Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005488.1 Corchorus capsularis cultivar CVL-1 contig05506, 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: 32795
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:440 original size:18 final size:18
Alignment explanation
Indices: 417--454 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
407 AGCTCATCAA
417 CACGATGCATCAAAATCC
1 CACGATGCATCAAAATCC
435 CACGATGCATCAAAATCC
1 CACGATGCATCAAAATCC
453 CA
1 CA
455 GTTTGAGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.34, G:0.11, T:0.16
Consensus pattern (18 bp):
CACGATGCATCAAAATCC
Found at i:1549 original size:11 final size:11
Alignment explanation
Indices: 1535--1571 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
1525 GTTTGTCCCT
1535 TTTTTTTTTTC
1 TTTTTTTTTTC
1546 TTTTTTTTTTCC
1 TTTTTTTTTT-C
*
1558 TTTTTTCTTTC
1 TTTTTTTTTTC
1569 TTT
1 TTT
1572 AACAACACAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:1550 original size:12 final size:12
Alignment explanation
Indices: 1532--1568 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1522 GCCGTTTGTC
1532 CCTTTTTTTTTT
1 CCTTTTTTTTTT
*
1544 TCTTTTTTTTTT
1 CCTTTTTTTTTT
*
1556 CCTTTTTTCTTT
1 CCTTTTTTTTTT
1568 C
1 C
1569 TTTAACAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (12 bp):
CCTTTTTTTTTT
Found at i:1766 original size:2 final size:2
Alignment explanation
Indices: 1759--1794 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1749 GGCACAAACA
1759 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1795 GAAGCTATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2804 original size:12 final size:12
Alignment explanation
Indices: 2787--2869 Score: 127
Period size: 12 Copynumber: 7.2 Consensus size: 12
2777 TGCAAAAAGC
2787 ACTAAAACAGCA
1 ACTAAAACAGCA
2799 ACTAAAACAGC-
1 ACTAAAACAGCA
2810 ACTAAAACAGC-
1 ACTAAAACAGCA
2821 ACTAAAACAGC-
1 ACTAAAACAGCA
*
2832 ACTAAAATAGCA
1 ACTAAAACAGCA
*
2844 ACTAACACAGCA
1 ACTAAAACAGCA
2856 ACTAAAACAGCA
1 ACTAAAACAGCA
2868 AC
1 AC
2870 CCGACCCGAC
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
11 32 0.48
12 34 0.52
ACGTcount: A:0.55, C:0.27, G:0.08, T:0.10
Consensus pattern (12 bp):
ACTAAAACAGCA
Found at i:2810 original size:23 final size:23
Alignment explanation
Indices: 2780--2869 Score: 139
Period size: 22 Copynumber: 4.0 Consensus size: 23
2770 TATGGGATGC
2780 AAAA-AGCACTAAAACAGCAACT
1 AAAACAGCACTAAAACAGCAACT
2802 AAAACAGCACTAAAACAGC-ACT
1 AAAACAGCACTAAAACAGCAACT
*
2824 AAAACAGCACTAAAATAGCAACT
1 AAAACAGCACTAAAACAGCAACT
*
2847 AACACAGCAACTAAAACAGCAAC
1 AAAACAGC-ACTAAAACAGCAAC
2870 CCGACCCGAC
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
22 25 0.40
23 24 0.39
24 13 0.21
ACGTcount: A:0.57, C:0.26, G:0.09, T:0.09
Consensus pattern (23 bp):
AAAACAGCACTAAAACAGCAACT
Found at i:4264 original size:14 final size:14
Alignment explanation
Indices: 4245--4271 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4235 GAGTAGTGAA
4245 CTTAAATGGGTAAG
1 CTTAAATGGGTAAG
4259 CTTAAATGGGTAA
1 CTTAAATGGGTAA
4272 CCTTGAGTTT
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:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (14 bp):
CTTAAATGGGTAAG
Found at i:6880 original size:12 final size:12
Alignment explanation
Indices: 6865--6967 Score: 133
Period size: 12 Copynumber: 8.9 Consensus size: 12
6855 AATAATTGTG
*
6865 GCTGTTTTTGTT
1 GCTGTTTTAGTT
6877 GCTGTTTTAG-T
1 GCTGTTTTAGTT
6888 GCTGTTTTAGTT
1 GCTGTTTTAGTT
*
6900 GCTGTGTTAGTT
1 GCTGTTTTAGTT
*
6912 GCTATTTTAG-T
1 GCTGTTTTAGTT
6923 GCTGTTTTAG-T
1 GCTGTTTTAGTT
* *
6934 GTTGTTTTA-AT
1 GCTGTTTTAGTT
6945 GCTGTTTTAGTT
1 GCTGTTTTAGTT
6957 GCTGTTTTAGT
1 GCTGTTTTAGT
6968 GCTTTTTGCA
Statistics
Matches: 80, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
11 39 0.49
12 41 0.51
ACGTcount: A:0.10, C:0.08, G:0.25, T:0.57
Consensus pattern (12 bp):
GCTGTTTTAGTT
Found at i:6890 original size:11 final size:11
Alignment explanation
Indices: 6865--6974 Score: 132
Period size: 11 Copynumber: 9.7 Consensus size: 11
6855 AATAATTGTG
*
6865 GCTGTTTTTGTT
1 GCTGTTTTAG-T
6877 GCTGTTTTAGT
1 GCTGTTTTAGT
6888 GCTGTTTTAGTT
1 GCTGTTTTAG-T
*
6900 GCTGTGTTAGTT
1 GCTGTTTTAG-T
*
6912 GCTATTTTAGT
1 GCTGTTTTAGT
6923 GCTGTTTTAGT
1 GCTGTTTTAGT
* *
6934 GTTGTTTTAAT
1 GCTGTTTTAGT
6945 GCTGTTTTAGTT
1 GCTGTTTTAG-T
6957 GCTGTTTTAGT
1 GCTGTTTTAGT
6968 GCT-TTTT
1 GCTGTTTT
6975 GCATCCCATA
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
10 4 0.05
11 43 0.49
12 40 0.46
ACGTcount: A:0.09, C:0.08, G:0.25, T:0.58
Consensus pattern (11 bp):
GCTGTTTTAGT
Found at i:6895 original size:23 final size:23
Alignment explanation
Indices: 6865--7043 Score: 127
Period size: 23 Copynumber: 7.9 Consensus size: 23
6855 AATAATTGTG
6865 GCTGTTTTTGTTGCTGTTTTAGT
1 GCTGTTTTTGTTGCTGTTTTAGT
* *
6888 GCTGTTTTAGTTGCTGTGTTAGTT
1 GCTGTTTTTGTTGCTGTTTTAG-T
* *
6912 GCTATTTTAG-TGCTGTTTTAGT
1 GCTGTTTTTGTTGCTGTTTTAGT
* **
6934 GTTG-TTTTAATGCTGTTTTAGTT
1 GCTGTTTTTGTTGCTGTTTTAG-T
*
6957 GCTGTTTTAG-TGCT-TTTT-GCAT
1 GCTGTTTTTGTTGCTGTTTTAG--T
* ** * *
6979 CCCATATTTGTGGCTGTTTTAGT
1 GCTGTTTTTGTTGCTGTTTTAGT
* * *
7002 GCTGTTATTGTTGCTG-TATATT
1 GCTGTTTTTGTTGCTGTTTTAGT
*
7024 CCTGTTTTTGTTGCTGTTTT
1 GCTGTTTTTGTTGCTGTTTT
7044 GTGTGAAGAT
Statistics
Matches: 118, Mismatches: 29, Indels: 18
0.72 0.18 0.11
Matches are distributed among these distances:
21 4 0.03
22 42 0.36
23 54 0.46
24 17 0.14
25 1 0.01
ACGTcount: A:0.09, C:0.11, G:0.23, T:0.56
Consensus pattern (23 bp):
GCTGTTTTTGTTGCTGTTTTAGT
Found at i:13160 original size:44 final size:44
Alignment explanation
Indices: 13110--13193 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
13100 TTACCGATGA
* *
13110 GGTTACCGAAATTTCATAGGAAGATTA-GTAAAATTTCATAGGGT
1 GGTTACCAAAATATCATAGGAAGATTACG-AAAATTTCATAGGGT
* * *
13154 GGTTACCAAAATATCATTGGAAGGTTACGGAAATTTCATA
1 GGTTACCAAAATATCATAGGAAGATTACGAAAATTTCATA
13194 AGAAGGTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 33 0.97
45 1 0.03
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (44 bp):
GGTTACCAAAATATCATAGGAAGATTACGAAAATTTCATAGGGT
Found at i:13164 original size:22 final size:22
Alignment explanation
Indices: 13109--13202 Score: 89
Period size: 22 Copynumber: 4.3 Consensus size: 22
13099 GTTACCGATG
*
13109 AGGTTACCGAAATTTCATAGGA
1 AGGTTACCAAAATTTCATAGGA
* ** *
13131 AGATTAGTAAAATTTCATAGGG
1 AGGTTACCAAAATTTCATAGGA
* * *
13153 TGGTTACCAAAATATCATTGGA
1 AGGTTACCAAAATTTCATAGGA
** *
13175 AGGTTACGGAAATTTCATAAGA
1 AGGTTACCAAAATTTCATAGGA
13197 AGGTTA
1 AGGTTA
13203 TCGAATGACT
Statistics
Matches: 54, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (22 bp):
AGGTTACCAAAATTTCATAGGA
Found at i:13202 original size:44 final size:44
Alignment explanation
Indices: 13109--13202 Score: 100
Period size: 44 Copynumber: 2.1 Consensus size: 44
13099 GTTACCGATG
* * * *
13109 AGGTTACCGAAATTTCATAGGAAGATTAGTAAAATTTCATAGGG
1 AGGTTACCAAAATATCATAGGAAGATTAGTAAAATTTCATAAGA
* * * *
13153 TGGTTACCAAAATATCATTGGAAGGTTACG-GAAATTTCATAAGA
1 AGGTTACCAAAATATCATAGGAAGATTA-GTAAAATTTCATAAGA
13197 AGGTTA
1 AGGTTA
13203 TCGAATGACT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
44 39 0.98
45 1 0.03
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (44 bp):
AGGTTACCAAAATATCATAGGAAGATTAGTAAAATTTCATAAGA
Found at i:14818 original size:97 final size:97
Alignment explanation
Indices: 14615--14810 Score: 302
Period size: 97 Copynumber: 2.0 Consensus size: 97
14605 GGAATAATTT
*
14615 GTATATACATAGGGTTTTATTATCGAAGGAACAAAAGAAATTATCCCGCTTAAAGCAAATAAAGT
1 GTATATACATAGGGTCTTATTATCGAAGGAACAAAAGAAATTATCCCGCTTAAAGCAAATAAAGT
* * **
14680 AAAATAGCAAATCAAACCCACAACATTGGTTA
66 AAAATAGCAAATAAAACCCACAACATTAGCGA
* * *
14712 GTATATACATAGGGTCTTATTATCGAAGGAATAAAAGAAATTATCCTGCTTAAAGCAAAATAAGG
1 GTATATACATAGGGTCTTATTATCGAAGGAACAAAAGAAATTATCCCGCTTAAAGC-AAATAAAG
*
14777 TAAAATAGCAACTAAAACCCACAACATTAGCGA
65 TAAAATAGCAAATAAAACCCACAACATTAGCGA
14810 G
1 G
14811 GTTTACATTA
Statistics
Matches: 89, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
97 53 0.60
98 36 0.40
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.24
Consensus pattern (97 bp):
GTATATACATAGGGTCTTATTATCGAAGGAACAAAAGAAATTATCCCGCTTAAAGCAAATAAAGT
AAAATAGCAAATAAAACCCACAACATTAGCGA
Found at i:15000 original size:22 final size:22
Alignment explanation
Indices: 14975--15412 Score: 216
Period size: 22 Copynumber: 19.9 Consensus size: 22
14965 GTTCATTTTA
14975 AGGTTACCAAAATTTCA-ATGGG
1 AGGTTACCAAAATTTCATA-GGG
* **
14997 AGGTTACTAAAATTTCATAGCA
1 AGGTTACCAAAATTTCATAGGG
* * * *
15019 AGATTGCCAATATTTCATATGG
1 AGGTTACCAAAATTTCATAGGG
** **
15041 AGGTTACCGTAATTTCATAGCA
1 AGGTTACCAAAATTTCATAGGG
15063 AGGTTACCAAAATTTCATAGGG
1 AGGTTACCAAAATTTCATAGGG
* * * * *
15085 AAGTTGCTAGAATTTCATAGGA
1 AGGTTACCAAAATTTCATAGGG
**
15107 AGGTTACCAAAATTTCATATCG
1 AGGTTACCAAAATTTCATAGGG
* * * *
15129 AGGTTACAAAAATTTCCTAAGT
1 AGGTTACCAAAATTTCATAGGG
* * * *
15151 AGTTTATCAAAATTTTCATAAGT
1 AGGTTACCAAAA-TTTCATAGGG
***
15174 AGGTTACTGGAATTTCATAGGG
1 AGGTTACCAAAATTTCATAGGG
* * ***
15196 CGGTTACTAAAATTTCATAACA
1 AGGTTACCAAAATTTCATAGGG
* ** ***
15218 AGGTTAGCGGAATTTCATAACA
1 AGGTTACCAAAATTTCATAGGG
*
15240 AGGTTACCAAAATTTCATATGG
1 AGGTTACCAAAATTTCATAGGG
** * **
15262 AGGTTATGAAAATTTTATAGTA
1 AGGTTACCAAAATTTCATAGGG
* *
15284 AGGTTA--AAGGAATTTCATATGA
1 AGGTTACCAA--AATTTCATAGGG
** * * * **
15306 AAATTACAAAAATTTTACAGCA
1 AGGTTACCAAAATTTCATAGGG
**
15328 AGGTTACCGGAATTTCATAGGG
1 AGGTTACCAAAATTTCATAGGG
* *** *
15350 ATGTTACCGGCATTTCATAGGA
1 AGGTTACCAAAATTTCATAGGG
* * **
15372 AGGTTACCAGAATTTCGTAGAT
1 AGGTTACCAAAATTTCATAGGG
*
15394 AGGTTATCAAAATTTCATA
1 AGGTTACCAAAATTTCATA
15413 AGTAGTTTAT
Statistics
Matches: 307, Mismatches: 103, Indels: 12
0.73 0.24 0.03
Matches are distributed among these distances:
20 2 0.01
22 286 0.93
23 17 0.06
24 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (22 bp):
AGGTTACCAAAATTTCATAGGG
Found at i:15014 original size:44 final size:44
Alignment explanation
Indices: 14955--15412 Score: 287
Period size: 44 Copynumber: 10.4 Consensus size: 44
14945 TTATAACATT
* ***
14955 GTTACCAAAAGTTCATTTTAAGGTTACCAAAATTTCA-ATGGGAG
1 GTTACCAAAATTTCATAGCAAGGTTACCAAAATTTCATAT-GGAG
* * * *
14999 GTTACTAAAATTTCATAGCAAGATTGCCAATATTTCATATGGAG
1 GTTACCAAAATTTCATAGCAAGGTTACCAAAATTTCATATGGAG
** * *
15043 GTTACCGTAATTTCATAGCAAGGTTACCAAAATTTCATAGGGAA
1 GTTACCAAAATTTCATAGCAAGGTTACCAAAATTTCATATGGAG
* * * * *
15087 GTTGCTAGAATTTCATAGGAAGGTTACCAAAATTTCATATCGAG
1 GTTACCAAAATTTCATAGCAAGGTTACCAAAATTTCATATGGAG
* * * * * * *
15131 GTTACAAAAATTTCCTAAG-TAGTTTATCAAAATTTTCATAAGTAG
1 GTTACCAAAATTTCAT-AGCAAGGTTACCAAAA-TTTCATATGGAG
*** *** * ***
15176 GTTACTGGAATTTCATAGGGCGGTTACTAAAATTTCATAACAAG
1 GTTACCAAAATTTCATAGCAAGGTTACCAAAATTTCATATGGAG
* ** *
15220 GTTAGCGGAATTTCATAACAAGGTTACCAAAATTTCATATGGAG
1 GTTACCAAAATTTCATAGCAAGGTTACCAAAATTTCATATGGAG
** * * * *
15264 GTTATGAAAATTTTATAGTAAGGTTA--AAGGAATTTCATATGAAA
1 GTTACCAAAATTTCATAGCAAGGTTACCAA--AATTTCATATGGAG
* * * * ** * *
15308 ATTACAAAAATTTTACAGCAAGGTTACCGGAATTTCATAGGGAT
1 GTTACCAAAATTTCATAGCAAGGTTACCAAAATTTCATATGGAG
*** * * * *
15352 GTTACCGGCATTTCATAGGAAGGTTACCAGAATTTCGTA-GATAG
1 GTTACCAAAATTTCATAGCAAGGTTACCAAAATTTCATATG-GAG
*
15396 GTTATCAAAATTTCATA
1 GTTACCAAAATTTCATA
15413 AGTAGTTTAT
Statistics
Matches: 315, Mismatches: 90, Indels: 18
0.74 0.21 0.04
Matches are distributed among these distances:
42 2 0.01
43 1 0.00
44 279 0.89
45 33 0.10
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.33
Consensus pattern (44 bp):
GTTACCAAAATTTCATAGCAAGGTTACCAAAATTTCATATGGAG
Found at i:15211 original size:111 final size:110
Alignment explanation
Indices: 14997--15346 Score: 283
Period size: 110 Copynumber: 3.2 Consensus size: 110
14987 TTTCAATGGG
* * * * * * * * ** * *
14997 AGGTTACTAAAATTTCATAGCAAGATTGCCAATATTTCATATGGAGGTTACCGTAATTTCATAGC
1 AGGTTACCAAAATTTCATAACAAGGTTACAAAAATTTCATAAGGAGGTTATCAAAATTTTATAGT
* * **
15062 AAGGTTACCAA--AATTTCATAGGGAAGTTGCTAGAATTTCATAGGA
66 AAGGTTA--AAGGAATTTCATAGGGAAGTTACTAAAATTTCATAACA
* * * * *
15107 AGGTTACCAAAATTTCATATCGAGGTTACAAAAATTTCCTAAGTAGTTTATCAAAATTTTCATAA
1 AGGTTACCAAAATTTCATAACAAGGTTACAAAAATTTCATAAGGAGGTTATCAAAATTTT-AT-A
** **
15172 GT-AGGTTACTGGAATTTCATAGGGCGGTTACTAAAATTTCATAACA
64 GTAAGGTTAAAGGAATTTCATAGGGAAGTTACTAAAATTTCATAACA
* ** * * *
15218 AGGTTAGCGGAATTTCATAACAAGGTTACCAAAATTTCATATGGAGGTTATGAAAATTTTATAGT
1 AGGTTACCAAAATTTCATAACAAGGTTACAAAAATTTCATAAGGAGGTTATCAAAATTTTATAGT
* * * * * * *
15283 AAGGTTAAAGGAATTTCATATGAAAATTACAAAAATTTTACAGCA
66 AAGGTTAAAGGAATTTCATAGGGAAGTTACTAAAATTTCATAACA
**
15328 AGGTTACCGGAATTTCATA
1 AGGTTACCAAAATTTCATA
15347 GGGATGTTAC
Statistics
Matches: 188, Mismatches: 47, Indels: 10
0.77 0.19 0.04
Matches are distributed among these distances:
109 3 0.02
110 98 0.52
111 85 0.45
112 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (110 bp):
AGGTTACCAAAATTTCATAACAAGGTTACAAAAATTTCATAAGGAGGTTATCAAAATTTTATAGT
AAGGTTAAAGGAATTTCATAGGGAAGTTACTAAAATTTCATAACA
Found at i:19267 original size:19 final size:19
Alignment explanation
Indices: 19256--19292 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
19246 AATTTTTAAG
19256 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
19275 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
19293 ACAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:21317 original size:21 final size:22
Alignment explanation
Indices: 21279--21324 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
21269 AAGAGGAGAA
* *
21279 TGTCAGAATTATGTTTAATGAC
1 TGTCAGAACTATGATTAATGAC
*
21301 TGTCAG-ACTATGATTAATTAC
1 TGTCAGAACTATGATTAATGAC
21322 TGT
1 TGT
21325 TTTAATCTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.41
Consensus pattern (22 bp):
TGTCAGAACTATGATTAATGAC
Found at i:23843 original size:83 final size:82
Alignment explanation
Indices: 23665--23836 Score: 283
Period size: 81 Copynumber: 2.1 Consensus size: 82
23655 TAGCTTGCTG
* **
23665 GCTGCTGCTAAACTTTTATGTACCAAAAAAATTTTTTCATTTAGAATCTCAAAGTCTCAACTCTT
1 GCTGCTGCTAAACTTTTATGTACCAAAAAAA-TATTTCATTTAGAATAGCAAAGTCTCAACTCTT
23730 AACTCCCCATTAATCTCT
65 AACTCCCCATTAATCTCT
* *
23748 ACTGCTGCTAAACTTTTATGTACCAAAAAAA-ATTTCATTTAGAATAGCGAAGTCTCAACTCTTA
1 GCTGCTGCTAAACTTTTATGTACCAAAAAAATATTTCATTTAGAATAGCAAAGTCTCAACTCTTA
23812 ACTCCCCATTAATCTCT
66 ACTCCCCATTAATCTCT
23829 GCTGCTGC
1 GCTGCTGC
23837 ATTAAACCAA
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
81 53 0.64
83 30 0.36
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.35
Consensus pattern (82 bp):
GCTGCTGCTAAACTTTTATGTACCAAAAAAATATTTCATTTAGAATAGCAAAGTCTCAACTCTTA
ACTCCCCATTAATCTCT
Found at i:23889 original size:2 final size:2
Alignment explanation
Indices: 23846--23876 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
23836 CATTAAACCA
23846 AT 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 AT A
23877 AAGAGCATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24055 original size:3 final size:3
Alignment explanation
Indices: 24047--24077 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
24037 TATGAGATGG
24047 ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
24078 TTTTGATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:25991 original size:41 final size:41
Alignment explanation
Indices: 25915--25994 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
25905 AGTGTAGGTG
* *
25915 CATGTAATTGAAAAAATTGAAAATTCAAGGATTAATTTAGT
1 CATGCAATTGAAAAAATTGAAAATTAAAGGATTAATTTAGT
* * *
25956 CATGCAATTG-AAAATTTTAAAATTTAAAGGGTTAATTTA
1 CATGCAATTGAAAAAATTGAAAA-TTAAAGGATTAATTTA
25995 ACCCTTTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 10 0.30
41 23 0.70
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (41 bp):
CATGCAATTGAAAAAATTGAAAATTAAAGGATTAATTTAGT
Found at i:28901 original size:12 final size:12
Alignment explanation
Indices: 28884--28910 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28874 TTAGAACATT
28884 GGAGGATATTGA
1 GGAGGATATTGA
28896 GGAGGATATTGA
1 GGAGGATATTGA
28908 GGA
1 GGA
28911 AGATTGGTTC
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:0.33, C:0.00, G:0.44, T:0.22
Consensus pattern (12 bp):
GGAGGATATTGA
Done.