Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010929.1 Corchorus capsularis cultivar CVL-1 contig10950, whole genome shotgun sequence
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: 45001
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1621 original size:20 final size:20
Alignment explanation
Indices: 1576--1626 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
1566 TTAATATCAA
*
1576 GTTTAGGGTTTTTAGGTTTAG
1 GTTTAGGG-TTATAGGTTTAG
1597 G-TTAGGGTTAT-GGTTTAGG
1 GTTTAGGGTTATAGGTTTA-G
1616 GTTTAGGGTTA
1 GTTTAGGGTTA
1627 GGTCTTTAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 6 0.22
19 5 0.19
20 15 0.56
21 1 0.04
ACGTcount: A:0.16, C:0.00, G:0.37, T:0.47
Consensus pattern (20 bp):
GTTTAGGGTTATAGGTTTAG
Found at i:4587 original size:72 final size:72
Alignment explanation
Indices: 4506--4640 Score: 184
Period size: 72 Copynumber: 1.9 Consensus size: 72
4496 ACCATCAAGA
*
4506 TCAATTTTTGACAATCT-AAAAATTTCAGCAGAAAA-TTTCGCATCCAAACCAGAATCCCACAAA
1 TCAATTTTTGACAATCTCAAAAATTT-AGCAGAAAACTTT-GCATCAAAACCAGAATCCCACAAA
4569 TCTTCAAAG
64 TCTTCAAAG
* * * * *
4578 TCAATTTTTGACAATTTCAAGACTTTAGCAGAAAACTTTGCATCAAAACTAGAATCCGACAAA
1 TCAATTTTTGACAATCTCAAAAATTTAGCAGAAAACTTTGCATCAAAACCAGAATCCCACAAA
4641 CCAAGATCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
72 46 0.84
73 9 0.16
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.27
Consensus pattern (72 bp):
TCAATTTTTGACAATCTCAAAAATTTAGCAGAAAACTTTGCATCAAAACCAGAATCCCACAAATC
TTCAAAG
Found at i:9656 original size:10 final size:10
Alignment explanation
Indices: 9637--9690 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
9627 TTTAGGTTTT
9637 AATTATTAAA
1 AATTATTAAA
*
9647 AATAATTAAA
1 AATTATTAAA
*
9657 TGATTATTAAA
1 -AATTATTAAA
9668 AATTA-TAAA
1 AATTATTAAA
*
9677 TATTATTAAGA
1 AATTATTAA-A
9688 AAT
1 AAT
9691 AAATTACACA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (10 bp):
AATTATTAAA
Found at i:9664 original size:21 final size:19
Alignment explanation
Indices: 9638--9692 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 19
9628 TTAGGTTTTA
9638 ATTATTAAAAATAATTAAAT
1 ATTATTAAAAATAA-TAAAT
*
9658 GATTATTAAAAATTATAAAT
1 -ATTATTAAAAATAATAAAT
9678 ATTATTAAGAAATAA
1 ATTATTAA-AAATAA
9693 ATTACACACA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 8 0.26
20 10 0.32
21 13 0.42
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (19 bp):
ATTATTAAAAATAATAAAT
Found at i:11130 original size:18 final size:18
Alignment explanation
Indices: 11107--11142 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11097 TCATCCTCGA
* *
11107 AAGATGAGGATGATTATG
1 AAGATGAAGATGAATATG
11125 AAGATGAAGATGAATATG
1 AAGATGAAGATGAATATG
11143 GAATATGAGA
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:0.44, C:0.00, G:0.31, T:0.25
Consensus pattern (18 bp):
AAGATGAAGATGAATATG
Found at i:12046 original size:407 final size:408
Alignment explanation
Indices: 11274--12169 Score: 1535
Period size: 407 Copynumber: 2.2 Consensus size: 408
11264 TACTACAAAT
*
11274 GGTTGGATTAAAAGTGGGATTCAAATATGACCGTTTGATTAAATCCTTATCTCTTTCACACCTTA
1 GGTTGGATTAAAAGTGGGATTCAAATATGACCGTTAGATTAAATCCTTATCTC-TT----CC--A
11339 TCCACCTTATCCAACAAAAGTCAGAAAATCCAACACAATATCCAATCACTTGCAAAGAATCTATC
59 --CACCTTATCCAACAAAAGTCAGAAAATCCAACACAATATCCAATCACTTGCAAAGAATCTATC
* *
11404 TTTATCTTATCCAACGGTTGGATTAAAAGTGGGATTCAAATATGACTGTTAGATTGAATCCTTAT
122 TTTATCTTATCCAACAGTTGGATTAAAAGTGGGATTCAAATATGACCGTTAGATTGAATCCTTAT
* * *
11469 CTCTTCCATACTCTATCCAACAAAAGTCAGAAAATCCAACACAATATCCAATTACTTGCATAGAA
187 CTCTTCCACACTCTATCCAACAAAAGTCAGAAAATCCAACACAATATCCAATCACTTGCAGAGAA
11534 TCTATCTTTATCTTATCCAACGGTTGGATTAAAAGTAGGATTCAAATATGACCGTTAAATTGAAT
252 TCTATCTTTATCTTATCCAACGGTTGGATTAAAAGTAGGATTCAAATATGACCGTTAAATTGAAT
*
11599 CCTTATCTCTTCCACACTCTATCCAACAAAAGTTAGAAAATACAACACAATATCCAATCACTTGC
317 CCTTATCTCTTCCACACTCTATCCAACAAAAGTCAGAAAATACAACACAATATCCAATCACTTGC
*
11664 AGAGAATCTATCTTTATTTTATCCAAC
382 AGAGAATCTATCTTTATCTTATCCAAC
* *
11691 GGTTGGATTCAAAGTAGGATTCAAATATGACCGTTAGATTAAATCCTTATCTCTTCCACACCTTA
1 GGTTGGATTAAAAGTGGGATTCAAATATGACCGTTAGATTAAATCCTTATCTCTTCCACACCTTA
*
11756 TCCAACCAAAGTCAGAAAATCCAACACAATATCCAATCACTTGCAAAG-ATCTATCTTTATCTTA
66 TCCAACAAAAGTCAGAAAATCCAACACAATATCCAATCACTTGCAAAGAATCTATCTTTATCTTA
11820 TCCAACAGTTGGATTAAAAGTGGGATTCAAATATGACCGTTAGATTGAATCCTTATCTCTTCCAC
131 TCCAACAGTTGGATTAAAAGTGGGATTCAAATATGACCGTTAGATTGAATCCTTATCTCTTCCAC
11885 ACTCTATCCAACAAAAGTCAGAAAATCCAACACAATATCCAATCACTTGCAGAGAATCTATCTTT
196 ACTCTATCCAACAAAAGTCAGAAAATCCAACACAATATCCAATCACTTGCAGAGAATCTATCTTT
*
11950 ATCTTATCCAACGGTTGGATTAAAAGTAGGATTCAAATATGACCGTTAGATTGAATCCTTATCTC
261 ATCTTATCCAACGGTTGGATTAAAAGTAGGATTCAAATATGACCGTTAAATTGAATCCTTATCTC
* * *
12015 TTCCACAC-CTTATCCAACCAAAGTCAGAAAATTCAACATAATATCCAATCACTTGCAGAGAATC
326 TTCCACACTC-TATCCAACAAAAGTCAGAAAATACAACACAATATCCAATCACTTGCAGAGAATC
12079 TATCTTTATCTTATCCAAC
390 TATCTTTATCTTATCCAAC
*
12098 GGTTGGATTAAAAGTGGGATTCAAATATGACCGTTAGATTGAATCCTTATCTCTTCCACACCTTA
1 GGTTGGATTAAAAGTGGGATTCAAATATGACCGTTAGATTAAATCCTTATCTCTTCCACACCTTA
*
12163 TCAAACA
66 TCCAACA
12170 TGTCTCTATA
Statistics
Matches: 458, Mismatches: 20, Indels: 12
0.93 0.04 0.02
Matches are distributed among these distances:
406 1 0.00
407 348 0.76
408 54 0.12
410 1 0.00
412 2 0.00
416 2 0.00
417 50 0.11
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (408 bp):
GGTTGGATTAAAAGTGGGATTCAAATATGACCGTTAGATTAAATCCTTATCTCTTCCACACCTTA
TCCAACAAAAGTCAGAAAATCCAACACAATATCCAATCACTTGCAAAGAATCTATCTTTATCTTA
TCCAACAGTTGGATTAAAAGTGGGATTCAAATATGACCGTTAGATTGAATCCTTATCTCTTCCAC
ACTCTATCCAACAAAAGTCAGAAAATCCAACACAATATCCAATCACTTGCAGAGAATCTATCTTT
ATCTTATCCAACGGTTGGATTAAAAGTAGGATTCAAATATGACCGTTAAATTGAATCCTTATCTC
TTCCACACTCTATCCAACAAAAGTCAGAAAATACAACACAATATCCAATCACTTGCAGAGAATCT
ATCTTTATCTTATCCAAC
Found at i:12159 original size:136 final size:136
Alignment explanation
Indices: 11341--12169 Score: 1414
Period size: 136 Copynumber: 6.1 Consensus size: 136
11331 ACACCTTATC
*
11341 CACCTTATCCAACAAAAGTCAGAAAATCCAACACAATATCCAATCACTTGCAAAGAATCTATCTT
1 CACCTTATCCAACAAAAGTCAGAAAATCCAACACAATATCCAATCACTTGCAGAGAATCTATCTT
* *
11406 TATCTTATCCAACGGTTGGATTAAAAGTGGGATTCAAATATGACTGTTAGATTGAATCCTTATCT
66 TATCTTATCCAACGGTTGGATTAAAAGTAGGATTCAAATATGACCGTTAGATTGAATCCTTATCT
11471 CTTCCA
131 CTTCCA
* * *
11477 TA-CTCTATCCAACAAAAGTCAGAAAATCCAACACAATATCCAATTACTTGCATAGAATCTATCT
1 CACCT-TATCCAACAAAAGTCAGAAAATCCAACACAATATCCAATCACTTGCAGAGAATCTATCT
*
11541 TTATCTTATCCAACGGTTGGATTAAAAGTAGGATTCAAATATGACCGTTAAATTGAATCCTTATC
65 TTATCTTATCCAACGGTTGGATTAAAAGTAGGATTCAAATATGACCGTTAGATTGAATCCTTATC
11606 TCTTCCA
130 TCTTCCA
* *
11613 CA-CTCTATCCAACAAAAGTTAGAAAATACAACACAATATCCAATCACTTGCAGAGAATCTATCT
1 CACCT-TATCCAACAAAAGTCAGAAAATCCAACACAATATCCAATCACTTGCAGAGAATCTATCT
* * *
11677 TTATTTTATCCAACGGTTGGATTCAAAGTAGGATTCAAATATGACCGTTAGATTAAATCCTTATC
65 TTATCTTATCCAACGGTTGGATTAAAAGTAGGATTCAAATATGACCGTTAGATTGAATCCTTATC
11742 TCTTCCA
130 TCTTCCA
* *
11749 CACCTTATCCAACCAAAGTCAGAAAATCCAACACAATATCCAATCACTTGCAAAG-ATCTATCTT
1 CACCTTATCCAACAAAAGTCAGAAAATCCAACACAATATCCAATCACTTGCAGAGAATCTATCTT
* *
11813 TATCTTATCCAACAGTTGGATTAAAAGTGGGATTCAAATATGACCGTTAGATTGAATCCTTATCT
66 TATCTTATCCAACGGTTGGATTAAAAGTAGGATTCAAATATGACCGTTAGATTGAATCCTTATCT
11878 CTTCCA
131 CTTCCA
11884 CA-CTCTATCCAACAAAAGTCAGAAAATCCAACACAATATCCAATCACTTGCAGAGAATCTATCT
1 CACCT-TATCCAACAAAAGTCAGAAAATCCAACACAATATCCAATCACTTGCAGAGAATCTATCT
11948 TTATCTTATCCAACGGTTGGATTAAAAGTAGGATTCAAATATGACCGTTAGATTGAATCCTTATC
65 TTATCTTATCCAACGGTTGGATTAAAAGTAGGATTCAAATATGACCGTTAGATTGAATCCTTATC
12013 TCTTCCA
130 TCTTCCA
* * *
12020 CACCTTATCCAACCAAAGTCAGAAAATTCAACATAATATCCAATCACTTGCAGAGAATCTATCTT
1 CACCTTATCCAACAAAAGTCAGAAAATCCAACACAATATCCAATCACTTGCAGAGAATCTATCTT
*
12085 TATCTTATCCAACGGTTGGATTAAAAGTGGGATTCAAATATGACCGTTAGATTGAATCCTTATCT
66 TATCTTATCCAACGGTTGGATTAAAAGTAGGATTCAAATATGACCGTTAGATTGAATCCTTATCT
12150 CTTCCA
131 CTTCCA
*
12156 CACCTTATCAAACA
1 CACCTTATCCAACA
12170 TGTCTCTATA
Statistics
Matches: 654, Mismatches: 34, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
134 2 0.00
135 127 0.19
136 521 0.80
137 4 0.01
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.30
Consensus pattern (136 bp):
CACCTTATCCAACAAAAGTCAGAAAATCCAACACAATATCCAATCACTTGCAGAGAATCTATCTT
TATCTTATCCAACGGTTGGATTAAAAGTAGGATTCAAATATGACCGTTAGATTGAATCCTTATCT
CTTCCA
Found at i:13558 original size:23 final size:23
Alignment explanation
Indices: 13528--13629 Score: 100
Period size: 23 Copynumber: 4.3 Consensus size: 23
13518 TTCGGGTTAT
* *
13528 TCGGGTCTCGGGTCGTTCGGGTC
1 TCGGGTCTCGAGTCATTCGGGTC
* * *
13551 TCGGGTCTCGGGTCATACGGGTT
1 TCGGGTCTCGAGTCATTCGGGTC
13574 TCGGGTCATTCGAGTC--TCGGGTC
1 TCGGGTC--TCGAGTCATTCGGGTC
*
13597 ATTCGGGTTTCGAGTCATTCGGGTC
1 --TCGGGTCTCGAGTCATTCGGGTC
13622 TCGGGTCT
1 TCGGGTCT
13630 ACCGGGTCTC
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
23 46 0.71
25 19 0.29
ACGTcount: A:0.07, C:0.24, G:0.37, T:0.32
Consensus pattern (23 bp):
TCGGGTCTCGAGTCATTCGGGTC
Found at i:13578 original size:39 final size:39
Alignment explanation
Indices: 13519--13596 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
13509 TCATCTAGGT
* * * *
13519 TCGGGTTATTCGGGTCTCGGGTCGTTCGGGTCTCGGGTC
1 TCGGGTCATACGGGTCTCGGGTCATTCGAGTCTCGGGTC
*
13558 TCGGGTCATACGGGTTTCGGGTCATTCGAGTCTCGGGTC
1 TCGGGTCATACGGGTCTCGGGTCATTCGAGTCTCGGGTC
13597 ATTCGGGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.06, C:0.23, G:0.38, T:0.32
Consensus pattern (39 bp):
TCGGGTCATACGGGTCTCGGGTCATTCGAGTCTCGGGTC
Found at i:13619 original size:71 final size:70
Alignment explanation
Indices: 13488--13629 Score: 196
Period size: 71 Copynumber: 2.0 Consensus size: 70
13478 TGCAGTTTTT
* * * * *
13488 TCGGGTCATTCGGATTTCGGGTCATCTAGGTTCGGGTTATTCGGGTCTCGGGTCGTTCGGGTCTC
1 TCGGGTCATACGGATTTCGGGTCATCGAGGTTCGGGTCATTCGGGTCTCGAGTCATTCGGGTCTC
13553 GGGTC
66 GGGTC
* *
13558 TCGGGTCATACGGGTTTCGGGTCATTCGA-GTCTCGGGTCATTCGGGTTTCGAGTCATTCGGGTC
1 TCGGGTCATACGGATTTCGGGTCA-TCGAGGT-TCGGGTCATTCGGGTCTCGAGTCATTCGGGTC
13622 TCGGGTC
64 TCGGGTC
13629 T
1 T
13630 ACCGGGTCTC
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
70 24 0.38
71 39 0.62
ACGTcount: A:0.08, C:0.22, G:0.36, T:0.34
Consensus pattern (70 bp):
TCGGGTCATACGGATTTCGGGTCATCGAGGTTCGGGTCATTCGGGTCTCGAGTCATTCGGGTCTC
GGGTC
Found at i:13635 original size:16 final size:16
Alignment explanation
Indices: 13488--13643 Score: 120
Period size: 16 Copynumber: 10.4 Consensus size: 16
13478 TGCAGTTTTT
* *
13488 TCGGGTCATTCGGATT
1 TCGGGTCATTCGGGTC
*
13504 TCGGGTCA-TCTAGGT-
1 TCGGGTCATTC-GGGTC
*
13519 TCGGGTTATTCGGGTC
1 TCGGGTCATTCGGGTC
13535 TCGGG----TC--GT-
1 TCGGGTCATTCGGGTC
13544 TCGGGTC--TCGGGTC
1 TCGGGTCATTCGGGTC
* *
13558 TCGGGTCATACGGGTT
1 TCGGGTCATTCGGGTC
*
13574 TCGGGTCATTCGAGTC
1 TCGGGTCATTCGGGTC
*
13590 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTC
*
13606 TCGAGTCATTCGGGTC
1 TCGGGTCATTCGGGTC
*
13622 TCGGGTC-TACCGGGTC
1 TCGGGTCAT-TCGGGTC
13638 TCGGGT
1 TCGGGT
13644 TGGGCGAGTT
Statistics
Matches: 114, Mismatches: 15, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
9 5 0.04
10 2 0.02
11 2 0.02
12 2 0.02
13 2 0.02
14 7 0.06
15 13 0.11
16 81 0.71
ACGTcount: A:0.08, C:0.22, G:0.37, T:0.33
Consensus pattern (16 bp):
TCGGGTCATTCGGGTC
Found at i:14115 original size:21 final size:21
Alignment explanation
Indices: 14090--14137 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
14080 TAGCCAATTT
*
14090 ATAATAGGTAAAATCATAACA
1 ATAATAGATAAAATCATAACA
* *
14111 ATAATTGATAAAATTATAACA
1 ATAATAGATAAAATCATAACA
14132 ATAATA
1 ATAATA
14138 TAAATTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (21 bp):
ATAATAGATAAAATCATAACA
Found at i:14199 original size:16 final size:16
Alignment explanation
Indices: 14180--14258 Score: 88
Period size: 16 Copynumber: 4.9 Consensus size: 16
14170 TATAATATTC
*
14180 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
**
14196 TCGGGTCATAAGGGTT
1 TCGGGTCATTCGGGTT
* *
14212 ACGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
14228 TCGGGTCA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
*
14244 GCGGGTCATTCGGGT
1 TCGGGTCATTCGGGT
14259 CACGGGTTCG
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
15 2 0.04
16 47 0.92
17 2 0.04
ACGTcount: A:0.10, C:0.18, G:0.39, T:0.33
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:14223 original size:32 final size:32
Alignment explanation
Indices: 14181--14265 Score: 116
Period size: 32 Copynumber: 2.7 Consensus size: 32
14171 ATAATATTCT
* *
14181 CGGGTTATTCGGGTTTCGGGTCATAAGGGTTA
1 CGGGTCATTCGGGTCTCGGGTCATAAGGGTTA
** *
14213 CGGGTCATTCGGGTCTCGGGTCATCTGGGTTG
1 CGGGTCATTCGGGTCTCGGGTCATAAGGGTTA
*
14245 CGGGTCATTCGGGTCACGGGT
1 CGGGTCATTCGGGTCTCGGGT
14266 TCGTCTGGTC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.11, C:0.19, G:0.40, T:0.31
Consensus pattern (32 bp):
CGGGTCATTCGGGTCTCGGGTCATAAGGGTTA
Found at i:14248 original size:23 final size:23
Alignment explanation
Indices: 14221--14282 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 23
14211 TACGGGTCAT
14221 TCGGGTCTCGGGTCATCTGGGTT-G
1 TCGGGTCTCGGGTCA-C-GGGTTCG
14245 -CGGGTCATTCGGGTCACGGGTTCG
1 TCGGGTC--TCGGGTCACGGGTTCG
*
14269 TCTGGTCTCGGGTC
1 TCGGGTCTCGGGTC
14283 GGGCGGGTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
23 18 0.55
24 2 0.06
25 13 0.39
ACGTcount: A:0.05, C:0.24, G:0.40, T:0.31
Consensus pattern (23 bp):
TCGGGTCTCGGGTCACGGGTTCG
Found at i:14264 original size:48 final size:48
Alignment explanation
Indices: 14178--14282 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 48
14168 TTTATAATAT
* * * *
14178 TCTCGGGTTATTCGGGTTTCGGGTCATAAGGGTTACGGG-TCATTCGGG
1 TCTCGGGTCATTCGGGTTGCGGGTCATAAGGGTCACGGGTTC-GTCGGG
** *
14226 TCTCGGGTCA-TCTGGGTTGCGGGTCATTCGGGTCACGGGTTCGTCTGG
1 TCTCGGGTCATTC-GGGTTGCGGGTCATAAGGGTCACGGGTTCGTCGGG
14274 TCTCGGGTC
1 TCTCGGGTC
14283 GGGCGGGTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
47 2 0.04
48 44 0.92
49 2 0.04
ACGTcount: A:0.09, C:0.21, G:0.38, T:0.32
Consensus pattern (48 bp):
TCTCGGGTCATTCGGGTTGCGGGTCATAAGGGTCACGGGTTCGTCGGG
Found at i:16190 original size:107 final size:106
Alignment explanation
Indices: 15996--16202 Score: 335
Period size: 107 Copynumber: 1.9 Consensus size: 106
15986 AAAAATTATA
* *
15996 TATTTTATTTCTAAAACCCTATAACAATATTATTAATTATGGAATTTACCCTTTAAAATGAAAAT
1 TATTTTATTTCTAAAACCCTATAACAATATTATTAATTATGAAATTTACCCTTTAAAATAAAAAT
16061 AAAATTTTAATTTGAGACTAAACTTAGTGAAATTAGTTTTG
66 AAAATTTTAATTTGAGACTAAACTTAGTGAAATTAGTTTTG
*
16102 TATTTTATTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTTACCC-TTAAAATAAAA
1 TATTTTATTTCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTTACCCTTTAAAATAAAA
* **
16166 ATAAAATTTTAATTTGGGGTTAAACTTAGTGAAATTA
64 ATAAAATTTTAATTTGAGACTAAACTTAGTGAAATTA
16203 AGGCTAAACT
Statistics
Matches: 93, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
106 28 0.30
107 44 0.47
108 21 0.23
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (106 bp):
TATTTTATTTCTAAAACCCTATAACAATATTATTAATTATGAAATTTACCCTTTAAAATAAAAAT
AAAATTTTAATTTGAGACTAAACTTAGTGAAATTAGTTTTG
Found at i:16960 original size:2 final size:2
Alignment explanation
Indices: 16953--16980 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16943 ATCATTTGTT
16953 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16981 CACATGTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18237 original size:2 final size:2
Alignment explanation
Indices: 18230--18258 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18220 AGTTTTAGAA
18230 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18259 GCGAGTTTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21245 original size:20 final size:23
Alignment explanation
Indices: 21222--21265 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
21212 TTTTTTTTAA
21222 CCAA-AATTTTTT-T-AGGATAG
1 CCAACAATTTTTTCTAAGGATAG
21242 CCAACAATTTTTTCTAAGGATAG
1 CCAACAATTTTTTCTAAGGATAG
21265 C
1 C
21266 AATTTCTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.19
21 8 0.38
22 1 0.05
23 8 0.38
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (23 bp):
CCAACAATTTTTTCTAAGGATAG
Found at i:21612 original size:12 final size:12
Alignment explanation
Indices: 21595--21621 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
21585 TGAAAGCAGA
21595 GCTGCATCTGTT
1 GCTGCATCTGTT
21607 GCTGCATCTGTT
1 GCTGCATCTGTT
21619 GCT
1 GCT
21622 TACCTTAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.26, G:0.26, T:0.41
Consensus pattern (12 bp):
GCTGCATCTGTT
Found at i:30398 original size:7 final size:7
Alignment explanation
Indices: 30386--30412 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
30376 TCCTTCACTC
30386 ATTTCTA
1 ATTTCTA
30393 ATTTCTA
1 ATTTCTA
30400 ATTTCTA
1 ATTTCTA
30407 ATTTCT
1 ATTTCT
30413 TTCGTTGAAA
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:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (7 bp):
ATTTCTA
Found at i:32147 original size:62 final size:62
Alignment explanation
Indices: 32050--32175 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
32040 ATTCTTGCCG
32050 AGGTGGAGGCTTGAAGATCACCAAAGGTTCGATGATTGTGATGAAAGGAGTGAAGAATTCGA
1 AGGTGGAGGCTTGAAGATCACCAAAGGTTCGATGATTGTGATGAAAGGAGTGAAGAATTCGA
*
32112 AGGTGGAGGCTTGAAGATCACCAAAGGTTCGATGATTGTGATGAAAGGGGTGAAGAATTCGA
1 AGGTGGAGGCTTGAAGATCACCAAAGGTTCGATGATTGTGATGAAAGGAGTGAAGAATTCGA
32174 AG
1 AG
32176 AATTTGTATG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.33, C:0.10, G:0.35, T:0.22
Consensus pattern (62 bp):
AGGTGGAGGCTTGAAGATCACCAAAGGTTCGATGATTGTGATGAAAGGAGTGAAGAATTCGA
Found at i:32823 original size:13 final size:14
Alignment explanation
Indices: 32793--32847 Score: 71
Period size: 13 Copynumber: 4.0 Consensus size: 14
32783 TTAAAAATTC
32793 ATATAT-ATAT-AT
1 ATATATAATATAAT
32805 ATATATAATATAAT
1 ATATATAATATAAT
32819 AATATATGAATATAAT
1 -ATATAT-AATATAAT
32835 ATA-ATAATATAAT
1 ATATATAATATAAT
32848 TAATTATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.15
13 12 0.31
14 4 0.10
15 9 0.23
16 8 0.21
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
ATATATAATATAAT
Found at i:32825 original size:21 final size:21
Alignment explanation
Indices: 32799--32845 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
32789 ATTCATATAT
32799 ATATAT-ATATATAATATAATA
1 ATATATGA-ATATAATATAATA
32820 ATATATGAATATAATATAATA
1 ATATATGAATATAATATAATA
32841 ATATA
1 ATATA
32846 ATTAATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
ATATATGAATATAATATAATA
Found at i:32846 original size:8 final size:8
Alignment explanation
Indices: 32793--32847 Score: 53
Period size: 8 Copynumber: 6.9 Consensus size: 8
32783 TTAAAAATTC
32793 ATATATATA
1 ATATA-ATA
32802 TATATATATA
1 -ATATA-ATA
32812 ATATAATA
1 ATATAATA
*
32820 ATAT-ATG
1 ATATAATA
32827 A-AT-ATA
1 ATATAATA
32833 ATATAATA
1 ATATAATA
32841 ATATAAT
1 ATATAAT
32848 TAATTATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
6 5 0.12
7 5 0.12
8 17 0.41
9 5 0.12
10 9 0.22
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (8 bp):
ATATAATA
Found at i:32869 original size:14 final size:14
Alignment explanation
Indices: 32850--32877 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
32840 AATATAATTA
32850 ATTATTTTATATAT
1 ATTATTTTATATAT
32864 ATTATTTTATATAT
1 ATTATTTTATATAT
32878 TAAAGTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTATTTTATATAT
Found at i:33897 original size:27 final size:27
Alignment explanation
Indices: 33867--33949 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 27
33857 TATAAGCTAC
33867 GCAAAATCAACTATCCTGATGTCCATA
1 GCAAAATCAACTATCCTGATGTCCATA
* ***
33894 GCAAACA-CAAC-A-GCT-ATAAAC-TA
1 GCAAA-ATCAACTATCCTGATGTCCATA
*
33917 CGCAAAATCAATTATCCTGATGTCCATA
1 -GCAAAATCAACTATCCTGATGTCCATA
33945 GCAAA
1 GCAAA
33950 TACAACAGCT
Statistics
Matches: 40, Mismatches: 9, Indels: 14
0.63 0.14 0.22
Matches are distributed among these distances:
23 3 0.08
24 11 0.28
25 3 0.08
26 3 0.08
27 17 0.43
28 3 0.08
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.22
Consensus pattern (27 bp):
GCAAAATCAACTATCCTGATGTCCATA
Found at i:33912 original size:51 final size:51
Alignment explanation
Indices: 33833--33983 Score: 257
Period size: 51 Copynumber: 3.0 Consensus size: 51
33823 CTATACTTCC
**
33833 GATGTCCATAGCAAATACAACAATTATAAGCTACGCAAAATCAACTATCCT
1 GATGTCCATAGCAAATACAACAGCTATAAGCTACGCAAAATCAACTATCCT
* * *
33884 GATGTCCATAGCAAACACAACAGCTATAAACTACGCAAAATCAATTATCCT
1 GATGTCCATAGCAAATACAACAGCTATAAGCTACGCAAAATCAACTATCCT
33935 GATGTCCATAGCAAATACAACAGCTATAAGCTACGCAAAATCAACTATC
1 GATGTCCATAGCAAATACAACAGCTATAAGCTACGCAAAATCAACTATC
33984 ATTACAGCTA
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 92 1.00
ACGTcount: A:0.43, C:0.25, G:0.11, T:0.22
Consensus pattern (51 bp):
GATGTCCATAGCAAATACAACAGCTATAAGCTACGCAAAATCAACTATCCT
Found at i:34073 original size:2 final size:2
Alignment explanation
Indices: 34066--34099 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
34056 TTGAGACTAG
34066 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34100 CTAGCTAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35162 original size:19 final size:19
Alignment explanation
Indices: 35135--35173 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
35125 CATTGTTTAA
*
35135 AAAGGTAAATTATATAAGT
1 AAAGCTAAATTATATAAGT
35154 AAAGCTAAATTATATAAGT
1 AAAGCTAAATTATATAAGT
35173 A
1 A
35174 TTGTCAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.54, C:0.03, G:0.13, T:0.31
Consensus pattern (19 bp):
AAAGCTAAATTATATAAGT
Found at i:40554 original size:40 final size:40
Alignment explanation
Indices: 40499--40579 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
40489 AACTAAGGGC
* *
40499 TAAATCTGAATTTAATTTCTTATC-TTAATTATTAGGGGGA
1 TAAATCTGAATTTAATTTATT-TCTTTAATTATTAGGAGGA
*
40539 TAAATCTGGATTTAATTTATTTCTTTAATTATTAGGAGGA
1 TAAATCTGAATTTAATTTATTTCTTTAATTATTAGGAGGA
40579 T
1 T
40580 CAAGTTGAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 2 0.05
40 35 0.95
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (40 bp):
TAAATCTGAATTTAATTTATTTCTTTAATTATTAGGAGGA
Found at i:41077 original size:16 final size:16
Alignment explanation
Indices: 41041--41115 Score: 100
Period size: 16 Copynumber: 4.8 Consensus size: 16
41031 TTCAGGCGGG
*
41041 TTCGGGTTCGGGTA-C
1 TTCGGGTTCGGGTATT
41056 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
41072 TTCGGGTTCGGGT-TAT
1 TTCGGGTTCGGGTAT-T
* *
41088 GTCGGATTCGGGTATT
1 TTCGGGTTCGGGTATT
41104 TTCGGGTTCGGG
1 TTCGGGTTCGGG
41116 CTCGGATTTG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
15 15 0.29
16 36 0.69
17 1 0.02
ACGTcount: A:0.07, C:0.15, G:0.40, T:0.39
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:41103 original size:32 final size:31
Alignment explanation
Indices: 41041--41115 Score: 116
Period size: 32 Copynumber: 2.4 Consensus size: 31
41031 TTCAGGCGGG
*
41041 TTCGGGTTCGGGTACTTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTACTTCGGATTCGGGTATT
41072 TTCGGGTTCGGGTTA-TGTCGGATTCGGGTATT
1 TTCGGGTTCGGG-TACT-TCGGATTCGGGTATT
41104 TTCGGGTTCGGG
1 TTCGGGTTCGGG
41116 CTCGGATTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
31 13 0.32
32 28 0.68
ACGTcount: A:0.07, C:0.15, G:0.40, T:0.39
Consensus pattern (31 bp):
TTCGGGTTCGGGTACTTCGGATTCGGGTATT
Found at i:41256 original size:2 final size:2
Alignment explanation
Indices: 41249--41321 Score: 54
Period size: 2 Copynumber: 39.5 Consensus size: 2
41239 AAATTTATTG
*
41249 AT AT AT AT A- AT AT A- AT A- AT AT A- AT AT A- AC AT -T AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
41284 AT CA- AT AT AT AT AT AT AT AT AT AT CT AT ACT AT AT AT A
1 AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
41322 AAAGTACAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 20
0.72 0.04 0.25
Matches are distributed among these distances:
1 8 0.14
2 47 0.81
3 3 0.05
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:41385 original size:31 final size:32
Alignment explanation
Indices: 41350--41416 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 32
41340 AACTTTATGT
* *
41350 TTTCCGATTGTACCCTTATTTTT-AAAAT-ATA
1 TTTCCAATTGTACCATT-TTTTTAAAAATCATA
41381 TTTCCAATTGTACCATTTTTTTAAAAATCATA
1 TTTCCAATTGTACCATTTTTTTAAAAATCATA
41413 TTTC
1 TTTC
41417 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 5 0.16
31 20 0.62
32 7 0.22
ACGTcount: A:0.30, C:0.16, G:0.04, T:0.49
Consensus pattern (32 bp):
TTTCCAATTGTACCATTTTTTTAAAAATCATA
Found at i:41428 original size:31 final size:29
Alignment explanation
Indices: 41368--41428 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 29
41358 TGTACCCTTA
*
41368 TTTTTAAAATATATTTCCAATTGTACCATT
1 TTTTTAAAATATATTTCAAATTG-ACCATT
41398 TTTTTAAAAATCATATTTCTAAATTG-CCATT
1 TTTTT-AAAAT-ATATTTC-AAATTGACCATT
41429 ACTAAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 5 0.19
31 10 0.37
32 7 0.26
33 5 0.19
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.49
Consensus pattern (29 bp):
TTTTTAAAATATATTTCAAATTGACCATT
Found at i:41576 original size:37 final size:36
Alignment explanation
Indices: 41531--41614 Score: 107
Period size: 36 Copynumber: 2.3 Consensus size: 36
41521 AATTTGTCTT
41531 TTTGTTTCCAAT-GTCCTATTTAATTTTGCCTTTTGTC
1 TTTGTTTCCAATCGTCCTATTTAATTTTG-C-TTTGTC
** *
41568 TTTGTTTCCAATCGTTGTATTTAATTTTGCTTTGTT
1 TTTGTTTCCAATCGTCCTATTTAATTTTGCTTTGTC
*
41604 TTTGTCTCCAA
1 TTTGTTTCCAA
41615 CATCTTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 15 0.36
37 13 0.31
38 14 0.33
ACGTcount: A:0.14, C:0.17, G:0.12, T:0.57
Consensus pattern (36 bp):
TTTGTTTCCAATCGTCCTATTTAATTTTGCTTTGTC
Found at i:42124 original size:22 final size:21
Alignment explanation
Indices: 41991--42360 Score: 103
Period size: 22 Copynumber: 16.7 Consensus size: 21
41981 CATTAGGCCA
* *
41991 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATA-TGAGG
* *
42013 TTAT-AAGAATTTCACAATGTGG
1 TTATCAA-AATTTCA-TATGAGG
* *
42035 TTAACAAAATTTCATTAGGAGG
1 TTATCAAAATTTCA-TATGAGG
* **
42057 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-ATGAGG
* * *
42079 TTATCAACATTTTATAGTGTGG
1 TTATCAAAATTTCATA-TGAGG
42101 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATATG-AGG
* *
42123 TTAT-AAAAGTCTCAATTTCATAAGG
1 TTATCAAAA-TTTC-A--T-ATGAGG
* * *
42148 AGTACCAAAATTTGATA-GAAGG
1 -TTATCAAAATTTCATATG-AGG
*
42170 TTATC-AAATCTCATA-GAGTG
1 TTATCAAAATTTCATATGAG-G
*
42190 ATTATCGAAATTTCATA-GAGATCAG
1 -TTATCAAAATTTCATATGAG----G
*
42215 ATTATCAAAATTT-ATA-GAAAGA
1 -TTATCAAAATTTCATATG--AGG
**
42237 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATA-TGAGG
* *
42259 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATA-TGAGG
* * *
42281 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCAT-ATGAGG
*
42303 TTATCAGAATTTCATA-GAGGGG
1 TTATCAAAATTTCATATGA--GG
* * * *
42325 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCAT-ATGAGG
*
42347 TTATCAAATTTTCA
1 TTATCAAAATTTCA
42361 AAATGTGATT
Statistics
Matches: 258, Mismatches: 58, Indels: 64
0.68 0.15 0.17
Matches are distributed among these distances:
19 2 0.01
20 11 0.04
21 31 0.12
22 169 0.66
23 8 0.03
24 7 0.03
25 18 0.07
26 8 0.03
27 4 0.02
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.34
Consensus pattern (21 bp):
TTATCAAAATTTCATATGAGG
Found at i:42194 original size:21 final size:23
Alignment explanation
Indices: 42153--42321 Score: 133
Period size: 22 Copynumber: 7.7 Consensus size: 23
42143 TAAGGAGTAC
* *
42153 CAAAATTTGATAGA-A-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
42174 C-AAATCTCATAGAG-TGATTAT
1 CAAAATTTCATAGAGATGATTAT
*
42195 CGAAATTTCATAGAGATCAGATTAT
1 CAAAATTTCATAGAGAT--GATTAT
*
42220 CAAAATTT-ATAGA-AAGATTAT
1 CAAAATTTCATAGAGATGATTAT
* *
42241 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAGATGATTAT
* * *
42263 CAAAATTTCAAAGCGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
42285 CAAAATTACATA-ATG-TGATTAT
1 CAAAATTTCATAGA-GATGATTAT
*
42307 CAGAATTTCATAGAG
1 CAAAATTTCATAGAG
42322 GGGTCAACAA
Statistics
Matches: 118, Mismatches: 18, Indels: 23
0.74 0.11 0.14
Matches are distributed among these distances:
20 10 0.08
21 22 0.19
22 64 0.54
23 4 0.03
24 5 0.04
25 13 0.11
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (23 bp):
CAAAATTTCATAGAGATGATTAT
Found at i:42333 original size:66 final size:66
Alignment explanation
Indices: 42235--42385 Score: 171
Period size: 66 Copynumber: 2.3 Consensus size: 66
42225 TTTATAGAAA
* ** * * * *
42235 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAAT
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAA-AGAGGTTATCAAAATTACAAAAT
42299 GT
65 GT
* * * *
42301 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGGTTATCAAATTTTCAAAATG
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACAAAATG
42366 T
66 T
42367 GATTA-CAAAATTTTCATAG
1 GATTATCAAAA-TTTCATAG
42386 TGGTATTTCT
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
65 4 0.06
66 65 0.92
67 2 0.03
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACAAAATG
T
Found at i:42513 original size:22 final size:22
Alignment explanation
Indices: 42485--43045 Score: 226
Period size: 22 Copynumber: 25.7 Consensus size: 22
42475 TCAGGGAGGA
*
42485 TATCAAAATTTCATATGAATGT
1 TATCAAAATTTCATATGAAGGT
**
42507 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
42529 TTTCAAAATTTCATAAGAATGT
1 TATCAAAATTTCATATGAAGGT
* ***
42551 TATCAAAATTTTATA-GTTTGT
1 TATCAAAATTTCATATGAAGGT
* * * *
42572 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
42595 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
42617 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
42639 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
42655 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
42677 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * * *
42700 TATAAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
*
42723 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
42745 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
42767 TATCAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* *
42789 TATTAATAA-TTCATATGGAGGT
1 TATCAA-AATTTCATATGAAGGT
* * * * *
42811 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
42833 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
42855 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
42878 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
42900 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
42922 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* *
42944 TAACAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
** **
42966 TAAAAAAATTT-ATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
* * * **
42987 TCTCGAAATTCCATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
* *
43009 TATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATATGAAGGT
43031 TATCAAAATTTCATA
1 TATCAAAATTTCATA
43046 ATGGGATCAT
Statistics
Matches: 411, Mismatches: 94, Indels: 68
0.72 0.16 0.12
Matches are distributed among these distances:
16 9 0.02
17 2 0.00
18 2 0.00
20 2 0.00
21 33 0.08
22 296 0.72
23 65 0.16
24 2 0.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:42622 original size:44 final size:44
Alignment explanation
Indices: 42466--43045 Score: 298
Period size: 44 Copynumber: 13.3 Consensus size: 44
42456 TTATGGAGTA
* * * *
42466 ATCAAAATTTC--AGGGAGGATATCAAAATTTCATATGAATG-TT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGA-GATT
* * * *
42508 ATCAAAATTTCATAGTTTA-GTTTTCAAAATTTCATAAGAATG-TT
1 ATCAAAATTTCATAG-TGAGGTTATCAAAATTTCATAGGGA-GATT
* ** *
42552 ATCAAAATTTTATAGT-TTGTAGATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGTGAGGT-TATCAAAATTTCATAGGGAGATT
* * ** *
42596 AACAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGATT
* * *
42640 ATCAAAA-TT--T-GT-A-GTTATCAAGATTTCATA-AGAAAGTT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGA-TT
* * * * *
42678 ATCAAAATTTTATAGGGAGGTTTATAAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGTGAGG-TTATCAAAATTTCATAGGGAGA-TT
* * * *
42724 ATCAAAATTTCATAGCGAGGTTATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGATT
* * * * * *
42768 ATCAAAATTTCAGAGTGTGATTATTAATAA-TTCATATGGAGGTT
1 ATCAAAATTTCATAGTGAGGTTATCAA-AATTTCATAGGGAGATT
* * * ** * * * * *
42812 TTTAAATTTTCATAACGTGGTTATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGATT
* * * *
42856 ATCAACATCTCATAGTGTTGGTTATCAAAATTTCATTGGGA-AGTT
1 ATCAAAATTTCATAGTG-AGGTTATCAAAATTTCATAGGGAGA-TT
* * * *
42901 ATCAAAATTTCATATTGAGGTCT-TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAGTGAGGT-TATCAAAATTTCATAGGGAGATT
* * ** *** *
42945 AACAAAATTTCATAAG-AAGGTTAAAAAAATTT-ATAAAAAGGTT
1 ATCAAAATTTCAT-AGTGAGGTTATCAAAATTTCATAGGGAGATT
* * * * * * *
42988 CTCGAAATTCCATAGT-ATCGTTATTAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATAGTGA-GGTTATCAAAATTTCATAGGGAGATT
43032 ATCAAAATTTCATA
1 ATCAAAATTTCATA
43046 ATGGGATCAT
Statistics
Matches: 405, Mismatches: 106, Indels: 52
0.72 0.19 0.09
Matches are distributed among these distances:
37 2 0.00
38 23 0.06
39 3 0.01
40 1 0.00
41 2 0.00
42 15 0.04
43 36 0.09
44 230 0.57
45 71 0.18
46 22 0.05
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (44 bp):
ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGATT
Found at i:42707 original size:23 final size:23
Alignment explanation
Indices: 42676--42777 Score: 100
Period size: 23 Copynumber: 4.5 Consensus size: 23
42666 CATAAGAAAG
42676 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* * *
42699 TTATAAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* *
42722 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
* * * * *
42744 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTTATAGGGAGGT
42766 TTATCAAAATTT
1 TTATCAAAATTT
42778 CAGAGTGTGA
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
21 1 0.02
22 28 0.42
23 37 0.56
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:42772 original size:128 final size:126
Alignment explanation
Indices: 42525--42777 Score: 308
Period size: 128 Copynumber: 2.0 Consensus size: 126
42515 TTTCATAGTT
* * *** *
42525 TAGTTTTCAAAATTTCATAAGAATGTTATCAAAATTTTATAGTTTGTAGATCAAAATTTCATAGG
1 TAGTTATCAAAATTTCATAAGAAAGTTATCAAAATTTTATAGGAGGTAGATAAAAATTTCATAGG
* * *
42590 GAGATTAACAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGAGGTTATCAAAATTTG
66 AAGATTAACAAAATTTCATAACGAGGTTATCAAAAAATCATAGGGAGATTATCAAAATTTG
* ** *
42651 TAGTTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGAGGTTTATAAAAATTTTATAG
1 TAGTTATCAAAATTTCATAAGAAAGTTATCAAAATTTTATA-GGAGGTAGATAAAAATTTCATAG
* * * ** * *
42716 GAAGATTTATCAAAATTTCATAGCGAGGTTATCACAATTTCATAGTGTGATTATCAAAATTT
65 GAAGA-TTAACAAAATTTCATAACGAGGTTATCAAAAAATCATAGGGAGATTATCAAAATTT
42778 CAGAGTGTGA
Statistics
Matches: 105, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
126 38 0.36
127 20 0.19
128 47 0.45
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (126 bp):
TAGTTATCAAAATTTCATAAGAAAGTTATCAAAATTTTATAGGAGGTAGATAAAAATTTCATAGG
AAGATTAACAAAATTTCATAACGAGGTTATCAAAAAATCATAGGGAGATTATCAAAATTTG
Done.