Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022438.1 Corchorus olitorius cultivar O-4 contig22471, 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: 55488
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:177 original size:21 final size:21
Alignment explanation
Indices: 141--184 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
131 ATTTTCTCAT
** *
141 TAAAGGTTATTGAGAAGATTA
1 TAAAGGTTATCAAGAACATTA
162 TAAAGGTTATCAAGAACATTA
1 TAAAGGTTATCAAGAACATTA
183 TA
1 TA
185 CTATTATCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (21 bp):
TAAAGGTTATCAAGAACATTA
Found at i:1681 original size:8 final size:8
Alignment explanation
Indices: 1645--1694 Score: 55
Period size: 8 Copynumber: 5.9 Consensus size: 8
1635 TTGCTTAAAC
1645 TAAAATTT
1 TAAAATTT
**
1653 TAAAAAAT
1 TAAAATTT
1661 TAAAAGGTATT
1 TAAAA--T-TT
1672 TAAAATTT
1 TAAAATTT
1680 TAAAATTT
1 TAAAATTT
1688 TAAAATT
1 TAAAATT
1695 AAAAGGGTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 28 0.80
9 1 0.03
11 6 0.17
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (8 bp):
TAAAATTT
Found at i:5286 original size:16 final size:16
Alignment explanation
Indices: 5238--5287 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
5228 AAAATTCGAT
5238 TAGTTTATTAGTAAAA
1 TAGTTTATTAGTAAAA
* * *
5254 TATTTTTTTTG-AGAAA
1 TAGTTTATTAGTA-AAA
5270 TAGTTTATTAGTAAAA
1 TAGTTTATTAGTAAAA
5286 TA
1 TA
5288 TTAATCGAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
15 1 0.04
16 24 0.92
17 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (16 bp):
TAGTTTATTAGTAAAA
Found at i:6647 original size:6 final size:6
Alignment explanation
Indices: 6636--6682 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
6626 TTGAGGTCCT
* * *
6636 CAAAAA CAAAAA CAAAAA CAAAAC CAAACA CCAAAA CAGAAAA CAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CA-AAAA CAAA
6683 GCTACACCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
6 28 0.82
7 6 0.18
ACGTcount: A:0.74, C:0.23, G:0.02, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:12022 original size:29 final size:30
Alignment explanation
Indices: 11959--12024 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
11949 TAAGAATTTT
* *
11959 TAATATTGACTTTTTTTTTTCATGGGTACA
1 TAATATTGACTTTTGTTTTTCATCGGTACA
* *
11989 AAATATTGA-TTTTGTTTTTCACTCGG-CCA
1 TAATATTGACTTTTGTTTTTCA-TCGGTACA
12018 TAATATT
1 TAATATT
12025 AAATGAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (30 bp):
TAATATTGACTTTTGTTTTTCATCGGTACA
Found at i:15097 original size:25 final size:26
Alignment explanation
Indices: 15069--15136 Score: 86
Period size: 25 Copynumber: 2.6 Consensus size: 26
15059 TATCTTGAAT
15069 AAAATAACACATTATT-ATCATGCCAA
1 AAAATAACACATTATTAAT-ATGCCAA
* *
15095 AAAA-AAAACATTATTAATGTGCCAAA
1 AAAATAACACATTATTAATATGCC-AA
15121 AAAATAACACATTATT
1 AAAATAACACATTATT
15137 TTTATAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 14 0.39
26 12 0.33
27 10 0.28
ACGTcount: A:0.54, C:0.15, G:0.04, T:0.26
Consensus pattern (26 bp):
AAAATAACACATTATTAATATGCCAA
Found at i:18463 original size:22 final size:22
Alignment explanation
Indices: 18433--18475 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
18423 GTATTTCAAG
18433 AAAACCTCCTCCATCCCCGAGA
1 AAAACCTCCTCCATCCCCGAGA
*
18455 AAAAGCTCCTCCATCCCCGAG
1 AAAACCTCCTCCATCCCCGAG
18476 GTAACTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.44, G:0.12, T:0.14
Consensus pattern (22 bp):
AAAACCTCCTCCATCCCCGAGA
Found at i:20277 original size:19 final size:19
Alignment explanation
Indices: 20253--20290 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
20243 TAAATAACTA
*
20253 AATATCATGCAATCCCTAC
1 AATATCATGCAAACCCTAC
*
20272 AATATCGTGCAAACCCTAC
1 AATATCATGCAAACCCTAC
20291 TAGACCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.32, G:0.08, T:0.24
Consensus pattern (19 bp):
AATATCATGCAAACCCTAC
Found at i:22324 original size:30 final size:30
Alignment explanation
Indices: 22282--22351 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
22272 ATAGGTCCCT
*
22282 CTACTTATAAAAAGGGATCAATTTGGCCCCC
1 CTACTTACAAAAAGGG-TCAATTTGGCCCCC
** * *
22313 CTAC-TACAAAAATTGTCAATTTGGTCCCT
1 CTACTTACAAAAAGGGTCAATTTGGCCCCC
22342 CTACTTACAA
1 CTACTTACAA
22352 TTTGGTATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 16 0.48
30 13 0.39
31 4 0.12
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.30
Consensus pattern (30 bp):
CTACTTACAAAAAGGGTCAATTTGGCCCCC
Found at i:22394 original size:31 final size:30
Alignment explanation
Indices: 22313--22397 Score: 79
Period size: 31 Copynumber: 2.8 Consensus size: 30
22303 TTTGGCCCCC
*
22313 CTAC-TACAAAAATTGTCAATTTG-GTCCCT
1 CTACTTACAAAATTTGTCAA-TTGAGTCCCT
22342 CTACTTAC--AATTTGGTATCAATTGAGTCCCT
1 CTACTTACAAAATTT-G--TCAATTGAGTCCCT
*
22373 TTACTTAACAAAATTTGTCAATTGA
1 CTACTT-ACAAAATTTGTCAATTGA
22398 TTATTTGTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
28 4 0.09
29 5 0.11
30 6 0.13
31 23 0.50
32 2 0.04
33 1 0.02
34 5 0.11
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (30 bp):
CTACTTACAAAATTTGTCAATTGAGTCCCT
Found at i:22719 original size:31 final size:31
Alignment explanation
Indices: 22616--22720 Score: 110
Period size: 31 Copynumber: 3.5 Consensus size: 31
22606 CAGATTCTAT
* *
22616 TAAGTAGAGGGACTC-AATTGA-CACCATATTG
1 TAAGTAGAGGGAC-CAAATTGATC-CCTTTTTG
** *
22647 TAAGTAGAGGGACCAAATTGAT-AGTTTCTG
1 TAAGTAGAGGGACCAAATTGATCCCTTTTTG
*
22677 T-AGTAGGGGGACCAAATTGATCCCTTTTTG
1 TAAGTAGAGGGACCAAATTGATCCCTTTTTG
22707 TAAGTAGAGGGACC
1 TAAGTAGAGGGACC
22721 TGTACGGTAT
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
29 19 0.32
30 11 0.18
31 30 0.50
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (31 bp):
TAAGTAGAGGGACCAAATTGATCCCTTTTTG
Found at i:24821 original size:12 final size:12
Alignment explanation
Indices: 24804--24828 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24794 GTTGTCCTGT
24804 TGAACTTGAGTA
1 TGAACTTGAGTA
24816 TGAACTTGAGTA
1 TGAACTTGAGTA
24828 T
1 T
24829 CGAGAGATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (12 bp):
TGAACTTGAGTA
Found at i:25524 original size:22 final size:20
Alignment explanation
Indices: 25475--25512 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25465 ATCATGGTAT
25475 TTAGTTGTAATGATTTTTAC
1 TTAGTTGTAATGATTTTTAC
* *
25495 TCACTTGTAATGATTTTT
1 TTAGTTGTAATGATTTTT
25513 TTCATTAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.08, G:0.13, T:0.55
Consensus pattern (20 bp):
TTAGTTGTAATGATTTTTAC
Found at i:25854 original size:21 final size:21
Alignment explanation
Indices: 25811--25854 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
25801 CCCTGAGACT
25811 TCGGGGATGGAGGAGCTTTTTC
1 TCGGGGATGGAGGAGC-TTTTC
25833 TCGGGGATGGAGGAAG-TTTTC
1 TCGGGGATGGAGG-AGCTTTTC
25854 T
1 T
25855 TGAAATACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.29
22 13 0.62
23 2 0.10
ACGTcount: A:0.16, C:0.11, G:0.41, T:0.32
Consensus pattern (21 bp):
TCGGGGATGGAGGAGCTTTTC
Found at i:41240 original size:107 final size:105
Alignment explanation
Indices: 41077--41338 Score: 366
Period size: 107 Copynumber: 2.5 Consensus size: 105
41067 AGTTTAGCCT
* * *
41077 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTGATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAACCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
* *
41142 AGTAATTTATTGTTATAGGATTTTAGAAATAAAATACAAAAC
66 AATAA--TAATGTTATAGGATTTTAGAAATAAAATACAAAAC
*
41184 TAATTTCACTAAGTTTAACCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAACCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
* * *
41249 AATAATAATGTTATAGGGTTTTAGAAATAAAATATATAAC
66 AATAATAATGTTATAGGATTTTAGAAATAAAATACAAAAC
** ** *
41289 TAA-TTCACTAAGTTT-AGTCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAACCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
41339 TAGAAAAATT
Statistics
Matches: 141, Mismatches: 14, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
103 30 0.21
104 12 0.09
105 34 0.24
107 65 0.46
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (105 bp):
TAATTTCACTAAGTTTAACCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
AATAATAATGTTATAGGATTTTAGAAATAAAATACAAAAC
Found at i:42845 original size:42 final size:43
Alignment explanation
Indices: 42793--42886 Score: 111
Period size: 45 Copynumber: 2.2 Consensus size: 43
42783 AGTGCATTAC
* *
42793 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAACG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
* *
42834 CTAATATTCTACTCCTCCATCTCTATATAATTGATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
*
42879 TTAATATT
1 CTAATATT
42887 AATTGTTGCT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.14
45 34 0.77
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.36
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:43937 original size:137 final size:138
Alignment explanation
Indices: 43672--43950 Score: 497
Period size: 137 Copynumber: 2.0 Consensus size: 138
43662 CAGCAGGAAA
43672 AGTAAGGGAGGAAATTCATCGAGGGCGTTTTTAGTCACCCGAAAAGTGAGAAAAGACCAAAAAAA
1 AGTAAGGGAGGAAATTCATCGAGGGCGTTTTTAGTCACCCGAAAAGTGAGAAAAGACCAAAAAAA
* * *
43737 GCCAAAAGGTGGCACCATATTAATCCTCAATTTGGCCTTTAAGTAATTTCCATAGTCACTAAAAA
66 GCCAAAAGGAGGCACCACATTAATCCTCAATTTGACCTTTAAGTAATTTCCATAGTCACTAAAAA
43802 TAATATAT
131 TAATATAT
*
43810 AGTAAGGGAGGAAATTCATCGATGGCGTTTTTAGTCACCCGAAAAGTGAGAAAAGACC-AAAAAA
1 AGTAAGGGAGGAAATTCATCGAGGGCGTTTTTAGTCACCCGAAAAGTGAGAAAAGACCAAAAAAA
* *
43874 GCCAAAAGGAGGCACCACATTAATTCTCAATTTGACCTTTAAGTAATTTCCATAGTCAGTAAAAA
66 GCCAAAAGGAGGCACCACATTAATCCTCAATTTGACCTTTAAGTAATTTCCATAGTCACTAAAAA
43939 TAATATAT
131 TAATATAT
43947 AGTA
1 AGTA
43951 TATATTATAT
Statistics
Matches: 135, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
137 78 0.58
138 57 0.42
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (138 bp):
AGTAAGGGAGGAAATTCATCGAGGGCGTTTTTAGTCACCCGAAAAGTGAGAAAAGACCAAAAAAA
GCCAAAAGGAGGCACCACATTAATCCTCAATTTGACCTTTAAGTAATTTCCATAGTCACTAAAAA
TAATATAT
Found at i:44015 original size:22 final size:23
Alignment explanation
Indices: 43987--44043 Score: 107
Period size: 22 Copynumber: 2.5 Consensus size: 23
43977 CTTAGAATAG
43987 AAAAGTGTAATTAGCTGAT-AAA
1 AAAAGTGTAATTAGCTGATAAAA
44009 AAAAGTGTAATTAGCTGATAAAA
1 AAAAGTGTAATTAGCTGATAAAA
44032 AAAAGTGTAATT
1 AAAAGTGTAATT
44044 GGAATATTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 19 0.56
23 15 0.44
ACGTcount: A:0.51, C:0.04, G:0.18, T:0.28
Consensus pattern (23 bp):
AAAAGTGTAATTAGCTGATAAAA
Found at i:49208 original size:11 final size:11
Alignment explanation
Indices: 49192--49217 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
49182 AGGGAGCAGA
49192 AATAAGAGAAG
1 AATAAGAGAAG
49203 AATAAGAGAAG
1 AATAAGAGAAG
49214 AATA
1 AATA
49218 TTGTTGACAA
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:0.65, C:0.00, G:0.23, T:0.12
Consensus pattern (11 bp):
AATAAGAGAAG
Done.