Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010115.1 Corchorus capsularis cultivar CVL-1 contig10136, 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: 25436
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:4571 original size:16 final size:16
Alignment explanation
Indices: 4552--4646 Score: 70
Period size: 16 Copynumber: 6.0 Consensus size: 16
4542 AACTCGTCTG
*
4552 AATCTGAACCCGAAAA
1 AATCTAAACCCGAAAA
*
4568 AATCCAAACCCGAAAA
1 AATCTAAACCCGAAAA
* *
4584 ACTC-AAATCCGAAAA
1 AATCTAAACCCGAAAA
* *
4599 AAT-TCGAACCTGAAAA
1 AATCT-AAACCCGAAAA
4615 AA-CTCAAACCCGAAAA
1 AATCT-AAACCCGAAAA
* * *
4631 AACCCAAATCCGAAAA
1 AATCTAAACCCGAAAA
4647 TTTATGAAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
15 12 0.19
16 50 0.79
17 1 0.02
ACGTcount: A:0.54, C:0.27, G:0.08, T:0.11
Consensus pattern (16 bp):
AATCTAAACCCGAAAA
Found at i:4616 original size:32 final size:31
Alignment explanation
Indices: 4558--4646 Score: 115
Period size: 32 Copynumber: 2.8 Consensus size: 31
4548 TCTGAATCTG
4558 AACCCGAAAAAATCCAAACCCGAAAAACTCA
1 AACCCGAAAAAATCCAAACCCGAAAAACTCA
* * * *
4589 AATCCGAAAAAATTCGAACCTGAAAAAACTCA
1 AACCCGAAAAAATCCAAACCCG-AAAAACTCA
* *
4621 AACCCGAAAAAACCCAAATCCGAAAA
1 AACCCGAAAAAATCCAAACCCGAAAA
4647 TTTATGAAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 22 0.47
32 25 0.53
ACGTcount: A:0.55, C:0.28, G:0.08, T:0.09
Consensus pattern (31 bp):
AACCCGAAAAAATCCAAACCCGAAAAACTCA
Found at i:4836 original size:32 final size:32
Alignment explanation
Indices: 4795--4871 Score: 136
Period size: 32 Copynumber: 2.4 Consensus size: 32
4785 ACCTAAACTG
* *
4795 AACCCGAACCCGAATTAACCTGACTCAAATTC
1 AACCCGAACCCGAATTAACATGACCCAAATTC
4827 AACCCGAACCCGAATTAACATGACCCAAATTC
1 AACCCGAACCCGAATTAACATGACCCAAATTC
4859 AACCCGAACCCGA
1 AACCCGAACCCGA
4872 TGACTCGAGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.39, C:0.36, G:0.10, T:0.14
Consensus pattern (32 bp):
AACCCGAACCCGAATTAACATGACCCAAATTC
Found at i:4857 original size:15 final size:15
Alignment explanation
Indices: 4802--4862 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
4792 CTGAACCCGA
*
4802 ACCCGAATTAACCTG
1 ACCCAAATTAACCTG
* *
4817 ACTCAAATTCAACCCG
1 ACCCAAATT-AACCTG
* *
4833 AACCCGAATTAACATG
1 -ACCCAAATTAACCTG
4849 ACCCAAATTCAACC
1 ACCCAAATT-AACC
4863 CGAACCCGAT
Statistics
Matches: 34, Mismatches: 9, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
15 15 0.44
16 12 0.35
17 7 0.21
ACGTcount: A:0.39, C:0.34, G:0.08, T:0.18
Consensus pattern (15 bp):
ACCCAAATTAACCTG
Found at i:5231 original size:23 final size:23
Alignment explanation
Indices: 5205--5271 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
5195 CTTTTATGGG
*
5205 ACTCCTTAGTGAGAGTTTTTTGA
1 ACTCCTTTGTGAGAGTTTTTTGA
* *
5228 ACTCCTTTGTGAGAGTTTTTGGG
1 ACTCCTTTGTGAGAGTTTTTTGA
*
5251 ACTCCTTTGTGAGAGCTTTTT
1 ACTCCTTTGTGAGAGTTTTTT
5272 CTATTGTCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.16, C:0.15, G:0.24, T:0.45
Consensus pattern (23 bp):
ACTCCTTTGTGAGAGTTTTTTGA
Found at i:5318 original size:59 final size:59
Alignment explanation
Indices: 5221--5339 Score: 211
Period size: 59 Copynumber: 2.0 Consensus size: 59
5211 TAGTGAGAGT
* *
5221 TTTTTGAACTCCTTTGTGAGAGTTTTTGGGACTCCTTTGTGAGAGCTTTTTCTATTGTC
1 TTTTGGAACTCCTTTGTGAGAGTTTTTGGGACTCCTTTGTGAGAACTTTTTCTATTGTC
*
5280 TTTTGGAACTCCTTTGTGAGAGTTTTTGGGGCTCCTTTGTGAGAACTTTTTCTATTGTC
1 TTTTGGAACTCCTTTGTGAGAGTTTTTGGGACTCCTTTGTGAGAACTTTTTCTATTGTC
5339 T
1 T
5340 CTGTACAAGT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.13, C:0.15, G:0.23, T:0.49
Consensus pattern (59 bp):
TTTTGGAACTCCTTTGTGAGAGTTTTTGGGACTCCTTTGTGAGAACTTTTTCTATTGTC
Found at i:5329 original size:23 final size:23
Alignment explanation
Indices: 5279--5329 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5269 TTTCTATTGT
*
5279 CTTTTGGAACTCCTTTGTGAGAG
1 CTTTTGGAACTCCTTTGTGAGAA
* **
5302 TTTTTGGGGCTCCTTTGTGAGAA
1 CTTTTGGAACTCCTTTGTGAGAA
5325 CTTTT
1 CTTTT
5330 TCTATTGTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.14, C:0.16, G:0.25, T:0.45
Consensus pattern (23 bp):
CTTTTGGAACTCCTTTGTGAGAA
Found at i:5675 original size:22 final size:22
Alignment explanation
Indices: 5649--5691 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5639 AAAGATGTCA
*
5649 GAAAAAAAA-ATAAAAAAAATC
1 GAAAAAAAACAAAAAAAAAATC
5670 GAAAAAAAACAAAAAAAAAATC
1 GAAAAAAAACAAAAAAAAAATC
5692 CTTGAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.81, C:0.07, G:0.05, T:0.07
Consensus pattern (22 bp):
GAAAAAAAACAAAAAAAAAATC
Found at i:5689 original size:11 final size:10
Alignment explanation
Indices: 5650--5688 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
5640 AAGATGTCAG
*
5650 AAAAAAAAAT
1 AAAAAAAAAC
*
5660 AAAAAAAATC
1 AAAAAAAAAC
*
5670 GAAAAAAAAC
1 AAAAAAAAAC
5680 AAAAAAAAA
1 AAAAAAAAA
5689 ATCCTTGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.87, C:0.05, G:0.03, T:0.05
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:10724 original size:19 final size:20
Alignment explanation
Indices: 10700--10740 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
10690 AAGAGGAAGA
*
10700 GGAAGAGGAAGACAT-GGTG
1 GGAAGAAGAAGACATAGGTG
*
10719 GGAAGAAGAAGAGATAGGTG
1 GGAAGAAGAAGACATAGGTG
10739 GG
1 GG
10741 GAAGGAGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.39, C:0.02, G:0.49, T:0.10
Consensus pattern (20 bp):
GGAAGAAGAAGACATAGGTG
Found at i:13643 original size:22 final size:21
Alignment explanation
Indices: 13592--13644 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 21
13582 GAATTTGTGT
* * *
13592 GGTTGTCAAAATTTATAGTGA
1 GGTTATCAAAATTAATAGGGA
* *
13613 GATTTTCAAAACTTAATAGGGA
1 GGTTATCAAAA-TTAATAGGGA
13635 GGTTATCAAA
1 GGTTATCAAA
13645 TTTTCATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.34
Consensus pattern (21 bp):
GGTTATCAAAATTAATAGGGA
Found at i:13704 original size:22 final size:22
Alignment explanation
Indices: 13674--13719 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
13664 TCGAAGATTG
*
13674 ATAATAATGTTATCAAAATTTC
1 ATAAAAATGTTATCAAAATTTC
*
13696 ATAAAAATGTTATCACAATTTC
1 ATAAAAATGTTATCAAAATTTC
13718 AT
1 AT
13720 GGTATGGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (22 bp):
ATAAAAATGTTATCAAAATTTC
Found at i:13823 original size:22 final size:22
Alignment explanation
Indices: 13797--13900 Score: 83
Period size: 22 Copynumber: 4.9 Consensus size: 22
13787 AATTATTAAG
13797 ATTTCATAAGTAGGTTATCAAA
1 ATTTCATAAGTAGGTTATCAAA
* *
13819 TTTTCATAGTGTA-GTTATCAAA
1 ATTTCATA-AGTAGGTTATCAAA
* **
13841 ATTCCAT-AGGGGGATTATCAAA
1 ATTTCATAAGTAGG-TTATCAAA
*
13863 ATTTCATAAGGA-G--ATCAAA
1 ATTTCATAAGTAGGTTATCAAA
* *
13882 ATTTCATAGGAAGGTTATC
1 ATTTCATAAGTAGGTTATC
13901 GAAACGTTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
19 16 0.25
20 2 0.03
21 1 0.02
22 39 0.61
23 6 0.09
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.35
Consensus pattern (22 bp):
ATTTCATAAGTAGGTTATCAAA
Found at i:14078 original size:22 final size:22
Alignment explanation
Indices: 14053--14097 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
14043 CATAGTATAA
* *
14053 TTATCAAATTTTCATAAAAAGG
1 TTATAAAAATTTCATAAAAAGG
*
14075 TTATAAAAATTTCATAAGAAGG
1 TTATAAAAATTTCATAAAAAGG
14097 T
1 T
14098 CATCGATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.36
Consensus pattern (22 bp):
TTATAAAAATTTCATAAAAAGG
Found at i:14188 original size:22 final size:22
Alignment explanation
Indices: 14163--14265 Score: 86
Period size: 22 Copynumber: 4.7 Consensus size: 22
14153 TAGAAGGATG
* *
14163 TTATCAAAATTTTATAGAGAGA
1 TTATCAAAATTTCATAGGGAGA
** * *
14185 TTATTTAAATTTCTTTATGTG-G-
1 TTATCAAAATTTC-ATA-GGGAGA
14207 TTATCAAAATTTCATAGGGAGA
1 TTATCAAAATTTCATAGGGAGA
* *
14229 TTAAT-AAAATTTCATTGGGAGG
1 TT-ATCAAAATTTCATAGGGAGA
14251 TTATCAAAATTTCAT
1 TTATCAAAATTTCAT
14266 TCTAAAGCTT
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
20 2 0.03
21 5 0.08
22 50 0.78
23 5 0.08
24 2 0.03
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGGAGA
Found at i:14210 original size:44 final size:44
Alignment explanation
Indices: 14157--14265 Score: 137
Period size: 44 Copynumber: 2.5 Consensus size: 44
14147 GCATTTTAGA
* * * * *
14157 AGGATGTTATCAAAATTTTATAGAGAGATTATTTAAATTTCTTT
1 AGGAGGTTATCAAAATTTCATAGAGAGATTAATAAAATTTCATT
* * *
14201 ATGTGGTTATCAAAATTTCATAGGGAGATTAATAAAATTTCATT
1 AGGAGGTTATCAAAATTTCATAGAGAGATTAATAAAATTTCATT
*
14245 GGGAGGTTATCAAAATTTCAT
1 AGGAGGTTATCAAAATTTCAT
14266 TCTAAAGCTT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.40
Consensus pattern (44 bp):
AGGAGGTTATCAAAATTTCATAGAGAGATTAATAAAATTTCATT
Found at i:14266 original size:22 final size:22
Alignment explanation
Indices: 14205--14266 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 22
14195 TTCTTTATGT
*
14205 GGTTATCAAAATTTCATAGGGA
1 GGTTATCAAAATTTCATTGGGA
*
14227 GATTAAT-AAAATTTCATTGGGA
1 GGTT-ATCAAAATTTCATTGGGA
14249 GGTTATCAAAATTTCATT
1 GGTTATCAAAATTTCATT
14267 CTAAAGCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (22 bp):
GGTTATCAAAATTTCATTGGGA
Found at i:15729 original size:120 final size:120
Alignment explanation
Indices: 15599--16609 Score: 1073
Period size: 120 Copynumber: 8.4 Consensus size: 120
15589 CTACATTTAT
* * * *
15599 AAGTCGCCTCCACCACCTCCATATGTTTACAAGTCACCACCACCTCCTCCATACGTCTACAAGTC
1 AAGTCACCTCCTCCTCCTCCATATGTCTACAAGTCACCACCACCTCCTCCATACGTCTACAAGTC
** * * *
15664 ACCTCCTCCTCCTCCATATATTTACAAGTCACCTCCACCACCACCATATGTGTAC
66 ACCTCCTCCTCCTCCATACGTCTACAAGTCACCTCCACCACCACCATACGTCTAC
* * * * *
15719 AAGTCACCTCCACCACCTCCATATGTCTACAAGTCACCTCCACCACCTCCATATGTCTACAAGTC
1 AAGTCACCTCCTCCTCCTCCATATGTCTACAAGTCACCACCACCTCCTCCATACGTCTACAAGTC
* * * *
15784 ACCTCCTCCTCCTCCATACGTTTATAAGTCACCTCCACCACCTCCATATGTCTAC
66 ACCTCCTCCTCCTCCATACGTCTACAAGTCACCTCCACCACCACCATACGTCTAC
* * * * * * *
15839 AAGTCATCTCCTCCCCCTCCATATGTCTACAAGTCACCTCCGCCACCACCATACGTGTACAAGTC
1 AAGTCACCTCCTCCTCCTCCATATGTCTACAAGTCACCACCACCTCCTCCATACGTCTACAAGTC
* *
15904 ACCTCCTCCTCCTCCATACGTGTACAAGTCACCTCCACCACCACCATACGTGTAC
66 ACCTCCTCCTCCTCCATACGTCTACAAGTCACCTCCACCACCACCATACGTCTAC
* * * * * *
15959 AAGTCACCTCCTCCTCCTCCATACGTGTATAAATCACCACCTCCTCCTCCATATGTCTACAAGTC
1 AAGTCACCTCCTCCTCCTCCATATGTCTACAAGTCACCACCACCTCCTCCATACGTCTACAAGTC
* * * * *
16024 ACCACCACCTCCTCCATACGTTTACAAGTCACCTCCACCACCACCATATGTGTAC
66 ACCTCCTCCTCCTCCATACGTCTACAAGTCACCTCCACCACCACCATACGTCTAC
* * * * * *
16079 AAGTCACCTCCTCCTCCTCCTTATGTTTACAAGTCCCCTCCACCTCCACCATACGTGTACAAGTC
1 AAGTCACCTCCTCCTCCTCCATATGTCTACAAGTCACCACCACCTCCTCCATACGTCTACAAGTC
* * * * * * * *
16144 ACC-CCACC-CCACCATACGTCTACAAGTCACCACCTCCTCCTCCATATGTGTAC
66 ACCTCCTCCTCCTCCATACGTCTACAAGTCACCTCCACCACCACCATACGTCTAC
* * ** *
16197 -AGATCACCTCCACCTCCACCATACCTCTACAATTCACCATCC-CCTCCTCCATACGTCTACAAG
1 AAG-TCACCTCCTCCTCCTCCATATGTCTACAAGTCACCA-CCACCTCCTCCATACGTCTACAAG
* * * * * * *
16260 TCACCACCCCCTCCTCCATACGTCTATAAATCACCCCCTCCACCACCATACCTCTAC
64 TCACCTCCTCCTCCTCCATACGTCTACAAGTCACCTCCACCACCACCATACGTCTAC
* * * * * * **
16317 AAGTCACCACCTCCTCCACCATATGTGTACAAATCACCCCCACCTCCACCATATTTCTACAAGTC
1 AAGTCACCTCCTCCTCCTCCATATGTCTACAAGTCACCACCACCTCCTCCATACGTCTACAAGTC
* * * * * * *
16382 ACCACCCCCTCCTCCATACGTCTATAAATCACCCCCTCCACCACCATACATCTAC
66 ACCTCCTCCTCCTCCATACGTCTACAAGTCACCTCCACCACCACCATACGTCTAC
* * * * * *
16437 AAGTCACCACCTCCTCCACCATATGTGTACAAGTCACCTCCACCACCACCATACGTCTACAAGTC
1 AAGTCACCTCCTCCTCCTCCATATGTCTACAAGTCACCACCACCTCCTCCATACGTCTACAAGTC
* * * * * *
16502 A-CTACCGCCTCCACCATACGTCTAC-AGCTCCCCTCCCCCTCCACCATACGTCTAT
66 ACCT-CCTCCTCCTCCATACGTCTACAAG-TCACCTCCACCACCACCATACGTCTAC
* * * *
16557 AAATCACCACCACCTCC-CTCATATGTCTACAAGTCACCACCACCACCTCCATA
1 AAGTCACCTCCTCCTCCTC-CATATGTCTACAAGTCACCACCACCTCCTCCATA
16610 TTACTACAAG
Statistics
Matches: 774, Mismatches: 108, Indels: 18
0.86 0.12 0.02
Matches are distributed among these distances:
117 2 0.00
118 90 0.12
119 16 0.02
120 664 0.86
121 2 0.00
ACGTcount: A:0.26, C:0.44, G:0.07, T:0.23
Consensus pattern (120 bp):
AAGTCACCTCCTCCTCCTCCATATGTCTACAAGTCACCACCACCTCCTCCATACGTCTACAAGTC
ACCTCCTCCTCCTCCATACGTCTACAAGTCACCTCCACCACCACCATACGTCTAC
Found at i:16610 original size:30 final size:30
Alignment explanation
Indices: 15599--16609 Score: 947
Period size: 30 Copynumber: 33.8 Consensus size: 30
15589 CTACATTTAT
* * * *
15599 AAGTCGCCTCCACCACCTCCATATGTTTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
*
15629 AAGTCACCACCACCTCCTCCATACGTCTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* ** *
15659 AAGTCACCTCCTCCTCCTCCATATATTTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* * * *
15689 AAGTCACCTCCACCACCACCATATGTGTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* *
15719 AAGTCACCTCCACCACCTCCATATGTCTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* *
15749 AAGTCACCTCCACCACCTCCATATGTCTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* * *
15779 AAGTCACCTCCTCCTCCTCCATACGTTTAT
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* *
15809 AAGTCACCTCCACCACCTCCATATGTCTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* * * *
15839 AAGTCATCTCCTCCCCCTCCATATGTCTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* * * *
15869 AAGTCACCTCCGCCACCACCATACGTGTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* *
15899 AAGTCACCTCCTCCTCCTCCATACGTGTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* * *
15929 AAGTCACCTCCACCACCACCATACGTGTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* * *
15959 AAGTCACCTCCTCCTCCTCCATACGTGTAT
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* * * *
15989 AAATCACCACCTCCTCCTCCATATGTCTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* *
16019 AAGTCACCACCACCTCCTCCATACGTTTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* * * *
16049 AAGTCACCTCCACCACCACCATATGTGTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* * * *
16079 AAGTCACCTCCTCCTCCTCCTTATGTTTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* * *
16109 AAGTCCCCTCCACCTCCACCATACGTGTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
*
16139 AAGTCACC-CCACC-CCACCATACGTCTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* * * *
16167 AAGTCACCACCTCCTCCTCCATATGTGTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* *
16197 -AGATCACCTCCACCTCCACCATACCTCTAC
1 AAG-TCACCTCCACCTCCTCCATACGTCTAC
*
16227 AATTCACCATCC-CCTCCTCCATACGTCTAC
1 AAGTCACC-TCCACCTCCTCCATACGTCTAC
* * *
16257 AAGTCACCACCCCCTCCTCCATACGTCTAT
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* * * * * *
16287 AAATCACCCCCTCCACCACCATACCTCTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* * * * *
16317 AAGTCACCACCTCCTCCACCATATGTGTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* * * **
16347 AAATCACCCCCACCTCCACCATATTTCTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* * *
16377 AAGTCACCACCCCCTCCTCCATACGTCTAT
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* * * * * *
16407 AAATCACCCCCTCCACCACCATACATCTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* * * * *
16437 AAGTCACCACCTCCTCCACCATATGTGTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* *
16467 AAGTCACCTCCACCACCACCATACGTCTAC
1 AAGTCACCTCCACCTCCTCCATACGTCTAC
* *
16497 AAGTCA-CTACCGCCTCCACCATACGTCTAC
1 AAGTCACCT-CCACCTCCTCCATACGTCTAC
* * * *
16527 -AGCTCCCCTCCCCCTCCACCATACGTCTAT
1 AAG-TCACCTCCACCTCCTCCATACGTCTAC
* * *
16557 AAATCACCACCACCTCC-CTCATATGTCTAC
1 AAGTCACCTCCACCTCCTC-CATACGTCTAC
* *
16587 AAGTCACCACCACCACCTCCATA
1 AAGTCACCTCCACCTCCTCCATA
16610 TTACTACAAG
Statistics
Matches: 824, Mismatches: 145, Indels: 24
0.83 0.15 0.02
Matches are distributed among these distances:
28 22 0.03
29 18 0.02
30 776 0.94
31 8 0.01
ACGTcount: A:0.26, C:0.44, G:0.07, T:0.23
Consensus pattern (30 bp):
AAGTCACCTCCACCTCCTCCATACGTCTAC
Found at i:17081 original size:2 final size:2
Alignment explanation
Indices: 17074--17106 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17064 GAATATGATT
17074 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17107 TGTCCTCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18528 original size:22 final size:23
Alignment explanation
Indices: 18490--18539 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
18480 CTTGAGAAAA
18490 ATCGAGCCGAACTCGAGTA-TTC
1 ATCGAGCCGAACTCGAGTAGTTC
*
18512 ATCGAGCCG-AGTCCGAGTAGTTC
1 ATCGAGCCGAACT-CGAGTAGTTC
18535 A-CGAG
1 ATCGAG
18540 TAGTATCATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 2 0.08
22 19 0.76
23 4 0.16
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
ATCGAGCCGAACTCGAGTAGTTC
Found at i:19817 original size:12 final size:12
Alignment explanation
Indices: 19800--19824 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19790 TTATGGGGTG
19800 AAATAATGGAGA
1 AAATAATGGAGA
19812 AAATAATGGAGA
1 AAATAATGGAGA
19824 A
1 A
19825 TCATTTGACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (12 bp):
AAATAATGGAGA
Found at i:21265 original size:111 final size:111
Alignment explanation
Indices: 21071--21293 Score: 419
Period size: 111 Copynumber: 2.0 Consensus size: 111
21061 GCGGAAGGTC
*
21071 CATGTACACTTTTTCCTCCAAGTCCCCATGTAAAAAAGCGTTCTTTATAAAGTGTCCAATTTAAA
1 CATGTACACTTCTTCCTCCAAGTCCCCATGTAAAAAAGCGTTCTTTATAAAGTGTCCAATTTAAA
*
21136 TTTGCAGCAACAGATAAGAGAACTCAAACAGTATTCATTTTTGCAA
66 TTTGCAGCAACAGATAAGAGAACTCAAACAGTATTCATATTTGCAA
21182 CATGTACACTTCTTCCTCCAAGTCCCCATGTAAAAAAGCGTTCTTTATAAAGTGTCCAATTTAAA
1 CATGTACACTTCTTCCTCCAAGTCCCCATGTAAAAAAGCGTTCTTTATAAAGTGTCCAATTTAAA
*
21247 TTTGCAGCAACAGATAAGAGAACTCGAACAGTATTCATATTTGCAA
66 TTTGCAGCAACAGATAAGAGAACTCAAACAGTATTCATATTTGCAA
21293 C
1 C
21294 TAGAGGAAAT
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 109 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (111 bp):
CATGTACACTTCTTCCTCCAAGTCCCCATGTAAAAAAGCGTTCTTTATAAAGTGTCCAATTTAAA
TTTGCAGCAACAGATAAGAGAACTCAAACAGTATTCATATTTGCAA
Found at i:24615 original size:18 final size:17
Alignment explanation
Indices: 24592--24625 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
24582 AATTTGTAAT
24592 AATAAATCATAAAAAATA
1 AATAAAT-ATAAAAAATA
*
24610 AATAAATATAATAAAT
1 AATAAATATAAAAAAT
24626 CGCATAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
AATAAATATAAAAAATA
Found at i:24644 original size:52 final size:51
Alignment explanation
Indices: 24543--24644 Score: 143
Period size: 52 Copynumber: 2.0 Consensus size: 51
24533 CAATAGTTCG
* * *
24543 TAAATCATAAAAAAAAAAAAGTATAATAAATCACATATTAATTTGTAATAA
1 TAAATCATAAAAAAAAAAAAGTATAATAAATCACATAATAATCTATAATAA
*
24594 TAAATCATAAAAAATAAATAAA-TATAATAAATCGCATAATAATCTATAATA
1 TAAATCATAAAAAA-AAA-AAAGTATAATAAATCACATAATAATCTATAATA
24645 TAACATTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
51 14 0.31
52 28 0.62
53 3 0.07
ACGTcount: A:0.61, C:0.07, G:0.03, T:0.29
Consensus pattern (51 bp):
TAAATCATAAAAAAAAAAAAGTATAATAAATCACATAATAATCTATAATAA
Done.