21 0.26
60 1 0.01
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.27
Consensus pattern (57 bp):
AAAAAAATTTAGATACCAAATTAGAAAAAATGTCAAGTTCGAGTATCAAATTGGATC
Found at i:3287456 original size:8 final size:8
Alignment explanation
Indices: 3287443--3287467 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3287433 GATTAGGTTG
3287443 ATTTAATT
1 ATTTAATT
3287451 ATTTAATT
1 ATTTAATT
3287459 ATTTAATT
1 ATTTAATT
3287467 A
1 A
3287468 ATATAATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTAATT
Found at i:3290532 original size:21 final size:20
Alignment explanation
Indices: 3290508--3290554 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
3290498 AACTACAACC
3290508 TTCTTCC-TTTCATCTCCACTT
1 TTCTTCCATTTCATCT-CA-TT
*
3290529 TTCTCCCATTTTCATCTCATT
1 TTCTTCCA-TTTCATCTCATT
3290550 TTCTT
1 TTCTT
3290555 TTCTGGGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 12 0.55
22 2 0.09
23 8 0.36
ACGTcount: A:0.11, C:0.34, G:0.00, T:0.55
Consensus pattern (20 bp):
TTCTTCCATTTCATCTCATT
Found at i:3297293 original size:13 final size:14
Alignment explanation
Indices: 3297275--3297307 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3297265 TTAAATTTTT
3297275 AAAAATTAAA-ATA
1 AAAAATTAAATATA
*
3297288 AAAAATTAAATTTA
1 AAAAATTAAATATA
3297302 AAAAAT
1 AAAAAT
3297308 ATATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAAATTAAATATA
Found at i:3302043 original size:2 final size:2
Alignment explanation
Indices: 3301991--3302024 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3301981 AAGTGTAGCA
*
3301991 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3302025 GTATTTCAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3315132 original size:28 final size:28
Alignment explanation
Indices: 3315101--3315156 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
3315091 AGAGATTTTA
3315101 AATTAT-T-TTAAATATAAAAATTAAAATT
1 AATTATATATTAAATA-AAAAA-TAAAATT
*
3315129 AATTATATATTAAATAAAAGATAAAATT
1 AATTATATATTAAATAAAAAATAAAATT
3315157 CGATTTTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 13 0.52
29 5 0.20
30 7 0.28
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (28 bp):
AATTATATATTAAATAAAAAATAAAATT
Found at i:3317723 original size:41 final size:41
Alignment explanation
Indices: 3317666--3317747 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
3317656 CCATATTACC
*
3317666 CTTCTTCCTCCTTCCTCATATATATACCCTATTATAGGGCA
1 CTTCTTCCTCCTTCCTCATATATATACCCTATTACAGGGCA
3317707 CTTCTTCCTCCTTCCTCATATATATACCCTATTACAGGGCA
1 CTTCTTCCTCCTTCCTCATATATATACCCTATTACAGGGCA
3317748 TTTAGGGTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.22, C:0.33, G:0.07, T:0.38
Consensus pattern (41 bp):
CTTCTTCCTCCTTCCTCATATATATACCCTATTACAGGGCA
Found at i:3318449 original size:2 final size:2
Alignment explanation
Indices: 3318442--3318471 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3318432 TCAGCAAAGA
*
3318442 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3318472 GGTACTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3326154 original size:144 final size:144
Alignment explanation
Indices: 3325894--3326175 Score: 546
Period size: 144 Copynumber: 2.0 Consensus size: 144
3325884 TTGGGGATGC
*
3325894 ATTCGCTTAGTTCTACCTTGTTTTGCATAGTTACACATTAATTCTTTAAGAAGAGTTAGAAGATG
1 ATTCGCTTAGTTCTACCTTGTTTTGCATAGTTACACATTAATTCTTCAAGAAGAGTTAGAAGATG
3325959 CAAATTGCTGGTGCAGTGTTGTTATCTCCCTCTCTCAACTTAGTTTATTTGCTCTCGTTGCAGAT
66 CAAATTGCTGGTGCAGTGTTGTTATCTCCCTCTCTCAACTTAGTTTATTTGCTCTCGTTGCAGAT
3326024 CCGCAAGTTAGTTT
131 CCGCAAGTTAGTTT
*
3326038 ATTCGCTTAGTTCTACCTTGTTTTGCATAGTTACACATTAATTCTTCAAGAAGAGTTCGAAGATG
1 ATTCGCTTAGTTCTACCTTGTTTTGCATAGTTACACATTAATTCTTCAAGAAGAGTTAGAAGATG
3326103 CAAATTGCTGGTGCAGTGTTGTTATCTCCCTCTCTCAACTTAGTTTATTTGCTCTCGTTGCAGAT
66 CAAATTGCTGGTGCAGTGTTGTTATCTCCCTCTCTCAACTTAGTTTATTTGCTCTCGTTGCAGAT
3326168 CCGCAAGT
131 CCGCAAGT
3326176 GGCTCTTTGG
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
144 136 1.00
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (144 bp):
ATTCGCTTAGTTCTACCTTGTTTTGCATAGTTACACATTAATTCTTCAAGAAGAGTTAGAAGATG
CAAATTGCTGGTGCAGTGTTGTTATCTCCCTCTCTCAACTTAGTTTATTTGCTCTCGTTGCAGAT
CCGCAAGTTAGTTT
Found at i:3329143 original size:20 final size:20
Alignment explanation
Indices: 3329113--3329164 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
3329103 TAGTGCGACA
* **
3329113 CAATTATACAAAACATTGGC
1 CAATTACACAAAACATTACC
* *
3329133 TAATTACACAAAATATTACC
1 CAATTACACAAAACATTACC
3329153 CAATTACACAAA
1 CAATTACACAAA
3329165 TTATTACAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.50, C:0.21, G:0.04, T:0.25
Consensus pattern (20 bp):
CAATTACACAAAACATTACC
Found at i:3329169 original size:20 final size:20
Alignment explanation
Indices: 3329134--3329171 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3329124 AACATTGGCT
3329134 AATTACACAAAATATTACCC
1 AATTACACAAAATATTACCC
*
3329154 AATTACACAAATTATTAC
1 AATTACACAAAATATTAC
3329172 AACATTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (20 bp):
AATTACACAAAATATTACCC
Found at i:3334176 original size:22 final size:23
Alignment explanation
Indices: 3334125--3334182 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
3334115 GCTAGGGAAA
*
3334125 CAGTAAGCACACACAGTGCAATC
1 CAGTAGGCACACACAGTGCAATC
*
3334148 CAGTAGGCACACACAGTGTAAT-
1 CAGTAGGCACACACAGTGCAATC
*
3334170 CAGTAGGCGCACA
1 CAGTAGGCACACA
3334183 TAGCACAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 12 0.38
23 20 0.62
ACGTcount: A:0.36, C:0.28, G:0.22, T:0.14
Consensus pattern (23 bp):
CAGTAGGCACACACAGTGCAATC
Found at i:3362513 original size:42 final size:42
Alignment explanation
Indices: 3362466--3362549 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
3362456 ATCCTCTAAC
3362466 TCCTTCAGCTGCTCAAGGAATTCATAGCAGTAAGAGCGATGA
1 TCCTTCAGCTGCTCAAGGAATTCATAGCAGTAAGAGCGATGA
*
3362508 TCCTTCTGCTGCTCAAGGAATTCATAGCAGTAAGAGCGATGA
1 TCCTTCAGCTGCTCAAGGAATTCATAGCAGTAAGAGCGATGA
3362550 AGCAGTGCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (42 bp):
TCCTTCAGCTGCTCAAGGAATTCATAGCAGTAAGAGCGATGA
Found at i:3383750 original size:31 final size:30
Alignment explanation
Indices: 3383707--3383764 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
3383697 AGAATGGTTA
3383707 AATTTTAGTTTTGATC-CTTATATTTTACTC
1 AATTTTAGTTTTGATCTC-TATATTTTACTC
3383737 AATTTTAAGTTTTGATCTCTATATTTTA
1 AATTTT-AGTTTTGATCTCTATATTTTA
3383765 ATTTTTGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 6 0.23
31 19 0.73
32 1 0.04
ACGTcount: A:0.26, C:0.10, G:0.07, T:0.57
Consensus pattern (30 bp):
AATTTTAGTTTTGATCTCTATATTTTACTC
Found at i:3388725 original size:25 final size:22
Alignment explanation
Indices: 3388697--3388741 Score: 63
Period size: 25 Copynumber: 1.9 Consensus size: 22
3388687 AGACGAGGAT
3388697 CGGCAATCTCTCATCTCTTTTTTAC
1 CGGCAATCT-T-AT-TCTTTTTTAC
3388722 CGGCAATCTTATTCTTTTTT
1 CGGCAATCTTATTCTTTTTT
3388742 GGATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 2 0.10
24 1 0.05
25 9 0.45
ACGTcount: A:0.16, C:0.27, G:0.09, T:0.49
Consensus pattern (22 bp):
CGGCAATCTTATTCTTTTTTAC
Found at i:3403863 original size:34 final size:34
Alignment explanation
Indices: 3403822--3403956 Score: 252
Period size: 34 Copynumber: 4.0 Consensus size: 34
3403812 TTATCTTGTC
*
3403822 TCTTAGTTAATGCTCAATATATTACTAACTGGTT
1 TCTTAGTTAATGCTCAATATGTTACTAACTGGTT
3403856 TCTTAGTTAATGCTCAATATGTTACTAACTGGTT
1 TCTTAGTTAATGCTCAATATGTTACTAACTGGTT
*
3403890 TCTTAGTTAATGCTCAATATGTTACTATCTGGTT
1 TCTTAGTTAATGCTCAATATGTTACTAACTGGTT
3403924 TCTTAGTTAATGCTCAATATGTTACTAACTGGT
1 TCTTAGTTAATGCTCAATATGTTACTAACTGGT
3403957 CTTTTCTTAG
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 98 1.00
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (34 bp):
TCTTAGTTAATGCTCAATATGTTACTAACTGGTT
Found at i:3413831 original size:29 final size:29
Alignment explanation
Indices: 3413798--3413856 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3413788 TATTTAACCT
3413798 AATTTCAGGAGCAGTTTTGAGTATTTTAG
1 AATTTCAGGAGCAGTTTTGAGTATTTTAG
3413827 AATTTCAGGAGCAGTTTTGAGTATTTTAG
1 AATTTCAGGAGCAGTTTTGAGTATTTTAG
3413856 A
1 A
3413857 CCTTAACTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.41
Consensus pattern (29 bp):
AATTTCAGGAGCAGTTTTGAGTATTTTAG
Found at i:3418654 original size:20 final size:19
Alignment explanation
Indices: 3418618--3418660 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
3418608 AAATGTATAT
**
3418618 AAAATAAATATTTTTTATC
1 AAAATAAATATAATTTATC
*
3418637 AAAATAATATATAATTTATT
1 AAAATAA-ATATAATTTATC
3418657 AAAA
1 AAAA
3418661 ACTAAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATAAATATAATTTATC
Found at i:3454668 original size:17 final size:17
Alignment explanation
Indices: 3454646--3454695 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
3454636 TGGTTGAATC
*
3454646 AATTAAATTAATGATTT
1 AATTAAATAAATGATTT
*
3454663 AATTAAATAAATTATTT
1 AATTAAATAAATGATTT
*
3454680 TATTAAA-AAATCGATT
1 AATTAAATAAAT-GATT
3454696 CGTACCAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 4 0.14
17 24 0.86
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (17 bp):
AATTAAATAAATGATTT
Found at i:3454805 original size:19 final size:19
Alignment explanation
Indices: 3454781--3454821 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
3454771 CCAACTGATT
3454781 AACCCAATTCGATACAAAC
1 AACCCAATTCGATACAAAC
3454800 AACCCAATTCGATACAAAC
1 AACCCAATTCGATACAAAC
3454819 AAC
1 AAC
3454822 TATTGTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.49, C:0.32, G:0.05, T:0.15
Consensus pattern (19 bp):
AACCCAATTCGATACAAAC
Found at i:3457547 original size:13 final size:13
Alignment explanation
Indices: 3457529--3457555 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3457519 AAAATTTGAT
3457529 TCAATTTTTATAA
1 TCAATTTTTATAA
3457542 TCAATTTTTATAA
1 TCAATTTTTATAA
3457555 T
1 T
3457556 AGATATAAAA
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:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (13 bp):
TCAATTTTTATAA
Found at i:3459060 original size:55 final size:59
Alignment explanation
Indices: 3458931--3459083 Score: 163
Period size: 55 Copynumber: 2.6 Consensus size: 59
3458921 AAAAAAATTG
* * *
3458931 GGGTGTTGGCCATGCAATGGTCGACACCCCCTTTTTATCAGAAAAAAAATTTCAGAATTTTT
1 GGGTGTAGGCCATGCAATGATCGACACCCCC-TATT-TCA-AAAAAAAATTTCAGAATTTTT
* *
3458993 GGGTGTAAGCCATGCAATGATCGACACCCCCTATTTC-AAAAAAAA-TT-A-CATTTTT
1 GGGTGTAGGCCATGCAATGATCGACACCCCCTATTTCAAAAAAAAATTTCAGAATTTTT
* * *
3459048 GGGTGTGGGCCAT-TACATGACCGACACCCCCTATTT
1 GGGTGTAGGCCATGCA-ATGATCGACACCCCCTATTT
3459084 TTCGAGAAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
54 1 0.01
55 36 0.44
56 1 0.01
57 2 0.02
58 8 0.10
60 2 0.02
61 3 0.04
62 28 0.35
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (59 bp):
GGGTGTAGGCCATGCAATGATCGACACCCCCTATTTCAAAAAAAAATTTCAGAATTTTT
Found at i:3459199 original size:102 final size:102
Alignment explanation
Indices: 3459024--3459224 Score: 314
Period size: 102 Copynumber: 2.0 Consensus size: 102
3459014 CGACACCCCC
*
3459024 TATTTCAAAAAAAATTACATTTTTGGGTGTGGGCCATTACATGACCGACACCCCCTATTTTTCGA
1 TATTTCAAAAAAAATTACATTTTTGGGTGTGGGCCATTACATGACCGACACCCCCTATTTCTCGA
* *
3459089 GAAAAAAA-TTCAATTTTTTTTTGTGTTGGCCATTTG
66 GAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATTTG
* * * * *
3459125 TATTTCAAAAAAAAATTGCATTTTTGGGTGTTGGCCATTGCATGGCCGACACCCCTTATTTCTCG
1 TATTTC-AAAAAAAATTACATTTTTGGGTGTGGGCCATTACATGACCGACACCCCCTATTTCTCG
3459190 AGAAAAAAATTTCAAATTTTTTTGGTGTTGGCCAT
65 AGAAAAAAATTTCAAATTTTTTTGGTGTTGGCCAT
3459225 CAAATGGCCG
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 6 0.07
102 61 0.68
103 23 0.26
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (102 bp):
TATTTCAAAAAAAATTACATTTTTGGGTGTGGGCCATTACATGACCGACACCCCCTATTTCTCGA
GAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATTTG
Found at i:3459232 original size:62 final size:60
Alignment explanation
Indices: 3459132--3459279 Score: 181
Period size: 62 Copynumber: 2.5 Consensus size: 60
3459122 TTGTATTTCA
** * *** * *
3459132 AAAAAAAATTGCA-TTTTTGGGTGTTGGCCATTGCATGGCCGACACCCCTTATTTCTCGAG
1 AAAAAAAATTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCT-GTTCTCGAG
* *
3459192 AAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTGTTCTGGAG
1 AAAAAAAATT-AAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTGTTCTCGAG
3459253 AAAAAAAATTAAATTTTTTTGGTGTTG
1 AAAAAAAATTAAATTTTTTTGGTGTTG
3459280 ATCATTTTTC
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
60 26 0.35
61 17 0.23
62 32 0.43
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (60 bp):
AAAAAAAATTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTGTTCTCGAG
Found at i:3460199 original size:30 final size:30
Alignment explanation
Indices: 3460139--3460230 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 30
3460129 TAATAATTAG
* * ** *
3460139 AATATACATGAAATTAGAAAGAAAAATTAA
1 AATATACAAGAAATTCGAAATTAAATTTAA
3460169 AATATACAAGAAATTCGAAATTAAATTTAA
1 AATATACAAGAAATTCGAAATTAAATTTAA
*
3460199 AATA-AAAATGAAATTAC-AAATTAAATTTAA
1 AATATACAA-GAAATT-CGAAATTAAATTTAA
3460229 AA
1 AA
3460231 AGTAAAGGGA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
29 3 0.06
30 50 0.93
31 1 0.02
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.27
Consensus pattern (30 bp):
AATATACAAGAAATTCGAAATTAAATTTAA
Found at i:3462398 original size:20 final size:20
Alignment explanation
Indices: 3462373--3462446 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
3462363 ATGATGGATG
3462373 AAAGTCGATCAACGGCGGAC
1 AAAGTCGATCAACGGCGGAC
3462393 AAAGTCGATCAACGGCGGAC
1 AAAGTCGATCAACGGCGGAC
* **
3462413 AAAGTCGGTCAACGGTAGAC
1 AAAGTCGATCAACGGCGGAC
*
3462433 AAAATCGATCAACG
1 AAAGTCGATCAACG
3462447 ACGGTCAACG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.38, C:0.23, G:0.27, T:0.12
Consensus pattern (20 bp):
AAAGTCGATCAACGGCGGAC
Done.