Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 123 of 144
Found at i:29234439 original size:31 final size:29
Alignment explanation
Indices: 29234389--29234450 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 29
29234379 ATTTCAAAAT
* *
29234389 TATACATGAATTTTGATTTAATGTGTAATTA
1 TATACATGAACTTTAATTT-A-GTGTAATTA
*
29234420 TATATATGAACTTTAATTTAGTGTAATTA
1 TATACATGAACTTTAATTTAGTGTAATTA
29234449 TA
1 TA
29234451 CACGTGAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 11 0.39
30 1 0.04
31 16 0.57
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.48
Consensus pattern (29 bp):
TATACATGAACTTTAATTTAGTGTAATTA
Found at i:29234685 original size:29 final size:30
Alignment explanation
Indices: 29234631--29234700 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
29234621 ATAATTTACA
* *
29234631 AAAATTACATC-AAATCGAAATTTCATTTAT
1 AAAATTACA-CAAAATCGAAAGTTCATGTAT
29234661 AAAATTACACAAAATC-AAAGTTCATGTAT
1 AAAATTACACAAAATCGAAAGTTCATGTAT
*
29234690 ACAATTACACA
1 AAAATTACACA
29234701 TTACCCTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.61
30 14 0.39
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.30
Consensus pattern (30 bp):
AAAATTACACAAAATCGAAAGTTCATGTAT
Found at i:29239014 original size:121 final size:122
Alignment explanation
Indices: 29238781--29239021 Score: 403
Period size: 121 Copynumber: 2.0 Consensus size: 122
29238771 TTTTTGTTTA
29238781 AGTCACTGGACTAGTCAAAAGTTTTTATTTAAGTCATTGGATCGTTAAGTTTTTTTTGATCCAGC
1 AGTCACTGGACTAGTCAAAAGTTTTTATTTAAGTCATTGGATCGTTAAGTTTTTTTTGATCCAGC
* * *
29238846 TATCAAGTTTTAAGTGATGATTTGATAATCGGTATAGTGAATCAATACCCAACGACG
66 TATCAAGTTTCAAGCGACGATTTGATAATCGGTATAGTGAATCAATACCCAACGACG
* * * *
29238903 AGTCATTGGACTATTCAAAAGTTTTTATTTAAGTCATTGGGTTGTTAAG-TTTTTTTGATCCAGC
1 AGTCACTGGACTAGTCAAAAGTTTTTATTTAAGTCATTGGATCGTTAAGTTTTTTTTGATCCAGC
*
29238967 TATCAAGTTTCAAGCGACGATTTGATAATCGGTATAGTGAATTAATACCCAACGA
66 TATCAAGTTTCAAGCGACGATTTGATAATCGGTATAGTGAATCAATACCCAACGA
29239022 TAAGTAGAAG
Statistics
Matches: 111, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
121 66 0.59
122 45 0.41
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (122 bp):
AGTCACTGGACTAGTCAAAAGTTTTTATTTAAGTCATTGGATCGTTAAGTTTTTTTTGATCCAGC
TATCAAGTTTCAAGCGACGATTTGATAATCGGTATAGTGAATCAATACCCAACGACG
Found at i:29239269 original size:14 final size:15
Alignment explanation
Indices: 29239232--29239261 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29239222 ACAACTCAAT
29239232 AACTTAAATGAAAAC
1 AACTTAAATGAAAAC
29239247 AACTTAAATGAAAAC
1 AACTTAAATGAAAAC
29239262 GTTTAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (15 bp):
AACTTAAATGAAAAC
Found at i:29240644 original size:24 final size:22
Alignment explanation
Indices: 29240602--29240647 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
29240592 AAATCCAAAT
29240602 TTAAAAATAAAAATAAAAATAA
1 TTAAAAATAAAAATAAAAATAA
29240624 TTAAAAA-AATAAATACCAAAATAA
1 TTAAAAATAA-AAATA--AAAATAA
29240648 ACTTAATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 2 0.10
22 12 0.57
24 7 0.33
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (22 bp):
TTAAAAATAAAAATAAAAATAA
Found at i:29240960 original size:23 final size:23
Alignment explanation
Indices: 29240934--29240989 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
29240924 GAAATTAAAT
*
29240934 TATAAATTTTATAATAATAAAAA
1 TATAAATTTTATAAGAATAAAAA
* * *
29240957 TATAATTTTTA-AAGGATTAAAA
1 TATAAATTTTATAAGAATAAAAA
29240979 TA-AAATTTTAT
1 TATAAATTTTAT
29240990 TAATTTTAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 7 0.26
22 10 0.37
23 10 0.37
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
TATAAATTTTATAAGAATAAAAA
Found at i:29240994 original size:31 final size:32
Alignment explanation
Indices: 29240959--29241028 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 32
29240949 AATAAAAATA
*
29240959 TAATTTTTAA-AG-GATTAAAATAAAATTTTAT
1 TAATTTTTAAGAGAGA-TAAAATAAAACTTTAT
*
29240990 TAA-TTTTAAGAGAGATAAAATATAACTTTAT
1 TAATTTTTAAGAGAGATAAAATAAAACTTTAT
29241021 T--TTTTTAA
1 TAATTTTTAA
29241029 TTTAAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
30 12 0.35
31 20 0.59
32 2 0.06
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (32 bp):
TAATTTTTAAGAGAGATAAAATAAAACTTTAT
Found at i:29241930 original size:25 final size:25
Alignment explanation
Indices: 29241862--29241916 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
29241852 CAAACCCATG
*
29241862 TTAATTATAATAATAAAATATTAAA
1 TTAATTACAATAATAAAATATTAAA
29241887 TTAATTACAATAATAAAATATTAAA
1 TTAATTACAATAATAAAATATTAAA
29241912 TTAAT
1 TTAAT
29241917 CACTCAATCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (25 bp):
TTAATTACAATAATAAAATATTAAA
Found at i:29247350 original size:4 final size:4
Alignment explanation
Indices: 29247341--29247408 Score: 55
Period size: 4 Copynumber: 16.8 Consensus size: 4
29247331 TTAAAAATAT
* * * ** *
29247341 TTTA TTTA TTTA TTTA TTTGT TTTA TTTA ATTA GTTA ACTA TTTA TATA
1 TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* *
29247390 TTTA GTTA TTTA GTTA TTT
1 TTTA TTTA TTTA TTTA TTT
29247409 GAGAGAGTTT
Statistics
Matches: 49, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
4 46 0.94
5 3 0.06
ACGTcount: A:0.26, C:0.01, G:0.06, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:29247567 original size:55 final size:55
Alignment explanation
Indices: 29247475--29247583 Score: 148
Period size: 55 Copynumber: 2.0 Consensus size: 55
29247465 CGTTGGGGTC
* * * *
29247475 AACAGTCAAATTTTTTATCGTTCAAAAAGTACATCCAGCTGGACGAGCTTTCCTG
1 AACAATCAAATTTTTTATCGTTCAAAAAGCACATCCAGCTGAACAAGCTTTCCTG
* *
29247530 AACAATCAAATTTTTTA-CTGTTCAAAAAGCACGTCCAGTTGAACAAGCTTTCCT
1 AACAATCAAATTTTTTATC-GTTCAAAAAGCACATCCAGCTGAACAAGCTTTCCT
29247584 TACATGTGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 1 0.02
55 46 0.98
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (55 bp):
AACAATCAAATTTTTTATCGTTCAAAAAGCACATCCAGCTGAACAAGCTTTCCTG
Found at i:29250994 original size:18 final size:17
Alignment explanation
Indices: 29250958--29251038 Score: 110
Period size: 17 Copynumber: 4.7 Consensus size: 17
29250948 GCTTTTTAAT
* *
29250958 TTTAATTTTAAAAT-TA
1 TTTAAATTTAAAATAAA
*
29250974 TTTCAAATTTAAACTAAA
1 TTT-AAATTTAAAATAAA
29250992 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
29251009 TTTAAATTTAAAAATAAA
1 TTTAAATTT-AAAATAAA
29251027 TTTAAATTTAAA
1 TTTAAATTTAAA
29251039 TTTAAAGTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
16 3 0.05
17 34 0.59
18 21 0.36
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:29250999 original size:6 final size:6
Alignment explanation
Indices: 29250952--29251044 Score: 86
Period size: 6 Copynumber: 16.0 Consensus size: 6
29250942 TTTTGGGCTT
* * * *
29250952 TTTAAT TTTAAT TTTAAA ATT--A TTTCAAA TTTAAA -CTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
* **
29250998 TTTAAA -ATAAA TTTAAA TTTAAA AATAAA TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
29251045 GTAAATCTAA
Statistics
Matches: 71, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
4 3 0.04
5 8 0.11
6 56 0.79
7 4 0.06
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:29251033 original size:41 final size:41
Alignment explanation
Indices: 29250988--29251073 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
29250978 AAATTTAAAC
*
29250988 TAAATTTAAATTTAAAATAAATTTAAATTTAAAAATAAATT
1 TAAATTTAAATTTAAAATAAATCTAAATTTAAAAATAAATT
* * *
29251029 TAAATTTAAATTTAAAGTAAATCTAATTTTAGAAATAAATT
1 TAAATTTAAATTTAAAATAAATCTAAATTTAAAAATAAATT
29251070 TAAA
1 TAAA
29251074 AATCATTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (41 bp):
TAAATTTAAATTTAAAATAAATCTAAATTTAAAAATAAATT
Found at i:29251076 original size:12 final size:12
Alignment explanation
Indices: 29251011--29251076 Score: 51
Period size: 12 Copynumber: 5.1 Consensus size: 12
29251001 AAAATAAATT
29251011 TAAATTTAAAAA
1 TAAATTTAAAAA
**
29251023 TAAATTTAAATT
1 TAAATTTAAAAA
29251035 TAAATTTAAAGTAAA
1 TAAATTT-AA--AAA
* *
29251050 TCTAATTTTAGAAA
1 --TAAATTTAAAAA
29251064 TAAATTTAAAAA
1 TAAATTTAAAAA
29251076 T
1 T
29251077 CATTTTAAAC
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
12 28 0.68
13 2 0.05
14 3 0.07
15 1 0.02
16 1 0.02
17 6 0.15
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (12 bp):
TAAATTTAAAAA
Found at i:29251084 original size:41 final size:41
Alignment explanation
Indices: 29250994--29251085 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
29250984 AAACTAAATT
* **
29250994 TAAATTTAAAATAAATTTAAATTTAAAAATAAATTTAAATT
1 TAAATTTAAAATAAATCTAAATTTAAAAATAAATTTAAAAA
* * *
29251035 TAAATTTAAAGTAAATCTAATTTTAGAAATAAATTTAAAAA
1 TAAATTTAAAATAAATCTAAATTTAAAAATAAATTTAAAAA
* *
29251076 TCATTTTAAA
1 TAAATTTAAA
29251086 CTTAAATTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (41 bp):
TAAATTTAAAATAAATCTAAATTTAAAAATAAATTTAAAAA
Found at i:29251091 original size:24 final size:24
Alignment explanation
Indices: 29251005--29251097 Score: 82
Period size: 24 Copynumber: 3.7 Consensus size: 24
29250995 AAATTTAAAA
* *
29251005 TAAATTTAAATTTAAAAATAAATT
1 TAAATTTAAATTTAAAAATCATTT
29251029 TAAATTTAAATTTAAAGTAAATCTAATTT
1 TAAATTTAAATTT-AA--AAATC--ATTT
*
29251058 TAGAA-ATAAATTTAAAAATCATTT
1 TA-AATTTAAATTTAAAAATCATTT
*
29251082 TAAACTTAAA-TTAAAA
1 TAAATTTAAATTTAAAA
29251098 TTGACCCAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 15
0.75 0.05 0.19
Matches are distributed among these distances:
23 8 0.14
24 23 0.40
25 2 0.03
26 5 0.09
27 4 0.07
28 2 0.03
29 12 0.21
30 2 0.03
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (24 bp):
TAAATTTAAATTTAAAAATCATTT
Found at i:29251877 original size:18 final size:18
Alignment explanation
Indices: 29251854--29251888 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
29251844 TATAAATTAA
29251854 AAAGTCCAATTACAAAAG
1 AAAGTCCAATTACAAAAG
29251872 AAAGTCCAATTACAAAA
1 AAAGTCCAATTACAAAA
29251889 TATAGGCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.17, G:0.09, T:0.17
Consensus pattern (18 bp):
AAAGTCCAATTACAAAAG
Found at i:29253613 original size:29 final size:30
Alignment explanation
Indices: 29253581--29253741 Score: 92
Period size: 29 Copynumber: 5.5 Consensus size: 30
29253571 CAAACCTTTC
29253581 AAAATT-CCATTTTTGACCCGATTTCACCA
1 AAAATTACCATTTTTGACCCGATTTCACCA
* * *** *
29253610 AAAATTACCA-TTTTGCCCCCAAACCTTCC-
1 AAAATTACCATTTTTGACCCGATTTC-ACCA
**
29253639 AAAATT-CCATTTTAAACCCCGATTTCACCA
1 AAAATTACCATTTTTGA-CCCGATTTCACCA
29253669 AAAATTACCA-TTTT-ACCTCCGAACCTTT---C-
1 AAAATTACCATTTTTGA-C-CCG-A--TTTCACCA
*
29253698 AAAGTT-CCATTTTTGACCTCGATTTCACCA
1 AAAATTACCATTTTTGACC-CGATTTCACCA
29253728 AAAATTACCATTTT
1 AAAATTACCATTTT
29253742 ACCCCGAAAC
Statistics
Matches: 97, Mismatches: 17, Indels: 34
0.66 0.11 0.23
Matches are distributed among these distances:
26 3 0.03
28 8 0.08
29 43 0.44
30 29 0.30
31 11 0.11
33 3 0.03
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (30 bp):
AAAATTACCATTTTTGACCCGATTTCACCA
Found at i:29253681 original size:59 final size:59
Alignment explanation
Indices: 29253550--29253768 Score: 314
Period size: 59 Copynumber: 3.7 Consensus size: 59
29253540 CCGAAACTAT
* * *
29253550 CAAAAATTACTATTTTATCCCCAAACCTTTCAAAATTCCATTTTTGA-CCCGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACCTTCCAAAATTCCATTTTTGACCCCGATTTCAC
* **
29253608 CAAAAATTACCATTTTGCCCCCAAACCTTCCAAAATTCCATTTTAAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACCTTCCAAAATTCCATTTTTGACCCCGATTTCAC
* * * * *
29253667 CAAAAATTACCATTTTACCTCCGAACCTTTCAAAGTTCCATTTTTGACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACCTTCCAAAATTCCATTTTTGACCCCGATTTCAC
* *
29253726 CAAAAATTACCATTTTACCCCGAAACCTTCCAAAATCCCATTT
1 CAAAAATTACCATTTTACCCCCAAACCTTCCAAAATTCCATTT
29253769 CTAATCTTGA
Statistics
Matches: 140, Mismatches: 20, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
58 41 0.29
59 99 0.71
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCCAAACCTTCCAAAATTCCATTTTTGACCCCGATTTCAC
Found at i:29253793 original size:118 final size:117
Alignment explanation
Indices: 29253550--29253768 Score: 359
Period size: 118 Copynumber: 1.9 Consensus size: 117
29253540 CCGAAACTAT
*
29253550 CAAAAATTACTATTTTATCCCCAAACCTTTCAAAATTCCATTTTTGACCCGATTTCACCAAAAAT
1 CAAAAATTACCATTTTATCCCCAAACCTTTCAAAATTCCATTTTTGACCCGATTTCACCAAAAAT
* *
29253615 TACCATTTTGCCCCCAAACCTTCCAAAATTCCATTTTAAACCCCGATTTCAC
66 TACCATTTTACCCCCAAACCTTCCAAAATCCCATTTTAAACCCCGATTTCAC
* *
29253667 CAAAAATTACCATTTTA-CCTCCGAACCTTTCAAAGTTCCATTTTTGACCTCGATTTCACCAAAA
1 CAAAAATTACCATTTTATCC-CCAAACCTTTCAAAATTCCATTTTTGACC-CGATTTCACCAAAA
*
29253731 ATTACCATTTTACCCCGAAACCTTCCAAAATCCCATTT
64 ATTACCATTTTACCCCCAAACCTTCCAAAATCCCATTT
29253769 CTAATCTTGA
Statistics
Matches: 94, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
116 2 0.02
117 43 0.46
118 49 0.52
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (117 bp):
CAAAAATTACCATTTTATCCCCAAACCTTTCAAAATTCCATTTTTGACCCGATTTCACCAAAAAT
TACCATTTTACCCCCAAACCTTCCAAAATCCCATTTTAAACCCCGATTTCAC
Found at i:29255721 original size:5 final size:5
Alignment explanation
Indices: 29255711--29255739 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
29255701 TATTAAATAT
29255711 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
29255740 TATTTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:29271940 original size:22 final size:23
Alignment explanation
Indices: 29271912--29271958 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
29271902 TATAGATAAA
29271912 TTTTATTTA-ATATAAAATTATT
1 TTTTATTTATATATAAAATTATT
*
29271934 TTTTATTTATTATATAAATTTATT
1 TTTTATTTA-TATATAAAATTATT
29271958 T
1 T
29271959 AATAAAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.41
24 13 0.59
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTTATTTATATATAAAATTATT
Found at i:29288272 original size:18 final size:18
Alignment explanation
Indices: 29288245--29288280 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29288235 TCTATTTGGG
*
29288245 TAGTTATGTCTTTATGAA
1 TAGTTATGTCCTTATGAA
*
29288263 TAGTTTTGTCCTTATGAA
1 TAGTTATGTCCTTATGAA
29288281 GACACATGCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.50
Consensus pattern (18 bp):
TAGTTATGTCCTTATGAA
Found at i:29294179 original size:23 final size:23
Alignment explanation
Indices: 29294153--29294228 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
29294143 ACTCGACCCA
*
29294153 TTGACCGAATCAAACTGTTGACT
1 TTGACCGAACCAAACTGTTGACT
* *
29294176 TTGACCGAACCAAACCGTTAACT
1 TTGACCGAACCAAACTGTTGACT
* *
29294199 TTGACTGAACCGAACTGTTGACT
1 TTGACCGAACCAAACTGTTGACT
29294222 TTGACCG
1 TTGACCG
29294229 TTGATTGTTG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (23 bp):
TTGACCGAACCAAACTGTTGACT
Found at i:29296731 original size:3 final size:3
Alignment explanation
Indices: 29296723--29296757 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
29296713 ACCCACTTGA
29296723 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATTC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC A-TC ATC A
29296758 AATTATAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:29297105 original size:2 final size:2
Alignment explanation
Indices: 29297098--29297137 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
29297088 TCATTTTTAA
29297098 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
29297138 TTGAGAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:29300058 original size:22 final size:21
Alignment explanation
Indices: 29300033--29300092 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
29300023 CTTATGACTA
*
29300033 TTAAATTATTATTCAAGATCAC
1 TTAAATTATTATTCAACA-CAC
*
29300055 TT-AATTATTTATATCATCACAC
1 TTAAATTA-TTAT-TCAACACAC
29300077 TTAAATTATTATTCAA
1 TTAAATTATTATTCAA
29300093 TTTAATCCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 8 0.25
22 15 0.47
23 9 0.28
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.45
Consensus pattern (21 bp):
TTAAATTATTATTCAACACAC
Found at i:29303045 original size:19 final size:19
Alignment explanation
Indices: 29303013--29303073 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
29303003 TTAAAAAATC
29303013 AAAAAATTGAAAAATATTTAA
1 AAAAAATT--AAAATATTTAA
29303034 AAAAAATTAAAATCA-TTAA
1 AAAAAATTAAAAT-ATTTAA
** * *
29303053 AATTATTTAAAATATATAA
1 AAAAAATTAAAATATTTAA
29303072 AA
1 AA
29303074 TAGTTTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 1 0.03
19 24 0.71
20 1 0.03
21 8 0.24
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAAAATTAAAATATTTAA
Found at i:29304724 original size:27 final size:28
Alignment explanation
Indices: 29304674--29304729 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
29304664 AAGGATTAAT
* *
29304674 ATCACAAATAATGCTTCCTTAAAA-AAA
1 ATCACAAATAATGCTACCTAAAAATAAA
**
29304701 ATCACAAATAATGCTAGGTAAAAATAAA
1 ATCACAAATAATGCTACCTAAAAATAAA
29304729 A
1 A
29304730 GCTCTAAAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.23
Consensus pattern (28 bp):
ATCACAAATAATGCTACCTAAAAATAAA
Found at i:29305148 original size:16 final size:16
Alignment explanation
Indices: 29305089--29305149 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
29305079 TGAAAACTTC
29305089 AAAATTAATATTTTTTA
1 AAAATTAAT-TTTTTTA
* * *
29305106 AAACGTTCATTTTTAT-
1 AAA-ATTAATTTTTTTA
* *
29305122 AATATTCATTTTTTTA
1 AAAATTAATTTTTTTA
29305138 AAAATTAATTTT
1 AAAATTAATTTT
29305150 AAATTATATC
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
15 10 0.29
16 12 0.35
17 8 0.24
18 4 0.12
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (16 bp):
AAAATTAATTTTTTTA
Found at i:29306847 original size:21 final size:21
Alignment explanation
Indices: 29306815--29306868 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
29306805 TCATTTTCCT
29306815 TTTGTA-ATATTACAATATAAA
1 TTTGTATA-ATTACAATATAAA
** *
29306836 TTTGTATAATTACTTTTTAAA
1 TTTGTATAATTACAATATAAA
*
29306857 GTTGTATAATTA
1 TTTGTATAATTA
29306869 TTTTAAACGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (21 bp):
TTTGTATAATTACAATATAAA
Found at i:29306874 original size:19 final size:20
Alignment explanation
Indices: 29306832--29306875 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
29306822 TATTACAATA
*
29306832 TAAATTTGTATAATTACTTTT
1 TAAAGTTGTATAATTAC-TTT
29306853 TAAAGTTGTATAATTA-TTT
1 TAAAGTTGTATAATTACTTT
29306872 TAAA
1 TAAA
29306876 CGTTAAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.32
21 15 0.68
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (20 bp):
TAAAGTTGTATAATTACTTT
Found at i:29313380 original size:28 final size:28
Alignment explanation
Indices: 29313349--29313408 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
29313339 AAAACGGGAC
* *
29313349 TTTTGGATACTCGGGGGCAAAATGGTAA
1 TTTTGGACACACGGGGGCAAAATGGTAA
*
29313377 TTTTGGACGCACGGGGGCAAAATGGTAA
1 TTTTGGACACACGGGGGCAAAATGGTAA
29313405 TTTT
1 TTTT
29313409 TGGTGAAACC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.27, C:0.12, G:0.32, T:0.30
Consensus pattern (28 bp):
TTTTGGACACACGGGGGCAAAATGGTAA
Found at i:29313458 original size:59 final size:59
Alignment explanation
Indices: 29313390--29313705 Score: 429
Period size: 59 Copynumber: 5.4 Consensus size: 59
29313380 TGGACGCACG
* * * *
29313390 GGGGCAAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATCTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
* * *
29313449 GGGGTAAAATGGTAATTTTTGATGAAATTGGGGTTAATAATGGAATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
* *
29313508 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG-TTC
1 GGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
* * * **
29313566 GAGGGTAAAATGGTACTTTTTGATGAAATTGGGGTTAAAAATGGAATTTTGGGAAGTTCGG
1 G-GGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT-TA
* * * *
29313627 GGGGTAAAATAGTAATTTTTGATGAAACCGAGGTT-AAAATAGAATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
*
29313685 GGGGTAAAATAGTAATTTTTG
1 GGGGTAAAATGGTAATTTTTG
29313706 GATAGTCCAG
Statistics
Matches: 227, Mismatches: 27, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
58 23 0.10
59 173 0.76
60 30 0.13
61 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
Found at i:29313496 original size:30 final size:29
Alignment explanation
Indices: 29313395--29313705 Score: 163
Period size: 30 Copynumber: 10.6 Consensus size: 29
29313385 GCACGGGGGC
**
29313395 AAAATGGTAATTTTTGGTGAAACCGGGGTT
1 AAAATGGTAATTTTT-GTGAAATTGGGGTT
*
29313425 AAAAATGG-AA-TCTTG-GAAAGTTTAGGGG-T
1 -AAAATGGTAATTTTTGTGAAA--TT-GGGGTT
29313454 AAAATGGTAATTTTTGATGAAATTGGGGTT
1 AAAATGGTAATTTTTG-TGAAATTGGGGTT
29313484 AATAATGG-AA-TTTTG-GAAAGTTCAGGGG-T
1 AA-AATGGTAATTTTTGTGAAA-TT--GGGGTT
*
29313513 AAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGGTAATTTTT-GTGAAATTGGGGTT
29313543 AAAAATGG-AA-TTTTG-GAAAGTTCGAGGG-T
1 -AAAATGGTAATTTTTGTGAAA-TT-G-GGGTT
*
29313572 AAAATGGTACTTTTTGATGAAATTGGGGTT
1 AAAATGGTAATTTTTG-TGAAATTGGGGTT
* * *
29313602 AAAAATGG-AA-TTTTGGGAAGTTCGGGGGGT
1 -AAAATGGTAATTTTTGTGAAATT--GGGGTT
* ** *
29313632 AAAATAGTAATTTTTGATGAAACCGAGGTT
1 AAAATGGTAATTTTTG-TGAAATTGGGGTT
*
29313662 AAAATAG-AA-TTTTG-GAAAGTTTAGGGG-T
1 AAAATGGTAATTTTTGTGAAA--TT-GGGGTT
*
29313690 AAAATAGTAATTTTTG
1 AAAATGGTAATTTTTG
29313706 GATAGTCCAG
Statistics
Matches: 222, Mismatches: 21, Indels: 75
0.70 0.07 0.24
Matches are distributed among these distances:
26 4 0.02
27 12 0.05
28 42 0.19
29 52 0.23
30 62 0.28
31 35 0.16
32 15 0.07
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (29 bp):
AAAATGGTAATTTTTGTGAAATTGGGGTT
Found at i:29313540 original size:118 final size:119
Alignment explanation
Indices: 29313390--29313705 Score: 485
Period size: 118 Copynumber: 2.7 Consensus size: 119
29313380 TGGACGCACG
* *
29313390 GGGGCAAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATCTTGGAAAGTTTAGGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTA
*
29313455 AAATGGTAATTTTTGATGAAATTGGGGTTAATAATGGAATTTTGGAAAGTTC-A
66 AAATGGTAATTTTTGATGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGA
* *
29313508 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG-TTCGAGGGT
1 GGGGTAAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG-GGGT
* * *
29313572 AAAATGGTACTTTTTGATGAAATTGGGGTTAAAAATGGAATTTTGGGAAGTTCGG
65 AAAATGGTAATTTTTGATGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGA
* * * *
29313627 GGGGTAAAATAGTAATTTTTGATGAAACCGAGGTT-AAAATAGAATTTTGGAAAGTTTAGGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTA
*
29313691 AAATAGTAATTTTTG
66 AAATGGTAATTTTTG
29313706 GATAGTCCAG
Statistics
Matches: 179, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
117 3 0.02
118 142 0.79
119 34 0.19
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.33
Consensus pattern (119 bp):
GGGGTAAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTA
AAATGGTAATTTTTGATGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGA
Found at i:29313628 original size:29 final size:29
Alignment explanation
Indices: 29313418--29313628 Score: 143
Period size: 29 Copynumber: 7.2 Consensus size: 29
29313408 TTGGTGAAAC
* *
29313418 CGGGGTTAAAAATGGAATCTTGGAAAGTTT
1 CGGGGTTAAAAATGGAATTTTGGGAAG-TT
* * *
29313448 AGGGG-T-AAAATGGTAATTTTTGATGAAATT
1 CGGGGTTAAAAATGG-AA-TTTTG-GGAAGTT
* *
29313478 -GGGGTTAATAATGGAATTTTGGAAAGTT
1 CGGGGTTAAAAATGGAATTTTGGGAAGTT
*
29313506 CAGGGG-T-AAAATGGTAATTTTTGGTGAA-AT
1 C-GGGGTTAAAAATGG-AA-TTTTGG-GAAGTT
*
29313536 CGGGGTTAAAAATGGAATTTTGGAAAGTT
1 CGGGGTTAAAAATGGAATTTTGGGAAGTT
* * *
29313565 CGAGGG-T-AAAATGGTACTTTTTGATGAAATT
1 CG-GGGTTAAAAATGG-A-ATTTTG-GGAAGTT
29313596 -GGGGTTAAAAATGGAATTTTGGGAAGTT
1 CGGGGTTAAAAATGGAATTTTGGGAAGTT
29313624 CGGGG
1 CGGGG
29313629 GGTAAAATAG
Statistics
Matches: 140, Mismatches: 21, Indels: 41
0.69 0.10 0.20
Matches are distributed among these distances:
28 31 0.22
29 42 0.30
30 39 0.28
31 28 0.20
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (29 bp):
CGGGGTTAAAAATGGAATTTTGGGAAGTT
Found at i:29314434 original size:14 final size:14
Alignment explanation
Indices: 29314415--29314461 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
29314405 AAAAGCCACC
*
29314415 CTTTTTCTTCTTTT
1 CTTTTTATTCTTTT
29314429 CTTTTTTATTCTTTT
1 C-TTTTTATTCTTTT
*
29314444 CTTTTGA-TCTTTT
1 CTTTTTATTCTTTT
29314457 ACTTT
1 -CTTT
29314462 AAAAGATCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 6 0.21
14 10 0.34
15 13 0.45
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.74
Consensus pattern (14 bp):
CTTTTTATTCTTTT
Found at i:29314440 original size:15 final size:15
Alignment explanation
Indices: 29314416--29314448 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
29314406 AAAGCCACCC
*
29314416 TTTTTCTTCTTTTCT
1 TTTTTATTCTTTTCT
29314431 TTTTTATTCTTTTCT
1 TTTTTATTCTTTTCT
29314446 TTT
1 TTT
29314449 GATCTTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTATTCTTTTCT
Found at i:29315605 original size:6 final size:6
Alignment explanation
Indices: 29315590--29315648 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
29315580 TTAAATTTGA
* * *
29315590 TTAAAC TTAAAT TTAAA- GTAAAT TTAAAT GAGTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
*
29315638 ATAAAT TTAAA
1 TTAAAT TTAAA
29315649 ACTCATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
8 5 0.12
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:29315625 original size:14 final size:14
Alignment explanation
Indices: 29315606--29315632 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29315596 TTAAATTTAA
29315606 AGTAAATTTAAATG
1 AGTAAATTTAAATG
29315620 AGTAAATTTAAAT
1 AGTAAATTTAAAT
29315633 TTAAAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (14 bp):
AGTAAATTTAAATG
Found at i:29317239 original size:177 final size:181
Alignment explanation
Indices: 29316919--29317277 Score: 636
Period size: 177 Copynumber: 2.0 Consensus size: 181
29316909 AATTAAAACA
*
29316919 ATATTTTAAAACAAAAAGAAAAACTTACGCGAATTTTGCCTTATAAATAAACACTTTACGTAGAA
1 ATATTTTAAAACAAAAAGAAAAACTTACGCGAATTTTACCTTATAAATAAACACTTTACGTAGAA
* * *
29316984 TTATATATAGACGACCTTTTTTATTATTTTCGCTTGTATAAGATTATTTTCACTTTTGAGAGTGA
66 TTATATATAGACAACCTTTTTCATTATTTTCGATTGTATAAGATTATTTTCACTTTTGAGAGTGA
*
29317049 TTGTTTAGATTTTCACTGAACTCTTAGTTTCATATTATTGAGGAGATTTGC
131 TTGCTTAGATTTTCACTGAACTCTTAGTTTCATATTATTGAGGAGATTTGC
29317100 ATATTTT-AAA-AAAAA-AAAAA-TTACGCGAATTTTACCTTATAAATAAACACTTTACGTAGAA
1 ATATTTTAAAACAAAAAGAAAAACTTACGCGAATTTTACCTTATAAATAAACACTTTACGTAGAA
29317161 TTATATATAGACAACCTTTTTCATTATTTTCGATTGTATAAGATTATTTTCACTTTTGAGAGTGA
66 TTATATATAGACAACCTTTTTCATTATTTTCGATTGTATAAGATTATTTTCACTTTTGAGAGTGA
*
29317226 TTGCTTAGATTTTCACTGAACTCTTAGTTTCATATTGTTGAGGAGATTTGC
131 TTGCTTAGATTTTCACTGAACTCTTAGTTTCATATTATTGAGGAGATTTGC
29317277 A
1 A
29317278 CTTCTAGTGG
Statistics
Matches: 172, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
177 152 0.88
178 5 0.03
179 5 0.03
180 3 0.02
181 7 0.04
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (181 bp):
ATATTTTAAAACAAAAAGAAAAACTTACGCGAATTTTACCTTATAAATAAACACTTTACGTAGAA
TTATATATAGACAACCTTTTTCATTATTTTCGATTGTATAAGATTATTTTCACTTTTGAGAGTGA
TTGCTTAGATTTTCACTGAACTCTTAGTTTCATATTATTGAGGAGATTTGC
Found at i:29318048 original size:18 final size:18
Alignment explanation
Indices: 29318025--29318060 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
29318015 ATTTAGGAAT
29318025 ATTTTTGT-TCCAAAAGTA
1 ATTTTTGTCT-CAAAAGTA
29318043 ATTTTTGTCTCAAAAGTA
1 ATTTTTGTCTCAAAAGTA
29318061 CTTCTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (18 bp):
ATTTTTGTCTCAAAAGTA
Found at i:29319166 original size:17 final size:17
Alignment explanation
Indices: 29319144--29319190 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
29319134 ATCACACAAT
29319144 TGAAACTCAACATCAAA
1 TGAAACTCAACATCAAA
*
29319161 TGAAAC-CACACATTAAA
1 TGAAACTCA-ACATCAAA
*
29319178 TAAAAACTCAACA
1 T-GAAACTCAACA
29319191 ATTATTCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 2 0.08
17 14 0.56
18 7 0.28
19 2 0.08
ACGTcount: A:0.55, C:0.23, G:0.04, T:0.17
Consensus pattern (17 bp):
TGAAACTCAACATCAAA
Found at i:29320758 original size:21 final size:19
Alignment explanation
Indices: 29320729--29320777 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
29320719 TTTTTTAATT
*
29320729 TAATTATTTAGTAGAATTTTA
1 TAATGATTTA-TA-AATTTTA
* *
29320750 TAATGATTTATAATTTTTT
1 TAATGATTTATAAATTTTA
29320769 TAATGATTT
1 TAATGATTT
29320778 TTTTAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 14 0.56
20 2 0.08
21 9 0.36
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (19 bp):
TAATGATTTATAAATTTTA
Found at i:29323117 original size:2 final size:2
Alignment explanation
Indices: 29323110--29323136 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29323100 CATCCACAAG
29323110 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
29323137 ACACACACAC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:29332054 original size:24 final size:24
Alignment explanation
Indices: 29332027--29332101 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
29332017 AGTTTGACTC
*
29332027 AAACAAATAAACAGAATTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
29332051 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* *
29332075 AAACAATTAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
29332099 AAA
1 AAA
29332102 GATTATTTGA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.56, C:0.09, G:0.11, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:29335174 original size:24 final size:24
Alignment explanation
Indices: 29335113--29335175 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
29335103 TAGAGTAATA
* *
29335113 AGAGTTTGACTCAAATAAATAAAC
1 AGAGTTTAACTGAAATAAATAAAC
* * *
29335137 AGAGTTTAATTGAAATAATTAAGC
1 AGAGTTTAACTGAAATAAATAAAC
29335161 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
29335176 GATTATTTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.29
Consensus pattern (24 bp):
AGAGTTTAACTGAAATAAATAAAC
Found at i:29349697 original size:25 final size:25
Alignment explanation
Indices: 29349663--29349748 Score: 120
Period size: 25 Copynumber: 3.5 Consensus size: 25
29349653 AAATAATTTC
*
29349663 TAAAACTAAATAGAATAATTAATAA
1 TAAAATTAAATAGAATAATTAATAA
*
29349688 TAAAATTAAATAGAACAATTAATAA
1 TAAAATTAAATAGAATAATTAATAA
* *
29349713 T-AAATTGAATACAATAATTAATAA
1 TAAAATTAAATAGAATAATTAATAA
*
29349737 TAAATTTAAATA
1 TAAAATTAAATA
29349749 CTTTTAAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
24 21 0.40
25 32 0.60
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (25 bp):
TAAAATTAAATAGAATAATTAATAA
Found at i:29360333 original size:53 final size:53
Alignment explanation
Indices: 29360270--29360376 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
29360260 AATCCGAGTC
29360270 TGAGGGTATATATATATATATAAATTCTCTTTTGTTTCCTTTTCTTTATGTTT
1 TGAGGGTATATATATATATATAAATTCTCTTTTGTTTCCTTTTCTTTATGTTT
29360323 TGAGGGTATATATATATATATAAATTCTCTTTTGTTTCCTTTTCTTTATGTTT
1 TGAGGGTATATATATATATATAAATTCTCTTTTGTTTCCTTTTCTTTATGTTT
29360376 T
1 T
29360377 TTTATTTTAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.22, C:0.09, G:0.11, T:0.57
Consensus pattern (53 bp):
TGAGGGTATATATATATATATAAATTCTCTTTTGTTTCCTTTTCTTTATGTTT
Found at i:29380139 original size:10 final size:10
Alignment explanation
Indices: 29380124--29380154 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
29380114 ATATATATGT
29380124 GTGTGTGTGC
1 GTGTGTGTGC
29380134 GTGTGTGTGC
1 GTGTGTGTGC
29380144 GTGTGTTGTGC
1 GTGTG-TGTGC
29380155 TGCTTTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.75
11 5 0.25
ACGTcount: A:0.00, C:0.10, G:0.48, T:0.42
Consensus pattern (10 bp):
GTGTGTGTGC
Found at i:29382467 original size:18 final size:17
Alignment explanation
Indices: 29382444--29382481 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
29382434 TTATTAAAAA
29382444 AAATTATA-AAGATTCTAT
1 AAATTATAGAAG-TTC-AT
29382462 AAATTATAGAAGTTCAT
1 AAATTATAGAAGTTCAT
29382479 AAA
1 AAA
29382482 AAAAAAACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 11 0.58
19 3 0.16
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.34
Consensus pattern (17 bp):
AAATTATAGAAGTTCAT
Found at i:29383242 original size:11 final size:10
Alignment explanation
Indices: 29383190--29383268 Score: 62
Period size: 9 Copynumber: 8.3 Consensus size: 10
29383180 AGCAAATGAT
29383190 TTTAAAATTA
1 TTTAAAATTA
*
29383200 -TT--AATTT
1 TTTAAAATTA
*
29383207 TTTAAAA-AA
1 TTTAAAATTA
*
29383216 TATAAAATTA
1 TTTAAAATTA
29383226 -TTAAAATTA
1 TTTAAAATTA
*
29383235 TTTTAAAATCAA
1 -TTTAAAAT-TA
29383247 TTTAAAATTA
1 TTTAAAATTA
29383257 -TTAAAATTA
1 TTTAAAATTA
29383266 TTT
1 TTT
29383269 TTTTGAAATA
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
7 4 0.08
8 2 0.04
9 25 0.47
10 6 0.11
11 15 0.28
12 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (10 bp):
TTTAAAATTA
Found at i:29383253 original size:31 final size:29
Alignment explanation
Indices: 29383190--29383269 Score: 112
Period size: 31 Copynumber: 2.8 Consensus size: 29
29383180 AGCAAATGAT
29383190 TTTAAAATTATT--AATT-TTTTAAAAAA
1 TTTAAAATTATTAAAATTATTTTAAAAAA
*
29383216 TATAAAATTATTAAAATTATTTTAAAATCAA
1 TTTAAAATTATTAAAATTATTTTAAAA--AA
29383247 TTTAAAATTATTAAAATTATTTT
1 TTTAAAATTATTAAAATTATTTT
29383270 TTTGAAATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
26 11 0.23
28 4 0.09
29 8 0.17
31 24 0.51
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (29 bp):
TTTAAAATTATTAAAATTATTTTAAAAAA
Found at i:29383284 original size:31 final size:28
Alignment explanation
Indices: 29383192--29383301 Score: 102
Period size: 31 Copynumber: 3.8 Consensus size: 28
29383182 CAAATGATTT
*
29383192 TAAAATTATT--AATT-TTTTAAAAAATA
1 TAAAATTATTAAAATTATTTTAAAATA-A
29383218 TAAAATTATTAAAATTATTTTAAAATCAA
1 TAAAATTATTAAAATTATTTTAAAAT-AA
*
29383247 TTTAAAATTATTAAAATTATTTTTTTGAAATAA
1 --TAAAATTATTAAAATTA---TTTTAAAATAA
*
29383280 TAAAATTATT-AAATAATTTTAA
1 TAAAATTATTAAAATTATTTTAA
29383302 TTTCCAATTT
Statistics
Matches: 71, Mismatches: 4, Indels: 17
0.77 0.04 0.18
Matches are distributed among these distances:
26 10 0.14
27 5 0.07
28 4 0.06
29 9 0.13
30 6 0.08
31 27 0.38
33 2 0.03
34 8 0.11
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (28 bp):
TAAAATTATTAAAATTATTTTAAAATAA
Found at i:29383616 original size:18 final size:18
Alignment explanation
Indices: 29383593--29383629 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29383583 TTACAAAATC
*
29383593 ACAAGCACAGTACTGGGA
1 ACAAGCACAATACTGGGA
*
29383611 ACAAGCTCAATACTGGGA
1 ACAAGCACAATACTGGGA
29383629 A
1 A
29383630 AAAGGTTGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAGCACAATACTGGGA
Found at i:29384053 original size:58 final size:58
Alignment explanation
Indices: 29383989--29384108 Score: 204
Period size: 58 Copynumber: 2.1 Consensus size: 58
29383979 ATCCATCAAC
*
29383989 AAACTAAACTCAAATATTTTTAAACCCAAATATAATTTCATTATTAAAAAACACTCAT
1 AAACTAAACTCAAATATTTTTAAACCCAAATATAATTTCATTACTAAAAAACACTCAT
* * *
29384047 AAACTAAACTCAAATATTTTTAAACCCAAATATAATTTTATTCCTAAATAACACTCAT
1 AAACTAAACTCAAATATTTTTAAACCCAAATATAATTTCATTACTAAAAAACACTCAT
29384105 AAAC
1 AAAC
29384109 AACTCCTTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (58 bp):
AAACTAAACTCAAATATTTTTAAACCCAAATATAATTTCATTACTAAAAAACACTCAT
Found at i:29385366 original size:9 final size:9
Alignment explanation
Indices: 29385352--29385401 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
29385342 ATTTCAAAAA
29385352 AATAATTTT
1 AATAATTTT
29385361 AATAATTTT
1 AATAATTTT
*
29385370 -AT-ATTTAAAA
1 AATAATTT---T
29385380 AATAATTTT
1 AATAATTTT
29385389 AATAATTTT
1 AATAATTTT
29385398 AATA
1 AATA
29385402 TTATTTGCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
7 4 0.12
8 2 0.06
9 22 0.65
11 2 0.06
12 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
AATAATTTT
Found at i:29385380 original size:28 final size:29
Alignment explanation
Indices: 29385327--29385403 Score: 111
Period size: 28 Copynumber: 2.6 Consensus size: 29
29385317 ATTAAAATTA
*
29385327 TTTAATACTTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTA-TATTT-AAAAAAATAAT
29385358 TTTAATAATTTTATATTT-AAAAAATAAT
1 TTTAATAATTTTATATTTAAAAAAATAAT
29385386 TTTAATAATTTTAATATT
1 TTTAATAATTTT-ATATT
29385404 ATTTGCTAAC
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
28 22 0.50
29 5 0.11
30 5 0.11
31 12 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTAATAATTTTATATTTAAAAAAATAAT
Found at i:29387134 original size:23 final size:23
Alignment explanation
Indices: 29387104--29387159 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
29387094 ACACTAGCGC
* *
29387104 GTCCTCTGTTTAGCAC-GTTTCGT
1 GTCCTCTGTTCAGCACTGTGT-GT
29387127 GTCCTCTGTTCAGCACTGTGTGT
1 GTCCTCTGTTCAGCACTGTGTGT
*
29387150 GCCCTCTGTT
1 GTCCTCTGTT
29387160 ACCCAGCACT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 26 0.90
24 3 0.10
ACGTcount: A:0.07, C:0.29, G:0.23, T:0.41
Consensus pattern (23 bp):
GTCCTCTGTTCAGCACTGTGTGT
Found at i:29387179 original size:25 final size:25
Alignment explanation
Indices: 29387147--29387210 Score: 119
Period size: 25 Copynumber: 2.6 Consensus size: 25
29387137 CAGCACTGTG
29387147 TGTGCCCTCTGTTACCCAGCACTCA
1 TGTGCCCTCTGTTACCCAGCACTCA
*
29387172 TGTGCCCTCTGTTACCCGGCACTCA
1 TGTGCCCTCTGTTACCCAGCACTCA
29387197 TGTGCCCTCTGTTA
1 TGTGCCCTCTGTTA
29387211 AGTACTTCGG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.12, C:0.38, G:0.19, T:0.31
Consensus pattern (25 bp):
TGTGCCCTCTGTTACCCAGCACTCA
Found at i:29397626 original size:19 final size:20
Alignment explanation
Indices: 29397552--29397627 Score: 59
Period size: 19 Copynumber: 4.0 Consensus size: 20
29397542 TAATGAAAGG
* *
29397552 TTACTTAAAACATTAAAATA
1 TTACTTAAAGCATTAAAAAA
* * *
29397572 TTTC-TAAAGAATTAAATAA
1 TTACTTAAAGCATTAAAAAA
** *
29397591 TT-CTTAAATTATGAAAAAA
1 TTACTTAAAGCATTAAAAAA
29397610 TTACTTAAA-CATTAAAAA
1 TTACTTAAAGCATTAAAAA
29397628 GTTTTTAAGA
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
18 1 0.02
19 33 0.77
20 9 0.21
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (20 bp):
TTACTTAAAGCATTAAAAAA
Found at i:29406490 original size:23 final size:23
Alignment explanation
Indices: 29406464--29406509 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
29406454 CTCAGCTCTC
*
29406464 AAAACCTGACATGCTATCAAAAG
1 AAAACCTGACATGCAATCAAAAG
29406487 AAAACCTGACATGCAATCAAAAG
1 AAAACCTGACATGCAATCAAAAG
29406510 GACTGGACTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.22, G:0.13, T:0.15
Consensus pattern (23 bp):
AAAACCTGACATGCAATCAAAAG
Found at i:29419074 original size:15 final size:16
Alignment explanation
Indices: 29419044--29419082 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
29419034 TAATAAAAAT
29419044 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
29419061 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
29419076 ATAATTT
1 ATAATTT
29419083 TAAATGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:29425265 original size:7 final size:7
Alignment explanation
Indices: 29425253--29425278 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29425243 ATCTAATGTC
29425253 TCAATAG
1 TCAATAG
29425260 TCAATAG
1 TCAATAG
29425267 TCAATAG
1 TCAATAG
29425274 TCAAT
1 TCAAT
29425279 TCAAAAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (7 bp):
TCAATAG
Found at i:29430504 original size:18 final size:19
Alignment explanation
Indices: 29430481--29430518 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
29430471 ATAGTTGAAA
29430481 TATTTTTAACATTAT-TTT
1 TATTTTTAACATTATATTT
*
29430499 TATTTTTTACATTATATTT
1 TATTTTTAACATTATATTT
29430518 T
1 T
29430519 TAATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTTTTAACATTATATTT
Found at i:29431576 original size:13 final size:13
Alignment explanation
Indices: 29431536--29431576 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
29431526 AAATATATAG
29431536 TATTTT-AAAAAA
1 TATTTTAAAAAAA
*
29431548 T-TATTAAAAAACA
1 TATTTTAAAAAA-A
29431561 TATTTTAAAAAAA
1 TATTTTAAAAAAA
29431574 TAT
1 TAT
29431577 AAATTACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
11 3 0.12
12 6 0.25
13 6 0.25
14 9 0.38
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (13 bp):
TATTTTAAAAAAA
Found at i:29432669 original size:10 final size:9
Alignment explanation
Indices: 29432647--29432689 Score: 59
Period size: 10 Copynumber: 4.6 Consensus size: 9
29432637 TAATTTTTTT
29432647 AAAATTATA
1 AAAATTATA
29432656 AAAATTATTA
1 AAAATTA-TA
29432666 AAAATTACTA
1 AAAATTA-TA
*
29432676 ACAATTATA
1 AAAATTATA
29432685 AAAAT
1 AAAAT
29432690 ATTAATAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
9 13 0.43
10 17 0.57
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAATTATA
Found at i:29432671 original size:19 final size:19
Alignment explanation
Indices: 29432647--29432689 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
29432637 TAATTTTTTT
29432647 AAAATTA-TAAAAATTATTA
1 AAAATTACTAAAAATTA-TA
*
29432666 AAAATTACTAACAATTATA
1 AAAATTACTAAAAATTATA
29432685 AAAAT
1 AAAAT
29432690 ATTAATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTACTAAAAATTATA
Found at i:29443584 original size:19 final size:20
Alignment explanation
Indices: 29443560--29443605 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
29443550 CATCCAAACA
29443560 CCAGAAAA-T-ATTAACTTTT
1 CCAGAAAAGTAATTAA-TTTT
*
29443579 CCAGAAAAGTAATTCATTTT
1 CCAGAAAAGTAATTAATTTT
29443599 CCAGAAA
1 CCAGAAA
29443606 TCATTTTCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 12 0.50
21 4 0.17
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.30
Consensus pattern (20 bp):
CCAGAAAAGTAATTAATTTT
Found at i:29447840 original size:3 final size:3
Alignment explanation
Indices: 29447832--29447872 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
29447822 TTAACCTCTT
29447832 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29447873 CAACAAGATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:29448060 original size:34 final size:34
Alignment explanation
Indices: 29448021--29448092 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
29448011 TCAAATCCAT
*
29448021 GAAATTTCATGAACCAATCGTTCTAAAAAGAATA
1 GAAATTTCATGAACCAATCATTCTAAAAAGAATA
* * *
29448055 GAAATTTTATGACCCAATCATTCTGAAAAGAATA
1 GAAATTTCATGAACCAATCATTCTAAAAAGAATA
29448089 GAAA
1 GAAA
29448093 CTTAATCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.26
Consensus pattern (34 bp):
GAAATTTCATGAACCAATCATTCTAAAAAGAATA
Found at i:29460426 original size:3 final size:3
Alignment explanation
Indices: 29460418--29460443 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29460408 GTACCCAAGG
29460418 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
29460444 CTGAAGCAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:29460572 original size:20 final size:20
Alignment explanation
Indices: 29460549--29460588 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
29460539 TCTGTATTCC
29460549 TTCTTCTTCTTCTTT-GTTAA
1 TTCTT-TTCTTCTTTAGTTAA
*
29460569 TTCTTTTCTTTTTTAGTTAA
1 TTCTTTTCTTCTTTAGTTAA
29460589 GGAGTCTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.12, C:0.15, G:0.05, T:0.68
Consensus pattern (20 bp):
TTCTTTTCTTCTTTAGTTAA
Found at i:29460603 original size:63 final size:63
Alignment explanation
Indices: 29460504--29460633 Score: 260
Period size: 63 Copynumber: 2.1 Consensus size: 63
29460494 GAAGCAGAGA
29460504 AATTCTTTTCTTTTTTAGTTAAGGAGTCTGTTCTTTCTGTATTCCTTCTTCTTCTTCTTTGTT
1 AATTCTTTTCTTTTTTAGTTAAGGAGTCTGTTCTTTCTGTATTCCTTCTTCTTCTTCTTTGTT
29460567 AATTCTTTTCTTTTTTAGTTAAGGAGTCTGTTCTTTCTGTATTCCTTCTTCTTCTTCTTTGTT
1 AATTCTTTTCTTTTTTAGTTAAGGAGTCTGTTCTTTCTGTATTCCTTCTTCTTCTTCTTTGTT
29460630 AATT
1 AATT
29460634 GTGAAACAGA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.12, C:0.17, G:0.11, T:0.60
Consensus pattern (63 bp):
AATTCTTTTCTTTTTTAGTTAAGGAGTCTGTTCTTTCTGTATTCCTTCTTCTTCTTCTTTGTT
Found at i:29473843 original size:41 final size:41
Alignment explanation
Indices: 29473786--29473877 Score: 175
Period size: 41 Copynumber: 2.2 Consensus size: 41
29473776 ATAAATTGAT
*
29473786 TCACACATCATGATCTTATACCATTTTCTCATCAATTTGCA
1 TCACATATCATGATCTTATACCATTTTCTCATCAATTTGCA
29473827 TCACATATCATGATCTTATACCATTTTCTCATCAATTTGCA
1 TCACATATCATGATCTTATACCATTTTCTCATCAATTTGCA
29473868 TCACATATCA
1 TCACATATCA
29473878 CATATCATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.39
Consensus pattern (41 bp):
TCACATATCATGATCTTATACCATTTTCTCATCAATTTGCA
Found at i:29474026 original size:4 final size:4
Alignment explanation
Indices: 29474017--29474082 Score: 123
Period size: 4 Copynumber: 16.5 Consensus size: 4
29474007 TGCAATAATC
*
29474017 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATAT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
29474065 ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT AT
29474083 TGAACTCTAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 60 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:29475881 original size:37 final size:38
Alignment explanation
Indices: 29475831--29475934 Score: 111
Period size: 37 Copynumber: 2.7 Consensus size: 38
29475821 TTCGAAGCAA
*
29475831 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAGTGACACCCAGTGTCTCATCGAACCTAGCCGAAG
** ** * *
29475868 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAGTGACACCCAGTGTCTCATCGAACCTAGCCGAAG
29475906 TAAAATAGTGACACCCAGTGTCTCATCGA
1 T--AA-AGTGACACCCAGTGTCTCATCGA
29475935 CTCGAGGTCG
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
37 21 0.40
38 10 0.19
40 2 0.04
41 19 0.37
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (38 bp):
TAAAGTGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:29476828 original size:11 final size:12
Alignment explanation
Indices: 29476795--29476853 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 12
29476785 ATATTAGTTA
29476795 ATAATAATAA-T
1 ATAATAATAATT
*
29476806 ATAATACTAATT
1 ATAATAATAATT
29476818 A-AATAATAATTT
1 ATAATAATAA-TT
* *
29476830 ATATTATTATATT
1 ATAATAATA-ATT
*
29476843 ATAATATTAAT
1 ATAATAATAAT
29476854 AAATTAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 16 0.41
12 7 0.18
13 15 0.38
14 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (12 bp):
ATAATAATAATT
Found at i:29477247 original size:54 final size:54
Alignment explanation
Indices: 29477153--29477264 Score: 170
Period size: 54 Copynumber: 2.1 Consensus size: 54
29477143 AATTTGGGTC
** *
29477153 ATTACATTTTGGTCCTTTGAATAATTGCTATATAGGTCCTCAAGCATTTCCTAA
1 ATTACATTTTGGTCCTTTGAATAATTGAAATATAGATCCTCAAGCATTTCCTAA
* * *
29477207 ATTACATTTTGGTCCTTTGGATAATTGAAATCTAGATCCTCAAGCATTTTCTAA
1 ATTACATTTTGGTCCTTTGAATAATTGAAATATAGATCCTCAAGCATTTCCTAA
29477261 ATTA
1 ATTA
29477265 AGACTCAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (54 bp):
ATTACATTTTGGTCCTTTGAATAATTGAAATATAGATCCTCAAGCATTTCCTAA
Found at i:29485682 original size:31 final size:31
Alignment explanation
Indices: 29485644--29485706 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
29485634 TTTTTTCCAC
29485644 ATAATTTCCATGTCAATTTATAATTAATATA
1 ATAATTTCCATGTCAATTTATAATTAATATA
29485675 ATAATTTCCATGTCAATTTATAATTAATATA
1 ATAATTTCCATGTCAATTTATAATTAATATA
29485706 A
1 A
29485707 ATAAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (31 bp):
ATAATTTCCATGTCAATTTATAATTAATATA
Found at i:29494201 original size:21 final size:22
Alignment explanation
Indices: 29494176--29494219 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
29494166 ATTTCAATGA
* *
29494176 TTTTAAGTTTTTAAAAA-TAAT
1 TTTTAAATTTTAAAAAATTAAT
29494197 TTTTAAATTTTAAAAAATTAAT
1 TTTTAAATTTTAAAAAATTAAT
29494219 T
1 T
29494220 AAATGATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTTAAATTTTAAAAAATTAAT
Found at i:29494446 original size:23 final size:23
Alignment explanation
Indices: 29494416--29494466 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
29494406 TTTATATTGC
** * *
29494416 TAAAAATTGTAATTTTTTAATAT
1 TAAAAATTAAAATTTTATAACAT
29494439 TAAAAATTAAAATTTTATAACAT
1 TAAAAATTAAAATTTTATAACAT
29494462 TAAAA
1 TAAAA
29494467 TCGATTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TAAAAATTAAAATTTTATAACAT
Found at i:29507956 original size:3 final size:3
Alignment explanation
Indices: 29507950--29507994 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
29507940 TCATGTCAGC
29507950 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA AT
29507995 GATTGTTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:29511035 original size:20 final size:20
Alignment explanation
Indices: 29511012--29511051 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
29511002 TCCTTAATTA
29511012 CTTAATTAAATTAACTTAAT
1 CTTAATTAAATTAACTTAAT
*
29511032 CTTAATTATATTAACTTAAT
1 CTTAATTAAATTAACTTAAT
29511052 TATTCATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.47
Consensus pattern (20 bp):
CTTAATTAAATTAACTTAAT
Found at i:29512313 original size:24 final size:25
Alignment explanation
Indices: 29512265--29512314 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
29512255 AAATAGCAAT
*
29512265 GGTGCTAAAATGGGATAAAAAAATTA
1 GGTGCTAAAAT-GGAGAAAAAAATTA
*
29512291 GGTGCTAAAAT-GAGAAAATAATTA
1 GGTGCTAAAATGGAGAAAAAAATTA
29512315 TAGCTTAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 11 0.50
26 11 0.50
ACGTcount: A:0.50, C:0.04, G:0.22, T:0.24
Consensus pattern (25 bp):
GGTGCTAAAATGGAGAAAAAAATTA
Found at i:29512862 original size:2 final size:2
Alignment explanation
Indices: 29512855--29512883 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29512845 TTTTCAGTAT
29512855 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
29512884 TGTGTGTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:29519173 original size:10 final size:9
Alignment explanation
Indices: 29519162--29519218 Score: 53
Period size: 9 Copynumber: 6.0 Consensus size: 9
29519152 ATTTTTATTA
29519162 TTTTAAATT
1 TTTTAAATT
*
29519171 ATTATAAACTT
1 -TTTTAAA-TT
29519182 TTTATAAATT
1 TTT-TAAATT
29519192 TTTTAAATT
1 TTTTAAATT
*
29519201 TTTT-TATAT
1 TTTTAAAT-T
29519210 TTTTAAATT
1 TTTTAAATT
29519219 ACTTATTGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
8 2 0.05
9 16 0.41
10 15 0.38
11 6 0.15
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTTAAATT
Found at i:29519188 original size:11 final size:10
Alignment explanation
Indices: 29519165--29519214 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
29519155 TTTATTATTT
*
29519165 TAAATTATTA
1 TAAATTTTTA
29519175 TAAACTTTTTA
1 TAAA-TTTTTA
29519186 TAAATTTTT-
1 TAAATTTTTA
*
29519195 TAAATTTTTT
1 TAAATTTTTA
*
29519205 TATATTTTTA
1 TAAATTTTTA
29519215 AATTACTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 9 0.26
10 17 0.49
11 9 0.26
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (10 bp):
TAAATTTTTA
Found at i:29519646 original size:29 final size:29
Alignment explanation
Indices: 29519613--29519668 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
29519603 ATTTTTTTAA
29519613 ATAAAAAATAATAAAAAATTATATAAAAC
1 ATAAAAAATAATAAAAAATTATATAAAAC
* **
29519642 ATAAAATATTTTAAAAAATTATATAAA
1 ATAAAAAATAATAAAAAATTATATAAA
29519669 CTTATAAATT
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:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (29 bp):
ATAAAAAATAATAAAAAATTATATAAAAC
Found at i:29529307 original size:64 final size:64
Alignment explanation
Indices: 29529171--29529317 Score: 181
Period size: 64 Copynumber: 2.3 Consensus size: 64
29529161 TCCCCTATGT
* * *
29529171 AGTGGACTATGGTTATCTCCCTACTATCAATGAAGTGACTCGCCATTTTAGTTCTCCCTTGTGC
1 AGTGGACTATGGTTATCTCCCTACCATCAATGAACTGACTCACCATTTTAGTTCTCCCTTGTGC
** * *
29529235 AGCAGACTATGGTTATCT-CCTCGCCATTAATGAAACTG-CTCACCATTTTAGTTCTCCCTTGTG
1 AGTGGACTATGGTTATCTCCCT-ACCATCAATG-AACTGACTCACCATTTTAGTTCTCCCTTGTG
29529298 C
64 C
* *
29529299 AGTGGACTACGATTATCTC
1 AGTGGACTATGGTTATCTC
29529318 GACATCAACG
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
63 3 0.04
64 62 0.90
65 4 0.06
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.35
Consensus pattern (64 bp):
AGTGGACTATGGTTATCTCCCTACCATCAATGAACTGACTCACCATTTTAGTTCTCCCTTGTGC
Found at i:29529902 original size:23 final size:23
Alignment explanation
Indices: 29529876--29529921 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
29529866 AATAAAACAC
29529876 CAAT-ATATGCCAAAAGCAAAAAT
1 CAATGATATGCCAAAAG-AAAAAT
* *
29529899 CAATGGTATGCTAAAAGAAAAAT
1 CAATGATATGCCAAAAGAAAAAT
29529922 GTTATTAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.54, C:0.13, G:0.13, T:0.20
Consensus pattern (23 bp):
CAATGATATGCCAAAAGAAAAAT
Found at i:29531024 original size:14 final size:14
Alignment explanation
Indices: 29530997--29531058 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 14
29530987 TTTTAGCATG
29530997 AACCTCGAACCCCA
1 AACCTCGAACCCCA
* *
29531011 AACCTTGAATCCCA
1 AACCTCGAACCCCA
* *
29531025 AACC-CAAACCCTA
1 AACCTCGAACCCCA
*
29531038 AACCTCGAA-TCCA
1 AACCTCGAACCCCA
29531051 AA-CTCGAA
1 AACCTCGAA
29531059 TCTGAACCCG
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
12 6 0.16
13 13 0.34
14 19 0.50
ACGTcount: A:0.40, C:0.40, G:0.06, T:0.13
Consensus pattern (14 bp):
AACCTCGAACCCCA
Found at i:29553247 original size:12 final size:12
Alignment explanation
Indices: 29553230--29553255 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29553220 GTCTATCTAC
29553230 AACCCAAACCTA
1 AACCCAAACCTA
29553242 AACCCAAACCTA
1 AACCCAAACCTA
29553254 AA
1 AA
29553256 TTTTGTAGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.38, G:0.00, T:0.08
Consensus pattern (12 bp):
AACCCAAACCTA
Found at i:29561582 original size:16 final size:16
Alignment explanation
Indices: 29561536--29561585 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
29561526 ACAAATTAAA
*
29561536 AAATAATTATAAAATAT
1 AAATAA-TATAAAAAAT
* * *
29561553 TAATTATATTAAAAAT
1 AAATAATATAAAAAAT
29561569 AAATAATATAAAAAAT
1 AAATAATATAAAAAAT
29561585 A
1 A
29561586 TTCAATATGG
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 22 0.85
17 4 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATAATATAAAAAAT
Found at i:29570377 original size:29 final size:30
Alignment explanation
Indices: 29570315--29570379 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
29570305 ACAATTAGAT
*
29570315 CTAAA-TTTTAAATTTAAAAAATAAAAAAA
1 CTAAATTTTTAAAATTAAAAAATAAAAAAA
* *
29570344 TTAAATTTTTAAAATT-AAAAATATAAAAA
1 CTAAATTTTTAAAATTAAAAAATAAAAAAA
29570373 CTAAATT
1 CTAAATT
29570380 CTCAATTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 22 0.71
30 9 0.29
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (30 bp):
CTAAATTTTTAAAATTAAAAAATAAAAAAA
Found at i:29570930 original size:3 final size:3
Alignment explanation
Indices: 29570924--29570958 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
29570914 GAGGAGGAGG
29570924 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
29570959 TAGCTGCTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:29573667 original size:138 final size:138
Alignment explanation
Indices: 29573453--29573868 Score: 771
Period size: 138 Copynumber: 3.0 Consensus size: 138
29573443 GCTTTGACTC
*
29573453 CATCGAATCTTGATGATCTATTTTCTGCTGAGAACTCATCTCTGCAGTACTCCGATCAAGCATTG
1 CATCGAATCTTGACGATCTATTTTCTGCTGAGAACTCATCTCTGCAGTACTCCGATCAAGCATTG
29573518 GCTGCGGCAGTTTACTCTCCCACCCATAAATCTGCTGTTTTAAATCAATTTCAGCAGCAGCAAAG
66 GCTGCGGCAGTTTACTCTCCCACCCATAAATCTGCTGTTTTAAATCAATTTCAGCAGCAGCAAAG
29573583 CATGTTAT
131 CATGTTAT
29573591 CATCGAATCTTGACGATCTATTTTCTGCTGAGAACTCATCTCTGCAGTACTCCGATCAAGCATTG
1 CATCGAATCTTGACGATCTATTTTCTGCTGAGAACTCATCTCTGCAGTACTCCGATCAAGCATTG
*
29573656 GCTGCGGCAGTTTACTCTCCCACCTATAAATCTGCTGTTTTAAATCAATTTCAGCAGCAGCAAAG
66 GCTGCGGCAGTTTACTCTCCCACCCATAAATCTGCTGTTTTAAATCAATTTCAGCAGCAGCAAAG
29573721 CATGTTAT
131 CATGTTAT
29573729 CATCGAATCTTGACGATCTATTTTCTGCTGAGAACTCATCTCTGCAGTACTCCGATCAAGCATTG
1 CATCGAATCTTGACGATCTATTTTCTGCTGAGAACTCATCTCTGCAGTACTCCGATCAAGCATTG
* **
29573794 GCTGCAGCAGTTTACTCTCCCACCCA-AAATTCCCCTGTTTTAAATCAATTTCAGCAGCAGCAAA
66 GCTGCGGCAGTTTACTCTCCCACCCATAAA-TCTGCTGTTTTAAATCAATTTCAGCAGCAGCAAA
29573858 GCATGTTAT
130 GCATGTTAT
29573867 CA
1 CA
29573869 CCTATAAACA
Statistics
Matches: 271, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
137 3 0.01
138 268 0.99
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31
Consensus pattern (138 bp):
CATCGAATCTTGACGATCTATTTTCTGCTGAGAACTCATCTCTGCAGTACTCCGATCAAGCATTG
GCTGCGGCAGTTTACTCTCCCACCCATAAATCTGCTGTTTTAAATCAATTTCAGCAGCAGCAAAG
CATGTTAT
Found at i:29574708 original size:3 final size:3
Alignment explanation
Indices: 29574700--29574724 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29574690 ATGATCCTTG
29574700 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
29574725 TAATATTCAA
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:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:29578255 original size:95 final size:95
Alignment explanation
Indices: 29578115--29578315 Score: 359
Period size: 95 Copynumber: 2.1 Consensus size: 95
29578105 AAATGTTTGA
*
29578115 ATGTCTCGAGACGATGTCATGTTCCTGTAGAACTTTAGCTTCAAAGTTGTCTTGTCTCAAGACAA
1 ATGTCTCGAGAAGATGTCATGTTCCTGTAGAACTTTAGCTTCAAAGTTGTCTTGTCTCAAGACAA
29578180 ATGAGTGTATGTCTCGAGACAAAGGGGCTT
66 ATGAGTGTATGTCTCGAGACAAAGGGGCTT
*
29578210 ATGTCTCGAGATAG-TGTCTTGTTCCTGTAGAACTTTAGCTTCAAAGTTGTCTTGTCTCAAGACA
1 ATGTCTCGAGA-AGATGTCATGTTCCTGTAGAACTTTAGCTTCAAAGTTGTCTTGTCTCAAGACA
*
29578274 AATGAGTGTATGTCTCGAGACAAAGGGGTTT
65 AATGAGTGTATGTCTCGAGACAAAGGGGCTT
29578305 ATGTCTCGAGA
1 ATGTCTCGAGA
29578316 CATGACCCTG
Statistics
Matches: 102, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
95 101 0.99
96 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (95 bp):
ATGTCTCGAGAAGATGTCATGTTCCTGTAGAACTTTAGCTTCAAAGTTGTCTTGTCTCAAGACAA
ATGAGTGTATGTCTCGAGACAAAGGGGCTT
Found at i:29578287 original size:22 final size:22
Alignment explanation
Indices: 29578262--29578317 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
29578252 AAAGTTGTCT
* *
29578262 TGTCTCAAGACAAATGAGTGTA
1 TGTCTCGAGACAAAGGAGTGTA
* *
29578284 TGTCTCGAGACAAAGGGGTTTA
1 TGTCTCGAGACAAAGGAGTGTA
29578306 TGTCTCGAGACA
1 TGTCTCGAGACA
29578318 TGACCCTGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (22 bp):
TGTCTCGAGACAAAGGAGTGTA
Found at i:29578352 original size:95 final size:94
Alignment explanation
Indices: 29578141--29578338 Score: 301
Period size: 95 Copynumber: 2.1 Consensus size: 94
29578131 TCATGTTCCT
29578141 GTAGAACTTTAGCTTCAAAGTTGTCTTGTCTCAAGACAAATGAGTGTATGTCTCGAGACAAAGGG
1 GTAGAACTTTAGCTTCAAAGTTGTCTTGTCTCAAGACAAATGAGTGTATGTCTCGAGACAAAGGG
* * * * *
29578206 GCTTATGTCTCGAGATAGTGTCTTGTTCC
66 GCTTATGTCTCGAGACAGTGCCCTGATAC
29578235 TGTAGAACTTTAGCTTCAAAGTTGTCTTGTCTCAAGACAAATGAGTGTATGTCTCGAGACAAAGG
1 -GTAGAACTTTAGCTTCAAAGTTGTCTTGTCTCAAGACAAATGAGTGTATGTCTCGAGACAAAGG
*
29578300 GGTTTATGTCTCGAGACA-TGACCCTGATAC
65 GGCTTATGTCTCGAGACAGTG-CCCTGATAC
*
29578330 -TATAACTTT
1 GTAGAACTTT
29578339 TTAGCTTTGA
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
93 8 0.08
94 2 0.02
95 85 0.89
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (94 bp):
GTAGAACTTTAGCTTCAAAGTTGTCTTGTCTCAAGACAAATGAGTGTATGTCTCGAGACAAAGGG
GCTTATGTCTCGAGACAGTGCCCTGATAC
Found at i:29604371 original size:30 final size:30
Alignment explanation
Indices: 29604335--29604391 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
29604325 AGCTGTTAAC
* *
29604335 TAATAGTCAACTGCATTTTTATCAAGTCTG
1 TAATAGTCAACTGAATATTTATCAAGTCTG
*
29604365 TAATAGTCGACTGAATATTTATCAAGT
1 TAATAGTCAACTGAATATTTATCAAGT
29604392 TTATATGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (30 bp):
TAATAGTCAACTGAATATTTATCAAGTCTG
Found at i:29619247 original size:26 final size:25
Alignment explanation
Indices: 29619217--29619266 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
29619207 TGGATGATTT
*
29619217 GATAAAAAAAATTTAAGAGCTAAAAA
1 GATAAAAAAAATGTAAGA-CTAAAAA
29619243 GATAAAAAAAATGTAAGACTAAAA
1 GATAAAAAAAATGTAAGACTAAAA
29619267 TGGTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.66, C:0.04, G:0.12, T:0.18
Consensus pattern (25 bp):
GATAAAAAAAATGTAAGACTAAAAA
Found at i:29623379 original size:29 final size:29
Alignment explanation
Indices: 29623337--29623421 Score: 170
Period size: 29 Copynumber: 2.9 Consensus size: 29
29623327 TGGGCCAAGG
29623337 ATGAAAACACATTAAAGGTAAAAGTTTAC
1 ATGAAAACACATTAAAGGTAAAAGTTTAC
29623366 ATGAAAACACATTAAAGGTAAAAGTTTAC
1 ATGAAAACACATTAAAGGTAAAAGTTTAC
29623395 ATGAAAACACATTAAAGGTAAAAGTTT
1 ATGAAAACACATTAAAGGTAAAAGTTT
29623422 GCTTTCAATT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.52, C:0.09, G:0.14, T:0.25
Consensus pattern (29 bp):
ATGAAAACACATTAAAGGTAAAAGTTTAC
Found at i:29633593 original size:92 final size:92
Alignment explanation
Indices: 29633415--29633613 Score: 285
Period size: 92 Copynumber: 2.1 Consensus size: 92
29633405 ATTATGATTG
* *
29633415 TGGGAATGGGATGATTGTTCCTACAGGAAACAATATAGGTATAGGAGCAACAATATATAGTACTA
1 TGGGAATGGGATGATTGTTCCTACAGGAAAAAAGATAGGTATAGGAGCAAC-A-ATATAGTACTA
*
29633480 CAACTAGTTCATATACGATGGTAAGGATA
64 CAACTAGTTCATATAAGATGGTAAGGATA
* * * *
29633509 TGGGAATGGGATGATTGTTCCTATAGGAAATTAAAGATAGGTATGGGAGTAAC-A-GTAGTACTA
1 TGGGAATGGGATGATTGTTCCTACAGGAAA--AAAGATAGGTATAGGAGCAACAATATAGTACTA
29633572 CAACTAGTTCATATAAGATGGTAAGGATA
64 CAACTAGTTCATATAAGATGGTAAGGATA
29633601 TGGGAATGGGATG
1 TGGGAATGGGATG
29633614 TATGCTGCAA
Statistics
Matches: 96, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
92 49 0.51
93 1 0.01
94 29 0.30
96 17 0.18
ACGTcount: A:0.37, C:0.09, G:0.27, T:0.27
Consensus pattern (92 bp):
TGGGAATGGGATGATTGTTCCTACAGGAAAAAAGATAGGTATAGGAGCAACAATATAGTACTACA
ACTAGTTCATATAAGATGGTAAGGATA
Found at i:29637932 original size:14 final size:14
Alignment explanation
Indices: 29637913--29637951 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
29637903 AAAAGAAAAG
29637913 GAAATCGAAAATCA
1 GAAATCGAAAATCA
29637927 GAAATC-AGAAATCA
1 GAAATCGA-AAATCA
29637941 GAAATCAGAAA
1 GAAATC-GAAA
29637952 GAAAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 2 0.09
16 1 0.05
ACGTcount: A:0.59, C:0.13, G:0.15, T:0.13
Consensus pattern (14 bp):
GAAATCGAAAATCA
Found at i:29642164 original size:22 final size:21
Alignment explanation
Indices: 29642136--29642178 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
29642126 TTCAAGGGGC
* *
29642136 TTTTTTTTTTCATTTTTAATAG
1 TTTTTTTTATCA-GTTTAATAG
29642158 TTTTTTTTATCAGTTTAATAG
1 TTTTTTTTATCAGTTTAATAG
29642179 ATTTAAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.67
Consensus pattern (21 bp):
TTTTTTTTATCAGTTTAATAG
Found at i:29646617 original size:23 final size:21
Alignment explanation
Indices: 29646591--29646641 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
29646581 TAGAATAAAT
*
29646591 TAAATTATTAATTTTCAGTTTAA
1 TAAATTATTAATTTT-A-TTGAA
* *
29646614 TAAATTTTTTATTTTATTGAA
1 TAAATTATTAATTTTATTGAA
29646635 TAAATTA
1 TAAATTA
29646642 ATAAAGAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 10 0.42
22 1 0.04
23 13 0.54
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (21 bp):
TAAATTATTAATTTTATTGAA
Found at i:29648864 original size:3 final size:3
Alignment explanation
Indices: 29648856--29648895 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
29648846 CTTTAATCAA
* * *
29648856 ATT ATT ATT ATT GTT GTT ATT GTT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
29648896 ATGTATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:29691857 original size:29 final size:27
Alignment explanation
Indices: 29691816--29691893 Score: 72
Period size: 29 Copynumber: 2.9 Consensus size: 27
29691806 TTTAAAAGTT
*
29691816 TTTTTTCAT-ATTTTTTAAAATTATAAT
1 TTTTTT-ATAATTTTTTAAAATTATAAA
* * *
29691843 TTTGATTTATAATTTTTGAACATTTTAAA
1 TTT--TTTATAATTTTTTAAAATTATAAA
29691872 TTTTTTATAA-TTTTT-AAATTAT
1 TTTTTTATAATTTTTTAAAATTAT
29691894 TTAATGACAT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
25 5 0.12
26 4 0.10
27 10 0.24
28 2 0.05
29 20 0.49
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (27 bp):
TTTTTTATAATTTTTTAAAATTATAAA
Found at i:29696356 original size:18 final size:20
Alignment explanation
Indices: 29696333--29696376 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
29696323 ATCAAGAGGT
29696333 AAGAAG-AAGCAAAA-AAGA
1 AAGAAGCAAGCAAAAGAAGA
*
29696351 AAGAAGCTGAGCAAAAGAAGA
1 AAGAAGC-AAGCAAAAGAAGA
29696372 AAGAA
1 AAGAA
29696377 ATAGTAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 6 0.27
20 7 0.32
21 9 0.41
ACGTcount: A:0.66, C:0.07, G:0.25, T:0.02
Consensus pattern (20 bp):
AAGAAGCAAGCAAAAGAAGA
Found at i:29700121 original size:22 final size:20
Alignment explanation
Indices: 29700084--29700127 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
29700074 ACATCAGAAT
29700084 TTTTTCACCTTTCTCAGTTGG
1 TTTTTCACCTTTCTCAG-TGG
29700105 TTTTTC-CCTTTAACTCAGTGG
1 TTTTTCACCTTT--CTCAGTGG
29700126 TT
1 TT
29700128 AGATATAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.24
21 11 0.52
22 5 0.24
ACGTcount: A:0.11, C:0.23, G:0.14, T:0.52
Consensus pattern (20 bp):
TTTTTCACCTTTCTCAGTGG
Found at i:29715191 original size:5 final size:5
Alignment explanation
Indices: 29715181--29715208 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
29715171 AATAAAGTTC
29715181 GTTGG GTTGG GTTGG GTTGG GTTGG GTT
1 GTTGG GTTGG GTTGG GTTGG GTTGG GTT
29715209 AGATGACGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.57, T:0.43
Consensus pattern (5 bp):
GTTGG
Found at i:29715643 original size:21 final size:21
Alignment explanation
Indices: 29715624--29715674 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 21
29715614 AACACATTAG
*
29715624 TAAAATTGATAAAAATATTAAA
1 TAAAATTCA-AAAAATATTAAA
29715646 TAAAATTCAAAAAATTAAATTAAA
1 TAAAATTCAAAAAA-T--ATTAAA
29715670 TAAAA
1 TAAAA
29715675 ACCATTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 5 0.20
22 9 0.36
24 11 0.44
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (21 bp):
TAAAATTCAAAAAATATTAAA
Found at i:29718233 original size:43 final size:44
Alignment explanation
Indices: 29718180--29718264 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 44
29718170 CACGTAACAC
* * * *
29718180 CTATTGATGGAAATTGAATCTTT-CATACATATAGAATTATAAT
1 CTATTAATGGAAATAGAATCTTTAAATACATATAGAAATATAAT
29718223 CTATTAATGGAAATAGAATCTTTAAATACATATAGAAATATA
1 CTATTAATGGAAATAGAATCTTTAAATACATATAGAAATATA
29718265 TTTGTTTGCA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 21 0.57
44 16 0.43
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (44 bp):
CTATTAATGGAAATAGAATCTTTAAATACATATAGAAATATAAT
Found at i:29722947 original size:2 final size:2
Alignment explanation
Indices: 29722940--29722971 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29722930 GTAAGAACAC
29722940 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
29722972 GGAGGGAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29727945 original size:27 final size:26
Alignment explanation
Indices: 29727892--29727946 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 26
29727882 TAAATTTTAA
*
29727892 AATTATATATGAATTTTAATTTGATAT
1 AATTATATATGAATTTT-ATTTAATAT
29727919 AATTATATACATGAATTTT-TTTAATAT
1 AATTATAT--ATGAATTTTATTTAATAT
29727946 A
1 A
29727947 CTATATGGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 16 0.64
29 9 0.36
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (26 bp):
AATTATATATGAATTTTATTTAATAT
Found at i:29728488 original size:16 final size:16
Alignment explanation
Indices: 29728467--29728518 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
29728457 ATACTTTATA
*
29728467 AAAATTATATTTAATT
1 AAAATTATATATAATT
*
29728483 AAAATTTTATAT-A-T
1 AAAATTATATATAATT
* *
29728497 AAAATTACATAAAATT
1 AAAATTATATATAATT
29728513 AAAATT
1 AAAATT
29728519 TATGTATACA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
14 10 0.34
15 2 0.07
16 17 0.59
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAATTATATATAATT
Found at i:29728521 original size:29 final size:30
Alignment explanation
Indices: 29728479--29728536 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
29728469 AATTATATTT
29728479 AATTAAAATTTTATATATAAAATTACATAA
1 AATTAAAATTTTATATATAAAATTACATAA
* *
29728509 AATTAAAA-TTTATGTATACAATTACATA
1 AATTAAAATTTTATATATAAAATTACATA
29728537 TTAAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (30 bp):
AATTAAAATTTTATATATAAAATTACATAA
Done.