Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008093.1 Corchorus capsularis cultivar CVL-1 contig08114, 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: 56611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:914 original size:331 final size:328
Alignment explanation
Indices: 6--1106 Score: 967
Period size: 331 Copynumber: 3.3 Consensus size: 328
1 CCAAA
* * *
6 AATAATCAT-TAAAAAATATATAGTTCAACGCCAAAAACATT-AGAGGGCTTTTCACGCTTCTAA
1 AATAATCATAAAAAAAATATATA-CTCAACGCC-AAAAGATTGA-AGGGCTTTTCACGCTTCTAA
* * *** * * * * * * * *
69 TCTCATTTTT-CTTTTT-TTTAATTAATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGT-T
63 TATAATTTTTCCTTTTTCCCGAAATAATTTCTAATAAAATCGAAACAAGATTCTGATACTCCTAA
* * * *** ** *
131 AAAAAATCCTTTTAAA-CCAATGTTGCGCAGATTTGGTTAGATGAATATAGATAGTTCAAGGAGT
128 AAAAAAT--TCTGAAATCAAATAAGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGT
* * ** *
195 CTTGGCA-CC--AAA-CACGCAAAACTGAGTTGGGGCCCAGGAACGCGTTTTTAGCCAGAAATCG
191 CTTGG-AGCCAAAAATCATGCAAAACTTAGCCGGGGCCCAGGAACGCGTTTTTAGCCAAAAATCG
*
256 TGATGGTTAGTACACGATTTCAGCTAAAACTTTGAAAAATTGTCTCGAAAGAGGATTTTTCCTCA
255 TGATGGTTAGTACACGATTTCGGCTAAAACTTTGAAAAATTGTCTCG-AA-A-GATTTTTCCTCA
*
321 ATTTTTAGTCAC
317 ATTTTTAGCCAC
* * * *
333 AATACTCATAAAAAAAATATATAATTCAATGCCAAAAGATTGGAGGGCTTTTCACGCTTCTAATA
1 AATAATCATAAAAAAAATATAT-ACTCAACGCCAAAAGATTGAAGGGCTTTTCACGCTTCTAATA
** * * *
398 TTGTTTTTCCTTTTTCCCGAAATAATTTCTAATAAAATTGAAACAAGATTCTGATGCTCCTTAAA
65 TAATTTTTCCTTTTTCCCGAAATAATTTCTAATAAAATCGAAACAAGATTCTGATACTCCTAAAA
*** *
463 AAAATTCTGAAATCAAATATTTCTAAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTG
130 AAAATTCTGAAATCAAATAAGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTG
* * * * ** * * *
528 GCGCCAAAAATCTTGTAAAACTTTGCCGGGTTCTATTG-ACGCGTTTTTAGCCAAAAACCGTGAT
195 GAGCCAAAAATCATGCAAAACTTAGCCGGGGCCCA-GGAACGCGTTTTTAGCCAAAAATCGTGAT
*
592 GGTTAGTACACGATTTCGGCTAAAACTTTGAAAAATTGTCTCGAAAGATTTTTCCACAATTTTTA
259 GGTTAGTACACGATTTCGGCTAAAACTTTGAAAAATTGTCTCGAAAGATTTTTCCTCAATTTTTA
657 GCCAC
324 GCCAC
* * ** * * * **
662 ATTAATCATAGACAGTAA-ATAT-CTCAACGTCAAAATGATTGAAGGGCTTTTCATGCTTGTTGT
1 AATAATCATA-AAAAAAATATATACTCAACGCCAAAA-GATTGAAGGGCTTTTCACGCTTCTAAT
* * * * * * * *
725 GTAATTTTTCTTTTTTTTCCCGAACTAATTTCTAATTAAATCGGAACAA-ATTTTATATACTCGT
64 ATAATTTTTC--CTTTTTCCCGAAATAATTTCTAATAAAATCGAAACAAGATTCT-GATACTCCT
* * * * * *
789 AAAAACAAA-TCTTTAAATCTAATAAGGCTTATATTTGCTTAGATGAAAATAGATATTTCAAGGA
126 AAAAA-AAATTC-TGAAATCAAATAAGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGA
*
853 GTCTTGGAGCCAAAAATCATGCAAAACTTAGCCGGGGCCCAGGAACGCATTTTTAGCCAAAAATC
189 GTCTTGGAGCCAAAAATCATGCAAAACTTAGCCGGGGCCCAGGAACGCGTTTTTAGCCAAAAATC
* * * * * *
918 GTGATGGTTTGTATACGATTTCGGCTAAAAATTTGCAAAAATTGACCCGAAAGATTTTCCCTCAA
254 GTGATGGTTAGTACACGATTTCGGCTAAAACTTTG-AAAAATTGTCTCGAAAGATTTTTCCTCAA
983 TTTTTAGCCAC
318 TTTTTAGCCAC
* * * * * * *
994 AATATTCAT-AAAAATATATATAATTCAACGCCTACAAGATTGGAA-GTCTTTTCCCGCTTCTAT
1 AATAATCATAAAAAAAATATAT-ACTCAACGCC-AAAAGATT-GAAGGGCTTTTCACGCTTCTAA
** * * * * * *
1057 TATTGTTTTTCTTATTTTTTCTGAATTAATTTCTAATTAAATCAAAACAA
63 TATAATTTTTC--CTTTTTCCCGAAATAATTTCTAATAAAATCGAAACAA
1107 TATTTAGATG
Statistics
Matches: 628, Mismatches: 120, Indels: 46
0.79 0.15 0.06
Matches are distributed among these distances:
327 52 0.08
328 59 0.09
329 124 0.20
330 60 0.10
331 139 0.22
332 123 0.20
333 65 0.10
334 6 0.01
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (328 bp):
AATAATCATAAAAAAAATATATACTCAACGCCAAAAGATTGAAGGGCTTTTCACGCTTCTAATAT
AATTTTTCCTTTTTCCCGAAATAATTTCTAATAAAATCGAAACAAGATTCTGATACTCCTAAAAA
AAATTCTGAAATCAAATAAGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGG
AGCCAAAAATCATGCAAAACTTAGCCGGGGCCCAGGAACGCGTTTTTAGCCAAAAATCGTGATGG
TTAGTACACGATTTCGGCTAAAACTTTGAAAAATTGTCTCGAAAGATTTTTCCTCAATTTTTAGC
CAC
Found at i:3434 original size:21 final size:21
Alignment explanation
Indices: 3350--3424 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
3340 TTGACACTGT
* * *
3350 TTAGGTACTATACAGATGAGA
1 TTAGGTACTGTACAGATCAAA
*
3371 TTA--TACTGTACATATCAAA
1 TTAGGTACTGTACAGATCAAA
3390 TTAGGTACTGTACAGATCAAA
1 TTAGGTACTGTACAGATCAAA
3411 TTAGGTACTGTACA
1 TTAGGTACTGTACA
3425 AATAAGATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 15 0.32
21 32 0.68
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32
Consensus pattern (21 bp):
TTAGGTACTGTACAGATCAAA
Found at i:4737 original size:32 final size:32
Alignment explanation
Indices: 4699--4763 Score: 87
Period size: 36 Copynumber: 1.9 Consensus size: 32
4689 TCTTAATCAA
4699 TTTTTTTGGC-AATTTATGACTCTGTGTTTTTT
1 TTTTTTTGGCAAATTTATGACTCTGT-TTTTTT
4731 TTTTTTTGGCATTAAATTTATGACTCTGTTTTT
1 TTTTTTTGGC---AAATTTATGACTCTGTTTTT
4764 GTGTGTGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 10 0.34
35 4 0.14
36 15 0.52
ACGTcount: A:0.15, C:0.09, G:0.14, T:0.62
Consensus pattern (32 bp):
TTTTTTTGGCAAATTTATGACTCTGTTTTTTT
Found at i:12001 original size:12 final size:12
Alignment explanation
Indices: 11984--12008 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11974 AATTAAAGTC
11984 ATTCTTATAAAT
1 ATTCTTATAAAT
11996 ATTCTTATAAAT
1 ATTCTTATAAAT
12008 A
1 A
12009 AGTAATAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTCTTATAAAT
Found at i:31293 original size:7 final size:7
Alignment explanation
Indices: 31274--31312 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
31264 GGCTAATAAG
31274 ATTCTC-
1 ATTCTCA
31280 ATCTCTCA
1 AT-TCTCA
31288 ATTCTCA
1 ATTCTCA
31295 ATTCTCA
1 ATTCTCA
31302 ATTCTCA
1 ATTCTCA
31309 ATTC
1 ATTC
31313 ACCACCACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 2 0.06
7 27 0.87
8 2 0.06
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTCTCA
Found at i:33563 original size:11 final size:10
Alignment explanation
Indices: 33547--33582 Score: 56
Period size: 11 Copynumber: 3.6 Consensus size: 10
33537 TTAGGGTTCT
33547 TTTTTTTTTC
1 TTTTTTTTTC
33557 ATTTTTTTTTC
1 -TTTTTTTTTC
33568 TTTTTTTTT-
1 TTTTTTTTTC
33577 TTTTTT
1 TTTTTT
33583 GGTTCCTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 6 0.24
10 9 0.36
11 10 0.40
ACGTcount: A:0.03, C:0.06, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:38512 original size:14 final size:14
Alignment explanation
Indices: 38493--38521 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
38483 ATCTTCTGTG
38493 TCAAAAATATTGAA
1 TCAAAAATATTGAA
38507 TCAAAAATATTGAA
1 TCAAAAATATTGAA
38521 T
1 T
38522 GGAGTGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (14 bp):
TCAAAAATATTGAA
Found at i:45316 original size:14 final size:14
Alignment explanation
Indices: 45297--45323 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
45287 TTGTCACTAT
45297 CTCCCCTGTTTTTC
1 CTCCCCTGTTTTTC
45311 CTCCCCTGTTTTT
1 CTCCCCTGTTTTT
45324 TGAAAGTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.41, G:0.07, T:0.52
Consensus pattern (14 bp):
CTCCCCTGTTTTTC
Found at i:48330 original size:31 final size:31
Alignment explanation
Indices: 48292--48356 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
48282 TTGGGTTATC
*
48292 AGTCTCCAAATCTTTAAATCTTGGATGTTTG
1 AGTCTCCAAATCTTTAAATCTTGGATATTTG
* *
48323 AGTCTCCAGATCTTTAGATCTTGGATATTTG
1 AGTCTCCAAATCTTTAAATCTTGGATATTTG
48354 AGT
1 AGT
48357 TAGTTCAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (31 bp):
AGTCTCCAAATCTTTAAATCTTGGATATTTG
Found at i:54033 original size:1 final size:1
Alignment explanation
Indices: 54027--54057 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
54017 ATTATGTAGC
54027 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
54058 GCCCGTGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:54867 original size:49 final size:49
Alignment explanation
Indices: 54786--54879 Score: 154
Period size: 49 Copynumber: 1.9 Consensus size: 49
54776 CTTTATTAAT
*
54786 GAAATGAAATGTGATCTGTGTGTTGTCAAAAAAAAAAAAAAAGAAAGAAA
1 GAAATGAAATGTGATCTGTGTGTTG-CCAAAAAAAAAAAAAAGAAAGAAA
*
54836 GAAA-GAAATGTGATCTGTGTGTTGCCCAAAAAAAAAAAAAGAAA
1 GAAATGAAATGTGATCTGTGTGTTGCCAAAAAAAAAAAAAAGAAA
54880 TGCGATCCGT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
48 18 0.43
49 20 0.48
50 4 0.10
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.19
Consensus pattern (49 bp):
GAAATGAAATGTGATCTGTGTGTTGCCAAAAAAAAAAAAAAGAAAGAAA
Done.