Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011043.1 Corchorus capsularis cultivar CVL-1 contig11064, 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: 7491
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Found at i:1166 original size:325 final size:320
Alignment explanation
Indices: 307--1269 Score: 1162
Period size: 325 Copynumber: 3.0 Consensus size: 320
297 AAACCATGAT
* * * * * * *
307 ACCCGAAAGGTTTTTCCTCAATTTTTGGCAAAAACACTCATAAAAATATATATAATTCAACACCA
1 ACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAA-ATATATAATTCAACACCA
* * * *
372 AAAAGATTGTA-GGACTTCTCACGCTTTTAATATCATTTTTCATA-TTTTTTCAGAATTAATTTC
65 AAAAGATTG-ACGGGCTTTTCACGCTTCTAATATCATTTTCCATATTTTTTTC-GAATTAATTTC
* ** * * * *
435 TGATTAAATCGAAACAAGATTCTGATGCAT-GTAAAAACAAATCCTTAAATCCAATGTGGCGGAG
128 TAATTAAATCGAAACAAGATTGAGATGC-TCGAAAAAACAAATCCTTATATCCAATATGGCTGAG
* * *
499 ATTTGATTAGACT-AATAAAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTG-TG
192 ATTTGGTTAGA-TGAATATAGATATTTCAAGGAGTTTTTC-GCCAAAAATCATGCAAAACTGAT-
* * * *
562 CCTGGGCCCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATGATTAC-TACACGATTTCGGCTAA
254 TC-GGG-GCCCGGAACGCGTTTTTAG-CCAAAAACCGTGATGGTT-CGTACACGATTTCGGCTAA
*
626 AAATTG
315 AAACTG
* * *
632 ACCCGAAAAGTCTTTTCTCAATTTTTTGCCACAATACTCAG-AAAAATATATAATTTAACTCCAA
1 ACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAA
* * *
696 AAAGATTGACGGGGTTTTCACGGTTCTAATATCGTTTTTCC--ATTTTTTTCGAATTAATTTCTA
66 AAAGATTGACGGGCTTTTCACGCTTCTAATATC-ATTTTCCATATTTTTTTCGAATTAATTTCTA
* * *
759 ATTAAATCGAAACAAGATTGGGATACTCGAAAAAAGAAATCCTTATATCCAATATGGCTGAGATT
130 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATT
* * *
824 TGGTTTGATGAATATAGATATTTTAAGGAGTTTTTGCGCCAAAAATCATGCAAAATTGATTCGGG
195 TGGTTAGATGAATATAGATATTTCAAGGAGTTTTT-CGCCAAAAATCATGCAAAACTGATTCGGG
889 GCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTCGTACACGATTTCGGCTAAAAACTG
259 GC-CCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTCGTACACGATTTCGGCTAAAAACTG
* * *
952 ACCCGGAAATTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATTATTCAACACCAA
1 ACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAA
1017 AAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTCCCATATTTTTTTTCTGAATTAATTGT
66 AAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTT-CCATA-TTTTTTTC-GAATTAATT-T
* * *
1082 -TAATTAAATTGAAACAAGATTGAGATGCTCGAAAAAACAAAT-CTTGGTATCCAATATGACTGA
127 CTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTT-ATATCCAATATGGCTGA
* * * * *
1145 GATTTGGTTCGATGAATATAGATATTTGAAGGAGTTTTTACGCCAAAAATCTTGTAAAACTGAGT
191 GATTTGGTTAGATGAATATAGATATTTCAAGGAGTTTTT-CGCCAAAAATCATGCAAAACTGATT
* * * *
1210 CGGGGCCTCAGAACGCGTTTTTAGCCAAAAACCGTAAT-G--AGTAAACGATTTCGGCTAAAA
255 CGGGGCC-CGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTCGTACACGATTTCGGCTAAAA
1270 TTTTGCAAAA
Statistics
Matches: 557, Mismatches: 63, Indels: 39
0.85 0.10 0.06
Matches are distributed among these distances:
319 1 0.00
320 82 0.15
321 74 0.13
322 137 0.25
323 53 0.10
324 22 0.04
325 187 0.34
326 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (320 bp):
ACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAA
AAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTCCATATTTTTTTCGAATTAATTTCTAA
TTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTT
GGTTAGATGAATATAGATATTTCAAGGAGTTTTTCGCCAAAAATCATGCAAAACTGATTCGGGGC
CCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTCGTACACGATTTCGGCTAAAAACTG
Found at i:2693 original size:325 final size:320
Alignment explanation
Indices: 1415--2718 Score: 1321
Period size: 325 Copynumber: 4.0 Consensus size: 320
1405 TTTAGCCACA
* * * * * ***
1415 CGTACACGATTTCGGCTAAAAACTGAGACGAAATTTTTTTTCTTGAATTTTTTATGACAATACTC
1 CGTACACGATTTCGACTAAAAACTGA-CCCAAAATTTTTTTC-TCAATTTTTTGCCACAATACTC
* * * *
1480 ATAAAAAATATATAATTCAACACCAAAAAAATTTAAGGGTTTGTCACGTTTCTAATATCGTTTTT
64 AGAAAAAATATATAATTCAACACCAAAAAAATTGACGGGTTT-TCACGCTTCTAATATCGTTTTT
* * * *
1545 CC-TTTTTTTCTGAATTAATTTCTAATTAAAACGAAACAAGATTCAGATGCTCGTAAAAATAAAT
128 CCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGAAAAAACAAAT
** * * * * * * * * *
1609 CAGTAAATCGAATTTGGCTGGGATTTGCTTCGATGAATATATATACTTCAAGGAGTCTTTATGCC
193 CCTTATATCTAATATGGCTGAGATTTGGTTCAATGAATATAGATATTTCAAGGAGTCTTTACGCC
** * * * *
1674 -AAAATCATGCAAAACTGAGCCGGGGCTTCGGAACGTGGTTTTAGCAAAAAAACTGTGATGGTT
258 AAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGC-CAAAAACCGTGATGGTT
* * * * * * * *
1737 AGTACATGATTTCAGGTAAAATTTTCCAAAAACTTACACGAAAAATTTTTCCTCATTTTTTTTGC
1 CGTACACGATTTC--G----A----CTAAAAACTGAC-CCAAAATTTTTTTCTCA-ATTTTTTGC
* ** * *
1802 CACAATATTCAG-AAAAATATATAATTCAACGCAAAAAAAAAAATGAAGGGTTTTTTCACGCTTC
54 CACAATACTCAGAAAAAATATATAATTCAA--CACCAAAAAAATTGACGGG--TTTTCACGCTTC
* ** * *
1866 AAATATTTTTTTTTCATTTTTTTCCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATG
115 TAATATCGTTTTTCCATTTTTTT--CCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG
* * * *
1931 CTCGTAAAAACAAATCCTTAAATCTAATGTGGTTGAGATTTGGTT-AGATGAATATAGATATTTC
178 CTCGAAAAAACAAATCCTTATATCTAATATGGCTGAGATTTGGTTCA-ATGAATATAGATATTTC
* *
1995 AAGGAGTCTTT-CTGCCAAAAATCATGCAAAACTGTGCCGGGGCCCCCGAAACGCGTTTTTAGCC
242 AAGGAGTCTTTAC-GCCAAAAATCATGCAAAACTGAGCCGGGG-CCCCGGAACGCGTTTTTAG-C
* *
2059 CAAAAATCATGATGGTT
304 CAAAAACCGTGATGGTT
* *
2076 AC-TACACGATTTCGACTAAAAACTGACCCGAAAAGTCTTTTCTCAATTTTTTGCCACAATACTC
1 -CGTACACGATTTCGACTAAAAACTGACCC-AAAATTTTTTTCTCAATTTTTTGCCACAATACTC
* * * *
2140 AGAAAAAATATATAATTTAACGCCAAAAAGATTGACGGGGTTTTCACGGTTCTAATATCGTTTTT
64 AGAAAAAATATATAATTCAACACCAAAAAAATTGAC-GGGTTTTCACGCTTCTAATATCGTTTTT
** ** * *
2205 CCA-TTTTTTCCGAATTAATTTCTAATTAAATAAAAACAAGATTGGGATACTCGAAAAAAGAAAT
128 CCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGAAAAAACAAAT
** * *
2269 CCTTATATCTAATATGGCTGAGATTTGGTTTGATGAATATAGATAGTTT-AAGGAGTTTTTGCGC
193 CCTTATATCTAATATGGCTGAGATTTGGTTCAATGAATATAGATA-TTTCAAGGAGTCTTTACGC
* * * * *
2333 CAAAAAACATGCAAAATTGATCCGGGGCTCCGGAACGCGTTTTTAGCCAATAACCGTGATGGTT
257 CAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTT
2397 CGTACACGATTTCGACTAAAAACTGACCCATAAATTTTTTTCTCAATTTTTTGCCACAATACTCA
1 CGTACACGATTTCGACTAAAAACTGACCCA-AAATTTTTTTCTCAATTTTTTGCCACAATACTCA
* * * * * * * *
2462 GGAAAAAGATATTATTCAACACCGAAAAGATTGACGGACTTTTCACGCTTCTAATATCATTTTCC
65 GAAAAAATATATAATTCAACACCAAAAAAATTGACGG-GTTTTCACGCTTCTAATATCGTTTTTC
* * * *
2527 CATTTTTTTTTTCTGAATTAATTGCTAATTAAATTGAAACAAGATTGAGATGCTCGAAAAAACAA
129 CA---TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGAAAAAACAA
* * * * *
2592 AT-CTTGGTATCCAATATGGCTGAGATTTAGTTCAATGAATATAGATATTTCAAGGGGTTTTTAC
191 ATCCTT-ATATCTAATATGGCTGAGATTTGGTTCAATGAATATAGATATTTCAAGGAGTCTTTAC
* * *
2656 GCCAAAAATCTTGTAAAATTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATG
255 GCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATG
2719 AGTAAACGAT
Statistics
Matches: 816, Mismatches: 126, Indels: 77
0.80 0.12 0.08
Matches are distributed among these distances:
320 4 0.00
321 128 0.16
322 28 0.03
323 122 0.15
324 11 0.01
325 164 0.20
326 23 0.03
327 10 0.01
328 23 0.03
329 38 0.05
331 19 0.02
332 35 0.04
333 16 0.02
334 19 0.02
335 10 0.01
337 104 0.13
338 24 0.03
339 37 0.05
340 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (320 bp):
CGTACACGATTTCGACTAAAAACTGACCCAAAATTTTTTTCTCAATTTTTTGCCACAATACTCAG
AAAAAATATATAATTCAACACCAAAAAAATTGACGGGTTTTCACGCTTCTAATATCGTTTTTCCA
TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGAAAAAACAAATCCT
TATATCTAATATGGCTGAGATTTGGTTCAATGAATATAGATATTTCAAGGAGTCTTTACGCCAAA
AATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTT
Found at i:4411 original size:2 final size:2
Alignment explanation
Indices: 4404--4429 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4394 AGTTTGATGA
4404 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
4430 TAAGGAGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4932 original size:253 final size:252
Alignment explanation
Indices: 4591--5050 Score: 694
Period size: 253 Copynumber: 1.8 Consensus size: 252
4581 GTTTTTCTAT
*
4591 TTTTTTTCCGAATTTATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT
1 TTTTTTTCCGAATTTATTTCTAATTAAATAGAAACAAGATTCAAATGCTCGTAAAAACAAATCCT
** *
4656 TAAATCTAATGTGGATGAGATTTGG-TACGATGAATATAGATATTTCAAGAATTCTTTATGCCAA
66 TAAATCTAATGTGGAAAAGATTTGGTTA-GATGAATATAGATATTTCAAGAAGTCTTTATGCCAA
* *
4720 AAATCATGCAAAACTGAGCCGGGACCCTAGAACGCGTTTTTAG-TAAAAAATCGTGATGCGTACA
130 AAATCATGCAAAACTGAGCCGGGACCCTAGAACGCGTTTTTAGCCAAAAAATCGTGA--CCTACA
4784 CAATTTCGGCTAAAATTTTGCAAAAACTGACTGGAAGGGTTTTTCACGCTTCTAATATTG
193 CAATTTCGGCTAAAATTTTGCAAAAACTGACTGGAAGGGTTTTTCACGCTTCTAATATTG
* *
4844 TTTTTTTCCGAATTTATTTCTAATTAAATCGAATCAAGATTCAAATGCTCGTAAAAACAAATCCT
1 TTTTTTTCCGAATTTATTTCTAATTAAATAGAAACAAGATTCAAATGCTCGTAAAAACAAATCCT
* * *
4909 TAAAT-TCAATGT-GACAAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGTCA
66 TAAATCT-AATGTGGA-AAAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTATGCCA
* * * * *
4972 AAACTCATGCAAAACTGAGCCGGGGCCCTGGAACGCGTTTTTAGCCCAAAAGTCGTGACCTACAC
129 AAAATCATGCAAAACTGAGCCGGGACCCTAGAACGCGTTTTTAGCCAAAAAATCGTGACCTACAC
*
5037 GATTTCGGCTAAAA
194 AATTTCGGCTAAAA
5051 ACTGACCCGA
Statistics
Matches: 186, Mismatches: 17, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
252 22 0.12
253 152 0.82
254 12 0.06
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (252 bp):
TTTTTTTCCGAATTTATTTCTAATTAAATAGAAACAAGATTCAAATGCTCGTAAAAACAAATCCT
TAAATCTAATGTGGAAAAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTATGCCAAA
AATCATGCAAAACTGAGCCGGGACCCTAGAACGCGTTTTTAGCCAAAAAATCGTGACCTACACAA
TTTCGGCTAAAATTTTGCAAAAACTGACTGGAAGGGTTTTTCACGCTTCTAATATTG
Found at i:5327 original size:320 final size:319
Alignment explanation
Indices: 4844--5493 Score: 828
Period size: 320 Copynumber: 2.0 Consensus size: 319
4834 TCTAATATTG
* * *
4844 TTTTTTTCCGAATTTATTTCTAATTAAATCGAATCAAGATTCAAATGCTCGTAAAAACAAATCCT
1 TTTTTTTCAGAATTTATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAAAAAATCCT
* * *
4909 TAAATTCAATGTGACAAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGTCAAA
66 TAAATCCAATGTGACAAACATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAA
* **
4974 ACTCATGCAAAACTGAGCCGGGGCCCTGGAACGCGTTTTTAGCCCAAAAGTCGTGACCT-AC-AC
131 ACTCATACAAAACTGAGCCGGGGCCCTGGAACGCGTTTTTA-CCCAAAAACCGTGACCTAACGAC
*** *
5037 G-ATTTCGGCTAAAAACTGACCCGAATTTTTTTTTTCTGAAATTTTTGCCACAATACT-TAGAAA
195 GTATTTCGGCTAAAAACTGA-CC-AAAAATTTTTTTCTCAAATTTTTGCCACAATACTATAGAAA
* * *
5100 AAATATATATTTCAATGCCAAAAATATTGATGGG-CTTTTCACGCTTCTAATATCATTTTTCCA
258 AAATATA-ATTT-AATGCCAAAAAGATTGAAGGGTCTTTTCACACTTCTAATATCATTTTTCCA
* *
5163 TTTTTTTCAGAATTTATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAAAAAAATCC
1 TTTTTTTCAGAATTTATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGT-AAAAAAAAATCC
*** * ** *
5228 TTTTGTCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGC-GCCA
65 TTAAATCCAATGTGACAAACATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT-CTGCCA
* * * **
5292 AAACTCATACAAAATTGAGCTGGGGCTCC-GGAACGCGTTTTTATCCAAAAACCGTGATGTAACG
129 AAACTCATACAAAACTGAGCCGGGGC-CCTGGAACGCGTTTTTACCCAAAAACCGTGACCTAACG
* * *
5356 TACGTTATTTCGGTTAAAAACTTACCAAAAATTTTTTTCTCAATTTTTTGCCACAATACTCATAG
193 -ACG-TATTTCGGCTAAAAACTGACCAAAAATTTTTTTCTCAAATTTTTGCCACAATACT-ATAG
* * *
5421 AAAATATATAATTTAATGTCAAAAAGATTGAAGGGTTTTTTCACACTTCTAATATCATTTTTCCA
255 AAAAAATATAATTTAATGCCAAAAAGATTGAAGGGTCTTTTCACACTTCTAATATCATTTTTCCA
5486 TTTTTTTC
1 TTTTTTTC
5494 GTTACATCGA
Statistics
Matches: 284, Mismatches: 36, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
319 60 0.21
320 102 0.36
321 3 0.01
322 50 0.18
323 41 0.14
324 28 0.10
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (319 bp):
TTTTTTTCAGAATTTATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAAAAAATCCT
TAAATCCAATGTGACAAACATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAA
ACTCATACAAAACTGAGCCGGGGCCCTGGAACGCGTTTTTACCCAAAAACCGTGACCTAACGACG
TATTTCGGCTAAAAACTGACCAAAAATTTTTTTCTCAAATTTTTGCCACAATACTATAGAAAAAA
TATAATTTAATGCCAAAAAGATTGAAGGGTCTTTTCACACTTCTAATATCATTTTTCCA
Found at i:6896 original size:15 final size:16
Alignment explanation
Indices: 6876--6912 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
6866 AAGTTTCATG
*
6876 ATTATAAATTATA-AT
1 ATTATAAATTAAATAT
6891 ATTAT-AATTAAATAT
1 ATTATAAATTAAATAT
6906 ATTATAA
1 ATTATAA
6913 TAGAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.32
15 12 0.63
16 1 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTATAAATTAAATAT
Found at i:7082 original size:29 final size:29
Alignment explanation
Indices: 7023--7078 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
7013 TTTCCATAAT
7023 TAATAAAAAAGTTAAATCATCTAAAAAGA
1 TAATAAAAAAGTTAAATCATCTAAAAAGA
*
7052 TAATAAAAAAGTTAAAT-GTCTAAAAAG
1 TAATAAAAAAGTTAAATCATCTAAAAAG
7079 GATACTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.61, C:0.05, G:0.09, T:0.25
Consensus pattern (29 bp):
TAATAAAAAAGTTAAATCATCTAAAAAGA
Done.