Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005884.1 Corchorus capsularis cultivar CVL-1 contig05902, 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: 8532
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:2505 original size:16 final size:16
Alignment explanation
Indices: 2444--2505 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
2434 GTCTGTTTGA
*
2444 TAGGGAGGAAA-GAAT
1 TAGGAAGGAAAGGAAT
*
2459 TAGGAAGGAAAGGAAA
1 TAGGAAGGAAAGGAAT
* *
2475 TAGCAAAGAAAGGAAT
1 TAGGAAGGAAAGGAAT
*
2491 TAGGAAGGAAGGGAA
1 TAGGAAGGAAAGGAA
2506 AGGAAGTCAC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
15 10 0.26
16 28 0.74
ACGTcount: A:0.52, C:0.02, G:0.37, T:0.10
Consensus pattern (16 bp):
TAGGAAGGAAAGGAAT
Found at i:2953 original size:27 final size:24
Alignment explanation
Indices: 2933--3024 Score: 89
Period size: 22 Copynumber: 3.7 Consensus size: 24
2923 CCCATTTCAC
2933 ACAAAAAAAAATAGCAGCCCATTT
1 ACAAAAAAAAATAGCAGCCCATTT
* *
2957 -C-AAAAAAAGTAGCAGGCCATTT
1 ACAAAAAAAAATAGCAGCCCATTT
*
2979 GAAAAAAAAAATAGTAGCAGCCCATTT
1 -ACAAAAAAAA-A-TAGCAGCCCATTT
*
3006 AACCAAAAAAAAGTAGCAG
1 -A-CAAAAAAAAATAGCAG
3025 TACAAGTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
22 19 0.35
23 1 0.02
25 7 0.13
26 6 0.11
27 13 0.24
28 8 0.15
ACGTcount: A:0.53, C:0.17, G:0.14, T:0.15
Consensus pattern (24 bp):
ACAAAAAAAAATAGCAGCCCATTT
Found at i:2987 original size:26 final size:26
Alignment explanation
Indices: 2923--3024 Score: 108
Period size: 27 Copynumber: 4.0 Consensus size: 26
2913 ACACTAGAAA
2923 CCCATTTCACACAAAAAAAAA-TAGCAG
1 CCCATTT-A-ACAAAAAAAAAGTAGCAG
2950 CCCATTT--C--AAAAAAAGTAGCAG
1 CCCATTTAACAAAAAAAAAGTAGCAG
*
2972 GCCATTTGAA-AAAAAAAATAGTAGCAG
1 CCCATTT-AACAAAAAAAA-AGTAGCAG
*
2999 CCCATTTAACCAAAAAAAAGTAGCAG
1 CCCATTTAACAAAAAAAAAGTAGCAG
3025 TACAAGTTTT
Statistics
Matches: 64, Mismatches: 3, Indels: 17
0.76 0.04 0.20
Matches are distributed among these distances:
21 7 0.11
22 12 0.19
23 1 0.02
26 16 0.25
27 28 0.44
ACGTcount: A:0.50, C:0.21, G:0.13, T:0.17
Consensus pattern (26 bp):
CCCATTTAACAAAAAAAAAGTAGCAG
Found at i:3319 original size:15 final size:15
Alignment explanation
Indices: 3274--3324 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
3264 AAAGAACTAT
3274 TTTCCTTCCCATTTC
1 TTTCCTTCCCATTTC
* *
3289 TTTCC-CCCCGTCTTC
1 TTTCCTTCCCAT-TTC
3304 TTTCCTTCCCATTTC
1 TTTCCTTCCCATTTC
3319 TTTCCT
1 TTTCCT
3325 ACCAAACACA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 4 0.13
15 22 0.73
16 4 0.13
ACGTcount: A:0.04, C:0.43, G:0.02, T:0.51
Consensus pattern (15 bp):
TTTCCTTCCCATTTC
Found at i:5193 original size:25 final size:25
Alignment explanation
Indices: 5159--5210 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
5149 TTGCATTAAA
5159 GGTGCTTATGGACCAGACCGAGTTT
1 GGTGCTTATGGACCAGACCGAGTTT
*
5184 GGTGCTTATGGACCGGACCGAGTTT
1 GGTGCTTATGGACCAGACCGAGTTT
5209 GG
1 GG
5211 ACGATTTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.17, C:0.19, G:0.37, T:0.27
Consensus pattern (25 bp):
GGTGCTTATGGACCAGACCGAGTTT
Found at i:5491 original size:6 final size:6
Alignment explanation
Indices: 5480--5517 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
5470 GGGAAATTAA
5480 AACTAC AACTAC AACTACC AGACT-C AACTAC AACTAC A
1 AACTAC AACTAC AACTA-C A-ACTAC AACTAC AACTAC A
5518 TAAACAAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 3 0.10
6 21 0.72
7 2 0.07
8 3 0.10
ACGTcount: A:0.47, C:0.34, G:0.03, T:0.16
Consensus pattern (6 bp):
AACTAC
Found at i:8215 original size:193 final size:193
Alignment explanation
Indices: 7879--8530 Score: 783
Period size: 192 Copynumber: 3.3 Consensus size: 193
7869 AATCACTTTA
* * *
7879 TATAATCTTTCTTATAGGATTATTATACAATACACTTTTCAGTGTAAATTTTACACTCC-TAAGC
1 TATAATTTTTCTTATAGGATTATTATACAATACAC-TGTCAGTGTAAATTTTAGACTCCATAAGC
*
7943 GGGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATTAATACATATTT
65 GGGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATTAATACATATTC
* * * *
8008 CTTAAGGGACACATGTCAACCTTTAAACCCTACACATGCAATCTGCTAAATTCGACT-TGTATAG
130 CCTAAGGGACACATGTCAACC-TTAAACCCCACACATGCAATCTGCTAAAATCCACTGTGTATAG
* * * * *
8072 TATAATTTTTCTTATAAGATTATTATGCAATCCACTGTCAGTATAAATTTTGGACTCCATAAGCG
1 TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTAGACTCCATAAGCG
* * * *
8137 GGTTAAGAAGTTGACATATACCCCA-TTCATAATTAACTCAATATTTAATATTAATACATATTCC
66 GGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATTAATACATATTCC
* * *
8201 CTAAGGGGACACATGTCAACCTTAAACCCCACACGTGCATTTTGCTAAAATCCACTAACGGTGTA
131 CTAA-GGGACACATGTCAACCTTAAACCCCACACATGCAATCTGCTAAAATCCACT----GTGTA
8266 TTA-
191 -TAG
* * * * * *
8269 TATAATTTTT-TTATATGATTATTATACAACACGCTGTTAGTGTAAATTTTAAACTCTATAAGCG
1 TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTAGACTCCATAAGCG
* * **
8333 GGTTAAGAAGTTGACACATACCTCATTTCATCATCAATTAAATAGATAATATTAATACATATTCC
66 GGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATTAATACATATTCC
** ** * *
8398 CTAAAGAAACACATGTCAACCCTTAAACCCGGCACATGCAGTCTGCTAAACTCCACTTACGGTGT
131 CT-AAGGGACACATGTCAA-CCTTAAACCCCACACATGCAATCTGCTAAAATCCAC-T---GTGT
8463 ATAG
190 ATAG
* * *
8467 TATAAATTTTTCTTATAGGATTATTATACAATAAACTTTCAGTGTAAATTTTGGACTCCATAAG
1 TAT-AATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTAGACTCCATAAG
8531 AG
Statistics
Matches: 389, Mismatches: 55, Indels: 23
0.83 0.12 0.05
Matches are distributed among these distances:
192 86 0.22
193 77 0.20
196 67 0.17
197 63 0.16
198 45 0.12
199 8 0.02
200 43 0.11
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (193 bp):
TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTAGACTCCATAAGCG
GGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATTAATACATATTCC
CTAAGGGACACATGTCAACCTTAAACCCCACACATGCAATCTGCTAAAATCCACTGTGTATAG
Done.