Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 114 of 126
Found at i:33981004 original size:31 final size:34
Alignment explanation
Indices: 33980930--33981008 Score: 96
Period size: 33 Copynumber: 2.4 Consensus size: 34
33980920 CTACCCATAA
*
33980930 AAGTGACTAAAATGTTAACGACAATTAACGGCTC
1 AAGTGACTAAAATGTTAACAACAATTAACGGCTC
*
33980964 AA-TGACTAAAATGTTAA-AACACGTTAA-GG-T-
1 AAGTGACTAAAATGTTAACAACA-ATTAACGGCTC
33980994 AAGTGACTAAAATGT
1 AAGTGACTAAAATGT
33981009 AACCTGAGGC
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
30 2 0.05
31 13 0.32
32 5 0.12
33 19 0.46
34 2 0.05
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.25
Consensus pattern (34 bp):
AAGTGACTAAAATGTTAACAACAATTAACGGCTC
Found at i:33997721 original size:2 final size:2
Alignment explanation
Indices: 33997714--33997749 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
33997704 TGGAAACTGG
33997714 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
33997750 CGGTGAGAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:33998023 original size:15 final size:14
Alignment explanation
Indices: 33997985--33998032 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
33997975 TTTTTCAAAA
33997985 TTTTAGAATTTAAT
1 TTTTAGAATTTAAT
* *
33997999 TTTTATAATTTTAT
1 TTTTAGAATTTAAT
33998013 TTTTAAGAATTTAAAT
1 TTTT-AGAATTT-AAT
33998029 TTTT
1 TTTT
33998033 TACTTTTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 16 0.57
15 6 0.21
16 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (14 bp):
TTTTAGAATTTAAT
Found at i:33998058 original size:29 final size:30
Alignment explanation
Indices: 33997970--33998058 Score: 76
Period size: 31 Copynumber: 3.0 Consensus size: 30
33997960 TCATAAGTTG
* * *
33997970 TTATATTTTTCAAAATTTTAGAATTTAATTT
1 TTATAATTTTC-AAATTTTAAAATTAAATTT
*
33998001 TTATAATTTT--ATTTTTAAGAATTTAAATTT
1 TTATAATTTTCAAATTTTAA-AA-TTAAATTT
* *
33998031 TT-TACTTTTCAAATTTTAAAATTCAATT
1 TTATAATTTTCAAATTTTAAAATTAAATT
33998059 CTAATTGTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
28 6 0.13
29 14 0.30
30 11 0.23
31 16 0.34
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.57
Consensus pattern (30 bp):
TTATAATTTTCAAATTTTAAAATTAAATTT
Found at i:33999681 original size:26 final size:27
Alignment explanation
Indices: 33999630--33999681 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
33999620 CATAAATTAA
* *
33999630 AAATCTAAAATTTTAAAACAGGAAAAG
1 AAATCTAAAACTTTAAAACAGCAAAAG
33999657 AAAT-TAAAACTTTAAAA-AGACAAAA
1 AAATCTAAAACTTTAAAACAG-CAAAA
33999682 ACCAGCCACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 2 0.09
26 16 0.73
27 4 0.18
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.21
Consensus pattern (27 bp):
AAATCTAAAACTTTAAAACAGCAAAAG
Found at i:34003876 original size:16 final size:16
Alignment explanation
Indices: 34003857--34003890 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
34003847 AATTTGCATG
*
34003857 TTTTATATTATATTAT
1 TTTTATATTATATAAT
34003873 TTTTATATTATATAAT
1 TTTTATATTATATAAT
34003889 TT
1 TT
34003891 ATAATACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTATATTATATAAT
Found at i:34003940 original size:2 final size:2
Alignment explanation
Indices: 34003928--34003965 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
34003918 AGAAATCATG
*
34003928 TA TA TA T- TA TA TA TA CA 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 TA TA T
34003966 TAAATATGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34018957 original size:16 final size:17
Alignment explanation
Indices: 34018919--34018957 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
34018909 AAATAAATAT
34018919 TAAAAAACCTTAAACCC
1 TAAAAAACCTTAAACCC
*
34018936 T-AAAAATCTTAAA-CC
1 TAAAAAACCTTAAACCC
34018951 TAAAAAA
1 TAAAAAA
34018958 AAGGGCCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 3 0.15
16 16 0.80
17 1 0.05
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (17 bp):
TAAAAAACCTTAAACCC
Found at i:34024690 original size:37 final size:38
Alignment explanation
Indices: 34024618--34024694 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 38
34024608 ATAAATGATT
34024618 TTAAAATTATTGAAATTATTTTTTTAAAATAAAAATTA
1 TTAAAATTATTGAAATTATTTTTTTAAAATAAAAATTA
*
34024656 TTAAAATTATTG-TATTA-TTTTTTAAAATATAAAATTA
1 TTAAAATTATTGAAATTATTTTTTTAAAATA-AAAATTA
34024693 TT
1 TT
34024695 TTATCCTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
36 12 0.32
37 13 0.35
38 12 0.32
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (38 bp):
TTAAAATTATTGAAATTATTTTTTTAAAATAAAAATTA
Found at i:34028545 original size:30 final size:30
Alignment explanation
Indices: 34028470--34028547 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
34028460 GGGTAACCTC
* *
34028470 GATATAATGCCAGCTTGTGTAAGCAACTCT
1 GATATAATGTCAGCTTGTGTAAGCAACCCT
*
34028500 GTTATAATGTCAGCTTGTG-AGAGCAACCCT
1 GATATAATGTCAGCTTGTGTA-AGCAACCCT
* *
34028530 GATATATTGTTAGCTTGT
1 GATATAATGTCAGCTTGT
34028548 TTGAGTAACA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 1 0.02
30 40 0.98
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (30 bp):
GATATAATGTCAGCTTGTGTAAGCAACCCT
Found at i:34037523 original size:37 final size:37
Alignment explanation
Indices: 34037473--34037617 Score: 182
Period size: 37 Copynumber: 3.9 Consensus size: 37
34037463 TTATACAAAT
34037473 TCAGGCTTGGTGCCTAGTAGGCTTTATGCCAGTGTTA
1 TCAGGCTTGGTGCCTAGTAGGCTTTATGCCAGTGTTA
* * *
34037510 TCAGGCTTGGTGCCTAGTAGGATTTATACCGGTGTTA
1 TCAGGCTTGGTGCCTAGTAGGCTTTATGCCAGTGTTA
* * * *
34037547 TCAGGCTTTGTGCCTAGTAGACTTTGTGCCGGTGTTA
1 TCAGGCTTGGTGCCTAGTAGGCTTTATGCCAGTGTTA
* ** * *
34037584 TCAGGCTTTGTGTTTAATAGGCTTGATGCCAGTG
1 TCAGGCTTGGTGCCTAGTAGGCTTTATGCCAGTG
34037618 ATCCAACAAT
Statistics
Matches: 93, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 93 1.00
ACGTcount: A:0.17, C:0.17, G:0.30, T:0.37
Consensus pattern (37 bp):
TCAGGCTTGGTGCCTAGTAGGCTTTATGCCAGTGTTA
Found at i:34037594 original size:21 final size:21
Alignment explanation
Indices: 34037538--34037595 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 21
34037528 AGGATTTATA
34037538 CCGGTGTTATCAGGCTTTGTG
1 CCGGTGTTATCAGGCTTTGTG
*
34037559 CC-----TAGT-AGACTTTGTG
1 CCGGTGTTA-TCAGGCTTTGTG
34037575 CCGGTGTTATCAGGCTTTGTG
1 CCGGTGTTATCAGGCTTTGTG
34037596 TTTAATAGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 14
0.64 0.05 0.32
Matches are distributed among these distances:
16 13 0.46
17 1 0.04
20 1 0.04
21 13 0.46
ACGTcount: A:0.12, C:0.19, G:0.31, T:0.38
Consensus pattern (21 bp):
CCGGTGTTATCAGGCTTTGTG
Found at i:34039047 original size:18 final size:16
Alignment explanation
Indices: 34039024--34039059 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
34039014 TGAACAGTCT
34039024 TTTAATTAATTAAATTTA
1 TTTAATTAA--AAATTTA
34039042 TTTAATTAAAAATTTA
1 TTTAATTAAAAATTTA
34039058 TT
1 TT
34039060 CTTATCCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAATTAAAAATTTA
Found at i:34040924 original size:26 final size:26
Alignment explanation
Indices: 34040895--34040952 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
34040885 TTACTTAGGA
34040895 TAAAATCATCAAAATTTT-ATCAGGGG
1 TAAAATCATCAAAATTTTAAT-AGGGG
* *
34040921 TAAAATCGTGAAAATTTTAATAGGGG
1 TAAAATCATCAAAATTTTAATAGGGG
34040947 TAAAAT
1 TAAAAT
34040953 AGGGATGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 27 0.93
27 2 0.07
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31
Consensus pattern (26 bp):
TAAAATCATCAAAATTTTAATAGGGG
Found at i:34042251 original size:22 final size:22
Alignment explanation
Indices: 34042226--34042280 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
34042216 ACCCACGTGG
34042226 CCTCCTTAAACAATTATGGCAA
1 CCTCCTTAAACAATTATGGCAA
34042248 CCTCCTTAAACAATTATGGCAA
1 CCTCCTTAAACAATTATGGCAA
34042270 CCTCCTCTAAA
1 CCTCCT-TAAA
34042281 TGTTGGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 28 0.88
23 4 0.12
ACGTcount: A:0.35, C:0.31, G:0.07, T:0.27
Consensus pattern (22 bp):
CCTCCTTAAACAATTATGGCAA
Found at i:34043097 original size:32 final size:33
Alignment explanation
Indices: 34043043--34043107 Score: 82
Period size: 32 Copynumber: 2.0 Consensus size: 33
34043033 AGATTTATTT
34043043 AAAATAAAAATATTAAATTTAAAT-TTAAAATA
1 AAAATAAAAATATTAAATTTAAATATTAAAATA
*
34043075 AAAAT-AAAA-ATTATAATATTAAATATTTAAATA
1 AAAATAAAAATATTA-AAT-TTAAATATTAAAATA
34043108 TTAAGAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 4 0.14
31 7 0.24
32 11 0.38
33 7 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (33 bp):
AAAATAAAAATATTAAATTTAAATATTAAAATA
Found at i:34043099 original size:7 final size:7
Alignment explanation
Indices: 34043050--34043111 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 7
34043040 TTTAAAATAA
34043050 AAATATT
1 AAATATT
34043057 AAAT-TT
1 AAATATT
34043063 AAAT-TT
1 AAATATT
34043069 AAA-A-T
1 AAATATT
*
34043074 AAA-AAT
1 AAATATT
*
34043080 AAAAATT
1 AAATATT
34043087 ATAATATT
1 A-AATATT
34043095 AAATATTT
1 AAATA-TT
34043103 AAATATT
1 AAATATT
34043110 AA
1 AA
34043112 GAAATATTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
5 5 0.10
6 15 0.31
7 15 0.31
8 13 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AAATATT
Found at i:34043121 original size:33 final size:30
Alignment explanation
Indices: 34043038--34043121 Score: 75
Period size: 33 Copynumber: 2.7 Consensus size: 30
34043028 CAGTCAGATT
34043038 TATTTAAA-ATAAAAATATTA-AATTTAAA
1 TATTTAAATATAAAAATATTATAATTTAAA
* * *
34043066 T-TTAAAATAAAAATAAAAATTATAATATTAAA
1 TATTTAAAT-ATAA-AAATATTATAAT-TTAAA
34043098 TATTTAAATATTAAGAAATATTAT
1 TATTTAAATA-TAA-AAATATTAT
34043122 TGACTTTGAT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 3 0.07
30 7 0.17
31 3 0.07
32 7 0.17
33 16 0.38
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (30 bp):
TATTTAAATATAAAAATATTATAATTTAAA
Found at i:34043382 original size:19 final size:20
Alignment explanation
Indices: 34043342--34043392 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
34043332 TTTTAAATTT
34043342 TAAAAATTGAAAATAATATA
1 TAAAAATTGAAAATAATATA
**
34043362 TAAAAATTGAAAATTGT-TA
1 TAAAAATTGAAAATAATATA
34043381 TAAAAATT-AAAA
1 TAAAAATTGAAAA
34043393 AAAAGTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 4 0.14
19 10 0.34
20 15 0.52
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (20 bp):
TAAAAATTGAAAATAATATA
Found at i:34043588 original size:17 final size:17
Alignment explanation
Indices: 34043566--34043618 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
34043556 TCGATTACCG
* *
34043566 TATTTTTTTGTAAATTT
1 TATTTTTTTATAAATTA
34043583 TA-TTTTTTATAAATTA
1 TATTTTTTTATAAATTA
* *
34043599 TATTTTTTTCTAGATTA
1 TATTTTTTTATAAATTA
34043616 TAT
1 TAT
34043619 ATAATGATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (17 bp):
TATTTTTTTATAAATTA
Found at i:34043590 original size:16 final size:16
Alignment explanation
Indices: 34043569--34043606 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
34043559 ATTACCGTAT
* *
34043569 TTTTTTGTAAATTTTA
1 TTTTTTATAAATTATA
34043585 TTTTTTATAAATTATA
1 TTTTTTATAAATTATA
34043601 TTTTTT
1 TTTTTT
34043607 TCTAGATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTTTATAAATTATA
Found at i:34043650 original size:20 final size:19
Alignment explanation
Indices: 34043625--34043679 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
34043615 ATATATAATG
34043625 ATTTTTATATATTTATTTCA
1 ATTTTTATATATTTATTT-A
34043645 ATTTTT-TCATATTT-TTTA
1 ATTTTTAT-ATATTTATTTA
*
34043663 ATGTGTCTATATATTTA
1 AT-T-TTTATATATTTA
34043680 ATAAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
18 3 0.10
19 5 0.17
20 20 0.69
21 1 0.03
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (19 bp):
ATTTTTATATATTTATTTA
Found at i:34049623 original size:2 final size:2
Alignment explanation
Indices: 34049616--34049648 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
34049606 CATCCAATCG
34049616 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
34049649 GCGTACGTAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:34057519 original size:66 final size:66
Alignment explanation
Indices: 34057442--34057573 Score: 228
Period size: 66 Copynumber: 2.0 Consensus size: 66
34057432 GTTGAATCGG
* * * *
34057442 ATTCTTCAACGAAAATAAAGCTCTTTTAACATTGTTTTCTTTGATTTTAATACTTGAACTCGAAA
1 ATTCTTCAACGAAAATAAAGCTCTTTTAACATTATTTTCTTCGATTTTAACACTTGAACCCGAAA
34057507 C
66 C
34057508 ATTCTTCAACGAAAATAAAGCTCTTTTAACATTATTTTCTTCGATTTTAACACTTGAACCCGAAA
1 ATTCTTCAACGAAAATAAAGCTCTTTTAACATTATTTTCTTCGATTTTAACACTTGAACCCGAAA
34057573 C
66 C
34057574 TTAAACTCTT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.39
Consensus pattern (66 bp):
ATTCTTCAACGAAAATAAAGCTCTTTTAACATTATTTTCTTCGATTTTAACACTTGAACCCGAAA
C
Found at i:34060913 original size:19 final size:19
Alignment explanation
Indices: 34060878--34060933 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
34060868 TTTTTAAAAA
*
34060878 TATAAAT-TTTAGAATTTT
1 TATAAATATTTTGAATTTT
34060896 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
34060915 TGA-AAATTATTTTGAATTT
1 T-ATAAA-TATTTTGAATTT
34060934 GTTTTTGTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.21
19 14 0.41
20 13 0.38
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:34060915 original size:20 final size:20
Alignment explanation
Indices: 34060878--34060933 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
34060868 TTTTTAAAAA
*
34060878 TATAAAT-TTTAGAA-TTTT
1 TATAAATATTTTGAATTTTT
34060896 TATAAATATTTTGAATTTTT
1 TATAAATATTTTGAATTTTT
*
34060916 GA-AAATTATTTTGAATTT
1 TATAAA-TATTTTGAATTT
34060934 GTTTTTGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.21
19 9 0.27
20 17 0.52
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
TATAAATATTTTGAATTTTT
Found at i:34079060 original size:15 final size:15
Alignment explanation
Indices: 34079040--34079070 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
34079030 ACTACATAAT
34079040 ATATAAAATATCATA
1 ATATAAAATATCATA
*
34079055 ATATAAAATATTATA
1 ATATAAAATATCATA
34079070 A
1 A
34079071 ACTTAAAATT
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:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATAAAATATCATA
Found at i:34082875 original size:38 final size:38
Alignment explanation
Indices: 34082824--34082930 Score: 101
Period size: 38 Copynumber: 2.8 Consensus size: 38
34082814 TCTAACATAT
* * *
34082824 TAAAAATACATAAA-AATAT-TTATATTAAAAATACTACTA
1 TAAATATA-ATAAATAATATATTATATTAAAAACA-TA-AA
* *
34082863 TAAATATAATAAATATTTTATTATATTAAAAACATAAA
1 TAAATATAATAAATAATATATTATATTAAAAACATAAA
** *
34082901 TAAATATAATAAATTTTTTATTATATTAAA
1 TAAATATAATAAATAATATATTATATTAAA
34082931 TAAAAATTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
38 35 0.58
39 12 0.20
40 13 0.22
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (38 bp):
TAAATATAATAAATAATATATTATATTAAAAACATAAA
Found at i:34086612 original size:5 final size:5
Alignment explanation
Indices: 34086602--34086645 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
34086592 TTCAAGCTTA
34086602 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
34086646 AAGTTAGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:34092828 original size:20 final size:21
Alignment explanation
Indices: 34092803--34092841 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
34092793 AGGCTCGAGA
34092803 TTTAATGTTT-AGGGTTTAAG
1 TTTAATGTTTAAGGGTTTAAG
34092823 TTTAATGTTTAAGGGTTTA
1 TTTAATGTTTAAGGGTTTA
34092842 GGGTTACGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (21 bp):
TTTAATGTTTAAGGGTTTAAG
Found at i:34096842 original size:23 final size:23
Alignment explanation
Indices: 34096816--34096859 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
34096806 ATGCAGTCCC
34096816 TTAAGAAAT-GATTAAATTATAAA
1 TTAAGAAATAG-TTAAATTATAAA
* *
34096839 TTAATATATAGTTAAATTATA
1 TTAAGAAATAGTTAAATTATA
34096860 TTTTGACCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 17 0.94
24 1 0.06
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (23 bp):
TTAAGAAATAGTTAAATTATAAA
Found at i:34106018 original size:6 final size:6
Alignment explanation
Indices: 34106000--34106094 Score: 81
Period size: 6 Copynumber: 16.0 Consensus size: 6
34105990 TTAAATTGAT
* *
34106000 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA TATCTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-T-TAAA
* ** *
34106047 TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
34106095 AATCCAAGTG
Statistics
Matches: 73, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.11
6 49 0.67
7 7 0.10
8 5 0.07
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:34106050 original size:31 final size:30
Alignment explanation
Indices: 34105990--34106071 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 30
34105980 GACTTTTGAG
*
34105990 TTAAATTGATTTTAAATTT--AT-TTAAAT
1 TTAATTTGATTTTAAATTTAAATATTAAAT
34106017 TTAGATTT-ATTTTAAATTTAAATATCTAAAT
1 TTA-ATTTGATTTTAAATTTAAATAT-TAAAT
*
34106048 TTAATTTGAATTTAAATTTAAATA
1 TTAATTTGATTTTAAATTTAAATA
34106072 AAAATTAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
27 14 0.30
28 3 0.06
29 2 0.04
30 5 0.11
31 23 0.49
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (30 bp):
TTAATTTGATTTTAAATTTAAATATTAAAT
Found at i:34106059 original size:25 final size:23
Alignment explanation
Indices: 34106009--34106094 Score: 82
Period size: 25 Copynumber: 3.6 Consensus size: 23
34105999 TTTTAAATTT
* *
34106009 ATTTAAATTTAGATTTATTTTAA
1 ATTTAAATTTAAATTTAATTTAA
*
34106032 ATTTAAATATCTAAATTTAATTTGA
1 ATTTAAAT-T-TAAATTTAATTTAA
** *
34106057 ATTTAAATTTAAATAAAAATTAAA
1 ATTTAAATTTAAAT-TTAATTTAA
34106081 ATATTAAATTTAAA
1 AT-TTAAATTTAAA
34106095 AATCCAAGTG
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
23 13 0.25
24 9 0.17
25 30 0.58
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTAAATTTAAATTTAATTTAA
Found at i:34106065 original size:17 final size:16
Alignment explanation
Indices: 34106004--34106068 Score: 64
Period size: 17 Copynumber: 4.1 Consensus size: 16
34105994 ATTGATTTTA
34106004 AATTT-ATTTAAATTT
1 AATTTAATTTAAATTT
*
34106019 AGATTTATTTTAAATTT
1 A-ATTTAATTTAAATTT
* *
34106036 AA-AT-ATCTAAATTT
1 AATTTAATTTAAATTT
34106050 AATTTGAATTTAAATTT
1 AATTT-AATTTAAATTT
34106067 AA
1 AA
34106069 ATAAAAATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
14 10 0.26
15 3 0.08
16 5 0.13
17 21 0.54
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (16 bp):
AATTTAATTTAAATTT
Found at i:34106067 original size:42 final size:42
Alignment explanation
Indices: 34106001--34106093 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
34105991 TAAATTGATT
* * ** *
34106001 TTAAATTT-ATTTAAATTTAGATTT-ATTTTAAATTTAAATA
1 TTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAAATA
*
34106041 TCTAAATTTAATTTGAATTTAAATTTAAATAAAAATTAAAATA
1 T-TAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAAATA
34106084 TTAAATTTAA
1 TTAAATTTAA
34106094 AAATCCAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
40 1 0.02
41 7 0.16
42 23 0.52
43 13 0.30
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (42 bp):
TTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAAATA
Found at i:34107758 original size:162 final size:163
Alignment explanation
Indices: 34107580--34107898 Score: 475
Period size: 162 Copynumber: 2.0 Consensus size: 163
34107570 TCTTTTAATT
* * *
34107580 TAGTCCTTTGACTGTTTGACTATACCAGAGATTGCCACGTGCCATGTTTTGGGATTATTTGTGCA
1 TAGTCCTTTGACTGTTTGACTACACCAGAGATTGCCACGTGCCATCTTTTGGGATTATTTCTGCA
*
34107645 TTTAGTCCTTTTTATTTCTAATTTATCTTAATTTAATCC-TAAATCAACTTAGT-TTTAATTACG
66 TTTAGTCCTTTTTATTTCTAATTTATCTTAATTTAATCCTTAAATCAAC-TAGTATTTAATTACA
34107708 AAATTGGCCCAAT-A-ATTTTTCAAGGTTTATAAAC
130 AAATTGGCCC--TGAGATTTTTCAAGGTTTATAAAC
* * * * *
34107742 TAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATCTTTTTGGATTATTTCTGTA
1 TAGTCCTTTGACTGTTTGACTACACCAGAGATTGCCACGTGCCATCTTTTGGGATTATTTCTGCA
* * *
34107807 TTTAGTCCTTTTTATTTCTCATTTGTCTTAATTTAATCCTTAAATCAACTATTATTTAATTACAA
66 TTTAGTCCTTTTTATTTCTAATTTATCTTAATTTAATCCTTAAATCAACTAGTATTTAATTACAA
34107872 AATTGGCCCTGAGATTTTTCAAGGTTT
131 AATTGGCCCTGAGATTTTTCAAGGTTT
34107899 TCAAATTGGT
Statistics
Matches: 141, Mismatches: 12, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
161 1 0.01
162 98 0.70
163 42 0.30
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.45
Consensus pattern (163 bp):
TAGTCCTTTGACTGTTTGACTACACCAGAGATTGCCACGTGCCATCTTTTGGGATTATTTCTGCA
TTTAGTCCTTTTTATTTCTAATTTATCTTAATTTAATCCTTAAATCAACTAGTATTTAATTACAA
AATTGGCCCTGAGATTTTTCAAGGTTTATAAAC
Found at i:34108027 original size:30 final size:30
Alignment explanation
Indices: 34107991--34108128 Score: 156
Period size: 30 Copynumber: 4.6 Consensus size: 30
34107981 AAACAATCCA
*
34107991 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
34108021 AAAATTACATTTTAACCCCAAAAACTTTTCC
1 AAAATTACATTTTAACCCC-AAAACTTTTCC
* *
34108052 AAAATTACATTTTAACCCTAAAAC-TTTCA
1 AAAATTACATTTTAACCCCAAAACTTTTCC
* * * *
34108081 AAAATTGCCATTTTACCCCCGAATCTTTT--
1 AAAATT-ACATTTTAACCCCAAAACTTTTCC
*
34108110 AAAATTCCATTTTTAACCC
1 AAAATTACA-TTTTAACCC
34108129 TAATTTCACC
Statistics
Matches: 95, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
28 3 0.03
29 24 0.25
30 36 0.38
31 32 0.34
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCAAAACTTTTCC
Found at i:34108130 original size:59 final size:57
Alignment explanation
Indices: 34108016--34108395 Score: 417
Period size: 59 Copynumber: 6.5 Consensus size: 57
34108006 CCCCAAAACT
** * * *
34108016 TTTC-CAAAATTA-CATTTTAACCCCAAAAACTTTTCCAAAATTACA-TTTTAACCCTAAAA
1 TTTCACAAAATTACCATTTT-ACCCCCGAATCTTTT--AAAATTCCATTTTTAACCC--CAA
* *
34108075 CTTTCA-AAAATTGCCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCTAA
1 -TTTCACAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCAA
*
34108132 TTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGA
1 TTTCA-C-AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCAA
* *
34108191 TTTCACCGAAAATTACCATTTTACCCCCGAAGCTTTTAAAATTCCATTTTTAACCCCGA
1 TTTCA-C-AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCAA
* * *
34108250 TTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGA
1 TTTCA-C-AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCAA
* * * **
34108309 TTTCACCAAAAATTACCATTATACCCCCGAATCTTTTAAAATTCTATTTTTAATCCTGA
1 TTTCA-C-AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCAA
* *
34108368 TTACATCAAAATTACCATTTTGCCCCCG
1 TTTCA-CAAAATTACCATTTTACCCCCG
34108396 GGTATCCATA
Statistics
Matches: 292, Mismatches: 22, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
56 5 0.02
57 2 0.01
58 27 0.09
59 230 0.79
60 22 0.08
61 6 0.02
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.35
Consensus pattern (57 bp):
TTTCACAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCAA
Found at i:34108154 original size:30 final size:30
Alignment explanation
Indices: 34108110--34108328 Score: 131
Period size: 30 Copynumber: 7.4 Consensus size: 30
34108100 CGAATCTTTT
*
34108110 AAAATTCCATTTTTAACCCTAATTTCACCG
1 AAAATTCCATTTTTAACCCCAATTTCACCG
* **
34108140 AAAATTACCA-TTTTACCCCCGAATCTT---TT
1 AAAATT-CCATTTTTAACCCC-AAT-TTCACCG
*
34108169 AAAATTCCATTTTTAACCCCGATTTCACCG
1 AAAATTCCATTTTTAACCCCAATTTCACCG
* *
34108199 AAAATTACCA-TTTTACCCCCGAAGCTTT----T
1 AAAATT-CCATTTTTAACCCC-AA--TTTCACCG
*
34108228 AAAATTCCATTTTTAACCCCGATTTCACCG
1 AAAATTCCATTTTTAACCCCAATTTCACCG
* * *
34108258 AAAATTACCA-TTTTACCCCCGAAGCTT---CT
1 AAAATT-CCATTTTTAACCCC-AA-TTTCACCG
* *
34108287 AAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTCCATTTTTAACCCCAATTTCACCG
34108317 AAAATTACCATT
1 AAAATT-CCATT
34108329 ATACCCCCGA
Statistics
Matches: 143, Mismatches: 22, Indels: 47
0.67 0.10 0.22
Matches are distributed among these distances:
26 3 0.02
27 4 0.03
28 13 0.09
29 46 0.32
30 51 0.36
31 19 0.13
32 4 0.03
33 3 0.02
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.34
Consensus pattern (30 bp):
AAAATTCCATTTTTAACCCCAATTTCACCG
Found at i:34108220 original size:118 final size:118
Alignment explanation
Indices: 34108079--34108395 Score: 510
Period size: 118 Copynumber: 2.7 Consensus size: 118
34108069 CTAAAACTTT
* *
34108079 CAAAAATTGCCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCTAATTTCACCGAAAA
1 CAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCTGATTTCACCGAAAA
* *
34108144 TTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCAC
66 TTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCAC
* * *
34108197 CGAAAATTACCATTTTACCCCCGAAGCTTTTAAAATTCCATTTTTAACCCCGATTTCACCGAAAA
1 CAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCTGATTTCACCGAAAA
34108262 TTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCAC
66 TTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCAC
* * * * *
34108315 CAAAAATTACCATTATACCCCCGAATCTTTTAAAATTCTATTTTTAATCCTGATTACATC-AAAA
1 CAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCTGATTTCACCGAAAA
*
34108379 TTACCATTTTGCCCCCG
66 TTACCATTTTACCCCCG
34108396 GGTATCCATA
Statistics
Matches: 183, Mismatches: 16, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
117 20 0.11
118 163 0.89
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (118 bp):
CAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCTGATTTCACCGAAAA
TTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCAC
Found at i:34110379 original size:16 final size:18
Alignment explanation
Indices: 34110358--34110397 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
34110348 ATCTAAAACA
*
34110358 TTTATTTT-TTATTTT-T
1 TTTATTTTCCTATTTTGT
34110374 TTTATTTTCCTATTTTGT
1 TTTATTTTCCTATTTTGT
34110392 TTTATT
1 TTTATT
34110398 GTTGATGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 6 0.29
18 7 0.33
ACGTcount: A:0.12, C:0.05, G:0.03, T:0.80
Consensus pattern (18 bp):
TTTATTTTCCTATTTTGT
Found at i:34110573 original size:30 final size:31
Alignment explanation
Indices: 34110522--34110589 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 31
34110512 GGTTTTAATT
34110522 CAGTCACTAAACTTTCGAAAAA-TAACAAAA
1 CAGTCACTAAACTTTCGAAAAAGTAACAAAA
** * *
34110552 CAGTCACTAATGTTATC-AAAAAGTGACAAAT
1 CAGTCACTAAACTT-TCGAAAAAGTAACAAAA
34110583 CAGTCAC
1 CAGTCAC
34110590 CATTAACATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.47, C:0.21, G:0.10, T:0.22
Consensus pattern (31 bp):
CAGTCACTAAACTTTCGAAAAAGTAACAAAA
Found at i:34112889 original size:15 final size:17
Alignment explanation
Indices: 34112864--34112896 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
34112854 TAATTTTGTC
34112864 ATTACTAAATTA-AAAT
1 ATTACTAAATTATAAAT
34112880 ATTA-TAAATTATAAAT
1 ATTACTAAATTATAAAT
34112896 A
1 A
34112897 GACTTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTACTAAATTATAAAT
Found at i:34123336 original size:50 final size:48
Alignment explanation
Indices: 34123282--34123375 Score: 118
Period size: 48 Copynumber: 1.9 Consensus size: 48
34123272 CTTACCTCCA
** *
34123282 AAAAT-TTTTACTTTCCCTCCCCTTTTATTTCAAAATATCAAAATCCCCCC
1 AAAATCTTTTA-TTT-CCTCCCC-TTTATCCCAAAAAATCAAAATCCCCCC
*
34123332 AAAATCTTTTATTTCTTCCCCTTTATCCCAAAAAATCAAAATCC
1 AAAATCTTTTATTTCCTCCCCTTTATCCCAAAAAATCAAAATCC
34123376 TTATTATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
48 20 0.51
49 6 0.15
50 8 0.21
51 5 0.13
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (48 bp):
AAAATCTTTTATTTCCTCCCCTTTATCCCAAAAAATCAAAATCCCCCC
Found at i:34125274 original size:30 final size:28
Alignment explanation
Indices: 34125234--34125298 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 28
34125224 GCTAATATTT
*
34125234 AATTAATTTTTAAAATTTAAAAATTATAAA
1 AATTATTTTTTAAAA-TT-AAAATTATAAA
*
34125264 AATTATTTTTTAAAATTAAAATTATTAA
1 AATTATTTTTTAAAATTAAAATTATAAA
34125292 AATTATT
1 AATTATT
34125299 AAAAAGTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 17 0.52
29 2 0.06
30 14 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
AATTATTTTTTAAAATTAAAATTATAAA
Found at i:34125303 original size:19 final size:19
Alignment explanation
Indices: 34125281--34125327 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
34125271 TTTTAAAATT
* *
34125281 AAAATTATTAAAATTATTA
1 AAAAATATTAAAATTATAA
* *
34125300 AAAAGTATGAAAATTATAA
1 AAAAATATTAAAATTATAA
34125319 AAAAATATT
1 AAAAATATT
34125328 TTTAAAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (19 bp):
AAAAATATTAAAATTATAA
Found at i:34126972 original size:7 final size:7
Alignment explanation
Indices: 34126960--34126999 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
34126950 TTACTAATAT
34126960 TAGAAAG
1 TAGAAAG
34126967 TAGAAAG
1 TAGAAAG
34126974 TAGAAAG
1 TAGAAAG
34126981 TAGAAAG
1 TAGAAAG
34126988 TAGAAAG
1 TAGAAAG
34126995 TAGAA
1 TAGAA
34127000 TTTTATAGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.57, C:0.00, G:0.28, T:0.15
Consensus pattern (7 bp):
TAGAAAG
Found at i:34129501 original size:12 final size:12
Alignment explanation
Indices: 34129484--34129523 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
34129474 TTAAAGAAAA
34129484 TCAAAATAATTT
1 TCAAAATAATTT
34129496 TCAAAA-AA-TT
1 TCAAAATAATTT
34129506 T-AAAATAATTT
1 TCAAAATAATTT
*
34129517 TTAAAAT
1 TCAAAAT
34129524 TTAAAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 4 0.16
10 5 0.20
11 5 0.20
12 11 0.44
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (12 bp):
TCAAAATAATTT
Found at i:34129502 original size:19 final size:19
Alignment explanation
Indices: 34129480--34129549 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
34129470 AAAATTAAAG
*
34129480 AAAATCAAAATAATTTTCAA
1 AAAATTAAAATAATTTT-AA
*
34129500 AAAATTTAAAATAATTTTTA
1 AAAA-TTAAAATAATTTTAA
*
34129520 AAATTTAAAAT-ATTTATAA
1 AAAATTAAAATAATTT-TAA
34129539 AAAATTAAAAT
1 AAAATTAAAAT
34129550 TTTATATTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
18 4 0.09
19 19 0.44
20 8 0.19
21 12 0.28
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATTAAAATAATTTTAA
Found at i:34129539 original size:18 final size:18
Alignment explanation
Indices: 34129500--34129555 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 18
34129490 TAATTTTCAA
*
34129500 AAAATTTAAAATAATTTTT
1 AAAATTTAAAAT-ATTTAT
34129519 AAAATTTAAAATATTTAT
1 AAAATTTAAAATATTTAT
*
34129537 AAAAAATTAAAAT-TTTAT
1 -AAAATTTAAAATATTTAT
34129555 A
1 A
34129556 TTTAAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 1 0.03
18 10 0.29
19 23 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAATTTAAAATATTTAT
Found at i:34129562 original size:20 final size:22
Alignment explanation
Indices: 34129500--34129562 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 22
34129490 TAATTTTCAA
*
34129500 AAAATTTAAAATA---ATTTTT
1 AAAATTTAAAATATTTATATTT
34129519 AAAATTTAAAATATTTATA---
1 AAAATTTAAAATATTTATATTT
*
34129538 AAAAATTAAAAT-TTTATATTT
1 AAAATTTAAAATATTTATATTT
34129559 AAAA
1 AAAA
34129563 AATATACAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
18 6 0.17
19 24 0.67
21 4 0.11
22 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAATTTAAAATATTTATATTT
Found at i:34129590 original size:17 final size:18
Alignment explanation
Indices: 34129558--34129609 Score: 70
Period size: 17 Copynumber: 2.8 Consensus size: 18
34129548 ATTTTATATT
*
34129558 TAAAAAATATACAAATTC
1 TAAAAAATATAAAAATTC
34129576 TAAAAAA-ATAAAAATTC
1 TAAAAAATATAAAAATTC
34129593 TAAAGAATATATAAAAA
1 TAAA-AA-ATATAAAAA
34129610 AATTTAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 13 0.43
18 9 0.30
19 1 0.03
20 7 0.23
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (18 bp):
TAAAAAATATAAAAATTC
Found at i:34132703 original size:20 final size:19
Alignment explanation
Indices: 34132665--34132723 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
34132655 GGATTAGTAT
34132665 GGTTTATATTAAG-TGTAAATA
1 GGTTTA-ATTAAGAT-TAAA-A
34132686 GGTTTAATTAAGATTAAAA
1 GGTTTAATTAAGATTAAAA
*
34132705 GTGATTAATTAAGACTTAA
1 G-GTTTAATTAAGA-TTAA
34132724 TGATGAAAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 2 0.06
20 21 0.62
21 11 0.32
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.39
Consensus pattern (19 bp):
GGTTTAATTAAGATTAAAA
Found at i:34134491 original size:21 final size:21
Alignment explanation
Indices: 34134465--34134518 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
34134455 GGAGTTTTTA
*
34134465 GTATCGGTAGATG-CATGACTT
1 GTATCGGTAGAAGTCAT-ACTT
*
34134486 GTATCGGTAGAAGTTATACTT
1 GTATCGGTAGAAGTCATACTT
34134507 GTATCGGTAGAA
1 GTATCGGTAGAA
34134519 CTAGCACAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGAAGTCATACTT
Found at i:34135982 original size:25 final size:23
Alignment explanation
Indices: 34135939--34136004 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 23
34135929 GACTTGGGTT
34135939 GTATCGGTAG-TTGTA--TAGAA
1 GTATCGGTAGTTTGTACTTAGAA
34135959 GGTATCGGTAGTTCTGTACTTAGAA
1 -GTATCGGTAGTT-TGTACTTAGAA
*
34135984 GTATCAGTAGTCTATGTACTT
1 GTATCGGTAGT-T-TGTACTT
34136005 GTATCGGTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 10 0.26
22 1 0.03
23 4 0.11
24 10 0.26
25 13 0.34
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.38
Consensus pattern (23 bp):
GTATCGGTAGTTTGTACTTAGAA
Found at i:34135993 original size:24 final size:26
Alignment explanation
Indices: 34135954--34136004 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
34135944 GGTAGTTGTA
* *
34135954 TAGAAGGTATCGGTAGT-TCTGTACT
1 TAGAAGGTATCAGTAGTCTATGTACT
34135979 TAGAA-GTATCAGTAGTCTATGTACT
1 TAGAAGGTATCAGTAGTCTATGTACT
34136004 T
1 T
34136005 GTATCGGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (26 bp):
TAGAAGGTATCAGTAGTCTATGTACT
Found at i:34136630 original size:18 final size:18
Alignment explanation
Indices: 34136598--34136648 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
34136588 TCACTATTAA
*
34136598 ATTCAATAATCATAATCAT
1 ATTCAATTATCATAAT-AT
*
34136617 ATTCTATT-TCATAAATAT
1 ATTCAATTATCAT-AATAT
34136635 ATTCAATTATCATA
1 ATTCAATTATCATA
34136649 CTTGTAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTCAATTATCATAATAT
Found at i:34139145 original size:20 final size:21
Alignment explanation
Indices: 34139129--34139175 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
34139119 TACAAAATAA
34139129 TCAAAAT-AATTTTAAAAAAT
1 TCAAAATAAATTTTAAAAAAT
34139149 TCAAAATAAATTTT-AAAAAT
1 TCAAAATAAATTTTAAAAAAT
34139169 T-AAAATA
1 TCAAAATA
34139176 TTTATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.23
20 14 0.54
21 6 0.23
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (21 bp):
TCAAAATAAATTTTAAAAAAT
Found at i:34139146 original size:21 final size:22
Alignment explanation
Indices: 34139122--34139168 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
34139112 CAAAAATTAC
34139122 AAAATAATCAAAAT-AATTTTA
1 AAAATAATCAAAATAAATTTTA
*
34139143 AAAA-ATTCAAAATAAATTTTA
1 AAAATAATCAAAATAAATTTTA
34139164 AAAAT
1 AAAAT
34139169 TAAAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAATAATCAAAATAAATTTTA
Found at i:34142223 original size:2 final size:2
Alignment explanation
Indices: 34142218--34142276 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
34142208 AAACAGGGAG
34142218 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
34142260 GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA G
34142277 GGGGGGGGGG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:34158062 original size:42 final size:42
Alignment explanation
Indices: 34158003--34158083 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
34157993 TTAAAAATAC
* *
34158003 CAATTCACTCCATTCTTGGTGTATTTCGATCCTAATATACAT
1 CAATTCACCCCATTCTTGGTGTATTTCGATCATAATATACAT
34158045 CAATTCACCCCATTCTTGGTGTATTTCGATCATAATATA
1 CAATTCACCCCATTCTTGGTGTATTTCGATCATAATATA
34158084 GATAATAGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (42 bp):
CAATTCACCCCATTCTTGGTGTATTTCGATCATAATATACAT
Found at i:34162187 original size:3 final size:3
Alignment explanation
Indices: 34162179--34162203 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
34162169 TTTGAATTTG
34162179 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
34162204 ACGCTGCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:34163439 original size:17 final size:18
Alignment explanation
Indices: 34163417--34163454 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
34163407 TTAAATTACA
34163417 AAAAAATTAAAA-ATTT-T
1 AAAAAA-TAAAATATTTAT
34163434 AAAAAATAAAATATTTAT
1 AAAAAATAAAATATTTAT
34163452 AAA
1 AAA
34163455 TTTATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.26
17 10 0.53
18 4 0.21
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAAATAAAATATTTAT
Found at i:34163444 original size:25 final size:25
Alignment explanation
Indices: 34163416--34163490 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
34163406 TTTAAATTAC
34163416 AAAAAAATTAAAAATTTTAAAAAAT
1 AAAAAAATTAAAAATTTTAAAAAAT
* * *
34163441 AAAATATTTATAAA-TTTATAAAAAT
1 AAAAAAATTAAAAATTTTA-AAAAAT
*
34163466 -AAGAAA-TAAAAATTATTTAAAAAAT
1 AAAAAAATTAAAAA-T-TTTAAAAAAT
34163491 TCGAGTTCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
23 5 0.13
24 7 0.18
25 23 0.59
26 4 0.10
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (25 bp):
AAAAAAATTAAAAATTTTAAAAAAT
Found at i:34168234 original size:32 final size:31
Alignment explanation
Indices: 34168192--34168258 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
34168182 AAAATTTTAA
** *
34168192 TAAATAAAAAATTCTATAAAATTATTAAATAT
1 TAAATAAAAAATAATATAAAAATA-TAAATAT
* *
34168224 TAAATGAAAAATAATATAAAAATATAAATTT
1 TAAATAAAAAATAATATAAAAATATAAATAT
34168255 TAAA
1 TAAA
34168259 AAATTAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 10 0.33
32 20 0.67
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (31 bp):
TAAATAAAAAATAATATAAAAATATAAATAT
Found at i:34171487 original size:14 final size:13
Alignment explanation
Indices: 34171462--34171513 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
34171452 TTTGTTTACA
34171462 ATTAAAATTTATT
1 ATTAAAATTTATT
34171475 ATTAAATATTTATT
1 ATTAAA-ATTTATT
*
34171489 AAAAATAAAATTTATT
1 ---ATTAAAATTTATT
*
34171505 ATAAAAATT
1 ATTAAAATT
34171514 AAATACATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 13 0.41
14 7 0.22
16 7 0.22
17 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTAAAATTTATT
Found at i:34171503 original size:16 final size:18
Alignment explanation
Indices: 34171477--34171510 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
34171467 AATTTATTAT
34171477 TAAATATTTATTA-AAAA
1 TAAATATTTATTATAAAA
34171494 TAAA-ATTTATTATAAAA
1 TAAATATTTATTATAAAA
34171511 ATTAAATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAATATTTATTATAAAA
Found at i:34184913 original size:14 final size:14
Alignment explanation
Indices: 34184863--34184914 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
34184853 ATGAACTCTC
34184863 AACTCTAAATCTTG
1 AACTCTAAATCTTG
* *
34184877 ATCCCTAAATCTTG
1 AACTCTAAATCTTG
*
34184891 AA-TATTAAATCTTG
1 AACT-CTAAATCTTG
34184905 AACTCTAAAT
1 AACTCTAAAT
34184915 TCCAAATCCT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 29 0.97
15 1 0.03
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (14 bp):
AACTCTAAATCTTG
Found at i:34184951 original size:42 final size:42
Alignment explanation
Indices: 34184896--34184992 Score: 97
Period size: 42 Copynumber: 2.3 Consensus size: 42
34184886 TCTTGAATAT
* * *
34184896 TAAATCTTGAACTCTAAAT-TCCAAATCCTAAACCCTAAACCT
1 TAAATCCTAAACTCTAAATCT-CAAATCCTAAACCCTAAACCC
* * ** *
34184938 TATATCCTAAACTCTGAATCTTGAATCTTAAACCCTAAACCC
1 TAAATCCTAAACTCTAAATCTCAAATCCTAAACCCTAAACCC
*
34184980 TAAATCTTAAACT
1 TAAATCCTAAACT
34184993 ATGGATCCCA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
42 43 0.98
43 1 0.02
ACGTcount: A:0.39, C:0.27, G:0.03, T:0.31
Consensus pattern (42 bp):
TAAATCCTAAACTCTAAATCTCAAATCCTAAACCCTAAACCC
Found at i:34184985 original size:21 final size:21
Alignment explanation
Indices: 34184896--34184991 Score: 68
Period size: 21 Copynumber: 4.6 Consensus size: 21
34184886 TCTTGAATAT
* * *
34184896 TAAATCTTGAACTCTAAATTCC
1 TAAATCTTAAACCCTAAA-CCC
* *
34184918 -AAATCCTAAACCCTAAACCT
1 TAAATCTTAAACCCTAAACCC
* * * * * *
34184938 TATATCCTAAACTCTGAATCT
1 TAAATCTTAAACCCTAAACCC
*
34184959 TGAATCTTAAACCCTAAACCC
1 TAAATCTTAAACCCTAAACCC
34184980 TAAATCTTAAAC
1 TAAATCTTAAAC
34184992 TATGGATCCC
Statistics
Matches: 56, Mismatches: 17, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 1 0.02
21 55 0.98
ACGTcount: A:0.40, C:0.27, G:0.03, T:0.30
Consensus pattern (21 bp):
TAAATCTTAAACCCTAAACCC
Found at i:34185005 original size:21 final size:21
Alignment explanation
Indices: 34184981--34185020 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34184971 CCTAAACCCT
*
34184981 AAATCTTAAACTATGGATCCC
1 AAATCTTAAACTATAGATCCC
*
34185002 AAATCTTGAACTATAGATC
1 AAATCTTAAACTATAGATC
34185021 ATAGGTCTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (21 bp):
AAATCTTAAACTATAGATCCC
Found at i:34185007 original size:42 final size:42
Alignment explanation
Indices: 34184916--34185008 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
34184906 ACTCTAAATT
* * * *
34184916 CCAAATCCTAAACCCTAAACCTTATATCCTAAACTCTGAATC
1 CCAAATCTTAAACCCTAAACCCTAAATCCTAAACTATGAATC
*** * *
34184958 TTGAATCTTAAACCCTAAACCCTAAATCTTAAACTATGGATC
1 CCAAATCTTAAACCCTAAACCCTAAATCCTAAACTATGAATC
34185000 CCAAATCTT
1 CCAAATCTT
34185009 GAACTATAGA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.29
Consensus pattern (42 bp):
CCAAATCTTAAACCCTAAACCCTAAATCCTAAACTATGAATC
Found at i:34193058 original size:4 final size:4
Alignment explanation
Indices: 34193051--34193077 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
34193041 CTACAATATA
34193051 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
34193078 ATAGTTTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:34204121 original size:22 final size:21
Alignment explanation
Indices: 34204096--34204155 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 21
34204086 AATTTGATAC
34204096 AATTTTCACAAATCATTAATAA
1 AATTTTCACAAATCA-TAATAA
*
34204118 AATTATCAACATAA-CATAATAA
1 AATTTTC-ACA-AATCATAATAA
*
34204140 AATTTTCTCAACATCA
1 AATTTTCACAA-ATCA
34204156 AGGGAGATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
20 1 0.03
21 3 0.10
22 20 0.65
23 5 0.16
24 2 0.06
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTTTCACAAATCATAATAA
Found at i:34208997 original size:58 final size:58
Alignment explanation
Indices: 34208928--34209042 Score: 169
Period size: 58 Copynumber: 2.0 Consensus size: 58
34208918 AAAGGAATTG
*
34208928 TTTATGAGTGTTATTT-ATGAATAAAATTATAATTGAGTTTAAAAATATTTGAGTTTAA
1 TTTATGAGTGTT-TTTGAAGAATAAAATTATAATTGAGTTTAAAAATATTTGAGTTTAA
* * * *
34208986 TTTATGAGTGTTTTTGAAGAATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
1 TTTATGAGTGTTTTTGAAGAATAAAATTATAATTGAGTTTAAAAATATTTGAGTTTA
34209043 GTTTGTTGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 3 0.06
58 48 0.94
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (58 bp):
TTTATGAGTGTTTTTGAAGAATAAAATTATAATTGAGTTTAAAAATATTTGAGTTTAA
Found at i:34216558 original size:50 final size:50
Alignment explanation
Indices: 34216504--34216603 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 50
34216494 GTCCAGAAAC
*
34216504 AACCAAGGA-ATATTTACTTAACCAAAAAAGCAAGACCGAGATCAAGAATA
1 AACCAAGGATA-AATTACTTAACCAAAAAAGCAAGACCGAGATCAAGAATA
* *
34216554 AACCAAGGATAAATTACTTAACCAAAAAAGCATGACCTAGATCAAGAATA
1 AACCAAGGATAAATTACTTAACCAAAAAAGCAAGACCGAGATCAAGAATA
34216604 TAGCTTGAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 45 0.98
51 1 0.02
ACGTcount: A:0.52, C:0.18, G:0.13, T:0.17
Consensus pattern (50 bp):
AACCAAGGATAAATTACTTAACCAAAAAAGCAAGACCGAGATCAAGAATA
Found at i:34235247 original size:37 final size:38
Alignment explanation
Indices: 34235197--34235280 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
34235187 CTTCTTCAAA
* * * *
34235197 CCCTAAGCCACCAAATTAA-ATTCTTCCTGCACGAAAT
1 CCCTAACCCACCAAATTAATATTATTCCCGCACAAAAT
*
34235234 CCCTAACCCACCAAATTAATTTTATTCCCGCACAAAAT
1 CCCTAACCCACCAAATTAATATTATTCCCGCACAAAAT
*
34235272 CCCTGACCC
1 CCCTAACCC
34235281 CATCCCTACT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
37 18 0.45
38 22 0.55
ACGTcount: A:0.33, C:0.37, G:0.06, T:0.24
Consensus pattern (38 bp):
CCCTAACCCACCAAATTAATATTATTCCCGCACAAAAT
Found at i:34238468 original size:21 final size:21
Alignment explanation
Indices: 34238439--34238478 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34238429 TGGTTTAGAG
*
34238439 GGATTCAAGATCTAATGTTCA
1 GGATCCAAGATCTAATGTTCA
*
34238460 GGATCCAAGATTTAATGTT
1 GGATCCAAGATCTAATGTT
34238479 TAAGGTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (21 bp):
GGATCCAAGATCTAATGTTCA
Found at i:34240482 original size:39 final size:39
Alignment explanation
Indices: 34240430--34240508 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
34240420 AGAGAATGTC
*
34240430 ATACATCAGCAATTTTAACAACTTAGTGGTTAAATGTAA
1 ATACATCAACAATTTTAACAACTTAGTGGTTAAATGTAA
34240469 ATACATCAACAATTTTAACAACTTAGTGGTTAAATGTAA
1 ATACATCAACAATTTTAACAACTTAGTGGTTAAATGTAA
34240508 A
1 A
34240509 CTTTCGAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (39 bp):
ATACATCAACAATTTTAACAACTTAGTGGTTAAATGTAA
Found at i:34243153 original size:33 final size:33
Alignment explanation
Indices: 34243115--34243201 Score: 83
Period size: 33 Copynumber: 2.7 Consensus size: 33
34243105 AGGTTCACCC
34243115 ATATTATTTTTTAAAAATTTTAAAAATTTATTT
1 ATATTATTTTTTAAAAATTTTAAAAATTTATTT
* *
34243148 ATATTATATATTTT-AATA-TTTAATAATTTATTT
1 ATATTAT-T-TTTTAAAAATTTTAAAAATTTATTT
* *
34243181 -T-TAATTTATTAAAATATTTTA
1 ATATTATTTTTTAAAA-ATTTTA
34243202 TATAATAATC
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
29 3 0.07
30 3 0.07
31 4 0.09
32 5 0.11
33 21 0.48
34 4 0.09
35 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (33 bp):
ATATTATTTTTTAAAAATTTTAAAAATTTATTT
Found at i:34248040 original size:17 final size:16
Alignment explanation
Indices: 34248007--34248040 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
34247997 TACTACATGT
*
34248007 ATTTTATTTACTTTTA
1 ATTTTATTTAATTTTA
34248023 ATTTTATCTTAATTTTA
1 ATTTTAT-TTAATTTTA
34248040 A
1 A
34248041 ATAATATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTTATTTAATTTTA
Found at i:34248592 original size:15 final size:17
Alignment explanation
Indices: 34248558--34248595 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
34248548 AATAAAAATG
34248558 TAATTTCATCATTTTAA
1 TAATTTCATCATTTTAA
*
34248575 TAATTT-AT-ATTTTTA
1 TAATTTCATCATTTTAA
34248590 TAATTT
1 TAATTT
34248596 TTAAAGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 2 0.10
17 6 0.30
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (17 bp):
TAATTTCATCATTTTAA
Found at i:34249036 original size:90 final size:89
Alignment explanation
Indices: 34248931--34249118 Score: 211
Period size: 90 Copynumber: 2.1 Consensus size: 89
34248921 TAAACCCCTA
* * * * ** *
34248931 CTTTTTTTTGCACTCACTTG-GTTA-TTAGAACTTTTAAAATGTATCAAAAAGGTCCTCAACCTT
1 CTTTTTTTTGCACTCAATTGAG-TACTT-GAACTTTCAAAATGCATAAAAAAGACCCTCAAACTT
*
34248994 TTTCAGAAA-AAGCAATTAAGCCATTG
64 TTT-AAAAAGAAGCAATTAAGCCATTG
* *
34249020 CTTTATTTTTGTACTCAATTGAGTACTTGAACTTTCAAAATGCATAAAAAATACCCTCAAACTTT
1 CTTT-TTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCATAAAAAAGACCCTCAAACTTT
*
34249085 TTAAAAAGAAGCAATTAAGCCCTTG
65 TTAAAAAGAAGCAATTAAGCCATTG
*
34249110 GTTTTTTTT
1 CTTTTTTTT
34249119 ATTGAATTGG
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
89 13 0.16
90 67 0.81
91 3 0.04
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (89 bp):
CTTTTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCATAAAAAAGACCCTCAAACTTTT
TAAAAAGAAGCAATTAAGCCATTG
Found at i:34249257 original size:20 final size:19
Alignment explanation
Indices: 34249233--34249287 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
34249223 GAATAAAAGC
*
34249233 TATAAAAATTATTAAATTT
1 TATAAAAATTATTAAATAT
**
34249252 TAATAAAAATATAGAAAATAT
1 T-ATAAAAAT-TATTAAATAT
34249273 T-TAAAAATTATTAAA
1 TATAAAAATTATTAAA
34249288 AAATAGAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 5 0.17
19 8 0.28
20 8 0.28
21 8 0.28
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
TATAAAAATTATTAAATAT
Found at i:34249269 original size:29 final size:29
Alignment explanation
Indices: 34249216--34249297 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 29
34249206 GATAAAAAAA
* *
34249216 TAAAAATGAATAAAAGCTATA-AAAAT-TAT
1 TAAAAATTAATAAAA-ATATAGAAAATAT-T
**
34249245 TAAATTTTAATAAAAATATAGAAAATATT
1 TAAAAATTAATAAAAATATAGAAAATATT
*
34249274 TAAAAATTATTAAAAA-ATAGAAAA
1 TAAAAATTAATAAAAATATAGAAAA
34249298 AAAATATAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
28 12 0.27
29 31 0.70
30 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.30
Consensus pattern (29 bp):
TAAAAATTAATAAAAATATAGAAAATATT
Found at i:34249649 original size:12 final size:11
Alignment explanation
Indices: 34249616--34249646 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
34249606 TTTATGATTT
34249616 ATAA-TTTTTA
1 ATAATTTTTTA
34249626 ATAATTTTTTA
1 ATAATTTTTTA
34249637 ATAATTTTTT
1 ATAATTTTTT
34249647 TAACTTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATAATTTTTTA
Found at i:34251945 original size:21 final size:20
Alignment explanation
Indices: 34251898--34251938 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
34251888 TTTGATTAGT
*
34251898 TTAATTAATCATGTTTTATGC
1 TTAATTAATCATGTTTAAT-C
34251919 TTAATTAATCATAGTTTAAT
1 TTAATTAATCAT-GTTTAAT
34251939 TATAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.51
Consensus pattern (20 bp):
TTAATTAATCATGTTTAATC
Found at i:34254036 original size:13 final size:13
Alignment explanation
Indices: 34254018--34254050 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
34254008 AAAAGTTAAA
34254018 AAAATAAAAAAAT
1 AAAATAAAAAAAT
*
34254031 AAAATAAAAAACT
1 AAAATAAAAAAAT
34254044 AAAATAA
1 AAAATAA
34254051 TTTTAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:34264250 original size:23 final size:22
Alignment explanation
Indices: 34264218--34264261 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
34264208 TTCTTAATCT
*
34264218 ATTAAAAATGATGAAATTATAC
1 ATTAAAAATGATAAAATTATAC
34264240 ATTAATAAATGATAAAATTATA
1 ATTAA-AAATGATAAAATTATA
34264262 TTTTGATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (22 bp):
ATTAAAAATGATAAAATTATAC
Found at i:34265864 original size:22 final size:25
Alignment explanation
Indices: 34265807--34265865 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
34265797 GGGATATGTC
*
34265807 TCGT-ATTATTCTCTCAGTTAAACT
1 TCGTGATTATTTTCTCAGTTAAACT
*
34265831 TCGTTATTATTTTCT-AGTTAAA-T
1 TCGTGATTATTTTCTCAGTTAAACT
34265854 TC-TGATTATTTT
1 TCGTGATTATTTT
34265866 AGAGATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 9 0.28
23 3 0.09
24 11 0.34
25 9 0.28
ACGTcount: A:0.24, C:0.14, G:0.08, T:0.54
Consensus pattern (25 bp):
TCGTGATTATTTTCTCAGTTAAACT
Found at i:34268207 original size:19 final size:19
Alignment explanation
Indices: 34268185--34268229 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
34268175 TTATATTAGG
*
34268185 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAAAAT-TGT
*
34268204 ATTTATTATTTAAAATTGT
1 ATTTAATATTTAAAATTGT
34268223 ATTTAAT
1 ATTTAAT
34268230 TTATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
ATTTAATATTTAAAATTGT
Found at i:34268248 original size:14 final size:14
Alignment explanation
Indices: 34268229--34268258 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
34268219 TTGTATTTAA
34268229 TTTATATTTATCTT
1 TTTATATTTATCTT
34268243 TTTATATTTATCTT
1 TTTATATTTATCTT
34268257 TT
1 TT
34268259 AGAGTTTAAA
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:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTATATTTATCTT
Found at i:34269043 original size:17 final size:17
Alignment explanation
Indices: 34269023--34269077 Score: 94
Period size: 17 Copynumber: 3.3 Consensus size: 17
34269013 CTTCTTCCCT
34269023 ATTTTCTATTTCTTTTA
1 ATTTTCTATTTCTTTTA
34269040 ATTTTCTATTTCTTTTA
1 ATTTTCTATTTCTTTTA
*
34269057 ATTTTAT-TTTCTTTTA
1 ATTTTCTATTTCTTTTA
34269073 ATTTT
1 ATTTT
34269078 AATTCCGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
16 14 0.38
17 23 0.62
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTCTATTTCTTTTA
Found at i:34269068 original size:22 final size:23
Alignment explanation
Indices: 34269035--34269081 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
34269025 TTTCTATTTC
*
34269035 TTTTAATTTTCTATTT-CTTTTAA
1 TTTTAATTTTCT-TTTAATTTTAA
34269058 TTTT-ATTTTCTTTTAATTTTAA
1 TTTTAATTTTCTTTTAATTTTAA
34269080 TT
1 TT
34269082 CCGTTTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 15 0.68
23 4 0.18
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTTAATTTTCTTTTAATTTTAA
Found at i:34270426 original size:21 final size:21
Alignment explanation
Indices: 34270402--34270452 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
34270392 GAATTTCAGC
*
34270402 AGCAATCTATAGATTTTCAAA
1 AGCAAACTATAGATTTTCAAA
* *
34270423 AGCAAACTGTTGATTTTCAAA
1 AGCAAACTATAGATTTTCAAA
*
34270444 AGAAAACTA
1 AGCAAACTA
34270453 AGGTATCTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (21 bp):
AGCAAACTATAGATTTTCAAA
Found at i:34273614 original size:27 final size:27
Alignment explanation
Indices: 34273577--34273641 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
34273567 AAATTAACAA
* *
34273577 AAAAAAAAATTTAGACCTTTAAAAGTT
1 AAAAAAAAATTTAGACCTGTAAAAATT
* * *
34273604 GATAAAAAATTTTGACCTGTAAAAATT
1 AAAAAAAAATTTAGACCTGTAAAAATT
34273631 AAAAAAAAATT
1 AAAAAAAAATT
34273642 ATACAGTGAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.57, C:0.06, G:0.08, T:0.29
Consensus pattern (27 bp):
AAAAAAAAATTTAGACCTGTAAAAATT
Found at i:34274954 original size:20 final size:21
Alignment explanation
Indices: 34274929--34275025 Score: 74
Period size: 20 Copynumber: 4.5 Consensus size: 21
34274919 AAAAACGCAT
*
34274929 AAAAATAACATCC-AAACAAC
1 AAAAATAACAACCAAAACAAC
* *
34274949 AAAAATAATAACCAAAACAGC
1 AAAAATAACAACCAAAACAAC
34274970 AAAAA-AACAACAACAAAACAAC
1 AAAAATAACAAC--CAAAACAAC
* *
34274992 ATTAAA-AACAACAAAAATAGCAAC
1 A-AAAATAACAAC-CAAA-A-CAAC
34275016 AAAAATAACA
1 AAAAATAACA
34275026 GCAAAAAGAG
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
20 16 0.26
21 11 0.18
22 13 0.21
23 13 0.21
24 9 0.15
ACGTcount: A:0.70, C:0.20, G:0.02, T:0.08
Consensus pattern (21 bp):
AAAAATAACAACCAAAACAAC
Found at i:34274978 original size:11 final size:11
Alignment explanation
Indices: 34274962--34275032 Score: 70
Period size: 12 Copynumber: 6.2 Consensus size: 11
34274952 AATAATAACC
*
34274962 AAAACAGCAAA
1 AAAACAACAAA
*
34274973 AAAACAACAAC
1 AAAACAACAAA
*
34274984 AAAACAACATTA
1 AAAACAACA-AA
34274996 AAAACAACAAA
1 AAAACAACAAA
*
34275007 AATAGCAACAAA
1 AA-AACAACAAA
*
34275019 AATAACAGCAAA
1 AA-AACAACAAA
34275031 AA
1 AA
34275033 GAGCACGAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
11 21 0.42
12 29 0.58
ACGTcount: A:0.72, C:0.18, G:0.04, T:0.06
Consensus pattern (11 bp):
AAAACAACAAA
Found at i:34275043 original size:24 final size:24
Alignment explanation
Indices: 34274945--34275037 Score: 72
Period size: 24 Copynumber: 4.1 Consensus size: 24
34274935 AACATCCAAA
* * *
34274945 CAACAAAAATAATAACCAAAACAG
1 CAACAAAAATAACAACAAAAAGAG
*
34274969 CAA-AAAAACAACAAC--AAA-A-
1 CAACAAAAATAACAACAAAAAGAG
* *
34274988 CAACATTAAA-AACAACAAAAATAG
1 CAACA-AAAATAACAACAAAAAGAG
*
34275012 CAACAAAAATAACAGCAAAAAGAG
1 CAACAAAAATAACAACAAAAAGAG
34275036 CA
1 CA
34275038 CGAAAACAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
19 3 0.05
20 8 0.14
21 6 0.11
22 3 0.05
23 14 0.25
24 22 0.39
ACGTcount: A:0.69, C:0.19, G:0.05, T:0.06
Consensus pattern (24 bp):
CAACAAAAATAACAACAAAAAGAG
Found at i:34275104 original size:22 final size:21
Alignment explanation
Indices: 34275079--34275119 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
34275069 TAAACAACAC
*
34275079 AAAAATCAGTAACCAAAACAGT
1 AAAAAACAG-AACCAAAACAGT
*
34275101 AAAAAACAGCACCAAAACA
1 AAAAAACAGAACCAAAACA
34275120 ACAATATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.63, C:0.22, G:0.07, T:0.07
Consensus pattern (21 bp):
AAAAAACAGAACCAAAACAGT
Found at i:34275559 original size:30 final size:28
Alignment explanation
Indices: 34275525--34275661 Score: 107
Period size: 29 Copynumber: 4.8 Consensus size: 28
34275515 AGTAAAATAA
34275525 TAAAAGTTGGAAAAAAAAATTTAAATCTTT
1 TAAAAGTT-GAAAAAAAAATTTAAA-CTTT
* *
34275555 TAAAAATTGGTAAAAAAAAATTTGAACTTT
1 TAAAAGTT-G-AAAAAAAAATTTAAACTTT
* * * *
34275585 TAAAAACTT-AAAAAAAAATTGAGACCTT
1 T-AAAAGTTGAAAAAAAAATTTAAACTTT
** **
34275613 TAAAAGTTGATAAAAAAAATTTTGACTCG
1 TAAAAGTTGA-AAAAAAAATTTAAACTTT
*
34275642 TAAAAATT-AAAAAAAAATTT
1 TAAAAGTTGAAAAAAAAATTT
34275662 GGACAGTTAT
Statistics
Matches: 89, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
27 17 0.19
28 18 0.20
29 20 0.22
30 14 0.16
31 20 0.22
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.31
Consensus pattern (28 bp):
TAAAAGTTGAAAAAAAAATTTAAACTTT
Found at i:34275598 original size:29 final size:28
Alignment explanation
Indices: 34275525--34275662 Score: 122
Period size: 28 Copynumber: 4.8 Consensus size: 28
34275515 AGTAAAATAA
* *
34275525 TAAAAGTTGGAAAAAAAAATTTAAATCTTT
1 TAAAAATT-GAAAAAAAAATTTGAA-CTTT
34275555 TAAAAATTGGTAAAAAAAAATTTGAACTTT
1 TAAAAATT-G-AAAAAAAAATTTGAACTTT
*
34275585 TAAAAACTT-AAAAAAAAA-TTGAGACCTT
1 TAAAAA-TTGAAAAAAAAATTTGA-ACTTT
* **
34275613 TAAAAGTTGATAAAAAAAATTTTG-ACTCG
1 TAAAAATTGA-AAAAAAAA-TTTGAACTTT
34275642 TAAAAATT-AAAAAAAAATTTG
1 TAAAAATTGAAAAAAAAATTTG
34275663 GACAGTTATT
Statistics
Matches: 93, Mismatches: 8, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
26 4 0.04
27 14 0.15
28 20 0.22
29 17 0.18
30 19 0.20
31 19 0.20
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.30
Consensus pattern (28 bp):
TAAAAATTGAAAAAAAAATTTGAACTTT
Found at i:34275615 original size:58 final size:57
Alignment explanation
Indices: 34275535--34275660 Score: 155
Period size: 58 Copynumber: 2.2 Consensus size: 57
34275525 TAAAAGTTGG
* * * **
34275535 AAAAAAAAATTTAAATCTTTTAAAAATTGGTAAAAAAAAATTTGAACTTTTAAAAACTT
1 AAAAAAAAATTGAAATCCTTTAAAAATTGATAAAAAAAAATTTG-ACTCGTAAAAA-TT
* * *
34275594 AAAAAAAAATTGAGA-CCTTTAAAAGTTGATAAAAAAAATTTTGACTCGTAAAAATT
1 AAAAAAAAATTGAAATCCTTTAAAAATTGATAAAAAAAAATTTGACTCGTAAAAATT
34275650 AAAAAAAAATT
1 AAAAAAAAATT
34275661 TGGACAGTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
56 13 0.22
57 9 0.15
58 24 0.41
59 13 0.22
ACGTcount: A:0.57, C:0.06, G:0.07, T:0.30
Consensus pattern (57 bp):
AAAAAAAAATTGAAATCCTTTAAAAATTGATAAAAAAAAATTTGACTCGTAAAAATT
Found at i:34280568 original size:10 final size:9
Alignment explanation
Indices: 34280525--34280671 Score: 63
Period size: 9 Copynumber: 15.6 Consensus size: 9
34280515 TATTATAAAT
34280525 TAAAAATTA
1 TAAAAATTA
34280534 TAAAAA-TA
1 TAAAAATTA
*
34280542 TAAGAAATTG
1 TAA-AAATTA
34280552 TAGAAAATTA
1 TA-AAAATTA
34280562 TTAAAAA-TA
1 -TAAAAATTA
34280571 -AAAGGAATTTA
1 TAAA--AA-TTA
34280582 TAAAAAAATTA
1 T--AAAAATTA
34280593 TATAAAATTA
1 TA-AAAATTA
*
34280603 CAAAAA-TA
1 TAAAAATTA
*
34280611 TAAAAACTA
1 TAAAAATTA
** *
34280620 TAAATTGTTT
1 TAAA-AATTA
**
34280630 TCTAAA-TA
1 TAAAAATTA
34280638 TTAAAAATTA
1 -TAAAAATTA
34280648 -AAAACATTA
1 TAAAA-ATTA
34280657 TAAAAAATTA
1 T-AAAAATTA
34280667 TAAAA
1 TAAAA
34280672 CAAGTTTAAA
Statistics
Matches: 104, Mismatches: 15, Indels: 38
0.66 0.10 0.24
Matches are distributed among these distances:
7 3 0.03
8 17 0.16
9 36 0.35
10 30 0.29
11 13 0.12
12 2 0.02
14 3 0.03
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:34280587 original size:29 final size:29
Alignment explanation
Indices: 34280525--34280587 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
34280515 TATTATAAAT
*
34280525 TAAAAATTATAAAAATATAAGAAATTGTA
1 TAAAAATTATAAAAATAAAAGAAATTGTA
* *
34280554 -GAAAATTATTAAAAATAAAAGGAATT-TA
1 TAAAAATTA-TAAAAATAAAAGAAATTGTA
34280582 TAAAAA
1 TAAAAA
34280588 AATTATATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (29 bp):
TAAAAATTATAAAAATAAAAGAAATTGTA
Found at i:34280662 original size:11 final size:10
Alignment explanation
Indices: 34280640--34280709 Score: 56
Period size: 10 Copynumber: 7.0 Consensus size: 10
34280630 TCTAAATATT
34280640 AAAAATTA-A
1 AAAAATTATA
*
34280649 AAACATTATA
1 AAAAATTATA
34280659 AAAAATTATA
1 AAAAATTATA
34280669 AAACAAGTT-TA
1 AAA-AA-TTATA
*
34280680 AAATA-TATGA
1 AAAAATTAT-A
*
34280690 AAAAAGTATA
1 AAAAATTATA
*
34280700 AAAAAATATA
1 AAAAATTATA
34280710 TTTGTCCCTG
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
8 1 0.02
9 8 0.16
10 29 0.58
11 10 0.20
12 2 0.04
ACGTcount: A:0.67, C:0.03, G:0.04, T:0.26
Consensus pattern (10 bp):
AAAAATTATA
Found at i:34280682 original size:20 final size:20
Alignment explanation
Indices: 34280638--34280703 Score: 52
Period size: 19 Copynumber: 3.4 Consensus size: 20
34280628 TTTCTAAATA
34280638 TTAAAAATTA-AAAAC-A-T
1 TTAAAAATTATAAAACAAGT
34280655 TATAAAAAATTATAAAACAAGT
1 T-T-AAAAATTATAAAACAAGT
34280677 TT-AAAATATATGAAAA-AAGT
1 TTAAAAAT-TAT-AAAACAAGT
*
34280697 ATAAAAA
1 TTAAAAA
34280704 AATATATTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
17 1 0.03
18 1 0.03
19 13 0.32
20 13 0.32
21 10 0.25
22 2 0.05
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (20 bp):
TTAAAAATTATAAAACAAGT
Found at i:34291234 original size:29 final size:29
Alignment explanation
Indices: 34291201--34291260 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
34291191 ACTTAATCAG
34291201 ATTTCTTCAAAGAATAGAAAACCAAAATA
1 ATTTCTTCAAAGAATAGAAAACCAAAATA
*
34291230 ATTTCTTGAAAGAATAGAAAACCAAAATA
1 ATTTCTTCAAAGAATAGAAAACCAAAATA
34291259 AT
1 AT
34291261 GCAAGTAGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.55, C:0.12, G:0.08, T:0.25
Consensus pattern (29 bp):
ATTTCTTCAAAGAATAGAAAACCAAAATA
Found at i:34304236 original size:14 final size:16
Alignment explanation
Indices: 34304212--34304243 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
34304202 AACACTCGCC
34304212 AAAATATATAAAT-AT
1 AAAATATATAAATCAT
34304227 AAAA-ATATAAATCAT
1 AAAATATATAAATCAT
34304242 AA
1 AA
34304244 CATAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAATATATAAATCAT
Found at i:34304446 original size:16 final size:16
Alignment explanation
Indices: 34304415--34304444 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34304405 TAATAAAAAT
34304415 ATAATTTATTATTTTA
1 ATAATTTATTATTTTA
34304431 ATAATTTA-TATTTT
1 ATAATTTATTATTTT
34304445 TATAGTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:34307109 original size:30 final size:31
Alignment explanation
Indices: 34307065--34307134 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
34307055 CAATTTTTAT
* * *
34307065 TTTTTGTAAATTTTCA-TAAATCTTTTAAAA
1 TTTTTGTAAATTTTCACTAAAACCTTCAAAA
34307095 TTTTTG-AAACTTTTCACTAAAACCTTCAAAA
1 TTTTTGTAAA-TTTTCACTAAAACCTTCAAAA
34307126 TTTTT-TAAA
1 TTTTTGTAAA
34307135 AAATTTAGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 3 0.09
30 12 0.35
31 19 0.56
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.49
Consensus pattern (31 bp):
TTTTTGTAAATTTTCACTAAAACCTTCAAAA
Found at i:34308946 original size:16 final size:16
Alignment explanation
Indices: 34308927--34308973 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
34308917 AATTTTTAAT
34308927 AAATAAAAAATATATA
1 AAATAAAAAATATATA
**
34308943 AAATTATTAAATAT-TA
1 AAA-TAAAAAATATATA
34308959 AAATAAAATAATATA
1 AAATAAAA-AATATA
34308974 AATATATGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 3 0.12
16 13 0.54
17 8 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATAAAAAATATATA
Found at i:34310624 original size:20 final size:20
Alignment explanation
Indices: 34310596--34310646 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
34310586 AATATATAAA
* *
34310596 TTTAAAATTTTTATAAATAT
1 TTTAGAATTTTTAGAAATAT
* *
34310616 TTTAGAATTTTAAGAATTAT
1 TTTAGAATTTTTAGAAATAT
34310636 TTT-GAATTTTT
1 TTTAGAATTTTT
34310647 TTTGTAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
TTTAGAATTTTTAGAAATAT
Found at i:34313789 original size:12 final size:12
Alignment explanation
Indices: 34313772--34313796 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34313762 ACGTAATTAC
34313772 TATTAATATATA
1 TATTAATATATA
34313784 TATTAATATATA
1 TATTAATATATA
34313796 T
1 T
34313797 GTGATGTCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TATTAATATATA
Found at i:34315356 original size:14 final size:14
Alignment explanation
Indices: 34315337--34315383 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
34315327 TCCTTTGAGA
34315337 TTTAATTTTTATAT
1 TTTAATTTTTATAT
*
34315351 TTTAATTTTATATAA
1 TTTAATTTT-TATAT
34315366 TTTAATTTATTAT-T
1 TTTAATTT-TTATAT
34315380 TTTA
1 TTTA
34315384 CAATGAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 13 0.45
15 15 0.52
16 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTAATTTTTATAT
Found at i:34320445 original size:26 final size:27
Alignment explanation
Indices: 34320415--34320474 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 27
34320405 TTTCATTTTT
*
34320415 TTAGGATTAAGGTTTTGT-TTTTTAAA
1 TTAGGATTAAGGTTTAGTGTTTTTAAA
*
34320441 TTAGGGTTAAGGTTTAGTGTTTTTAAA
1 TTAGGATTAAGGTTTAGTGTTTTTAAA
*
34320468 ATAGGAT
1 TTAGGAT
34320475 CTGGGTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 16 0.55
27 13 0.45
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.48
Consensus pattern (27 bp):
TTAGGATTAAGGTTTAGTGTTTTTAAA
Found at i:34334997 original size:67 final size:67
Alignment explanation
Indices: 34334916--34335047 Score: 246
Period size: 67 Copynumber: 2.0 Consensus size: 67
34334906 AAAAAATTCG
34334916 ACTACTTATAGGATTGAAAAACCCTACTATTCTATACAAATTCAACTTGCGCAATATGCTCCGTA
1 ACTACTTATAGGATTGAAAAACCCTACTATTCTATACAAATTCAACTTGCGCAATATGCTCCGTA
34334981 AC
66 AC
* *
34334983 ACTACTTATAGGATTGAAAAACCCTACTATTCTATACAGATTCAACTTGCGCAATATGTTCCGTA
1 ACTACTTATAGGATTGAAAAACCCTACTATTCTATACAAATTCAACTTGCGCAATATGCTCCGTA
34335048 CCACAAAAGC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (67 bp):
ACTACTTATAGGATTGAAAAACCCTACTATTCTATACAAATTCAACTTGCGCAATATGCTCCGTA
AC
Found at i:34339005 original size:59 final size:59
Alignment explanation
Indices: 34338923--34339037 Score: 144
Period size: 59 Copynumber: 1.9 Consensus size: 59
34338913 TAAAATATTC
* * *
34338923 AATAATTTTAGCCATTAATATTTACAAAACTTG-TAATTTTAGTTTGAATTCTAAAAAAT
1 AATAAATTTAGCCATTAAAATTTACAAAACTTGTTAA-TTTAGTTTGAATTATAAAAAAT
* * *
34338982 AATAAATTTAGCC-TTCAAAATTTATAAAATTTGTTAATTTAGTTTTAATTATAAAA
1 AATAAATTTAGCCATT-AAAATTTACAAAACTTGTTAATTTAGTTTGAATTATAAAA
34339038 TATTCAATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
58 2 0.04
59 43 0.90
60 3 0.06
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.43
Consensus pattern (59 bp):
AATAAATTTAGCCATTAAAATTTACAAAACTTGTTAATTTAGTTTGAATTATAAAAAAT
Found at i:34343302 original size:52 final size:52
Alignment explanation
Indices: 34343186--34343379 Score: 262
Period size: 52 Copynumber: 3.7 Consensus size: 52
34343176 TTCTCATTTG
* * ** *
34343186 ATACTCACGATGGCATATAGTCATCGGACCTCATAATCCAAAAAGGATTTAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * * *
34343238 ATGCTCATGATGACACATGGTCATCGGACCTCATAATTCGTAAAGAATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
34343290 ATACTCACGATGACACATAGTCATCGAACCTCATAGTCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
34343342 ATACTCACGATGACACATAATCATCAGACCTCATAATC
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATC
34343380 TGTACACATA
Statistics
Matches: 121, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 121 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Done.