Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004937.1 Corchorus capsularis cultivar CVL-1 contig04955, 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: 19261
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Found at i:787 original size:318 final size:319
Alignment explanation
Indices: 80--1583 Score: 1573
Period size: 323 Copynumber: 4.7 Consensus size: 319
70 TTTGGCCAGA
* * * *
80 TGGCGCAAAGACTCCTTGAAATATCTATATTTATCAAAGCAAATCTCAACCATATTGGATATAAG
1 TGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAATCAAATCTCAGCCATATTGGATATAAG
* * *
145 GATTTGTTTTTGCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTGATTCAGAAAAAAATG
66 GATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTAATTAGAAATTAATTCA-AAAAAAATG
* * * * ** *
210 GAAAAATGATATTAGAAGCATG-AAAAGCCATCAATCTCCTTGGCGTTGAATTATATATTGTTTC
130 GAAAAACGATATTAGAAGCGTGAAAAACCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTC
* * *
274 TAAGTGTTGTGGCAAAAAATTGAGAAAAAAACTTTTCCGATCAGTTTTTAGCCGAAATC----AC
195 TGAGTATTGTGGCAAAAAATTGAGAAAAAAACTTTT-CGGTCAGTTTTTAGCCGAAATCGTGTAC
* * * *
335 TAACCATCATGTTTTTTTTTTTTGCTAAAAACGCATTCTTGAGCCCCGGGTCAATTTCGCATGAT
259 TAACCATCATG------ATTTTTGCTAAAAACGC-TTCTGGAGCCCCGGCTCAATTTTGCATGAT
*
400 TTG
317 TTT
* * * *
403 TGGCGCAAAGATTCCTTGAAA-ATTCTATATTCATCGAAACAAATCTCAGCAATAATGGATATAA
1 TGGCGCAAAGACTCCTTGAAATA-TCTATATTCATCGAATCAAATCTCAGCCATATTGGATATAA
* *
467 GGATTTTTTTTTTCGAGCATCTTAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAAAA
65 GGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTAATTAGAAATTAATTC--AAAAAAAA
*
532 TGGAAAAACGATATTAGAAGCGTGAAAAACCCGTCAATCTTTTTGTCGTTGAATTATATATTTTT
128 TGGAAAAACGATATTAGAAGCGTGAAAAACCCGTCAATCTTTTTGGCGTTGAATTATATATTTTT
* * * *
597 TCTGTGTATTGTGGCAAAAAATTTAG-AAAAAACTTTTCGTGTCAGTTTTTAACCGAAATCGTAT
193 TCTGAGTATTGTGGCAAAAAATTGAGAAAAAAACTTTTCG-GTCAGTTTTTAGCCGAAATCGTGT
* * * *
661 ACTAACCATCATGATGTTTGGT-TAAA-G-TTCTGGAGCCCCGGCTCATTTTTGCATGATTTT
257 ACTAACCATCATGATTTTTGCTAAAAACGCTTCTGGAGCCCCGGCTCAATTTTGCATGATTTT
* * * *
721 TGGCGCAAAAACTCATTGAAATATCTATATTCATCGAATCAAATGAT-AGCCATAATGGATATAA
1 TGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAATCAAAT-CTCAGCCATATTGGATATAA
* * ** * * *
785 GGATTTGTTTTTACAAGTATCTGCATTTTGTTTCGTTTTAATTAGAATTTAATTCAAAAAAAATG
65 GGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAAATG
* * *
850 GAAAAACAATATTAGAAGTGTGAAAAACCCGTCAATCTTTTTGTCGTTGAATTATATATTTTTTC
130 GAAAAACGATATTAGAAGCGTGAAAAACCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTC
* * **
915 TGAGTATTGTGGCAAAAAAATTGAGAAAAAAACTTTTCGGGTTAGTTTTTAGTCGAAATTATGTA
195 TGAGTATTGTGGC-AAAAAATTGAGAAAAAAACTTTTC-GGTCAGTTTTTAGCCGAAATCGTGTA
* * * * * *
980 CTAACCATCACGGTTTTTGGCTAAAAATG-TGTTTCGGAGTCCCGACTCAATTTTGCATGATTTT
258 CTAACCATCATGATTTTT-GCTAAAAACGCT-TCT-GGAGCCCCGGCTCAATTTTGCATGATTTT
* * * * * *
1044 TGGTGCAAAGACTTCTTGAAATATCTTTATTCATCGAACCGAATGTCAGCC-TCATTGGATATAA
1 TGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAATCAAATCTCAGCCAT-ATTGGATATAA
* *
1108 GAATTTGTTTTTACGAGCATC-TATATCTTGTTTCGATTTAATTAGAAATTAATTCGGGAAAAAA
65 GGATTTGTTTTTACGAGCATCTTA-ATCTTGTTTCGATTTAATTAGAAATTAATTC--AAAAAAA
* * * * *
1172 ATGAAAAAACGATATTAGAAGCGTGAAAAGCCCGTTAATCTTTTTGGCGTTCAATTATATAATTT
127 ATGGAAAAACGATATTAGAAGCGTGAAAAACCCGTCAATCTTTTTGGCGTTGAATTATATATTTT
* *
1237 TTCTGAGTATTGTGGCAAAAAATTGAG--AAAAAC-TTTCAGGTTAGTTTTTACCCGAAATCGTG
192 TTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAACTTTTC-GGTCAGTTTTTAGCCGAAATCGTG
* * * * **
1299 TAATAACCATCA-CAGTTTTTGACTAAAAAAGCCTTCCAGGA-CCACC--CTTCTGTTTTGCATG
256 TACTAACCATCATGA-TTTTTG-CTAAAAACG-CTT-CTGGAGCC-CCGGC-TCAATTTTGCAT-
*
1360 GTTTTT
314 GATTTT
* ** * * * * * *
1366 TTGCGCTGAGACTCCTTGAAATATCTTTATT-AGTCTAATCAAATTTTAGCCACATTGGATTTAA
1 TGGCGCAAAGACTCCTTGAAATATCTATATTCA-TCGAATCAAATCTCAGCCATATTGGATATAA
** * *
1430 GGATTTGTTTTTACTTGCATCATAATCTTGTTTCGATTTAAATAGAAATTAATT-AAAAAAAATA
65 GGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAAAT-
* * * *
1494 CGAAAAACGATATTAAAAGCGTGAAAAGA-CCTTCAATCTTTTT-GCATTGAATTATATATATTT
129 GGAAAAACGATATTAGAAGCGTGAAAA-ACCCGTCAATCTTTTTGGCGTTGAATTATATAT-TTT
* * * * *
1557 TTATGAGTGTTTTTGCCAAAAATTGAG
192 TTCTGAGTATTGTGGCAAAAAATTGAG
1584 GAAACTCCGA
Statistics
Matches: 1003, Mismatches: 140, Indels: 79
0.82 0.11 0.06
Matches are distributed among these distances:
316 85 0.08
317 10 0.01
318 174 0.17
319 26 0.03
320 67 0.07
321 65 0.06
322 124 0.12
323 234 0.23
324 69 0.07
325 136 0.14
328 13 0.01
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (319 bp):
TGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAATCAAATCTCAGCCATATTGGATATAAG
GATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAAATGG
AAAAACGATATTAGAAGCGTGAAAAACCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCT
GAGTATTGTGGCAAAAAATTGAGAAAAAAACTTTTCGGTCAGTTTTTAGCCGAAATCGTGTACTA
ACCATCATGATTTTTGCTAAAAACGCTTCTGGAGCCCCGGCTCAATTTTGCATGATTTT
Found at i:2372 original size:32 final size:32
Alignment explanation
Indices: 2336--2400 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
2326 TAATTGTAGT
2336 CAGAAAGACTTAGTTTTTGGTTCATTTTCTAC
1 CAGAAAGACTTAGTTTTTGGTTCATTTTCTAC
2368 CAGAAAGACTTAGTTTTTGGTTCATTTTCTAC
1 CAGAAAGACTTAGTTTTTGGTTCATTTTCTAC
2400 C
1 C
2401 CTAATTGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.43
Consensus pattern (32 bp):
CAGAAAGACTTAGTTTTTGGTTCATTTTCTAC
Found at i:10263 original size:31 final size:31
Alignment explanation
Indices: 10225--10376 Score: 160
Period size: 31 Copynumber: 4.9 Consensus size: 31
10215 TTTGTACCCA
*
10225 ACTTTTTGAAACATATGGCATGCCACGTGTC
1 ACTTTTTGAAACATGTGGCATGCCACGTGTC
10256 ACTTTTTGAAACATGTGGCATGCCACGTGTC
1 ACTTTTTGAAACATGTGGCATGCCACGTGTC
** * * * * *
10287 ACTTTTTGGTACACGTGACGTGACATGTGTC
1 ACTTTTTGAAACATGTGGCATGCCACGTGTC
** * *
10318 ACTTTTTGGTACATGTGGCGTGCCACATGTC
1 ACTTTTTGAAACATGTGGCATGCCACGTGTC
** * *
10349 ACTTTTTGGTACACGTGGCGTGCCACGT
1 ACTTTTTGAAACATGTGGCATGCCACGT
10377 CGGAAACCGT
Statistics
Matches: 106, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 106 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (31 bp):
ACTTTTTGAAACATGTGGCATGCCACGTGTC
Found at i:10318 original size:62 final size:62
Alignment explanation
Indices: 10251--10370 Score: 195
Period size: 62 Copynumber: 1.9 Consensus size: 62
10241 GGCATGCCAC
*
10251 GTGTCACTTTTTGAAACATGTGGCATGCCACGTGTCACTTTTTGGTACACGTGACGTGACAT
1 GTGTCACTTTTTGAAACATGTGGCATGCCACATGTCACTTTTTGGTACACGTGACGTGACAT
** * *
10313 GTGTCACTTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGCGTG
1 GTGTCACTTTTTGAAACATGTGGCATGCCACATGTCACTTTTTGGTACACGTGACGTG
10371 CCACGTCGGA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (62 bp):
GTGTCACTTTTTGAAACATGTGGCATGCCACATGTCACTTTTTGGTACACGTGACGTGACAT
Found at i:10969 original size:31 final size:30
Alignment explanation
Indices: 10927--11056 Score: 151
Period size: 30 Copynumber: 4.4 Consensus size: 30
10917 CACAGTGTCC
10927 GACATG-G-CATGCCACGTGTACCAAAAAGT
1 GACATGTGTCATGCCACGTGTACC-AAAAGT
*
10956 AACATGTGTCATGCCACGTGTACCAAAAGT
1 GACATGTGTCATGCCACGTGTACCAAAAGT
*** *
10986 GACCCATGTCATGCCATGTGTACCAAAAGT
1 GACATGTGTCATGCCACGTGTACCAAAAGT
* *
11016 GACATGTGGT-ATGCCACGTGCACAAAAAG-
1 GACATGT-GTCATGCCACGTGTACCAAAAGT
11045 GACATGTGTCAT
1 GACATGTGTCAT
11057 TTTTGTCCAC
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
28 2 0.02
29 14 0.16
30 52 0.61
31 17 0.20
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (30 bp):
GACATGTGTCATGCCACGTGTACCAAAAGT
Done.