Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009228.1 Corchorus capsularis cultivar CVL-1 contig09249, 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: 36124
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:6499 original size:10 final size:10
Alignment explanation
Indices: 6484--6511 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
6474 TAATATACTC
6484 TCTCTGTCTT
1 TCTCTGTCTT
6494 TCTCTGTCTT
1 TCTCTGTCTT
6504 TCTCTGTC
1 TCTCTGTC
6512 AGCTAGGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.32, G:0.11, T:0.57
Consensus pattern (10 bp):
TCTCTGTCTT
Found at i:35994 original size:317 final size:318
Alignment explanation
Indices: 34644--36124 Score: 1459
Period size: 317 Copynumber: 4.6 Consensus size: 318
34634 CTTTTTTTAT
* * * ** *
34644 ATCGAAACGAGATTCAGATGCACGTAA-GAACAAATCCTTAAACCCAATGTGG-TAGAGATTTGA
1 ATCGAAACAAGATTCAGATGCTCGTAATG-GCAAATCCTTAAATGCAATGTGGCT-GAGATTTGG
* * * * * ** * * * * *
34707 TTAGATAAATAAAGATATTTAAAGGAGACTCGATGCCAAAAATCATGCGAAAC-AGAGCTGTGGC
64 TTAGATGAATATATATATTTCAAGGAGTCTTTAAGCCAAAAATCATTCAAAACTA-AGCCGAGGC
** * * * * * *
34771 ACTTG-AACGCGTTTTTAGTC-AAAAATCGTGATGGTTA-GTACATGATTTCGGC-AAAACACTG
128 -CCCGAAACGCATTTTTAG-CAAAAAACCGTGATAGTAACATACACGATTTCGGCTAAAA-ACTG
* * * * ** *
34832 ACCCGAAATGTTTTTTTTTTCTCAA-TTTTTGCAACAATACTAATAAA-AATTATATATTTCGAC
190 ACCCGAAA----ATTTTTTTCTCAATTTTTTGCCACAATACTCATAAATAA-TATATAATTAAAT
* * * * * * *
34895 ACCAACAAGATTG-ACGGTTTTTCATGCTTCTAATATCGTTTTTTTTTTCTGAATTAATCTCTAA
250 GCCAAAAAGATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTTTTTTTCTGAATTTATTTCTAA
34959 TTAA
315 TTAA
*** * * * *
34963 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATATGGAC-GACATTTGGT
1 ATCGAAACAAGATTCAGATGCTCGTAATGGCAAATCCTTAAATGCAATGTGG-CTGAGATTTGGT
* * * * * * * * * *
35027 TTGATTAATATAAAAATTTCAAGGAGT-TTTCACGCCAAAAATCATGCAAAATTGAGCCGGGGCT
65 TAGATGAATATATATATTTCAAGGAGTCTTT-AAGCCAAAAATCATTCAAAACTAAGCCGAGGCC
* * * * * *
35091 CCGAAACGCGTTTTTAGCCAAAAATCGTGATGGGTTA-ATACATGATTTCGGC-AAAAATTTTGC
129 CCGAAACGCATTTTTAGCAAAAAACCGTGAT-AGTAACATACACGATTTCGGCTAAAAA-----C
** * * * * * *
35154 AGAAATTGACCCGAAAGGTTTTTCCTCCACTTTCTGCCACAATACTAAGGAAA-AATATATAATT
188 ------TGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCA-TAAATAATATATAATT
*
35218 AACA-GCCAAAAAAATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCAAATTTTTTTTTCT
246 AA-ATGCCAAAAAGATTGAAGGGGTTTTCACGCTTCTAATATCG----T-----TTTTTTTTTCT
35282 GAATTTATTTCTAATTAA
301 GAATTTATTTCTAATTAA
* * * *
35300 ATCGAAACAAGATTCATATGCTCGTAAAGCCAAATCCTTAAATCCAATGTGGCTGAGATTTGGTT
1 ATCGAAACAAGATTCAGATGCTCGTAATGGCAAATCCTTAAATGCAATGTGGCTGAGATTTGGTT
* * *
35365 AGATGAATGTAGATATTTCAAGGAGTCTTTATGCCAAAAAT-ATTCAAAACTGAA-CCGAGGCCC
66 AGATGAATATATATATTTCAAGGAGTCTTTAAGCCAAAAATCATTCAAAACT-AAGCCGAGGCCC
*
35428 CGAAACG-AGTTTTTAGTC-AAAAACCGTGATAGTTAAC--ACATGATTTCGGCTAAAAACTGAC
130 CGAAACGCA-TTTTTAG-CAAAAAACCGTGATAG-TAACATACACGATTTCGGCTAAAAACTGAC
* * *
35489 CCG-AAATTTTTTTCTCAATTTTTTGTCACATTACTCATAAATAATATATAATTCAATGCCAAAA
192 CCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCATAAATAATATATAATTAAATGCCAAAA
*
35553 AGATTGAAGGGGTTTTCACGCTTCTAATATC--ATTTTTTTTCTGAATTTATTTCTAATTAA
257 AGATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTTTTTTTCTGAATTTATTTCTAATTAA
* * *
35613 ATCGAAACAAGATTAAGATGCTCGTAATGGCAAATCCTTTAATGCAATGTGGCTGAGCTTTGGTT
1 ATCGAAACAAGATTCAGATGCTCGTAATGGCAAATCCTTAAATGCAATGTGGCTGAGATTTGGTT
*
35678 AGATGAATATATATATTTGAAGGAGTCTTTAAGCCAAAAATCATTCAAAACTAAGCCGAGGCCCC
66 AGATGAATATATATATTTCAAGGAGTCTTTAAGCCAAAAATCATTCAAAACTAAGCCGAGGCCCC
* *
35743 GAAACGCATTTTTAGCAAAAAACTGTGAT-GTAACATACACGATTTCAGCTAAAAACTGACCCGA
131 GAAACGCATTTTTAGCAAAAAACCGTGATAGTAACATACACGATTTCGGCTAAAAACTGACCCGA
*
35807 AAATTTTTTTCTCAATTTTTTGCCACAATACTCCTAAATAATATATAATTAAATGCCAAAAAGAT
196 AAATTTTTTTCTCAATTTTTTGCCACAATACTCATAAATAATATATAATTAAATGCCAAAAAGAT
* * *
35872 TGTAGTGGTTTTCACGCTTCTAATATCGTTTTTTTTTTATGAATTTATTTCTAATTAA
261 TGAAGGGGTTTTCACGCTTCTAATATCGTTTTTTTTTTCTGAATTTATTTCTAATTAA
*
35930 ATCGAAACAAGATTCGGATGCTCGTAATGGCAAATCCTTAAATGCAATGTGGCTGAGATTTGGTT
1 ATCGAAACAAGATTCAGATGCTCGTAATGGCAAATCCTTAAATGCAATGTGGCTGAGATTTGGTT
* * * * *
35995 GGATGAATATATATATTTCAAGGAGTCTTTAGGCCAAAAATCATTCAATACTGAGTCGAGGCCCC
66 AGATGAATATATATATTTCAAGGAGTCTTTAAGCCAAAAATCATTCAAAACTAAGCCGAGGCCCC
* * * * * *
36060 AAAACGCGTTTTTAGCAAAAAACCGTGATGGTTA-ATACACGATTTTGGCTAAAAATTGACCCGA
131 GAAACGCATTTTTAGCAAAAAACCGTGATAGTAACATACACGATTTCGGCTAAAAACTGACCCGA
36124 A
196 A
Statistics
Matches: 992, Mismatches: 118, Indels: 106
0.82 0.10 0.09
Matches are distributed among these distances:
312 4 0.00
313 127 0.13
314 69 0.07
315 87 0.09
317 201 0.20
318 6 0.01
319 124 0.12
320 23 0.02
323 4 0.00
324 75 0.08
325 7 0.01
326 9 0.01
327 34 0.03
328 28 0.03
330 10 0.01
331 1 0.00
332 1 0.00
335 14 0.01
336 48 0.05
337 117 0.12
338 3 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (318 bp):
ATCGAAACAAGATTCAGATGCTCGTAATGGCAAATCCTTAAATGCAATGTGGCTGAGATTTGGTT
AGATGAATATATATATTTCAAGGAGTCTTTAAGCCAAAAATCATTCAAAACTAAGCCGAGGCCCC
GAAACGCATTTTTAGCAAAAAACCGTGATAGTAACATACACGATTTCGGCTAAAAACTGACCCGA
AAATTTTTTTCTCAATTTTTTGCCACAATACTCATAAATAATATATAATTAAATGCCAAAAAGAT
TGAAGGGGTTTTCACGCTTCTAATATCGTTTTTTTTTTCTGAATTTATTTCTAATTAA
Done.