Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012683.1 Corchorus olitorius cultivar O-4 contig12716, 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: 49401
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:347 original size:17 final size:17
Alignment explanation
Indices: 327--361 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
317 GGTAGTTTAA
*
327 AAAAAAAATTAGTTTTC
1 AAAAAAAAGTAGTTTTC
*
344 AAAAAGAAGTAGTTTTC
1 AAAAAAAAGTAGTTTTC
361 A
1 A
362 TGCAAGAGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.31
Consensus pattern (17 bp):
AAAAAAAAGTAGTTTTC
Found at i:2205 original size:11 final size:11
Alignment explanation
Indices: 2165--2198 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
2155 AGGAGTAGGG
2165 TCCTTCCTAGC
1 TCCTTCCTAGC
2176 TCCTTCCTAGC
1 TCCTTCCTAGC
2187 TCCTTCCTAGC
1 TCCTTCCTAGC
2198 T
1 T
2199 TTTTCCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.09, C:0.44, G:0.09, T:0.38
Consensus pattern (11 bp):
TCCTTCCTAGC
Found at i:3679 original size:15 final size:15
Alignment explanation
Indices: 3659--3687 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3649 TTGTTTTCTA
3659 GTTTAATTGCTTTCC
1 GTTTAATTGCTTTCC
3674 GTTTAATTGCTTTC
1 GTTTAATTGCTTTC
3688 TGTCAATCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (15 bp):
GTTTAATTGCTTTCC
Found at i:8955 original size:15 final size:15
Alignment explanation
Indices: 8932--8961 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8922 TACGGTTGAA
*
8932 ATATTGTGTATCGTG
1 ATATCGTGTATCGTG
8947 ATATCGTGTATCGTG
1 ATATCGTGTATCGTG
8962 GCAGCCTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (15 bp):
ATATCGTGTATCGTG
Found at i:11813 original size:15 final size:15
Alignment explanation
Indices: 11793--11823 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11783 CTACTCCTAC
*
11793 ATCCTTGGTAGCTCT
1 ATCCTTGGCAGCTCT
11808 ATCCTTGGCAGCTCT
1 ATCCTTGGCAGCTCT
11823 A
1 A
11824 GTACTTAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.29, G:0.19, T:0.35
Consensus pattern (15 bp):
ATCCTTGGCAGCTCT
Found at i:13371 original size:40 final size:40
Alignment explanation
Indices: 13327--13407 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
13317 TAAATTTCAT
13327 CGCAAAAGCCAAGCCAACCTGAAAAGTTAATCTTTAGGTG
1 CGCAAAAGCCAAGCCAACCTGAAAAGTTAATCTTTAGGTG
*
13367 CGCAAAAGCCAAGCCAACCTGAAAAGTTAATTTTTAGGTG
1 CGCAAAAGCCAAGCCAACCTGAAAAGTTAATCTTTAGGTG
13407 C
1 C
13408 TTTTGCGTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (40 bp):
CGCAAAAGCCAAGCCAACCTGAAAAGTTAATCTTTAGGTG
Found at i:13576 original size:13 final size:13
Alignment explanation
Indices: 13560--13584 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13550 TCTACCCCAA
13560 TTTTCAAAAACAC
1 TTTTCAAAAACAC
13573 TTTTCAAAAACA
1 TTTTCAAAAACA
13585 ATTCTTCCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (13 bp):
TTTTCAAAAACAC
Found at i:15205 original size:11 final size:11
Alignment explanation
Indices: 15181--15215 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
15171 TTGACAGTGC
15181 AACAAAAACAA
1 AACAAAAACAA
* *
15192 AACGAAAACGA
1 AACAAAAACAA
15203 AACAAAAACAA
1 AACAAAAACAA
15214 AA
1 AA
15216 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:15463 original size:4 final size:4
Alignment explanation
Indices: 15451--15482 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
15441 ATCCAAAAAA
15451 AAAT AAAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAA
15483 CCACCTGTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:16840 original size:11 final size:11
Alignment explanation
Indices: 16824--16849 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16814 GAGTTTAGTA
16824 TAATTTGACTT
1 TAATTTGACTT
16835 TAATTTGACTT
1 TAATTTGACTT
16846 TAAT
1 TAAT
16850 GACAACAAAC
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:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (11 bp):
TAATTTGACTT
Found at i:19224 original size:2 final size:2
Alignment explanation
Indices: 19217--19255 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
19207 AGTGGCTGCT
19217 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
19256 TTTTCTTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:21019 original size:1 final size:1
Alignment explanation
Indices: 21013--21037 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
21003 TACTTATTTC
21013 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
21038 GAAAGAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29610 original size:21 final size:22
Alignment explanation
Indices: 29584--29637 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
29574 CATATGGAGT
* *
29584 TTATCACAATTTTATA-GGTAA
1 TTATCAAAATTTAATAGGGTAA
29605 TTATCAAAATTTAATAGGGTAA
1 TTATCAAAATTTAATAGGGTAA
29627 -TATCAAAATTT
1 TTATCAAAATTT
29638 CATAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTTAATAGGGTAA
Found at i:29750 original size:2 final size:2
Alignment explanation
Indices: 29741--29792 Score: 61
Period size: 2 Copynumber: 26.0 Consensus size: 2
29731 TTTTGATGGG
* *
29741 TA TA -A TA TA TA TA TA TA TA TA CTA AA TA TA TA TA TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
*
29783 TA TA TT TA TA
1 TA TA TA TA TA
29793 AATCAATATT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31467 original size:80 final size:80
Alignment explanation
Indices: 31308--31463 Score: 251
Period size: 80 Copynumber: 2.0 Consensus size: 80
31298 AAAGTGGTTT
31308 CGGATCTTAGACGACTTTTGAAGATAAGTCGGCTGGAAAACCTATTTTAGGAAGAGAAATAAAAA
1 CGGATCTTAGACGACTTTTGAAGATAAGTCGGCTGGAAAACCTATTTTAGGAAGAGAAATAAAAA
31373 CGAGGGGGAGTTGCA
66 CGAGGGGGAGTTGCA
** * * * *
31388 CGGATCTTAGACGACTTTTGAAGATGGGTTGGCTGGAAAACCTATTTTGGGAAGGGAAATGAAAA
1 CGGATCTTAGACGACTTTTGAAGATAAGTCGGCTGGAAAACCTATTTTAGGAAGAGAAATAAAAA
31453 CGA-GGGGAGTT
66 CGAGGGGGAGTT
31464 TGCATAACGA
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
79 8 0.11
80 62 0.89
ACGTcount: A:0.33, C:0.12, G:0.31, T:0.24
Consensus pattern (80 bp):
CGGATCTTAGACGACTTTTGAAGATAAGTCGGCTGGAAAACCTATTTTAGGAAGAGAAATAAAAA
CGAGGGGGAGTTGCA
Found at i:39894 original size:24 final size:24
Alignment explanation
Indices: 39867--39916 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
39857 CAATCACATT
*
39867 TGGAAATCTATTATTCATCAATCA
1 TGGAAATCTATTATCCATCAATCA
*
39891 TGGAGATCTATTATCCATCAATCA
1 TGGAAATCTATTATCCATCAATCA
39915 TG
1 TG
39917 AATATAAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (24 bp):
TGGAAATCTATTATCCATCAATCA
Found at i:39940 original size:2 final size:2
Alignment explanation
Indices: 39933--39973 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
39923 AGACATTCTT
39933 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
39974 CCAAAAGGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42309 original size:53 final size:52
Alignment explanation
Indices: 42251--42391 Score: 140
Period size: 53 Copynumber: 2.7 Consensus size: 52
42241 AAAGCAATCC
* * * *
42251 ATAAAAAGATTTCATAAAAGCATTTAAGGTCACATGTAAAA-TCCCAACAGAAA
1 ATAAAAAG-TTCCATAACAGCATTTAAGGTCACATATAAAACT-CCAACACAAA
* * * * * *
42304 ATAAAAAGGTTCCACAACAGTATTTAAGGCCAAATATAATACTCTAACACAAA
1 ATAAAAA-GTTCCATAACAGCATTTAAGGTCACATATAAAACTCCAACACAAA
* *
42357 ATAAAAAGTTCCATAGCAGCATTGAAGGTCACATA
1 ATAAAAAGTTCCATAACAGCATTTAAGGTCACATA
42392 AAACAGGCCA
Statistics
Matches: 70, Mismatches: 16, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
52 22 0.31
53 46 0.66
54 2 0.03
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (52 bp):
ATAAAAAGTTCCATAACAGCATTTAAGGTCACATATAAAACTCCAACACAAA
Found at i:42604 original size:17 final size:17
Alignment explanation
Indices: 42582--42616 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
42572 CAAATATTGC
*
42582 TGATAAAATAGCTGCAA
1 TGATAAAATAGCTCCAA
42599 TGATAAAATAGCTCCAA
1 TGATAAAATAGCTCCAA
42616 T
1 T
42617 AATTGTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (17 bp):
TGATAAAATAGCTCCAA
Found at i:48496 original size:80 final size:80
Alignment explanation
Indices: 48337--48492 Score: 251
Period size: 80 Copynumber: 2.0 Consensus size: 80
48327 AAAGTGGTTT
48337 CGGATCTTAGACGACTTTTGAAGATAAGTCGGCTGGAAAACCTATTTTAGGAAGAGAAATAAAAA
1 CGGATCTTAGACGACTTTTGAAGATAAGTCGGCTGGAAAACCTATTTTAGGAAGAGAAATAAAAA
48402 CGAGGGGGAGTTGCA
66 CGAGGGGGAGTTGCA
** * * * *
48417 CGGATCTTAGACGACTTTTGAAGATGGGTTGGCTGGAAAACCTATTTTGGGAAGGGAAATGAAAA
1 CGGATCTTAGACGACTTTTGAAGATAAGTCGGCTGGAAAACCTATTTTAGGAAGAGAAATAAAAA
48482 CGA-GGGGAGTT
66 CGAGGGGGAGTT
48493 TGCATAACGA
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
79 8 0.11
80 62 0.89
ACGTcount: A:0.33, C:0.12, G:0.31, T:0.24
Consensus pattern (80 bp):
CGGATCTTAGACGACTTTTGAAGATAAGTCGGCTGGAAAACCTATTTTAGGAAGAGAAATAAAAA
CGAGGGGGAGTTGCA
Done.