Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014328.1 Corchorus capsularis cultivar CVL-1 contig14349, 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: 17456
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:198 original size:25 final size:24
Alignment explanation
Indices: 170--221 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
160 TTCAAACCCT
*
170 AAACTTAATTTCTAACAACTTCTTC
1 AAACTTAATTTCTAACAA-ATCTTC
* *
195 AAACTTCATTTTTAACAAATCTTC
1 AAACTTAATTTCTAACAAATCTTC
219 AAA
1 AAA
222 TTCATTTTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.38
Consensus pattern (24 bp):
AAACTTAATTTCTAACAAATCTTC
Found at i:267 original size:18 final size:18
Alignment explanation
Indices: 244--278 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
234 CATTTTAATC
244 ATAAACTAATTAAATACA
1 ATAAACTAATTAAATACA
*
262 ATAAACTAATTAGATAC
1 ATAAACTAATTAAATAC
279 TAATTAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.11, G:0.03, T:0.29
Consensus pattern (18 bp):
ATAAACTAATTAAATACA
Found at i:622 original size:10 final size:10
Alignment explanation
Indices: 592--622 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
582 ACTAATTAAT
592 ATTAAAAAAA
1 ATTAAAAAAA
*
602 ATTTAAAAAA
1 ATTAAAAAAA
612 ATTAAAAAAA
1 ATTAAAAAAA
622 A
1 A
623 AAAACAAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
ATTAAAAAAA
Found at i:1024 original size:22 final size:21
Alignment explanation
Indices: 999--1548 Score: 161
Period size: 22 Copynumber: 25.7 Consensus size: 21
989 ATGATCTCAT
999 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACC-TCC
* *
1021 TATGAAATTTTAATAA--TAC
1 TATGAAATTTTGATAACCTCC
* * * * **
1040 TATGGAATTTCGAGAATCTTTT
1 TATGAAATTTTGATAA-CCTCC
** *
1062 TAT-AAATTTTTTTTAACCTTCT
1 TATGAAA-TTTTGATAACC-TCC
*
1084 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCT-CC
* * *
1106 TAAGGAATTTTGA-AGACCTCAA
1 TATGAAATTTTGATA-ACCTC-C
* *
1128 TGTGAAATTTTGATAACTTCCC
1 TATGAAATTTTGATAACCT-CC
* * *
1150 AATTAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TC-C
* *
1173 TATGAGATGTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
*
1194 ATATG--A-TAT-AT-ACCTCC
1 -TATGAAATTTTGATAACCTCC
* *
1211 ATATG-AATTGTT-AGTAATCGCAC
1 -TATGAAATT-TTGA-TAACCTC-C
** * *
1234 TCCGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCTC-C
*
1256 TATG-AATTTGTGATAATCTCGC
1 TATGAAATTT-TGATAACCTC-C
* *
1278 TATGAAATTTTGATAAATCTTTC
1 TATGAAATTTTGAT-AA-CCTCC
* *
1301 TATAAAATTTTGATAAATCTCCC
1 TATGAAATTTTGAT-AACCT-CC
* * *
1324 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAAC-CTCC
*
1346 TATTG-AATCTTGATAA----C
1 TA-TGAAATTTTGATAACCTCC
*
1363 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCT-CC
** *
1384 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTC-C
* *
1406 TATGGAAATTTTGTTAATCTTCC
1 TAT-GAAATTTTGATAA-CCTCC
* * *
1429 TATGAAATTTTGATCTACGTAC
1 TATGAAATTTTGAT-AACCTCC
*
1451 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAA-CCTCC
* * *
1473 TATAAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT--CC
* *
1495 TATGAAATTTTAATATCCTCC
1 TATGAAATTTTGATAACCTCC
* *
1516 -CTGAAATTTTGATATCCT-C
1 TATGAAATTTTGATAACCTCC
*
1535 TCTGAAATTTTGAT
1 TATGAAATTTTGAT
1549 TACTCCATAA
Statistics
Matches: 392, Mismatches: 91, Indels: 92
0.68 0.16 0.16
Matches are distributed among these distances:
16 10 0.03
17 13 0.03
18 3 0.01
19 17 0.04
20 34 0.09
21 21 0.05
22 206 0.53
23 84 0.21
24 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (21 bp):
TATGAAATTTTGATAACCTCC
Found at i:1296 original size:23 final size:23
Alignment explanation
Indices: 1237--1339 Score: 113
Period size: 23 Copynumber: 4.6 Consensus size: 23
1227 ATCGCACTCC
*
1237 GAAATTTTGAT-AATCACACTAT
1 GAAATTTTGATAAATCTCACTAT
*
1259 G-AATTTGTGAT-AATCTCGCTAT
1 GAAATTT-TGATAAATCTCACTAT
**
1281 GAAATTTTGATAAATCTTTCTAT
1 GAAATTTTGATAAATCTCACTAT
* *
1304 AAAATTTTGATAAATCTCCCTAT
1 GAAATTTTGATAAATCTCACTAT
*
1327 AAAATTTTGATAA
1 GAAATTTTGATAA
1340 CTTTCTTATT
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
21 5 0.07
22 19 0.27
23 47 0.66
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.41
Consensus pattern (23 bp):
GAAATTTTGATAAATCTCACTAT
Found at i:1546 original size:20 final size:20
Alignment explanation
Indices: 1497--1548 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1487 AACTAAACTA
*
1497 TGAAATTTTAATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
1517 TGAAATTTTGATATCCTCTC
1 TGAAATTTTGATATCCTCCC
1537 TGAAATTTTGAT
1 TGAAATTTTGAT
1549 TACTCCATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.44
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:4091 original size:30 final size:31
Alignment explanation
Indices: 4057--4121 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
4047 TGGCAATTTA
* *
4057 GAAATATGTTTTAAAAA-AAGGGTACAATTG
1 GAAATATATTTTAAAAATAAGGGTACAATCG
4087 GAAATATATTTTAAAAATAAGGGTACAATCG
1 GAAATATATTTTAAAAATAAGGGTACAATCG
4118 GAAA
1 GAAA
4122 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.49, C:0.05, G:0.18, T:0.28
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATCG
Found at i:4699 original size:19 final size:20
Alignment explanation
Indices: 4677--4715 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4667 TTATTGAGTT
4677 GTTTT-CTTTTAAATAGGTA
1 GTTTTACTTTTAAATAGGTA
*
4696 GTTTTATTTTTAAATAGGTA
1 GTTTTACTTTTAAATAGGTA
4716 ATTTAAGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.54
Consensus pattern (20 bp):
GTTTTACTTTTAAATAGGTA
Found at i:4720 original size:19 final size:20
Alignment explanation
Indices: 4683--4720 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4673 AGTTGTTTTC
*
4683 TTTTAAATAGGTAGTTTTAT
1 TTTTAAATAGGTAGATTTAT
4703 TTTTAAATAGGTA-ATTTA
1 TTTTAAATAGGTAGATTTA
4721 AGAACTGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (20 bp):
TTTTAAATAGGTAGATTTAT
Found at i:4779 original size:2 final size:2
Alignment explanation
Indices: 4772--4806 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4762 AAATCCGTGC
4772 AT AT 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 AT AT A
4807 CTAAATATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5926 original size:12 final size:12
Alignment explanation
Indices: 5909--5936 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5899 TTTTGAAAAA
5909 TATAGTATTATT
1 TATAGTATTATT
5921 TATAGTATTATT
1 TATAGTATTATT
5933 TATA
1 TATA
5937 TTAAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (12 bp):
TATAGTATTATT
Found at i:6596 original size:3 final size:3
Alignment explanation
Indices: 6588--6623 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
6578 TTCTTAACCT
6588 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6624 TATTAGTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:8038 original size:13 final size:13
Alignment explanation
Indices: 8020--8046 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8010 AAACAACTGA
8020 AAAGCACTTCTGG
1 AAAGCACTTCTGG
8033 AAAGCACTTCTGG
1 AAAGCACTTCTGG
8046 A
1 A
8047 TTTTCTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (13 bp):
AAAGCACTTCTGG
Found at i:8638 original size:2 final size:2
Alignment explanation
Indices: 8631--8657 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8621 AAATAATTAA
8631 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 A
8658 AGGGGCCGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10236 original size:30 final size:30
Alignment explanation
Indices: 10192--10259 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
10182 ATCATTCCTT
*
10192 TGGCAATATCCAAGACGATCGTCGTTCTTG
1 TGGCAATGTCCAAGACGATCGTCGTTCTTG
* * * *
10222 TGGTAATGTCCAAGATGTTCGTCGTTCTTT
1 TGGCAATGTCCAAGACGATCGTCGTTCTTG
10252 TGGCAATG
1 TGGCAATG
10260 CCCAGGAGGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (30 bp):
TGGCAATGTCCAAGACGATCGTCGTTCTTG
Found at i:12883 original size:18 final size:18
Alignment explanation
Indices: 12860--12895 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
12850 TCTTGCACAT
*
12860 GATCAGGAGTTGCTGACA
1 GATCAGGAGCTGCTGACA
12878 GATCAGGAGCTGCTGACA
1 GATCAGGAGCTGCTGACA
12896 AAAATGATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.19, G:0.33, T:0.19
Consensus pattern (18 bp):
GATCAGGAGCTGCTGACA
Found at i:13309 original size:68 final size:68
Alignment explanation
Indices: 13197--13327 Score: 183
Period size: 68 Copynumber: 1.9 Consensus size: 68
13187 ATTCCATATT
* *
13197 CAGCAAGGATCACAGCCATAAGTGCTTTCCTTTGTGATGCTTCTGCCTTATGTAGCCAATTAAGA
1 CAGCAAGGATCACAGCCAAAAGTGCTTTCCTTTGTGATGATTCTGCCTTATGTAGCCAATTAAGA
13262 TTC
66 TTC
** * * *
13265 CAGCAAGGATCGTAGCCAAAAGTGTCTTTCCTTT-TGTTGATTCTGGCTTATGTAGCCCATTAA
1 CAGCAAGGATCACAGCCAAAAGTG-CTTTCCTTTGTGATGATTCTGCCTTATGTAGCCAATTAA
13328 AAAATCTATA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
68 46 0.84
69 9 0.16
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (68 bp):
CAGCAAGGATCACAGCCAAAAGTGCTTTCCTTTGTGATGATTCTGCCTTATGTAGCCAATTAAGA
TTC
Found at i:13494 original size:110 final size:109
Alignment explanation
Indices: 13292--13520 Score: 338
Period size: 110 Copynumber: 2.1 Consensus size: 109
13282 AAAAGTGTCT
* * *
13292 TTCCTT-TTGTTGATTCTGGCTTATGTAGCCCATTAAAAAATCTATATTTTGACTTGGAGTGAGT
1 TTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTAAAAAATCTATATTTTGACTTGGAGAGAGT
*
13356 GCACCCATAGGAGTGTTGCACTGGTTGCACCTCCAGGAGTGCCC
66 GCACCCATAGGAGTGTTGCACTGATTGCACCTCCAGGAGTGCCC
13400 TTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTAAAAACAAT-TATATTTTGACTTGGAGCAG
1 TTCCTTGTTGATGATTCTGGCCTATGTAGCCCATT-AAAA-AATCTATATTTTGACTTGGAG-AG
* * *
13464 -GTGCACCCTTAGGAGTGTTGTACTGATTGCACCTCCAGTAGTGCCC
63 AGTGCACCCATAGGAGTGTTGCACTGATTGCACCTCCAGGAGTGCCC
*
13510 CTCCTTGTTGA
1 TTCCTTGTTGA
13521 CACTTCTAGC
Statistics
Matches: 109, Mismatches: 8, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
108 6 0.06
109 26 0.24
110 73 0.67
111 4 0.04
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (109 bp):
TTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTAAAAAATCTATATTTTGACTTGGAGAGAGT
GCACCCATAGGAGTGTTGCACTGATTGCACCTCCAGGAGTGCCC
Found at i:13650 original size:39 final size:38
Alignment explanation
Indices: 13549--13830 Score: 361
Period size: 37 Copynumber: 7.3 Consensus size: 38
13539 CTTTAAGAAA
*
13549 AAAAAAAAGGCTTACAATGCCTATAGCCAATGTAGCTT
1 AAAAAAAAGGCTTACAATGCCTATAGCCTATGTAGCTT
* * * * * *
13587 -GAAAGAGGGCGTACAACGCCTATAGCCTATGCAGCTT
1 AAAAAAAAGGCTTACAATGCCTATAGCCTATGTAGCTT
13624 AAAAAAAATGGCTTACAATGCCTATAGCCTATGTAGCTTT
1 AAAAAAAA-GGCTTACAATGCCTATAGCCTATGTAGC-TT
* *
13664 AAAAAAAAAGCTTACAATGCCTATAGCCAATGTAGCTT
1 AAAAAAAAGGCTTACAATGCCTATAGCCTATGTAGCTT
* * * * *
13702 -GAAAGAGGGCGTACAATGCCTATAGCCTATGCAGCTT
1 AAAAAAAAGGCTTACAATGCCTATAGCCTATGTAGCTT
*
13739 AAAAAAATGGCTTACAATGCCTATAGCCTATGTAGCTT
1 AAAAAAAAGGCTTACAATGCCTATAGCCTATGTAGCTT
*
13777 AAAAAAGAAAAGGCTTACAATGCCTATAGCTTATGTAGCTT
1 --AAAA-AAAAGGCTTACAATGCCTATAGCCTATGTAGCTT
13818 AAAAAAAAGGCTT
1 AAAAAAAAGGCTT
13831 TTTATGCCTA
Statistics
Matches: 208, Mismatches: 29, Indels: 14
0.83 0.12 0.06
Matches are distributed among these distances:
37 60 0.29
38 47 0.23
39 55 0.26
40 14 0.07
41 32 0.15
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (38 bp):
AAAAAAAAGGCTTACAATGCCTATAGCCTATGTAGCTT
Found at i:13658 original size:76 final size:77
Alignment explanation
Indices: 13548--13830 Score: 365
Period size: 76 Copynumber: 3.7 Consensus size: 77
13538 GCTTTAAGAA
* * * * * *
13548 AAAAAAAAAGGCTTACAATGCCTATAGCCAATGTAGCTT-GAAAGAGGGCGTACAACGCCTATAG
1 AAAAAAAAAGGCTTACAATGCCTATAGCCTATGTAGCTTAAAAAAAAGGCTTACAATGCCTATAG
*
13612 CCTATGCAGCTT
66 CCTATGTAGCTT
* *
13624 AAAAAAAATGGCTTACAATGCCTATAGCCTATGTAGCTTTAAAAAAAAAGCTTACAATGCCTATA
1 AAAAAAAAAGGCTTACAATGCCTATAGCCTATGTAGC-TTAAAAAAAAGGCTTACAATGCCTATA
*
13689 GCCAATGTAGCTT
65 GCCTATGTAGCTT
* * * * * *
13702 --GAAAGAGGGCGTACAATGCCTATAGCCTATGCAGCTTAAAAAAATGGCTTACAATGCCTATAG
1 AAAAAAAAAGGCTTACAATGCCTATAGCCTATGTAGCTTAAAAAAAAGGCTTACAATGCCTATAG
13765 CCTATGTAGCTT
66 CCTATGTAGCTT
*
13777 AAAAAAGAAAAGGCTTACAATGCCTATAGCTTATGTAGCTTAAAAAAAAGGCTT
1 -AAAAA-AAAAGGCTTACAATGCCTATAGCCTATGTAGCTTAAAAAAAAGGCTT
13831 TTTATGCCTA
Statistics
Matches: 176, Mismatches: 25, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
75 37 0.21
76 65 0.37
77 2 0.01
78 31 0.18
79 41 0.23
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (77 bp):
AAAAAAAAAGGCTTACAATGCCTATAGCCTATGTAGCTTAAAAAAAAGGCTTACAATGCCTATAG
CCTATGTAGCTT
Found at i:13735 original size:115 final size:115
Alignment explanation
Indices: 13547--13817 Score: 481
Period size: 115 Copynumber: 2.3 Consensus size: 115
13537 AGCTTTAAGA
13547 AAAAAAAAAAGGCTTACAATGCCTATAGCCAATGTAGCTTGAAAGAGGGCGTACAACGCCTATAG
1 AAAAAAAAAAGGCTTACAATGCCTATAGCCAATGTAGCTTGAAAGAGGGCGTACAACGCCTATAG
13612 CCTATGCAGCTTAAAAAAAATGGCTTACAATGCCTATAGCCTATGTAGCTT
66 CCTATGCAGCTT-AAAAAAATGGCTTACAATGCCTATAGCCTATGTAGCTT
* *
13663 TAAAAAAAAA-GCTTACAATGCCTATAGCCAATGTAGCTTGAAAGAGGGCGTACAATGCCTATAG
1 AAAAAAAAAAGGCTTACAATGCCTATAGCCAATGTAGCTTGAAAGAGGGCGTACAACGCCTATAG
13727 CCTATGCAGCTTAAAAAAATGGCTTACAATGCCTATAGCCTATGTAGCTT
66 CCTATGCAGCTTAAAAAAATGGCTTACAATGCCTATAGCCTATGTAGCTT
**
13777 AAAAAAGAAAAGGCTTACAATGCCTATAGCTTATGTAGCTT
1 AAAAAA-AAAAGGCTTACAATGCCTATAGCCAATGTAGCTT
13818 AAAAAAAAGG
Statistics
Matches: 148, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
114 43 0.29
115 69 0.47
116 36 0.24
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (115 bp):
AAAAAAAAAAGGCTTACAATGCCTATAGCCAATGTAGCTTGAAAGAGGGCGTACAACGCCTATAG
CCTATGCAGCTTAAAAAAATGGCTTACAATGCCTATAGCCTATGTAGCTT
Found at i:14630 original size:20 final size:17
Alignment explanation
Indices: 14586--14634 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 17
14576 AAAATTTATA
*
14586 TGCGCTTCCAACATGGT
1 TGCGCTTCCAACATGGC
14603 TGCGCTTCCAACATGATGC
1 TGCGCTTCCAACATG--GC
14622 TGACGCTTCCAAC
1 TG-CGCTTCCAAC
14635 GGAAAGAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 15 0.54
19 3 0.11
20 10 0.36
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.27
Consensus pattern (17 bp):
TGCGCTTCCAACATGGC
Found at i:14714 original size:37 final size:37
Alignment explanation
Indices: 14653--14737 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 37
14643 TTTATACTTT
* * *
14653 TTCCAACATGGGATAGCGTTTTTCTGCTGACTTCTTC
1 TTCCAACATGGGATAGCGTCTTTCTGCGGACTCCTTC
*
14690 TTCCAACATGGAGGTAGCG-CTTTCTGCGGACTCCTTC
1 TTCCAACATGG-GATAGCGTCTTTCTGCGGACTCCTTC
*
14727 TTCCAATATGG
1 TTCCAACATGG
14738 TGACAGCGCT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
37 36 0.86
38 6 0.14
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (37 bp):
TTCCAACATGGGATAGCGTCTTTCTGCGGACTCCTTC
Found at i:14746 original size:37 final size:37
Alignment explanation
Indices: 14653--14748 Score: 104
Period size: 37 Copynumber: 2.6 Consensus size: 37
14643 TTTATACTTT
* * * *
14653 TTCCAACATGG-GATAGCGTTTTTCTGCTGACTTCTTC
1 TTCCAACATGGAGACAGCG-CTTTCTGCGGACTCCTTC
**
14690 TTCCAACATGGAGGTAGCGCTTTCTGCGGACTCCTTC
1 TTCCAACATGGAGACAGCGCTTTCTGCGGACTCCTTC
* *
14727 TTCCAATATGGTGACAGCGCTT
1 TTCCAACATGGAGACAGCGCTT
14749 CCAATCTCAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
37 44 0.88
38 6 0.12
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (37 bp):
TTCCAACATGGAGACAGCGCTTTCTGCGGACTCCTTC
Found at i:14848 original size:40 final size:40
Alignment explanation
Indices: 14779--14896 Score: 130
Period size: 45 Copynumber: 2.8 Consensus size: 40
14769 CTCTTCCAGG
* ** *
14779 GTGGTGGCGCTTCCAACGACATTATTTATACTCCAACATGA
1 GTGGTGGCGCTTCCAATGACAAGAATTATACTCCAACAT-A
14820 G-GGTGGCGCTTCCAATGACAAGAATTATACCCTCTTCCAACATA
1 GTGGTGGCGCTTCCAATGACAAGAATTATA----C-TCCAACATA
*
14864 GTGGTGGTGCTTCCAATGACAAGAATTATACTC
1 GTGGTGGCGCTTCCAATGACAAGAATTATACTC
14897 TCTTCCACAT
Statistics
Matches: 66, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
40 26 0.39
41 2 0.03
44 3 0.05
45 35 0.53
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (40 bp):
GTGGTGGCGCTTCCAATGACAAGAATTATACTCCAACATA
Found at i:14861 original size:45 final size:46
Alignment explanation
Indices: 14810--14915 Score: 157
Period size: 45 Copynumber: 2.4 Consensus size: 46
14800 TTATTTATAC
14810 TCCAACATGAG-GGTGGCGCTTCCAATGACAAGAATTATACCCTCT
1 TCCAACATGAGTGGTGGCGCTTCCAATGACAAGAATTATACCCTCT
* *
14855 TCCAACAT-AGTGGTGGTGCTTCCAATGACAAGAATTATACTCTCT
1 TCCAACATGAGTGGTGGCGCTTCCAATGACAAGAATTATACCCTCT
*
14900 TCC-ACATG-GTGTTGGC
1 TCCAACATGAGTGGTGGC
14916 AAACTGTTAC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
44 12 0.22
45 43 0.78
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (46 bp):
TCCAACATGAGTGGTGGCGCTTCCAATGACAAGAATTATACCCTCT
Found at i:15591 original size:46 final size:46
Alignment explanation
Indices: 15459--15597 Score: 188
Period size: 46 Copynumber: 3.0 Consensus size: 46
15449 AGGAGATGCA
* * * **
15459 TCTTATGTGAGCATACTTCTGCAGAAAAAATACTCTATACAATAGC
1 TCTTATGTGAGCACACTTCTTCAGAAAGAATACTCTATACGGTAGC
*
15505 TTTTATGTGAGCACACTTCTTCAGAAAGAATACTCTATACGGTAGC
1 TCTTATGTGAGCACACTTCTTCAGAAAGAATACTCTATACGGTAGC
* * * *
15551 TCTTATGTGAGCACCCATCTTCAGAAGGAATTCTCTATACGGTAGC
1 TCTTATGTGAGCACACTTCTTCAGAAAGAATACTCTATACGGTAGC
15597 T
1 T
15598 TCTTGCAAAG
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 82 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (46 bp):
TCTTATGTGAGCACACTTCTTCAGAAAGAATACTCTATACGGTAGC
Found at i:17063 original size:18 final size:18
Alignment explanation
Indices: 17029--17074 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
17019 GAAGACTACG
*
17029 GTGTTGGAA-AGCTATAC
1 GTGTTGGAAGAGCCATAC
17046 GTGTTGGAAGAGCCATAC
1 GTGTTGGAAGAGCCATAC
*
17064 GTATTGGAAGA
1 GTGTTGGAAGA
17075 CTATCATCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.30, C:0.11, G:0.33, T:0.26
Consensus pattern (18 bp):
GTGTTGGAAGAGCCATAC
Found at i:17394 original size:2 final size:2
Alignment explanation
Indices: 17389--17456 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
17379 AATTTTTTTA
17389 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
17431 AG AG AG AG AG AG AG AG AG AG AG -G AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.