Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010386.1 Corchorus capsularis cultivar CVL-1 contig10407, 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: 40157
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Found at i:2617 original size:19 final size:19
Alignment explanation
Indices: 2578--2617 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2568 AGTTGAGTTT
** *
2578 TTTGAGTCAGTTTGTTGAG
1 TTTGAGTCAGTCAGTTCAG
2597 TTTGAGTCAGTCAGTTCAG
1 TTTGAGTCAGTCAGTTCAG
2616 TT
1 TT
2618 AGTCACACTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.17, C:0.10, G:0.28, T:0.45
Consensus pattern (19 bp):
TTTGAGTCAGTCAGTTCAG
Found at i:7294 original size:1 final size:1
Alignment explanation
Indices: 7288--7317 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
7278 GCAATGAGCC
*
7288 TTTTTTTTTTTTTTTTTTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
7318 CAGGTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:10445 original size:8 final size:8
Alignment explanation
Indices: 10404--10446 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
10394 TACATACATA
*
10404 TATGTATG
1 TATGTCTG
10412 TATGTCTG
1 TATGTCTG
*
10420 TCTGTCTG
1 TATGTCTG
*
10428 TCTGTCTG
1 TATGTCTG
*
10436 TATGTATG
1 TATGTCTG
10444 TAT
1 TAT
10447 TAATATCTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.14, C:0.12, G:0.23, T:0.51
Consensus pattern (8 bp):
TATGTCTG
Found at i:15966 original size:42 final size:42
Alignment explanation
Indices: 15907--16038 Score: 255
Period size: 42 Copynumber: 3.1 Consensus size: 42
15897 AAGGTTCAGC
15907 GCTATGAGGCTGAGTGGTTGACATTATTTCTGCCCCAAACTG
1 GCTATGAGGCTGAGTGGTTGACATTATTTCTGCCCCAAACTG
15949 GCTATGAGGCTGAGTGGTTGACATTATTTCTGCCCCAAACTG
1 GCTATGAGGCTGAGTGGTTGACATTATTTCTGCCCCAAACTG
15991 GCTATGAGGCTGAGTGGTTGACATTATTTCTGCCCCAAACTG
1 GCTATGAGGCTGAGTGGTTGACATTATTTCTGCCCCAAACTG
*
16033 GTTATG
1 GCTATG
16039 CGAAATACAT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 89 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (42 bp):
GCTATGAGGCTGAGTGGTTGACATTATTTCTGCCCCAAACTG
Found at i:18471 original size:69 final size:69
Alignment explanation
Indices: 18360--18499 Score: 262
Period size: 69 Copynumber: 2.0 Consensus size: 69
18350 ACGGCCGCCG
*
18360 CGTACTTCTTACGCGCGTTCTCCGACAGTGGAGATTTGCTTGTTGATCCATTGGCCTTCTGCAGA
1 CGTACTTCTTACGCGCGTTCTCCAACAGTGGAGATTTGCTTGTTGATCCATTGGCCTTCTGCAGA
18425 GGGA
66 GGGA
*
18429 CGTACTTCTTACGCGCGTTCTCCAAGAGTGGAGATTTGCTTGTTGATCCATTGGCCTTCTGCAGA
1 CGTACTTCTTACGCGCGTTCTCCAACAGTGGAGATTTGCTTGTTGATCCATTGGCCTTCTGCAGA
18494 GGGA
66 GGGA
18498 CG
1 CG
18500 CGTTTTGGTA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.31
Consensus pattern (69 bp):
CGTACTTCTTACGCGCGTTCTCCAACAGTGGAGATTTGCTTGTTGATCCATTGGCCTTCTGCAGA
GGGA
Found at i:20624 original size:71 final size:71
Alignment explanation
Indices: 20502--20643 Score: 239
Period size: 71 Copynumber: 2.0 Consensus size: 71
20492 AGATCATGGA
20502 TATAACCTTGAACACCTGTATGCATATATCTGAGGCCAAGGATAATACTGCCTGATTTTGAACTG
1 TATAACCTTGAACACCTGTATGCATATATCTGAGGCCAAGGATAATACTGCCTGATTTTGAACTG
20567 TGAGTT
66 TGAGTT
* * * * *
20573 TATACCCTTGAAGACCTGTATGCATGTATCTGAGGCCAAGGATAATGCTGCCTGATTTTGAACTT
1 TATAACCTTGAACACCTGTATGCATATATCTGAGGCCAAGGATAATACTGCCTGATTTTGAACTG
20638 TGAGTT
66 TGAGTT
20644 ATCTTCTGTA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (71 bp):
TATAACCTTGAACACCTGTATGCATATATCTGAGGCCAAGGATAATACTGCCTGATTTTGAACTG
TGAGTT
Found at i:32478 original size:1 final size:1
Alignment explanation
Indices: 32474--32503 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
32464 AAGCAAAAGC
32474 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
32504 CGGAAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:33259 original size:22 final size:23
Alignment explanation
Indices: 33229--33274 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
33219 TGAAACCAGA
*
33229 GAAAGTGGC-GAAATCGAGGAGT
1 GAAACTGGCAGAAATCGAGGAGT
33251 GAAACTGGCAGAAATCGAGGAGT
1 GAAACTGGCAGAAATCGAGGAGT
33274 G
1 G
33275 CTACTACTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.37, C:0.11, G:0.39, T:0.13
Consensus pattern (23 bp):
GAAACTGGCAGAAATCGAGGAGT
Found at i:34819 original size:24 final size:24
Alignment explanation
Indices: 34787--34868 Score: 71
Period size: 24 Copynumber: 3.4 Consensus size: 24
34777 AATTTGAGTC
*
34787 TTCATAAACCAAACCAGGCAATAG
1 TTCATAAACCAAACCAAGCAATAG
***
34811 TTCATAAA-CAATGTACCTTTTC-ATA-
1 TTCATAAACCAA---ACC-AAGCAATAG
34836 TTCATAAACCAAACCAAGCAATAG
1 TTCATAAACCAAACCAAGCAATAG
34860 TTCATAAAC
1 TTCATAAAC
34869 AATGTAACTT
Statistics
Matches: 45, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
22 1 0.02
23 9 0.20
24 17 0.38
25 8 0.18
26 9 0.20
27 1 0.02
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.26
Consensus pattern (24 bp):
TTCATAAACCAAACCAAGCAATAG
Found at i:37969 original size:321 final size:320
Alignment explanation
Indices: 37305--40157 Score: 3082
Period size: 321 Copynumber: 8.9 Consensus size: 320
37295 ACCCGAAAGT
* * ** * * * **
37305 CTCATTCAAATGTCTATATTCATCTAAAAAAATCTCTATCGA-ATTGCATTTAAGGATTCATTTT
1 CTCATTGAAATATCTATATTCATCTAATTAAATCTC-AGCCACATTGGATTTAAGGATTTGTTTT
* * * *
37369 TACGAGCATCTTAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAATAATAGGAAAAACAA
65 TACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATAGGAAAAACAA
* * * *
37434 TATTAGAAGTGTGAAAAGCTCTTCAATCAT-TTTGGCA-TTGAATTATA-ATTTTTTATGATTA-
130 TATTAGAAGTGT-AAAAGCCCTTCAATC-TCTTT-GAAGTTGAATTATATA-TTATTATGAGTAT
* * * * * * ***
37495 TTGAGACAAGAAATTAAGGGAAAAACTTTCGGGTCAATTTTTG-C-AAAAAAAT-T--TAACC--
191 TTGGGCCAA-AAATTGAGGAAAAAAATTTCGGGTCAATTTTAGCCGAAAATCGTGTACTAACCAT
* * * * * * * *
37553 CACGGTTTTTTGGCTAAAAATGTGTACCGGGGCCCAGTCTCAGTTTTGCATGATTTTTGGCGCCA
255 CACGG-TTTTTGGCTAAAAACGCGT-TCTGGGCCCCGACTTAGTTTTGCATGGTTTTTGGCGCCA
37618 AGA
318 AGA
* ** * * * *
37621 CTCATTAAAATATCTATATTCATCTAACAAAATCCCATCCGCATTGGATTTGAGGATTTGTTTTT
1 CTCATTGAAATATCTATATTCATCTAATTAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
*
37686 ACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATT-A-AAAAAAATAGGAAAAACGAT
66 ACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATAGGAAAAACAAT
* * ** * * * **
37749 ATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTAGAATTATATATTTTTATTAGTATTTAA
131 ATTAGAAGTGT-AAAAGCCCTTCAATCTCTTTGAAGTTGAATTATATATTATTATGAGTATTTGG
* * * *
37814 GCCAAAAATTGAGGGAAAAAAATTTCGAGTCAATTTTAGCCG-AAATCATGTACGAATCATCACA
195 GCCAAAAATTGA-GGAAAAAAATTTCGGGTCAATTTTAGCCGAAAATCGTGTACTAACCATCAC-
* * * * ** * *
37878 GTTTTTTTGCTAAAAACGTGTTCCGAGGCTACGACTCAGTTTTGCATAGTTTTTGGCGCCAAGA
258 GGTTTTTGGCTAAAAACGCGTTCTG-GGCCCCGACTTAGTTTTGCATGGTTTTTGGCGCCAAGA
** * *
37942 CTCATTGAAATATCTATATTCATCTAACCAAATCTCAACCACATTGGGTTTAAGGATTTGTTTTT
1 CTCATTGAAATATCTATATTCATCTAATTAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
* * * * **
38007 ACGAGCATCTAAATATTTTTTTTCGATTTAATTAGAAATTAATTCAGAGAAAAATAGAAAAAATG
66 ACGAGCATCTGAATA--TTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATAGGAAAAACA
* ** * * * *
38072 ATATTACAAGCAATAAAATCCCATCAATCTTTTTGACA-TTGAATTATATA-TATTTATGAGTTT
129 ATATTAGAAG-TGTAAAAGCCCTTCAATCTCTTTGA-AGTTGAATTATATATTA-TTATGAGTAT
* * * *
38135 TTGGGCCAGACATTGAGGAAAAAAATTTCGGGTTAATTTTAGCTC--AAATCGTGTACGAACCAT
191 TTGGGCCAAAAATTGAGGAAAAAAATTTCGGGTCAATTTTAGC-CGAAAATCGTGTACTAACCAT
* ** * * * *
38198 CACGATTTTTGGCTAAAAACTTGTTATGGAACCCCGAATTAGTTTTGCAT-ATGTTTTGGCGCCA
255 CACGGTTTTTGGCTAAAAACGCGTTCTGG-GCCCCGACTTAGTTTTGCATGGT-TTTTGGCGCCA
*
38262 AGT
318 AGA
* * * *
38265 CTCATTGAATTATCTATATTCATCTAATTAATTCTCAGCAACATTGGATTTAAAGATTTGTTTTT
1 CTCATTGAAATATCTATATTCATCTAATTAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
* * * *
38330 ACAAGCATCTGAATATTGTTTCGATTTAATTAAAAATTAATTCAGAAAAAAATAGGGAAAACGAT
66 ACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATAGGAAAAACAAT
* * * **
38395 ATTAGAAAAGTG-AAAAACCCTTCAACCTTTTTGGCGTTGAATTATATATGT-TTATGAGTATTT
131 ATTAG--AAGTGTAAAAGCCCTTCAATCTCTTTGAAGTTGAATTATATAT-TATTATGAGTATTT
* * * * * * *
38458 TGGTCACAAATTGAGGAAAAAACATTTCGGGTTAATTTTAGTCG-AAATCGTGCACTAATTAACT
193 GGGCCAAAAATTGAGGAAAAAA-ATTTCGGGTCAATTTTAGCCGAAAATCGTG---T-ACTAACC
* * ** * * * * *
38522 ATCACAGTTTTTGGTTAAAAACGTATTCCGGAACCCCAACTCAGTTTTGCATGGTTTTTGGCGAC
253 ATCACGGTTTTTGGCTAAAAACGCGTTCTGG-GCCCCGACTTAGTTTTGCATGGTTTTTGGCGCC
38587 AAGA
317 AAGA
* * * * *
38591 CCCATTGAAATATC--CATTCATTTAATTAAATCTTAGCCA-AGTTGGATTTAACGATTTGTTTT
1 CTCATTGAAATATCTATATTCATCTAATTAAATCTCAGCCACA-TTGGATTTAAGGATTTGTTTT
* * *
38653 TACGAGCATCTAAATATTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATTGAAAAAACAA
65 TACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATAGGAAAAACAA
* * *
38718 TATTAGAAGTGATAAAATCCCTTCAATC-ATATGAAGTTGAATTATATATTATTATGAGTATTTG
130 TATTAGAAGTG-TAAAAGCCCTTCAATCTCTTTGAAGTTGAATTATATATTATTATGAGTATTTG
* * *
38782 GGCCATAAATTTAGGAAAAAAAAAGTTCGGGTCAATTTTAGCCGAAAATCGTGTACTAACCATCA
194 GGCCAAAAATTGAGG--AAAAAAATTTCGGGTCAATTTTAGCCGAAAATCGTGTACTAACCATCA
* * * * *
38847 CAGTTTTTTGGCTGAAAACGCGTTCTTGTGCCCCGACTTAGTTTTGAAGGGTTTCTT-GCGCCAA
257 C-GGTTTTTGGCTAAAAACGCGTTC-TGGGCCCCGACTTAGTTTTGCATGGTTT-TTGGCGCCAA
38911 GA
319 GA
* *
38913 CTCATTG-AATCATCTATATTCATCTAATTGAATCTCAGCCA-AGTTGGATTTAAAGATTTGTTT
1 CTCATTGAAAT-ATCTATATTCATCTAATTAAATCTCAGCCACA-TTGGATTTAAGGATTTGTTT
*
38976 TTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAAATAAGAAAAACA
64 TTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATAGGAAAAACA
* *
39040 ATATTAGAAGTGATAAAAGCCTTTCAATCTCTTTGAAGTTAAATTATATATTATTATGAGTATTT
129 ATATTAGAAGTG-TAAAAGCCCTTCAATCTCTTTGAAGTTGAATTATATATTATTATGAGTATTT
* * ** *
39105 GGGCCAGAAATTTAGGAAAAAAATTTCTTGTCAATTTTAGCTGAAAATCGTGTACTAACCATCAC
193 GGGCCAAAAATTGAGGAAAAAAATTTCGGGTCAATTTTAGCCGAAAATCGTGTACTAACCATCAC
* ** *
39170 GGGTTTTGGCTAAAAACGCGTTCTTGGGCCCCGACTTAGTTTTGCATGGTTTTTGGAACAAAGA
258 GGTTTTTGGCTAAAAACGCGTTC-TGGGCCCCGACTTAGTTTTGCATGGTTTTTGGCGCCAAGA
* * * *
39234 CTCATTGAATTATCTACATTCATCTAATTAAATCTCAGGCACGTTGGATTTAAGGATTTGTTTTT
1 CTCATTGAAATATCTATATTCATCTAATTAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
* * *
39299 ACGAGCCTTTGAATATTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAAATAAGAAAAACAAT
66 ACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATAGGAAAAACAAT
* * * *
39363 ATTAGAAGTGATAAAAACCTTTTAATCTCTTTGAAGTTTAATTATATATTATTATGAGTATTTGG
131 ATTAGAAGTG-TAAAAGCCCTTCAATCTCTTTGAAGTTGAATTATATATTATTATGAGTATTTGG
* * * * * *
39428 GCCAGAAATTAAGAAAAAAAATTTCTGGTTAATTTTAGCTGAAAATCGTGTACTAACCATCACGG
195 GCCAAAAATTGAGGAAAAAAATTTCGGGTCAATTTTAGCCGAAAATCGTGTACTAACCATCACGG
* * *
39493 ATTTTGGCTAAAAACGCATTCTTGGGCCCCGACTTAGTTTTGCATGGTTTTTGGCACCAAGA
260 TTTTTGGCTAAAAACGCGTTC-TGGGCCCCGACTTAGTTTTGCATGGTTTTTGGCGCCAAGA
* * * * ** *
39555 CTCATTGAATTATCTACATTAATCTAATTAAATCTTAGCCATGTTGGATTTAAGGATTTGATTTT
1 CTCATTGAAATATCTATATTCATCTAATTAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
* * *
39620 ACGAGCATTTGAATATTGTTTTGATTTAATTATAAATTAATTCAGAAAAATAA-A--AAAAACAA
66 ACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCAGAAAAA-AATAGGAAAAACAA
* * * *
39682 TATTAAAAGTTATAAAAGCCTTTCAATCTCTTTGAAGTTAAATTATATATTATTATGAGTATTTG
130 TATTAGAAG-TGTAAAAGCCCTTCAATCTCTTTGAAGTTGAATTATATATTATTATGAGTATTTG
* * * * ** *
39747 CGCCATAAATTAAGAAAAAAAAATTTCTTGTCAATTTTAGCTGAAAATCGTGTACTAACCATCAC
194 GGCCAAAAATTGAG-GAAAAAAATTTCGGGTCAATTTTAGCCGAAAATCGTGTACTAACCATCAC
* * *
39812 AGG-TTTTGGCTAAAAACGCCTTATTGGGCCCCGACTTAGTTTTGCATGGTTTTTGGCGCTAAGA
258 -GGTTTTTGGCTAAAAACGCGTT-CTGGGCCCCGACTTAGTTTTGCATGGTTTTTGGCGCCAAGA
* * * * *
39876 CTCATTGAATTGTCTGTATTCATCTAATTAAATCTCAGCCACGTTGGATTAAAGGATTTGTTTTT
1 CTCATTGAAATATCTATATTCATCTAATTAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
* *
39941 ACGAGCATTTGAATATTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATAAGAAAAACAAT
66 ACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATAGGAAAAACAAT
* * *
40006 ATTAGAAGTGATAAAAGCCTTTCAATCTCTTTGAAATCGAATTATATATTATTATGAGTATTTGG
131 ATTAGAAGTG-TAAAAGCCCTTCAATCTCTTTGAAGTTGAATTATATATTATTATGAGTATTTGG
* * *
40071 G-CAAAAATTTGAGGAAAAAAGTTTCGGGTC-ATATTTAGTCGAAAATCGTGTACTAACCTTCAC
195 GCCAAAAA-TTGAGGAAAAAAATTTCGGGTCAAT-TTTAGCCGAAAATCGTGTACTAACCATCAC
*
40134 GGTTTTTGGCTAAAAACACGTTCT
258 GGTTTTTGGCTAAAAACGCGTTCT
Statistics
Matches: 2196, Mismatches: 274, Indels: 129
0.84 0.11 0.05
Matches are distributed among these distances:
313 2 0.00
314 71 0.03
315 34 0.02
316 96 0.04
317 1 0.00
319 3 0.00
320 84 0.04
321 913 0.42
322 207 0.09
323 307 0.14
324 316 0.14
325 90 0.04
326 71 0.03
327 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36
Consensus pattern (320 bp):
CTCATTGAAATATCTATATTCATCTAATTAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
ACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATAGGAAAAACAAT
ATTAGAAGTGTAAAAGCCCTTCAATCTCTTTGAAGTTGAATTATATATTATTATGAGTATTTGGG
CCAAAAATTGAGGAAAAAAATTTCGGGTCAATTTTAGCCGAAAATCGTGTACTAACCATCACGGT
TTTTGGCTAAAAACGCGTTCTGGGCCCCGACTTAGTTTTGCATGGTTTTTGGCGCCAAGA
Done.