Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013234.1 Corchorus olitorius cultivar O-4 contig13267, 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: 27833
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Found at i:1005 original size:11 final size:11
Alignment explanation
Indices: 989--1030 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
979 TTCGTTTTTC
989 TGTTTTT-TTT
1 TGTTTTTGTTT
999 TGTTTTTGTTT
1 TGTTTTTGTTT
* *
1010 CGTTTTCGTTT
1 TGTTTTTGTTT
1021 TGTTTTTGTT
1 TGTTTTTGTT
1031 ACTGTTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
10 7 0.26
11 20 0.74
ACGTcount: A:0.00, C:0.05, G:0.17, T:0.79
Consensus pattern (11 bp):
TGTTTTTGTTT
Found at i:1036 original size:28 final size:29
Alignment explanation
Indices: 978--1037 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
968 TTGGCATCGT
**
978 TTTCGTTTTTCTGTTTTTTTTTGTTTTTG
1 TTTCGTTTTTCTGTTTTTTTTTGTTACTG
1007 TTTCG-TTTTC-GTTTTGTTTTTGTTACTG
1 TTTCGTTTTTCTGTTTT-TTTTTGTTACTG
1035 TTT
1 TTT
1038 ATACTCAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 5 0.18
28 18 0.64
29 5 0.18
ACGTcount: A:0.02, C:0.08, G:0.15, T:0.75
Consensus pattern (29 bp):
TTTCGTTTTTCTGTTTTTTTTTGTTACTG
Found at i:2697 original size:51 final size:50
Alignment explanation
Indices: 2596--2697 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 50
2586 GTTCATCAAA
* **
2596 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGT
1 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
* *
2646 TTCTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTCTC-CTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGT
2697 T
1 T
2698 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 7 0.16
51 36 0.82
52 1 0.02
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.39
Consensus pattern (50 bp):
TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
Found at i:4021 original size:15 final size:15
Alignment explanation
Indices: 4003--4033 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3993 CAAGGGCTGA
*
4003 AATTAATTAATTATT
1 AATTAAATAATTATT
4018 AATTAAATAATTATT
1 AATTAAATAATTATT
4033 A
1 A
4034 TTTTCTTGAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTAAATAATTATT
Found at i:8230 original size:179 final size:179
Alignment explanation
Indices: 7923--8277 Score: 683
Period size: 179 Copynumber: 2.0 Consensus size: 179
7913 GAAACAACTC
7923 CCAAAAAGGCGAACTTGGCTCCAAGCACCTCCTTGGCAGCCAACCCTCAACATGAAGGTAAGTCT
1 CCAAAAAGGCGAACTTGGCTCCAAGCACCTCCTTGGCAGCCAACCCTCAACATGAAGGTAAGTCT
* *
7988 TATCACCACTCTGCTAAAGTCAAGAAGTTGGTTGATAAAGCTAAATCTAAAACTCTGGGTGTGCA
66 TATCACCACTCTGCTAAAGCCAAGAAGTTGGATGATAAAGCTAAATCTAAAACTCTGGGTGTGCA
8053 TTCAGATCGGCCTTGGAATCCAAACATGGCCGCTGACAGACTTAAAGCA
131 TTCAGATCGGCCTTGGAATCCAAACATGGCCGCTGACAGACTTAAAGCA
*
8102 CCAAAAGGGCGAACTTGGCTCCAAGCACCTCCTTGGCAGCCAACCCTCAACATGAAGGTAAGTCT
1 CCAAAAAGGCGAACTTGGCTCCAAGCACCTCCTTGGCAGCCAACCCTCAACATGAAGGTAAGTCT
8167 TATCACCACTCTGCTAAAGCCAAGAAGTTGGATGATAAAGCTAAATCTAAAACTCTGGGTGTGCA
66 TATCACCACTCTGCTAAAGCCAAGAAGTTGGATGATAAAGCTAAATCTAAAACTCTGGGTGTGCA
8232 TTCAGATCGGCCTTGGAATCCAAACATGGCCGCTGACAGACTTAAA
131 TTCAGATCGGCCTTGGAATCCAAACATGGCCGCTGACAGACTTAAA
8278 TCCTTTCCCA
Statistics
Matches: 173, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
179 173 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (179 bp):
CCAAAAAGGCGAACTTGGCTCCAAGCACCTCCTTGGCAGCCAACCCTCAACATGAAGGTAAGTCT
TATCACCACTCTGCTAAAGCCAAGAAGTTGGATGATAAAGCTAAATCTAAAACTCTGGGTGTGCA
TTCAGATCGGCCTTGGAATCCAAACATGGCCGCTGACAGACTTAAAGCA
Found at i:19323 original size:13 final size:13
Alignment explanation
Indices: 19305--19330 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19295 CTTGGCTTGA
19305 GTGATGATTTTTG
1 GTGATGATTTTTG
19318 GTGATGATTTTTG
1 GTGATGATTTTTG
19331 TTGTTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:21823 original size:1 final size:1
Alignment explanation
Indices: 21817--21841 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
21807 ATGAATTCTG
21817 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
21842 TTATGTACTT
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:25707 original size:22 final size:22
Alignment explanation
Indices: 25675--25777 Score: 86
Period size: 22 Copynumber: 4.7 Consensus size: 22
25665 TGAATATTTT
*
25675 TATGAAATTTTGATAA-CTACCC
1 TATGAAATTTTGATAATC-ACCA
*
25697 TATTAAATTTTGATAATCACCA
1 TATGAAATTTTGATAATCACCA
*
25719 TATGAAATTTTGATAAGT-AAC-
1 TATGAAATTTTGATAA-TCACCA
* * * *
25740 TATAAAATTGTGATAAACTCCA
1 TATGAAATTTTGATAATCACCA
* *
25762 TAAGAAACTTTGATAA
1 TATGAAATTTTGATAA
25778 CCTAACTATG
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
21 15 0.23
22 47 0.73
23 2 0.03
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACCA
Found at i:25763 original size:43 final size:43
Alignment explanation
Indices: 25675--25786 Score: 134
Period size: 43 Copynumber: 2.6 Consensus size: 43
25665 TGAATATTTT
* * * *
25675 TATGAAATTTTGATAACTACCCTATTAAATTTTGATAATCACCA
1 TATGAAATTTTGATAACTA-ACTATAAAATTGTGATAAACACCA
* *
25719 TATGAAATTTTGATAAGTAACTATAAAATTGTGATAAACTCCA
1 TATGAAATTTTGATAACTAACTATAAAATTGTGATAAACACCA
* *
25762 TAAGAAACTTTGATAACCTAACTAT
1 TATGAAATTTTGATAA-CTAACTAT
25787 GAACTTTTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 33 0.57
44 25 0.43
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (43 bp):
TATGAAATTTTGATAACTAACTATAAAATTGTGATAAACACCA
Found at i:25800 original size:44 final size:43
Alignment explanation
Indices: 25678--25802 Score: 106
Period size: 44 Copynumber: 2.9 Consensus size: 43
25668 ATATTTTTAT
* * * * * * * *
25678 GAAATTTTGATAACTACCCTATTAAATTTTGATAATCACCATAT
1 GAAACTTTGATAACTA-ACTATAAAATTGTAATAAACTCCATAA
* * *
25722 GAAATTTTGATAAGTAACTATAAAATTGTGATAAACTCCATAA
1 GAAACTTTGATAACTAACTATAAAATTGTAATAAACTCCATAA
* * *
25765 GAAACTTTGATAACCTAACTATGAACTTTTAATAAACT
1 GAAACTTTGATAA-CTAACTATAAAATTGTAATAAACT
25803 TTCCTAAGAA
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
43 33 0.49
44 34 0.51
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (43 bp):
GAAACTTTGATAACTAACTATAAAATTGTAATAAACTCCATAA
Found at i:27074 original size:14 final size:15
Alignment explanation
Indices: 27055--27088 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
27045 AATTTTCAAT
27055 CAACACAAATTAAA-
1 CAACACAAATTAAAG
*
27069 CAACACAGATTAAAG
1 CAACACAAATTAAAG
27084 CAACA
1 CAACA
27089 ATTTTCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.59, C:0.24, G:0.06, T:0.12
Consensus pattern (15 bp):
CAACACAAATTAAAG
Found at i:27183 original size:2 final size:2
Alignment explanation
Indices: 27176--27204 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27166 CAAAAGATTC
27176 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27205 ACATATCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.