Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 89 of 145
Found at i:29692428 original size:28 final size:28
Alignment explanation
Indices: 29692387--29692441 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
29692377 AAGGAGTATA
29692387 AAACTTATACTTTATTTTATTTCCTATC
1 AAACTTATACTTTATTTTATTTCCTATC
*
29692415 AAACTTATATTTTATTTTATTTCCTAT
1 AAACTTATACTTTATTTTATTTCCTAT
29692442 TTTTTGTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (28 bp):
AAACTTATACTTTATTTTATTTCCTATC
Found at i:29698742 original size:21 final size:21
Alignment explanation
Indices: 29698701--29698743 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29698691 TTCATTGCAT
* *
29698701 AATCAAATAACAATTATGCTC
1 AATCAAATAACAATAAAGCTC
*
29698722 AATCAAATAGCAATAAAGCTC
1 AATCAAATAACAATAAAGCTC
29698743 A
1 A
29698744 CTCTCTCGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.19, G:0.07, T:0.23
Consensus pattern (21 bp):
AATCAAATAACAATAAAGCTC
Found at i:29705068 original size:11 final size:11
Alignment explanation
Indices: 29705048--29705076 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
29705038 TTTCATGTCA
29705048 AAAATA-GGGG
1 AAAATAGGGGG
29705058 AAAATAGGGGG
1 AAAATAGGGGG
29705069 AAAATAGG
1 AAAATAGG
29705077 CTGATTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.52, C:0.00, G:0.38, T:0.10
Consensus pattern (11 bp):
AAAATAGGGGG
Found at i:29708272 original size:17 final size:17
Alignment explanation
Indices: 29708216--29708272 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
29708206 GCCCAATATT
29708216 CCCACACGCTCGTGTGG
1 CCCACACGCTCGTGTGG
** * *
29708233 TTCACCCG-T-GTGAGG
1 CCCACACGCTCGTGTGG
*
29708248 CCCGCACGCTCGTGTGG
1 CCCACACGCTCGTGTGG
29708265 CCCACACG
1 CCCACACG
29708273 GCCCAATTCG
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
15 9 0.32
16 2 0.07
17 17 0.61
ACGTcount: A:0.12, C:0.40, G:0.30, T:0.18
Consensus pattern (17 bp):
CCCACACGCTCGTGTGG
Found at i:29713495 original size:25 final size:25
Alignment explanation
Indices: 29713467--29713515 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
29713457 ATGCTCATTT
*
29713467 GAGCTA-AAGATCGGTATGCTCTCAC
1 GAGCTATAA-ATCAGTATGCTCTCAC
29713492 GAGCTATAAATCAGTATGCTCTCA
1 GAGCTATAAATCAGTATGCTCTCA
29713516 TAAGCCATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (25 bp):
GAGCTATAAATCAGTATGCTCTCAC
Found at i:29713525 original size:25 final size:25
Alignment explanation
Indices: 29713480--29713528 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
29713470 CTAAAGATCG
* *
29713480 GTATGCTCTCACGAGCTATAAATCA
1 GTATGCTCTCACAAGCCATAAATCA
*
29713505 GTATGCTCTCATAAGCCATAAATC
1 GTATGCTCTCACAAGCCATAAATC
29713529 GGTAATCCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (25 bp):
GTATGCTCTCACAAGCCATAAATCA
Found at i:29716546 original size:23 final size:24
Alignment explanation
Indices: 29716519--29716627 Score: 107
Period size: 25 Copynumber: 4.5 Consensus size: 24
29716509 CTTAATATAT
*
29716519 TTTTAAACTTATCATCA-A-TATTA
1 TTTTAAATTTATCAT-ATATTATTA
*
29716542 TTTT-AATTTATAATATATTATTA
1 TTTTAAATTTATCATATATTATTA
* * *
29716565 TTTTAAATTTATCATGTATTTTTT
1 TTTTAAATTTATCATATATTATTA
* *
29716589 TATTTAAATTCATCATGTATTATTA
1 T-TTTAAATTTATCATATATTATTA
29716614 TTTTAAAATTTATC
1 TTTT-AAATTTATC
29716628 GTCTATGATT
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.01
22 9 0.13
23 13 0.18
24 19 0.27
25 29 0.41
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTTAAATTTATCATATATTATTA
Found at i:29716623 original size:25 final size:24
Alignment explanation
Indices: 29716537--29716620 Score: 98
Period size: 24 Copynumber: 3.5 Consensus size: 24
29716527 TTATCATCAA
* * *
29716537 TATTATTTT-AATTTATAATATAT
1 TATTATTTTAAATTCATCATGTAT
*
29716560 TATTATTTTAAATTTATCATGTAT
1 TATTATTTTAAATTCATCATGTAT
* *
29716584 TTTTTTATTTAAATTCATCATGTAT
1 TATTAT-TTTAAATTCATCATGTAT
29716609 TATTATTTTAAA
1 TATTATTTTAAA
29716621 ATTTATCGTC
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
23 9 0.17
24 22 0.42
25 21 0.40
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (24 bp):
TATTATTTTAAATTCATCATGTAT
Found at i:29716909 original size:24 final size:24
Alignment explanation
Indices: 29716881--29716926 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
29716871 GTTTAAATTC
*
29716881 TCTTTTAAATATGTTTATATATCT
1 TCTTTTAAATATATTTATATATCT
*
29716905 TCTTTTAAATCTATTTATATAT
1 TCTTTTAAATATATTTATATAT
29716927 ATAATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (24 bp):
TCTTTTAAATATATTTATATATCT
Found at i:29728919 original size:12 final size:11
Alignment explanation
Indices: 29728895--29728937 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
29728885 CTGACAGAAG
29728895 AAAATAAAATA
1 AAAATAAAATA
*
29728906 AAAATTAAACTA
1 AAAA-TAAAATA
* *
29728918 AAAACAAGATA
1 AAAATAAAATA
29728929 AAAATAAAA
1 AAAATAAAA
29728938 AAATGGCTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:29733091 original size:29 final size:29
Alignment explanation
Indices: 29733037--29733092 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
29733027 AACCCTGTTA
* *
29733037 AAAGCCTTTTTGGTTGTTTCTATTAAATT
1 AAAGCCTTTGTGGTTGTTTATATTAAATT
*
29733066 AAAGCCTTTGTGGTTGTTTATGTTAAA
1 AAAGCCTTTGTGGTTGTTTATATTAAA
29733093 AGGATGTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.25, C:0.09, G:0.18, T:0.48
Consensus pattern (29 bp):
AAAGCCTTTGTGGTTGTTTATATTAAATT
Found at i:29746000 original size:21 final size:21
Alignment explanation
Indices: 29745976--29746027 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
29745966 CAAATAACAT
*
29745976 ATCATACTTAAAATAATACGG
1 ATCATACTTAAAATAATACAG
* **
29745997 ATCATAGTTACCATAATACAG
1 ATCATACTTAAAATAATACAG
*
29746018 ATCACACTTA
1 ATCATACTTA
29746028 GCTTATAACT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (21 bp):
ATCATACTTAAAATAATACAG
Found at i:29751309 original size:40 final size:40
Alignment explanation
Indices: 29751249--29751443 Score: 293
Period size: 40 Copynumber: 4.9 Consensus size: 40
29751239 GTTAATTTTA
* *
29751249 CCTGATTGCACATACGTGCCCCTATTTGAAATTCGGTACC
1 CCTGATTGCACATACGTGCCCCTGTTTGAACTTCGGTACC
* *
29751289 CCTGATTGCACATACATGCCCCTGTTTGAACTTCGGTACT
1 CCTGATTGCACATACGTGCCCCTGTTTGAACTTCGGTACC
* *
29751329 CCTGATTGCACATACGTGCCTCTGTTTGTACTTCGGTACC
1 CCTGATTGCACATACGTGCCCCTGTTTGAACTTCGGTACC
* **
29751369 CCTGATTGCACATACGTGCCCCTGTTTGTACTTTAGTACC
1 CCTGATTGCACATACGTGCCCCTGTTTGAACTTCGGTACC
29751409 CCTGATTGCACATACGTGCCCCTGTTT-ATACTTCG
1 CCTGATTGCACATACGTGCCCCTGTTTGA-ACTTCG
29751444 ATAATTTCAA
Statistics
Matches: 140, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 140 1.00
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.33
Consensus pattern (40 bp):
CCTGATTGCACATACGTGCCCCTGTTTGAACTTCGGTACC
Found at i:29751310 original size:20 final size:20
Alignment explanation
Indices: 29751249--29751432 Score: 126
Period size: 20 Copynumber: 9.2 Consensus size: 20
29751239 GTTAATTTTA
29751249 CCTGATTGCACATACGTGCC
1 CCTGATTGCACATACGTGCC
* * *
29751269 CCT-ATTTG-AAATTCGGTACC
1 CCTGA-TTGCACATAC-GTGCC
*
29751289 CCTGATTGCACATACATGCC
1 CCTGATTGCACATACGTGCC
* * * * *
29751309 CCTGTTTGAAC-TTCGGTACT
1 CCTGATTGCACATAC-GTGCC
29751329 CCTGATTGCACATACGTGCC
1 CCTGATTGCACATACGTGCC
* * * * *
29751349 TCTGTTTGTAC-TTCGGTACC
1 CCTGATTGCACATAC-GTGCC
29751369 CCTGATTGCACATACGTGCC
1 CCTGATTGCACATACGTGCC
* * * *
29751389 CCTGTTTGTACTTTA-GTACC
1 CCTGATTGCAC-ATACGTGCC
29751409 CCTGATTGCACATACGTGCC
1 CCTGATTGCACATACGTGCC
29751429 CCTG
1 CCTG
29751433 TTTATACTTC
Statistics
Matches: 118, Mismatches: 36, Indels: 20
0.68 0.21 0.11
Matches are distributed among these distances:
19 11 0.09
20 96 0.81
21 11 0.09
ACGTcount: A:0.18, C:0.31, G:0.18, T:0.32
Consensus pattern (20 bp):
CCTGATTGCACATACGTGCC
Found at i:29758480 original size:15 final size:15
Alignment explanation
Indices: 29758456--29758493 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
29758446 CCCACCACGC
*
29758456 CCACGAGTACCTCGT
1 CCACGAGTACCTCAT
*
29758471 CCATGAGTACCTCAT
1 CCACGAGTACCTCAT
29758486 CCACGAGT
1 CCACGAGT
29758494 TCTACGCATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.21
Consensus pattern (15 bp):
CCACGAGTACCTCAT
Found at i:29759806 original size:21 final size:21
Alignment explanation
Indices: 29759782--29759835 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
29759772 ATAACATATT
*
29759782 ATACTTAACATAATATGGATC
1 ATACTTAACATAATATAGATC
*
29759803 ATACTTACCATAATATAGATC
1 ATACTTAACATAATATAGATC
* *
29759824 ATTCTTAGCATA
1 ATACTTAACATA
29759836 TAACTTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.35
Consensus pattern (21 bp):
ATACTTAACATAATATAGATC
Found at i:29762930 original size:26 final size:25
Alignment explanation
Indices: 29762879--29762930 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
29762869 TTATTTTTAA
* * *
29762879 TTTTAAAATATATATTTTTAATAAT
1 TTTTAAAATATAAATTTTAAAAAAT
*
29762904 TTTTAAAATTTTAAATTTTAAAAAAT
1 TTTTAAAA-TATAAATTTTAAAAAAT
29762930 T
1 T
29762931 AATTAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTTAAAATATAAATTTTAAAAAAT
Found at i:29764510 original size:27 final size:27
Alignment explanation
Indices: 29764475--29764528 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
29764465 TATTATTGAA
29764475 TTAAAGATTAATTTTATAGTTTACTTT
1 TTAAAGATTAATTTTATAGTTTACTTT
* *
29764502 TTAATGATTAATTTTGTAGTTTACTTT
1 TTAAAGATTAATTTTATAGTTTACTTT
29764529 CATAACTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (27 bp):
TTAAAGATTAATTTTATAGTTTACTTT
Found at i:29768488 original size:22 final size:21
Alignment explanation
Indices: 29768456--29768524 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 21
29768446 TATGCATTAT
*
29768456 TAAACAAAGAGCATTAAAGTGC
1 TAAACAGAGAGCA-TAAAGTGC
* *
29768478 TATACAGAGAGCACAAATGTGC
1 TAAACAGAGAGCATAAA-GTGC
* *
29768500 TAAACGGAGAGCACTAATGTGC
1 TAAACAGAGAGCA-TAAAGTGC
29768522 TAA
1 TAA
29768525 TAAGCAGAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 3 0.08
22 33 0.87
23 2 0.05
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (21 bp):
TAAACAGAGAGCATAAAGTGC
Found at i:29773027 original size:27 final size:27
Alignment explanation
Indices: 29772989--29773044 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
29772979 GCGACATTTC
*
29772989 TTGTCTTGTTTCCTTGATGCTACCAAA
1 TTGTCTTATTTCCTTGATGCTACCAAA
29773016 TTGTCTTATTTCCTTGATGCTACCAAA
1 TTGTCTTATTTCCTTGATGCTACCAAA
29773043 TT
1 TT
29773045 CAAGGTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.20, C:0.21, G:0.12, T:0.46
Consensus pattern (27 bp):
TTGTCTTATTTCCTTGATGCTACCAAA
Found at i:29778271 original size:22 final size:22
Alignment explanation
Indices: 29778246--29778287 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
29778236 AAAAGGCCTT
29778246 TATTTTA-TTATTAAAGTAAATA
1 TATTTTACTTATTAAA-TAAATA
*
29778268 TATTTTACTTCTTAAATAAA
1 TATTTTACTTATTAAATAAA
29778288 CTATTCTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (22 bp):
TATTTTACTTATTAAATAAATA
Found at i:29778691 original size:27 final size:27
Alignment explanation
Indices: 29778653--29778709 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
29778643 ATTTTAGTCC
29778653 GGTCAGGCCAATCACTTTGGCACCTTT
1 GGTCAGGCCAATCACTTTGGCACCTTT
29778680 GGTCAGGCCAATCACTTTGGCACCTTT
1 GGTCAGGCCAATCACTTTGGCACCTTT
29778707 GGT
1 GGT
29778710 GCCGCCAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.18, C:0.28, G:0.25, T:0.30
Consensus pattern (27 bp):
GGTCAGGCCAATCACTTTGGCACCTTT
Found at i:29778716 original size:27 final size:27
Alignment explanation
Indices: 29778653--29778718 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
29778643 ATTTTAGTCC
*
29778653 GGTCAGGCCAATCACTTTGGCACCTTT
1 GGTCACGCCAATCACTTTGGCACCTTT
*
29778680 GGTCAGGCCAATCACTTTGGCACCTTT
1 GGTCACGCCAATCACTTTGGCACCTTT
29778707 GGTGC-CGCCAAT
1 GGT-CACGCCAAT
29778719 GTGATTGGCC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
27 36 0.97
28 1 0.03
ACGTcount: A:0.18, C:0.30, G:0.24, T:0.27
Consensus pattern (27 bp):
GGTCACGCCAATCACTTTGGCACCTTT
Found at i:29778805 original size:27 final size:27
Alignment explanation
Indices: 29778775--29778829 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 27
29778765 TTATTTTTTT
29778775 ATTTTGAT-ATATTTTGGTAAATAAAAA
1 ATTTT-ATAATATTTTGGTAAATAAAAA
29778802 ATTTTATAATATTTTGGTAAATAAAAA
1 ATTTTATAATATTTTGGTAAATAAAAA
29778829 A
1 A
29778830 ATAACATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (27 bp):
ATTTTATAATATTTTGGTAAATAAAAA
Found at i:29778833 original size:23 final size:24
Alignment explanation
Indices: 29778783--29778842 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 24
29778773 TTATTTTGAT
29778783 ATATTTTGGTAAATAAAAAATTTTATA
1 ATATTTTGGTAAATAAAAAA---TATA
29778810 ATATTTTGGTAAATAAAAAA-ATA
1 ATATTTTGGTAAATAAAAAATATA
*
29778833 ACATTTTGGT
1 ATATTTTGGT
29778843 TATTTTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 12 0.38
27 20 0.62
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.42
Consensus pattern (24 bp):
ATATTTTGGTAAATAAAAAATATA
Found at i:29785677 original size:15 final size:16
Alignment explanation
Indices: 29785646--29785683 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
29785636 TATATATATA
29785646 TTATTTTAAATTAATT
1 TTATTTTAAATTAATT
*
29785662 TTATTTT-AATTTATT
1 TTATTTTAAATTAATT
*
29785677 TTCTTTT
1 TTATTTT
29785684 CCCGAATCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTTTAAATTAATT
Found at i:29795618 original size:28 final size:27
Alignment explanation
Indices: 29795584--29795675 Score: 80
Period size: 29 Copynumber: 3.3 Consensus size: 27
29795574 AAATATTAAT
*
29795584 ATTTTTATAATTTTTATACTTTTTAAATA
1 ATTTTAATAATTTTTA-A-TTTTTAAATA
* *
29795613 ATTTTAATGATTTTTAATTTTTAAAAATC
1 ATTTTAATAATTTTTAATTTTT--AAATA
*
29795642 ATTTTTATATATTTTTGAA-TTTTAAA-A
1 ATTTTAATA-ATTTTT-AATTTTTAAATA
29795669 ATTTTAA
1 ATTTTAA
29795676 AAAATTAATA
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
27 11 0.21
28 4 0.08
29 25 0.48
30 10 0.19
31 2 0.04
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (27 bp):
ATTTTAATAATTTTTAATTTTTAAATA
Found at i:29795626 original size:20 final size:19
Alignment explanation
Indices: 29795568--29795629 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
29795558 TTTTTTAAAA
*
29795568 TTTTAAA-AATATTAATAT
1 TTTTAAATAATTTTAATAT
*
29795586 TTTT--ATAATTTTTATACT
1 TTTTAAATAATTTTAATA-T
29795604 TTTTAAATAATTTTAATGAT
1 TTTTAAATAATTTTAAT-AT
29795624 TTTTAA
1 TTTTAA
29795630 TTTTTAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
16 1 0.03
17 8 0.22
18 9 0.25
20 17 0.47
21 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTTAAATAATTTTAATAT
Found at i:29795656 original size:30 final size:29
Alignment explanation
Indices: 29795581--29795670 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 29
29795571 TAAAAATATT
29795581 AATATTTTTATA-ATTTTTATACTTTTT--A
1 AATATTTTTATATATTTTTA-A-TTTTTAAA
*
29795609 AATAATTTTA-ATGATTTTTAATTTTTAAA
1 AATATTTTTATAT-ATTTTTAATTTTTAAA
29795638 AATCATTTTTATATATTTTTGAA-TTTTAAA
1 AAT-ATTTTTATATATTTTT-AATTTTTAAA
29795668 AAT
1 AAT
29795671 TTTAAAAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
27 6 0.11
28 10 0.19
29 11 0.21
30 22 0.42
31 4 0.08
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (29 bp):
AATATTTTTATATATTTTTAATTTTTAAA
Found at i:29796185 original size:31 final size:30
Alignment explanation
Indices: 29796122--29796188 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
29796112 ATCCCAAAAT
29796122 TATACATGAACTTTGATTTAATATGCAATTA
1 TATACATGAACTTTGATTT-ATATGCAATTA
* * *
29796153 TATACATGAACTTTGATTT-TGTGTAATTT
1 TATACATGAACTTTGATTTATATGCAATTA
29796182 TATACAT
1 TATACAT
29796189 AAAAGTTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 14 0.42
31 19 0.58
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (30 bp):
TATACATGAACTTTGATTTATATGCAATTA
Found at i:29797481 original size:20 final size:20
Alignment explanation
Indices: 29797446--29797500 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
29797436 TAAATTGTTG
*
29797446 AATATC-ATTAAAATA-TATT
1 AATATCAATTCAAATATTA-T
29797465 AATATCAATTCAAATATTAT
1 AATATCAATTCAAATATTAT
*
29797485 AATAGACAATTCAAAT
1 AATA-TCAATTCAAAT
29797501 CATAATTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.19
20 13 0.42
21 12 0.39
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (20 bp):
AATATCAATTCAAATATTAT
Found at i:29798893 original size:30 final size:30
Alignment explanation
Indices: 29798831--29798893 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
29798821 ACTTTTCCCT
* * * *
29798831 CAAAACTTTTACTCCTTCTCGCTTTCCCCC
1 CAAAACTTTTACTCCTCCTCCCCTCCCCCC
29798861 CAAAACTTTTACTCC-CCTCCCCTCCCCTCC
1 CAAAACTTTTACTCCTCCTCCCCTCCCC-CC
29798891 CAA
1 CAA
29798894 CCCCTCAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.19, C:0.49, G:0.02, T:0.30
Consensus pattern (30 bp):
CAAAACTTTTACTCCTCCTCCCCTCCCCCC
Found at i:29804011 original size:11 final size:11
Alignment explanation
Indices: 29803995--29804041 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
29803985 AATTGCATAT
29803995 ATATAATGTTC
1 ATATAATGTTC
29804006 ATATAATGTTC
1 ATATAATGTTC
* *
29804017 ATAAACAT-ATC
1 ATATA-ATGTTC
29804028 ATATAATGTTC
1 ATATAATGTTC
29804039 ATA
1 ATA
29804042 ATTAACAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
10 2 0.07
11 26 0.87
12 2 0.07
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (11 bp):
ATATAATGTTC
Found at i:29804205 original size:45 final size:45
Alignment explanation
Indices: 29804136--29804351 Score: 247
Period size: 45 Copynumber: 4.8 Consensus size: 45
29804126 TTGTTCAAGA
* * * * * **
29804136 TGCCATAGCGCCTTTCAGCCATGGTCTTATTTATTTCTAACAT-G
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTGGCATAG
* * *
29804180 ATGTCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGTCAT-G
1 -TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTGGCATAG
* *
29804225 TTGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTCGTATAG
1 -TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTGGCATAG
* * *
29804271 TGCCATAGTGTCCTTCACCTATGGTCTTATTCATTTCTGGTATAG
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTGGCATAG
* *
29804316 TGCCATGGTGCCTTTCAACTATGGTCTTATTCATTT
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTT
29804352 TTCAAGCCAA
Statistics
Matches: 148, Mismatches: 22, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
45 147 0.99
46 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (45 bp):
TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTGGCATAG
Found at i:29805529 original size:17 final size:17
Alignment explanation
Indices: 29805504--29805547 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
29805494 AATTCGTTTG
* *
29805504 TTTATTTTTCTTTATTTC
1 TTTATTTTT-GTTATTTA
29805522 TTTATTTTTGTTATTTA
1 TTTATTTTTGTTATTTA
29805539 TTTATTTTT
1 TTTATTTTT
29805548 ATTCCCCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.80
Consensus pattern (17 bp):
TTTATTTTTGTTATTTA
Found at i:29820915 original size:13 final size:12
Alignment explanation
Indices: 29820891--29820923 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
29820881 AATTAAAATT
29820891 AAATTAAATTAA
1 AAATTAAATTAA
29820903 AAATTATAATTAA
1 AAATTA-AATTAA
29820916 AAATTAAA
1 AAATTAAA
29820924 GTAGTTTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATTAAATTAA
Found at i:29821303 original size:2 final size:2
Alignment explanation
Indices: 29821296--29821328 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
29821286 ACATACATAC
29821296 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29821329 GGGTTATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:29823723 original size:27 final size:28
Alignment explanation
Indices: 29823693--29823750 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
29823683 GCACCTCTAA
*
29823693 TGGAT-GGTTGGGCTTATTTCTCCCTAG
1 TGGATAGGTTGGGCTCATTTCTCCCTAG
* * *
29823720 TGGATAGTTTGGGCTCCTTTCTCCTTAG
1 TGGATAGGTTGGGCTCATTTCTCCCTAG
29823748 TGG
1 TGG
29823751 GCTATCTAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.10, C:0.19, G:0.29, T:0.41
Consensus pattern (28 bp):
TGGATAGGTTGGGCTCATTTCTCCCTAG
Found at i:29826823 original size:17 final size:17
Alignment explanation
Indices: 29826803--29826837 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
29826793 GTATAAGTAC
29826803 AATCATGGTATTATTTA
1 AATCATGGTATTATTTA
29826820 AATCATGGTATTATTTA
1 AATCATGGTATTATTTA
29826837 A
1 A
29826838 CCTTAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (17 bp):
AATCATGGTATTATTTA
Found at i:29827705 original size:96 final size:96
Alignment explanation
Indices: 29827541--29827728 Score: 304
Period size: 96 Copynumber: 2.0 Consensus size: 96
29827531 AACCAAAAAT
* * *
29827541 CGAAAGGGACGACCTCTAGACAAGGTAACTTCCGAGAAAAGGGAGATGAGAAGTGGTCTATGATC
1 CGAAAGGGACGACCTCTAGACAAGGTAACCTCCGAGAAAAGGGAGAGGAGAAGGGGTCTATGATC
29827606 AGACTTGATCTTTGGAAGGTAAGTAATAAAC
66 AGACTTGATCTTTGGAAGGTAAGTAATAAAC
* * * *
29827637 CGAAAGGGATGACCTCTAGACAAGGTAACCTCCGGGAAATGGGAGAGGCGAAGGGGTCTATGATC
1 CGAAAGGGACGACCTCTAGACAAGGTAACCTCCGAGAAAAGGGAGAGGAGAAGGGGTCTATGATC
*
29827702 AGACTTGATCTTTGGAAGGTGAGTAAT
66 AGACTTGATCTTTGGAAGGTAAGTAAT
29827729 CGAACAAGTT
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 84 1.00
ACGTcount: A:0.34, C:0.15, G:0.31, T:0.21
Consensus pattern (96 bp):
CGAAAGGGACGACCTCTAGACAAGGTAACCTCCGAGAAAAGGGAGAGGAGAAGGGGTCTATGATC
AGACTTGATCTTTGGAAGGTAAGTAATAAAC
Found at i:29829705 original size:31 final size:29
Alignment explanation
Indices: 29829665--29829738 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 29
29829655 TTAATGGCTC
*
29829665 AGTGCCTAAAATGTTACAACACGTT-AACATA
1 AGTGACTAAAATGTT--AACA-GTTAAACATA
* *
29829696 AGTGACTAAAACG-TAACATTTGAAACATA
1 AGTGACTAAAATGTTAACAGTT-AAACATA
29829725 AGTGACTAAAATGT
1 AGTGACTAAAATGT
29829739 AACCTGAGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
27 2 0.06
28 4 0.11
29 18 0.50
30 1 0.03
31 11 0.31
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.26
Consensus pattern (29 bp):
AGTGACTAAAATGTTAACAGTTAAACATA
Found at i:29829867 original size:22 final size:20
Alignment explanation
Indices: 29829826--29829897 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 20
29829816 ATTAATTTGC
29829826 ATATTTATCATAATA--T-AT
1 ATATTTA-CATAATAGTTAAT
29829844 ATATTTACCATAATCAGTTAAT
1 ATATTTA-CATAAT-AGTTAAT
* *
29829866 ATAATCACA-AATAGTTAAT
1 ATATTTACATAATAGTTAAT
*
29829885 ACATTTATCATAA
1 ATATTTA-CATAA
29829898 CTAATGCAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
18 13 0.31
19 12 0.29
20 5 0.12
21 5 0.12
22 7 0.17
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (20 bp):
ATATTTACATAATAGTTAAT
Found at i:29829980 original size:24 final size:24
Alignment explanation
Indices: 29829950--29830004 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
29829940 TTAATTTTCA
*
29829950 TAATATA-AATTCACCATAATTAGT
1 TAATATATAATT-ACCATAATTAAT
*
29829974 TAATATATAATTATCATAATTAAT
1 TAATATATAATTACCATAATTAAT
29829998 TAATATA
1 TAATATA
29830005 GGCTAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (24 bp):
TAATATATAATTACCATAATTAAT
Found at i:29831880 original size:3 final size:3
Alignment explanation
Indices: 29831872--29831903 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
29831862 GTCATTTCAT
*
29831872 TTC TTC TTC TCC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
29831904 TTGCATTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:29834783 original size:45 final size:45
Alignment explanation
Indices: 29834693--29834785 Score: 134
Period size: 46 Copynumber: 2.0 Consensus size: 45
29834683 GCTACATGTG
* * *
29834693 AAGAGGAGGATAAGTTTTTATGGCTGTCTTAGTTTGTGTTTGGTTT
1 AAGAGGAGGATAAGTTTCTATGCCTG-CTTAGTTTATGTTTGGTTT
29834739 AAGAGGAGGATAAGTTTCTATGACCTG-TTAGTTTATGTTTGGTTT
1 AAGAGGAGGATAAGTTTCTATG-CCTGCTTAGTTTATGTTTGGTTT
29834784 AA
1 AA
29834786 AAGAATTATG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
45 19 0.44
46 21 0.49
47 3 0.07
ACGTcount: A:0.24, C:0.05, G:0.28, T:0.43
Consensus pattern (45 bp):
AAGAGGAGGATAAGTTTCTATGCCTGCTTAGTTTATGTTTGGTTT
Found at i:29853657 original size:43 final size:43
Alignment explanation
Indices: 29853607--29853829 Score: 136
Period size: 43 Copynumber: 5.2 Consensus size: 43
29853597 ATAGCAGGTA
29853607 TTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCC
1 TTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCC
* * * * * * ** * *
29853650 TTGCCTTCATTG-GTT-GCAGTGGAGCTGGTTAAAGAAGCAGA-TC
1 TTGCCTTC-CTGCGTTAACAGCGAAGCAGATCGAA-AA-CAAAGCC
29853693 TTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCC
1 TTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCC
* ** * * * ** * *
29853736 TTGCCTTCATTG-GTT-GTAG-TAGAGCTGGTTAAAGAAGCAGA-TC
1 TTGCCTTC-CTGCGTTAACAGCGA-AGCAGATCGAA-AA-CAAAGCC
*
29853779 TTGCCTTCCTGCGTTAACAGCAAAGCAGATCGAAAACAAAGCC
1 TTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCC
*
29853822 TTACCTTC
1 TTGCCTTC
29853830 ATTGGTTGCA
Statistics
Matches: 125, Mismatches: 41, Indels: 28
0.64 0.21 0.14
Matches are distributed among these distances:
41 1 0.01
42 30 0.24
43 63 0.50
44 30 0.24
45 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (43 bp):
TTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCC
Found at i:29853729 original size:86 final size:87
Alignment explanation
Indices: 29853546--29854237 Score: 645
Period size: 88 Copynumber: 7.9 Consensus size: 87
29853536 AGATCAGTGA
* ** * * * *
29853546 AGATCGAAA-ATAAAGCCTTGCCTTCATTAGTTGTAGTGGAGCTGGTTAAAGATAGCAGGTATTG
1 AGATCGAAACACAAAGCCTTGCCTTCATCGGTTG-AGTGGAGCTGGTTAAAGACAACAGATCTTG
* *
29853610 CCTTCCTGCGTTAACAGCGAAGC
65 CCTTCCTGCATTGACAGCGAAGC
* *
29853633 AGATCGAAA-ACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGA-AGCAGATCTTG
1 AGATCGAAACACAAAGCCTTGCCTTCATCGGTTG-AGTGGAGCTGGTTAAAGACAACAGATCTTG
* *
29853696 CCTTCCTGCGTTAACAGCGAAGC
65 CCTTCCTGCATTGACAGCGAAGC
* * *
29853719 AGATCGAAA-ACAAAGCCTTGCCTTCATTGGTTGTAGTAGAGCTGGTTAAAGA-AGCAGATCTTG
1 AGATCGAAACACAAAGCCTTGCCTTCATCGGTTG-AGTGGAGCTGGTTAAAGACAACAGATCTTG
* * *
29853782 CCTTCCTGCGTTAACAGCAAAGC
65 CCTTCCTGCATTGACAGCGAAGC
* * *
29853805 AGATCGAAA-ACAAAGCCTTACCTTCATTGGTTGCAGTGGAGCTGGTTAAAGACAAAAGATCTTG
1 AGATCGAAACACAAAGCCTTGCCTTCATCGGTTG-AGTGGAGCTGGTTAAAGACAACAGATCTTG
* *
29853869 CCTTCTTGCATTGACGGCGAAGC
65 CCTTCCTGCATTGACAGCGAAGC
* * * * * * * *
29853892 AGGTCAAAGATACAAA-CCTTGCCGCTC-TCGGTTGTGATGGAGCTGATTGAAGACAAAAGATCT
1 AGATCGAA-ACACAAAGCCTTGCC-TTCATCGGTTGAG-TGGAGCTGGTTAAAGACAACAGATCT
* *
29853955 TGCCTTCCTGCATTGACGGCGAAAC
63 TGCCTTCCTGCATTGACAGCGAAGC
* * * * * *
29853980 AGGTCAAAGACACAAA-CCTTACCTCTC-TCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCT
1 AGATCGAA-ACACAAAGCCTTGCCT-TCATCGGTTGAG-TGGAGCTGGTTAAAGACAACAGATCT
29854043 TGCCTTCCTGCATTGACAGCGAAGC
63 TGCCTTCCTGCATTGACAGCGAAGC
* * * * *
29854068 CGGTCGAAGACACAAA-CCTTGCCTTCCTCGGTTGTGATGGAGCTGGTTGAAGACAACAGATCTT
1 AGATCGAA-ACACAAAGCCTTGCCTTCATCGGTTGAG-TGGAGCTGGTTAAAGACAACAGATCTT
* * *
29854132 GCCTTCTTGCATTGACAGTGAAAC
64 GCCTTCCTGCATTGACAGCGAAGC
* * * * ** *
29854156 AGGTCGAAGACACAAA-CCTTGCCTCTC-TCGGTTGTGGTGAAGCTGGTTGAAGACAGTAGATAT
1 AGATCGAA-ACACAAAGCCTTGCCT-TCATCGGTTG-AGTGGAGCTGGTTAAAGACAACAGATCT
* *
29854219 TGCCCTCCTGCATCGACAG
63 TGCCTTCCTGCATTGACAG
29854238 TGGGGCAGAT
Statistics
Matches: 546, Mismatches: 50, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
86 164 0.30
87 85 0.16
88 287 0.53
89 10 0.02
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (87 bp):
AGATCGAAACACAAAGCCTTGCCTTCATCGGTTGAGTGGAGCTGGTTAAAGACAACAGATCTTGC
CTTCCTGCATTGACAGCGAAGC
Found at i:29854133 original size:44 final size:44
Alignment explanation
Indices: 29853918--29854137 Score: 148
Period size: 44 Copynumber: 5.0 Consensus size: 44
29853908 CCTTGCCGCT
* *
29853918 CTCGGTTGTGATGGAGCTGATTGAAGACAAAAGATCTTGCCTTC
1 CTCGGTTGTGATGGAGCTGGTTGAAGACAACAGATCTTGCCTTC
** * * * ** * * *
29853962 CT-GCAT-TGACGGCGAAACAGGTCAAAGAC-ACAAACCTTACC-TC
1 CTCGGTTGTGA-TG-G-AGCTGGTTGAAGACAACAGATCTTGCCTTC
*
29854005 TCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTC
1 -CTCGGTTGTGATGGAGCTGGTTGAAGACAACAGATCTTGCCTTC
** * * * * *
29854050 CT-GCAT-TGACAGCGAAGCCGGTCGAAGAC-ACAAACCTTGCCTTC
1 CTCGGTTGTGA-TG-G-AGCTGGTTGAAGACAACAGATCTTGCCTTC
29854094 CTCGGTTGTGATGGAGCTGGTTGAAGACAACAGATCTTGCCTTC
1 CTCGGTTGTGATGGAGCTGGTTGAAGACAACAGATCTTGCCTTC
29854138 TTGCATTGAC
Statistics
Matches: 124, Mismatches: 38, Indels: 28
0.65 0.20 0.15
Matches are distributed among these distances:
42 6 0.05
43 30 0.24
44 53 0.43
45 29 0.23
46 6 0.05
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (44 bp):
CTCGGTTGTGATGGAGCTGGTTGAAGACAACAGATCTTGCCTTC
Found at i:29854177 original size:44 final size:44
Alignment explanation
Indices: 29853953--29854179 Score: 149
Period size: 44 Copynumber: 5.2 Consensus size: 44
29853943 GACAAAAGAT
* * * *
29853953 CTTGCCTTCCTGCATTGACGGCGAAACAGGTCAAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAAC
* * ** * * * * *
29853997 CTTACC-TCTCT-CGGTTGTGA-TGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTC-CTGC-ATTGACAGTGAAGCAGGTCGAAGACACAA-AC
* *
29854041 CTTGCCTTCCTGCATTGACAGCGAAGCCGGTCGAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAAC
* ** * * * * *
29854085 CTTGCCTTCCT-CGGTTGTGA-TGGAGCTGGTTGAAGACAACAGAT
1 CTTGCCTTCCTGC-ATTGACAGTGAAGCAGGTCGAAGAC-ACAAAC
* *
29854129 CTTGCCTTCTTGCATTGACAGTGAAACAGGTCGAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAAC
29854173 CTTGCCT
1 CTTGCCT
29854180 CTCTCGGTTG
Statistics
Matches: 131, Mismatches: 42, Indels: 20
0.68 0.22 0.10
Matches are distributed among these distances:
43 31 0.24
44 67 0.51
45 33 0.25
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (44 bp):
CTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAAC
Found at i:29854390 original size:52 final size:52
Alignment explanation
Indices: 29854334--29854486 Score: 146
Period size: 52 Copynumber: 3.1 Consensus size: 52
29854324 AGTAGAATGG
29854334 ATTGAAAATCGAAGATGGCAAATTTTACCTCCCTGTGACTACAGTAGAGTAC
1 ATTGAAAATCGAAGATGGCAAATTTTACCTCCCTGTGACTACAGTAGAGTAC
* * * * * * * **
29854386 ATTG--AAGC-CA-AT----AATTCTATCTCCCTG-G-TTGGCAGTAGAATGG
1 ATTGAAAATCGAAGATGGCAAATTTTACCTCCCTGTGACT-ACAGTAGAGTAC
29854429 ATTGAAAATCGAAGATGGCAAATTTTACCTCCCTGTGACTACAGTAGAGTAC
1 ATTGAAAATCGAAGATGGCAAATTTTACCTCCCTGTGACTACAGTAGAGTAC
29854481 ATTGAA
1 ATTGAA
29854487 GCCGATAATT
Statistics
Matches: 72, Mismatches: 18, Indels: 22
0.64 0.16 0.20
Matches are distributed among these distances:
42 1 0.01
43 13 0.18
44 13 0.18
45 3 0.04
46 1 0.01
47 2 0.03
48 2 0.03
49 1 0.01
50 3 0.04
51 13 0.18
52 19 0.26
53 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (52 bp):
ATTGAAAATCGAAGATGGCAAATTTTACCTCCCTGTGACTACAGTAGAGTAC
Found at i:29854416 original size:95 final size:95
Alignment explanation
Indices: 29854253--29854510 Score: 498
Period size: 95 Copynumber: 2.7 Consensus size: 95
29854243 CAGATCAAAT
*
29854253 ATGGCAAATTTTACCTCCTTGTGACTACAGTAGAGTACATTGAAGCCAATAATTCTATCTCCCTG
1 ATGGCAAATTTTACCTCCCTGTGACTACAGTAGAGTACATTGAAGCCAATAATTCTATCTCCCTG
29854318 GTTGGCAGTAGAATGGATTGAAAATCGAAG
66 GTTGGCAGTAGAATGGATTGAAAATCGAAG
29854348 ATGGCAAATTTTACCTCCCTGTGACTACAGTAGAGTACATTGAAGCCAATAATTCTATCTCCCTG
1 ATGGCAAATTTTACCTCCCTGTGACTACAGTAGAGTACATTGAAGCCAATAATTCTATCTCCCTG
29854413 GTTGGCAGTAGAATGGATTGAAAATCGAAG
66 GTTGGCAGTAGAATGGATTGAAAATCGAAG
*
29854443 ATGGCAAATTTTACCTCCCTGTGACTACAGTAGAGTACATTGAAGCCGATAATTCTATCTCCCTG
1 ATGGCAAATTTTACCTCCCTGTGACTACAGTAGAGTACATTGAAGCCAATAATTCTATCTCCCTG
29854508 GTT
66 GTT
29854511 NNNNNNNNNN
Statistics
Matches: 161, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 161 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (95 bp):
ATGGCAAATTTTACCTCCCTGTGACTACAGTAGAGTACATTGAAGCCAATAATTCTATCTCCCTG
GTTGGCAGTAGAATGGATTGAAAATCGAAG
Found at i:29858835 original size:12 final size:12
Alignment explanation
Indices: 29858818--29858868 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
29858808 ACTTAATCAT
29858818 TTTAATATTAAA
1 TTTAATATTAAA
*
29858830 TTTAATCTAATAAA
1 TTTAA--TATTAAA
*
29858844 TATT-AGATTAAA
1 T-TTAATATTAAA
29858856 TTTAATATTAAA
1 TTTAATATTAAA
29858868 T
1 T
29858869 ATTATTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
11 2 0.06
12 19 0.61
14 8 0.26
15 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:29858845 original size:21 final size:21
Alignment explanation
Indices: 29858821--29858862 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29858811 TAATCATTTT
*
29858821 AATATTAAATTTAATCTAATA
1 AATATTAAATTAAATCTAATA
* *
29858842 AATATTAGATTAAATTTAATA
1 AATATTAAATTAAATCTAATA
29858863 TTAAATATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
AATATTAAATTAAATCTAATA
Found at i:29859383 original size:19 final size:19
Alignment explanation
Indices: 29859345--29859384 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
29859335 AAAATATCAT
* *
29859345 ATTAATTTTAATTGATTTG
1 ATTAATTTAAATTGACTTG
*
29859364 ATTAATTTAAATTTACTTG
1 ATTAATTTAAATTGACTTG
29859383 AT
1 AT
29859385 CAAAATTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (19 bp):
ATTAATTTAAATTGACTTG
Found at i:29860583 original size:4 final size:4
Alignment explanation
Indices: 29860574--29860598 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
29860564 AGAAATTAGC
29860574 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
29860599 CGTTCAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:29868445 original size:187 final size:188
Alignment explanation
Indices: 29867690--29868430 Score: 1196
Period size: 188 Copynumber: 3.9 Consensus size: 188
29867680 ATTAGATACC
* * * *
29867690 TTAAGCTCTTATGGTCTGAAAACACACGACACTTCTCCCTATAAAGGTAGTGTCTTTAGATCTTT
1 TTAAGCTCTTATGGTCTAAAAACACATGACACTTCTCCCCATAAAGGTAGTGTCTCTAGATCTTT
** * * ** *
29867755 AGTGCCAACACTACCATTGCAAGCTTTAAGTCTTGAGTTGGATAATTCTTTTAATGTGGCTTGAG
66 AGCACCAACACTACCACTGCAAGCTTTAAGTCTTGAGTTGGATAATTATTTTAATGCAGCTTGAT
* * **
29867820 CTAGCGAGATGTATAGGCCACAACCTTTTCTCTTTGCATAAGCACACACCCTAGCCCA
131 CTGGCGAGATGCATACACCACAACCTTTTCTCTTTGCATAAGCACACACCCTAGCCCA
*
29867878 TTAAGTTCTTATGGTCTAAAAACACATGACACTTCTCCCCATAAAGGTAGTGTCTCTAGATCTTT
1 TTAAGCTCTTATGGTCTAAAAACACATGACACTTCTCCCCATAAAGGTAGTGTCTCTAGATCTTT
* * * * *
29867943 AGCACCAACACTACCACTGAAAGCTTTATGTCTTGAGTTGGATAATTATTTTAATGCGGCCTCAT
66 AGCACCAACACTACCACTGCAAGCTTTAAGTCTTGAGTTGGATAATTATTTTAATGCAGCTTGAT
* *
29868008 CTGGCAAGATGCATACACCACAACCTTTTCTCTTTGCATAAGCATACACCCTAGCCCA
131 CTGGCGAGATGCATACACCACAACCTTTTCTCTTTGCATAAGCACACACCCTAGCCCA
* * *
29868066 TTAAGCTTTTATGGTCTAAAAACACATGACCCTTCTCCCCATAAAGGTAGTTTCTCTAGATCTTT
1 TTAAGCTCTTATGGTCTAAAAACACATGACACTTCTCCCCATAAAGGTAGTGTCTCTAGATCTTT
29868131 AGCACCAACACTACCACTGCAAGCTTTAAGTCTTGAGTTGGATAATTATTTTAATGCAGCTTGAT
66 AGCACCAACACTACCACTGCAAGCTTTAAGTCTTGAGTTGGATAATTATTTTAATGCAGCTTGAT
29868196 CTGGCGAGATGCATACACCACAACCTTTTCTCTTTGCATAAGCACACACCCTAGCCCA
131 CTGGCGAGATGCATACACCACAACCTTTTCTCTTTGCATAAGCACACACCCTAGCCCA
* *
29868254 TTAAGCTCTTATGGTCTAAAAACACATGACCCTTCT-CCCATAAAGGTAGTATCTCTAGATCTTT
1 TTAAGCTCTTATGGTCTAAAAACACATGACACTTCTCCCCATAAAGGTAGTGTCTCTAGATCTTT
29868318 AGCACCAACACTACCACTGCAAGCTTTAAGTCTTGAGTTGGATAATTATTTTAATGCAGCTTGAT
66 AGCACCAACACTACCACTGCAAGCTTTAAGTCTTGAGTTGGATAATTATTTTAATGCAGCTTGAT
* * *
29868383 CTGGCGAGATGCATTCACCATAACCTTTTCTTTTTGCATAAGCACACA
131 CTGGCGAGATGCATACACCACAACCTTTTCTCTTTGCATAAGCACACA
29868431 TCCAAAACCA
Statistics
Matches: 516, Mismatches: 37, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
187 137 0.27
188 379 0.73
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.32
Consensus pattern (188 bp):
TTAAGCTCTTATGGTCTAAAAACACATGACACTTCTCCCCATAAAGGTAGTGTCTCTAGATCTTT
AGCACCAACACTACCACTGCAAGCTTTAAGTCTTGAGTTGGATAATTATTTTAATGCAGCTTGAT
CTGGCGAGATGCATACACCACAACCTTTTCTCTTTGCATAAGCACACACCCTAGCCCA
Found at i:29876128 original size:26 final size:26
Alignment explanation
Indices: 29876099--29876167 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 26
29876089 CATTTCAACG
* * * *
29876099 CACATCTCGTTTGAGTAGGCCTATTT
1 CACAGCTCGTGTGAGCAGACCTATTT
* *
29876125 CACAGCTTGTGTGAGCATACCTATTT
1 CACAGCTCGTGTGAGCAGACCTATTT
29876151 CACAGCTCGTGTGAGCA
1 CACAGCTCGTGTGAGCA
29876168 ACTATGTGTA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (26 bp):
CACAGCTCGTGTGAGCAGACCTATTT
Found at i:29877726 original size:20 final size:20
Alignment explanation
Indices: 29877687--29877725 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
29877677 TTTAATAAGG
29877687 TATCGATACCCAACATAAAA
1 TATCGATACCCAACATAAAA
*
29877707 TATCGATA-CCAACTTAAAA
1 TATCGATACCCAACATAAAA
29877726 ACTTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.49, C:0.23, G:0.05, T:0.23
Consensus pattern (20 bp):
TATCGATACCCAACATAAAA
Found at i:29881381 original size:116 final size:116
Alignment explanation
Indices: 29881009--29881439 Score: 576
Period size: 116 Copynumber: 3.7 Consensus size: 116
29880999 ATATTTGGCA
* * * * **
29881009 ATTTGGTTTAAACGAG--AAATCGAAATCCAGCACCTTAGGACACG-TCCCTCGAATTTCCAAAC
1 ATTTGG-TTAAGCGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAAC
* * *
29881071 GC-AAAGCATTGCCTTATTTCG-AA--TTT--TTTTTAAAAGGATATTTAGCC
65 GCTAAA-CATTGCCTTATTTTGAAATTTTTAATTTTTTAAAGGATATTAAGCC
29881118 ATTTGGTTGAA-CGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCCAAA
1 ATTTGGTT-AAGCGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTT-CCAAA
* *
29881182 CGCAAAACATTGCCTTATTTTTAAAATTATTTTAAAATTTTTTAAAGGATATTAAGCC
64 CGCTAAACATTGCCTTA-TTTTGAAA-T-TTTT--AATTTTTTAAAGGATATTAAGCC
29881240 ATTTGGTTAAGCGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACG
1 ATTTGGTTAAGCGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACG
*
29881305 CTAAATATTGCCTTATTTTGAAATTTTTAATTTTTTAAAGGATATTAAGCC
66 CTAAACATTGCCTTATTTTGAAATTTTTAATTTTTTAAAGGATATTAAGCC
29881356 ATTTGGTTAAGCGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACG
1 ATTTGGTTAAGCGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACG
* * *
29881421 CTAAATATTACATTATTTT
66 CTAAACATTGCCTTATTTT
29881440 AAAAAAAATT
Statistics
Matches: 291, Mismatches: 14, Indels: 27
0.88 0.04 0.08
Matches are distributed among these distances:
108 6 0.02
109 8 0.03
110 25 0.09
111 10 0.03
112 18 0.06
113 6 0.02
114 2 0.01
116 105 0.36
118 7 0.02
119 1 0.00
120 7 0.02
121 22 0.08
122 74 0.25
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (116 bp):
ATTTGGTTAAGCGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACG
CTAAACATTGCCTTATTTTGAAATTTTTAATTTTTTAAAGGATATTAAGCC
Found at i:29881407 original size:238 final size:230
Alignment explanation
Indices: 29881009--29881444 Score: 617
Period size: 238 Copynumber: 1.9 Consensus size: 230
29880999 ATATTTGGCA
*
29881009 ATTTGGTTTAAACGAGAAATCGAAATCCAGCACCTTAGGACACGTCCCTCGAATTTCCAAACGCA
1 ATTTGGTTTAAACGAGAAATCGAAACCCAGCACCTTAGGACACGTCCCTCGAATTTCCAAACGCA
*
29881074 AAGCATTGCCTTATTTCGAATTTTTTTTAAAAGGATATTTAGCCATTTGGTTGAACGAGAAAAAT
66 AAGCATTGCCTTATTTCGAATTTTTTTTAAAAGGATATTAAGCCATTTGGTTGAACGAGAAAAAT
* * *
29881139 CGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCCAAACGCAAAACATTGCCTTATTTTT
131 CGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTT-CCAAACGCAAAACATTACATTATTTTA
29881204 AAAATTATTTTAAAATTTTTTAAAGGATATTAAGCC
195 AAAATTATTTTAAAATTTTTTAAAGGATATTAAGCC
* * * **
29881240 ATTTGG-TTAAGCGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAAC
1 ATTTGGTTTAAACGAG--AAATCGAAACCCAGCACCTTAGGACACG-TCCCTCGAATTTCCAAAC
* * *
29881304 GCTAAA-TATTGCCTTATTTTGAAATTTTTAATTTTTTAAAGGATATTAAGCCATTTGGTT-AAG
63 GC-AAAGCATTGCCTTATTTCG-AA--TTT--TTTTTAAAAGGATATTAAGCCATTTGGTTGAA-
* *
29881367 CGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGCTAAATATTAC
121 CGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTAC
29881432 ATTATTTTAAAAA
186 ATTATTTTAAAAA
29881445 AAATTTAGAA
Statistics
Matches: 180, Mismatches: 15, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
230 8 0.04
231 6 0.03
232 25 0.14
233 31 0.17
234 5 0.03
236 3 0.02
237 28 0.16
238 74 0.41
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (230 bp):
ATTTGGTTTAAACGAGAAATCGAAACCCAGCACCTTAGGACACGTCCCTCGAATTTCCAAACGCA
AAGCATTGCCTTATTTCGAATTTTTTTTAAAAGGATATTAAGCCATTTGGTTGAACGAGAAAAAT
CGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTACATTATTTTAA
AAATTATTTTAAAATTTTTTAAAGGATATTAAGCC
Found at i:29882397 original size:3 final size:3
Alignment explanation
Indices: 29882389--29882448 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
29882379 AATATTAAGG
29882389 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29882437 ATA ATA ATA ATA
1 ATA ATA ATA ATA
29882449 GAATTACTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:29885385 original size:4 final size:4
Alignment explanation
Indices: 29885376--29885400 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
29885366 TAATGAAGAA
29885376 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
29885401 TACCCACCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:29891013 original size:60 final size:60
Alignment explanation
Indices: 29890886--29891013 Score: 168
Period size: 60 Copynumber: 2.1 Consensus size: 60
29890876 ATGTGCAGTT
* * * * * *
29890886 AGGGGCATCGAAGTGTTAACAGGGGCATAGACATGCAAATAGGGACACCGAAGTGTATAC
1 AGGGGCACCGAAGTGTGAACAGGAGCACAGACATGCAAATAGAGACACCGAAGTGGATAC
* *
29890946 AGAGGCACCGAAGTGTGAACAGGAGCACAGGCATGCAAATAGAGACACCGAAGTGCGA-AC
1 AGGGGCACCGAAGTGTGAACAGGAGCACAGACATGCAAATAGAGACACCGAAGTG-GATAC
29891006 AGGGGCAC
1 AGGGGCAC
29891014 AGTTGTGCAA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 57 0.98
61 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.33, T:0.12
Consensus pattern (60 bp):
AGGGGCACCGAAGTGTGAACAGGAGCACAGACATGCAAATAGAGACACCGAAGTGGATAC
Found at i:29891027 original size:60 final size:60
Alignment explanation
Indices: 29890903--29891033 Score: 147
Period size: 60 Copynumber: 2.2 Consensus size: 60
29890893 TCGAAGTGTT
* * * * **
29890903 AACAGGGGCATAGACATGCAAATAGGGACACCGAAGTGTATACAGAGGCACCGAAGTGTG
1 AACAGGGGCACAGACATGCAAATAGAGACACCGAAGTGGATACAGAGGCACAGAAGTGCA
* * * **
29890963 AACAGGAGCACAGGCATGCAAATAGAGACACCGAAGTGCGA-ACAGGGGCACAGTTGTGCA
1 AACAGGGGCACAGACATGCAAATAGAGACACCGAAGTG-GATACAGAGGCACAGAAGTGCA
29891023 AACAGGGGCAC
1 AACAGGGGCAC
29891034 TTCTTCATTT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
60 57 0.98
61 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.32, T:0.11
Consensus pattern (60 bp):
AACAGGGGCACAGACATGCAAATAGAGACACCGAAGTGGATACAGAGGCACAGAAGTGCA
Found at i:29891112 original size:2 final size:2
Alignment explanation
Indices: 29891105--29891131 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29891095 TCTTAATTTC
29891105 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
29891132 CATGTATAAT
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:29897557 original size:24 final size:24
Alignment explanation
Indices: 29897530--29897581 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
29897520 ACAAATTTTT
29897530 TTTAATTTTATTAAATTTTAAATA
1 TTTAATTTTATTAAATTTTAAATA
* * * *
29897554 TTTATTTTTTTTAAGTTTTATATA
1 TTTAATTTTATTAAATTTTAAATA
29897578 TTTA
1 TTTA
29897582 CCTGAACTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTAATTTTATTAAATTTTAAATA
Found at i:29900561 original size:16 final size:16
Alignment explanation
Indices: 29900540--29900572 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
29900530 TTCGCTGTAT
29900540 TGGAATAGATGCGTAA
1 TGGAATAGATGCGTAA
29900556 TGGAATAGATGCGTAA
1 TGGAATAGATGCGTAA
29900572 T
1 T
29900573 AGCAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.30, T:0.27
Consensus pattern (16 bp):
TGGAATAGATGCGTAA
Found at i:29900647 original size:44 final size:45
Alignment explanation
Indices: 29900554--29900648 Score: 131
Period size: 44 Copynumber: 2.1 Consensus size: 45
29900544 ATAGATGCGT
*
29900554 AATGGAATAGATGCGTAATAGCAAATCAATTGTTTGGTTGAATGT
1 AATGGAATAGATGCGTAATAGCAAATCAATTGTTTGGTTGAATGG
* * *
29900599 AATGGAATAGATGCGTAATAG-TATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGATGCGTAATAGCAAATCAAT-TGTTTGGTTGAATGG
29900643 AATGGA
1 AATGGA
29900649 GGTGTAATAG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 21 0.47
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (45 bp):
AATGGAATAGATGCGTAATAGCAAATCAATTGTTTGGTTGAATGG
Found at i:29901086 original size:47 final size:47
Alignment explanation
Indices: 29901033--29901172 Score: 148
Period size: 47 Copynumber: 3.0 Consensus size: 47
29901023 TTAATAATGA
*
29901033 TATATAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATT
1 TATATAATTTCATAAAATTCTTAATAATAAATTTTCTTATATGAATT
** * * *
29901080 TATATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATGA
1 TATATAATTTCATAAAATTCTTAATAATAAAT-T-TTCTTATATGAAT-T
*
29901124 TATATAATTTCATAAAATTCTTAATAATAAATATTCTTATATGAATT
1 TATATAATTTCATAAAATTCTTAATAATAAATTTTCTTATATGAATT
29901171 TA
1 TA
29901173 CTAAAATCAT
Statistics
Matches: 72, Mismatches: 12, Indels: 18
0.71 0.12 0.18
Matches are distributed among these distances:
43 3 0.04
44 25 0.35
45 7 0.10
46 6 0.08
47 28 0.39
48 3 0.04
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (47 bp):
TATATAATTTCATAAAATTCTTAATAATAAATTTTCTTATATGAATT
Found at i:29901128 original size:44 final size:44
Alignment explanation
Indices: 29901010--29901133 Score: 119
Period size: 44 Copynumber: 2.8 Consensus size: 44
29901000 NNNNNNNNNN
** *
29901010 TATTAAATATAATTTAATAATGATATATAATTTCATAAAATTCTTGA
1 TATTAAATATAATTTAATAATGATATATAA-TT--TAAAATAATTAA
* * *
29901057 TAATAAAT-T-TTCTTATATGAAT-TTATATAATTTAAAATAATTAA
1 TATTAAATATAAT-TTA-AT-AATGATATATAATTTAAAATAATTAA
29901101 TATTAAATATAATTTAATAATGATATATAATTT
1 TATTAAATATAATTTAATAATGATATATAATTT
29901134 CATAAAATTC
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
43 3 0.05
44 28 0.45
45 5 0.08
46 7 0.11
47 16 0.26
48 3 0.05
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (44 bp):
TATTAAATATAATTTAATAATGATATATAATTTAAAATAATTAA
Found at i:29911594 original size:15 final size:16
Alignment explanation
Indices: 29911574--29911611 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
29911564 ATTAAACTAG
29911574 TTTAATTAACTTAA-C
1 TTTAATTAACTTAAGC
29911589 TTTAATT-ACTTAAGC
1 TTTAATTAACTTAAGC
29911604 TTTAATTA
1 TTTAATTA
29911612 CCAATTAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.50
Consensus pattern (16 bp):
TTTAATTAACTTAAGC
Found at i:29915070 original size:24 final size:24
Alignment explanation
Indices: 29915038--29915089 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
29915028 GTAGGGGTCA
29915038 ACACGCCCGTATTGAAGGAGGTAT
1 ACACGCCCGTATTGAAGGAGGTAT
29915062 ACACGCCCGTATTGAAGGAGGTAT
1 ACACGCCCGTATTGAAGGAGGTAT
29915086 ACAC
1 ACAC
29915090 CCGTGTGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (24 bp):
ACACGCCCGTATTGAAGGAGGTAT
Found at i:29922344 original size:25 final size:25
Alignment explanation
Indices: 29922302--29922363 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 25
29922292 TATAATAAAT
* * *
29922302 TTAAAT-ATTATATTTATATTTATA
1 TTAAATAAATATAATTATATTAATA
29922326 TTAAATAAATATAATTATATTAATA
1 TTAAATAAATATAATTATATTAATA
*
29922351 TTAAGTAAA-ATAA
1 TTAAATAAATATAA
29922364 AAATTCCCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 10 0.30
25 23 0.70
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
TTAAATAAATATAATTATATTAATA
Found at i:29931562 original size:43 final size:43
Alignment explanation
Indices: 29931514--29931627 Score: 140
Period size: 43 Copynumber: 2.6 Consensus size: 43
29931504 ATGTTCCAAT
*
29931514 ATCGATTTCAGATTTTGTGTAAGACCACAGCTGGGATATTGGC
1 ATCGATTTCAGATTTCGTGTAAGACCACAGCTGGGATATTGGC
* * * *
29931557 ATCGATTTGAGATTTCGTGTAAGACCATAGTTGGGCTATTGGC
1 ATCGATTTCAGATTTCGTGTAAGACCACAGCTGGGATATTGGC
* *
29931600 ATCGA-TACGAGATTTCCATGTAAGACCA
1 ATCGATTTC-AGATTT-CGTGTAAGACCA
29931628 TGTCTAGGAC
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
42 1 0.02
43 49 0.80
44 11 0.18
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.32
Consensus pattern (43 bp):
ATCGATTTCAGATTTCGTGTAAGACCACAGCTGGGATATTGGC
Found at i:29939827 original size:18 final size:19
Alignment explanation
Indices: 29939790--29939827 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
29939780 AATATTAACA
29939790 TAAATATTAATATAATATT
1 TAAATATTAATATAATATT
* *
29939809 TAAAT-TTATTATCATATT
1 TAAATATTAATATAATATT
29939827 T
1 T
29939828 TTAAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TAAATATTAATATAATATT
Found at i:29941789 original size:23 final size:23
Alignment explanation
Indices: 29941755--29941808 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
29941745 ATTTTAAAAA
29941755 TAAAAC-TTATTTAAGTACAAAT
1 TAAAACATTATTTAAGTACAAAT
**
29941777 TAAAACATTATTTTGGTACAAAT
1 TAAAACATTATTTAAGTACAAAT
29941800 TAAAA-ATTA
1 TAAAACATTA
29941809 AGCATTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.37
Consensus pattern (23 bp):
TAAAACATTATTTAAGTACAAAT
Found at i:29942185 original size:149 final size:150
Alignment explanation
Indices: 29941971--29942271 Score: 595
Period size: 149 Copynumber: 2.0 Consensus size: 150
29941961 TAAACTTTAA
29941971 AAGGCTTTATTTTTCATTACTTCCCAAAATTACTGTTAGAAGTTTTTTTTTATTGAAAAGTTTTA
1 AAGGCTTTATTTTTCATTACTTCCCAAAATTACTGTTAGAAGTTTTTTTTTATTGAAAAGTTTTA
29942036 AAAGTTTTTAGAATTTTAAAATATTGGTATTTTAGAATTCATAAATTTAAAATGTTAGATTTGTA
66 AAAGTTTTTAGAATTTTAAAATATTGGTATTTTAGAATTCATAAATTTAAAATGTTAGATTTGTA
29942101 ATTACTTTG-TTGAATAAAT
131 ATTACTTTGTTTGAATAAAT
29942120 AAGGCTTTATTTTTCATTACTTCCCAAAATTACTGTTAGAAGTTTTTTTTTATTGAAAAGTTTTA
1 AAGGCTTTATTTTTCATTACTTCCCAAAATTACTGTTAGAAGTTTTTTTTTATTGAAAAGTTTTA
29942185 AAAGTTTTTAGAATTTTAAAATATTGGTATTTTAGAATTCATAAATTTAAAATGTTAGATTTGTA
66 AAAGTTTTTAGAATTTTAAAATATTGGTATTTTAGAATTCATAAATTTAAAATGTTAGATTTGTA
29942250 ATTACTTTGTTTGAATAAAT
131 ATTACTTTGTTTGAATAAAT
29942270 AA
1 AA
29942272 TTGGTGTAGA
Statistics
Matches: 151, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
149 139 0.92
150 12 0.08
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (150 bp):
AAGGCTTTATTTTTCATTACTTCCCAAAATTACTGTTAGAAGTTTTTTTTTATTGAAAAGTTTTA
AAAGTTTTTAGAATTTTAAAATATTGGTATTTTAGAATTCATAAATTTAAAATGTTAGATTTGTA
ATTACTTTGTTTGAATAAAT
Found at i:29946910 original size:21 final size:20
Alignment explanation
Indices: 29946880--29946925 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
29946870 AACCCCTGAT
29946880 CTTAAACACATAAACAGAGCA
1 CTTAAACACATAAACAGAG-A
* * *
29946901 CTTAACCACATATATAGAGA
1 CTTAAACACATAAACAGAGA
29946921 CTTAA
1 CTTAA
29946926 TTATTAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.48, C:0.22, G:0.09, T:0.22
Consensus pattern (20 bp):
CTTAAACACATAAACAGAGA
Found at i:29947321 original size:30 final size:28
Alignment explanation
Indices: 29947266--29947341 Score: 71
Period size: 31 Copynumber: 2.6 Consensus size: 28
29947256 AAATCAATTC
* * ** *
29947266 AAATTTCAAAACATTTATAAAAAAAAAA
1 AAATTTTAAAAAATTTATTTAAAAATAA
*
29947294 CAAATTTTCATAAAAATTTATTTAAAAATTA
1 -AAATTTT-A-AAAAATTTATTTAAAAATAA
29947325 AAATTTTAAAAAATTTA
1 AAATTTTAAAAAATTTA
29947342 AAATTCTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 9 0.23
29 7 0.18
30 8 0.21
31 15 0.38
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (28 bp):
AAATTTTAAAAAATTTATTTAAAAATAA
Found at i:29947338 original size:16 final size:17
Alignment explanation
Indices: 29947317--29947351 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
29947307 AAATTTATTT
*
29947317 AAAAA-TTAAAATTTTA
1 AAAAATTTAAAATTCTA
29947333 AAAAATTTAAAATTCTA
1 AAAAATTTAAAATTCTA
29947350 AA
1 AA
29947352 GAAGATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAAATTTAAAATTCTA
Found at i:29951197 original size:20 final size:20
Alignment explanation
Indices: 29951174--29951220 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
29951164 AACTACAATA
*
29951174 ATAATGAGAATA-CTAATTTT
1 ATAATAAGAATATC-AATTTT
*
29951194 ATAATAATAATATCAATTTT
1 ATAATAAGAATATCAATTTT
29951214 ATAATAA
1 ATAATAA
29951221 TATCGATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (20 bp):
ATAATAAGAATATCAATTTT
Found at i:29957654 original size:31 final size:31
Alignment explanation
Indices: 29957619--29957686 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
29957609 TTTACAGCCT
*
29957619 AGTGACTTGAAT-AAAAATTTCTAAATAGTTC
1 AGTGACTTAAATGAAAAATTT-TAAATAGTTC
** *
29957650 AGTGACTTAAATGAAACCTTTTGAATAGTTC
1 AGTGACTTAAATGAAAAATTTTAAATAGTTC
29957681 AGTGAC
1 AGTGAC
29957687 CAAATTGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 26 0.81
32 6 0.19
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (31 bp):
AGTGACTTAAATGAAAAATTTTAAATAGTTC
Found at i:29970387 original size:21 final size:21
Alignment explanation
Indices: 29970363--29970462 Score: 94
Period size: 21 Copynumber: 4.8 Consensus size: 21
29970353 GCTTCTGTTT
*
29970363 AACTCATATGAGTTTCCGTTC
1 AACTCTTATGAGTTTCCGTTC
* ** *
29970384 AACTC-TATTGAGCTTCTTTTT
1 AACTCTTA-TGAGTTTCCGTTC
*
29970405 AACTCTTATGGGTTTCCGTTC
1 AACTCTTATGAGTTTCCGTTC
* *
29970426 AGCTCTTATGAGTTTCCATTC
1 AACTCTTATGAGTTTCCGTTC
* *
29970447 AACCCTTATGGGTTTC
1 AACTCTTATGAGTTTC
29970463 TATTTAGCTC
Statistics
Matches: 62, Mismatches: 15, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
20 2 0.03
21 58 0.94
22 2 0.03
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.43
Consensus pattern (21 bp):
AACTCTTATGAGTTTCCGTTC
Found at i:29970399 original size:42 final size:42
Alignment explanation
Indices: 29970352--29970431 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
29970342 AGCTCTCACA
29970352 AGCTTCTGTTTAACTCATATGAGTTTCCGTTCAACTCTATTG
1 AGCTTCTGTTTAACTCATATGAGTTTCCGTTCAACTCTATTG
* * * *
29970394 AGCTTCTTTTTAACTCTTATGGGTTTCCGTTCAGCTCT
1 AGCTTCTGTTTAACTCATATGAGTTTCCGTTCAACTCT
29970432 TATGAGTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.17, C:0.23, G:0.15, T:0.45
Consensus pattern (42 bp):
AGCTTCTGTTTAACTCATATGAGTTTCCGTTCAACTCTATTG
Found at i:29970455 original size:42 final size:42
Alignment explanation
Indices: 29970369--29970489 Score: 127
Period size: 42 Copynumber: 2.9 Consensus size: 42
29970359 GTTTAACTCA
* * * * *
29970369 TATGAGTTTCCGTTCAACTC-TATTGAGCTTCTTTTTAACTCT
1 TATGGGTTTCCGTTCAGCTCTTA-TGAGCTTCTATTCAACCCT
* *
29970411 TATGGGTTTCCGTTCAGCTCTTATGAGTTTCCATTCAACCCT
1 TATGGGTTTCCGTTCAGCTCTTATGAGCTTCTATTCAACCCT
** * *
29970453 TATGGGTTTCTATTTAGCTCTCATGAGCTTCTATTCA
1 TATGGGTTTCCGTTCAGCTCTTATGAGCTTCTATTCA
29970490 GGCTTCGGGC
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 63 0.97
43 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.45
Consensus pattern (42 bp):
TATGGGTTTCCGTTCAGCTCTTATGAGCTTCTATTCAACCCT
Found at i:29970490 original size:63 final size:63
Alignment explanation
Indices: 29970333--29970490 Score: 156
Period size: 63 Copynumber: 2.5 Consensus size: 63
29970323 TCATGTTTAC
** * * * *
29970333 TTTCTATTTAGCTCTCACAAGCTTCTGTTTAACTCATATGAGTTTCCGTTCAACTCTATTGAG
1 TTTCTATTTAGCTCTCATGAGCTTCTGTTCAGCTCATATGAGTTTCCATTCAACCCTATTGAG
* * * * * * * * *
29970396 CTTCTTTTTAACTCTTATGGGTTTCCGTTCAGCTCTTATGAGTTTCCATTCAACCCT-TATGGG
1 TTTCTATTTAGCTCTCATGAGCTTCTGTTCAGCTCATATGAGTTTCCATTCAACCCTAT-TGAG
*
29970459 TTTCTATTTAGCTCTCATGAGCTTCTATTCAG
1 TTTCTATTTAGCTCTCATGAGCTTCTGTTCAG
29970491 GCTTCGGGCT
Statistics
Matches: 71, Mismatches: 23, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
62 1 0.01
63 70 0.99
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.44
Consensus pattern (63 bp):
TTTCTATTTAGCTCTCATGAGCTTCTGTTCAGCTCATATGAGTTTCCATTCAACCCTATTGAG
Found at i:29971118 original size:14 final size:14
Alignment explanation
Indices: 29971099--29971128 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
29971089 TTTTGACCGT
29971099 AATATATTTCAAAA
1 AATATATTTCAAAA
29971113 AATATATTTCAAAA
1 AATATATTTCAAAA
29971127 AA
1 AA
29971129 GAAAAGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (14 bp):
AATATATTTCAAAA
Found at i:29972767 original size:50 final size:50
Alignment explanation
Indices: 29972686--29973342 Score: 487
Period size: 50 Copynumber: 13.2 Consensus size: 50
29972676 ACAGTTAAAT
* * * * *
29972686 AGATTAAAGTTACAACAGCAAATATTACTTCCCTAGCGGTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTAGCAGTGCAGTGGAAC
* * * **
29972736 AGATTGAAGCTACAACGGCGAATCTTGCTTCCCT-GACATTGCAGTTAAAC
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTAG-CAGTGCAGTGGAAC
* * *
29972786 AGATTGAAGCTATAACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTAGCAGTGCAGTGGAAC
* * * * * ** *
29972836 AGATTGAAGCTACAACGGCAAATCTTGCTTTCCCGA-CATTGCAGTTAAAT
1 AGATTGAAGCTACAACAGCGAATCTTAC-TTCCCTAGCAGTGCAGTGGAAC
** * *
29972886 AGATTGAAGCTATGACAGCGAATGTTACTTCCCTCGCAGTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTAGCAGTGCAGTGGAAC
* * * * * ** *
29972936 AGATTGAAGCTACAACGGCGAATCTTGCATCCC-CGACATTGCAGTTAAAT
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTAG-CAGTGCAGTGGAAC
* * *
29972986 AGATTGAAGCTACGACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTAGCAGTGCAGTGGAAC
* ** * * * * ** *
29973036 AAATTGAAGCTACAATGGTGAATCTTGCTTCCGCGA-CATTGCAGTTAAAT
1 AGATTGAAGCTACAACAGCGAATCTTACTTCC-CTAGCAGTGCAGTGGAAC
* *
29973086 AGATTGAAGCTACAACAGCAAATCTTACTTCCCTAGCGGTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTAGCAGTGCAGTGGAAC
** * ** * * **
29973136 AGATTGAAGCTACAATGGCCAATCTTGTTTCCC-CGACATTGCAGTTAAAC
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTAG-CAGTGCAGTGGAAC
* * *
29973186 AGATTGAAACTACGACAGCGAATATTACTTCCCT-G-ATGGTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTAGCA--GTGCAGTGGAAC
** * * * * ** *
29973236 AGATTGAAGCTACAATGGCGAATCTTGCTTCTCCGA-CATTGTAGTTAAAT
1 AGATTGAAGCTACAACAGCGAATCTTACTTC-CCTAGCAGTGCAGTGGAAC
* * *
29973286 AGATTGAAG--A-TA-A-CGAATCTTATTTCCCT-GAAGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTAGCAG-TGCAGTGGAAC
29973331 AGATTGAAGCTA
1 AGATTGAAGCTA
29973343 TAAATTACAG
Statistics
Matches: 459, Mismatches: 129, Indels: 41
0.73 0.21 0.07
Matches are distributed among these distances:
44 3 0.01
45 27 0.06
47 2 0.00
48 2 0.00
49 11 0.02
50 403 0.88
51 10 0.02
52 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCTACAACAGCGAATCTTACTTCCCTAGCAGTGCAGTGGAAC
Found at i:29972803 original size:100 final size:98
Alignment explanation
Indices: 29972672--29973342 Score: 902
Period size: 100 Copynumber: 6.8 Consensus size: 98
29972662 ATCTCTTTGG
* * * * *
29972672 CATTACAGTTAAATAGATTAAAGTTACAACAGCAAATATTACTTCCCTAGCGGTGCAGTGGAACA
1 CATTGCAGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCT-GCGGTGCAGTGGAACA
29972737 GATTGAAGCTACAACGGCGAATCTTGCTTCCCTGA
65 GATTGAAGCTACAACGGCGAATCTTGCTTCCC-GA
* *
29972772 CATTGCAGTTAAACAGATTGAAGCTATAACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACA
1 CATTGCAGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCT-GCGGTGCAGTGGAACA
*
29972837 GATTGAAGCTACAACGGCAAATCTTGCTTTCCCGA
65 GATTGAAGCTACAACGGCGAATCTTGC-TTCCCGA
** * *
29972872 CATTGCAGTTAAATAGATTGAAGCTATGACAGCGAATGTTACTTCCCTCGCAGTGCAGTGGAACA
1 CATTGCAGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCT-GCGGTGCAGTGGAACA
*
29972937 GATTGAAGCTACAACGGCGAATCTTGCATCCCCGA
65 GATTGAAGCTACAACGGCGAATCTTGC-TTCCCGA
*
29972972 CATTGCAGTTAAATAGATTGAAGCTACGACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACA
1 CATTGCAGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCT-GCGGTGCAGTGGAACA
* * *
29973037 AATTGAAGCTACAATGGTGAATCTTGCTTCCGCGA
65 GATTGAAGCTACAACGGCGAATCTTGCTTCC-CGA
*
29973072 CATTGCAGTTAAATAGATTGAAGCTACAACAGCAAATCTTACTTCCCTAGCGGTGCAGTGGAACA
1 CATTGCAGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCT-GCGGTGCAGTGGAACA
* * *
29973137 GATTGAAGCTACAATGGCCAATCTTGTTTCCCCGA
65 GATTGAAGCTACAACGGCGAATCTTGCTT-CCCGA
* * * * *
29973172 CATTGCAGTTAAACAGATTGAAACTACGACAGCGAATATTACTTCCCTGATGGTGCAGTGGAACA
1 CATTGCAGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCTG-CGGTGCAGTGGAACA
*
29973237 GATTGAAGCTACAATGGCGAATCTTGCTTCTCCGA
65 GATTGAAGCTACAACGGCGAATCTTGCTTC-CCGA
* * * * *
29973272 CATTGTAGTTAAATAGATTGAAG--A-TA-A-CGAATCTTATTTCCCTGAAGTTGCAGTGGAACA
1 CATTGCAGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCTG-CGGTGCAGTGGAACA
29973332 GATTGAAGCTA
65 GATTGAAGCTA
29973343 TAAATTACAG
Statistics
Matches: 518, Mismatches: 48, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
95 40 0.08
96 1 0.00
97 1 0.00
98 1 0.00
99 5 0.01
100 463 0.89
101 7 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (98 bp):
CATTGCAGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGCGGTGCAGTGGAACAG
ATTGAAGCTACAACGGCGAATCTTGCTTCCCGA
Found at i:29974247 original size:6 final size:6
Alignment explanation
Indices: 29974238--29974277 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
29974228 TGTTTTGTTC
29974238 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
29974278 TTCGAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:29974972 original size:3 final size:3
Alignment explanation
Indices: 29974966--29975018 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
29974956 AAACTAATAA
*
29974966 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29975014 ATT AT
1 ATT AT
29975019 CATATTTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:29976262 original size:21 final size:21
Alignment explanation
Indices: 29976237--29976280 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
29976227 ATCTTCGAGG
29976237 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
29976258 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
29976279 AT
1 AT
29976281 GTAATCTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:29976286 original size:19 final size:19
Alignment explanation
Indices: 29976236--29976291 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
29976226 AATCTTCGAG
29976236 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29976255 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
29976276 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
29976292 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 15 0.44
21 19 0.56
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:29976298 original size:22 final size:23
Alignment explanation
Indices: 29976249--29976314 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
29976239 ATGCAATCTT
*
29976249 AGATATGATATATGCAATCTT---
1 AGATATGAT-TATGTAATCTTAGA
29976270 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
29976292 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
29976315 GATTTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 10 0.26
21 8 0.21
22 8 0.21
23 13 0.33
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:29976324 original size:22 final size:23
Alignment explanation
Indices: 29976280--29976324 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
29976270 AGATATGATA
*
29976280 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
29976303 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
29976325 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:29977941 original size:21 final size:21
Alignment explanation
Indices: 29977889--29977941 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
29977879 TTTTACATTT
* *
29977889 TTATAATTTTATTCATTTTAT
1 TTATTATTTTATTCATTTTAG
* *
29977910 TTATT-TATTTATTTATTTTCG
1 TTATTAT-TTTATTCATTTTAG
29977931 TTATTATTTTA
1 TTATTATTTTA
29977942 AAAGAATGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.70
Consensus pattern (21 bp):
TTATTATTTTATTCATTTTAG
Found at i:29979076 original size:87 final size:87
Alignment explanation
Indices: 29978976--29979142 Score: 219
Period size: 87 Copynumber: 1.9 Consensus size: 87
29978966 TCTCTCTCTT
* * *
29978976 TTTTTTTTGCACTCAATTAAGCACTTGAACTTTAAAAATGTATAAAAAAGGCCCTCAAACTTCTT
1 TTTTTTTTGCACTCAATTAAGCACTTGAACTTTAAAAATGCATAAAAAAGACCCTCAAAATTCTT
29979041 CAAAGAAACCAATTAAACCCCTA
66 CAAA-AAACCAATTAAACCCCTA
** * * * * *
29979064 TTTTTTTT-CACTCAATTGGGTACTTGAACTTTCAAAATGCATGAAAAAGACCCTTAAAATTTTT
1 TTTTTTTTGCACTCAATTAAGCACTTGAACTTTAAAAATGCATAAAAAAGACCCTCAAAATTCTT
*
29979128 CAAAAAAGCAATTAA
66 CAAAAAACCAATTAA
29979143 TAAAAAATAT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
86 10 0.15
87 50 0.74
88 8 0.12
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.33
Consensus pattern (87 bp):
TTTTTTTTGCACTCAATTAAGCACTTGAACTTTAAAAATGCATAAAAAAGACCCTCAAAATTCTT
CAAAAAACCAATTAAACCCCTA
Found at i:29979502 original size:8 final size:8
Alignment explanation
Indices: 29979491--29979563 Score: 58
Period size: 8 Copynumber: 8.9 Consensus size: 8
29979481 CAATTTTACC
29979491 ATTTTTAT
1 ATTTTTAT
29979499 ATTTTT-T
1 ATTTTTAT
** *
29979506 AAATCTAT
1 ATTTTTAT
29979514 ATTTTTAT
1 ATTTTTAT
*
29979522 ATTTTTTACG
1 A-TTTTTA-T
29979532 ATTTTTAT
1 ATTTTTAT
29979540 ATTTTTAT
1 ATTTTTAT
* *
29979548 TTTTTTCT
1 ATTTTTAT
29979556 AATTTTTA
1 -ATTTTTA
29979564 ATAAAAATAG
Statistics
Matches: 49, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
7 4 0.08
8 27 0.55
9 17 0.35
10 1 0.02
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.70
Consensus pattern (8 bp):
ATTTTTAT
Found at i:29979562 original size:26 final size:26
Alignment explanation
Indices: 29979460--29979563 Score: 103
Period size: 26 Copynumber: 4.1 Consensus size: 26
29979450 TATGTTTCTA
29979460 TATATTTTATATATTTTTTTACAA-TTT
1 TATATTTT-TATA-TTTTTTACAATTTT
* *
29979487 TACCATTTTTATATTTTTTA-AA--TC
1 TA-TATTTTTATATTTTTTACAATTTT
*
29979511 TATATTTTTATATTTTTTACGATTTT
1 TATATTTTTATATTTTTTACAATTTT
29979537 TATATTTTTAT-TTTTTT-CTAATTTT
1 TATATTTTTATATTTTTTAC-AATTTT
29979562 TA
1 TA
29979564 ATAAAAATAG
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
23 16 0.24
24 5 0.08
25 15 0.23
26 19 0.29
27 6 0.09
28 5 0.08
ACGTcount: A:0.26, C:0.06, G:0.01, T:0.67
Consensus pattern (26 bp):
TATATTTTTATATTTTTTACAATTTT
Found at i:29985122 original size:60 final size:61
Alignment explanation
Indices: 29985009--29985122 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 61
29984999 ATGCTAACAA
** **
29985009 TTTAATTCAAAATATAAAATATTCAACAAATTTAGTGCTCAATGTTTACAAAATTTGTCAT
1 TTTAATTCAAAATATAAAATATTCAACAAATTTAGCCCTCAAAATTTACAAAATTTGTCAT
* * * * *
29985070 TTTAGTTCAAATTCTAAAAT-TTCAATAAATTTAGCCCTCAAAATTTAGAAAAT
1 TTTAATTCAAAATATAAAATATTCAACAAATTTAGCCCTCAAAATTTACAAAAT
29985123 GACTAAATTT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
60 27 0.61
61 17 0.39
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39
Consensus pattern (61 bp):
TTTAATTCAAAATATAAAATATTCAACAAATTTAGCCCTCAAAATTTACAAAATTTGTCAT
Found at i:29985606 original size:21 final size:18
Alignment explanation
Indices: 29985580--29985619 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
29985570 AGAGATGTGG
29985580 AAATATCTAAGAAAAAATGGA
1 AAATAT-TAA-AAAAAA-GGA
29985601 AAATATTAAAAAAAAGGA
1 AAATATTAAAAAAAAGGA
29985619 A
1 A
29985620 TAAAGGGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 6 0.32
20 3 0.16
21 6 0.32
ACGTcount: A:0.68, C:0.03, G:0.12, T:0.17
Consensus pattern (18 bp):
AAATATTAAAAAAAAGGA
Found at i:29986478 original size:16 final size:16
Alignment explanation
Indices: 29986459--29986489 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29986449 ATTATTTTAA
29986459 ATTTTAATTAGATAAT
1 ATTTTAATTAGATAAT
*
29986475 ATTTTATTTAGATAA
1 ATTTTAATTAGATAA
29986490 ATAAATAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
ATTTTAATTAGATAAT
Found at i:29994462 original size:20 final size:20
Alignment explanation
Indices: 29994433--29994492 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
29994423 ATTTTAAAAT
* *
29994433 CAAGTGAAAATTATTTTAAC
1 CAAGTTAAAATCATTTTAAC
* * *
29994453 CAAGTTAAAATGATCTTAAT
1 CAAGTTAAAATCATTTTAAC
*
29994473 TAAGTTAAAATCATTTTAAC
1 CAAGTTAAAATCATTTTAAC
29994493 ACATCAAAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (20 bp):
CAAGTTAAAATCATTTTAAC
Found at i:29996960 original size:13 final size:12
Alignment explanation
Indices: 29996919--29996967 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
29996909 TTTAAAATTT
*
29996919 AAAATTTATTAA
1 AAAATTTATAAA
29996931 AAAA--T-TAAA
1 AAAATTTATAAA
29996940 AAAA-TTATAAA
1 AAAATTTATAAA
29996951 CAAAATTTATAAA
1 -AAAATTTATAAA
29996964 AAAA
1 AAAA
29996968 ATTAAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
9 7 0.22
10 2 0.06
11 4 0.12
12 12 0.38
13 7 0.22
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (12 bp):
AAAATTTATAAA
Found at i:29996968 original size:13 final size:13
Alignment explanation
Indices: 29996937--29996970 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
29996927 TTAAAAAATT
29996937 AAAAAAA-TTATA
1 AAAAAAATTTATA
*
29996949 AACAAAATTTATA
1 AAAAAAATTTATA
29996962 AAAAAAATT
1 AAAAAAATT
29996971 AAAATTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAAAAATTTATA
Found at i:29997488 original size:6 final size:6
Alignment explanation
Indices: 29997479--29997503 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29997469 TAAAGTATTA
29997479 TTAAAT TTAAAT TTAAAT TTAAAT T
1 TTAAAT TTAAAT TTAAAT TTAAAT T
29997504 AACTATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:29997833 original size:17 final size:17
Alignment explanation
Indices: 29997813--29997845 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29997803 AAAATTATTA
29997813 AAAATACAA-AAATATAG
1 AAAATA-AATAAATATAG
29997830 AAAATAAATAAATATA
1 AAAATAAATAAATATA
29997846 TATTATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAATAAATAAATATAG
Found at i:29998275 original size:18 final size:17
Alignment explanation
Indices: 29998252--29998294 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
29998242 AGGTTGTATA
*
29998252 TAAAATTGTAAGTATTTT
1 TAAAATTGTAACT-TTTT
*
29998270 TAAAATTTGTATCTTTTT
1 TAAAA-TTGTAACTTTTT
29998288 TAAAATT
1 TAAAATT
29998295 TTCTATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 14 0.64
19 6 0.27
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.53
Consensus pattern (17 bp):
TAAAATTGTAACTTTTT
Found at i:29998306 original size:19 final size:20
Alignment explanation
Indices: 29998264--29998315 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 20
29998254 AAATTGTAAG
*
29998264 TATTTTTAAAA-TTTGTATC
1 TATTTTTAAAATTTTCTATC
29998283 T-TTTTTAAAATTTTCTAT-
1 TATTTTTAAAATTTTCTATC
29998301 TA-TTTTAAATATTTT
1 TATTTTTAAA-ATTTT
29998316 TTGCACTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 17 0.59
19 12 0.41
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (20 bp):
TATTTTTAAAATTTTCTATC
Found at i:29998363 original size:17 final size:19
Alignment explanation
Indices: 29998322--29998392 Score: 78
Period size: 17 Copynumber: 3.8 Consensus size: 19
29998312 TTTTTTGCAC
*
29998322 TTTTCTATATTTTTATAATAA
1 TTTTCTATA-TTTT-TAACAA
29998343 TTTTCTATA-TTTTAA-AA
1 TTTTCTATATTTTTAACAA
*
29998360 TTTTCCATATTTTTAACAA
1 TTTTCTATATTTTTAACAA
29998379 TTTT-T-TATTTTTAA
1 TTTTCTATATTTTTAA
29998393 TTCATATAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
17 19 0.41
18 9 0.20
19 9 0.20
21 9 0.20
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTCTATATTTTTAACAA
Found at i:29998411 original size:17 final size:17
Alignment explanation
Indices: 29998390--29998437 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 17
29998380 TTTTTATTTT
29998390 TAATTCATATAATTTTAA
1 TAATT-ATATAATTTTAA
*
29998408 -AATTAT-TCATTTTAA
1 TAATTATATAATTTTAA
29998423 TAATTTATATAATTT
1 TAA-TTATATAATTT
29998438 GTATAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 8 0.32
16 4 0.16
17 8 0.32
18 5 0.20
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (17 bp):
TAATTATATAATTTTAA
Found at i:29998490 original size:31 final size:28
Alignment explanation
Indices: 29998439--29998510 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 28
29998429 ATATAATTTG
*
29998439 TATAATTTTTGAGACATTTATACTGTTTTTTTT
1 TATAATTTTT--G-CATTTATA-T-TTATTTTT
29998472 TATATATTTTTGCATTTATATTTATTTTT
1 TATA-ATTTTTGCATTTATATTTATTTTT
29998501 TATAATTTTT
1 TATAATTTTT
29998511 TTTGTGATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
28 6 0.16
29 11 0.30
30 1 0.03
31 8 0.22
32 1 0.03
33 4 0.11
34 6 0.16
ACGTcount: A:0.25, C:0.04, G:0.06, T:0.65
Consensus pattern (28 bp):
TATAATTTTTGCATTTATATTTATTTTT
Found at i:29998514 original size:31 final size:31
Alignment explanation
Indices: 29998453--29998510 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
29998443 ATTTTTGAGA
*
29998453 CATTTATACTGTTTTTTTTTATATATTTTTG
1 CATTTATACTGTTATTTTTTATATATTTTTG
29998484 CATTTATA-T-TTATTTTTTATA-ATTTTT
1 CATTTATACTGTTATTTTTTATATATTTTT
29998511 TTTGTGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 6 0.23
29 11 0.42
30 1 0.04
31 8 0.31
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.69
Consensus pattern (31 bp):
CATTTATACTGTTATTTTTTATATATTTTTG
Found at i:29998558 original size:38 final size:36
Alignment explanation
Indices: 29998492--29998568 Score: 91
Period size: 38 Copynumber: 2.1 Consensus size: 36
29998482 TGCATTTATA
* ** *
29998492 TTTATTTTTTATAATTTTTTTTGTGATTTTGAATAT
1 TTTATTTTTTATAATTTCTTTTACGATTTTCAATAT
*
29998528 TTTAGTTTTTTAATAATTTCTTTTACGATTTTCAGTAT
1 TTTA-TTTTTT-ATAATTTCTTTTACGATTTTCAATAT
29998566 TTT
1 TTT
29998569 TTACCGATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 4 0.12
37 6 0.18
38 24 0.71
ACGTcount: A:0.22, C:0.04, G:0.08, T:0.66
Consensus pattern (36 bp):
TTTATTTTTTATAATTTCTTTTACGATTTTCAATAT
Found at i:30002381 original size:21 final size:20
Alignment explanation
Indices: 30002340--30002382 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
30002330 ATTTTTTTAC
**
30002340 TATTTTAAATATAAAGTATT
1 TATTTTAAATATAAAAAATT
*
30002360 TATTTTATATTATAAAAAATT
1 TATTTTA-AATATAAAAAATT
30002381 TA
1 TA
30002383 AATTATTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TATTTTAAATATAAAAAATT
Found at i:30002412 original size:27 final size:26
Alignment explanation
Indices: 30002359--30002413 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
30002349 TATAAAGTAT
* *
30002359 TTATTTTATATTATAAAAAATTTAAA
1 TTATTTTATATTATAAAAAAATAAAA
30002385 TTATTTATATATTA-AATAAAAATAAAA
1 TTATTT-TATATTATAA-AAAAATAAAA
30002412 TT
1 TT
30002414 TAATTCAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TTATTTTATATTATAAAAAAATAAAA
Found at i:30007059 original size:15 final size:15
Alignment explanation
Indices: 30007039--30007072 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
30007029 TTTCCTGCAC
30007039 TGGGCTGGTGGT-TAT
1 TGGGCTGG-GGTGTAT
30007054 TGGGCTGGGGTGTAT
1 TGGGCTGGGGTGTAT
30007069 TGGG
1 TGGG
30007073 TAATTCGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.06, C:0.06, G:0.53, T:0.35
Consensus pattern (15 bp):
TGGGCTGGGGTGTAT
Found at i:30011110 original size:111 final size:112
Alignment explanation
Indices: 30010985--30011210 Score: 445
Period size: 111 Copynumber: 2.0 Consensus size: 112
30010975 TATAACAATT
30010985 TTAAAAGTACAAAATAATATTATAACACAATTCATTTATTTTCGTTTAAGTTATTTTTTAATCTC
1 TTAAAAGTACAAAATAATATTATAACACAATTCATTTATTTTCGTTTAAGTTATTTTTTAATCTC
30011050 GATCCAATTCAGCATGAGCGGAATTTAAATTAAATAA-TTTAAAATA
66 GATCCAATTCAGCATGAGCGGAATTTAAATTAAATAATTTTAAAATA
30011096 TTAAAAGTACAAAATAATATTATAACACAATTCATTTATTTTCGTTTAAGTTATTTTTTAATCTC
1 TTAAAAGTACAAAATAATATTATAACACAATTCATTTATTTTCGTTTAAGTTATTTTTTAATCTC
30011161 GATCCAATTCAGCATGAGCGGAATTTAAATTAAATAATTTTAAAATA
66 GATCCAATTCAGCATGAGCGGAATTTAAATTAAATAATTTTAAAATA
30011208 TTA
1 TTA
30011211 TTATATAAAA
Statistics
Matches: 114, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
111 102 0.89
112 12 0.11
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (112 bp):
TTAAAAGTACAAAATAATATTATAACACAATTCATTTATTTTCGTTTAAGTTATTTTTTAATCTC
GATCCAATTCAGCATGAGCGGAATTTAAATTAAATAATTTTAAAATA
Found at i:30022535 original size:33 final size:33
Alignment explanation
Indices: 30022493--30022561 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
30022483 TAAGGGGTGT
* *
30022493 TACATCACTGTTCAATTTTTTTACTTGTTTTGG
1 TACATCACTGCTCAATTTTTTTACTTGTATTGG
*
30022526 TACATCACTGCTCAGTTTTTTTACTTGTATTGG
1 TACATCACTGCTCAATTTTTTTACTTGTATTGG
30022559 TAC
1 TAC
30022562 TTTGGTTCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.19, C:0.17, G:0.13, T:0.51
Consensus pattern (33 bp):
TACATCACTGCTCAATTTTTTTACTTGTATTGG
Found at i:30022720 original size:15 final size:15
Alignment explanation
Indices: 30022702--30022731 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30022692 TTTTACCATA
30022702 TTGAATGTTGAATTT
1 TTGAATGTTGAATTT
*
30022717 TTGAATGTTTAATTT
1 TTGAATGTTGAATTT
30022732 GTATATTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.57
Consensus pattern (15 bp):
TTGAATGTTGAATTT
Done.