Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009382.1 Corchorus capsularis cultivar CVL-1 contig09403, 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: 11067
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:6638 original size:17 final size:18
Alignment explanation
Indices: 6605--6638 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6595 AGTAGTATGT
6605 TTCTTTTAGCTAAAACCC
1 TTCTTTTAGCTAAAACCC
6623 TTCTTTTAGC-AAAACC
1 TTCTTTTAGCTAAAACC
6639 TGTGACAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.38
Consensus pattern (18 bp):
TTCTTTTAGCTAAAACCC
Found at i:9512 original size:331 final size:329
Alignment explanation
Indices: 8788--9996 Score: 922
Period size: 331 Copynumber: 3.7 Consensus size: 329
8778 ACCATGATGC
* * * * * *
8788 CAAAAA-TAACCCGAAAGATTTTTCCTCAATTATT-GGAAAAATTACTCATAAAATATATATAAT
1 CAAAAATTGACCCAAAAGATATTTCCTCAATTTTTAGCAAAAA-TACTCATAAAAAATATATAAT
* * * *
8851 TCAACGCCAAAAAGATTGAATGACTTTTTACGCTTTTAATATCGTTTTTCATATTTTTTCAGAAT
65 TCAACGCCAAAAAGATTGAAAGGCTTTTTACGCTTCTAATATCGTTTTTCCTATTTTTTC-GAAT
* * * *
8916 CAAATTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAATAAATCCTTAAATCCAATGTG
129 TAAATTTTAATTAAATCGAAACAAGATTCAAATGCTCGAAAAAACAAATCCTTAAATCCAATGTG
* * * *
8981 TCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTCGGCGCCAAAAATTATGCAAAACAG
194 GCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTCGGCACAAAAAATCATGCAAAACAG
* **** ** *
9046 ATCCGTGGTCCCAAAACACATTTTTAGCCAAAAACCGTGATGGTTAGTATACGATTTCGGATAAA
259 ATCCGTGGCCCCAAAACACATTTTTAGCCAAAAACAAAAAAAGTTAGTACACGATTTCGGATAAA
9111 ATTTTG
324 ATTTTG
* * * * * *
9117 CAAAAATTGACCCGAAAGATATTTCCTTAATTTTTGGCAAAAATTCTTATAAAAAAAAATATAAT
1 CAAAAATTGACCCAAAAGATATTTCCTCAATTTTTAGCAAAAATACTCAT-AAAAAATATATAAT
* * * * * *
9182 TTAACGCCAAAAATATT-AGAGGGTTTTTTACGCTTCTAATATCGTTTTCCCTACTTTTTCTGAA
65 TCAACGCCAAAAAGATTGA-AAGGCTTTTTACGCTTCTAATATCGTTTTTCCTATTTTTTC-GAA
***
9246 TTAAATTTTAATTAAATCGAAACAAGATTTGGATGCTC-AAAAAACAAATCCTTAAATCCAATGT
128 TTAAATTTTAATTAAATCGAAACAAGATTCAAATGCTCGAAAAAACAAATCCTTAAATCCAATGT
* *
9310 GGCTGATATTTGATTAGATGAATATAA-ATATTTCAAGGAGTCTTGGCATAAAAAATCATGCAAA
193 GGCTGAGATTTGATTAGATGAATA-AAGATATTTCAAGGAGTC--GGCACAAAAAATCATGCAAA
* ** * * * *
9374 ACTGA-CC-TGGAGCCCCGTAACGCGTTTTTAG-TAAAAA-AAAAAAAGTAATGGTACACGATTT
255 ACAGATCCGT-G-GCCCCAAAACACATTTTTAGCCAAAAACAAAAAAAGT--TAGTACACGATTT
* *
9435 CGGTTAATATTTTG
316 CGGATAAAATTTTG
* * * * **
9449 -AGAAAATTGACCCAAAATATTTTTCCTCAATTTTTAGCCACAATACTCATAAAACGTATATAAT
1 CA-AAAATTGACCCAAAAGATATTTCCTCAATTTTTAGCAAAAATACTCATAAAAAATATATAAT
* * * * *
9513 TCAACGCCAAAAAGATTGCAAGGCTTTTCACTCTTCCAATAATTGTTTTTCCTATTTTTTCGAAT
65 TCAACGCCAAAAAGATTGAAAGGCTTTTTACGCTTCTAAT-ATCGTTTTTCCTATTTTTTCGAAT
* * * *
9578 T-AATTTCTAATTAAATCGAAACATGATTCAGATGCT------------T-GTTAAA-ACAA--T
129 TAAATTT-TAATTAAATCGAAACAAGATTCAAATGCTCGAAAAAACAAATCCTTAAATCCAATGT
* * * * * *
9626 GGCTGGGATTTGGTTACATTAATATAGATATTTCAATGAGTCTCGGTGCA-AAAAAATCATGCAA
193 GGCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAG--TC-G-GCACAAAAAATCATGCAA
* * * *** * * **** * ** * *
9690 AACTGAACCG-AGTTTCGAAACACGTTTTTAGCCAAAAAC-CGTGATGTTTTTACATGTTTTCGG
254 AACAGATCCGTGGCCCCAAAACACATTTTTAGCCAAAAACAAAAAAAGTTAGTACACGATTTCGG
* *
9753 CTAAAATTCTG
319 ATAAAATTTTG
* * * * *
9764 CAAAAATTGACCTAAAAGATATTTTCTCAAATTTTAGCCACAATTA-TCAT-AAAAATATATAAT
1 CAAAAATTGACCCAAAAGATATTTCCTCAATTTTTAG-CAAAAATACTCATAAAAAATATATAAT
* * * * * * *
9827 TCAAAGCCGAAAAGATTGAAGGGCTTTTCACGCTTCTAATATTGTTTTTCATA-TTTTTCTGGAT
65 TCAACGCCAAAAAGATTGAAAGGCTTTTTACGCTTCTAATATCGTTTTTCCTATTTTTTC-GAAT
* * ** * *
9891 T-AATTTCTAATTAAATCGAAACAAGAATCAGATGCTCCTAAAAACAAATCATTAAAATGCAATG
129 TAAATTT-TAATTAAATCGAAACAAGATTCAAATGCTCGAAAAAACAAATCCTT-AAATCCAATG
* * * * *
9955 TGGATAAGATTTTATTAGAAGAATATAGATAATTT-AAGGAGT
192 TGGCTGAGATTTGATTAGATGAATAAAGAT-ATTTCAAGGAGT
9997 TTGGGCGTCA
Statistics
Matches: 700, Mismatches: 136, Indels: 89
0.76 0.15 0.10
Matches are distributed among these distances:
312 6 0.01
313 49 0.07
314 45 0.06
315 55 0.08
316 52 0.07
317 29 0.04
318 10 0.01
319 5 0.01
320 1 0.00
325 1 0.00
326 2 0.00
327 3 0.00
328 4 0.01
329 6 0.01
330 127 0.18
331 191 0.27
332 114 0.16
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (329 bp):
CAAAAATTGACCCAAAAGATATTTCCTCAATTTTTAGCAAAAATACTCATAAAAAATATATAATT
CAACGCCAAAAAGATTGAAAGGCTTTTTACGCTTCTAATATCGTTTTTCCTATTTTTTCGAATTA
AATTTTAATTAAATCGAAACAAGATTCAAATGCTCGAAAAAACAAATCCTTAAATCCAATGTGGC
TGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTCGGCACAAAAAATCATGCAAAACAGAT
CCGTGGCCCCAAAACACATTTTTAGCCAAAAACAAAAAAAGTTAGTACACGATTTCGGATAAAAT
TTTG
Found at i:11008 original size:338 final size:329
Alignment explanation
Indices: 10086--11067 Score: 1396
Period size: 331 Copynumber: 2.9 Consensus size: 329
10076 TTTTCAATAT
* * * * *
10086 TTTTTGGATAAAATACTCATAAAAAATATATAATTTAACGTCAAAAAGATTGGAGGG-TTTTTCA
1 TTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGATTTTTAA
* * *
10150 CGCTTGTAATATCG-TTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAAAAAGATTCA
66 CGTTTCTAATATCGTTTTTCATA-TTTTTCCGAATTAATTTCTAATTAAATC-AAAAAAGATTCA
* ** *
10214 GATACTCATAAAAACAAATCCTTAAGTCCAATGTGACTGAGATTTGATCAGATGAATATAGATAT
129 GATGCTCGGAAAAACAAATCCTTAAGTCCAATGTGACTGAGATTTGATTAGATGAATATAGATAT
* * * * * * *
10279 TTCAAGTAGTCTCGGAACAAAAAAATCATGCAAAACTCAGCTGCGTACCCGAAACGCGTTTTTAG
194 TTCAAGTAGTCTCGGAGC-AAAAAATCATGCAAAATTGAGCCGGGTACTCGGAACGCGTTTTTAG
* * *
10344 CCAAACCCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAACTTGCCACGAAAGATTT
258 CCAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTG-AAAAATTGCCACAAAAGATTT
*
10409 TTCCTCAA
322 CTCCTCAA
* * * *
10417 TTTTTGGCTAAAATACTAATAAAAAATATATAATTCACCGCCAAAAAGATTCATGGGA-TTTTAA
1 TTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGATTTTTAA
* * * *
10481 CGTTTCTAATATCGTTTTTCCTATATTTCCGAATTATTTTCTAATTAAATCAAAAAAAGATTAAG
66 CGTTTCTAATATCGTTTTTCATATTTTTCCGAATTAATTTCTAATTAAATC-AAAAAAGATTCAG
*
10546 ATGCTCGGAAAAACAAATCTTTAAGTCCAATGTGACTGAGATTTGATTAGATGAATATAGATATT
130 ATGCTCGGAAAAACAAATCCTTAAGTCCAATGTGACTGAGATTTGATTAGATGAATATAGATATT
* *
10611 TCAAGTAGTCTCGGAGCAAAAAATCATGCAAAATTGAGCCAGGTA-TCCAGAACGCGTTTTTAGC
195 TCAAGTAGTCTCGGAGCAAAAAATCATGCAAAATTGAGCCGGGTACT-CGGAACGCGTTTTTAGC
10675 CAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGCCACAAAAGATTTC
259 CAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTG-AAAAATTGCCACAAAAGATTTC
10740 TCCTCAA
323 TCCTCAA
10747 TTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGATTTTAAT
1 TTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGG------AT
*
10812 TTTTAACGTTTCTAATATCGTTTTTCTTATTTTTCCCGAATTAATTTCTAATTAAATCAAAACAA
60 TTTTAACGTTTCTAATATCGTTTTTCATATTTTT-CCGAATTAATTTCTAATTAAATCAAAA-AA
** * *
10877 GATTCCCATGCTCGGAAAAACAAATCCTTCAGTCCAATGTGACTAAGATTTGATTAGATGAATAT
123 GATTCAGATGCTCGGAAAAACAAATCCTTAAGTCCAATGTGACTGAGATTTGATTAGATGAATAT
* * *
10942 AAATATTTCAAGTAGTCTCGGAGCCAAAAATTATGCAAAATTGAGCCGGGTACTCGGAACGCGTT
188 AGATATTTCAAGTAGTCTCGGAGCAAAAAATCATGCAAAATTGAGCCGGGTACTCGGAACGCGTT
*
11007 TTTAGCCAAAACCGTGATGGTTAGTACACGATTTCAAGCTAAAATTTTGAAAGAATTGCCA
253 TTTAGCCAAAACCGTGATGGTTAGTACACGATTTC-GGCTAAAATTTTGAAA-AATTGCCA
Statistics
Matches: 581, Mismatches: 55, Indels: 22
0.88 0.08 0.03
Matches are distributed among these distances:
330 158 0.27
331 179 0.31
332 7 0.01
336 1 0.00
337 36 0.06
338 179 0.31
339 21 0.04
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (329 bp):
TTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGATTTTTAA
CGTTTCTAATATCGTTTTTCATATTTTTCCGAATTAATTTCTAATTAAATCAAAAAAGATTCAGA
TGCTCGGAAAAACAAATCCTTAAGTCCAATGTGACTGAGATTTGATTAGATGAATATAGATATTT
CAAGTAGTCTCGGAGCAAAAAATCATGCAAAATTGAGCCGGGTACTCGGAACGCGTTTTTAGCCA
AAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGAAAAATTGCCACAAAAGATTTCTCC
TCAA
Done.