Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 84 of 163
Found at i:23333072 original size:10 final size:10
Alignment explanation
Indices: 23333057--23333118 Score: 54
Period size: 10 Copynumber: 6.0 Consensus size: 10
23333047 ATAATATATA
23333057 TTCTTTCTTT
1 TTCTTTCTTT
23333067 TTCTTTCTTT
1 TTCTTTCTTT
* **
23333077 TTATCAAC-TT
1 TTCT-TTCTTT
23333087 TTCTTTCTTT
1 TTCTTTCTTT
*
23333097 TTTTTCTCTTT
1 TTCTT-TCTTT
23333108 TTCTTTTCTTT
1 TTC-TTTCTTT
23333119 ATGTGACTGA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
9 1 0.03
10 24 0.60
11 13 0.32
12 2 0.05
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (10 bp):
TTCTTTCTTT
Found at i:23333109 original size:21 final size:22
Alignment explanation
Indices: 23333062--23333118 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
23333052 ATATATTCTT
23333062 TCTTTTTCTTTC-TTTTTATCA
1 TCTTTTTCTTTCTTTTTTATCA
* *
23333083 AC-TTTTCTTTCTTTTTTTTC-
1 TCTTTTTCTTTCTTTTTTATCA
23333103 TCTTTTTCTTTTCTTT
1 TCTTTTTC-TTTCTTT
23333119 ATGTGACTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 10 0.33
21 13 0.43
22 7 0.23
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.75
Consensus pattern (22 bp):
TCTTTTTCTTTCTTTTTTATCA
Found at i:23341171 original size:24 final size:24
Alignment explanation
Indices: 23341143--23341194 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
23341133 TGGGTATCTA
*
23341143 CTTGTTTTTCATTTTCATTTTCTT
1 CTTGTTTTTCATTTTCATTTTCCT
*
23341167 CTTGTTTTTCATTTTCTTTTTCCT
1 CTTGTTTTTCATTTTCATTTTCCT
23341191 CTTG
1 CTTG
23341195 AGAACTCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.06, C:0.19, G:0.06, T:0.69
Consensus pattern (24 bp):
CTTGTTTTTCATTTTCATTTTCCT
Found at i:23344759 original size:14 final size:14
Alignment explanation
Indices: 23344740--23344766 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23344730 CACAAAAACT
23344740 GAAATGAAAATAAA
1 GAAATGAAAATAAA
23344754 GAAATGAAAATAA
1 GAAATGAAAATAA
23344767 CTAAAAACCT
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:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (14 bp):
GAAATGAAAATAAA
Found at i:23347715 original size:22 final size:23
Alignment explanation
Indices: 23347678--23347720 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
23347668 TAAAGTGGTC
23347678 CATGAAAATTAAATTAATTAAAG
1 CATGAAAATTAAATTAATTAAAG
* *
23347701 CATG-AAATTATATTATTTAA
1 CATGAAAATTAAATTAATTAA
23347721 TGGACATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (23 bp):
CATGAAAATTAAATTAATTAAAG
Found at i:23354585 original size:21 final size:21
Alignment explanation
Indices: 23354561--23354607 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
23354551 TCAAAGCAAC
* *
23354561 TACAACCTAAAACAAGGGAAT
1 TACAACCCAAAACAAGAGAAT
* *
23354582 TACAACCCACAACAATAGAAT
1 TACAACCCAAAACAAGAGAAT
23354603 TACAA
1 TACAA
23354608 TCAACAAAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.23, G:0.09, T:0.15
Consensus pattern (21 bp):
TACAACCCAAAACAAGAGAAT
Found at i:23360404 original size:18 final size:18
Alignment explanation
Indices: 23360381--23360419 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
23360371 ATAATTTATT
23360381 CTACGCCTACACTAGGGC
1 CTACGCCTACACTAGGGC
23360399 CTACGCCTACACTAGGGC
1 CTACGCCTACACTAGGGC
23360417 CTA
1 CTA
23360420 GAATAGTGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.38, G:0.21, T:0.18
Consensus pattern (18 bp):
CTACGCCTACACTAGGGC
Found at i:23361255 original size:17 final size:17
Alignment explanation
Indices: 23361184--23361255 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
23361174 TGTTAATAAG
* * *
23361184 CATTGTCATCGTATTCC
1 CATTGTCATTGCATTTC
* *
23361201 CATTGTCATTACATTTT
1 CATTGTCATTGCATTTC
* * *
23361218 AATTGTCATAGCATTTG
1 CATTGTCATTGCATTTC
23361235 CATTGTCATTGCATTTC
1 CATTGTCATTGCATTTC
23361252 CATT
1 CATT
23361256 TGTCCTTATA
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.22, C:0.21, G:0.11, T:0.46
Consensus pattern (17 bp):
CATTGTCATTGCATTTC
Found at i:23367805 original size:21 final size:21
Alignment explanation
Indices: 23367761--23367807 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
23367751 GGTTGGTTTG
* * **
23367761 AAGGACAAGAAGAGGAAGTGC
1 AAGGACAAAAAGAAGAAGCAC
23367782 AAGGACAAAAAGAAGAAGCAC
1 AAGGACAAAAAGAAGAAGCAC
23367803 AAGGA
1 AAGGA
23367808 GGAAAGAGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.55, C:0.11, G:0.32, T:0.02
Consensus pattern (21 bp):
AAGGACAAAAAGAAGAAGCAC
Found at i:23377393 original size:12 final size:12
Alignment explanation
Indices: 23377376--23377417 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
23377366 TATCTTCTTG
23377376 TTTTTCATTTTC
1 TTTTTCATTTTC
*
23377388 TTTTTC-TTCTTG
1 TTTTTCATT-TTC
23377400 TTTTTCATTTTC
1 TTTTTCATTTTC
23377412 TTTTTC
1 TTTTTC
23377418 CTCTTGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 2 0.08
12 22 0.85
13 2 0.08
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTTTCATTTTC
Found at i:23377400 original size:24 final size:24
Alignment explanation
Indices: 23377368--23377423 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
23377358 TGTATGGGTA
23377368 TCTTCTTGTTTTTCATTTTCTTTT
1 TCTTCTTGTTTTTCATTTTCTTTT
23377392 TCTTCTTGTTTTTCATTTTCTTTT
1 TCTTCTTGTTTTTCATTTTCTTTT
*
23377416 TCCTCTTG
1 TCTTCTTG
23377424 AGAACTCTCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.04, C:0.20, G:0.05, T:0.71
Consensus pattern (24 bp):
TCTTCTTGTTTTTCATTTTCTTTT
Found at i:23379036 original size:19 final size:19
Alignment explanation
Indices: 23379012--23379049 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
23379002 ACCCACAGAA
23379012 TATTTTT-TTATTTTTCTCG
1 TATTTTTCTT-TTTTTCTCG
23379031 TATTTTTCTTTTTTTCTCG
1 TATTTTTCTTTTTTTCTCG
23379050 ACTTTTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.08, C:0.13, G:0.05, T:0.74
Consensus pattern (19 bp):
TATTTTTCTTTTTTTCTCG
Found at i:23383971 original size:22 final size:23
Alignment explanation
Indices: 23383941--23383983 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
23383931 TAAAGTGGTC
23383941 CATGCAAATTAAATTAATTAAAG
1 CATGCAAATTAAATTAATTAAAG
* *
23383964 CATG-AAATTATATTATTTAA
1 CATGCAAATTAAATTAATTAA
23383984 TGGACATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (23 bp):
CATGCAAATTAAATTAATTAAAG
Found at i:23397440 original size:17 final size:17
Alignment explanation
Indices: 23397386--23397440 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
23397376 ATCGTATTCC
*
23397386 CATTGTCATTACATTTT
1 CATTGTCATTGCATTTT
* * *
23397403 AATTGTCATAGCATTTG
1 CATTGTCATTGCATTTT
23397420 CATTGTCATTGCATTTT
1 CATTGTCATTGCATTTT
23397437 CATT
1 CATT
23397441 TGTCCTTATA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.49
Consensus pattern (17 bp):
CATTGTCATTGCATTTT
Found at i:23406058 original size:22 final size:23
Alignment explanation
Indices: 23406028--23406070 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
23406018 TAAAGTGGGT
23406028 CATGCAAATTAAATTAATTAAAG
1 CATGCAAATTAAATTAATTAAAG
* *
23406051 CATG-AAATTATATTATTTAA
1 CATGCAAATTAAATTAATTAA
23406071 TGGACATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (23 bp):
CATGCAAATTAAATTAATTAAAG
Found at i:23410291 original size:271 final size:271
Alignment explanation
Indices: 23409808--23410347 Score: 936
Period size: 271 Copynumber: 2.0 Consensus size: 271
23409798 GAATCGCGGT
**
23409808 TTTCTTCCTTTTTCGTGGAGGAATTATAATCTGCAAATAATGAACAGGGATGAACAGTAATCAAT
1 TTTCTTCCTTTTTCGAAGAGGAATTATAATCTGCAAATAATGAACAGGGATGAACAGTAATCAAT
* * * * * *
23409873 GGAACAGTGACAGTCAAGAGATACCTTAATCCCAATTTTGTGCTTGCTGATTCACTCGACTATCT
66 AGAACAGTAACAGTCAAGAAATACCTTAATCCCAATTTCGAGCTTGCTGAATCACTCGACTATCT
*
23409938 CTTCAATATTGAACTTGTTACTTCCGTCCTCTTATTCTTTGAAAAATGGGTATGAAAATTTGGGG
131 CTTCAATATTGAACTTGTTACTTCCATCCTCTTATTCTTTGAAAAATGGGTATGAAAATTTGGGG
23410003 GATTTTGGGTATGGTTGAGAGTGGATGAGAGAGTTTGGAGGAGATATAAGTGTTTAAAGAGGTTT
196 GATTTTGGGTATGGTTGAGAGTGGATGAGAGAGTTTGGAGGAGATATAAGTGTTTAAAGAGGTTT
*
23410068 AGGCGTAGGGC
261 AGGCATAGGGC
* *
23410079 TTTCTTCCTTTTTCGAATAGGAATTATAATCTGCAAATATTGAACAGGGATGAACAGTAATCAAT
1 TTTCTTCCTTTTTCGAAGAGGAATTATAATCTGCAAATAATGAACAGGGATGAACAGTAATCAAT
*
23410144 AGAATAGTAACAGTCAAGAAATACCTTAATCCCAATTTCGAGCTTGCTGAATCACTCGACTATCT
66 AGAACAGTAACAGTCAAGAAATACCTTAATCCCAATTTCGAGCTTGCTGAATCACTCGACTATCT
* *
23410209 CTTCAATATTGAACTTGTTACTTCCATCCTCTTATTCTTTGAACAATGGGTATGAAAGTTTGGGG
131 CTTCAATATTGAACTTGTTACTTCCATCCTCTTATTCTTTGAAAAATGGGTATGAAAATTTGGGG
*
23410274 GATTTTGGGTATGGTTGAGAGTTGATGAGAGAGTTTGGAGGAGATATAAGTGTTTAAAGAGGTTT
196 GATTTTGGGTATGGTTGAGAGTGGATGAGAGAGTTTGGAGGAGATATAAGTGTTTAAAGAGGTTT
23410339 AGGCATAGG
261 AGGCATAGG
23410348 TTAGTATTTA
Statistics
Matches: 253, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
271 253 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (271 bp):
TTTCTTCCTTTTTCGAAGAGGAATTATAATCTGCAAATAATGAACAGGGATGAACAGTAATCAAT
AGAACAGTAACAGTCAAGAAATACCTTAATCCCAATTTCGAGCTTGCTGAATCACTCGACTATCT
CTTCAATATTGAACTTGTTACTTCCATCCTCTTATTCTTTGAAAAATGGGTATGAAAATTTGGGG
GATTTTGGGTATGGTTGAGAGTGGATGAGAGAGTTTGGAGGAGATATAAGTGTTTAAAGAGGTTT
AGGCATAGGGC
Found at i:23418891 original size:9 final size:9
Alignment explanation
Indices: 23418879--23418903 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
23418869 TCATAATAAT
23418879 TTTAATTAA
1 TTTAATTAA
23418888 TTTAATTAA
1 TTTAATTAA
23418897 TTTAATT
1 TTTAATT
23418904 TTACTTTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTAATTAA
Found at i:23423571 original size:20 final size:20
Alignment explanation
Indices: 23423522--23423591 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
23423512 ACCATAAAAT
*
23423522 GGTATCGATACCT-TGTCAAG
1 GGTATCGATA-CTATGACAAG
* *
23423542 GGTAAT-GATACTTTGAGGAA-
1 GGT-ATCGATACTATGA-CAAG
23423562 GGTATCGATACTATGACAAG
1 GGTATCGATACTATGACAAG
23423582 GGTATCGATA
1 GGTATCGATA
23423592 ATTTTGATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 6 0.15
20 31 0.76
21 4 0.10
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (20 bp):
GGTATCGATACTATGACAAG
Found at i:23426072 original size:23 final size:22
Alignment explanation
Indices: 23426042--23426085 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
23426032 ATTATAAATA
*
23426042 TTTTTTTTCTTTTCTCTTTCTCT
1 TTTTTTTTC-TTTCTATTTCTCT
23426065 TTTCTTTTTCTTTCTATTTCT
1 TTT-TTTTTCTTTCTATTTCT
23426086 GTGACTGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTTTTTCTTTCTATTTCTCT
Found at i:23431789 original size:19 final size:19
Alignment explanation
Indices: 23431765--23431805 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
23431755 CTAAAATTAC
23431765 TTTGAAGTTTCGTTAAGTA
1 TTTGAAGTTTCGTTAAGTA
23431784 TTTGAAGTTTCGTTAAGTA
1 TTTGAAGTTTCGTTAAGTA
23431803 TTT
1 TTT
23431806 ATCGAGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.05, G:0.20, T:0.51
Consensus pattern (19 bp):
TTTGAAGTTTCGTTAAGTA
Found at i:23438714 original size:19 final size:19
Alignment explanation
Indices: 23438672--23438714 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
23438662 ACATGTTAAG
* * *
23438672 AAAAAAACTTAGAAAATTT
1 AAAAAAAATCAGAAAAATT
*
23438691 TAAAAAAATCAGAAAAATT
1 AAAAAAAATCAGAAAAATT
23438710 AAAAA
1 AAAAA
23438715 CCTTTTAAAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.21
Consensus pattern (19 bp):
AAAAAAAATCAGAAAAATT
Found at i:23440347 original size:26 final size:26
Alignment explanation
Indices: 23440306--23440402 Score: 122
Period size: 26 Copynumber: 3.7 Consensus size: 26
23440296 TTCCGAGTAG
** **
23440306 TAGGCTTTGTTTCGGTGATTACCTAT
1 TAGGCTTTGTGCCGGTGATTATATAT
*
23440332 CAGGCTTTGTGCCGGTGATTATATAT
1 TAGGCTTTGTGCCGGTGATTATATAT
*
23440358 TAGGCTTTGTGCCAGTGATTATATAT
1 TAGGCTTTGTGCCGGTGATTATATAT
* *
23440384 TAGGCTTTGAGCCGATGAT
1 TAGGCTTTGTGCCGGTGAT
23440403 ACAGACTGTA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 61 1.00
ACGTcount: A:0.20, C:0.14, G:0.26, T:0.40
Consensus pattern (26 bp):
TAGGCTTTGTGCCGGTGATTATATAT
Found at i:23441431 original size:21 final size:21
Alignment explanation
Indices: 23441375--23441431 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
23441365 CACAGGTGGA
* *
23441375 CACAGAGGCGTGTGAAGTAGT
1 CACACAGGCGTGTGGAGTAGT
* *
23441396 CAAACGGGCGTGTGGAGTAGT
1 CACACAGGCGTGTGGAGTAGT
23441417 CACACAGGCGTGTGG
1 CACACAGGCGTGTGG
23441432 GAGTGCCACA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.40, T:0.18
Consensus pattern (21 bp):
CACACAGGCGTGTGGAGTAGT
Found at i:23441441 original size:21 final size:21
Alignment explanation
Indices: 23441375--23441442 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
23441365 CACAGGTGGA
* * *
23441375 CACAGAGGCGTGTGAAGTAGT
1 CACACAGGCGTGTGGAGTAGC
* * *
23441396 CAAACGGGCGTGTGGAGTAGT
1 CACACAGGCGTGTGGAGTAGC
23441417 CACACAGGCGTGTGGGAGT-GC
1 CACACAGGCGTGT-GGAGTAGC
23441438 CACAC
1 CACAC
23441443 GAGCTAGGCT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 34 0.87
22 5 0.13
ACGTcount: A:0.25, C:0.21, G:0.38, T:0.16
Consensus pattern (21 bp):
CACACAGGCGTGTGGAGTAGC
Found at i:23449137 original size:20 final size:20
Alignment explanation
Indices: 23449101--23449138 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
23449091 ATTTATGATT
*
23449101 CCTTATTTCTATCTCATTAG
1 CCTTATTTCAATCTCATTAG
*
23449121 CCTTATTTCAATTTCATT
1 CCTTATTTCAATCTCATT
23449139 TCGTATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.03, T:0.53
Consensus pattern (20 bp):
CCTTATTTCAATCTCATTAG
Found at i:23449392 original size:14 final size:14
Alignment explanation
Indices: 23449369--23449405 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
23449359 TTCTATTATA
23449369 TATT-TATATATTC
1 TATTATATATATTC
23449382 TATTATATATATTC
1 TATTATATATATTC
*
23449396 TAATATATAT
1 TATTATATAT
23449406 TAGAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTATATATATTC
Found at i:23449423 original size:20 final size:20
Alignment explanation
Indices: 23449398--23449447 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
23449388 ATATATTCTA
23449398 ATATATATTA-GAATTTATTT
1 ATATATATTATGAATTT-TTT
* *
23449418 ATATATTTTATTAATTTTTT
1 ATATATATTATGAATTTTTT
23449438 ATATAT-TTAT
1 ATATATATTAT
23449448 TTATAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 4 0.15
20 18 0.67
21 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
ATATATATTATGAATTTTTT
Found at i:23449490 original size:22 final size:22
Alignment explanation
Indices: 23449362--23449491 Score: 89
Period size: 22 Copynumber: 6.0 Consensus size: 22
23449352 ATATTAATTC
*
23449362 TATT-ATA-TATTTATATATTC
1 TATTAATATTATTTATATATTA
23449382 TATT-ATATATATTCTA-ATA-TA
1 TATTAATAT-TATT-TATATATTA
*
23449403 TATTAGA-ATTTATTTATATATTT
1 TATTA-ATA-TTATTTATATATTA
23449426 TATTAAT-TT-TTTATATATT-
1 TATTAATATTATTTATATATTA
* * *
23449445 TATTTATAATATATTAGAATATTA
1 TATTAATATTAT-TTA-TATATTA
*
23449469 TATTAATATTATTTTTATATTA
1 TATTAATATTATTTATATATTA
23449491 T
1 T
23449492 TGATATATTT
Statistics
Matches: 87, Mismatches: 9, Indels: 26
0.71 0.07 0.21
Matches are distributed among these distances:
19 6 0.07
20 18 0.21
21 10 0.11
22 26 0.30
23 17 0.20
24 10 0.11
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
TATTAATATTATTTATATATTA
Found at i:23449523 original size:39 final size:39
Alignment explanation
Indices: 23449480--23449556 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
23449470 ATTAATATTA
*
23449480 TTTTTATATTATTGATATATTTCTATTTTATTTATTTCC
1 TTTTTATATTATTGATATATTTCTATTTCATTTATTTCC
* *
23449519 TTTTTATATTATTTATCTATTTCTATTTCATTTATTTC
1 TTTTTATATTATTGATATATTTCTATTTCATTTATTTC
23449557 ATTTGCATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.22, C:0.09, G:0.01, T:0.68
Consensus pattern (39 bp):
TTTTTATATTATTGATATATTTCTATTTCATTTATTTCC
Found at i:23449532 original size:20 final size:19
Alignment explanation
Indices: 23449364--23449553 Score: 72
Period size: 19 Copynumber: 9.7 Consensus size: 19
23449354 ATTAATTCTA
23449364 TTATA-TATTTATATATTCT
1 TTATATTATTTATATATT-T
*
23449383 ATTATATATATTCTA-ATATATA
1 -TTATAT-TATT-TATATAT-TT
*
23449405 TTAGAATTTATTTATATA-TT
1 TTA-TA-TTATTTATATATTT
*
23449425 TTATTAATT-TTT-TATATAT
1 TTA-T-ATTATTTATATATTT
* *
23449444 TTAT-TTA-TAATATATTA
1 TTATATTATTTATATATTT
**
23449461 GAATATTATATTAATATTATTT
1 TTATATTAT-TT-ATA-TATTT
*
23449483 TTATATTATTGATATATTT
1 TTATATTATTTATATATTT
* * * *
23449502 CTATTTTATTTATTTCCTTT
1 TTATATTATTTATAT-ATTT
*
23449522 TTATATTATTTATCTATTT
1 TTATATTATTTATATATTT
*
23449541 CTAT-TTCATTTAT
1 TTATATT-ATTTAT
23449554 TTCATTTGCA
Statistics
Matches: 126, Mismatches: 26, Indels: 37
0.67 0.14 0.20
Matches are distributed among these distances:
16 3 0.02
17 7 0.06
18 10 0.08
19 35 0.28
20 30 0.24
21 10 0.08
22 27 0.21
23 4 0.03
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (19 bp):
TTATATTATTTATATATTT
Found at i:23460638 original size:13 final size:13
Alignment explanation
Indices: 23460620--23460650 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
23460610 TACGACTATA
23460620 ATAGGCTTAATAT
1 ATAGGCTTAATAT
23460633 ATAGGCTTAATAT
1 ATAGGCTTAATAT
23460646 ATAGG
1 ATAGG
23460651 GTGAACTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (13 bp):
ATAGGCTTAATAT
Found at i:23462169 original size:32 final size:33
Alignment explanation
Indices: 23462107--23462179 Score: 112
Period size: 32 Copynumber: 2.2 Consensus size: 33
23462097 ACAAAGCTTT
*
23462107 AAGGGTTTTTCTTGGACAATAAAAGAATAGGATC
1 AAGGG-TTGTCTTGGACAATAAAAGAATAGGATC
*
23462141 AAGGGTTGTCTTGGACAAT-AAAGAATAGGGTC
1 AAGGGTTGTCTTGGACAATAAAAGAATAGGATC
23462173 AAGGGTT
1 AAGGGTT
23462180 TTGATTTCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 19 0.51
33 13 0.35
34 5 0.14
ACGTcount: A:0.36, C:0.08, G:0.29, T:0.27
Consensus pattern (33 bp):
AAGGGTTGTCTTGGACAATAAAAGAATAGGATC
Found at i:23463327 original size:17 final size:17
Alignment explanation
Indices: 23463305--23463340 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
23463295 GTAGAAGTAG
*
23463305 GGAATTGACTCTTGATA
1 GGAATTGACTCCTGATA
23463322 GGAATTGACTCCTGATA
1 GGAATTGACTCCTGATA
23463339 GG
1 GG
23463341 GAACAAGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (17 bp):
GGAATTGACTCCTGATA
Found at i:23469347 original size:104 final size:104
Alignment explanation
Indices: 23469166--23469372 Score: 326
Period size: 104 Copynumber: 2.0 Consensus size: 104
23469156 TGCCAATGCA
*
23469166 GTGCTTACACCACTTTATAATCTAGCGGATGGATGCCTTAAATTAAGGGCTAGTTAGCATTGCTT
1 GTGCTTACACCACTTTATAATCTAGCGGATGGATGACTTAAATTAAGGGCTAGTTAGCATTGCTT
* *
23469231 TTGTTAAGTGATTTTGAGAAGAATG-TTTCTGAAAAGTTG
66 TTGATAAATGATTTTGAGAAGAATGATTT-TGAAAAGTTG
* * * *
23469270 GTGCTTACACCACTTTATAATTTAGCGGATGTATGACTTAGATTAAGGGCTAGTTAGCATTGTTT
1 GTGCTTACACCACTTTATAATCTAGCGGATGGATGACTTAAATTAAGGGCTAGTTAGCATTGCTT
*
23469335 TTGATAAATGATTTTGAGAAGAATGATTTTGAGAAGTT
66 TTGATAAATGATTTTGAGAAGAATGATTTTGAAAAGTT
23469373 CGGTTTGGTT
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
104 91 0.97
105 3 0.03
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.38
Consensus pattern (104 bp):
GTGCTTACACCACTTTATAATCTAGCGGATGGATGACTTAAATTAAGGGCTAGTTAGCATTGCTT
TTGATAAATGATTTTGAGAAGAATGATTTTGAAAAGTTG
Found at i:23469361 original size:15 final size:15
Alignment explanation
Indices: 23469341--23469370 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
23469331 GTTTTTGATA
23469341 AATGATTTTGAGAAG
1 AATGATTTTGAGAAG
23469356 AATGATTTTGAGAAG
1 AATGATTTTGAGAAG
23469371 TTCGGTTTGG
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:0.40, C:0.00, G:0.27, T:0.33
Consensus pattern (15 bp):
AATGATTTTGAGAAG
Found at i:23476295 original size:16 final size:17
Alignment explanation
Indices: 23476274--23476305 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
23476264 AATTGGGTTG
23476274 GGAAAATT-ATTTAATT
1 GGAAAATTAATTTAATT
23476290 GGAAAATTAATTTAAT
1 GGAAAATTAATTTAAT
23476306 AATATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (17 bp):
GGAAAATTAATTTAATT
Found at i:23478336 original size:16 final size:18
Alignment explanation
Indices: 23478317--23478354 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
23478307 TTTACTTCTT
23478317 GTTTAGA-TTAATT-AGA
1 GTTTAGATTTAATTAAGA
*
23478333 GTTTTGATTTAATTAAGA
1 GTTTAGATTTAATTAAGA
23478351 GTTT
1 GTTT
23478355 TATTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 6 0.32
18 7 0.37
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (18 bp):
GTTTAGATTTAATTAAGA
Found at i:23478364 original size:18 final size:17
Alignment explanation
Indices: 23478324--23478361 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
23478314 CTTGTTTAGA
23478324 TTAATTAGAGTTTTGAT
1 TTAATTAGAGTTTTGAT
23478341 TTAATTAAGAGTTTT-AT
1 TTAATT-AGAGTTTTGAT
23478358 TTAA
1 TTAA
23478362 ATTTATTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (17 bp):
TTAATTAGAGTTTTGAT
Found at i:23480179 original size:30 final size:30
Alignment explanation
Indices: 23480145--23480208 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
23480135 ATTATCTCTT
* *
23480145 AAATTCTCTCAAATTCTTAAATCATTCTAA
1 AAATTCTCTCAAATTCTCAAATCACTCTAA
*
23480175 AAATTCTCTCAAATTCTCAAATCACTCTCA
1 AAATTCTCTCAAATTCTCAAATCACTCTAA
23480205 AAAT
1 AAAT
23480209 ATTTTTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.23, G:0.00, T:0.36
Consensus pattern (30 bp):
AAATTCTCTCAAATTCTCAAATCACTCTAA
Found at i:23481036 original size:3 final size:3
Alignment explanation
Indices: 23481028--23481057 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
23481018 TTTTCTTTTA
23481028 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
23481058 TCAACTCACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:23483306 original size:2 final size:2
Alignment explanation
Indices: 23483299--23483328 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
23483289 TTATTCCAAC
23483299 TA TA TA TA TA TA -A 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 T
23483329 CGATTTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23484176 original size:13 final size:13
Alignment explanation
Indices: 23484160--23484184 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23484150 TTTTTTAGGC
23484160 CATTTTCATTTTT
1 CATTTTCATTTTT
23484173 CATTTTCATTTT
1 CATTTTCATTTT
23484185 GGAGAAAACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (13 bp):
CATTTTCATTTTT
Found at i:23484229 original size:56 final size:57
Alignment explanation
Indices: 23484169--23484285 Score: 168
Period size: 56 Copynumber: 2.1 Consensus size: 57
23484159 CCATTTTCAT
* *
23484169 TTTTCATTTTCATTTTGGAGAAAACC-ACATTATTTCCAAATGATTT-C-ATTTTTCCA
1 TTTTCATTTTCATTTTGGAGAAAACCTA-ATCATTTCCAAATG-TTTCCTATTTCTCCA
23484225 TTTTCATTTTCATTTTGGAGAAAACCTTAATCATTTCCAAATGTTTCCTATTTCTCCA
1 TTTTCATTTTCATTTTGGAGAAAACC-TAATCATTTCCAAATGTTTCCTATTTCTCCA
23484283 TTT
1 TTT
23484286 CACCATTTCT
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
56 29 0.53
57 14 0.25
58 12 0.22
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (57 bp):
TTTTCATTTTCATTTTGGAGAAAACCTAATCATTTCCAAATGTTTCCTATTTCTCCA
Found at i:23486178 original size:110 final size:110
Alignment explanation
Indices: 23485876--23486178 Score: 408
Period size: 110 Copynumber: 2.8 Consensus size: 110
23485866 CGACCCCTCA
* * * **
23485876 CAGATAAAAGCTACCAGAGAAAATCGTGGATGCTCCATTCATATAGTCATTGTTGGAATCTACTA
1 CAGATAAAAGTTATCAGAGAAAATCGTGGATGCTTCATTCATATAGTCACAGTTGGAATCTACTA
* * * * *
23485941 ATCTGTGAATATAGATCAGATTGATTGAGGATCCACAATCCCTTG
66 ATTTGTGAATACACAGCGGATTGATTGAGGATCCACAATCCCTTG
* * * * * * * *
23485986 CAAATAAAAGTTGTTAGAGGAAATCATGGATGCTTCATTCATATAGTCACAATTGGAATCCATTA
1 CAGATAAAAGTTATCAGAGAAAATCGTGGATGCTTCATTCATATAGTCACAGTTGGAATCTACTA
23486051 ATTTGTGAATACACAGCGGATTGATTGAGGATCCACAATCCCTTG
66 ATTTGTGAATACACAGCGGATTGATTGAGGATCCACAATCCCTTG
* * **
23486096 CAGATAAAAGTTATCAGAGAAAATCGTGGATGCTTCGTTCATATAGTCGCAGTTGGAATCTGGTA
1 CAGATAAAAGTTATCAGAGAAAATCGTGGATGCTTCATTCATATAGTCACAGTTGGAATCTACTA
23486161 ATTTGTGAATACACAGCG
66 ATTTGTGAATACACAGCG
23486179 AACAAACATA
Statistics
Matches: 164, Mismatches: 29, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
110 164 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (110 bp):
CAGATAAAAGTTATCAGAGAAAATCGTGGATGCTTCATTCATATAGTCACAGTTGGAATCTACTA
ATTTGTGAATACACAGCGGATTGATTGAGGATCCACAATCCCTTG
Found at i:23486697 original size:29 final size:29
Alignment explanation
Indices: 23486662--23486761 Score: 114
Period size: 29 Copynumber: 3.4 Consensus size: 29
23486652 AATTTTTTTG
*
23486662 AAAAATAGTGGCAAAACTATGAAATCTGA
1 AAAAATAGTGGCAAAACTATAAAATCTGA
* *
23486691 AAAAATAGTAGCAGAACTGA-AAAATCT-A
1 AAAAATAGTGGCAAAACT-ATAAAATCTGA
* *
23486719 GAAAACTAGTGGCAAAACTATAAAATTTGA
1 -AAAAATAGTGGCAAAACTATAAAATCTGA
*
23486749 AAAAGTAGTGGCA
1 AAAAATAGTGGCA
23486762 GAATTGTAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
28 2 0.03
29 55 0.93
30 2 0.03
ACGTcount: A:0.52, C:0.10, G:0.18, T:0.20
Consensus pattern (29 bp):
AAAAATAGTGGCAAAACTATAAAATCTGA
Found at i:23486729 original size:58 final size:59
Alignment explanation
Indices: 23486661--23486774 Score: 167
Period size: 58 Copynumber: 1.9 Consensus size: 59
23486651 TAATTTTTTT
*
23486661 GAAAAATAGTGGCAAAACTATGAAATCTGAAAAAATAGTAGCAGAACTG-AAAAATCTA
1 GAAAAATAGTGGCAAAACTATAAAATCTGAAAAAATAGTAGCAGAACTGTAAAAATCTA
* * * * *
23486719 GAAAACTAGTGGCAAAACTATAAAATTTGAAAAAGTAGTGGCAGAATTGTAAAAAT
1 GAAAAATAGTGGCAAAACTATAAAATCTGAAAAAATAGTAGCAGAACTGTAAAAAT
23486775 TGTAAAATCT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
58 43 0.88
59 6 0.12
ACGTcount: A:0.52, C:0.09, G:0.18, T:0.21
Consensus pattern (59 bp):
GAAAAATAGTGGCAAAACTATAAAATCTGAAAAAATAGTAGCAGAACTGTAAAAATCTA
Found at i:23486781 original size:29 final size:29
Alignment explanation
Indices: 23486659--23486781 Score: 92
Period size: 29 Copynumber: 4.3 Consensus size: 29
23486649 TGTAATTTTT
*
23486659 TTGAAAAA-TAGTGGCAAAACTAT-GAAA
1 TTGAAAAACTAGTGGCAAAACTATAAAAA
* * * *
23486686 TCTGAAAAAATAGTAGCAGAACT-GAAAAA
1 T-TGAAAAACTAGTGGCAAAACTATAAAAA
*
23486715 TCT-AGAAAACTAGTGGCAAAACTATAAAAT
1 T-TGA-AAAACTAGTGGCAAAACTATAAAAA
* * * *
23486745 TTGAAAAAGTAGTGGCAGAATTGTAAAAA
1 TTGAAAAACTAGTGGCAAAACTATAAAAA
*
23486774 TTGTAAAA
1 TTGAAAAA
23486782 TCTAAAAAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
27 1 0.01
28 8 0.11
29 60 0.80
30 6 0.08
ACGTcount: A:0.51, C:0.08, G:0.18, T:0.23
Consensus pattern (29 bp):
TTGAAAAACTAGTGGCAAAACTATAAAAA
Found at i:23487273 original size:32 final size:33
Alignment explanation
Indices: 23487235--23487305 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
23487225 GAAAGAAAGA
*
23487235 TAAATTCT-TTTAGGATT-TGAAAAGGATTAATT
1 TAAATTCTAGTTAGGATTGT-AAAAGGATTAATT
*
23487267 TGAATTCTAGTTAGGATTGTAAAAGGATTAATT
1 TAAATTCTAGTTAGGATTGTAAAAGGATTAATT
23487300 TAAATT
1 TAAATT
23487306 TTAAATTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 7 0.21
33 26 0.76
34 1 0.03
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.42
Consensus pattern (33 bp):
TAAATTCTAGTTAGGATTGTAAAAGGATTAATT
Found at i:23487454 original size:14 final size:14
Alignment explanation
Indices: 23487432--23487464 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
23487422 AAATAAGATT
*
23487432 ATTCTTACATAAGG
1 ATTCCTACATAAGG
23487446 ATTCCTACATAAGG
1 ATTCCTACATAAGG
23487460 ATTCC
1 ATTCC
23487465 CAAGTTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (14 bp):
ATTCCTACATAAGG
Found at i:23497413 original size:17 final size:17
Alignment explanation
Indices: 23497371--23497413 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
23497361 AAATAAACTA
*
23497371 ACAAGTAAAATGCAACG
1 ACAACTAAAATGCAACG
* *
23497388 ATAACTAAAATGCAATG
1 ACAACTAAAATGCAACG
*
23497405 ACAATTAAA
1 ACAACTAAA
23497414 TGAGATGCAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.56, C:0.14, G:0.12, T:0.19
Consensus pattern (17 bp):
ACAACTAAAATGCAACG
Found at i:23497538 original size:21 final size:21
Alignment explanation
Indices: 23497514--23497558 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
23497504 GGGAGCTCTT
23497514 CTTTACGCTTT-TTTTCTTGTC
1 CTTT-CGCTTTCTTTTCTTGTC
* *
23497535 CTTTCTCTTTCTTTTCTTTTC
1 CTTTCGCTTTCTTTTCTTGTC
23497556 CTT
1 CTT
23497559 GGAGTCAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.02, C:0.27, G:0.04, T:0.67
Consensus pattern (21 bp):
CTTTCGCTTTCTTTTCTTGTC
Found at i:23503437 original size:18 final size:18
Alignment explanation
Indices: 23503414--23503448 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
23503404 AAGGATTCGG
23503414 TTACGTCGACATGGGCAA
1 TTACGTCGACATGGGCAA
23503432 TTACGTCGACATGGGCA
1 TTACGTCGACATGGGCA
23503449 GTTGCATCGA
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:0.26, C:0.23, G:0.29, T:0.23
Consensus pattern (18 bp):
TTACGTCGACATGGGCAA
Found at i:23503458 original size:18 final size:18
Alignment explanation
Indices: 23503414--23503461 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
23503404 AAGGATTCGG
*
23503414 TTACGTCGACATGGGCAA
1 TTACATCGACATGGGCAA
* *
23503432 TTACGTCGACATGGGCAG
1 TTACATCGACATGGGCAA
*
23503450 TTGCATCGACAT
1 TTACATCGACAT
23503462 CTTTGTTGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (18 bp):
TTACATCGACATGGGCAA
Found at i:23506983 original size:50 final size:50
Alignment explanation
Indices: 23506927--23507023 Score: 185
Period size: 50 Copynumber: 1.9 Consensus size: 50
23506917 TACGAGAGGC
*
23506927 AGTAGCCAAAGGAATTGTAGATGTTATGAAAGTAGCTTCTGAAGATAGGT
1 AGTAGCCAAAGGAATTGTAGATGTTATGAAAGTAGCTCCTGAAGATAGGT
23506977 AGTAGCCAAAGGAATTGTAGATGTTATGAAAGTAGCTCCTGAAGATA
1 AGTAGCCAAAGGAATTGTAGATGTTATGAAAGTAGCTCCTGAAGATA
23507024 ACCTTGCGGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.37, C:0.09, G:0.27, T:0.27
Consensus pattern (50 bp):
AGTAGCCAAAGGAATTGTAGATGTTATGAAAGTAGCTCCTGAAGATAGGT
Found at i:23519595 original size:20 final size:21
Alignment explanation
Indices: 23519559--23519608 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
23519549 TCATTTAGCT
*
23519559 TTAATT-AATCATTTTTA-ATC
1 TTAATTAAATCATATTTACA-C
23519579 TTAATTAAATC-TATTTACAC
1 TTAATTAAATCATATTTACAC
23519599 TTAATATAAA
1 TTAAT-TAAA
23519609 CCATGTCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAATTAAATCATATTTACAC
Found at i:23526375 original size:20 final size:21
Alignment explanation
Indices: 23526339--23526388 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
23526329 TCATTAAGCT
*
23526339 TTAATT-AATCATTTTTA-ATC
1 TTAATTAAATCATATTTACA-C
23526359 TTAATTAAATC-TATTTACAC
1 TTAATTAAATCATATTTACAC
23526379 TTAATATAAA
1 TTAAT-TAAA
23526389 CCATGCCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAATTAAATCATATTTACAC
Found at i:23528969 original size:11 final size:11
Alignment explanation
Indices: 23528897--23528971 Score: 50
Period size: 11 Copynumber: 6.7 Consensus size: 11
23528887 ATTCCAAAAA
*
23528897 AATATTATTTT
1 AATATTAATTT
23528908 AATAGTTTAATATT
1 AATA--TTAAT-TT
23528922 AA-ATTTAATTT
1 AATA-TTAATTT
*
23528933 AATACTTATTTT
1 AATA-TTAATTT
*
23528945 AGTATT-ATTT
1 AATATTAATTT
23528955 --TATTAATTT
1 AATATTAATTT
23528964 AATATTAA
1 AATATTAA
23528972 AGTGATTATC
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
8 4 0.08
9 4 0.08
10 3 0.06
11 16 0.31
12 16 0.31
13 5 0.10
14 4 0.08
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (11 bp):
AATATTAATTT
Found at i:23537817 original size:20 final size:20
Alignment explanation
Indices: 23537764--23537818 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
23537754 TTTTCTTTAA
*
23537764 TTTATAATT-AAATATAATT
1 TTTATATTTAAAATATAATT
*
23537783 TTTATGATATAAAATA-AATAT
1 TTTAT-ATTTAAAATATAAT-T
23537804 TTTATATTTAAAATA
1 TTTATATTTAAAATA
23537819 GTGAGAGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 5 0.17
20 14 0.47
21 11 0.37
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TTTATATTTAAAATATAATT
Found at i:23541471 original size:1 final size:1
Alignment explanation
Indices: 23541465--23541489 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
23541455 TGCATTTTGC
23541465 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
23541490 TCGTTGGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:23556743 original size:15 final size:15
Alignment explanation
Indices: 23556652--23556746 Score: 57
Period size: 15 Copynumber: 6.3 Consensus size: 15
23556642 GATCGATCAG
* *
23556652 TGCTCGCAACTTTCA
1 TGCTCGCAACATCCA
* *
23556667 TGCTCACAATATCCA
1 TGCTCGCAACATCCA
* *
23556682 CGCTTGCAACATCCA
1 TGCTCGCAACATCCA
* ** *
23556697 TGATCGCAATGT-TA
1 TGCTCGCAACATCCA
** *
23556711 GTGCTCGCAATTTTCA
1 -TGCTCGCAACATCCA
23556727 TGCTCGCAACATCCA
1 TGCTCGCAACATCCA
23556742 TGCTC
1 TGCTC
23556747 ACATTATTCA
Statistics
Matches: 58, Mismatches: 20, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
14 1 0.02
15 56 0.97
16 1 0.02
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (15 bp):
TGCTCGCAACATCCA
Found at i:23556764 original size:60 final size:61
Alignment explanation
Indices: 23556650--23556870 Score: 184
Period size: 60 Copynumber: 3.7 Consensus size: 61
23556640 TGGATCGATC
* * * * * ** * *
23556650 AGTGCTCGCAACTTTCATGCTCACAATATCCACGCTTGCAACATCCATGATCGC-A-ATGTT
1 AGTGCTCGCAATTTTCATGCTCGCAACATCCATGCTCGCATTATTCATGTTCGCAACATG-T
*
23556710 AGTGCTCGCAATTTTCATGCTCGCAACATCCATGCTCACATTATTCATGTTCGCAACATGT
1 AGTGCTCGCAATTTTCATGCTCGCAACATCCATGCTCGCATTATTCATGTTCGCAACATGT
* * * ** *
23556771 A-TGCTCACACTTTTCATGTTCGCAACATGTATGCTCGCACTT-TTCATGTTCGTAACATGT
1 AGTGCTCGCAATTTTCATGCTCGCAACATCCATGCTCGCA-TTATTCATGTTCGCAACATGT
* * * * *
23556831 A-TGCTCACACTTTTCATGTTTGC-ACTATTCATGCTCGCAT
1 AGTGCTCGCAATTTTCATGCTCGCAAC-ATCCATGCTCGCAT
23556871 CATCCCCTCC
Statistics
Matches: 137, Mismatches: 20, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
59 3 0.02
60 126 0.92
61 5 0.04
62 3 0.02
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34
Consensus pattern (61 bp):
AGTGCTCGCAATTTTCATGCTCGCAACATCCATGCTCGCATTATTCATGTTCGCAACATGT
Found at i:23556866 original size:30 final size:30
Alignment explanation
Indices: 23556712--23556850 Score: 199
Period size: 30 Copynumber: 4.6 Consensus size: 30
23556702 GCAATGTTAG
* * * **
23556712 TGCTCGCAATTTTCATGCTCGCAACATCCA
1 TGCTCACACTTTTCATGTTCGCAACATGTA
23556742 TGCTCACA-TTATTCATGTTCGCAACATGTA
1 TGCTCACACTT-TTCATGTTCGCAACATGTA
23556772 TGCTCACACTTTTCATGTTCGCAACATGTA
1 TGCTCACACTTTTCATGTTCGCAACATGTA
* *
23556802 TGCTCGCACTTTTCATGTTCGTAACATGTA
1 TGCTCACACTTTTCATGTTCGCAACATGTA
23556832 TGCTCACACTTTTCATGTT
1 TGCTCACACTTTTCATGTT
23556851 TGCACTATTC
Statistics
Matches: 100, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
29 2 0.02
30 96 0.96
31 2 0.02
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.37
Consensus pattern (30 bp):
TGCTCACACTTTTCATGTTCGCAACATGTA
Found at i:23560064 original size:15 final size:15
Alignment explanation
Indices: 23560042--23560244 Score: 96
Period size: 15 Copynumber: 13.5 Consensus size: 15
23560032 TGGTTGGGTC
23560042 CATGCTCGCAACATT
1 CATGCTCGCAACATT
*
23560057 -AGTGCTCGTAACATT
1 CA-TGCTCGCAACATT
* *
23560072 CATGCTCTCAACGTT
1 CATGCTCGCAACATT
*
23560087 -AGTGCTCGCAACTTT
1 CA-TGCTCGCAACATT
* *
23560102 CATGCTCGCAATATC
1 CATGCTCGCAACATT
* **
23560117 CATGCTCACATTATT
1 CATGCTCGCAACATT
*
23560132 CATGTTCGCAACATGT
1 CATGCTCGCAACAT-T
*
23560148 -ATGCTCGC-ACTTTT
1 CATGCTCGCAAC-ATT
* *
23560162 CATGTTTGCAACATGT
1 CATGCTCGCAACAT-T
* *
23560178 -ACGCTCGC-ACTTTT
1 CATGCTCGCAAC-ATT
* * *
23560192 CATGTTCGCAATATC
1 CATGCTCGCAACATT
* **
23560207 CATGCTCACATTATT
1 CATGCTCGCAACATT
*
23560222 CATGTTCGCAACATGT
1 CATGCTCGCAACAT-T
23560238 -ATGCTCG
1 CATGCTCG
23560245 TACTTTTCAT
Statistics
Matches: 136, Mismatches: 39, Indels: 26
0.68 0.19 0.13
Matches are distributed among these distances:
14 8 0.06
15 120 0.88
16 8 0.06
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.34
Consensus pattern (15 bp):
CATGCTCGCAACATT
Found at i:23560078 original size:30 final size:30
Alignment explanation
Indices: 23560042--23560156 Score: 108
Period size: 30 Copynumber: 3.8 Consensus size: 30
23560032 TGGTTGGGTC
*
23560042 CATGCTCGCAACATTAGTGCTCGTAACATT
1 CATGCTCGCAACATTAGTGCTCGCAACATT
* * *
23560072 CATGCTCTCAACGTTAGTGCTCGCAACTTT
1 CATGCTCGCAACATTAGTGCTCGCAACATT
* * * **
23560102 CATGCTCGCAATATCCA-TGCTCACATTATT
1 CATGCTCGCAACAT-TAGTGCTCGCAACATT
*
23560132 CATGTTCGCAACATGTA-TGCTCGCA
1 CATGCTCGCAACAT-TAGTGCTCGCA
23560157 CTTTTCATGT
Statistics
Matches: 67, Mismatches: 17, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
30 66 0.99
31 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (30 bp):
CATGCTCGCAACATTAGTGCTCGCAACATT
Found at i:23560164 original size:30 final size:30
Alignment explanation
Indices: 23560089--23560291 Score: 214
Period size: 30 Copynumber: 6.8 Consensus size: 30
23560079 TCAACGTTAG
* * **
23560089 TGCTCGCAAC-TTTCATGCTCGCAATATCCA
1 TGCTCGC-ACTTTTCATGTTCGCAACATGTA
*
23560119 TGCTCACA-TTATTCATGTTCGCAACATGTA
1 TGCTCGCACTT-TTCATGTTCGCAACATGTA
*
23560149 TGCTCGCACTTTTCATGTTTGCAACATGTA
1 TGCTCGCACTTTTCATGTTCGCAACATGTA
* * **
23560179 CGCTCGCACTTTTCATGTTCGCAATATCCA
1 TGCTCGCACTTTTCATGTTCGCAACATGTA
*
23560209 TGCTCACA-TTATTCATGTTCGCAACATGTA
1 TGCTCGCACTT-TTCATGTTCGCAACATGTA
* * *
23560239 TGCTCGTACTTTTCATGTTTGTAACATGTA
1 TGCTCGCACTTTTCATGTTCGCAACATGTA
* *
23560269 CGCTCACACTTTTCATGTTCGCA
1 TGCTCGCACTTTTCATGTTCGCA
23560292 CTATTCATGC
Statistics
Matches: 142, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
29 4 0.03
30 134 0.94
31 4 0.03
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.37
Consensus pattern (30 bp):
TGCTCGCACTTTTCATGTTCGCAACATGTA
Found at i:23560201 original size:90 final size:90
Alignment explanation
Indices: 23560090--23560303 Score: 358
Period size: 90 Copynumber: 2.4 Consensus size: 90
23560080 CAACGTTAGT
*
23560090 GCTCGCAAC-TTTCATGCTCGCAATATCCATGCTCACATTATTCATGTTCGCAACATGTATGCTC
1 GCTCGC-ACTTTTCATGTTCGCAATATCCATGCTCACATTATTCATGTTCGCAACATGTATGCTC
23560154 GCACTTTTCATGTTTGCAACATGTAC
65 GCACTTTTCATGTTTGCAACATGTAC
23560180 GCTCGCACTTTTCATGTTCGCAATATCCATGCTCACATTATTCATGTTCGCAACATGTATGCTCG
1 GCTCGCACTTTTCATGTTCGCAATATCCATGCTCACATTATTCATGTTCGCAACATGTATGCTCG
* *
23560245 TACTTTTCATGTTTGTAACATGTAC
66 CACTTTTCATGTTTGCAACATGTAC
* * *
23560270 GCTCACACTTTTCATGTTCGCACTATTCATGCTC
1 GCTCGCACTTTTCATGTTCGCAATATCCATGCTC
23560304 GCATCAAACC
Statistics
Matches: 117, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
89 2 0.02
90 115 0.98
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.37
Consensus pattern (90 bp):
GCTCGCACTTTTCATGTTCGCAATATCCATGCTCACATTATTCATGTTCGCAACATGTATGCTCG
CACTTTTCATGTTTGCAACATGTAC
Found at i:23561366 original size:12 final size:12
Alignment explanation
Indices: 23561349--23561374 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
23561339 TACATATACT
23561349 TAACATATCATC
1 TAACATATCATC
23561361 TAACATATCATC
1 TAACATATCATC
23561373 TA
1 TA
23561375 TCAACTCTCG
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:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (12 bp):
TAACATATCATC
Found at i:23568309 original size:16 final size:16
Alignment explanation
Indices: 23568288--23568318 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23568278 ATAATGTGAA
23568288 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
23568304 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
23568319 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:23569154 original size:26 final size:26
Alignment explanation
Indices: 23569112--23569165 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
23569102 ATTCTGGGCG
23569112 CAATTCTGGACACGTTCATGCAGCGA
1 CAATTCTGGACACGTTCATGCAGCGA
* *
23569138 CAATTCTGTACATGTTCATGCAGCGA
1 CAATTCTGGACACGTTCATGCAGCGA
23569164 CA
1 CA
23569166 TTACTAGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (26 bp):
CAATTCTGGACACGTTCATGCAGCGA
Found at i:23569196 original size:37 final size:38
Alignment explanation
Indices: 23569155--23569242 Score: 101
Period size: 38 Copynumber: 2.3 Consensus size: 38
23569145 GTACATGTTC
*
23569155 ATGCAGCGACA-TTACTAGG-TGCAA-TTGAAGAATACTT
1 ATGCAGCGACAGTT-CT-GGATGCAATTTAAAGAATACTT
* *
23569192 ATGCAGCGATAGTTCTGGATGCAATTTAAAGAATATTT
1 ATGCAGCGACAGTTCTGGATGCAATTTAAAGAATACTT
*
23569230 ATGCAGTGACAGT
1 ATGCAGCGACAGT
23569243 CTTGGGCGCA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
36 2 0.05
37 17 0.40
38 24 0.56
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (38 bp):
ATGCAGCGACAGTTCTGGATGCAATTTAAAGAATACTT
Found at i:23569320 original size:37 final size:36
Alignment explanation
Indices: 23569279--23569371 Score: 96
Period size: 37 Copynumber: 2.5 Consensus size: 36
23569269 GTGGCAACAG
* *
23569279 TTTTGGGTGCAATTTGGAAGTACTCATGCGGCGATAA
1 TTTTGGGTGCAATTTAGAAGTACTCATGCAGCGA-AA
* * * *
23569316 TTTTGGGTGTAATCTAGAAGTGCTCATGCAGCGACA
1 TTTTGGGTGCAATTTAGAAGTACTCATGCAGCGAAA
*
23569352 TGTTTAGGTGCAATTCTAGA
1 T-TTTGGGTGCAATT-TAGA
23569372 TTAAAATTAC
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
36 2 0.04
37 39 0.87
38 4 0.09
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (36 bp):
TTTTGGGTGCAATTTAGAAGTACTCATGCAGCGAAA
Found at i:23572056 original size:14 final size:15
Alignment explanation
Indices: 23572024--23572063 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
23572014 TTAAAAAAAT
23572024 ATTTTTCTTTTACAA
1 ATTTTTCTTTTACAA
*
23572039 ATTTTTCTTTTA-AC
1 ATTTTTCTTTTACAA
*
23572053 ATTTTTATTTT
1 ATTTTTCTTTT
23572064 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTTTCTTTTACAA
Found at i:23573318 original size:26 final size:26
Alignment explanation
Indices: 23573215--23573321 Score: 90
Period size: 26 Copynumber: 4.1 Consensus size: 26
23573205 AATTCTGGGC
* *
23573215 ACAATTCTAGAGATGCTCATACAGCG
1 ACAATTCTAGACATGCTCATGCAGCG
* * **
23573241 ACAACTCTGGACATTTTCATGCAGCG
1 ACAATTCTAGACATGCTCATGCAGCG
* * * * * *
23573267 ATAATTCTGGATAAGTTTCA-GTAGCG
1 ACAATTCTAGACATG-CTCATGCAGCG
23573293 ACAATTCTAGACATGCTCATGCAGCG
1 ACAATTCTAGACATGCTCATGCAGCG
23573319 ACA
1 ACA
23573322 TTAGTAGTAA
Statistics
Matches: 61, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
25 3 0.05
26 54 0.89
27 4 0.07
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (26 bp):
ACAATTCTAGACATGCTCATGCAGCG
Found at i:23594789 original size:15 final size:16
Alignment explanation
Indices: 23594769--23594802 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
23594759 CATTAAATTC
*
23594769 TTTTTATTC-CTTTTA
1 TTTTTATTCTCTTATA
23594784 TTTTTATTCTCTTATA
1 TTTTTATTCTCTTATA
23594800 TTT
1 TTT
23594803 AGCTTTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTATTCTCTTATA
Found at i:23598716 original size:28 final size:28
Alignment explanation
Indices: 23598658--23598717 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
23598648 AAATGAGGGC
** *
23598658 AAACAAAAACATGTTATGACAAAAACAA
1 AAACAAAAACACATTATCACAAAAACAA
*
23598686 AAACAAAAACACATATATCACAAAAATAA
1 AAACAAAAACACAT-TATCACAAAAACAA
23598715 AAA
1 AAA
23598718 AAATTTGGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.68, C:0.15, G:0.03, T:0.13
Consensus pattern (28 bp):
AAACAAAAACACATTATCACAAAAACAA
Found at i:23600229 original size:319 final size:319
Alignment explanation
Indices: 23599650--23600294 Score: 1281
Period size: 319 Copynumber: 2.0 Consensus size: 319
23599640 TGTACTCTTA
23599650 ATTTTTGAGACTAAATGATATCTTATTCAAGCTTGCTTTTACTGTTTAATCTTTGAGTTTGATTG
1 ATTTTTGAGACTAAATGATATCTTATTCAAGCTTGCTTTTACTGTTTAATCTTTGAGTTTGATTG
23599715 TTTTCTTAGTTTTCCTAGGAATAGTATTCTTAGTTTTCTACTGACTATTTATGTCAGGGACCCTA
66 TTTTCTTAGTTTTCCTAGGAATAGTATTCTTAGTTTTCTACTGACTATTTATGTCAGGGACCCTA
23599780 TTTCATTATTACTGCATTACTTCTTTAATTTTACATTATTGCTTCGATAATTCAATCTCACAATT
131 TTTCATTATTACTGCATTACTTCTTTAATTTTACATTATTGCTTCGATAATTCAATCTCACAATT
23599845 TTATTTCATTTACTTGTTCATTGCACTGACAATTATAGACAACAAACATCCATCATCGTAGGATC
196 TTATTTCATTTACTTGTTCATTGCACTGACAATTATAGACAACAAACATCCATCATCGTAGGATC
23599910 GATATCTGATAGGTTACATATCTGTCTACTATACTTGCATTGACAGTGTACGCTTGCAC
261 GATATCTGATAGGTTACATATCTGTCTACTATACTTGCATTGACAGTGTACGCTTGCAC
23599969 ATTTTTGAGACTAAATGATATCTTATTCAAGCTTGCTTTTACTGTTTAATCTTTGAGTTTGATTG
1 ATTTTTGAGACTAAATGATATCTTATTCAAGCTTGCTTTTACTGTTTAATCTTTGAGTTTGATTG
23600034 TTTTCTTAGTTTTCCTAGGAATAGTATTCTTAGTTTTCTACTGACTATTTATGTCAGGGACCCTA
66 TTTTCTTAGTTTTCCTAGGAATAGTATTCTTAGTTTTCTACTGACTATTTATGTCAGGGACCCTA
23600099 TTTCATTATTACTGCATTACTTCTTTAATTTTACATTATTGCTTCGATAATTCAATCTCACAATT
131 TTTCATTATTACTGCATTACTTCTTTAATTTTACATTATTGCTTCGATAATTCAATCTCACAATT
23600164 TTATTTCATTTACTTGTTCATTGCACTGACAATTATAGACAACAAACATCCATCATCGTAGGATC
196 TTATTTCATTTACTTGTTCATTGCACTGACAATTATAGACAACAAACATCCATCATCGTAGGATC
23600229 GATATCTGATAGGTTACATATCTGTCTACTATACTTGCATTGACAGTGTACGCTTGCAC
261 GATATCTGATAGGTTACATATCTGTCTACTATACTTGCATTGACAGTGTACGCTTGCAC
*
23600288 ATATTTG
1 ATTTTTG
23600295 CTGTGATCTT
Statistics
Matches: 325, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
319 325 1.00
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.43
Consensus pattern (319 bp):
ATTTTTGAGACTAAATGATATCTTATTCAAGCTTGCTTTTACTGTTTAATCTTTGAGTTTGATTG
TTTTCTTAGTTTTCCTAGGAATAGTATTCTTAGTTTTCTACTGACTATTTATGTCAGGGACCCTA
TTTCATTATTACTGCATTACTTCTTTAATTTTACATTATTGCTTCGATAATTCAATCTCACAATT
TTATTTCATTTACTTGTTCATTGCACTGACAATTATAGACAACAAACATCCATCATCGTAGGATC
GATATCTGATAGGTTACATATCTGTCTACTATACTTGCATTGACAGTGTACGCTTGCAC
Found at i:23629966 original size:3 final size:3
Alignment explanation
Indices: 23629958--23629986 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
23629948 CTCGTCATGA
23629958 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
23629987 GTTATTATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:23644395 original size:20 final size:21
Alignment explanation
Indices: 23644357--23644396 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
23644347 CTTAACAACA
23644357 CTTTAGAACAACCTCCAAATT
1 CTTTAGAACAACCTCCAAATT
23644378 CTTTA-AACAATCCT-CAAAT
1 CTTTAGAACAA-CCTCCAAAT
23644397 GTATCTCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.40, C:0.28, G:0.03, T:0.30
Consensus pattern (21 bp):
CTTTAGAACAACCTCCAAATT
Found at i:23653661 original size:18 final size:17
Alignment explanation
Indices: 23653638--23653689 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
23653628 TAACAATTTT
23653638 TTTCTTCTTCTTTTCTCA
1 TTTCTTCTTCTTTTCT-A
*
23653656 TTTCTTCTTC-TTTCTT
1 TTTCTTCTTCTTTTCTA
23653672 TTTCTTC-TCTTTT-TA
1 TTTCTTCTTCTTTTCTA
23653687 TTT
1 TTT
23653690 TATAAGTGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 6 0.19
16 10 0.32
17 5 0.16
18 10 0.32
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTCTTCTTCTTTTCTA
Found at i:23654310 original size:18 final size:18
Alignment explanation
Indices: 23654255--23654302 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
23654245 ATGCAACTAC
23654255 AATGCAAATGCACTAAAT-AA
1 AATGC-AATG-AC-AAATAAA
*
23654275 AATGCAGTGACAAATAAA
1 AATGCAATGACAAATAAA
23654293 AATGCAATGA
1 AATGCAATGA
23654303 TAACTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 4 0.16
18 13 0.52
19 3 0.12
20 5 0.20
ACGTcount: A:0.54, C:0.12, G:0.15, T:0.19
Consensus pattern (18 bp):
AATGCAATGACAAATAAA
Found at i:23660973 original size:15 final size:14
Alignment explanation
Indices: 23660949--23660980 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
23660939 CTATTGATTA
23660949 TTGTTATAACTCCC
1 TTGTTATAACTCCC
23660963 TTGTCTATAACTCCC
1 TTGT-TATAACTCCC
23660978 TTG
1 TTG
23660981 CTGTGAGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (14 bp):
TTGTTATAACTCCC
Found at i:23665603 original size:15 final size:16
Alignment explanation
Indices: 23665570--23665613 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
23665560 TTTAAAAAGA
*
23665570 AAAAGAAAAAAATGTT
1 AAAAGAAAAATATGTT
*
23665586 AAAAGAAAAATTTG-T
1 AAAAGAAAAATATGTT
23665601 AAAAGGAAAAATA
1 AAAA-GAAAAATA
23665614 GTTTTTTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (16 bp):
AAAAGAAAAATATGTT
Found at i:23671586 original size:16 final size:17
Alignment explanation
Indices: 23671565--23671600 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
23671555 AGATGATTAT
*
23671565 ATAAAAAATTTA-AAAA
1 ATAAAAAATGTATAAAA
23671581 ATAAAAAATGTATAAAA
1 ATAAAAAATGTATAAAA
23671598 ATA
1 ATA
23671601 TTAAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (17 bp):
ATAAAAAATGTATAAAA
Found at i:23671634 original size:22 final size:25
Alignment explanation
Indices: 23671594--23671638 Score: 69
Period size: 22 Copynumber: 1.9 Consensus size: 25
23671584 AAAAATGTAT
23671594 AAAAATATTAAATATTAAATATTAA
1 AAAAATATTAAATATTAAATATTAA
23671619 AAAAATA-T-AATA-TAAATATT
1 AAAAATATTAAATATTAAATATT
23671639 TTTTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 4 0.20
24 1 0.05
25 7 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
AAAAATATTAAATATTAAATATTAA
Found at i:23675707 original size:81 final size:83
Alignment explanation
Indices: 23675582--23675747 Score: 318
Period size: 81 Copynumber: 2.0 Consensus size: 83
23675572 AATGTTTGTT
23675582 AATATTTGTCAAGTTAACATATTTTTTTTTTATTAATCATATGTTATACTACATGGAGACAACCT
1 AATATTTGTCAAGTTAACATATTTTTTTTTTATTAATCATATGTTATACTACATGGAGACAACCT
23675647 AATCAATTTGTCAAATTG
66 AATCAATTTGTCAAATTG
23675665 AATATTTGT-AAGTTAACATA-TTTTTTTTTATTAATCATATGTTATACTACATGGAGACAACCT
1 AATATTTGTCAAGTTAACATATTTTTTTTTTATTAATCATATGTTATACTACATGGAGACAACCT
23675728 AATCAATTTGTCAAATTG
66 AATCAATTTGTCAAATTG
23675746 AA
1 AA
23675748 AAAATATTGA
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
81 63 0.76
82 11 0.13
83 9 0.11
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (83 bp):
AATATTTGTCAAGTTAACATATTTTTTTTTTATTAATCATATGTTATACTACATGGAGACAACCT
AATCAATTTGTCAAATTG
Found at i:23678235 original size:3 final size:3
Alignment explanation
Indices: 23678227--23678267 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
23678217 TTTTTGTCAT
23678227 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
23678268 TTTAAAGTGG
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:23684729 original size:17 final size:19
Alignment explanation
Indices: 23684709--23684743 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
23684699 GTTTCAATTT
23684709 TAAAA-AATATTT-TAATA
1 TAAAACAATATTTGTAATA
23684726 TAAAACAATATTTGTAAT
1 TAAAACAATATTTGTAAT
23684744 GCTTTTAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 7 0.44
19 4 0.25
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (19 bp):
TAAAACAATATTTGTAATA
Found at i:23688461 original size:16 final size:17
Alignment explanation
Indices: 23688437--23688471 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
23688427 ATAAACCAAG
*
23688437 TACTTAAAA-TAAATGA
1 TACTGAAAAGTAAATGA
23688453 TACTGAAAAGTAAATGA
1 TACTGAAAAGTAAATGA
23688470 TA
1 TA
23688472 AACAAAGCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (17 bp):
TACTGAAAAGTAAATGA
Found at i:23689258 original size:27 final size:26
Alignment explanation
Indices: 23689221--23689272 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
23689211 GCTGAGTTAA
23689221 CACTCCAAGATTG-CTGTGACAATAAG
1 CACTCCAAGATTGCCT-TGACAATAAG
23689247 CACTCCCAAGATTGCCTTGACAATAA
1 CACT-CCAAGATTGCCTTGACAATAA
23689273 ACCTTTGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 4 0.17
27 18 0.75
28 2 0.08
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (26 bp):
CACTCCAAGATTGCCTTGACAATAAG
Found at i:23690099 original size:3 final size:3
Alignment explanation
Indices: 23690093--23690131 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
23690083 AGTGATGATT
23690093 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
23690132 AACATAGTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:23703948 original size:7 final size:7
Alignment explanation
Indices: 23703936--23703962 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
23703926 TCTTGATGAT
23703936 TTCTTCA
1 TTCTTCA
23703943 TTCTTCA
1 TTCTTCA
23703950 TTCTTCA
1 TTCTTCA
23703957 TTCTTC
1 TTCTTC
23703963 TATTTATAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.30, G:0.00, T:0.59
Consensus pattern (7 bp):
TTCTTCA
Found at i:23711184 original size:20 final size:20
Alignment explanation
Indices: 23711159--23711201 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
23711149 CTTTGTTGTT
23711159 TTTATTCTTACTCTC-ACAAG
1 TTTATTCTT-CTCTCTACAAG
*
23711179 TTTATTCTTTTCTCTACAAG
1 TTTATTCTTCTCTCTACAAG
23711199 TTT
1 TTT
23711202 CTTTTAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTATTCTTCTCTCTACAAG
Found at i:23713825 original size:10 final size:10
Alignment explanation
Indices: 23713812--23713860 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
23713802 GAAAAATCAC
23713812 AAAAAGAAAG
1 AAAAAGAAAG
23713822 AAAAA-AAAG
1 AAAAAGAAAG
23713831 AAAGAAG-AAG
1 AAA-AAGAAAG
23713841 AAAAGAGAAA-
1 AAAA-AGAAAG
23713851 AGAAAAGAAA
1 A-AAAAGAAA
23713861 TATATTACCA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
9 8 0.24
10 21 0.62
11 5 0.15
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:23713836 original size:17 final size:18
Alignment explanation
Indices: 23713813--23713860 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
23713803 AAAAATCACA
23713813 AAAAGAAAGAAAAAAAAG
1 AAAAGAAAGAAAAAAAAG
*
23713831 -AAAG-AAGAAGAAAAGAG
1 AAAAGAAAGAA-AAAAAAG
23713848 AAAAGAAAAGAAA
1 AAAAG-AAAGAAA
23713861 TATATTACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 5 0.20
17 10 0.40
18 4 0.16
19 1 0.04
20 5 0.20
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAAGAAAGAAAAAAAAG
Found at i:23725912 original size:3 final size:3
Alignment explanation
Indices: 23725904--23725942 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
23725894 CTGCACAGTG
* * *
23725904 CTT CTT CTT CTT CTT CTT CCT CTT CTT CTC CTC CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
23725943 GCACTTTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (3 bp):
CTT
Found at i:23733578 original size:54 final size:54
Alignment explanation
Indices: 23733515--23733624 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
23733505 ATGCATCCTG
23733515 TAGTGCTATTATCTCCAAGGTAATTCCCCCAAAACTAAAGGATCCTGGTAGCTT
1 TAGTGCTATTATCTCCAAGGTAATTCCCCCAAAACTAAAGGATCCTGGTAGCTT
*
23733569 TAGTGCTATTATCTCCAAGGTAATTCCCCCAAAACTGAAGGATCCTGGTAGCTT
1 TAGTGCTATTATCTCCAAGGTAATTCCCCCAAAACTAAAGGATCCTGGTAGCTT
23733623 TA
1 TA
23733625 CTATTCCTAG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (54 bp):
TAGTGCTATTATCTCCAAGGTAATTCCCCCAAAACTAAAGGATCCTGGTAGCTT
Found at i:23734453 original size:22 final size:22
Alignment explanation
Indices: 23734422--23734475 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
23734412 GTTGAGGAAA
*
23734422 ATGTCACGACAAGCACTCCATT
1 ATGTCGCGACAAGCACTCCATT
23734444 ATGTCGCGACAAGCACTCCATT
1 ATGTCGCGACAAGCACTCCATT
23734466 ATGTCGCGAC
1 ATGTCGCGAC
23734476 CTAGAGATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (22 bp):
ATGTCGCGACAAGCACTCCATT
Found at i:23734638 original size:16 final size:17
Alignment explanation
Indices: 23734617--23734650 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
23734607 CTTAAAACCC
*
23734617 TAAATA-CTAACCATTA
1 TAAATATCTAAACATTA
23734633 TAAATATCTAAACATTA
1 TAAATATCTAAACATTA
23734650 T
1 T
23734651 TCTACTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAATATCTAAACATTA
Found at i:23737679 original size:11 final size:11
Alignment explanation
Indices: 23737663--23737689 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
23737653 GAAATCAAGT
23737663 ATTTTCATAAA
1 ATTTTCATAAA
23737674 ATTTTCATAAA
1 ATTTTCATAAA
23737685 ATTTT
1 ATTTT
23737690 GTCGATTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTTTCATAAA
Found at i:23747847 original size:11 final size:11
Alignment explanation
Indices: 23747831--23747857 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
23747821 AGAAGATGAC
23747831 AGAAGTTGTTA
1 AGAAGTTGTTA
23747842 AGAAGTTGTTA
1 AGAAGTTGTTA
23747853 AGAAG
1 AGAAG
23747858 GAAATGGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (11 bp):
AGAAGTTGTTA
Found at i:23753975 original size:38 final size:38
Alignment explanation
Indices: 23753932--23754012 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
23753922 CTGTTTGATG
23753932 TTTGGGGTATGGATTTTATGGGACCATTTCCAAGTTCA
1 TTTGGGGTATGGATTTTATGGGACCATTTCCAAGTTCA
*
23753970 TTTGGGGTATGTATTTTATGGGACCATTTCCAAGTTCA
1 TTTGGGGTATGGATTTTATGGGACCATTTCCAAGTTCA
23754008 TTTGG
1 TTTGG
23754013 ACATCTTTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.20, C:0.12, G:0.26, T:0.42
Consensus pattern (38 bp):
TTTGGGGTATGGATTTTATGGGACCATTTCCAAGTTCA
Found at i:23754988 original size:22 final size:23
Alignment explanation
Indices: 23754962--23755004 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
23754952 ATTAGATCCG
*
23754962 ATTATCGACGC-ATTTGTACTTT
1 ATTATCAACGCAATTTGTACTTT
23754984 ATTATCAACGCAATTTGTACT
1 ATTATCAACGCAATTTGTACT
23755005 ATTGTATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.42
Consensus pattern (23 bp):
ATTATCAACGCAATTTGTACTTT
Found at i:23774344 original size:26 final size:26
Alignment explanation
Indices: 23774315--23774379 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
23774305 TTACTACTAA
* * * *
23774315 TGTCGTTGTATGAGCATGTTCAGAAT
1 TGTCGCTGCATGAACATGTCCAGAAT
23774341 TGTCGCTGCATGAACATGTCCAGAAT
1 TGTCGCTGCATGAACATGTCCAGAAT
* *
23774367 GGTCACTGCATGA
1 TGTCGCTGCATGA
23774380 GCACATCCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (26 bp):
TGTCGCTGCATGAACATGTCCAGAAT
Found at i:23774388 original size:26 final size:26
Alignment explanation
Indices: 23774335--23774388 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
23774325 TGAGCATGTT
* * **
23774335 CAGAATTGTCGCTGCATGAACATGTC
1 CAGAATGGTCACTGCATGAACACATC
*
23774361 CAGAATGGTCACTGCATGAGCACATC
1 CAGAATGGTCACTGCATGAACACATC
23774387 CA
1 CA
23774389 AAATTACGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (26 bp):
CAGAATGGTCACTGCATGAACACATC
Found at i:23779780 original size:19 final size:19
Alignment explanation
Indices: 23779756--23779802 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
23779746 CTATCTTAAC
*
23779756 AAAAATGCAATGAGAAAAT
1 AAAAATGCAATGACAAAAT
*
23779775 AAAAATGTAATGACAAAAT
1 AAAAATGCAATGACAAAAT
23779794 AAAAATGCA
1 AAAAATGCA
23779803 TGAAAACTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.64, C:0.06, G:0.13, T:0.17
Consensus pattern (19 bp):
AAAAATGCAATGACAAAAT
Found at i:23781586 original size:18 final size:18
Alignment explanation
Indices: 23781563--23781605 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
23781553 TCTGAGCCAC
23781563 TGTGGTTGAAGTTGAAAG
1 TGTGGTTGAAGTTGAAAG
23781581 TGTGGTTGAAGTTGAAAG
1 TGTGGTTGAAGTTGAAAG
*
23781599 TATGGTT
1 TGTGGTT
23781606 TTACAAGGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (18 bp):
TGTGGTTGAAGTTGAAAG
Found at i:23793681 original size:52 final size:51
Alignment explanation
Indices: 23793595--23793878 Score: 316
Period size: 52 Copynumber: 5.5 Consensus size: 51
23793585 ATTTCACTTC
* * *
23793595 ATTCATATACTCACGATGACACATAGCCACCGGACCTTATAATCTGTAAGGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTT-TAATCCGTAAAGG
** * * *
23793647 ATTGGTATACTCACGATGACACAGAGTCAACGGACCTCTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCT-TTAATCCGTAAAGG
** * * * *
23793699 AGCCATATACTCATGATGACACTTAGCCATTGGACTTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTTTAATCCGTAAAGG
* * * * * * *
23793750 ATTTATATACTCATGATGACACTTAGTCATCAGACCGTTTAATCTGTAATGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACC-TTTAATCCGTAAAGG
*
23793802 ATTCATATACTCACGATGACACATAGCCATTGGACCGTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACC-TTTAATCCGTAAAGG
* *
23793854 ATGCATATACTCACGATGACTCATA
1 ATTCATATACTCACGATGACACATA
23793879 ATCATCGAAC
Statistics
Matches: 193, Mismatches: 37, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
51 43 0.22
52 149 0.77
53 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.28
Consensus pattern (51 bp):
ATTCATATACTCACGATGACACATAGCCATCGGACCTTTAATCCGTAAAGG
Found at i:23793778 original size:103 final size:104
Alignment explanation
Indices: 23793598--23793873 Score: 340
Period size: 103 Copynumber: 2.7 Consensus size: 104
23793588 TCACTTCATT
** * * * **
23793598 CATATACTCACGATGACACATAGCCACCGGACCTTATAATCTGTAAGGGATTGGTATACTCACGA
1 CATATACTCACGATGACACATAGCCATTGGACCTTTTAATCCGTAAAGGATTCATATACTCACGA
*
23793663 TGACACAGAGTCAACGGACC-TCTTAATCCGTAAAGGAGC
66 TGACACAGAGTCAACAGACCGT-TTAATCCGTAAAGGAGC
* * * *
23793702 CATATACTCATGATGACACTTAGCCATTGGA-CTTTTAATCCGTAAAGGATTTATATACTCATGA
1 CATATACTCACGATGACACATAGCCATTGGACCTTTTAATCCGTAAAGGATTCATATACTCACGA
** * * * **
23793766 TGACACTTAGTCATCAGACCGTTTAATCTGTAATGGATT
66 TGACACAGAGTCAACAGACCGTTTAATCCGTAAAGGAGC
* *
23793805 CATATACTCACGATGACACATAGCCATTGGACCGTTTAATCCGTAAAGGATGCATATACTCACGA
1 CATATACTCACGATGACACATAGCCATTGGACCTTTTAATCCGTAAAGGATTCATATACTCACGA
23793870 TGAC
66 TGAC
23793874 TCATAATCAT
Statistics
Matches: 146, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
103 85 0.58
104 61 0.42
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (104 bp):
CATATACTCACGATGACACATAGCCATTGGACCTTTTAATCCGTAAAGGATTCATATACTCACGA
TGACACAGAGTCAACAGACCGTTTAATCCGTAAAGGAGC
Found at i:23800890 original size:52 final size:52
Alignment explanation
Indices: 23800802--23801097 Score: 337
Period size: 52 Copynumber: 5.7 Consensus size: 52
23800792 TGTTCACTTC
* * * * *
23800802 ATTCATATACTCACTATGACACATAGCCACCGGACC-TTATAATCCGCAAGGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCGTT-TAATCCGTAAAGG
* * *
23800854 ATTCGTATACTCACGATGTCACAGAGTCATCGGACC-TCTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCGT-TTAATCCGTAAAGG
** * *
23800906 ACCCATATACTCACGATGACACTTAGTCATCGGACCGTTTAATCTGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCGTTTAATCCGTAAAGG
* ** *
23800958 ATTTATATACTCACGATGACATTTAGTCATCAGG-CCGTTTAATCCATAAAGG
1 ATTCATATACTCACGATGACACATAGTCATC-GGACCGTTTAATCCGTAAAGG
* * *
23801010 ATTCATATACTCACGATGACACATAGCCATCGGACCATTTAATCCATAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCGTTTAATCCGTAAAGG
* * * *
23801062 ATTCATATACTCACGATGGCTCATAATCATTGGACC
1 ATTCATATACTCACGATGACACATAGTCATCGGACC
23801098 TCTTCATTTA
Statistics
Matches: 209, Mismatches: 31, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
51 2 0.01
52 203 0.97
53 4 0.02
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACATAGTCATCGGACCGTTTAATCCGTAAAGG
Found at i:23804586 original size:24 final size:24
Alignment explanation
Indices: 23804552--23804598 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
23804542 ATTCATCTTT
*
23804552 TATTAATTTGCTCTGAC-ATTTTA
1 TATTAATTTGCACTGACAATTTTA
23804575 TATTACATTTGCACTGACAATTTT
1 TATTA-ATTTGCACTGACAATTTT
23804599 TAATCTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 11 0.52
25 5 0.24
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.49
Consensus pattern (24 bp):
TATTAATTTGCACTGACAATTTTA
Found at i:23812804 original size:18 final size:17
Alignment explanation
Indices: 23812750--23812800 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
23812740 TGCATGCATT
*
23812750 TTTTTATTGTCAT-TGCA
1 TTTTTATTGTC-TCTACA
23812767 TTTTTATTGTCTCTACA
1 TTTTTATTGTCTCTACA
23812784 TTTTTATTTGT-TCTACA
1 TTTTTA-TTGTCTCTACA
23812801 ATTTGCATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 1 0.03
17 26 0.84
18 4 0.13
ACGTcount: A:0.18, C:0.14, G:0.08, T:0.61
Consensus pattern (17 bp):
TTTTTATTGTCTCTACA
Found at i:23816717 original size:37 final size:37
Alignment explanation
Indices: 23816662--23816741 Score: 115
Period size: 37 Copynumber: 2.2 Consensus size: 37
23816652 TAATGTAGCT
* ** * *
23816662 GCATGAGCACTTCTAGATTGTGCCCAAATCTGTCGCC
1 GCATGAGCACTTCCAGATTGCACCCAAAACTGTCGCA
23816699 GCATGAGCACTTCCAGATTGCACCCAAAACTGTCGCA
1 GCATGAGCACTTCCAGATTGCACCCAAAACTGTCGCA
23816736 GCATGA
1 GCATGA
23816742 ATAGTTTTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (37 bp):
GCATGAGCACTTCCAGATTGCACCCAAAACTGTCGCA
Found at i:23816813 original size:37 final size:37
Alignment explanation
Indices: 23816715--23816838 Score: 135
Period size: 37 Copynumber: 3.4 Consensus size: 37
23816705 GCACTTCCAG
* * * *
23816715 ATTGCACCCAAAACTGTCGCAGCATGAATAGTT-TT-A
1 ATTGCACCCAAGACTATCGCTGCATAAATA-TTCTTCA
* * *
23816751 GAATGCACCCAAGACTATTGTTGCATAAATATTCTTCA
1 -ATTGCACCCAAGACTATCGCTGCATAAATATTCTTCA
* *
23816789 ATTGCATCCAAGACTATCGCTGCATAAGTATTCTTCA
1 ATTGCACCCAAGACTATCGCTGCATAAATATTCTTCA
23816826 ATTGCACCCAAGA
1 ATTGCACCCAAGA
23816839 ATGTCACTGT
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
36 2 0.03
37 69 0.96
38 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (37 bp):
ATTGCACCCAAGACTATCGCTGCATAAATATTCTTCA
Found at i:23816890 original size:13 final size:13
Alignment explanation
Indices: 23816859--23816893 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
23816849 ATGAACATGT
23816859 CCAGAATTG-AGC
1 CCAGAATTGTAGC
23816871 CCAGAATTGTAGC
1 CCAGAATTGTAGC
*
23816884 TCAGAATTGT
1 CCAGAATTGT
23816894 CATTGCATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (13 bp):
CCAGAATTGTAGC
Found at i:23817706 original size:16 final size:16
Alignment explanation
Indices: 23817685--23817715 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23817675 TTGTGGATCT
23817685 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
23817701 CATTTTATCTTTATT
1 CATTTTACCTTTATT
23817716 TTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:23820300 original size:10 final size:10
Alignment explanation
Indices: 23820277--23820320 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
23820267 AGTCACATAT
23820277 AAAAAA-AGA
1 AAAAAAGAGA
23820286 AAAAAAGAGA
1 AAAAAAGAGA
*
23820296 GAAAAAGAGA
1 AAAAAAGAGA
*
23820306 AAAGAAGA-A
1 AAAAAAGAGA
23820315 AAAAAA
1 AAAAAA
23820321 ATATCTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 12 0.40
10 18 0.60
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAAGAGA
Found at i:23820799 original size:37 final size:37
Alignment explanation
Indices: 23820757--23820870 Score: 104
Period size: 37 Copynumber: 3.1 Consensus size: 37
23820747 AATGTCGCTG
** * * * *
23820757 CATGAGCACTTTTAGATTGCGCCCAAAACTGTCGCCA
1 CATGAGCACTTCCAAATTGCACCCAAAACTATCGCAA
23820794 CATGAGCACTTCCAAATTGCACCCAAAACTATCGCAA
1 CATGAGCACTTCCAAATTGCACCCAAAACTATCGCAA
** * * * *
23820831 CATGAATATTTCTAGAA-TGCACCCAAGACTATCGCTA
1 CATGAGCACTTCCA-AATTGCACCCAAAACTATCGCAA
23820868 CAT
1 CAT
23820871 AAATATTCTT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
37 62 0.97
38 2 0.03
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (37 bp):
CATGAGCACTTCCAAATTGCACCCAAAACTATCGCAA
Found at i:23820876 original size:37 final size:37
Alignment explanation
Indices: 23820808--23820899 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
23820798 AGCACTTCCA
* * *
23820808 AATTGCACCCAAAACTATCGCAACATGAATATTTCTAG
1 AATTGCACCCAAGACTATCGCAACATAAATA-TTCTAC
* *
23820846 AA-TGCACCCAAGACTATCGCTACATAAATATTCTTC
1 AATTGCACCCAAGACTATCGCAACATAAATATTCTAC
*
23820882 AATTGCATCCAAGACTAT
1 AATTGCACCCAAGACTAT
23820900 TACTGCATGA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
36 6 0.13
37 39 0.83
38 2 0.04
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.27
Consensus pattern (37 bp):
AATTGCACCCAAGACTATCGCAACATAAATATTCTAC
Found at i:23830445 original size:37 final size:37
Alignment explanation
Indices: 23830395--23830499 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 37
23830385 ATGTAGCTGT
** * *
23830395 ATGAGCACTTCTAGATTGTGCCCAAATCTTTCACCGC
1 ATGAGCACTTCTAGATTGCACCCAAAACTATCACCGC
23830432 ATGAGCACTTCTAGATTGCACCCAAAACTATCACCGC
1 ATGAGCACTTCTAGATTGCACCCAAAACTATCACCGC
** * * * *
23830469 ATGAATATTTCTGGAATGCACCCAAGACTAT
1 ATGAGCACTTCTAGATTGCACCCAAAACTAT
23830500 TACTGCATAA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (37 bp):
ATGAGCACTTCTAGATTGCACCCAAAACTATCACCGC
Found at i:23830535 original size:37 final size:37
Alignment explanation
Indices: 23830446--23830567 Score: 120
Period size: 37 Copynumber: 3.3 Consensus size: 37
23830436 GCACTTCTAG
** * * **
23830446 ATTGCACCCAAAACTATCACCGCATGAATATTTCTGGA
1 ATTGCACCCAGGACTATCACAGCATAAATA-TTCTTCA
* * *
23830484 A-TGCACCCAAGACTATTACTGCATAAATATTCTTCA
1 ATTGCACCCAGGACTATCACAGCATAAATATTCTTCA
* * *
23830520 ATTGCATCCAGGACTATCGCAGCATAAGTATTCTTCA
1 ATTGCACCCAGGACTATCACAGCATAAATATTCTTCA
23830557 ATTGCACCCAG
1 ATTGCACCCAG
23830568 TAATGTCACT
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
36 6 0.09
37 63 0.90
38 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (37 bp):
ATTGCACCCAGGACTATCACAGCATAAATATTCTTCA
Done.