Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009212.1 Corchorus capsularis cultivar CVL-1 contig09233, 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: 65594
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:13286 original size:11 final size:11
Alignment explanation
Indices: 13270--13294 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13260 ATTATTAGAG
13270 TTTCTTTCTTT
1 TTTCTTTCTTT
13281 TTTCTTTCTTT
1 TTTCTTTCTTT
13292 TTT
1 TTT
13295 TGCTCTTCGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTCTTTCTTT
Found at i:50833 original size:2 final size:2
Alignment explanation
Indices: 50826--50856 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
50816 CACAATTCAA
*
50826 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
50857 AATTTGTGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:54302 original size:35 final size:37
Alignment explanation
Indices: 54243--54318 Score: 120
Period size: 35 Copynumber: 2.1 Consensus size: 37
54233 AAATGAGAAT
54243 CCAACCCAAACTAAGAAATTACCTTAAATAAGGTAAACC
1 CCAACCCAAACTAAG-AA-TACCTTAAATAAGGTAAACC
54282 CCAACCCAAACTAAG-A-ACCTTAAATAAGGTAAACC
1 CCAACCCAAACTAAGAATACCTTAAATAAGGTAAACC
54317 CC
1 CC
54319 GTGAGATTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
35 21 0.57
37 1 0.03
39 15 0.41
ACGTcount: A:0.47, C:0.29, G:0.08, T:0.16
Consensus pattern (37 bp):
CCAACCCAAACTAAGAATACCTTAAATAAGGTAAACC
Found at i:55471 original size:333 final size:326
Alignment explanation
Indices: 54855--56322 Score: 960
Period size: 330 Copynumber: 4.5 Consensus size: 326
54845 CATACTTTTA
* * * * *
54855 ATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATC-AAAACAAGATTCAGAT-ATAC
1 ATATTGTTTTCCATATTTTTCTGAATTAATTTCTAATTAAATCGAACA-AAGATTCAAATGCT-C
* * *** * *
54918 ATAAAAACAAATCCTTAAATCCAATGTTTCTGAGATTTGATTAGATG-AATAAAGATATTTCAAG
64 GTAAAAA-AAATCCTTAAATTCAATGTGGATGAGATTTGAGTAGATGAAATATAGATATTTCAAG
* * * * *
54982 GAGTCTCGACGC-------CATGCAAAA-TAGAGCCGTGGCCCCGGAACGCGTTTTTAGCCAAAA
128 GAGTCTCGGCGCAAAAAATCATGCAAAACT-GAGCCG-GGTCCCGGAACGCATTTTTAACCGAAA
* * ** *
55039 ATCGTGATGGTTAGTATATGATTTCGGCA-AAAATTTTGCAAAAATTGATCCGAAAGATATTTCC
191 A-C-TG-T-G---GTACACGATTTC-TAATAAAATTTTGCAAAAATTGACCCGAAAGATATTTCC
* * * * ***
55103 TCAATTATTGGCTAAAATACTCATAAAAAATATATAATTCGAC-ATAAAAAAGATTG-AAGGGTT
248 TCAATTATTAGCGAAAATACTCATAAAAAATATATAATTCAACGACAAAAAA-ATTGAAAACCTT
55166 TTTAACGCTTCTAAT
312 TTTAACGCTTCTAAT
*
55181 AATATTGTTTTCCCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAATAGATTCAAATGC
1 -ATATTGTTTTCCATA-TTTTTCTGAATTAATTTCTAATTAAATCG-AACAA-AGATTCAAATGC
*
55246 TCGTAAAAATAAATCCTTAAA-TCTAATGTGGATGAGATTTGGGTAGATG-AATATAGATATTTC
62 TCGTAAAAA-AAATCCTTAAATTC-AATGTGGATGAGATTTGAGTAGATGAAATATAGATATTTC
*
55309 AAGGAGTCTTGGCATGCACCAAAAATCATGCAAAACTGAGCCGGGTCCCGGAACGCATTTTTAAC
125 AAGGAGTCTCGGC--GCA--AAAAATCATGCAAAACTGAGCCGGGTCCCGGAACGCATTTTTAAC
*
55374 CGAAAACTGTGGTACACGATTTCTAATAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCA
186 CGAAAACTGTGGTACACGATTTCTAATAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCA
*
55439 ATT-TCTAGCGAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAAACCTTTTT
251 ATTAT-TAGCGAAAATACTCATAAAAAATATATAATTCAACGACAAAAAAATTGAAAACCTTTTT
* *
55503 CACGCTTTTAAT
315 AACGCTTCTAAT
* * * **
55515 ATTTTTTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAATTAAGATTCAAATGCTCGT
1 ATATTGTTTTCCATATTTTTCTGAATTAATTTCTAATTAAATCGAACAAAGATTCAAATGCTCGT
* *
55580 AAAAAAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAAATATAGATATTTCAAGGAG
66 AAAAAAAATCCTTAAATTCAATGTGGATGAGATTTGAGTAGATGAAATATAGATATTTCAAGGAG
* * * * ** * **
55645 TCTCGGCGCAAAAAATCATGCAAAATTAAGCCTGGACTCCAAAACGCGTTTTTATATAGCAAAAA
131 TCTCGGCGCAAAAAATCATGCAAAACTGAGCCGGGTC-CCGGAACGC-ATTTT-TA-A-CCGAAA
*** * * * *
55710 ACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAAATG-CCCCAAAAATTTTTTT
191 A-C-TG-T-G---GTACACGATTTCTAATAAAATTTTGC-AAAAATTGACCCGAAAGA--TATTT
* * * * * * * * **
55774 CATCAATTTTTGGCTAAAATACTCATAATATATATATAATT-AACG-CAAAAGAGATAGGAGGA-
246 CCTCAATTATTAGCGAAAATACTCATAAAAAATATATAATTCAACGACAAAA-AAAT-TGAAAAC
* *
55836 C-TTTTCACGCTTTTAAT
309 CTTTTTAACGCTTCTAAT
* * * *
55853 ATA--GTTTTTCATA-TTTTCTGAATTAATTTCTAACTAAAACGAA-ACAAGATTCAGATGCTCG
1 ATATTGTTTTCCATATTTTTCTGAATTAATTTCTAATTAAATCGAACA-AAGATTCAAATGCTCG
* * * * * * * *
55914 TAAAAACAAATTCTTAAATCCAA--T-G-T-AG--TTGATTAAAT-AAATATGGACATCTCAAAG
65 TAAAAA-AAATCCTTAAATTCAATGTGGATGAGATTTGAGTAGATGAAATATAGATATTTCAAGG
* ** * * * * * *
55971 AGTCTTGGCGTTAAAAATCATGCAAAACTTAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAAT
129 AGTCTCGGCGCAAAAAATCATGCAAAACTGAG-CCGGGTCCCGGAACGCATTTTTAACCGAAAA-
* * ** * * *
56036 CGTGATGATTATTACACGATTTC-AGCTTGAATTTTTCAAAAATTGACTCGAAAGTTATTTCCTC
192 C-TG-TG----GTACACGATTTCTA-ATAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTC
* * * * * * * * * *
56100 AATTTTTAGCCACAATACTCATAAAAATTATATAATTCAAAGCCAAAAAGATTGAAGATCTTTTC
250 AATTATTAGCGAAAATACTCATAAAAAATATATAATTCAACGACAAAAAAATTGAAAACCTTTTT
56165 ATA--CTTCTAAT
315 A-ACGCTTCTAAT
** * * * *
56176 ATCGT-TTTTCCTATTATTTTT-TGAATTAA---GT--TTAAATCGAA-ACATGATTTAGATGCT
1 ATATTGTTTTCC-A-TATTTTTCTGAATTAATTTCTAATTAAATCGAACA-AAGATTCAAATGCT
* *** * * * * *
56233 TGTTTTACAAATCCTTAAATCCAATGT-GACTGAGATTTGATTAGAT-AAATGTAGATATTTTAA
63 CGTAAAAAAAATCCTTAAATTCAATGTGGA-TGAGATTTGAGTAGATGAAATATAGATATTTCAA
*
56296 GGAGTCTCGGTGCAAAAAATCATGCAA
127 GGAGTCTCGGCGCAAAAAATCATGCAA
56323 CACCGAACCG
Statistics
Matches: 930, Mismatches: 146, Indels: 130
0.77 0.12 0.11
Matches are distributed among these distances:
320 15 0.02
321 25 0.03
322 44 0.05
323 26 0.03
324 54 0.06
325 4 0.00
326 35 0.04
327 70 0.08
328 84 0.09
329 50 0.05
330 124 0.13
331 11 0.01
332 35 0.04
333 99 0.11
334 25 0.03
335 50 0.05
336 24 0.03
337 1 0.00
338 55 0.06
339 16 0.02
340 66 0.07
341 16 0.02
342 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (326 bp):
ATATTGTTTTCCATATTTTTCTGAATTAATTTCTAATTAAATCGAACAAAGATTCAAATGCTCGT
AAAAAAAATCCTTAAATTCAATGTGGATGAGATTTGAGTAGATGAAATATAGATATTTCAAGGAG
TCTCGGCGCAAAAAATCATGCAAAACTGAGCCGGGTCCCGGAACGCATTTTTAACCGAAAACTGT
GGTACACGATTTCTAATAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTATTAGCG
AAAATACTCATAAAAAATATATAATTCAACGACAAAAAAATTGAAAACCTTTTTAACGCTTCTAA
T
Found at i:58948 original size:2 final size:2
Alignment explanation
Indices: 58937--58969 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
58927 ATTCCTTCTC
58937 AT AT -T AT 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 AT AT AT AT
58970 TCTACATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Done.