Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007607.1 Corchorus capsularis cultivar CVL-1 contig07628, 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: 49297
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:289 original size:14 final size:14
Alignment explanation
Indices: 272--299 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
262 CTAACTATCA
272 TATTAAATTAGCAT
1 TATTAAATTAGCAT
286 TATTAAATTAGCAT
1 TATTAAATTAGCAT
300 ATATGTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
TATTAAATTAGCAT
Found at i:6573 original size:16 final size:17
Alignment explanation
Indices: 6552--6583 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
6542 ACTTTATGAA
6552 AAAAAAAAGGA-AAAAG
1 AAAAAAAAGGAGAAAAG
6568 AAAAAAAAGGAGAAAA
1 AAAAAAAAGGAGAAAA
6584 TGATGAGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGGAGAAAAG
Found at i:10465 original size:2 final size:2
Alignment explanation
Indices: 10453--10494 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
10443 TCTGGTGATT
*
10453 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10495 ATCTGAAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:10886 original size:13 final size:13
Alignment explanation
Indices: 10870--10896 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10860 TAAAATATTG
10870 ATGAAAGCATTTA
1 ATGAAAGCATTTA
10883 ATGAAAGCATTTA
1 ATGAAAGCATTTA
10896 A
1 A
10897 AGATAGGGTT
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:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGAAAGCATTTA
Found at i:12653 original size:17 final size:16
Alignment explanation
Indices: 12613--12661 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
12603 CATGTAATCT
12613 TTGATCA-TCGGTGATC
1 TTGATCACT-GGTGATC
12629 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
12646 TTAGATCACTAGTGAT
1 TT-GATCACTGGTGAT
12662 GTAAGTGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 3 0.10
17 24 0.83
18 2 0.07
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:15464 original size:99 final size:99
Alignment explanation
Indices: 15291--15484 Score: 264
Period size: 99 Copynumber: 2.0 Consensus size: 99
15281 AGCATTCCAA
* * * *
15291 AGTCGGGCTGTTGGTATTATTTCGAGGATGACCGTTGGCCTGCTTTGGTGTAGATTCCGCTACCT
1 AGTCGGGCTGCTGGTATTATTTCGAAGATGACCGTTGGCCTGCTTTGGTGGAGATTCCGATACCT
* *
15356 CTTTTCGGCTTTCTAGTAAAACAGAGTCATTCAG
66 CTTTCCGGCTCTCTAGTAAAACAGAGTCATTCAG
* * * **
15390 AGTCGGGCTGCTGGTATTGA-TTCGAAGATGATCGTTGGCCTGTTTTGGTGGAGGTTCCGATATT
1 AGTCGGGCTGCTGGTATT-ATTTCGAAGATGACCGTTGGCCTGCTTTGGTGGAGATTCCGATACC
*
15454 TCTTTCCGGCTCTCTGGTAAAACAGAGTCAT
65 TCTTTCCGGCTCTCTAGTAAAACAGAGTCAT
15485 CACTCTCAAC
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
99 81 0.99
100 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.35
Consensus pattern (99 bp):
AGTCGGGCTGCTGGTATTATTTCGAAGATGACCGTTGGCCTGCTTTGGTGGAGATTCCGATACCT
CTTTCCGGCTCTCTAGTAAAACAGAGTCATTCAG
Found at i:22109 original size:21 final size:21
Alignment explanation
Indices: 22084--22136 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
22074 TGTAATCATA
22084 AATAAATATATTATAATTAAT
1 AATAAATATATTATAATTAAT
* * * * *
22105 TATAAGTTTAATATTATTAAT
1 AATAAATATATTATAATTAAT
*
22126 AATAATTATAT
1 AATAAATATAT
22137 ATCTATATAC
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
AATAAATATATTATAATTAAT
Found at i:32733 original size:78 final size:70
Alignment explanation
Indices: 32656--32810 Score: 224
Period size: 70 Copynumber: 2.2 Consensus size: 70
32646 TAACTAAAAT
* * * * *
32656 AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAG-ATTTAATTATATAAAAATAGAGTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATT-GTATTTAATTAAATAAAAATAGAGTTTT
*
32720 TAGTTG
65 TAGTCG
32726 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTGTATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTGTATTTAATTAAATAAAAATAGAGTTTTT
32791 AGTCG
66 AGTCG
32796 AGTAAAACTA-TAAAA
1 AGTAAAA-TAGTAAAA
32811 ACCTAAACAA
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
69 1 0.01
70 74 0.96
71 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.13, T:0.35
Consensus pattern (70 bp):
AGTAAAATAGTAAAATAAAATAATTATAAAGATATTGTATTTAATTAAATAAAAATAGAGTTTTT
AGTCG
Found at i:35276 original size:22 final size:22
Alignment explanation
Indices: 35251--35349 Score: 67
Period size: 22 Copynumber: 4.3 Consensus size: 22
35241 TGTGGTTACT
35251 AAAATTTTATAGTGTGATTATC
1 AAAATTTTATAGTGTGATTATC
* * *
35273 AAAATTTTATAATGAGGTTAATTACC
1 AAAATTTTAT-A-G-TG-TGATTATC
* * *
35299 AAAATTTTATTG-GTAGAATATT
1 AAAATTTTATAGTGT-GATTATC
35321 AAAATTTTATAGTGT-ATTTATC
1 AAAATTTTATAGTGTGA-TTATC
*
35343 ACAATTT
1 AAAATTT
35350 CATGAGAAGT
Statistics
Matches: 58, Mismatches: 12, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
21 2 0.03
22 34 0.59
23 3 0.05
24 2 0.03
25 1 0.02
26 16 0.28
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.44
Consensus pattern (22 bp):
AAAATTTTATAGTGTGATTATC
Found at i:35389 original size:22 final size:22
Alignment explanation
Indices: 35338--35615 Score: 170
Period size: 22 Copynumber: 12.5 Consensus size: 22
35328 TATAGTGTAT
* * *
35338 TTATCACAATTTCATGA-GAAG
1 TTATCAAAATTTCATAAGGAGG
35359 TTATCAAAATTTCATAAGGAGG
1 TTATCAAAATTTCATAAGGAGG
* *
35381 TTATTAAAATAAAATTTCATAAGGATG
1 TTA-T----CAAAATTTCATAAGGAGG
* *
35408 TTATGAAAATTTCATATGGAGG
1 TTATCAAAATTTCATAAGGAGG
35430 TTATCAAAATTTCATAAGGAGG
1 TTATCAAAATTTCATAAGGAGG
* ** *
35452 TTATCGAAA-TTCATGCGAAGG
1 TTATCAAAATTTCATAAGGAGG
* *
35473 TTATCAAAATTTCACATGGAGG
1 TTATCAAAATTTCATAAGGAGG
****
35495 TTA-CTAAAATTTCATACTTTGG
1 TTATC-AAAATTTCATAAGGAGG
* * *
35517 TTGTCAAAATTTCATAGGGCA-A
1 TTATCAAAATTTCATAAGG-AGG
** * * **
35539 TTATTGAAATTTTATATGGAAA
1 TTATCAAAATTTCATAAGGAGG
* * *
35561 TTATCAAAATTACATAAGAAGA
1 TTATCAAAATTTCATAAGGAGG
*
35583 TTATCAAAATTTCAT-AGTGTGG
1 TTATCAAAATTTCATAAG-GAGG
*
35605 TTATAAAAATT
1 TTATCAAAATT
35616 ACATTGTGAG
Statistics
Matches: 198, Mismatches: 47, Indels: 23
0.74 0.18 0.09
Matches are distributed among these distances:
21 36 0.18
22 140 0.71
23 2 0.01
26 1 0.01
27 19 0.10
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGGAGG
Found at i:35402 original size:27 final size:27
Alignment explanation
Indices: 35364--35417 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
35354 AGAAGTTATC
*
35364 AAAATTTCATAAGGAGGTTATTAAAAT
1 AAAATTTCATAAGGAGGTTATGAAAAT
*
35391 AAAATTTCATAAGGATGTTATGAAAAT
1 AAAATTTCATAAGGAGGTTATGAAAAT
35418 TTCATATGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (27 bp):
AAAATTTCATAAGGAGGTTATGAAAAT
Found at i:35417 original size:49 final size:48
Alignment explanation
Indices: 35345--35439 Score: 136
Period size: 49 Copynumber: 2.0 Consensus size: 48
35335 TATTTATCAC
* *
35345 AATTTCATGAGAAGTTATCAAAATTTCATAAGGAGGTTATTAAAATAA
1 AATTTCATAAGAAGTTATCAAAATTTCATAAGGAGGTTATCAAAATAA
* * *
35393 AATTTCATAAGGATGTTATGAAAATTTCATATGGAGGTTATCAAAAT
1 AATTTCATAA-GAAGTTATCAAAATTTCATAAGGAGGTTATCAAAAT
35440 TTCATAAGGA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 9 0.22
49 32 0.78
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (48 bp):
AATTTCATAAGAAGTTATCAAAATTTCATAAGGAGGTTATCAAAATAA
Found at i:35767 original size:22 final size:22
Alignment explanation
Indices: 35742--35786 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
35732 TAGAGGGAGA
35742 TTATCAAAATTTCATAATGTGG
1 TTATCAAAATTTCATAATGTGG
35764 TTATCAAAATTTCATAATGTGG
1 TTATCAAAATTTCATAATGTGG
35786 T
1 T
35787 ACAGAGGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTCATAATGTGG
Found at i:35821 original size:58 final size:56
Alignment explanation
Indices: 35733--35840 Score: 137
Period size: 58 Copynumber: 1.9 Consensus size: 56
35723 TCAAAATTTT
*
35733 AGAGGGAGATTATCAAAATTTCATAATGTGGTTATCAAAATTTCATAATGTGGTAC
1 AGAGGGAGATTATCAAAATTTCATAATGTGGTAATCAAAATTTCATAATGTGGTAC
** * *
35789 AGAGGGAGAGGTTATC-AAATCTTCATCGTGTGGTAATTAAATTTTCATAATG
1 AGAGGGAGA--TTATCAAAAT-TTCATAATGTGGTAATCAAAATTTCATAATG
35841 AGTAAAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
56 9 0.20
57 4 0.09
58 31 0.70
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.34
Consensus pattern (56 bp):
AGAGGGAGATTATCAAAATTTCATAATGTGGTAATCAAAATTTCATAATGTGGTAC
Found at i:35870 original size:21 final size:22
Alignment explanation
Indices: 35844--35920 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
35834 CATAATGAGT
35844 AAAATTT-ATAGTGAGATTAAC
1 AAAATTTCATAGTGAGATTAAC
* * * * **
35865 AAAATTTGATTGTGTGGTTCTC
1 AAAATTTCATAGTGAGATTAAC
* *
35887 AAAATTTTATAGGGAGATTAAC
1 AAAATTTCATAGTGAGATTAAC
35909 AAAATTTCATAG
1 AAAATTTCATAG
35921 GTAAGTTATC
Statistics
Matches: 42, Mismatches: 13, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
21 7 0.17
22 35 0.83
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.36
Consensus pattern (22 bp):
AAAATTTCATAGTGAGATTAAC
Found at i:35937 original size:44 final size:44
Alignment explanation
Indices: 35844--35940 Score: 108
Period size: 44 Copynumber: 2.2 Consensus size: 44
35834 CATAATGAGT
* * * * *
35844 AAAA-TTTATAGTGAGATTAACAAAATTTGATTGTGTGGTTCTC
1 AAAATTTTATAGGGAGATTAACAAAATTTCATAGTGTAGTTATC
35887 AAAATTTTATAGGGAGATTAACAAAATTTCATAG-GTAAGTTATC
1 AAAATTTTATAGGGAGATTAACAAAATTTCATAGTGT-AGTTATC
**
35931 GTAATTTTAT
1 AAAATTTTAT
35941 GGTATAGTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
43 6 0.13
44 39 0.87
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.39
Consensus pattern (44 bp):
AAAATTTTATAGGGAGATTAACAAAATTTCATAGTGTAGTTATC
Found at i:44127 original size:169 final size:166
Alignment explanation
Indices: 43646--44311 Score: 474
Period size: 169 Copynumber: 3.9 Consensus size: 166
43636 GCCAAACCAC
** * * * *
43646 TAATTTTTCGAAAGCATTTTTTATACATGAAACATCAAATTTAGCTTTTGAGCTC-TCAATGAAA
1 TAATTTTTCGAAAATATTTTTGATTC-TGAAACATCAAATTTAGCTTTCGAACTCTTC-ATGAAA
* * * * * * * * *
43710 GTTGTAGGTCATGAAATAATCTTTTAATAAACAATTTGATTCACCTTAATCAGATATTTGGAGCA
64 GTTGTAGATCATGGAACAATCTTTTAATAAAC-ACTTGAATCATCTTAATCAGATATCTAGAACA
* * * *
43775 AAAACTT-TATAATATTAAGTAGACTATTCACCAAAACCAC
128 AAAA-TTATATAATATTAAGTAGACCATCCACTAAAA-CAA
** * * * * *
43815 TAATTTTTCGAAGGTATTTTCTAAATT-TGAAACATCAAATTTAACTTTTG-AGTACTACATGAA
1 TAATTTTTCGAAAATATTTT-T-GATTCTGAAACATCAAATTTAGCTTTCGAACT-CTTCATGAA
* * * * * ** *
43878 AGTTGTAAATTATGGAA-AAACATATTAATAGACACTTGAATCAAGTTAATCAGATATCCAGAGA
63 AGTTGTAGATCATGGAACAATC-TTTTAATAAACACTTGAATCATCTTAATCAGATATCTAGA-A
* *
43942 -AAATACTATATAATATTGAA-TAGACCATCCACTAAAACAA
126 CAAAAATTATATAATATT-AAGTAGACCATCCACTAAAACAA
*
43982 TTAATTTTTCCGAAAATATTTTTGATTCCCGAAACATCAAATTTAGCTTTCGAACTCTTCATGAA
1 -TAATTTTT-CGAAAATATTTTTGATT-CTGAAACATCAAATTTAGCTTTCGAACTCTTCATGAA
* *
44047 AGTTGTAGATCATGGAACAA-CTTTTTAATAAACACTTGAATCATCTCAATCGGACT-TCTAGAA
63 AGTTGTAGATCATGGAACAATC-TTTTAATAAACACTTGAATCATCTTAATCAGA-TATCTAGAA
* * *
44110 CAAAAATTATGTAATATTAAGTTGACCGTCCATTCCCGCTAACCGATACAA
126 CAAAAATTATATAATATTAAG-T-A--GACCA-T-CCACTAA---A-ACAA
* * * * * *
44161 CAAATTTTCGAAAGCA-ATTTTGGATACTTGAAACATCAAATTTAGCTTTC-AAGTCTTTAATGA
1 TAATTTTTCGAAA--ATATTTTTGATTC-TGAAACATCAAATTTAGCTTTCGAACTC-TTCATGA
* * * * * *
44224 AAGTT-TAGATTATGGAACAATCTTTTAATAGACACTTGAATCATCTTAATCGGACATCTATAGC
62 AAGTTGTAGATCATGGAACAATCTTTTAATAAACACTTGAATCATCTTAATCAGATATCTAGAAC
**
44288 AAAAATTAGGTAATATTAAGTAGA
127 AAAAATTATATAATATTAAGTAGA
44312 TTGTCCATTC
Statistics
Matches: 397, Mismatches: 67, Indels: 62
0.75 0.13 0.12
Matches are distributed among these distances:
167 6 0.02
168 65 0.16
169 169 0.43
170 8 0.02
171 3 0.01
173 5 0.01
174 1 0.00
175 7 0.02
176 1 0.00
177 79 0.20
178 48 0.12
179 5 0.01
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (166 bp):
TAATTTTTCGAAAATATTTTTGATTCTGAAACATCAAATTTAGCTTTCGAACTCTTCATGAAAGT
TGTAGATCATGGAACAATCTTTTAATAAACACTTGAATCATCTTAATCAGATATCTAGAACAAAA
ATTATATAATATTAAGTAGACCATCCACTAAAACAA
Found at i:44565 original size:68 final size:68
Alignment explanation
Indices: 44456--44585 Score: 251
Period size: 68 Copynumber: 1.9 Consensus size: 68
44446 CTATTAGACC
44456 TTAAATTCTTATCACATAGATCATGTATGTCAAATTTCAAGTTAATTGAAAATATTTAACTACAG
1 TTAAATTCTTATCACATAGATCATGTATGTCAAATTTCAAGTTAATTGAAAATATTTAACTACAG
44521 ATT
66 ATT
*
44524 TTAAATTCTTATCACATAGATCATGTATGTCAAATTTCAAGTTAATTGAAGATATTTAACTA
1 TTAAATTCTTATCACATAGATCATGTATGTCAAATTTCAAGTTAATTGAAAATATTTAACTA
44586 TATATGTTTG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (68 bp):
TTAAATTCTTATCACATAGATCATGTATGTCAAATTTCAAGTTAATTGAAAATATTTAACTACAG
ATT
Found at i:45001 original size:27 final size:27
Alignment explanation
Indices: 44963--45017 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
44953 AGCATATTGT
44963 TCATCCCATTCTTATCAAGTCCAATTA
1 TCATCCCATTCTTATCAAGTCCAATTA
*
44990 TCATCCCATTCTTATCAAGTCCGATTA
1 TCATCCCATTCTTATCAAGTCCAATTA
45017 T
1 T
45018 GATTCAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.29, G:0.05, T:0.38
Consensus pattern (27 bp):
TCATCCCATTCTTATCAAGTCCAATTA
Found at i:47427 original size:2 final size:2
Alignment explanation
Indices: 47415--47467 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
47405 GATGGCGAAA
* *
47415 AG AG GG AG AG AG AG AG AG GG 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
47457 AG AG AG AG AG A
1 AG AG AG AG AG A
47468 ACTGAAGTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Done.