Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023068.1 Corchorus olitorius cultivar O-4 contig23101, 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: 21679
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Found at i:671 original size:153 final size:162
Alignment explanation
Indices: 492--783 Score: 395
Period size: 166 Copynumber: 1.8 Consensus size: 162
482 TATGACAGTA
492 CCTTTTTTTCAAATATATTTCTAAATTGACATTATTAAAA-T-T-T-A-TTA-TA-TAAAAATT-
1 CCTTTTTTTCAAATATATTTCTAAATTGACATTATTAAAATTATATAATTTATTATTAAAAATTA
* *
549 A-AAAAATTTCAGTTTAGACCGAATTATAAGTTTGTAAAATTGATTTTCATTGATGAACATGCAA
66 ATAAAAATTTCAATTTAGACCAAATTATAAGTTTGTAAAATTGATTTTCATTGATGAACATGCAA
613 ATTTCTACTAACTTTATGTTTTCCGATTGTAT
131 ATTTCTACTAACTTTATGTTTTCCGATTGTAT
* * * **
645 CCTTTTTTTCGATTATTTTTCTAAATTTCCATTATTAAAATTTAGTATAATTTATTATTTAAAAA
1 CCTTTTTTTCAAATATATTTCTAAATTGACATTATTAAAA-TTA-TATAATTTATTA-TTAAAAA
* *
710 TTAATTAAAAATTTCAATTTAGACCAAATTATAAGTTTGTCAAATTGATTTTCGTTGATGAACAT
63 TTAA-TAAAAATTTCAATTTAGACCAAATTATAAGTTTGTAAAATTGATTTTCATTGATGAACAT
*
775 TCAAATTTC
127 GCAAATTTC
784 CTTTACTATT
Statistics
Matches: 116, Mismatches: 10, Indels: 13
0.83 0.07 0.09
Matches are distributed among these distances:
153 35 0.30
155 1 0.01
157 1 0.01
158 1 0.01
159 1 0.01
160 3 0.03
161 2 0.02
163 8 0.07
164 1 0.01
166 63 0.54
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (162 bp):
CCTTTTTTTCAAATATATTTCTAAATTGACATTATTAAAATTATATAATTTATTATTAAAAATTA
ATAAAAATTTCAATTTAGACCAAATTATAAGTTTGTAAAATTGATTTTCATTGATGAACATGCAA
ATTTCTACTAACTTTATGTTTTCCGATTGTAT
Found at i:1058 original size:22 final size:21
Alignment explanation
Indices: 1002--1209 Score: 128
Period size: 22 Copynumber: 9.5 Consensus size: 21
992 GTATCTGTGT
*
1002 GGTTATCAAAATTTCATAAGA
1 GGTTATCAAAATTTCATAGGA
* * *
1023 TAGTTATTATAATTTCATGAGGA
1 -GGTTATCAAAATTTCAT-AGGA
* *
1046 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
1068 GGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATA-GGA
* *
1090 AGTTATCAAAATTTCATGGGAA
1 GGTTATCAAAATTTCATAGG-A
* * *
1112 GGTTACCAAAATTTCACAGTGT
1 GGTTATCAAAATTTCATAG-GA
* * *
1134 GGTTACCAAAATTTCTTAGAAA
1 GGTTATCAAAATTTCATAG-GA
** * *
1156 GGTTATTGAAATTTCATAATGT
1 GGTTATCAAAATTTCAT-AGGA
* * * *
1178 GATTATCACAATTTTATAGAAA
1 GGTTATCAAAATTTCATAG-GA
1200 GGTTATCAAA
1 GGTTATCAAA
1210 GAGATTATCA
Statistics
Matches: 137, Mismatches: 42, Indels: 14
0.71 0.22 0.07
Matches are distributed among these distances:
21 5 0.04
22 126 0.92
23 6 0.04
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:1161 original size:66 final size:65
Alignment explanation
Indices: 998--1172 Score: 208
Period size: 66 Copynumber: 2.6 Consensus size: 65
988 TCTTGTATCT
* * * * * *
998 GTGTGGTTATCAAAATTTCATAAGATAGTTATTATAATTTCATGAGGAGGTTATCAAAATTCCAT
1 GTGTGGTTACCAAAATTTC-TTAGAAAGTTATTAAAATTTCATGAGGAGGTTACCAAAATTCCAC
1063 A
65 A
* * * *
1064 GTGTGGTTACCAAAATTTCATATGGAAGTTATCAAAATTTCATG-GGAAGGTTACCAAAATTTCA
1 GTGTGGTTACCAAAATTTCTTA-GAAAGTTATTAAAATTTCATGAGG-AGGTTACCAAAATTCCA
1128 CA
64 CA
*
1130 GTGTGGTTACCAAAATTTCTTAGAAAGGTTATTGAAATTTCAT
1 GTGTGGTTACCAAAATTTCTTAGAAA-GTTATTAAAATTTCAT
1173 AATGTGATTA
Statistics
Matches: 92, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
65 6 0.07
66 86 0.93
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (65 bp):
GTGTGGTTACCAAAATTTCTTAGAAAGTTATTAAAATTTCATGAGGAGGTTACCAAAATTCCACA
Found at i:1313 original size:122 final size:121
Alignment explanation
Indices: 1092--1318 Score: 264
Period size: 122 Copynumber: 1.9 Consensus size: 121
1082 CATATGGAAG
* * * * *
1092 TTATCAAAATTTCATGGGAAGGTTACCAAAATTTCACAGTGTGGTTACCAAAATTTCTTAGAAAG
1 TTATCAAAATGTCATAGCAAGGTTACCAAAATTTCACAGTGTGGTTAACAAAATTTCATAGAAAG
* * * *
1157 GTTATTGAAATTTCATAATGTGATTATCACAATTTTATAGAAAGGTTATCAAAGAGA
66 GTTACTGAAATTTCAT-ATGGGATTATCAAAATTTCATAGAAAGGTTATCAAAGAGA
* * *
1214 TTATCAAAATGTCATAGCAAGGTTA-TAAGAATTTCATAGTGTGGTTAACAAAATTTCATATG-G
1 TTATCAAAATGTCATAGCAAGGTTACCAA-AATTTCACAGTGTGGTTAACAAAATTTCATA-GAA
1277 AGGTTACT-AATATTTCAT-TGGGATGTTATCAAAATTTCATAG
64 AGGTTACTGAA-ATTTCATATGGGA--TTATCAAAATTTCATAG
1319 TATGGTTACC
Statistics
Matches: 88, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
120 4 0.05
121 4 0.05
122 79 0.90
123 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (121 bp):
TTATCAAAATGTCATAGCAAGGTTACCAAAATTTCACAGTGTGGTTAACAAAATTTCATAGAAAG
GTTACTGAAATTTCATATGGGATTATCAAAATTTCATAGAAAGGTTATCAAAGAGA
Found at i:1326 original size:22 final size:22
Alignment explanation
Indices: 1214--1634 Score: 108
Period size: 22 Copynumber: 19.6 Consensus size: 22
1204 ATCAAAGAGA
* * *
1214 TTATCAAAATGTCATAGCAAGG
1 TTATCAAAATTTCATAGGATGG
1236 TTAT-AAGAATTTCATAGTG-TGG
1 TTATCAA-AATTTCATAG-GATGG
*
1258 TTAACAAAATTTCATATGGA-GG
1 TTATCAAAATTTCATA-GGATGG
* *
1280 TTA-CTAATATTTCATTGGGAT-G
1 TTATC-AAAATTTCA-TAGGATGG
*
1302 TTATCAAAATTTCATAGTATGG
1 TTATCAAAATTTCATAGGATGG
* * *
1324 TTA-CCAAA--T--TAGGAAGC
1 TTATCAAAATTTCATAGGATGG
* * *
1341 TTATTAAACTTTTACTATGGA--G
1 TTATCAAAATTTCA-TA-GGATGG
* *
1363 TAATCAAAATTTCA-CGGA-GG
1 TTATCAAAATTTCATAGGATGG
* * **
1383 ATATCAAAATTTCATATGAAAG
1 TTATCAAAATTTCATAGGATGG
** **
1405 TTATCAAAATTTCATAAGTTTAA
1 TTATCAAAATTTCAT-AGGATGG
* * *
1428 TTTTCAAATTTTTATA-G-TGTG
1 TTATCAAAATTTCATAGGATG-G
* *
1449 TAGATCAAAATTTCATAGGGA-GA
1 T-TATCAAAATTTCATA-GGATGG
* *
1472 TTAACAAAATTTCATAATGA-GG
1 TTATCAAAATTTCAT-AGGATGG
**
1494 TTATCAAAAAATCATAGGGA-GG
1 TTATCAAAATTTCATA-GGATGG
*
1516 TTATCAAAA-TT--T--G-TAG
1 TTATCAAAATTTCATAGGATGG
* *
1532 CTATCAAGATTTCATAAGGA-GG
1 TTATCAAAATTTCAT-AGGATGG
*
1554 TTATCAAAATTTTATAGGGA-GG
1 TTATCAAAATTTCATA-GGATGG
*
1576 TTTATCAAAATTTTATAGCGA-GG
1 -TTATCAAAATTTCATAG-GATGG
* * *
1599 TTATCACAACTTCATAGTG-TGA
1 TTATCAAAATTTCATAG-GATGG
*
1621 CTATCAAAATTTCA
1 TTATCAAAATTTCA
1635 GAGTGTGATT
Statistics
Matches: 291, Mismatches: 68, Indels: 80
0.66 0.15 0.18
Matches are distributed among these distances:
16 9 0.03
17 10 0.03
18 2 0.01
19 6 0.02
20 15 0.05
21 17 0.06
22 184 0.63
23 43 0.15
24 5 0.02
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGATGG
Found at i:1547 original size:82 final size:83
Alignment explanation
Indices: 1452--1604 Score: 200
Period size: 82 Copynumber: 1.9 Consensus size: 83
1442 TAGTGTGTAG
* * *
1452 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGG-TTATCAAAAAATCATAGGGAGG
1 ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGAGGTTTATCAAAAAATCATAGCGAGG
1516 TTATCAAAATTTGTAGCT
66 TTATCAAAATTTGTAGCT
* * * * * ** *
1534 ATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGCGAGG
1 ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGAGGTTTATCAAAAAATCATAGCGAGG
1599 TTATCA
66 TTATCA
1605 CAACTTCATA
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
82 35 0.59
83 24 0.41
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (83 bp):
ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGAGGTTTATCAAAAAATCATAGCGAGG
TTATCAAAATTTGTAGCT
Found at i:1584 original size:23 final size:22
Alignment explanation
Indices: 1452--1604 Score: 120
Period size: 22 Copynumber: 7.2 Consensus size: 22
1442 TAGTGTGTAG
* *
1452 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTTATAGGGAGGTT
* * **
1474 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTTATAGGGAGGTT
** *
1496 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTTATAGGGAGGTT
* *
1518 ATCAAAA--TT-T--GTA-GCT
1 ATCAAAATTTTATAGGGAGGTT
* * *
1534 ATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTTATAGGGAGGTT
1556 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTTATAGGGAGG-TT
*
1579 ATCAAAATTTTATAGCGAGGTT
1 ATCAAAATTTTATAGGGAGGTT
1601 ATCA
1 ATCA
1605 CAACTTCATA
Statistics
Matches: 104, Mismatches: 20, Indels: 14
0.75 0.14 0.10
Matches are distributed among these distances:
16 8 0.08
17 2 0.02
18 1 0.01
19 2 0.02
20 1 0.01
21 2 0.02
22 67 0.64
23 21 0.20
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (22 bp):
ATCAAAATTTTATAGGGAGGTT
Found at i:1639 original size:22 final size:22
Alignment explanation
Indices: 1600--1642 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1590 ATAGCGAGGT
* *
1600 TATCACAACTTCATAGTGTGAC
1 TATCAAAACTTCAGAGTGTGAC
*
1622 TATCAAAATTTCAGAGTGTGA
1 TATCAAAACTTCAGAGTGTGA
1643 TTACTAACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (22 bp):
TATCAAAACTTCAGAGTGTGAC
Found at i:2461 original size:22 final size:22
Alignment explanation
Indices: 2428--2483 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
2418 TTCCGGTGGC
*
2428 GGTGACGGTGGCAATTATGGTG
1 GGTGGCGGTGGCAATTATGGTG
* *
2450 GTTGGCGGTGGCAGTTATGGTG
1 GGTGGCGGTGGCAATTATGGTG
*
2472 GGTGGCTGTGGC
1 GGTGGCGGTGGC
2484 GTTGACAGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.11, C:0.11, G:0.50, T:0.29
Consensus pattern (22 bp):
GGTGGCGGTGGCAATTATGGTG
Found at i:6984 original size:7 final size:7
Alignment explanation
Indices: 6972--7012 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
6962 AGAACTGCTT
6972 TCTCCAA
1 TCTCCAA
6979 TCTCCAA
1 TCTCCAA
6986 TCTCCAA
1 TCTCCAA
6993 TCTCCAA
1 TCTCCAA
7000 TCTCCAA
1 TCTCCAA
7007 TCTCCA
1 TCTCCA
7013 GTTCTGATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.27, C:0.44, G:0.00, T:0.29
Consensus pattern (7 bp):
TCTCCAA
Found at i:15441 original size:27 final size:27
Alignment explanation
Indices: 15406--15463 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
15396 TTTGCTATCC
* * **
15406 AACTTTTCCTAATCCTTTACATTACCA
1 AACTGTTCCTAATCCTTAACAACACCA
*
15433 AACTGTTCCTACTCCTTAACAACACCA
1 AACTGTTCCTAATCCTTAACAACACCA
15460 AACT
1 AACT
15464 ACACCAAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.33, G:0.02, T:0.33
Consensus pattern (27 bp):
AACTGTTCCTAATCCTTAACAACACCA
Found at i:16729 original size:108 final size:110
Alignment explanation
Indices: 16527--16733 Score: 305
Period size: 108 Copynumber: 1.9 Consensus size: 110
16517 TCGAATTTGC
*
16527 TAACCATCTACTCACATATATGATAAGAATCGAGAGAAAAAAAAAACTCTATAACTAAAATGATT
1 TAACCACCTACTCACATATATGATAAGAATCGAGAGAAAAAAAAAACTCTATAACTAAAATGATT
* *
16592 TGCTAGCCACACATCAAGAATACTTGACGCGCCAGCGCAAGCCGA
66 TGCTAGCCACAAATCAAGAATACTCGACGCGCCAGCGCAAGCCGA
*
16637 TAACCACCTACTCACATATATGATAAG-AGCTGAGAG-AAAAAAAAA-TCTA-AATCTAAAATGA
1 TAACCACCTACTCACATATATGATAAGAATC-GAGAGAAAAAAAAAACTCTATAA-CTAAAATGA
* * *
16698 TTTGTTAGCCATAAATCAAGAATGCTCGACGCGCCA
64 TTTGCTAGCCACAAATCAAGAATACTCGACGCGCCA
16734 ACGTGAGCCG
Statistics
Matches: 88, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
107 2 0.02
108 44 0.50
109 11 0.12
110 31 0.35
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (110 bp):
TAACCACCTACTCACATATATGATAAGAATCGAGAGAAAAAAAAAACTCTATAACTAAAATGATT
TGCTAGCCACAAATCAAGAATACTCGACGCGCCAGCGCAAGCCGA
Found at i:16929 original size:2 final size:2
Alignment explanation
Indices: 16922--16948 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16912 TGTATGTATG
16922 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 T
16949 TATTCAACTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19177 original size:25 final size:25
Alignment explanation
Indices: 19149--19197 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
19139 GCTTGTTTTG
19149 TAGAGACCAAGCGAGAGTGCTCAAA
1 TAGAGACCAAGCGAGAGTGCTCAAA
*
19174 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCAAGCGAGAGTGCTCAA
19198 GATTGTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.31, T:0.12
Consensus pattern (25 bp):
TAGAGACCAAGCGAGAGTGCTCAAA
Found at i:20198 original size:33 final size:33
Alignment explanation
Indices: 20082--20212 Score: 174
Period size: 33 Copynumber: 4.0 Consensus size: 33
20072 GGCGTCGTCG
*
20082 CCATGGCGGTGTCGCCCAACTT-GGGCGGCACCA
1 CCATGGCGGTGTCGCCCTA-TTGGGGCGGCACCA
* *
20115 CCATAGCGGTGTCGCCCTGTTGGGGCGGCACCA
1 CCATGGCGGTGTCGCCCTATTGGGGCGGCACCA
* * *
20148 CCTTGGCGGTGTCGCCCTATTGGGGTGGCACAA
1 CCATGGCGGTGTCGCCCTATTGGGGCGGCACCA
* *
20181 CCATGGCGGCGTCGCCCTGTTGGGGCGGCACC
1 CCATGGCGGTGTCGCCCTATTGGGGCGGCACC
20213 GCCACAAAGT
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
32 2 0.02
33 82 0.98
ACGTcount: A:0.11, C:0.34, G:0.37, T:0.18
Consensus pattern (33 bp):
CCATGGCGGTGTCGCCCTATTGGGGCGGCACCA
Done.