Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016860.1 Corchorus olitorius cultivar O-4 contig16893, 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: 35295
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Found at i:6229 original size:27 final size:28
Alignment explanation
Indices: 6198--6263 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
6188 TCTTTCGACT
* *
6198 TTGCATTTGGGGCA-TTTTGGTTTGTGA
1 TTGCATTTGGGGCATTTTTAGTTTGGGA
*
6225 TTGCATTT-GGACATTTTTAGTTTGGGA
1 TTGCATTTGGGGCATTTTTAGTTTGGGA
6252 TTGCATTTGGGG
1 TTGCATTTGGGG
6264 ACACATTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 4 0.12
27 27 0.82
28 2 0.06
ACGTcount: A:0.14, C:0.08, G:0.32, T:0.47
Consensus pattern (28 bp):
TTGCATTTGGGGCATTTTTAGTTTGGGA
Found at i:8041 original size:15 final size:16
Alignment explanation
Indices: 8021--8060 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
8011 AGAGGTTGAA
8021 AGAAAACAATTAAAC-
1 AGAAAACAATTAAACT
*
8036 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
8052 AGAAAACAA
1 AGAAAACAA
8061 AGCAAAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:11386 original size:21 final size:21
Alignment explanation
Indices: 11343--11397 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
11333 GGCTTGGAAT
* **
11343 GGTGATGGCACGGGCATGGCC
1 GGTGGTGGCACGGGCATAACC
*
11364 GGTGGTGGCACGGGCTTAACC
1 GGTGGTGGCACGGGCATAACC
*
11385 GGTGGTGTCACGG
1 GGTGGTGGCACGG
11398 TGAATGTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.13, C:0.22, G:0.47, T:0.18
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATAACC
Found at i:14554 original size:24 final size:24
Alignment explanation
Indices: 14527--14586 Score: 59
Period size: 27 Copynumber: 2.4 Consensus size: 24
14517 TTTTAGAACA
**
14527 ACGCAAAAACCTTTTTTTTTAAT-G
1 ACGCAAAAAAATTTTTTTTT-ATCG
14551 ACGCAGAAACAAAATTTTTTTTTATCG
1 ACGC--AAA-AAAATTTTTTTTTATCG
14578 ACGCAAAAA
1 ACGCAAAAA
14587 TCAAAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
24 6 0.20
25 3 0.10
26 5 0.17
27 16 0.53
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (24 bp):
ACGCAAAAAAATTTTTTTTTATCG
Found at i:14568 original size:27 final size:28
Alignment explanation
Indices: 14538--14592 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
14528 CGCAAAAACC
*
14538 TTTTTTTTTAAT-GACGCAGAAA-CAAAA
1 TTTTTTTTT-ATCGACGCAAAAATCAAAA
14565 TTTTTTTTTATCGACGCAAAAATCAAAA
1 TTTTTTTTTATCGACGCAAAAATCAAAA
14593 AATTAAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 2 0.08
27 18 0.72
28 5 0.20
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (28 bp):
TTTTTTTTTATCGACGCAAAAATCAAAA
Found at i:15006 original size:15 final size:16
Alignment explanation
Indices: 14986--15025 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
14976 AGAGGTTGAA
14986 AGAAAACAATTAAAC-
1 AGAAAACAATTAAACT
*
15001 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
15017 AGAAAACAA
1 AGAAAACAA
15026 AGCAAAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:17597 original size:167 final size:166
Alignment explanation
Indices: 17314--17643 Score: 572
Period size: 167 Copynumber: 2.0 Consensus size: 166
17304 TCAACTGAGA
*
17314 ATTGTATGAGGTTGAAGCGAGAGGTGCAAGCTCTGGTGAAGGGTGGGAAACTCAGTTTTCCAAAA
1 ATTGTATGAGGTTGAAGCGAGAGATGCAAGCTCTGGTGAAGGGTGGGAAACTCAGTTTTCCAAAA
* * *
17379 ACGGCACAACCGAATACAGCTGGAAATGCGCTATCTAATCATAACGGGGGCAAGTTGGGGCTGTA
66 ACGGCAAAACCGAATACAGCTGGAAATCCGCTACCTAATCATAACGGGGGCAAGTTGGGGCTGTA
17444 TACGGTGGAGAATTTGTGGTAAGAGATGTCAGTAAG
131 TACGGTGGAGAATTTGTGGTAAGAGATGTCAGTAAG
*
17480 ATTGTTATGAGGTTGAAGCGAGAGATGCAAGCTCTGGTGAAGGGTGGGAAACTTAG-TTTCCAAA
1 ATTG-TATGAGGTTGAAGCGAGAGATGCAAGCTCTGGTGAAGGGTGGGAAACTCAGTTTTCCAAA
*
17544 AGCGGCAAAACCGAATACAGCTGGAAATCCGCTACCTAATCATAACGGGGGGCAAGTTGGGGCTG
65 AACGGCAAAACCGAATACAGCTGGAAATCCGCTACCTAATCATAAC-GGGGGCAAGTTGGGGCTG
*
17609 TATACGGTGGATAATTTGTGGTAAGAGATGTCAGT
129 TATACGGTGGAGAATTTGTGGTAAGAGATGTCAGT
17644 GAGGTTTTTA
Statistics
Matches: 155, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
166 54 0.35
167 101 0.65
ACGTcount: A:0.30, C:0.15, G:0.32, T:0.23
Consensus pattern (166 bp):
ATTGTATGAGGTTGAAGCGAGAGATGCAAGCTCTGGTGAAGGGTGGGAAACTCAGTTTTCCAAAA
ACGGCAAAACCGAATACAGCTGGAAATCCGCTACCTAATCATAACGGGGGCAAGTTGGGGCTGTA
TACGGTGGAGAATTTGTGGTAAGAGATGTCAGTAAG
Found at i:19595 original size:32 final size:32
Alignment explanation
Indices: 19554--19619 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
19544 TATTCAAATA
19554 CTTAATATCCTAAAACA-AAACACACCAATTTC
1 CTTAATATCCTAAAACATAAA-ACACCAATTTC
*
19586 CTTAATATCCTAAAACATGAAACACCAATTTC
1 CTTAATATCCTAAAACATAAAACACCAATTTC
19618 CT
1 CT
19620 AAAATGTTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 30 0.94
33 2 0.06
ACGTcount: A:0.44, C:0.27, G:0.02, T:0.27
Consensus pattern (32 bp):
CTTAATATCCTAAAACATAAAACACCAATTTC
Found at i:21690 original size:24 final size:24
Alignment explanation
Indices: 21654--21728 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
21644 GTTGCACTTC
*
21654 TTCTCCAATAGCCCTTGGCGCTTG
1 TTCTCCAACAGCCCTTGGCGCTTG
21678 TTCTCCAACAGCCCTTGGCGCTTG
1 TTCTCCAACAGCCCTTGGCGCTTG
* **
21702 TTCTCTAACAGCCCTTGGTACTTG
1 TTCTCCAACAGCCCTTGGCGCTTG
21726 TTC
1 TTC
21729 ATTTGCAGCC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.13, C:0.33, G:0.19, T:0.35
Consensus pattern (24 bp):
TTCTCCAACAGCCCTTGGCGCTTG
Found at i:22347 original size:2 final size:2
Alignment explanation
Indices: 22340--22381 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
22330 GGAAAGAGAA
22340 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
22382 GCAACAAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23419 original size:63 final size:63
Alignment explanation
Indices: 23341--23466 Score: 225
Period size: 63 Copynumber: 2.0 Consensus size: 63
23331 CAAGACCCAT
23341 GATTTCTATTGAACAATAATTGGAGAAGATTTGATGTAAGAACGTGTGAATAAAAATGGGAAA
1 GATTTCTATTGAACAATAATTGGAGAAGATTTGATGTAAGAACGTGTGAATAAAAATGGGAAA
* * *
23404 GATTTCTATTGAACAATAATTGGAGAAGATTTGATGTAAGAATGTGTGAATTAACATGGGAAA
1 GATTTCTATTGAACAATAATTGGAGAAGATTTGATGTAAGAACGTGTGAATAAAAATGGGAAA
23467 TATGGGTAGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.41, C:0.05, G:0.24, T:0.30
Consensus pattern (63 bp):
GATTTCTATTGAACAATAATTGGAGAAGATTTGATGTAAGAACGTGTGAATAAAAATGGGAAA
Found at i:29225 original size:16 final size:18
Alignment explanation
Indices: 29191--29225 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29181 CTCCTCTTGC
29191 ATGAAAACACTTCTTTTT
1 ATGAAAACACTTCTTTTT
29209 ATGAAAACA-TT-TTTTT
1 ATGAAAACACTTCTTTTT
29225 A
1 A
29226 ACTACCCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 2 0.12
18 9 0.53
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (18 bp):
ATGAAAACACTTCTTTTT
Found at i:32161 original size:21 final size:22
Alignment explanation
Indices: 32089--32167 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
32079 GAAAACTCTT
32089 TTTTTTTTTTCAAAAACGCAAAAACA
1 TTTTTTTTTTCAAAAACGC---AA-A
* **
32115 ATTTTTTTTTCCGAAACGCAAA
1 TTTTTTTTTTCAAAAACGCAAA
*
32137 TTTTTTTTTTCAAAAACG-AAT
1 TTTTTTTTTTCAAAAACGCAAA
32158 TTTTTTTTTT
1 TTTTTTTTTT
32168 AGGAAAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
21 12 0.26
22 16 0.35
23 2 0.04
26 16 0.35
ACGTcount: A:0.32, C:0.13, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTTTTTTTTCAAAAACGCAAA
Found at i:35207 original size:29 final size:28
Alignment explanation
Indices: 35163--35218 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
35153 TTCTTCAAAC
*
35163 TTTCTAATTTCAAGAACACTCAAGAACA
1 TTTCTAATTTCAAGAACACTAAAGAACA
*
35191 TTTCTAATCTTCAAGAACGCTAAAGAAC
1 TTTCTAAT-TTCAAGAACACTAAAGAAC
35219 GTGGAATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (28 bp):
TTTCTAATTTCAAGAACACTAAAGAACA
Done.