Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018577.1 Corchorus olitorius cultivar O-4 contig18610, 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: 41808
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2576 original size:23 final size:22
Alignment explanation
Indices: 2527--2577 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
2517 CTTTATTCTT
* *
2527 GTTGGGCCTTGATTGTTACTTG
1 GTTGGGCCTTGATTGTGACTTA
*
2549 GTTGGGCCTTGTATTGTGAGTTA
1 GTTGGGCCTTG-ATTGTGACTTA
*
2572 TTTGGG
1 GTTGGG
2578 TAAAGAGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.10, C:0.10, G:0.35, T:0.45
Consensus pattern (22 bp):
GTTGGGCCTTGATTGTGACTTA
Found at i:3263 original size:33 final size:33
Alignment explanation
Indices: 3212--3304 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 33
3202 TTTAAGTTTT
*
3212 TTTTTAATTGGGAAAGTTCCCATCAAGTATTAA
1 TTTTCAATTGGGAAAGTTCCCATCAAGTATTAA
* * * * *
3245 TTTTCAATTGGGATAGTTCTCACCAAGTTTTAG
1 TTTTCAATTGGGAAAGTTCCCATCAAGTATTAA
3278 TTTTCAATTTAGGGAAAGTTCCCATCA
1 TTTTCAA-TT-GGGAAAGTTCCCATCA
3305 TTTTCGGTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 34 0.69
34 2 0.04
35 13 0.27
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (33 bp):
TTTTCAATTGGGAAAGTTCCCATCAAGTATTAA
Found at i:5049 original size:30 final size:30
Alignment explanation
Indices: 5015--5081 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
5005 TGCCCTTAAC
* * *
5015 TGTAAAATACGAATACGTTTTACCCTCATT
1 TGTAAAACACGAAAACGTTTAACCCTCATT
* * *
5045 TGTAATACCCGAAAACGTTTAACCCTTATT
1 TGTAAAACACGAAAACGTTTAACCCTCATT
5075 TGCTAAA
1 TG-TAAA
5082 CCGTTCAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (30 bp):
TGTAAAACACGAAAACGTTTAACCCTCATT
Found at i:6989 original size:16 final size:16
Alignment explanation
Indices: 6968--7005 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
6958 CATTTTCAGC
*
6968 TTCGGGTATTCTCGGG
1 TTCGGGTATTCTCGGA
*
6984 TTCGGGTATTTTCGGA
1 TTCGGGTATTCTCGGA
7000 TTCGGG
1 TTCGGG
7006 AATCTTTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.08, C:0.16, G:0.37, T:0.39
Consensus pattern (16 bp):
TTCGGGTATTCTCGGA
Found at i:9984 original size:21 final size:21
Alignment explanation
Indices: 9950--9990 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9940 CCCACATGGA
* *
9950 TTGCCTGAAGACCCATGTGGT
1 TTGCCTGAACACCCAGGTGGT
*
9971 TTGCCTGATCACCCAGGTGG
1 TTGCCTGAACACCCAGGTGG
9991 GCTGTGTCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (21 bp):
TTGCCTGAACACCCAGGTGGT
Found at i:14320 original size:19 final size:18
Alignment explanation
Indices: 14291--14326 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
14281 TGAAAATAAT
14291 TCTTCAATTGTCTTCAAA
1 TCTTCAATTGTCTTCAAA
14309 TCTTCAAATTGTCTTCAA
1 TCTTC-AATTGTCTTCAA
14327 TAAGTCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (18 bp):
TCTTCAATTGTCTTCAAA
Found at i:20009 original size:15 final size:16
Alignment explanation
Indices: 19989--20022 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
19979 TGAAAGATAG
19989 CAATTAAAC-AGAAAA
1 CAATTAAACTAGAAAA
*
20004 CAATTATACTAGAAAA
1 CAATTAAACTAGAAAA
20020 CAA
1 CAA
20023 AGCAAAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.62, C:0.15, G:0.06, T:0.18
Consensus pattern (16 bp):
CAATTAAACTAGAAAA
Found at i:22215 original size:16 final size:16
Alignment explanation
Indices: 22194--22228 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
22184 AACAGTCATC
22194 AAAAGCATTCAAAGTT
1 AAAAGCATTCAAAGTT
*
22210 AAAAGCATTCAAATTT
1 AAAAGCATTCAAAGTT
22226 AAA
1 AAA
22229 TTCTTGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.54, C:0.11, G:0.09, T:0.26
Consensus pattern (16 bp):
AAAAGCATTCAAAGTT
Found at i:23805 original size:21 final size:20
Alignment explanation
Indices: 23780--23839 Score: 50
Period size: 21 Copynumber: 3.0 Consensus size: 20
23770 GAATTGATTG
23780 AAATTTCGGTTTGGGCCTCA
1 AAATTTCGGTTTGGGCCTCA
**** *
23800 ATAATTGATATTTGGG-CTTA
1 A-AATTTCGGTTTGGGCCTCA
*
23820 AGATTTCGGTTTGGGCCTCA
1 AAATTTCGGTTTGGGCCTCA
23840 TGGGTTGTAC
Statistics
Matches: 27, Mismatches: 11, Indels: 4
0.64 0.26 0.10
Matches are distributed among these distances:
19 9 0.33
20 8 0.30
21 10 0.37
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.38
Consensus pattern (20 bp):
AAATTTCGGTTTGGGCCTCA
Found at i:26207 original size:23 final size:25
Alignment explanation
Indices: 26162--26210 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
26152 CTTTTTGTGT
* *
26162 TTTCCTTTTTCTTTTAGCGTTTTTG
1 TTTCCTTCTTCTTTTAGCATTTTTG
26187 TTTCCTTCTT-TTTT-GCATTTTTG
1 TTTCCTTCTTCTTTTAGCATTTTTG
26210 T
1 T
26211 GGCATTGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.41
24 4 0.18
25 9 0.41
ACGTcount: A:0.04, C:0.16, G:0.10, T:0.69
Consensus pattern (25 bp):
TTTCCTTCTTCTTTTAGCATTTTTG
Found at i:32863 original size:2 final size:2
Alignment explanation
Indices: 32856--32880 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32846 TCTTTCTATG
32856 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 T
32881 CTTGCTATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.