Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 10 of 770
Found at i:2702727 original size:10 final size:10
Alignment explanation
Indices: 2702714--2702749 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
2702704 AAAGTATATA
2702714 TATATATAGG
1 TATATATAGG
2702724 TATATATA--
1 TATATATAGG
2702732 TATATATAGG
1 TATATATAGG
2702742 TATATATA
1 TATATATA
2702750 ATTTTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.33
10 16 0.67
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (10 bp):
TATATATAGG
Found at i:2702731 original size:18 final size:18
Alignment explanation
Indices: 2702708--2702749 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
2702698 ATTTTTAAAG
2702708 TATATATATATATAGGTA
1 TATATATATATATAGGTA
2702726 TATATATATATATAGGTA
1 TATATATATATATAGGTA
2702744 TATATA
1 TATATA
2702750 ATTTTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (18 bp):
TATATATATATATAGGTA
Found at i:2708009 original size:21 final size:21
Alignment explanation
Indices: 2707979--2708020 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2707969 CTGTTCTGAA
*
2707979 TTTAAAAAATCATTAA-AAAT
1 TTTAAAAAATAATTAAGAAAT
2707999 TTTACAAAAATAATTAAGAAAT
1 TTTA-AAAAATAATTAAGAAAT
2708021 ATAGTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (21 bp):
TTTAAAAAATAATTAAGAAAT
Found at i:2716729 original size:16 final size:18
Alignment explanation
Indices: 2716691--2716729 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2716681 TATCTAGACT
*
2716691 TTTATCCAACACTTATAA
1 TTTATCCAACACTAATAA
2716709 TTTATCCAAC-CTAAT-A
1 TTTATCCAACACTAATAA
2716725 TTTAT
1 TTTAT
2716730 TTTTTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 4 0.20
18 10 0.50
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTATCCAACACTAATAA
Found at i:2716735 original size:23 final size:20
Alignment explanation
Indices: 2716709--2716756 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 20
2716699 ACACTTATAA
*
2716709 TTTATCCAACCTAATATTTATTT
1 TTTAT-CAACC-AATATAT-TTT
*
2716732 TTTATTAACCAATATATTTT
1 TTTATCAACCAATATATTTT
2716752 TTTAT
1 TTTAT
2716757 TAAATTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 8 0.35
21 6 0.26
22 4 0.17
23 5 0.22
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTATCAACCAATATATTTT
Found at i:2717169 original size:15 final size:15
Alignment explanation
Indices: 2717149--2717179 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2717139 TAGGCTTAAA
2717149 TAATTATAACATTAT
1 TAATTATAACATTAT
*
2717164 TAATTATAATATTAT
1 TAATTATAACATTAT
2717179 T
1 T
2717180 CAGCCATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATTATAACATTAT
Found at i:2717452 original size:6 final size:6
Alignment explanation
Indices: 2717436--2717481 Score: 65
Period size: 6 Copynumber: 7.5 Consensus size: 6
2717426 ACAAATACAT
* *
2717436 ATGATCC ATGACC ATGATC ATGACC ATAACC ATGACC ATGACC ATG
1 ATGA-CC ATGACC ATGACC ATGACC ATGACC ATGACC ATGACC ATG
2717482 TTTACTTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
6 31 0.89
7 4 0.11
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (6 bp):
ATGACC
Found at i:2720465 original size:85 final size:85
Alignment explanation
Indices: 2720294--2720519 Score: 292
Period size: 85 Copynumber: 2.6 Consensus size: 85
2720284 TATGTAGCAT
* * *
2720294 CACCAAGGTGGTCATGCCAAAGAGAATGGCTCTACCAAAATAAAAATAAAAACTTTATTTTTATG
1 CACCAAAGTGGTCACGCCAAAGAGAAT-GCTCCACCAAAATAAAAA-AAAAA---TATTTTTATG
** *
2720359 GTGGTCACATTATTTTCAATGGCAC
61 GTGGTCACACCATTCTCAATGGCAC
* * *
2720384 CATCAAAGTGGTCACGCCAAAGAGAATAGCTCCATCAAAATAAAAAAATAA-ATTTTTATGGTGG
1 CACCAAAGTGGTCACGCCAAAGAGAAT-GCTCCACCAAAATAAAAAAAAAATATTTTTATGGTGG
2720448 TCACACCATTCTCAATGGCAC
65 TCACACCATTCTCAATGGCAC
*
2720469 CACCAAAGTGGCCACGCCAAAGAGAATGACTCCACCAAAATAAAAAAAAAA
1 CACCAAAGTGGTCACGCCAAAGAGAATG-CTCCACCAAAATAAAAAAAAAA
2720520 AATTAAAAAA
Statistics
Matches: 121, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
84 1 0.01
85 76 0.63
89 4 0.03
90 40 0.33
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.22
Consensus pattern (85 bp):
CACCAAAGTGGTCACGCCAAAGAGAATGCTCCACCAAAATAAAAAAAAAATATTTTTATGGTGGT
CACACCATTCTCAATGGCAC
Found at i:2720542 original size:12 final size:12
Alignment explanation
Indices: 2720505--2720553 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
2720495 TGACTCCACC
2720505 AAAATAAA--AA
1 AAAATAAATTAA
2720515 AAAA-AAATTAA
1 AAAATAAATTAA
*
2720526 AAAATAATTTAA
1 AAAATAAATTAA
**
2720538 AAAATCTATTAA
1 AAAATAAATTAA
2720550 AAAA
1 AAAA
2720554 AGTCTGGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 3 0.09
10 4 0.12
11 6 0.19
12 19 0.59
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAATAAATTAA
Found at i:2722770 original size:16 final size:17
Alignment explanation
Indices: 2722749--2722782 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2722739 AATAATTAAA
2722749 AATAATCTTTA-AAAAT
1 AATAATCTTTATAAAAT
*
2722765 AATAATTTTTATAAAAT
1 AATAATCTTTATAAAAT
2722782 A
1 A
2722783 TTTTTTCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAATCTTTATAAAAT
Found at i:2723980 original size:29 final size:29
Alignment explanation
Indices: 2723948--2724025 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
2723938 ACTTTAACCC
* *
2723948 AAAAATATAAAATTTAATTTAATTTTTTT
1 AAAAATATAAAATTTAATTTAATTATTAT
* *
2723977 AAAAAT-TAAAATTATATTTTTATTATTAT
1 AAAAATATAAAATT-TAATTTAATTATTAT
* *
2724006 AAAAATATATAATTCAATTT
1 AAAAATATAAAATTTAATTT
2724026 CTGCTCTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 7 0.17
29 27 0.68
30 6 0.15
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (29 bp):
AAAAATATAAAATTTAATTTAATTATTAT
Found at i:2730203 original size:20 final size:17
Alignment explanation
Indices: 2730155--2730194 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
2730145 TGAGGGTTGA
2730155 GGGGAAGTAAAATTGTT
1 GGGGAAGTAAAATTGTT
2730172 GGGGAAGTAAAATTGTT
1 GGGGAAGTAAAATTGTT
2730189 GGGGAA
1 GGGGAA
2730195 AAAGTAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.40, T:0.25
Consensus pattern (17 bp):
GGGGAAGTAAAATTGTT
Found at i:2733925 original size:19 final size:20
Alignment explanation
Indices: 2733891--2733934 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
2733881 AAATTTAAGT
2733891 TTTTAATTAAATAAATATAA
1 TTTTAATTAAATAAATATAA
*
2733911 TTTTAA-TATATAAATATAA
1 TTTTAATTAAATAAATATAA
2733930 TTTTA
1 TTTTA
2733935 TTTTAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTAATTAAATAAATATAA
Found at i:2734134 original size:15 final size:16
Alignment explanation
Indices: 2734111--2734154 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
2734101 AATATAAAAA
*
2734111 TATTATATATATTAAAT
1 TATTATAAAT-TTAAAT
2734128 TATTATAAATTTAAAT
1 TATTATAAATTTAAAT
2734144 T-TTATACAATT
1 TATTATA-AATT
2734155 AACAAAACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 5 0.20
16 11 0.44
17 9 0.36
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTATAAATTTAAAT
Found at i:2737349 original size:26 final size:26
Alignment explanation
Indices: 2737294--2737349 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
2737284 AAAATTAATT
*
2737294 TATTTTAATGATCAAAATAATTTTAA
1 TATTTTAATGATAAAAATAATTTTAA
2737320 -ATTTTAAATGATTAAAAAT-A-TTTAA
1 TATTTT-AATGA-TAAAAATAATTTTAA
2737345 TATTT
1 TATTT
2737350 ATTTATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
25 10 0.38
26 10 0.38
27 6 0.23
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (26 bp):
TATTTTAATGATAAAAATAATTTTAA
Found at i:2738645 original size:17 final size:18
Alignment explanation
Indices: 2738623--2738662 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2738613 CATAATTTAC
*
2738623 AATAAAAAATTAAGA-GA
1 AATAAAAAATTAAAATGA
*
2738640 AATAAAATATTAAAATGA
1 AATAAAAAATTAAAATGA
2738658 AATAA
1 AATAA
2738663 TAAGAAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (18 bp):
AATAAAAAATTAAAATGA
Found at i:2740331 original size:6 final size:6
Alignment explanation
Indices: 2740320--2740893 Score: 256
Period size: 6 Copynumber: 95.8 Consensus size: 6
2740310 CTTTATTAAA
* * * *
2740320 TATTAT TATTAT T-TCTAA TATTAT TAATAT TATCAC TATTAT TATATAT
1 TATTAT TATTAT TAT-TAT TATTAT TATTAT TATTAT TATTAT TAT-TAT
*
2740369 TAGTGTA- TATTTT TATTAT CTATGTA- TATGTA- TATATAT T-TATAT
1 TA-T-TAT TATTAT TATTAT -TAT-TAT TAT-TAT TAT-TAT TAT-TAT
* * * * *
2740414 ATAATAT TATTTT TAATTAC T-TTAT T-TTAA TATTTT TATTA- TATTA-
1 -TATTAT TATTAT T-ATTAT TATTAT TATTAT TATTAT TATTAT TATTAT
* * * * *
2740460 TATTTACT T-TT-T GTATT-T CAATAA TATTAC TATTAC TATTAT TATTAT
1 TA-TTA-T TATTAT -TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT
2740508 TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATATAT
1 TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TAT-TAT
2740557 ATACTGTA- TATT-T T-TTAT TATATAT GTA-TAT GTA-TAT ATATT-T
1 -TA-T-TAT TATTAT TATTAT TAT-TAT -TATTAT -TATTAT -TATTAT
* * * * *
2740600 ATATATAG TATTAT TTTTAAT TACT-T TATT-T TAATAT TTTTAT TA-TAT
1 -TAT-TAT TATTAT TATT-AT TATTAT TATTAT TATTAT TATTAT TATTAT
* * *
2740648 TATTTT TGCTT-T T-TGTAT T-TTAA TATTAT TATTAT TATTAT TATTAT
1 TATTAT T-ATTAT TAT-TAT TATTAT TATTAT TATTAT TATTAT TATTAT
2740695 TATTAT TATTAT TATTAT TATTAT TATATAT TAGTGT-T TATT-T T-TTA-
1 TATTAT TATTAT TATTAT TATTAT TAT-TAT TA-T-TAT TATTAT TATTAT
*
2740742 TATATAT GTA-TAT GTA-TAT ATATT-T ATATATAG TATTAAT T-TTAAT
1 TAT-TAT -TATTAT -TATTAT -TATTAT -TAT-TAT TATT-AT TATT-AT
* * * **
2740788 TACT-T TATT-T TAATAT TTTTAT TA-TAT TA-TAT T-TGCT T-TT-T
1 TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT
2740829 GTATT-T TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT
1 -TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT
2740877 TATTAT TATTAT TATTA
1 TATTAT TATTAT TATTA
2740894 GTGTATATTT
Statistics
Matches: 457, Mismatches: 58, Indels: 106
0.74 0.09 0.17
Matches are distributed among these distances:
4 8 0.02
5 70 0.15
6 307 0.67
7 55 0.12
8 14 0.03
9 3 0.01
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.62
Consensus pattern (6 bp):
TATTAT
Found at i:2740341 original size:9 final size:9
Alignment explanation
Indices: 2740312--2740370 Score: 57
Period size: 9 Copynumber: 6.3 Consensus size: 9
2740302 TTTCGTTTCT
2740312 TTATTAAATA
1 TTATT-AATA
*
2740322 TTATTATTA
1 TTATTAATA
2740331 TT-TCTAATA
1 TTAT-TAATA
2740340 TTATTAATA
1 TTATTAATA
* *
2740349 TTATCACTA
1 TTATTAATA
2740358 TTATTATATA
1 TTATTA-ATA
2740368 TTA
1 TTA
2740371 GTGTATATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
8 1 0.03
9 28 0.70
10 11 0.28
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (9 bp):
TTATTAATA
Found at i:2740341 original size:18 final size:17
Alignment explanation
Indices: 2740318--2740979 Score: 145
Period size: 18 Copynumber: 37.8 Consensus size: 17
2740308 TTCTTTATTA
2740318 AATATTATTATTATTTCT
1 AATATTATTATTATTT-T
* *
2740336 AATATTATTAATATTATC
1 AATATTATTATTATT-TT
*
2740354 ACTATTATTATATATTAGTGT
1 AATATTATTAT-TATT--T-T
*
2740375 -ATATTTTTATTATCTATGT
1 AATATTATTATTAT-T-T-T
2740394 -ATATGTA-TA-TATATTT
1 AATAT-TATTATTAT-TTT
*
2740410 -ATATATAATATTATTTT
1 AATAT-TATTATTATTTT
* *
2740427 TA-ATTACT-TTATTTT
1 AATATTATTATTATTTT
* *
2740442 AATATTTTTATTATATT
1 AATATTATTATTATTTT
* *
2740459 -ATATTTACTTTTTGTATTTC
1 AATA-TTA--TTAT-TATTTT
* * *
2740479 AATAATATTACTATTACT
1 AATATTATTATTATT-TT
*
2740497 ATTATTATTATTATTATT
1 AATATTATTATTATT-TT
*
2740515 ATTATTATTATTATTATT
1 AATATTATTATTATT-TT
*
2740533 ATTATTATTATTATTATT
1 AATATTATTATTATT-TT
2740551 ATATATATACTGTA-TATTTT
1 A-ATAT-TA-T-TATTATTTT
* *
2740571 -TTATTA-TA-TA-TGT
1 AATATTATTATTATTTT
2740584 -ATATGTA-TA-TATATTT
1 AATAT-TATTATTAT-TTT
*
2740600 -ATATATAGTATTATTTT
1 AATAT-TATTATTATTTT
* *
2740617 TA-ATTACT-TTATTTT
1 AATATTATTATTATTTT
* *
2740632 AATATTTTTATTATATT
1 AATATTATTATTATTTT
* * * *
2740649 ATTTTTGCTTTTTGTATTTT
1 AATATT--ATTAT-TATTTT
2740669 AATATTATTATTATTATT
1 AATATTATTATTATT-TT
*
2740687 ATTATTATTATTATTATT
1 AATATTATTATTATT-TT
* *
2740705 ATTATTATTATTATTAT
1 AATATTATTATTATTTT
2740722 -ATATTAGTGT-TTATTTTT
1 AATATTA-T-TATTA-TTTT
* *
2740740 TATATATATGTA-TATGTAT
1 AATAT-TAT-TATTAT-TTT
*
2740759 ATATATT-TATATATAGTATT
1 A-ATATTAT-TAT-TA-TTTT
*
2740779 AATTTTAATTACTTTATTTT
1 AATATT-ATTA--TTATTTT
* *
2740799 AATATTTTTATTATATT
1 AATATTATTATTATTTT
**
2740816 -ATATT-TGCTT-TTTGT
1 AATATTATTATTATTT-T
*
2740831 -ATTTTATTATTATTATT
1 AATATTATTATTATT-TT
*
2740848 ATTATTATTATTATTATT
1 AATATTATTATTATT-TT
*
2740866 ATTATTATTATTATTATT
1 AATATTATTATTATT-TT
*
2740884 ATTATTATTAGTGTATATTT
1 AATATTATTA-T-TAT-TTT
*
2740904 --T-TTATTATCTA-TGT
1 AATATTATTAT-TATTTT
*
2740918 -ATATGTA-TATATATTTA
1 AATAT-TATTAT-TATTTT
*
2740935 AATA-TAGTATTATTTT
1 AATATTATTATTATTTT
* *
2740951 TA-ATTACT-TTATTTT
1 AATATTATTATTATTTT
2740966 AATATTATTATTAT
1 AATATTATTATTAT
2740980 ATTATATTTG
Statistics
Matches: 498, Mismatches: 81, Indels: 131
0.70 0.11 0.18
Matches are distributed among these distances:
13 5 0.01
14 14 0.03
15 34 0.07
16 70 0.14
17 73 0.15
18 184 0.37
19 47 0.09
20 55 0.11
21 13 0.03
22 3 0.01
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.62
Consensus pattern (17 bp):
AATATTATTATTATTTT
Found at i:2740602 original size:190 final size:186
Alignment explanation
Indices: 2740320--2740754 Score: 655
Period size: 190 Copynumber: 2.3 Consensus size: 186
2740310 CTTTATTAAA
* * * *
2740320 TATTATTATTATT-TCTAATATTATTAATATTATCACTATTATTATATAT-TAGTGTATA-TTTT
1 TATTATTATTATTAT-TATTATTATTATTATTATTATTATTATTATATATATA-TGTATATTTTT
*
2740382 TATTATCTATGTATATGTATATATATTTATATATAATATTATTTTTAATTACTTTATTTTAATAT
64 TATTATATATGTATATGTATATATATTTATATATAATATTATTTTTAATTACTTTATTTTAATAT
2740447 TTTTATTATATTATATTTACTTTTTGTATTTCAATAATATTACTATTACTATTATTATTAT
129 TTTTATTATATTATATTTACTTTTTGTATTT---TAATATTACTATTACTATTATTATTAT
2740508 TATTATTATTATTATTATTATTATTATTATTATTATTATTATTATATATATACTGTATATTTTTT
1 TATTATTATTATTATTATTATTATTATTATTATTATTATTATTATATATATA-TGTATATTTTTT
*
2740573 ATTATATATGTATATGTATATATATTTATATATAGTATTATTTTTAATTACTTTATTTTAATATT
65 ATTATATATGTATATGTATATATATTTATATATAATATTATTTTTAATTACTTTATTTTAATATT
* * * *
2740638 TTTATTATATTATTTTTGCTTTTTGTATTTTAATATTATTATTATTATTATTATTAT
130 TTTATTATATTATATTTACTTTTTGTATTTTAATATTACTATTACTATTATTATTAT
*
2740695 TATTATTATTATTATTATTATTATTATATATTAGTGT-TTATT-TTTTATATATATGTATAT
1 TATTATTATTATTATTATTATTATTAT-TATTA-T-TATTATTATTATATATATATGTATAT
2740755 GTATATATAT
Statistics
Matches: 229, Mismatches: 12, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
187 59 0.26
188 58 0.25
189 15 0.07
190 97 0.42
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (186 bp):
TATTATTATTATTATTATTATTATTATTATTATTATTATTATTATATATATATGTATATTTTTTA
TTATATATGTATATGTATATATATTTATATATAATATTATTTTTAATTACTTTATTTTAATATTT
TTATTATATTATATTTACTTTTTGTATTTTAATATTACTATTACTATTATTATTAT
Found at i:2740771 original size:167 final size:168
Alignment explanation
Indices: 2740498--2741042 Score: 941
Period size: 167 Copynumber: 3.2 Consensus size: 168
2740488 ACTATTACTA
*
2740498 TTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATATATATACTG
1 TTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATATAT-TAGTG
2740563 TATATTTTTTATTATATATGTATATGTATATATATTTATATATAGTATTATTTTTAATTACTTTA
65 TATATTTTTTATTATATATGTATATGTATATATATTTATATATAGTATTATTTTTAATTACTTTA
*
2740628 TTTTAATATTTTTATTATATTATTTTTGCTTTTTGTATT
130 TTTTAATATTTTTATTATATTATATTTGCTTTTTGTATT
*
2740667 TTAATATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATATATTAGTGT
1 TTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATATATTAGTGT
* *
2740732 TTATTTTTTA-TATATATGTATATGTATATATATTTATATATAGTATTAATTTTAATTACTTTAT
66 ATATTTTTTATTATATATGTATATGTATATATATTTATATATAGTATTATTTTTAATTACTTTAT
2740796 TTTAATATTTTTATTATATTATATTTGCTTTTTGTATT
131 TTTAATATTTTTATTATATTATATTTGCTTTTTGTATT
2740834 TTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTAT-TATTAGTGT
1 TTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATATATTAGTGT
* *
2740898 ATATTTTTTATTATCTATGTATATGTATATATATTTAAATATAGTATTATTTTTAATTACTTTAT
66 ATATTTTTTATTATATATGTATATGTATATATATTTATATATAGTATTATTTTTAATTACTTTAT
*
2740963 TTTAATATTATTATTATATTATATTTGCTTTTTGTATT
131 TTTAATATTTTTATTATATTATATTTGCTTTTTGTATT
** * * * *
2741001 TTATTATTATTGCTAGTATTATTATCATTATCATCATTATTA
1 TTATTATTATTATTATTATTATTATTATTATTATTATTATTA
2741043 ACATATATAT
Statistics
Matches: 358, Mismatches: 17, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
166 18 0.05
167 268 0.75
168 14 0.04
169 58 0.16
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (168 bp):
TTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATATATTAGTGT
ATATTTTTTATTATATATGTATATGTATATATATTTATATATAGTATTATTTTTAATTACTTTAT
TTTAATATTTTTATTATATTATATTTGCTTTTTGTATT
Found at i:2741008 original size:357 final size:357
Alignment explanation
Indices: 2740320--2740983 Score: 948
Period size: 357 Copynumber: 1.8 Consensus size: 357
2740310 CTTTATTAAA
2740320 TATTATTATTATTTCTAATATTATTAATATTATCACTATTATTATATATTAGTGTATATTTTTAT
1 TATTATTATTATTTCTAATATTATTAATATTATCACTATTATTATATATTAGTGTATATTTTTAT
* *
2740385 TATCTATGTATATGTATATATATTTATATATAATATTATTTTTAATTACTTTATTTTAATATTTT
66 TATATATGTATATGTATATATATTTATATATAATATTAATTTTAATTACTTTATTTTAATATTTT
2740450 TATTATATTATATTTACTTTTTGTATTTCAATAATATTACTATTACTATTATTATTATTATTATT
131 TATTATATTATATTTACTTTTTGTATTTCAATAATATTACTATTACTATTATTATTATTATTATT
* *
2740515 ATTATTATTATTATTATTATTATTATTATTATTATTATATATATACTGTATATTTTTTATTATAT
196 ATTATTATTATTATTATTATTATTATTATTATTATTATATATATACTGTATATTTTTAAATATAT
* *
2740580 ATGTATATGTATATATATTTATATATAGTATTATTTTTAATTACTTTATTTTAATATTTTTATTA
261 ATGTATATGTATATATATTTATATATAATATTATTATTAATTACTTTATTTTAATATTTTTATTA
*
2740645 TATTATTTTTGCTTTTTGTATTTTAATATTAT
326 TATTATTATTGCTTTTTGTATTTTAATATTAT
* * * * *
2740677 TATTATTATTATTAT-TATTATTATTATTATTATTATTATTATTATATATTAGTGTTTATTTTT-
1 TATTATTATTATT-TCTAATATTATTAATATTATCACTATTATTATATATTAGTGTATATTTTTA
*
2740740 TATATATATGTATATGTATATATATTTATATATAGTATTAATTTTAATTACTTTATTTTAATATT
65 T-TATATATGTATATGTATATATATTTATATATAATATTAATTTTAATTACTTTATTTTAATATT
* * * * * *
2740805 TTTATTATATTATATTTGCTTTTTGTATTTTATTATTATTATTATTATTATTATTATTATTATTA
129 TTTATTATATTATATTTACTTTTTGTATTTCAATAATATTACTATTACTATTATTATTATTATTA
* *
2740870 TTATTATTATTATTATTATTATTAGTGTA-TATTTTTTATTATCTATGTATA-TGTATATATATT
194 TTATTATTATTATTATTATTATTA-T-TATTA-TTATTATTA--TATATATACTGTATAT-T-TT
* * *
2740933 TAAATATAGTAT-TATTTTTA-AT-TACTTTAT-TTTAATATTATTATTATATTA
252 TAAATATA-TATGTATATGTATATATA-TTTATATATAATATTATTATTA-ATTA
2740984 TATTTGCTTT
Statistics
Matches: 272, Mismatches: 23, Indels: 20
0.86 0.07 0.06
Matches are distributed among these distances:
356 1 0.00
357 199 0.73
358 4 0.01
359 10 0.04
360 22 0.08
361 19 0.07
362 14 0.05
363 3 0.01
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.62
Consensus pattern (357 bp):
TATTATTATTATTTCTAATATTATTAATATTATCACTATTATTATATATTAGTGTATATTTTTAT
TATATATGTATATGTATATATATTTATATATAATATTAATTTTAATTACTTTATTTTAATATTTT
TATTATATTATATTTACTTTTTGTATTTCAATAATATTACTATTACTATTATTATTATTATTATT
ATTATTATTATTATTATTATTATTATTATTATTATTATATATATACTGTATATTTTTAAATATAT
ATGTATATGTATATATATTTATATATAATATTATTATTAATTACTTTATTTTAATATTTTTATTA
TATTATTATTGCTTTTTGTATTTTAATATTAT
Found at i:2744838 original size:8 final size:8
Alignment explanation
Indices: 2744825--2744855 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
2744815 ATTCATTTGT
2744825 CATTCATC
1 CATTCATC
2744833 CATTCATC
1 CATTCATC
2744841 CATTCATC
1 CATTCATC
*
2744849 CGTTCAT
1 CATTCAT
2744856 TGCATGTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.23, C:0.35, G:0.03, T:0.39
Consensus pattern (8 bp):
CATTCATC
Found at i:2751004 original size:39 final size:39
Alignment explanation
Indices: 2750950--2751062 Score: 208
Period size: 39 Copynumber: 2.9 Consensus size: 39
2750940 TGCCTCTTCA
*
2750950 AATGAGCATATATGAAGTCCCTACACATTGTTTTAATAC
1 AATGAGCATATATGAAGTCCCTACACATTGTTTCAATAC
2750989 AATGAGCATATATGAAGTCCCTACACATTGTTTCAATAC
1 AATGAGCATATATGAAGTCCCTACACATTGTTTCAATAC
*
2751028 AATGAGCATATATGAAGTCCCTACACATTATTTCA
1 AATGAGCATATATGAAGTCCCTACACATTGTTTCA
2751063 GTATTGAAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 72 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.32
Consensus pattern (39 bp):
AATGAGCATATATGAAGTCCCTACACATTGTTTCAATAC
Found at i:2753303 original size:78 final size:78
Alignment explanation
Indices: 2753214--2753514 Score: 367
Period size: 77 Copynumber: 3.9 Consensus size: 78
2753204 TTTTTTTTTT
*
2753214 AAAAATGAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACACTGAGGTATCTTTAGTT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACACTGAGGTATCTTTAGTT
2753279 CCTATTTTTCAAA
66 CCTATTTTTCAAA
** *** * * *
2753292 AAAAATCAACTCATATTGGGAGAGGTGAGTTGAGCCTCAAATCACGCACTAAGGTAT-TTTCAAT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACACTGAGGTATCTTT-AGT
** *
2753356 T--TATGATTAAAA
65 TCCTATTTTTCAAA
* * * *
2753368 AAAAATCAACTCATATTGTAAGAGGTGAGTTGAGCCTCGGGTTACACGCTGATGTATCTTTAGTT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACACTGAGGTATCTTTAGTT
2753433 CCTATTTTTC-AA
66 CCTATTTTTCAAA
* *** *
2753445 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGTTGAGGTATTTTTAGTT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACACTGAGGTATCTTTAGTT
*
2753510 TCTAT
66 CCTAT
2753515 CAACTCATAT
Statistics
Matches: 185, Mismatches: 34, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
76 58 0.31
77 70 0.38
78 57 0.31
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (78 bp):
AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACACTGAGGTATCTTTAGTT
CCTATTTTTCAAA
Found at i:2753396 original size:76 final size:77
Alignment explanation
Indices: 2753214--2753482 Score: 265
Period size: 76 Copynumber: 3.5 Consensus size: 77
2753204 TTTTTTTTTT
* *** * *
2753214 AAAAATGAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACACTGAGGTATCTTTAGTT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAATCACACACTAAGGTATCTTTAATT
** *
2753279 CCTATTTTTCAAA
66 -CTATGATTAAAA
** *
2753292 AAAAATCAACTCATATTGGGAGAGGTGAGTTGAGCCTCAAATCACGCACTAAGGTAT-TTTCAAT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAATCACACACTAAGGTATCTTT-AAT
2753356 T-TATGATTAAAA
65 TCTATGATTAAAA
* *** * * * * *
2753368 AAAAATCAACTCATATTGTAAGAGGTGAGTTGAGCCTCGGGTTACACGCTGATGTATCTTTAGTT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAATCACACACTAAGGTATCTTTAATT
* **
2753433 CCTAT-TTTTCAA
66 -CTATGATTAAAA
*
2753445 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC
2753483 GGGTCACATG
Statistics
Matches: 159, Mismatches: 28, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
76 58 0.36
77 46 0.29
78 55 0.35
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (77 bp):
AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAATCACACACTAAGGTATCTTTAATT
CTATGATTAAAA
Found at i:2753567 original size:64 final size:64
Alignment explanation
Indices: 2753449--2753568 Score: 195
Period size: 64 Copynumber: 1.9 Consensus size: 64
2753439 TTTCAAAAAA
* *** *
2753449 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGTTGAGGTATTTTTAGTTTCT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACACTGAGATATTTTTAGTTTCT
2753513 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACACTGAGATATTTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACACTGAGATATTTT
2753569 CAATTTTTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (64 bp):
ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACACTGAGATATTTTTAGTTTCT
Found at i:2753917 original size:26 final size:26
Alignment explanation
Indices: 2753881--2753942 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
2753871 CTACAAAAGA
*
2753881 TCTCCTTGAAGTTTCAATGGATCTCT
1 TCTCCTTGAAGTTTCAATAGATCTCT
*
2753907 TCTCCTTGAAGTTTCAGTAGATCTCT
1 TCTCCTTGAAGTTTCAATAGATCTCT
*
2753933 TCTCCCTGAA
1 TCTCCTTGAA
2753943 ATGGCATTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.40
Consensus pattern (26 bp):
TCTCCTTGAAGTTTCAATAGATCTCT
Found at i:2754030 original size:44 final size:45
Alignment explanation
Indices: 2753975--2754085 Score: 111
Period size: 45 Copynumber: 2.5 Consensus size: 45
2753965 CCACAACAAA
* * *
2753975 ATCTCCTTGAAGTTTCAGCGGAG-AACATTGAAG-TCA-CAAGTCTT
1 ATCTCCCTGAAGTTCCAGCGGAGCAACA-TGAAGAT-AGCAAATCTT
* * **
2754019 ATCTCCCTGAAGTTGCAGTGGAGCAGGATGAAGATAGCAAATCTT
1 ATCTCCCTGAAGTTCCAGCGGAGCAACATGAAGATAGCAAATCTT
*
2754064 ATTTCCCTGAAGTTCCAGCGGA
1 ATCTCCCTGAAGTTCCAGCGGA
2754086 TTAGATAGAA
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
44 26 0.47
45 29 0.53
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (45 bp):
ATCTCCCTGAAGTTCCAGCGGAGCAACATGAAGATAGCAAATCTT
Found at i:2755503 original size:3 final size:3
Alignment explanation
Indices: 2755495--2755732 Score: 160
Period size: 3 Copynumber: 79.7 Consensus size: 3
2755485 CTTTATTAAA
* * * *
2755495 TAT TAT TAT T-T CTAA TAT TAT TAA TAT TAT CAC TAT TAT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2755540 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TAGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA-T
* *
2755587 GTA- TAT TTT TAT TAT CTAT GTA- TAT GTA- TAT ATAT T-T ATAT ATAG
1 -TAT TAT TAT TAT TAT -TAT -TAT TAT -TAT TAT -TAT TAT -TAT -TAT
* * * *
2755632 TAT TAT TTT TAAT TAC T-T TAT T-T TAA TAT TTT TAT TA- TAT TA-
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
** *
2755674 TAT T-T GCT T-T T-T GTAT T-T CAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2755716 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
2755733 ATACTAGTGT
Statistics
Matches: 188, Mismatches: 25, Indels: 44
0.73 0.10 0.17
Matches are distributed among these distances:
2 20 0.11
3 145 0.77
4 21 0.11
5 2 0.01
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2755751 original size:155 final size:155
Alignment explanation
Indices: 2755538--2755889 Score: 589
Period size: 155 Copynumber: 2.3 Consensus size: 155
2755528 TATTATTATT
*
2755538 ATTATTATTATTATTATTATTATTATTATTATTATTATTATATATTAGTGTATATTTTTATTATC
1 ATTATTATTATTATTATTATTATTATTATTATTATTATTA-ATACTAGTGTATATTTTTATTATC
* *
2755603 TATGTATATGTATATATATTTATATATAGTATTATTTTTAATTACTTTATTTTAATATTTTTATT
65 TATGTATATGTATATATATTTAAATATAGTATTATTTTTAATTACTTTATTTTAATATTATTATT
2755668 ATATTATATTTGC-TTTTTGTATTTC
130 ATATTATATTTGCTTTTTTGTATTTC
2755693 ATTATTATTATTATTATTATTATTATTATTATTATTATTAATACTAGTGTATATTTTTTATTATC
1 ATTATTATTATTATTATTATTATTATTATTATTATTATTAATACTAGTGTATA-TTTTTATTATC
2755758 TATGTATATGTATATATATTTAAATATAGTATTATTTTTAATTACTTTATTTTAATATTATTATT
65 TATGTATATGTATATATATTTAAATATAGTATTATTTTTAATTACTTTATTTTAATATTATTATT
*
2755823 ATATTATATTTGCTTTTTTGTATTTT
130 ATATTATATTTGCTTTTTTGTATTTC
** * * * *
2755849 ATTATTATTGCTAGTATTATTATCATTATCATCATTATTAA
1 ATTATTATTATTATTATTATTATTATTATTATTATTATTAA
2755890 CATATATATG
Statistics
Matches: 185, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
154 12 0.06
155 127 0.69
156 46 0.25
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (155 bp):
ATTATTATTATTATTATTATTATTATTATTATTATTATTAATACTAGTGTATATTTTTATTATCT
ATGTATATGTATATATATTTAAATATAGTATTATTTTTAATTACTTTATTTTAATATTATTATTA
TATTATATTTGCTTTTTTGTATTTC
Found at i:2755797 original size:18 final size:20
Alignment explanation
Indices: 2755762--2755798 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
2755752 ATTATCTATG
2755762 TATATGTATATATATTTAAA
1 TATATGTATATATATTTAAA
*
2755782 TATA-GTAT-TATTTTTAA
1 TATATGTATATATATTTAA
2755799 TTACTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 4 0.25
20 4 0.25
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TATATGTATATATATTTAAA
Found at i:2756974 original size:16 final size:16
Alignment explanation
Indices: 2756930--2756968 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
2756920 GGAGAGCAGG
* *
2756930 GGAAAGAAAGAAGGAA
1 GGAAAAAAAGAAAGAA
2756946 GGAAAAAAAGAAAGAA
1 GGAAAAAAAGAAAGAA
2756962 GGAAAAA
1 GGAAAAA
2756969 GGGAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (16 bp):
GGAAAAAAAGAAAGAA
Found at i:2759101 original size:46 final size:46
Alignment explanation
Indices: 2759049--2759278 Score: 370
Period size: 46 Copynumber: 5.0 Consensus size: 46
2759039 AGTGTGCTCT
2759049 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
2759095 CTGATATGAAATGTGTAGGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
2759141 CTAATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
***
2759187 CTGATATGAAATGAAAAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * **
2759233 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
2759279 ATGACAGAAA
Statistics
Matches: 173, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 173 1.00
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:2759338 original size:92 final size:90
Alignment explanation
Indices: 2759064--2759326 Score: 276
Period size: 92 Copynumber: 2.8 Consensus size: 90
2759054 ATGAAATGTG
* * *** * *
2759064 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAGGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAAAAAGACCATAGTTGAAAGA
* * * **
2759129 TACCATGGCAACCTAATATGAAATGTG
66 CACCATGGCAA-CT-ACATGAAAAGAA
* * *
2759156 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGAAAAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAAAAAGACCATAGTTGAAAGA
*
2759221 TACCATGGCAACGTGACATGAAAAGAA
66 CACCATGGCAAC-T-ACATGAAAAGAA
2759248 TAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAATGAGTAAGACCATAGTTG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATG-AAATGAA--A--AAGACCATAGTTG
* *
2759312 AAAGGCACTATGGCA
61 AAAGACACCATGGCA
2759327 TCATGTCAAA
Statistics
Matches: 150, Mismatches: 15, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
91 2 0.01
92 123 0.82
94 1 0.01
96 24 0.16
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.21
Consensus pattern (90 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAAAAAGACCATAGTTGAAAGA
CACCATGGCAACTACATGAAAAGAA
Found at i:2764053 original size:28 final size:28
Alignment explanation
Indices: 2764000--2764083 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
2763990 CACTTTGTGC
2764000 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
* *
2764029 TATTCTTGTGTGTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* *
2764057 GATACTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
2764084 CTGGTGTGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
28 32 0.65
29 17 0.35
ACGTcount: A:0.19, C:0.04, G:0.30, T:0.48
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:2767742 original size:15 final size:16
Alignment explanation
Indices: 2767711--2767747 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
2767701 AATTAATAAA
2767711 TAAAAATTTATAATAT
1 TAAAAATTTATAATAT
*
2767727 TAAATATTTA-AATAT
1 TAAAAATTTATAATAT
2767742 TAAAAA
1 TAAAAA
2767748 ACACTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAAATTTATAATAT
Found at i:2768652 original size:73 final size:74
Alignment explanation
Indices: 2768555--2768695 Score: 196
Period size: 73 Copynumber: 1.9 Consensus size: 74
2768545 ATTCATCTAA
*
2768555 TCTAGAATTTCTTACTTTTTATTTGTAATTTAAATAAATAATTGCAAATATAATT-TTTAAATTA
1 TCTAGAATTTCTTACTTTTTATTTGTAATTTAAATAAATAATT-CAAATATAATTATTAAAATTA
2768619 ATATTTATAG
65 ATATTTATAG
* * * * **
2768629 TCTAGAGTTTGTTA-TTTTTATTTGTAATTTATATAATTAATTTTAATATAATTATTAAAATTAA
1 TCTAGAATTTCTTACTTTTTATTTGTAATTTAAATAAATAATTCAAATATAATTATTAAAATTAA
2768693 TAT
66 TAT
2768696 ATGTTTTTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
72 9 0.15
73 38 0.64
74 12 0.20
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (74 bp):
TCTAGAATTTCTTACTTTTTATTTGTAATTTAAATAAATAATTCAAATATAATTATTAAAATTAA
TATTTATAG
Found at i:2776794 original size:20 final size:20
Alignment explanation
Indices: 2776743--2776794 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
2776733 ATCTATATCG
**
2776743 AAGTATCGATACTTTTCCTA
1 AAGTATCGATACTTTGACTA
* *
2776763 TAGTATCAATACTTTGACTA
1 AAGTATCGATACTTTGACTA
*
2776783 AAGTATTGATAC
1 AAGTATCGATAC
2776795 CTTCCTTAAG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (20 bp):
AAGTATCGATACTTTGACTA
Found at i:2781060 original size:47 final size:47
Alignment explanation
Indices: 2780796--2781053 Score: 297
Period size: 47 Copynumber: 5.5 Consensus size: 47
2780786 TGCACATAGT
* * * ** * *
2780796 CACATATCACACACCGAAGCCATAGCCCAGCCATGGTCTTACACGG-AT
1 CACATAT--CACACTGATGCCATATCCCAGATATGGTCTTATACGGAAG
* * *
2780844 CACAGATCACACTGATGCCATATCCCAGATATGGTCTTACACAGAAG
1 CACATATCACACTGATGCCATATCCCAGATATGGTCTTATACGGAAG
*
2780891 CACATATCACACCGATGCCATATCCCAGATATGGTCTTATACGGAAG
1 CACATATCACACTGATGCCATATCCCAGATATGGTCTTATACGGAAG
* * *
2780938 CTCATATCACACCGATGTCATATCCCAGATATGGTCTTATACGGAAG
1 CACATATCACACTGATGCCATATCCCAGATATGGTCTTATACGGAAG
* * *
2780985 CTCATATCACACTGATGCCATAGCCCA-ACTATGGTCTTATACGGAAAT
1 CACATATCACACTGATGCCATATCCCAGA-TATGGTCTTATACGG-AAG
*
2781033 CACATATCACA-TGTTGCCATA
1 CACATATCACACTGATGCCATA
2781054 GTCCAACCAT
Statistics
Matches: 187, Mismatches: 20, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
46 32 0.17
47 137 0.73
48 18 0.10
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.24
Consensus pattern (47 bp):
CACATATCACACTGATGCCATATCCCAGATATGGTCTTATACGGAAG
Found at i:2785188 original size:8 final size:8
Alignment explanation
Indices: 2785175--2785227 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
2785165 TTTTTAAACA
2785175 ATTTTTAT
1 ATTTTTAT
2785183 ATTTTT-T
1 ATTTTTAT
*
2785190 AATTTTAT
1 ATTTTTAT
2785198 A--TTTAT
1 ATTTTTAT
2785204 A-TTTTAT
1 ATTTTTAT
2785211 AGTTTTTAT
1 A-TTTTTAT
*
2785220 AATTTTAT
1 ATTTTTAT
2785228 TCTATTTAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 6 0.15
7 12 0.31
8 14 0.36
9 7 0.18
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (8 bp):
ATTTTTAT
Found at i:2785201 original size:7 final size:7
Alignment explanation
Indices: 2785177--2785227 Score: 50
Period size: 7 Copynumber: 6.9 Consensus size: 7
2785167 TTTAAACAAT
2785177 TTTTATA
1 TTTTATA
*
2785184 TTTTTTAA
1 TTTTAT-A
2785192 TTTTATA
1 TTTTATA
2785199 -TTTATA
1 TTTTATA
2785205 TTTTATA
1 TTTTATA
2785212 GTTTTTATAA
1 --TTTTAT-A
2785222 TTTTAT
1 TTTTAT
2785228 TCTATTTAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
6 6 0.16
7 12 0.32
8 12 0.32
9 6 0.16
10 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (7 bp):
TTTTATA
Found at i:2785209 original size:13 final size:15
Alignment explanation
Indices: 2785177--2785227 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 15
2785167 TTTAAACAAT
*
2785177 TTTTATATTTTTTAA
1 TTTTATATTTTATAA
2785192 TTTTATA-TTTAT-A
1 TTTTATATTTTATAA
2785205 TTTTATAGTTTTTATAA
1 TTTTATA--TTTTATAA
2785222 TTTTAT
1 TTTTAT
2785228 TCTATTTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
13 8 0.26
14 4 0.13
15 7 0.23
16 5 0.16
17 7 0.23
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTTATATTTTATAA
Found at i:2785496 original size:23 final size:24
Alignment explanation
Indices: 2785453--2785501 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
2785443 TCATTATTCT
*
2785453 AAATATTAAAAAATTATAATTATA
1 AAATATTAAAAAATGATAATTATA
2785477 AAATATT-AAAAATGGA-AATTATA
1 AAATATTAAAAAAT-GATAATTATA
2785500 AA
1 AA
2785502 CTTATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATATTAAAAAATGATAATTATA
Found at i:2791948 original size:11 final size:11
Alignment explanation
Indices: 2791932--2791956 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2791922 TTACAATTGT
2791932 TTTTGTAATTA
1 TTTTGTAATTA
2791943 TTTTGTAATTA
1 TTTTGTAATTA
2791954 TTT
1 TTT
2791957 CTTTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTGTAATTA
Found at i:2809992 original size:24 final size:23
Alignment explanation
Indices: 2809963--2810010 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 23
2809953 TATAATACGT
2809963 AAATAAAGTAAAAATAATATTAAA
1 AAATAAAGTAAAAATAATA-TAAA
2809987 AAATAAAGTAAAAATAATATAAA
1 AAATAAAGTAAAAATAATATAAA
2810010 A
1 A
2810011 TTTATAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (23 bp):
AAATAAAGTAAAAATAATATAAA
Found at i:2810009 original size:11 final size:12
Alignment explanation
Indices: 2809963--2810010 Score: 57
Period size: 11 Copynumber: 4.2 Consensus size: 12
2809953 TATAATACGT
2809963 AAATAA-AGTAA
1 AAATAATAGTAA
*
2809974 AAATAATATTAAA
1 AAATAATAGT-AA
2809987 AAATAA-AGTAA
1 AAATAATAGTAA
2809998 AAATAATA-TAA
1 AAATAATAGTAA
2810009 AA
1 AA
2810011 TTTATAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 19 0.59
12 5 0.16
13 8 0.25
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (12 bp):
AAATAATAGTAA
Found at i:2812633 original size:35 final size:35
Alignment explanation
Indices: 2812587--2812923 Score: 415
Period size: 35 Copynumber: 9.6 Consensus size: 35
2812577 CATGGCAAAG
* * *
2812587 TGTGAAACGTAGGTATAGTATTAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
* * * *
2812622 TGTGAAACGTAGGCATGGAATCATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
* *
2812657 TGTGAAACGTAGGCATGGTATCATCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
* *
2812692 TGTGAAATGTAGGTATGGTATCATCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
* *
2812727 TGTGAAACGTAGGTATGATATCATCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
* ** *
2812762 TGTGAAACGTAGGTATGGTATTAACTGTACCGAGA
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
* * *
2812797 TGTGAAACGTAGGTATGGTATTAACCGTACTGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
*
2812832 TGTGAAACGTAGGTATGGTATTATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
** * **
2812867 TAAGAAATGTAGGTATGACATT-TCCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATTAT-CCATACCGAGT
*
2812902 TGTGAAATGTAGGTATGGTATT
1 TGTGAAACGTAGGTATGGTATT
2812924 TCAATGAGGA
Statistics
Matches: 269, Mismatches: 32, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
34 1 0.00
35 268 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.30
Consensus pattern (35 bp):
TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
Found at i:2813100 original size:31 final size:31
Alignment explanation
Indices: 2813019--2813110 Score: 141
Period size: 31 Copynumber: 3.0 Consensus size: 31
2813009 ATAAGTAATT
* *
2813019 TGATCAGTGAGAAGTGGTACCTCTGGCTACT
1 TGATCAGTGAGAAGTGGTAGCTCTGGCTACC
2813050 TGATCAGTGAGAAGTGGTAGCTCTGGCTACC
1 TGATCAGTGAGAAGTGGTAGCTCTGGCTACC
*
2813081 TGATCAGTGAGTAGTGGTAGCT-TCGGCTAC
1 TGATCAGTGAGAAGTGGTAGCTCT-GGCTAC
2813111 AAGTGACAAG
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
30 1 0.02
31 56 0.98
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (31 bp):
TGATCAGTGAGAAGTGGTAGCTCTGGCTACC
Found at i:2816150 original size:24 final size:25
Alignment explanation
Indices: 2816120--2816179 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
2816110 AGAGAGCCAT
2816120 TAACGGGAAGCTT-ATA-CGAGCTAA
1 TAACGGGAAGCTTCA-AGCGAGCTAA
* *
2816144 TATCGGGAAG-TTCAAGTGAGCTAA
1 TAACGGGAAGCTTCAAGCGAGCTAA
2816168 TAACGGGAAGCT
1 TAACGGGAAGCT
2816180 CATAAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 3 0.10
24 26 0.87
25 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (25 bp):
TAACGGGAAGCTTCAAGCGAGCTAA
Found at i:2816680 original size:21 final size:21
Alignment explanation
Indices: 2816654--2816694 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2816644 GAATTTAACA
*
2816654 TCAATTTAATACAAATCATAG
1 TCAATTCAATACAAATCATAG
* *
2816675 TCAATTCAATCCAATTCATA
1 TCAATTCAATACAAATCATA
2816695 TCCTAGACAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.20, G:0.02, T:0.34
Consensus pattern (21 bp):
TCAATTCAATACAAATCATAG
Found at i:2830083 original size:21 final size:20
Alignment explanation
Indices: 2830036--2830085 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
2830026 AGTTTGTCTA
2830036 GTAAATTTTGTGAATATTTT
1 GTAAATTTTGTGAATATTTT
*
2830056 G-AAATTTTGT-ATGATTTTTT
1 GTAAATTTTGTGA--ATATTTT
2830076 GTAAATTTTG
1 GTAAATTTTG
2830086 ATAATAGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 1 0.04
19 9 0.35
20 8 0.31
21 8 0.31
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (20 bp):
GTAAATTTTGTGAATATTTT
Found at i:2852711 original size:92 final size:89
Alignment explanation
Indices: 2852506--2852791 Score: 277
Period size: 93 Copynumber: 3.1 Consensus size: 89
2852496 TTAAGGGTGT
* *
2852506 AAAAGGCCCTAAAACTTTTTCAAAAAAAAAGAAGCAATTAAGCCCT-TATTTTTTTTTGCACTCA
1 AAAAGGCCCTCAAACTTTTTC----AAAAA-AAGCAATTAAGCCCTGTTTTTTTTTTTGCACTCA
* * * *
2852570 ATTGGGTACTTGAACTTTTAAAATGCATA
61 ATTGGATAATTGAACTGTCAAAATGCATA
* * *
2852599 AAAAGGCCCTCAAACTTTTTCAAATAAAGCAATTAAGCCCCTAGTTTTTTTTTTTGTACTTAATT
1 AAAAGGCCCTCAAACTTTTTCAAAAAAAGCAATTAAG-CCCT-GTTTTTTTTTTTGCACTCAATT
* *
2852664 GGATAATTGAACTGTCCAGATGCATCA
64 GGATAATTGAACTGTCAAAATGCAT-A
* ** *
2852691 AAAAGGCCCTCGAACTTTTTCAAAAAAATTAATTAAGTCACTGTTTTTTTTTTTTTGCACTCAAT
1 AAAAGGCCCTCAAACTTTTTCAAAAAAAGCAATTAAG-CCCTG--TTTTTTTTTTTGCACTCAAT
* * * **
2852756 TGAATACTTGAACTGCCAAAATATATCA
63 TGGATAATTGAACTGTCAAAATGCAT-A
2852784 AAAAGGCC
1 AAAAGGCC
2852792 AGGGGTGAAT
Statistics
Matches: 161, Mismatches: 26, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
88 11 0.07
89 8 0.05
91 38 0.24
92 37 0.23
93 67 0.42
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (89 bp):
AAAAGGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCTGTTTTTTTTTTTGCACTCAATTGG
ATAATTGAACTGTCAAAATGCATA
Found at i:2853269 original size:47 final size:47
Alignment explanation
Indices: 2853202--2853294 Score: 186
Period size: 47 Copynumber: 2.0 Consensus size: 47
2853192 AATTATTTTA
2853202 ATATATATATATTAAAATAATTAGAATTGAAAACGAGGTATCGAGAT
1 ATATATATATATTAAAATAATTAGAATTGAAAACGAGGTATCGAGAT
2853249 ATATATATATATTAAAATAATTAGAATTGAAAACGAGGTATCGAGA
1 ATATATATATATTAAAATAATTAGAATTGAAAACGAGGTATCGAGA
2853295 CCTCGGGAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.31
Consensus pattern (47 bp):
ATATATATATATTAAAATAATTAGAATTGAAAACGAGGTATCGAGAT
Found at i:2855556 original size:18 final size:19
Alignment explanation
Indices: 2855533--2855585 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
2855523 TACGATAATT
2855533 TTTATAATTTTTTACA-AA
1 TTTATAATTTTTTACATAA
**
2855551 TTTAT-ATTTCTTTACATTT
1 TTTATAATTT-TTTACATAA
2855570 TTTATAATTTTCTTAC
1 TTTATAATTTT-TTAC
2855586 GGCTTTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 4 0.14
18 11 0.38
19 6 0.21
20 8 0.28
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATAATTTTTTACATAA
Found at i:2857591 original size:85 final size:86
Alignment explanation
Indices: 2857421--2857736 Score: 338
Period size: 89 Copynumber: 3.6 Consensus size: 86
2857411 GTTCCTAGCT
* *
2857421 TTTTTTATGCATTTTGGCAGTTCAAGTAC-CTAATT-AGT-ACTAAAAAAGAGCAGAGGCTTAAT
1 TTTTTTATGCATTTTGACAGTTCAAGTACAC-AATTGAGTGA--AAAAAA-A--AGA-GATTAAT
* *
2857483 TG-CTTTTTTTGAAAAAGTTTGAGGGAC
59 TGTTTTTTTTTGAAAAATTTTGAGGGAC
** * * * *
2857510 TTTTAAATACATTTTGACAGTTCAAATACCCAATTGAGTGAAAAAAAAGGAGATTAATTGTTTTT
1 TTTTTTATGCATTTTGACAGTTCAAGTACACAATTGAGTGAAAAAAAAAGAGATTAATTGTTTTT
**
2857575 TTTTG-AAAATTTTGAGGTCC
66 TTTTGAAAAATTTTGAGGGAC
* *
2857595 TTTTTTATGCATTTTGAAAGTTCAAGTACTCAATTGAGTGAAAAAAAAAGAGATTAATTGTTTTT
1 TTTTTTATGCATTTTGACAGTTCAAGTACACAATTGAGTGAAAAAAAAAGAGATTAATTG---TT
*
2857660 TTTTTTTGAAAAATTTTGA-GGTC
63 TTTTTTTGAAAAATTTTGAGGGAC
**
2857683 ATTTTTTATGCATTTTGACAGTTCAAGTGTACAATTGAGTGAAAAAAAAAGAGA
1 -TTTTTTATGCATTTTGACAGTTCAAGTACACAATTGAGTGAAAAAAAAAGAGA
2857737 GCAAGTCTTA
Statistics
Matches: 194, Mismatches: 24, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
85 73 0.38
86 10 0.05
88 13 0.07
89 93 0.48
90 4 0.02
91 1 0.01
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (86 bp):
TTTTTTATGCATTTTGACAGTTCAAGTACACAATTGAGTGAAAAAAAAAGAGATTAATTGTTTTT
TTTTGAAAAATTTTGAGGGAC
Found at i:2858281 original size:19 final size:20
Alignment explanation
Indices: 2858250--2858293 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
2858240 ACCAATAAGC
2858250 TTAACGTGATGCCAAAATCT
1 TTAACGTGATGCCAAAATCT
2858270 TTAACG-GATGCCAAAATCT
1 TTAACGTGATGCCAAAATCT
*
2858289 CTAAC
1 TTAAC
2858294 AAATATCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (20 bp):
TTAACGTGATGCCAAAATCT
Found at i:2858305 original size:19 final size:19
Alignment explanation
Indices: 2858261--2858412 Score: 70
Period size: 19 Copynumber: 7.9 Consensus size: 19
2858251 TAACGTGATG
* ** *
2858261 CCAAAATCTTTAACGGATG
1 CCAAAATCTCTAACAAATA
2858280 CCAAAATCTCTAACAAATA
1 CCAAAATCTCTAACAAATA
* * * *
2858299 TCGAAATTTCTAACAGATA
1 CCAAAATCTCTAACAAATA
*
2858318 CCAAAATCTCAAACCAAATA
1 CCAAAATCTCTAA-CAAATA
** * * ***
2858338 CTGAAGTCTATAATTGATA
1 CCAAAATCTCTAACAAATA
* ***
2858357 CCAAAATATCTAATGGATA
1 CCAAAATCTCTAACAAATA
* **
2858376 CCAAAATTTGAAACCAAATA
1 CCAAAATCTCTAA-CAAATA
*
2858396 CCACAATCTCTAACAAA
1 CCAAAATCTCTAACAAA
2858413 AATCTCTAAC
Statistics
Matches: 94, Mismatches: 37, Indels: 4
0.70 0.27 0.03
Matches are distributed among these distances:
19 69 0.73
20 25 0.27
ACGTcount: A:0.47, C:0.22, G:0.07, T:0.24
Consensus pattern (19 bp):
CCAAAATCTCTAACAAATA
Found at i:2860411 original size:22 final size:22
Alignment explanation
Indices: 2860386--2860439 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
2860376 TGAGGCAAAG
2860386 CCTCCAGTACGTGGACAAGCCA
1 CCTCCAGTACGTGGACAAGCCA
2860408 CCTCCAGTACGTGGACAAGCCA
1 CCTCCAGTACGTGGACAAGCCA
* *
2860430 CTTTCAGTAC
1 CCTCCAGTAC
2860440 TTTCTCCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.26, C:0.35, G:0.20, T:0.19
Consensus pattern (22 bp):
CCTCCAGTACGTGGACAAGCCA
Found at i:2860565 original size:26 final size:26
Alignment explanation
Indices: 2860518--2860570 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
2860508 TCAAACATGC
*
2860518 ATTTAGGTCAATTTAACTCTAGGGGT
1 ATTTAGGTCAATTTAACTCTAGAGGT
* *
2860544 ATTTCGGT-AATTTATCTACTAGAGGT
1 ATTTAGGTCAATTTAACT-CTAGAGGT
2860570 A
1 A
2860571 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACTCTAGAGGT
Found at i:2862093 original size:26 final size:26
Alignment explanation
Indices: 2862057--2862164 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
2862047 TGAAATGCTC
*
2862057 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
2862083 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
2862109 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
2862135 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
2862161 ATCA
1 ATCA
2862165 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:2864294 original size:3 final size:3
Alignment explanation
Indices: 2864286--2864338 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
2864276 ATGAATTAAA
* *
2864286 TAT TAT TAT TAT AAT TA- TAT TAT TAT TAT AATT TAT TAT TAT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT T-AT
2864332 T-T TAT TA
1 TAT TAT TA
2864339 ATTAATTCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 4 0.10
3 33 0.79
4 5 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2864305 original size:17 final size:17
Alignment explanation
Indices: 2864285--2864329 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
2864275 TATGAATTAA
2864285 ATATTATTATTATAATT
1 ATATTATTATTATAATT
2864302 ATATTATTATTATAATT
1 ATATTATTATTATAATT
2864319 -TATTATTATTA
1 ATATTATTATTA
2864330 ATTTTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATTATTATTATAATT
Found at i:2864385 original size:16 final size:16
Alignment explanation
Indices: 2864364--2864396 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2864354 AAATAAAGTA
*
2864364 AAAGAATAAAAGAAAC
1 AAAGAAGAAAAGAAAC
2864380 AAAGAAGAAAAGAAAC
1 AAAGAAGAAAAGAAAC
2864396 A
1 A
2864397 GAGACTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAGAAGAAAAGAAAC
Found at i:2864435 original size:14 final size:15
Alignment explanation
Indices: 2864416--2864445 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2864406 CGAAACAGGG
2864416 GAAAGAAAAA-GAAA
1 GAAAGAAAAATGAAA
2864430 GAAAGAAAAATGAAA
1 GAAAGAAAAATGAAA
2864445 G
1 G
2864446 GAAAAACTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.03
Consensus pattern (15 bp):
GAAAGAAAAATGAAA
Found at i:2867908 original size:17 final size:19
Alignment explanation
Indices: 2867882--2867924 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2867872 ACTTTCCCTC
2867882 AAAC-TTTTA-TTCC-CCG
1 AAACTTTTTATTTCCTCCG
*
2867898 AAACTTTTTATTTCCTCCT
1 AAACTTTTTATTTCCTCCG
2867917 AAACTTTT
1 AAACTTTT
2867925 ACTTCTCACC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 5 0.22
18 4 0.17
19 10 0.43
ACGTcount: A:0.26, C:0.26, G:0.02, T:0.47
Consensus pattern (19 bp):
AAACTTTTTATTTCCTCCG
Found at i:2867924 original size:18 final size:16
Alignment explanation
Indices: 2867882--2867925 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
2867872 ACTTTCCCTC
2867882 AAACTTTTATTCCCCG
1 AAACTTTTATTCCCCG
*
2867898 AAACTTTTTATTTCCTCCT
1 AAAC-TTTTA-TTCC-CCG
2867917 AAACTTTTA
1 AAACTTTTA
2867926 CTTCTCACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 4 0.17
17 5 0.21
18 9 0.38
19 6 0.25
ACGTcount: A:0.27, C:0.25, G:0.02, T:0.45
Consensus pattern (16 bp):
AAACTTTTATTCCCCG
Found at i:2868439 original size:5 final size:5
Alignment explanation
Indices: 2868429--2868459 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
2868419 GAACAAATAT
2868429 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
2868460 ATTCTATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (5 bp):
ATTCG
Found at i:2870226 original size:29 final size:30
Alignment explanation
Indices: 2870193--2870261 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
2870183 TTAATAAAAG
* *
2870193 TAAAATTATATTTTAACTTTTT-AACATTA
1 TAAAATTATAATTTAACTTTTTAAAAATTA
*
2870222 TAAAAATT-TAATTTAATTTTTTAAAAATTA
1 T-AAAATTATAATTTAACTTTTTAAAAATTA
*
2870252 TAAAAATATA
1 TAAAATTATA
2870262 GAACATAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
29 18 0.55
30 15 0.45
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (30 bp):
TAAAATTATAATTTAACTTTTTAAAAATTA
Found at i:2870228 original size:30 final size:30
Alignment explanation
Indices: 2870194--2870258 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
2870184 TAATAAAAGT
* *
2870194 AAAATTATATTTTAACTTTTT-AACATTATA
1 AAAATT-TAATTTAACTTTTTAAAAATTATA
*
2870224 AAAATTTAATTTAATTTTTTAAAAATTATA
1 AAAATTTAATTTAACTTTTTAAAAATTATA
2870254 AAAAT
1 AAAAT
2870259 ATAGAACATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 12 0.39
30 19 0.61
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (30 bp):
AAAATTTAATTTAACTTTTTAAAAATTATA
Found at i:2873654 original size:2 final size:2
Alignment explanation
Indices: 2873647--2873681 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2873637 TTCATTGCAA
2873647 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2873682 CCACCAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2878912 original size:7 final size:7
Alignment explanation
Indices: 2878902--2878945 Score: 52
Period size: 7 Copynumber: 5.9 Consensus size: 7
2878892 AACAAATACC
2878902 AAAAAAT
1 AAAAAAT
*
2878909 AAAAAGCAA
1 AAAAA--AT
2878918 AAAAAAT
1 AAAAAAT
2878925 AAAAAAAT
1 -AAAAAAT
2878933 AAAAAAT
1 AAAAAAT
2878940 AAAAAA
1 AAAAAA
2878946 ACAAAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 19 0.59
8 7 0.22
9 6 0.19
ACGTcount: A:0.86, C:0.02, G:0.02, T:0.09
Consensus pattern (7 bp):
AAAAAAT
Found at i:2878923 original size:16 final size:15
Alignment explanation
Indices: 2878902--2878954 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
2878892 AACAAATACC
2878902 AAAAAATAAAAAGCAA-
1 AAAAAATAAAAA--AAT
2878918 AAAAAATAAAAAAAT
1 AAAAAATAAAAAAAT
*
2878933 AAAAAATAAAAAAAC
1 AAAAAATAAAAAAAT
2878948 AAAAAAT
1 AAAAAAT
2878955 TAGAATTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
14 2 0.06
15 21 0.60
16 12 0.34
ACGTcount: A:0.85, C:0.04, G:0.02, T:0.09
Consensus pattern (15 bp):
AAAAAATAAAAAAAT
Found at i:2878928 original size:8 final size:8
Alignment explanation
Indices: 2878902--2878953 Score: 63
Period size: 8 Copynumber: 6.6 Consensus size: 8
2878892 AACAAATACC
2878902 AAAAAATA
1 AAAAAATA
*
2878910 AAAAGCA-A
1 AAAA-AATA
2878918 AAAAAATA
1 AAAAAATA
2878926 AAAAAAT-
1 AAAAAATA
2878933 AAAAAATA
1 AAAAAATA
*
2878941 AAAAAACA
1 AAAAAATA
2878949 AAAAA
1 AAAAA
2878954 TTAGAATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
7 8 0.21
8 29 0.76
9 1 0.03
ACGTcount: A:0.87, C:0.04, G:0.02, T:0.08
Consensus pattern (8 bp):
AAAAAATA
Found at i:2879872 original size:2 final size:2
Alignment explanation
Indices: 2879865--2879891 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2879855 TGTATATTAC
2879865 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2879892 ATGTTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2880298 original size:18 final size:19
Alignment explanation
Indices: 2880253--2880301 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 19
2880243 ACACTATTAC
2880253 TATTCATATATATATTTATA
1 TATT-ATATATATATTTATA
2880273 TA-TATATATATATTCT-TAA
1 TATTATATATATATT-TAT-A
2880292 TATTATATAT
1 TATTATATAT
2880302 TGTATGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 12 0.46
19 5 0.19
20 9 0.35
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTATATATATATTTATA
Found at i:2880373 original size:60 final size:59
Alignment explanation
Indices: 2880260--2880423 Score: 151
Period size: 58 Copynumber: 2.8 Consensus size: 59
2880250 TACTATTCAT
* * *
2880260 ATATATATTTATATATA-TA-TATATATTC-TTAATATTATATATTGTATGTATTTTCTT-A
1 ATATATGTATATATATAGTAGTACATATTCTTTAATATTAT-TA-TGTATGTATTTT-TTAA
* * *
2880318 TTATATGTGTATGTATAGTATGTACATATTCTTTAATATTATTATGTAT-TAATTTTTTAA
1 ATATATGTATATATATAGTA-GTACATATTCTTTAATATTATTATGTATGT-ATTTTTTAA
* * * *
2880378 ATATATGTATATATATATTAGTACTTA-TATTTAGTATTATTATGTA
1 ATATATGTATATATATAGTAGTACATATTCTTTAATATTATTATGTA
2880424 AACGTCTTTC
Statistics
Matches: 88, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
58 30 0.34
59 11 0.12
60 27 0.31
61 10 0.11
62 10 0.11
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (59 bp):
ATATATGTATATATATAGTAGTACATATTCTTTAATATTATTATGTATGTATTTTTTAA
Found at i:2881261 original size:2 final size:2
Alignment explanation
Indices: 2881256--2881291 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2881246 TGTGTGATTG
*
2881256 AT AT AT AT AT GT 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 AT
2881292 GAGTGAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2884061 original size:3 final size:3
Alignment explanation
Indices: 2884045--2884088 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
2884035 CATTTTAAAG
*
2884045 TAT TAT TCT T-T TAT TAT TAT TAT TAT TAT TATT TAT ATAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT -TAT TAT T
2884089 TATTTATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
2 2 0.05
3 29 0.78
4 6 0.16
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2884091 original size:15 final size:13
Alignment explanation
Indices: 2884045--2884096 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 13
2884035 CATTTTAAAG
*
2884045 TATTATTCTTTTAT
1 TATTATT-TATTAT
2884059 TATTA-TTATTAT
1 TATTATTTATTAT
2884071 TATTATTTATATAT
1 TATTATTTAT-TAT
2884085 TATTTATTTATT
1 TA-TTATTTATT
2884097 TTAAACTATC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
12 10 0.29
13 5 0.15
14 11 0.32
15 8 0.24
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTATTTATTAT
Found at i:2884354 original size:2 final size:2
Alignment explanation
Indices: 2884307--2884341 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2884297 CTAAATTGTT
2884307 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
2884342 CCTTTATATA
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:2895139 original size:39 final size:39
Alignment explanation
Indices: 2895096--2895179 Score: 168
Period size: 39 Copynumber: 2.2 Consensus size: 39
2895086 GCAATTAGCT
2895096 TGCTAGGTATAAACCTGAACTTATCACCGGCACGAGGCC
1 TGCTAGGTATAAACCTGAACTTATCACCGGCACGAGGCC
2895135 TGCTAGGTATAAACCTGAACTTATCACCGGCACGAGGCC
1 TGCTAGGTATAAACCTGAACTTATCACCGGCACGAGGCC
2895174 TGCTAG
1 TGCTAG
2895180 ACATTAAGCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.21
Consensus pattern (39 bp):
TGCTAGGTATAAACCTGAACTTATCACCGGCACGAGGCC
Found at i:2908488 original size:19 final size:19
Alignment explanation
Indices: 2908451--2908488 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2908441 GTAAAGTATT
*
2908451 TAATTTATAGCGTAAATAA
1 TAATTTATAGCATAAATAA
2908470 TAATTTA-AGCATAATATAA
1 TAATTTATAGCATAA-ATAA
2908489 GGAACAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (19 bp):
TAATTTATAGCATAAATAA
Found at i:2909545 original size:17 final size:18
Alignment explanation
Indices: 2909511--2909563 Score: 81
Period size: 17 Copynumber: 2.9 Consensus size: 18
2909501 AATCATATCT
2909511 TCTAAGATTGCAATCATA
1 TCTAAGATTGCAATCATA
*
2909529 TCTAAGATTG-TATCATA
1 TCTAAGATTGCAATCATA
2909546 TCTAAGATTGCATATCAT
1 TCTAAGATTGCA-ATCAT
2909564 TGAAGATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 16 0.52
18 10 0.32
19 5 0.16
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (18 bp):
TCTAAGATTGCAATCATA
Found at i:2910178 original size:45 final size:45
Alignment explanation
Indices: 2910114--2910310 Score: 236
Period size: 45 Copynumber: 4.4 Consensus size: 45
2910104 GGAAAGTGAT
* * * * *
2910114 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATAAAGAGACACTAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
2910159 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * * *
2910204 ATCTGCTTA--TTCAATCTGCTCACCGTCTAATACAGATATGCCAA
1 ATCTG-TTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * * *
2910248 ATCTATTATCTCCGATTTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* *
2910293 ATCTGTCATCTTGGATCT
1 ATCTGTTATCTTCGATCT
2910311 ACTTCGATGT
Statistics
Matches: 129, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
43 3 0.02
44 35 0.27
45 88 0.68
46 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (45 bp):
ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
Found at i:2910279 original size:89 final size:89
Alignment explanation
Indices: 2910128--2910297 Score: 250
Period size: 89 Copynumber: 1.9 Consensus size: 89
2910118 GCTATCTTTG
* * * *
2910128 ATCTGCTCCCCGTCTAATAAAGAGACACTAAATCTGTTATCTTCGATCTGCTCCCCGTCTAATAC
1 ATCTGCTCACCGTCTAATAAAGAGACACCAAATCTATTATCTCCGATCTGCTCCCCGTCTAATAC
2910193 AGAGACGCCAAATCTGCTTATTCA
66 AGAGACGCCAAATCTGCTTATTCA
* * ** *
2910217 ATCTGCTCACCGTCTAATACAGATATGCCAAATCTATTATCTCCGATTTGCTCCCCGTCTAATAC
1 ATCTGCTCACCGTCTAATAAAGAGACACCAAATCTATTATCTCCGATCTGCTCCCCGTCTAATAC
*
2910282 AGAGATGCCAAATCTG
66 AGAGACGCCAAATCTG
2910298 TCATCTTGGA
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
89 71 1.00
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (89 bp):
ATCTGCTCACCGTCTAATAAAGAGACACCAAATCTATTATCTCCGATCTGCTCCCCGTCTAATAC
AGAGACGCCAAATCTGCTTATTCA
Found at i:2910469 original size:78 final size:77
Alignment explanation
Indices: 2910327--2910620 Score: 464
Period size: 78 Copynumber: 3.8 Consensus size: 77
2910317 ATGTAAACGC
*
2910327 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCGTCTAATACAGAGATACCAAATCATCTT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCGTCTAATACAGAGATGCCAAATCATCTT
2910392 GGATCTGCTTCA
66 GGATCTGCTTCA
*
2910404 ATGAAGGTCCA-ATCTGTTATGTCTTCGATCTGCTTCCCGTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGC-TCCCGTCTAATACAGAGATGCCAAATCATC
2910468 TTGGATCTGCTTCA
64 TTGGATCTGCTTCA
* * *
2910482 ATGAAGGTCAGATCTACTATGTCTTCGATCTGTTCCCCGTCTAATACAGAGATGCCAAATCATAT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCT-CCCGTCTAATACAGAGATGCCAAATCATCT
2910547 TGGATCTGCTTCA
65 TGGATCTGCTTCA
* * * *
2910560 ATGAAGGTCATATCTGTTATGTCTTCGATCTGCTCTCCGTCGAATATAGAGATGCCAAATC
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTC-CCGTCTAATACAGAGATGCCAAATC
2910621 TGTTTCTTCG
Statistics
Matches: 200, Mismatches: 12, Indels: 9
0.90 0.05 0.04
Matches are distributed among these distances:
77 33 0.17
78 167 0.83
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.32
Consensus pattern (77 bp):
ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCGTCTAATACAGAGATGCCAAATCATCTT
GGATCTGCTTCA
Found at i:2911346 original size:12 final size:12
Alignment explanation
Indices: 2911329--2911360 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2911319 CACTTACGTG
*
2911329 AATTCTTCGAAC
1 AATTCTTCAAAC
2911341 AATTCTTCAAAC
1 AATTCTTCAAAC
2911353 AATTCTTC
1 AATTCTTC
2911361 TATTTTAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (12 bp):
AATTCTTCAAAC
Found at i:2919484 original size:23 final size:21
Alignment explanation
Indices: 2919443--2919501 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
2919433 CATCAACGGT
2919443 TAAGATTACAA--A-ATC-TC
1 TAAGATTACAATCATATCTTC
2919460 TAAGATTACAAAATCATATCTTC
1 TAAGATTAC--AATCATATCTTC
*
2919483 TAAGATTGCAATCATATCT
1 TAAGATTACAATCATATCT
2919502 AAGGTTGTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
17 9 0.26
19 2 0.06
21 11 0.31
22 3 0.09
23 10 0.29
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.34
Consensus pattern (21 bp):
TAAGATTACAATCATATCTTC
Found at i:2919516 original size:38 final size:37
Alignment explanation
Indices: 2919480--2919571 Score: 136
Period size: 36 Copynumber: 2.5 Consensus size: 37
2919470 AAATCATATC
*
2919480 TTCTAAGATTGCA-ATCATATCTAAGGTTGTATCATA
1 TTCTAAGATTGCATATCATATCTAAGATTGTATCATA
2919516 -TCTAAGATTGCATATCATATCTAAGATTGTAT-ATCA
1 TTCTAAGATTGCATATCATATCTAAGATTGTATCAT-A
2919552 TATCTAAGATTGCATATCAT
1 T-TCTAAGATTGCATATCAT
2919572 TGAAGATTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
35 14 0.27
36 19 0.37
38 18 0.35
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (37 bp):
TTCTAAGATTGCATATCATATCTAAGATTGTATCATA
Found at i:2919533 original size:19 final size:19
Alignment explanation
Indices: 2919481--2919571 Score: 143
Period size: 19 Copynumber: 4.9 Consensus size: 19
2919471 AATCATATCT
2919481 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
*
2919499 TCTAAGGTTG--TATCATA
1 TCTAAGATTGCATATCATA
2919516 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
2919535 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
2919554 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
2919572 TGAAGATTAT
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
17 15 0.23
18 9 0.14
19 42 0.64
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:2919729 original size:21 final size:21
Alignment explanation
Indices: 2919690--2919730 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2919680 TTGGACTTCG
* **
2919690 TTTTTTTTTTTGGGTTTATTA
1 TTTTTGTTTTTGGACTTATTA
2919711 TTTTTGTTTTTGGACTTATT
1 TTTTTGTTTTTGGACTTATT
2919731 TCTGGGCCCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.02, G:0.15, T:0.73
Consensus pattern (21 bp):
TTTTTGTTTTTGGACTTATTA
Found at i:2929658 original size:3 final size:3
Alignment explanation
Indices: 2929652--2929694 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
2929642 ATTATTATTA
*
2929652 TTG TTG TTG TTG TTTG TTG TTTG TTG TTG TTG CTG TTG TTG TT
1 TTG TTG TTG TTG -TTG TTG -TTG TTG TTG TTG TTG TTG TTG TT
2929695 AAAACTTCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 30 0.83
4 6 0.17
ACGTcount: A:0.00, C:0.02, G:0.30, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:2930042 original size:41 final size:41
Alignment explanation
Indices: 2929970--2930048 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
2929960 ACCGTAAAAT
* * * ** *
2929970 AAAGATAATTTTATCTAATTAAAGTTGAAAAGTTTAAATTC
1 AAAGACAATTTTATCTAAATAAAATCCAAAAGCTTAAATTC
*
2930011 AAAGACAATTTTGTCTAAATAAAATCCAAAAGCTTAAA
1 AAAGACAATTTTATCTAAATAAAATCCAAAAGCTTAAA
2930049 GCCTAAAAAG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (41 bp):
AAAGACAATTTTATCTAAATAAAATCCAAAAGCTTAAATTC
Found at i:2931991 original size:2 final size:2
Alignment explanation
Indices: 2931984--2932008 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2931974 ACCTGAACCA
2931984 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2932009 AGCAACACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2932488 original size:17 final size:16
Alignment explanation
Indices: 2932464--2932507 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
2932454 CAAATTTTAT
2932464 TTACTTTCCTT-AGAA
1 TTACTTTCCTTAAGAA
2932479 TCTAACTTTCCCTTAAGAA
1 T-T-ACTTT-CCTTAAGAA
2932498 TTACTTTCCT
1 TTACTTTCCT
2932508 ATAAACATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
15 1 0.04
16 4 0.16
17 10 0.40
18 5 0.20
19 5 0.20
ACGTcount: A:0.25, C:0.25, G:0.05, T:0.45
Consensus pattern (16 bp):
TTACTTTCCTTAAGAA
Found at i:2936890 original size:38 final size:38
Alignment explanation
Indices: 2936816--2936890 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
2936806 GATCTTCTGA
* * * *
2936816 GCTTCTTGAACTTGTGAATATTTTGAATGGCGAGAAAG
1 GCTTCTTGAACTTATGAATATATTGAATAGCAAGAAAG
*
2936854 GCTTCTTGAACTTATGAATATATTGAATAGTAAGAAA
1 GCTTCTTGAACTTATGAATATATTGAATAGCAAGAAA
2936891 AGATTGTATG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (38 bp):
GCTTCTTGAACTTATGAATATATTGAATAGCAAGAAAG
Found at i:2938359 original size:21 final size:19
Alignment explanation
Indices: 2938314--2938356 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
2938304 TTCAGTAGAT
*
2938314 TTATATATAGGTCAATATG
1 TTATAAATAGGTCAATATG
*
2938333 TTATAAATAGGTCAATATA
1 TTATAAATAGGTCAATATG
2938352 TTATA
1 TTATA
2938357 TAAGCCAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.42
Consensus pattern (19 bp):
TTATAAATAGGTCAATATG
Found at i:2940124 original size:45 final size:45
Alignment explanation
Indices: 2940074--2940162 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
2940064 AACTCGTAAA
* *
2940074 AGAAAATTCATAGATGTAG-AGAATTCATACATGTGAATTCATAGT
1 AGAAAATTCATAGATATAGCAG-ACTCATACATGTGAATTCATAGT
* *
2940119 AGAAAATTCATAGATATGGCAGACTCATACATGTGGATTCATAG
1 AGAAAATTCATAGATATAGCAGACTCATACATGTGAATTCATAG
2940163 ATATAGTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 37 0.95
46 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.29
Consensus pattern (45 bp):
AGAAAATTCATAGATATAGCAGACTCATACATGTGAATTCATAGT
Found at i:2940159 original size:31 final size:31
Alignment explanation
Indices: 2940123--2940275 Score: 148
Period size: 31 Copynumber: 4.9 Consensus size: 31
2940113 CATAGTAGAA
*
2940123 AATTCATAGATATGGCAGACTCATACATGTG
1 AATTCATAGATATGGCAAACTCATACATGTG
* * ** * ***
2940154 GATTCATAGATATAGTGAACTTATACATACA
1 AATTCATAGATATGGCAAACTCATACATGTG
**
2940185 AATTCATAGATATGGCAAACTCATACAAATG
1 AATTCATAGATATGGCAAACTCATACATGTG
* * *
2940216 GATTCATAGATATAGTAAACTCATACATGCT-
1 AATTCATAGATATGGCAAACTCATACATG-TG
2940247 AATTCATAGATATGGCGAAA-TCATACATG
1 AATTCATAGATATGGC-AAACTCATACATG
2940276 CGGACTATGT
Statistics
Matches: 95, Mismatches: 25, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
31 91 0.96
32 4 0.04
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (31 bp):
AATTCATAGATATGGCAAACTCATACATGTG
Found at i:2940188 original size:62 final size:62
Alignment explanation
Indices: 2940122--2940275 Score: 220
Period size: 62 Copynumber: 2.5 Consensus size: 62
2940112 TCATAGTAGA
* *
2940122 AAATTCATAGATATGGCAGACTCATACATGTGGATTCATAGATATAGTGAACTTATACATAC
1 AAATTCATAGATATGGCAGACTCATACATGTGGATTCATAGATATAGTAAACTCATACATAC
* ** *
2940184 AAATTCATAGATATGGCAAACTCATACAAATGGATTCATAGATATAGTAAACTCATACATGC
1 AAATTCATAGATATGGCAGACTCATACATGTGGATTCATAGATATAGTAAACTCATACATAC
* *
2940246 TAATTCATAGATATGGC-GAAATCATACATG
1 AAATTCATAGATATGGCAG-ACTCATACATG
2940276 CGGACTATGT
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
62 80 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (62 bp):
AAATTCATAGATATGGCAGACTCATACATGTGGATTCATAGATATAGTAAACTCATACATAC
Found at i:2948490 original size:22 final size:22
Alignment explanation
Indices: 2948439--2948499 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
2948429 ATAAGTAAAT
* *
2948439 ACAAAAATAA-AGGAAAATATA
1 ACAAAAATAATAGAAAAATACA
* *
2948460 ATAACAATAATAGAAAAATACA
1 ACAAAAATAATAGAAAAATACA
* *
2948482 ACAATAATAATAGTAAAA
1 ACAAAAATAATAGAAAAA
2948500 GATATAATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 8 0.25
22 24 0.75
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.18
Consensus pattern (22 bp):
ACAAAAATAATAGAAAAATACA
Found at i:2948600 original size:3 final size:3
Alignment explanation
Indices: 2948592--2948801 Score: 151
Period size: 3 Copynumber: 69.7 Consensus size: 3
2948582 AAAGTAGTGC
2948592 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
2948640 TAA TAA TAA TAA TAA TAA T-C TAT TAA GTTA TAA TGAA -AA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA T-AA TAA TAA TAA
* * * * *
2948685 TAA TGA TGA T-A TAT TAGA TAA TAA TAG TAA -AA TAA TAA GTAA CAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA -TAA TAA
* * * * * * * * *
2948730 TAA TAAA TTA TAA TAA TAG TGA TGA TAA TAA CAG TAA CAA TAG TAG
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
2948776 TAA TAA T-A TAT TAG TAA TACA TAA TA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TA
2948802 GAGGTAGTAA
Statistics
Matches: 165, Mismatches: 31, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
2 9 0.05
3 141 0.85
4 15 0.09
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2948895 original size:16 final size:15
Alignment explanation
Indices: 2948866--2948907 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
2948856 TATACGTATG
*
2948866 AAAAATAATGATAGT
1 AAAAATAATAATAGT
2948881 AAAATATAATAATAGT
1 AAAA-ATAATAATAGT
*
2948897 AATAATAATAA
1 AAAAATAATAA
2948908 AGGAATGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (15 bp):
AAAAATAATAATAGT
Found at i:2949014 original size:3 final size:3
Alignment explanation
Indices: 2949006--2949038 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2948996 CTACCATATT
2949006 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2949039 TAGAAATACA
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:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2949147 original size:3 final size:3
Alignment explanation
Indices: 2949133--2949165 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
2949123 AAATATACAC
2949133 TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TA
2949166 TATATTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2949174 original size:3 final size:3
Alignment explanation
Indices: 2949168--2949193 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2949158 TAATAATATA
2949168 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
2949194 AAATGCAGAA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2949703 original size:27 final size:27
Alignment explanation
Indices: 2949665--2949725 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
2949655 AATCTCAAAA
2949665 AAAAAAAAAAATCCCCTCTTGAATCTC
1 AAAAAAAAAAATCCCCTCTTGAATCTC
* * *
2949692 AAAAAAAAAAATCTCTTCTTGAATCTT
1 AAAAAAAAAAATCCCCTCTTGAATCTC
2949719 AAAAAAA
1 AAAAAAA
2949726 TTTCTTCTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.54, C:0.18, G:0.03, T:0.25
Consensus pattern (27 bp):
AAAAAAAAAAATCCCCTCTTGAATCTC
Found at i:2950153 original size:2 final size:2
Alignment explanation
Indices: 2950146--2950178 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2950136 TGAATTCTTT
2950146 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2950179 CAAAGTTTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2951780 original size:10 final size:10
Alignment explanation
Indices: 2951765--2951795 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
2951755 AAATATCTAT
2951765 ATTTCTCTTC
1 ATTTCTCTTC
2951775 ATTTCTCTTC
1 ATTTCTCTTC
2951785 ATTTCTCTTC
1 ATTTCTCTTC
2951795 A
1 A
2951796 ATTCCAGCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.13, C:0.29, G:0.00, T:0.58
Consensus pattern (10 bp):
ATTTCTCTTC
Found at i:2954066 original size:46 final size:46
Alignment explanation
Indices: 2954006--2954224 Score: 276
Period size: 46 Copynumber: 4.9 Consensus size: 46
2953996 TTTGACATGA
* * * * * *
2954006 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** *
2954052 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
2954098 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
2954144 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C---TCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
2954182 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
2954225 AGAGCACACT
Statistics
Matches: 153, Mismatches: 11, Indels: 18
0.84 0.06 0.10
Matches are distributed among these distances:
38 34 0.22
40 3 0.02
41 1 0.01
43 1 0.01
44 3 0.02
45 4 0.03
46 107 0.70
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:2954189 original size:38 final size:38
Alignment explanation
Indices: 2954138--2954213 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
2954128 ACATTTCATA
2954138 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
2954176 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
2954214 ATTTCATATC
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:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (38 bp):
TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:2954324 original size:54 final size:54
Alignment explanation
Indices: 2954257--2954397 Score: 282
Period size: 54 Copynumber: 2.6 Consensus size: 54
2954247 ATCCTTGCAG
2954257 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
2954311 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
2954365 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAA
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAA
2954398 CGACAATTAC
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 87 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.24
Consensus pattern (54 bp):
CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
Found at i:2956428 original size:11 final size:11
Alignment explanation
Indices: 2956412--2956463 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
2956402 TATACTAAAT
2956412 AAATAATAATA
1 AAATAATAATA
*
2956423 AAATAAT-ATT
1 AAATAATAATA
* *
2956433 AAATATCTCATA
1 AAATA-ATAATA
*
2956445 AAATATTAATA
1 AAATAATAATA
2956456 AAATAATA
1 AAATAATA
2956464 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:2964937 original size:22 final size:21
Alignment explanation
Indices: 2964912--2964960 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
2964902 AATTAAAATT
2964912 AAAATTAA-TCTGAATAATAATA
1 AAAATTAACTC-GAAT-ATAATA
2964934 AAAA--AACTCGAATATAATA
1 AAAATTAACTCGAATATAATA
2964953 AAAATTAA
1 AAAATTAA
2964961 ATTCAGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 10 0.42
20 6 0.25
21 4 0.17
22 4 0.17
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (21 bp):
AAAATTAACTCGAATATAATA
Found at i:2965518 original size:25 final size:25
Alignment explanation
Indices: 2965463--2965521 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
2965453 TCTAAAAAAT
*
2965463 TTAAAGAAATATATAAAAATTAATA
1 TTAAATAAATATATAAAAATTAATA
*
2965488 TTAAATAAATATA-AATATATTAATA
1 TTAAATAAATATATAA-AAATTAATA
2965513 TTAAATAAA
1 TTAAATAAA
2965522 AATCCCCCGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 2 0.06
25 29 0.94
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (25 bp):
TTAAATAAATATATAAAAATTAATA
Found at i:2965524 original size:21 final size:20
Alignment explanation
Indices: 2965469--2965524 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
2965459 AAATTTAAAG
*
2965469 AAATATATAAAAATTAATATT
1 AAATAAATAAAAA-TAATATT
*
2965490 AAATAAATATAAAT-ATATT
1 AAATAAATAAAAATAATATT
2965509 AATATTAAATAAAAAT
1 AA-A-TAAATAAAAAT
2965525 CCCCCGTCCC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 7 0.23
20 2 0.07
21 21 0.70
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATAAATAAAAATAATATT
Found at i:2969923 original size:13 final size:13
Alignment explanation
Indices: 2969888--2969932 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
2969878 AAAATACAGT
2969888 AAAATAATAAA-A
1 AAAATAATAAACA
*
2969900 TAAA-AAT-AACA
1 AAAATAATAAACA
2969911 AAAATAATAAACA
1 AAAATAATAAACA
*
2969924 AAAAAAATA
1 AAAATAATA
2969933 GAATTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
10 2 0.07
11 7 0.26
12 6 0.22
13 12 0.44
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAATAATAAACA
Found at i:2970746 original size:26 final size:26
Alignment explanation
Indices: 2970713--2970769 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 26
2970703 TTCTAATACT
2970713 ATATTATATATATATACAT--TTTT-
1 ATATTATATATATATACATACTTTTA
2970736 AT-TTATATATATATACATACTTTTA
1 ATATTATATATATATACATACTTTTA
2970761 ATATTATAT
1 ATATTATAT
2970770 TCCACATGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 16 0.53
23 2 0.07
24 4 0.13
25 2 0.07
26 6 0.20
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.54
Consensus pattern (26 bp):
ATATTATATATATATACATACTTTTA
Found at i:2970768 original size:22 final size:24
Alignment explanation
Indices: 2970712--2970769 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
2970702 ATTCTAATAC
*
2970712 TATATTATATATATATACATTTTTA
1 TATATTATATATACATACA-TTTTA
*
2970737 TTTATATATATATACATAC-TTTTA
1 TATAT-TATATATACATACATTTTA
2970761 -ATATTATAT
1 TATATTATAT
2970770 TCCACATGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 5 0.17
23 3 0.10
24 5 0.17
25 4 0.14
26 12 0.41
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (24 bp):
TATATTATATATACATACATTTTA
Done.