Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000974.1 Corchorus capsularis cultivar CVL-1 contig00974, 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: 5319
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Found at i:109 original size:37 final size:37
Alignment explanation
Indices: 14--109 Score: 129
Period size: 38 Copynumber: 2.6 Consensus size: 37
4 AATTTGCCTT
*
14 TTTATTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
1 TTTATTTCCAATGTCCTATTTAATTTTGCCTTTTGTC
* ** *
51 TTTGTTTCCAATCGTTGTATTTAATTTTGCTTTTTGTC
1 TTTATTTCCAAT-GTCCTATTTAATTTTGCCTTTTGTC
*
89 TTTATCTCCAATGTCCTATTT
1 TTTATTTCCAATGTCCTATTT
110 GGGCTTAACT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
37 17 0.35
38 32 0.65
ACGTcount: A:0.16, C:0.19, G:0.09, T:0.56
Consensus pattern (37 bp):
TTTATTTCCAATGTCCTATTTAATTTTGCCTTTTGTC
Found at i:273 original size:19 final size:20
Alignment explanation
Indices: 246--283 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
236 TACTATTATT
246 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
266 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
284 ACCGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:519 original size:44 final size:44
Alignment explanation
Indices: 450--577 Score: 145
Period size: 44 Copynumber: 2.9 Consensus size: 44
440 GTCTTTATGT
* **
450 GGTTATCAAAATTTCATAAG-ATGGTTATTATAA-TTTCATGA-GGA
1 GGTTATCAAAATTTCAT-AGTGTGGTTACCA-AATTTTCAT-ATGGA
*
494 GGTTATCAAAATTCCATAGTGTGGTTACCAAATTTTCATATGGA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAATTTTCATATGGA
* * *
538 AGTTATCAAACTTTCATAGTGTGGTTACCAAAATTTCATA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAATTTTCATA
578 GAATCGGGTT
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
43 5 0.07
44 68 0.93
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAGTGTGGTTACCAAATTTTCATATGGA
Found at i:543 original size:66 final size:66
Alignment explanation
Indices: 447--578 Score: 144
Period size: 66 Copynumber: 2.0 Consensus size: 66
437 CTTGTCTTTA
* * * *
447 TGTGGTTATCAAAATTTCATAAGATGGTTATTATAA-TTTCATGAG-GAGGTTATCAAAATTCCA
1 TGTGGTTACCAAAATTTCATAAGATAGTTATCA-AACTTTCAT-AGTGAGGTTACCAAAATTCCA
510 TAG
64 TAG
* * * *
513 TGTGGTTACCAAATTTTCATATGGA-AGTTATCAAACTTTCATAGTGTGGTTACCAAAATTTCAT
1 TGTGGTTACCAAAATTTCATA-AGATAGTTATCAAACTTTCATAGTGAGGTTACCAAAATTCCAT
577 AG
65 AG
579 AATCGGGTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
65 4 0.07
66 49 0.89
67 2 0.04
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.38
Consensus pattern (66 bp):
TGTGGTTACCAAAATTTCATAAGATAGTTATCAAACTTTCATAGTGAGGTTACCAAAATTCCATA
G
Found at i:578 original size:22 final size:22
Alignment explanation
Indices: 447--578 Score: 119
Period size: 22 Copynumber: 6.0 Consensus size: 22
437 CTTGTCTTTA
447 TGTGGTTATCAAAATTTCATAAG
1 TGTGGTTATCAAAATTTCAT-AG
* * *
470 -ATGGTTATTATAATTTCATGAG
1 TGTGGTTATCAAAATTTCAT-AG
* *
492 -GAGGTTATCAAAATTCCATAG
1 TGTGGTTATCAAAATTTCATAG
* *
513 TGTGGTTACCAAATTTTCATA-
1 TGTGGTTATCAAAATTTCATAG
*
534 TG-GAAGTTATCAAACTTTCATAG
1 TGTG--GTTATCAAAATTTCATAG
*
557 TGTGGTTACCAAAATTTCATAG
1 TGTGGTTATCAAAATTTCATAG
579 AATCGGGTTA
Statistics
Matches: 87, Mismatches: 17, Indels: 11
0.76 0.15 0.10
Matches are distributed among these distances:
20 1 0.01
21 4 0.05
22 79 0.91
23 2 0.02
24 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.38
Consensus pattern (22 bp):
TGTGGTTATCAAAATTTCATAG
Found at i:693 original size:22 final size:22
Alignment explanation
Indices: 668--1656 Score: 225
Period size: 22 Copynumber: 44.6 Consensus size: 22
658 ATCAAAGAAA
* *
668 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
690 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
*
712 TTAACAAAATTTCATTAG-GAGG
1 TTATCAAAATTTCA-TAGTGAGG
* * *
734 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
* *
756 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
778 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* * *
800 TTATAAAAAGTCTCAATTCCA-TAAGG
1 TTATCAAAA-TTTC-A-T--AGTGAGG
* * *
826 AGTACCAAAATTTCATAG-AAGG
1 -TTATCAAAATTTCATAGTGAGG
* * * *
848 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
869 TTATCGAAATTTCATAGAGATCAGA
1 TTATCAAAATTTCAT--AG-TGAGG
*
894 TTATCAAAATTT-ATAG-GAAGA
1 TTATCAAAATTTCATAGTG-AGG
**
915 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGAGG
* * *
937 TTATCAAAATTTTAAAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
959 TTATCAAAATTAT-ATAACGT-A-A
1 TTATCAAAATT-TCAT-A-GTGAGG
* *
981 TTATCAGAATTTCATAGAG-GG
1 TTATCAAAATTTCATAGTGAGG
* * * **
1002 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
**
1024 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
1046 TTATCAAAATTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
1068 TTA-CAAAAATTTCATAGT--GG
1 TTATC-AAAATTTCATAGTGAGG
* * ** *
1088 TATTTCTGGGAGGTTATCA-A---A-A
1 T-TATC---AAAATT-TCATAGTGAGG
*
1110 TT-TCATAGTATGGTTACCAAATTAG-GAAGG
1 TTATCA-A-AAT--TT--C--A-TAGTG-AGG
* * *
1140 TTATTAAATTTTTATTA-TG-GAG
1 TTATCAAAATTTCA-TAGTGAG-G
*
1162 TAATCAAAATTTCA-AG-GAGG
1 TTATCAAAATTTCATAGTGAGG
* *
1182 ATATCAAAATTTC--AGGGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
1202 ATATCACAATTTCATAGTTTA-G
1 TTATCAAAATTTCATAG-TGAGG
* *
1224 TTTTCAAAATTTCATA-AGAGGG
1 TTATCAAAATTTCATAGTGA-GG
**
1246 TTATCAAAATTTCATAGT-ATA
1 TTATCAAAATTTCATAGTGAGG
* *
1267 TAGATCAAAATTTCATAGGGAGG
1 T-TATCAAAATTTCATAGTGAGG
* * * *
1290 TTAACAAAATTTCATAATAATG
1 TTATCAAAATTTCATAGTGAGG
** *
1312 TTATCAAAAAATCATAGGGAGG
1 TTATCAAAATTTCATAGTGAGG
1334 TTATCAAAA-TT--T-GT-A-G
1 TTATCAAAATTTCATAGTGAGG
* * *
1350 TTATCAAGATTTCATAAG-AAAG
1 TTATCAAAATTTCAT-AGTGAGG
* *
1372 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
1394 TTTATGAAAATTTTATAG-GAAGAT
1 -TTATCAAAATTTCATAGTG-AG-G
*
1418 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
1440 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
1462 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAGTGAGG
1484 TTA-CTAACAA-TTCATA-TGGAGG
1 TTATC-AA-AATTTCATAGT-GAGG
* * * * ** *
1506 TTTTTAAATTTTCGTAACGTGG
1 TTATCAAAATTTCATAGTGAGG
* *
1528 TTATCAATATATCATA-TGGAGG
1 TTATCAAAATTTCATAGT-GAGG
* * *
1550 TTAATTATCAATATCTCATAGTGTTGG
1 ----TTATCAAAATTTCATAGTG-AGG
* * *
1577 TTATCAAAATTTCGTTG-GAAAG
1 TTATCAAAATTTCATAGTG-AGG
*
1599 TTATCAAAATTTCATAATGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
1621 TCT-TCAAAAATCCTTAGGGAGG
1 T-TATCAAAATTTCATAGTGAGG
*
1643 TTAACAAAATTTCA
1 TTATCAAAATTTCA
1657 CAAGAAGATT
Statistics
Matches: 707, Mismatches: 168, Indels: 184
0.67 0.16 0.17
Matches are distributed among these distances:
16 9 0.01
17 3 0.00
18 2 0.00
19 5 0.01
20 47 0.07
21 63 0.09
22 431 0.61
23 73 0.10
24 13 0.02
25 18 0.03
26 23 0.03
27 13 0.02
29 2 0.00
30 3 0.00
31 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:1050 original size:65 final size:63
Alignment explanation
Indices: 894--1059 Score: 174
Period size: 65 Copynumber: 2.5 Consensus size: 63
884 AGAGATCAGA
* * * * *
894 TTATCAAAATTTATAGGAAGATTATCAAAATTTCATAGTGTTGTTATCAAAATTTTAAAGCGAGG
1 TTATCAAAATTTATA--AAGATTATCAAAATTTCATAGAGTGGTCAACAAAATTTTAAAGAGAGG
* *
959 TTATCAAAATTATATAACGTAATTATCAGAATTTCATAGAG-GGTCAACAAAATTTTATAA-AGA
1 TTATCAAAATT-TATAAAG--ATTATCAAAATTTCATAGAGTGGTCAACAAAATTTTA-AAGAGA
1022 GG
62 GG
1024 TTATCAAAATTTCATAAAGAGGTTATCAAAATTTCA
1 TTATCAAAATTT-ATAAAGA--TTATCAAAATTTCA
1060 AAATGTGATT
Statistics
Matches: 85, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
63 1 0.01
64 3 0.04
65 57 0.67
66 24 0.28
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (63 bp):
TTATCAAAATTTATAAAGATTATCAAAATTTCATAGAGTGGTCAACAAAATTTTAAAGAGAGG
Found at i:1189 original size:20 final size:20
Alignment explanation
Indices: 1164--1215 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1154 TTATGGAGTA
1164 ATCAAAATTTCAAGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
*
1184 ATCAAAATTTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
*
1204 ATCACAATTTCA
1 ATCAAAATTTCA
1216 TAGTTTAGTT
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:0.42, C:0.13, G:0.17, T:0.27
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:1391 original size:60 final size:61
Alignment explanation
Indices: 1289--1406 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 61
1279 TCATAGGGAG
* *
1289 GTTAACAAAATTTCATAATAATGTTATCAAAAAATCATAGGGAGG-TTATCAAAATTTGTA
1 GTTAACAAAATTTCATAAGAAAGTTATCAAAAAATCATAGGGAGGTTTATCAAAATTTGTA
* * ** * *
1349 GTTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGAGGTTTATGAAAATTT
1 GTTAACAAAATTTCATAAGAAAGTTATCAAAAAATCATAGGGAGGTTTATCAAAATTT
1407 TATAGGAAGA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
60 38 0.78
61 11 0.22
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (61 bp):
GTTAACAAAATTTCATAAGAAAGTTATCAAAAAATCATAGGGAGGTTTATCAAAATTTGTA
Found at i:1403 original size:23 final size:23
Alignment explanation
Indices: 1372--1473 Score: 100
Period size: 23 Copynumber: 4.5 Consensus size: 23
1362 CATAAGAAAG
1372 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* * *
1395 TTATGAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* *
1418 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
* * * * *
1440 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTTATAGGGAGGT
1462 TTATCAAAATTT
1 TTATCAAAATTT
1474 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:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:3912 original size:21 final size:21
Alignment explanation
Indices: 3888--3934 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3878 TTTCAGAGAG
*
3888 AGGTTATAAAAAATCATAGGA
1 AGGTTACAAAAAATCATAGGA
**
3909 AGGTTACAAAATTTCATAGGA
1 AGGTTACAAAAAATCATAGGA
3930 AGGTT
1 AGGTT
3935 TATTAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.28
Consensus pattern (21 bp):
AGGTTACAAAAAATCATAGGA
Found at i:3949 original size:23 final size:21
Alignment explanation
Indices: 3902--3950 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
3892 TATAAAAAAT
*
3902 CATAGGAAGGTTACAAAATTT
1 CATAGGAAGGTTACAAAATTC
*
3923 CATAGGAAGGTTTATTAAAATTC
1 CATAGGAAGG-TTA-CAAAATTC
3946 CATAG
1 CATAG
3951 TTAGGTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.42
22 3 0.12
23 11 0.46
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (21 bp):
CATAGGAAGGTTACAAAATTC
Done.