Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008127.1 Corchorus capsularis cultivar CVL-1 contig08148, 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: 30850
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:2267 original size:28 final size:26
Alignment explanation
Indices: 2175--2280 Score: 108
Period size: 28 Copynumber: 4.0 Consensus size: 26
2165 AGGTGTACTA
* * *
2175 AAAATTACCAAAATGTCCCTAAATATGC
1 AAAATGACCAAAATGCCCCT--AGATGC
* *
2203 -AAATGACCAAAATACCCTTAG-TGC
1 AAAATGACCAAAATGCCCCTAGATGC
2227 AAGAATGACCAAAATGCCCCTATGATGC
1 AA-AATGACCAAAATGCCCCTA-GATGC
2255 GAAAATGACCAAAATGCCCCTAGATG
1 -AAAATGACCAAAATGCCCCTAGATG
2281 ACCCTAATGC
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
24 3 0.05
25 2 0.03
26 17 0.26
27 20 0.30
28 22 0.33
29 2 0.03
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (26 bp):
AAAATGACCAAAATGCCCCTAGATGC
Found at i:4589 original size:18 final size:18
Alignment explanation
Indices: 4566--4600 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4556 AAGTTCGTGA
* *
4566 TTGAAGATATTTGAAGAT
1 TTGAAGACAATTGAAGAT
4584 TTGAAGACAATTGAAGA
1 TTGAAGACAATTGAAGA
4601 ATTAATTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.31
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:5945 original size:6 final size:6
Alignment explanation
Indices: 5934--5971 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
5924 ATTAATTTGC
5934 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
5972 GCTTTGCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (6 bp):
TTTAGA
Found at i:8647 original size:19 final size:18
Alignment explanation
Indices: 8623--8659 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
8613 TTGAAGATTT
8623 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
8642 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
8660 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:10797 original size:156 final size:153
Alignment explanation
Indices: 10384--10798 Score: 376
Period size: 156 Copynumber: 2.7 Consensus size: 153
10374 TAGGTCATCC
* * * * * * *
10384 TGGCTAAATTTCATCTCAAACAGACTTAGGATGAAGAACTTATGTAAGTTTTTAAGTTAAGGACA
1 TGGCGAAATTTCAGCTCAATCAGACTTAGG-TGAAAAACTTATGCAAGTTTTTCATTTAAGGACA
* * * **
10449 GTTTGGGGTGTGAAACCAACTTCACTATGATAGGAACTTCGGTTTTACTTAGAATTTTTTCCATA
65 GTTTGAGGTGTGAAACCAAGTTCACTATGA-AGGGAGGTCGGTTTTACTTAGAATTTTTTCCATA
*
10514 GTTTAATGGGAATAATCTAAGCCTA
129 GTTTAATGGGAATAATATAAGCCTA
* ** * *
10539 CTGGCGGAAA-ATCAGCTTC-ATTGGACTTAGAATGAAAAACTTATGCAAGTTGTTCATTTAAGG
1 -TGGC-GAAATTTCAGC-TCAATCAGACTTAG-GTGAAAAACTTATGCAAGTTTTTCATTTAAGG
* * * * * * * *
10602 ACAATTT-AGGGAGAGAAACCAAGATCACCATCAAGGGGAGGTCGGTTTTACTTGGGATTTTTTC
62 ACAGTTTGA-GGTGTGAAACCAAGTTCACTATGAA-GGGAGGTCGGTTTTACTTAGAATTTTTTC
*
10666 CATAGTCTT-GTGGAGAA-AATATAAGTCCCT-
125 CATAGT-TTAATGG-GAATAATATAAG--CCTA
* *
10696 TGGC-AAAGTTTCAGCTCAATCAGACTTAAGGTGAAAAAACTTAGGGAAGTTTTTCATTTAAGGA
1 TGGCGAAA-TTTCAGCTCAATCAGACTT-AGGTG-AAAAACTTATGCAAGTTTTTCATTTAAGGA
*
10760 CAGTTTGAGGTGTGAAACCTAGTTCACTATGAAGGGAGG
63 CAGTTTGAGGTGTGAAACCAAGTTCACTATGAAGGGAGG
10799 CTCGAACCAG
Statistics
Matches: 203, Mismatches: 41, Indels: 30
0.74 0.15 0.11
Matches are distributed among these distances:
154 3 0.01
155 3 0.01
156 130 0.64
157 63 0.31
158 4 0.02
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (153 bp):
TGGCGAAATTTCAGCTCAATCAGACTTAGGTGAAAAACTTATGCAAGTTTTTCATTTAAGGACAG
TTTGAGGTGTGAAACCAAGTTCACTATGAAGGGAGGTCGGTTTTACTTAGAATTTTTTCCATAGT
TTAATGGGAATAATATAAGCCTA
Found at i:12435 original size:120 final size:120
Alignment explanation
Indices: 12218--12458 Score: 385
Period size: 120 Copynumber: 2.0 Consensus size: 120
12208 AGAGAAAACA
*
12218 TCATGGCTCGAATTGGTCTCATCGATGAAAGACTTGGGGGGCAAAACCAACAACTGCTTGGTGCC
1 TCATGGCTCGAATTGGTCTCATCGATGAAAGACTTGAGGGGCAAAACCAACAACTGCTTGGTGCC
* * *
12283 TAACCCGGTGCTCTGCCTCTTCGACAAGTCAACCATCAGGTGAACAACCAACAAG
66 CAACCCGGTGCTCTGCCTCTTCAACAAGTCAACAATCAGGTGAACAACCAACAAG
**
12338 TCATGGCTC-AGATTGGTCTCATCGATGAAAGACTTGAGGGGCAAAACCAACGGCTGCTTGGTGC
1 TCATGGCTCGA-ATTGGTCTCATCGATGAAAGACTTGAGGGGCAAAACCAACAACTGCTTGGTGC
* * *
12402 CCAGCCCGGTGCTCTGCCTCTTCAACAATTCAACAATGAGGTGAACAACCAACAAG
65 CCAACCCGGTGCTCTGCCTCTTCAACAAGTCAACAATCAGGTGAACAACCAACAAG
12458 T
1 T
12459 TCCACCTCCA
Statistics
Matches: 111, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
119 1 0.01
120 110 0.99
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.21
Consensus pattern (120 bp):
TCATGGCTCGAATTGGTCTCATCGATGAAAGACTTGAGGGGCAAAACCAACAACTGCTTGGTGCC
CAACCCGGTGCTCTGCCTCTTCAACAAGTCAACAATCAGGTGAACAACCAACAAG
Found at i:15262 original size:20 final size:21
Alignment explanation
Indices: 15223--15262 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
15213 CAAATGCTCA
*
15223 ACTTAAGGAGTCAAACGACTT
1 ACTTAAAGAGTCAAACGACTT
*
15244 ACTTAAAGAG-CAAATGACT
1 ACTTAAAGAGTCAAACGACT
15263 CGAGACCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23
Consensus pattern (21 bp):
ACTTAAAGAGTCAAACGACTT
Found at i:17165 original size:156 final size:156
Alignment explanation
Indices: 16881--17167 Score: 373
Period size: 156 Copynumber: 1.8 Consensus size: 156
16871 ATCTCAAACA
** * * * * * **
16881 GACTTAGGCTGAAGAACTTATGCAAGTTTTTCAATTAAGGACAGTTTGGGGTGTGAAACCAATTT
1 GACTTAGAATGAAAAACTTATGCAAGCTTTTCAATTAAGGACAGTTTAGGGAGAGAAACCAAGAT
* * *
16946 CACTATGATAGGAAGTTCAGTTTTACTTAGAATTTTTTCCATAGATTTATGGGAATAATCTAAGT
66 CACCATCATAGGAAGCTCAGTTTTACTTAGAATTTTTTCCATAGATTTATGGGAATAATCTAAGT
17011 CTACTAGCGAAAAATCAGCTTCATTG
131 CTACTAGCGAAAAATCAGCTTCATTG
*
17037 GACTTAGAATGAAAAACTTATGCAAGCTTTTCATTTAAGGACAGTTTAGGGAGAGAAACCAAGAT
1 GACTTAGAATGAAAAACTTATGCAAGCTTTTCAATTAAGGACAGTTTAGGGAGAGAAACCAAGAT
* * * *
17102 CACCATCA-AGGGGAGCTCAGTTTTACTTGGGATTTTTTCCATAG-TCTTGTGGAGAA-AATCTA
66 CACCATCATA-GGAAGCTCAGTTTTACTTAGAATTTTTTCCATAGAT-TTATGG-GAATAATCTA
17164 AGTC
128 AGTC
17168 CACCCTGCAA
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
155 2 0.02
156 106 0.95
157 3 0.03
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Consensus pattern (156 bp):
GACTTAGAATGAAAAACTTATGCAAGCTTTTCAATTAAGGACAGTTTAGGGAGAGAAACCAAGAT
CACCATCATAGGAAGCTCAGTTTTACTTAGAATTTTTTCCATAGATTTATGGGAATAATCTAAGT
CTACTAGCGAAAAATCAGCTTCATTG
Found at i:21755 original size:16 final size:16
Alignment explanation
Indices: 21734--21767 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
21724 TATATTTATT
21734 ACCAAATGAAAATGCA
1 ACCAAATGAAAATGCA
21750 ACCAAATGAAAATGCA
1 ACCAAATGAAAATGCA
21766 AC
1 AC
21768 TGGAAATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.12
Consensus pattern (16 bp):
ACCAAATGAAAATGCA
Found at i:22282 original size:45 final size:43
Alignment explanation
Indices: 22179--22294 Score: 152
Period size: 45 Copynumber: 2.7 Consensus size: 43
22169 ATTTTATTAA
*
22179 TTTCCAAAAATCTTCTTTTGG-ATTTCTT---AAAAACTTTTAT
1 TTTCC-AAAATCTTCTTTTGGAATTACTTAAAAAAAACTTTTAT
22219 TTTCCAAAATCTTCTTTTGGAATTACTTAAAAGAAAATCTTTGT-T
1 TTTCCAAAATCTTCTTTTGGAATTACTTAAAA-AAAA-CTTT-TAT
22264 TTTCCAAAATCTTCTTTTGGAATTACTTAAA
1 TTTCCAAAATCTTCTTTTGGAATTACTTAAA
22295 TATAAAACGT
Statistics
Matches: 68, Mismatches: 1, Indels: 9
0.87 0.01 0.12
Matches are distributed among these distances:
39 15 0.22
40 11 0.16
43 1 0.01
44 4 0.06
45 36 0.53
46 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.47
Consensus pattern (43 bp):
TTTCCAAAATCTTCTTTTGGAATTACTTAAAAAAAACTTTTAT
Found at i:24225 original size:30 final size:29
Alignment explanation
Indices: 24162--24235 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 29
24152 GAGGATGTCG
* **
24162 TCGCACAAGACCGGCCATTGCATGGAGGGA
1 TCGCAC-AGACCGGCCATGGCATGGAGCAA
24192 TCGCACATGACCGGCCATGGCATGG-GCCAA
1 TCGCACA-GACCGGCCATGGCATGGAG-CAA
24222 TCGCACGAGACCGG
1 TCGCAC-AGACCGG
24236 GCACAACCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
29 2 0.05
30 35 0.92
31 1 0.03
ACGTcount: A:0.24, C:0.31, G:0.32, T:0.12
Consensus pattern (29 bp):
TCGCACAGACCGGCCATGGCATGGAGCAA
Found at i:28919 original size:2 final size:2
Alignment explanation
Indices: 28912--28939 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28902 TGTACAACTC
28912 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28940 GATAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29861 original size:16 final size:16
Alignment explanation
Indices: 29840--29875 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
29830 TGTTTAGGTG
29840 CATTCTTCCTAAATAA
1 CATTCTTCCTAAATAA
* *
29856 CATTCTTCCTGAATAG
1 CATTCTTCCTAAATAA
29872 CATT
1 CATT
29876 AATACCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.39
Consensus pattern (16 bp):
CATTCTTCCTAAATAA
Found at i:30054 original size:26 final size:26
Alignment explanation
Indices: 30025--30092 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
30015 TACTTAGTTT
* *
30025 ATTAGTTTATGTTTAGTTAGTATCTA
1 ATTAGTTTATGATTAATTAGTATCTA
*
30051 ATTAGTTTATGATTAATTAGTATTTA
1 ATTAGTTTATGATTAATTAGTATCTA
30077 ATTAGTTTATGATTAA
1 ATTAGTTTATGATTAA
30093 AATGAAGGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.53
Consensus pattern (26 bp):
ATTAGTTTATGATTAATTAGTATCTA
Found at i:30067 original size:15 final size:15
Alignment explanation
Indices: 30049--30092 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
30039 AGTTAGTATC
30049 TAATTAGTTTATGAT
1 TAATTAGTTTATGAT
30064 TAATTAG--TAT--T
1 TAATTAGTTTATGAT
30075 TAATTAGTTTATGAT
1 TAATTAGTTTATGAT
30090 TAA
1 TAA
30093 AATGAAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 8 0.32
13 6 0.24
15 11 0.44
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.52
Consensus pattern (15 bp):
TAATTAGTTTATGAT
Found at i:30146 original size:23 final size:23
Alignment explanation
Indices: 30102--30146 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
30092 AAATGAAGGA
**
30102 AAATGAATTTGAAGATTTTTTAG
1 AAATGAATTTGAAGATAATTTAG
30125 AAATGAAGTTTGAAGA-AATTTA
1 AAATGAA-TTTGAAGATAATTTA
30147 AAGAAGTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.18, T:0.38
Consensus pattern (23 bp):
AAATGAATTTGAAGATAATTTAG
Done.