Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022089.1 Corchorus olitorius cultivar O-4 contig22122, 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: 37519
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1469 original size:11 final size:11
Alignment explanation
Indices: 1453--1478 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1443 TAGATAATTT
1453 TTTTCTTCTAG
1 TTTTCTTCTAG
1464 TTTTCTTCTAG
1 TTTTCTTCTAG
1475 TTTT
1 TTTT
1479 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:2268 original size:15 final size:15
Alignment explanation
Indices: 2238--2279 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
2228 TTACTCTGCT
2238 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
2254 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
2269 TTGCTTTCTGT
1 TTGTTTTCTGT
2280 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:2747 original size:28 final size:28
Alignment explanation
Indices: 2690--2748 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
2680 TGCGTCATAT
** **
2690 AAAAAGAGTTTTTGCGTTTTTCTAAAAA
1 AAAAAGAGTTTTTGCGTTCATAAAAAAA
*
2718 AAAAAGAGTTTTTGCG-TCATAAAAAGA
1 AAAAAGAGTTTTTGCGTTCATAAAAAAA
2745 AAAA
1 AAAA
2749 GAAAAAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (28 bp):
AAAAAGAGTTTTTGCGTTCATAAAAAAA
Found at i:5942 original size:21 final size:21
Alignment explanation
Indices: 5895--5944 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
5885 CGGCCATTCA
* * *
5895 CCGTGACACCACCGGTTAAGC
1 CCGTGCCACCAACGGCTAAGC
*
5916 CCGTGCCACCAACGGCTATGC
1 CCGTGCCACCAACGGCTAAGC
5937 CCGTGCCA
1 CCGTGCCA
5945 TCACCATTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.20, C:0.42, G:0.24, T:0.14
Consensus pattern (21 bp):
CCGTGCCACCAACGGCTAAGC
Found at i:8483 original size:11 final size:11
Alignment explanation
Indices: 8467--8492 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
8457 AGATAATTTT
8467 TTTTCTTCTAG
1 TTTTCTTCTAG
8478 TTTTCTTCTAG
1 TTTTCTTCTAG
8489 TTTT
1 TTTT
8493 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:13436 original size:15 final size:15
Alignment explanation
Indices: 13392--13446 Score: 74
Period size: 15 Copynumber: 3.6 Consensus size: 15
13382 CCAAGTGTCT
13392 GCAGTATTTCCTACG
1 GCAGTATTTCCTACG
* *
13407 GCAAATATTTACTACG
1 GC-AGTATTTCCTACG
13423 GCAGTATTTCCTACG
1 GCAGTATTTCCTACG
*
13438 GTAGTATTT
1 GCAGTATTT
13447 GTTGATTTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
15 21 0.62
16 13 0.38
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (15 bp):
GCAGTATTTCCTACG
Found at i:14254 original size:28 final size:27
Alignment explanation
Indices: 14210--14372 Score: 127
Period size: 28 Copynumber: 5.9 Consensus size: 27
14200 GAATGAGGGT
*
14210 CACA-TAGGGGGCATTTTAGTCATTTG
1 CACATTAGGGGGCATTTTGGTCATTTG
*
14236 CACGTCTAGGGGGCATTTTGGTCATTTTG
1 CACAT-TAGGGGGCATTTTGGTCA-TTTG
* * *
14265 CATATTTGGGGGCATTTTGGTCATTTTA
1 CACATTAGGGGGCATTTTGGTCA-TTTG
* *
14293 TATATTCA-GGGGCATTTTGGTCATTTG
1 CACATT-AGGGGGCATTTTGGTCATTTG
* * *
14320 TAC-TTCA-GAGGAATTTTGGTCATTTG
1 CACATT-AGGGGGCATTTTGGTCATTTG
**
14346 TGCATTTAGAGGGGCATTTTGGTCATT
1 CACA-TTAG-GGGGCATTTTGGTCATT
14373 GGGTCCCTTA
Statistics
Matches: 114, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
26 26 0.23
27 6 0.05
28 60 0.53
29 22 0.19
ACGTcount: A:0.19, C:0.13, G:0.27, T:0.41
Consensus pattern (27 bp):
CACATTAGGGGGCATTTTGGTCATTTG
Found at i:31223 original size:41 final size:39
Alignment explanation
Indices: 31178--31310 Score: 142
Period size: 40 Copynumber: 3.3 Consensus size: 39
31168 GTTCAACATG
*
31178 GTCCCTGATTTAGGATACTATCTTCTATTTGATGCAATTTT
1 GTCCCTGATTTAGGAT-TTAT-TTCTATTTGATGCAATTTT
* * ** *
31219 GTCCCTGATCTAGGATTTTATTTTTGATTT-ATGCAGCTTA
1 GTCCCTGATTTAGGA-TTTATTTCT-ATTTGATGCAATTTT
* *
31259 GTCCCTGATTCAAGATTTATTTACTATTTGATGCAATTTT
1 GTCCCTGATTTAGGATTTATTT-CTATTTGATGCAATTTT
31299 GTCCCTGATTTA
1 GTCCCTGATTTA
31311 TGTTATTGAT
Statistics
Matches: 74, Mismatches: 14, Indels: 9
0.76 0.14 0.09
Matches are distributed among these distances:
39 11 0.15
40 41 0.55
41 21 0.28
42 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.47
Consensus pattern (39 bp):
GTCCCTGATTTAGGATTTATTTCTATTTGATGCAATTTT
Found at i:32251 original size:16 final size:17
Alignment explanation
Indices: 32230--32261 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
32220 TGATTTTCCT
32230 TTTTTCT-TTTATAATC
1 TTTTTCTATTTATAATC
32246 TTTTTCTATTTATAAT
1 TTTTTCTATTTATAAT
32262 TAAGATCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTCTATTTATAATC
Found at i:35189 original size:24 final size:25
Alignment explanation
Indices: 35161--35211 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
35151 AAAGAGTAAC
*
35161 AATAAAATAAATAAACAAGA-AAAT
1 AATAAAATAAAGAAACAAGATAAAT
*
35185 AATAAAATTAAGAAACAAGATAAAT
1 AATAAAATAAAGAAACAAGATAAAT
35210 AA
1 AA
35212 ATACTCCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.18
Consensus pattern (25 bp):
AATAAAATAAAGAAACAAGATAAAT
Found at i:35689 original size:27 final size:28
Alignment explanation
Indices: 35639--35691 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
35629 AAATCAATTA
*
35639 GAAATCATAAAAACATAAAGATAAATCT
1 GAAATCATAAAAACACAAAGATAAATCT
35667 GAAATCATAAAATAC-CAAA-ATAAAT
1 GAAATCATAAAA-ACACAAAGATAAAT
35692 AATCAGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 6 0.26
28 15 0.65
29 2 0.09
ACGTcount: A:0.62, C:0.11, G:0.06, T:0.21
Consensus pattern (28 bp):
GAAATCATAAAAACACAAAGATAAATCT
Done.