Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009522.1 Corchorus capsularis cultivar CVL-1 contig09543, 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: 19742
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1764 original size:2 final size:2
Alignment explanation
Indices: 1757--1782 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1747 CTCTAGCCAC
1757 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
1783 CTAGAAATAT
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:2093 original size:4 final size:4
Alignment explanation
Indices: 2084--2109 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2074 TCATGATCAT
2084 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
2110 ATGGGATTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:3298 original size:2 final size:2
Alignment explanation
Indices: 3291--3315 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3281 ACGAAGTTAC
3291 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3316 GGTAGAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3476 original size:9 final size:9
Alignment explanation
Indices: 3462--3488 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
3452 CTGAAAATTG
3462 AAAAAGACA
1 AAAAAGACA
3471 AAAAAGACA
1 AAAAAGACA
3480 AAAAAGACA
1 AAAAAGACA
3489 GTGGTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.11, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAAAGACA
Found at i:6245 original size:10 final size:10
Alignment explanation
Indices: 6230--6254 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6220 AGACATAGCT
6230 AGAAAGAGAG
1 AGAAAGAGAG
6240 AGAAAGAGAG
1 AGAAAGAGAG
6250 AGAAA
1 AGAAA
6255 TAGTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (10 bp):
AGAAAGAGAG
Found at i:8217 original size:324 final size:322
Alignment explanation
Indices: 6878--8313 Score: 1193
Period size: 324 Copynumber: 4.5 Consensus size: 322
6868 ATCTTGGGTT
* * * * * * * * * *
6878 CGAATGAATCTCTACTTAAATCTAAAACAAGATTCAAATGCCCGTTAAAACAAAACCTTATATTC
1 CGAATTAATTTCTAATTAAATC-GAAACAAGATTCAAATTCTCGTAAAAACAAATCCTTTTATCC
** ** * * **
6943 AATGTGGCTGGGATTTGGTTCCATGAATATTGATATTTGAAGGAGTCTTTCTGTTAAAAATCATG
65 AATGTGGCTGAAATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATG
* * ** *
7008 CAAAACTGAGTC-GGGTCCCGAAACACGTTTTT-TC-----CCAAAAACCGTG--A-C-GA-TTC
130 CAAAACTGAGTCTGGGCCCCGAAACACGTTTTTAGCAAAAAAAAAAAACAGTGATATCAGACTT-
** * ** * *
7061 CGGCAAAAAACTGACC-CGATATTTTTTTT-TGATTTTTTTAACACAATACTCAGAAAAAAATAT
194 CAACTAAAAACTGACCATAATTTTTTTTTTCTGAATTTTTTAACACAATACTCAG-AAAAAATAT
* * * *
7124 ATAATTCAACT-CAAAAAAGATTGACAGGTTTTTCACACTTCTAATATCGTTTTCCCATTTTTTT
258 ATAATTCAA-TGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTT
7188 C
322 C
* *
7189 CGAATTAATTTATAATTAAATCGAAACAAGATTCAGATTCTCGTAAAAACAAATCCTTTTA-CGC
1 CGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATTCTCGTAAAAACAAATCCTTTTATC-C
*
7253 AATGTGGCTGAAATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGTCAAAAATCATG
65 AATGTGGCTGAAATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATG
* * * *
7318 CAAAATTGA-ACTGGGCCCCGAAACACGTTTTTAGC------AAGAAACCGTGAT-TCA-ACTTA
130 CAAAACTGAGTCTGGGCCCCGAAACACGTTTTTAGCAAAAAAAAAAAACAGTGATATCAGACTT-
** * *** * * **
7374 CATTTTGCAAAAACTTACC-TGAA-AAATTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAA
194 CA-ACT--AAAAACTGACCAT-AATTTTTTTTTTCTGAATTTTTTAACACAATACTCAGAAAAAA
* * * ** * *
7437 TACATAATTCAATGCGAAAAAAATTGA-AGAATTTTCACGGTTCTAATATCATTTTTCCA-TTTT
255 TATATAATTCAATGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTT
**
7500 CCC
320 TTC
* * * * * * * ** *
7503 CGAATTTATTTCTAATTAAATTGTAATAAGATTCAAATGCTTGTAAAATCAAATCCTTAAATCTA
1 CGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATTCTCGTAAAAACAAATCCTTTTATCCA
* * * * *
7568 ATGCGGCTGAGATTTGGTTATATGAATATAGATATTTCAAGGAGTCATTT-TGCCGAAAATCATT
66 ATGTGGCTGAAATTTGGTTAGATGAATATAGATATTTCAAGGAGTC-TTTCTGCCAAAAATCATG
* * * * ** **** * *
7632 TAAAACTGAAT-TGGAGCCCCGAAACGCATTTTTAGCCCAAAAACCGTA-ATTGTTAATGCATGA
130 CAAAACTGAGTCTGG-GCCCCGAAACACGTTTTTAGCAAAAAAAAAAAACAGTGAT-AT-CA-GA
* ** * * * *
7695 TTTCGGCTAAACACTGACCCGA-AGATTTTTTTTTTTTTGAATTTTTCAACATAATACTCAGAAA
191 CTTCAACTAAAAACTGA-CC-ATA-A-TTTTTTTTTTCTGAATTTTTTAACACAATACTCAGAAA
** * * *
7759 AAATATATAATTCAACCCCTAAAAGATTGACGGGC-TTT-----TTC-ACTATCGTTTTTCCATT
252 AAATATATAATTCAATGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCATT
7817 TTTTTC
317 TTTTTC
* * * **
7823 CGAATAAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAAC-AATTTTTTATATCC
1 CGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATTCTCGTAAAAACAAATCCTTT-TATCC
** * *
7887 AATGTGGCTGAAATTTGGTTAGATGAAT-TCAGATATTTTGAGGATTCTTTCTGCCAAAAATCAC
65 AATGTGGCTGAAATTTGGTTAGATGAATAT-AGATATTTCAAGGAGTCTTTCTGCCAAAAATCAT
*
7951 ACAAAACTGAGTCAT-GGCCCCGAAACACGTTTTTAGCAAAAAAAAAAAACAGTGATGAGTACAC
129 GCAAAACTGAGTC-TGGGCCCCGAAACACGTTTTTAGCAAAAAAAAAAAACAGTGAT-A-T-CA-
*
8015 GACTTCAACTAAAAACTGACCATAATTTTTTTTTTCTGAATTTTTTAACACAATACTCA-TAAAA
189 GACTTCAACTAAAAACTGACCATAATTTTTTTTTTCTGAATTTTTTAACACAATACTCAGAAAAA
* * * *
8079 ATATATAATTCATTGCCAAAAAGATTGACGGGCTATTCACGCTTCTAATATTGTTTTTCCA-TTT
254 ATATATAATTCAATGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTT
8143 TTTC
319 TTTC
*
8147 CGAATTAATTTCTAATTAAATCAAAACAAGATTCAAATTCTCGTAAAAACAAATCCTTTTA-CGC
1 CGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATTCTCGTAAAAACAAATCCTTTTATC-C
* * * *
8211 AATGTGGCTGAAATTTGGTTGGATGCATATAAATATTTAAAGGAGTCTTTCTGCCAAAAATCATG
65 AATGTGGCTGAAATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATG
* * *
8276 CAAAATTGAG-CAGGACTCCCGAAACACGTTTTTAGCAA
130 CAAAACTGAGTCTGGGC-CCCGAAACACGTTTTTAGCAA
8314 GAATTACAAA
Statistics
Matches: 888, Mismatches: 180, Indels: 101
0.76 0.15 0.09
Matches are distributed among these distances:
309 1 0.00
310 127 0.14
311 19 0.02
312 2 0.00
313 3 0.00
314 120 0.14
315 50 0.06
316 44 0.05
317 21 0.02
318 33 0.04
319 55 0.06
320 141 0.16
321 18 0.02
322 23 0.03
323 8 0.01
324 145 0.16
325 77 0.09
326 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (322 bp):
CGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATTCTCGTAAAAACAAATCCTTTTATCCA
ATGTGGCTGAAATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGC
AAAACTGAGTCTGGGCCCCGAAACACGTTTTTAGCAAAAAAAAAAAACAGTGATATCAGACTTCA
ACTAAAAACTGACCATAATTTTTTTTTTCTGAATTTTTTAACACAATACTCAGAAAAAATATATA
ATTCAATGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTC
Found at i:8310 original size:644 final size:618
Alignment explanation
Indices: 6878--8311 Score: 1444
Period size: 644 Copynumber: 2.3 Consensus size: 618
6868 ATCTTGGGTT
* * * * * * *
6878 CGAATGAATCTCTACTTAAATCTAAAACAAGATTCAAATGCCCGTTAAAACAAAACCTTATATTC
1 CGAATTAATTTCTAATTAAATC-AAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTATA-CC
* * * * **
6943 AATGTGGCTGGGATTTGGTTCCATGAATATTGATATTTGAAGGAGTCTTTCTGTTAAAAATCATG
64 AATGTGGCTGAGATTTGGTTACATGAATATAGATATTTAAAGGAGTCTTTCTGCCAAAAATCATG
* *
7008 CAAAACTGAGTCGG-GTCCCGAAACACGTTTTT-TCCCAAAAACCGTGACGATTCCGGCAAAAAA
129 CAAAACTGAG-CGGACTCCCGAAACACGTTTTTAGCCCAAAAACCGTGACGATTCCGGCAAAAAA
* * *
7071 CTGACCCGATATTTTTTTTTGATTTTTTTAACACAATACTCAGAAAAAAATATATAATTCAACTC
193 CTGACCCGATATTTTTTTTTGAATTTTTCAACACAATACTCAGAAAAAAATATATAATTCAACCC
*
7136 AAAAAAGATTGACAGGTTTTTCACACTTCTAATATCGTTTTCCCATTTTTTTCCGAATTAATTTA
258 AAAAAAGATTGACAGGTTTTT-ACA--TC--ATATCGTTTTCCCATTTTTTTCCGAATAAATTTA
*
7201 TAATTAAATCGAAACAAGATTCAGATTCTCGTAAAAACAAATCCTTTTACGCAATGTGGCTGAAA
318 TAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTTTACGCAATGTGGCTGAAA
* ** *
7266 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGTCAAAAATCATGCAAAATTGAACTG
383 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCACACAAAACTGAACTG
* * ** *
7331 GGCCCCGAAACACGTTTTTAGCAAGAAACCGTGATTCAACTTACATTTTGCAAAAACTTACCTGA
448 GGCCCCGAAACACGTTTTTAGCAAAAAACAGTGATTCAACTTACATACT-CAAAAACTGACCTGA
** *
7396 AAAATTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATACATAATTCAATGCGAAAAAAAT
512 AAAATTTTTCCTCAATTTTTTAACACAATACTCAGAAAAAATACATAATTCAATGCCAAAAAAAT
* *
7461 TGAAGAATTTTCACGGTTCTAATATCATTTTTCCATTTTCCC
577 TGAAGAATATTCACGCTTCTAATATCATTTTTCCATTTTCCC
* *** * * * * *
7503 CGAATTTATTTCTAATTAAATTGTAATAAGATTCAAATGCTTGTAAAATCAAATCCTTAAATCTA
1 CGAATTAATTTCTAATTAAATCAAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTATA-CCA
* * * * *
7568 ATGCGGCTGAGATTTGGTTATATGAATATAGATATTTCAAGGAGTCATTT-TGCCGAAAATCATT
65 ATGTGGCTGAGATTTGGTTACATGAATATAGATATTTAAAGGAGTC-TTTCTGCCAAAAATCATG
* ** * *
7632 TAAAACTGAATTGGAGC-CCCGAAACGCATTTTTAGCCCAAAAACCGTAATTGTTAATGCATGAT
129 CAAAACTG-AGCGGA-CTCCCGAAACACGTTTTTAGCCCAAAAACCG----TG---A--C--GAT
* * * * *
7696 TTCGGCTAAACACTGACCCGAAGATTTTTTTTTTTTTGAATTTTTCAACATAATACTCAG-AAAA
181 TCCGGCAAAAAACTGACCC---GA--TATTTTTTTTTGAATTTTTCAACACAATACTCAGAAAAA
** * *
7760 AATATATAATTCAACCCCTAAAAGATTGACGGGCTTTTT-CA-C-TATCGTTTTTCCATTTTTTT
241 AATATATAATTCAACCCAAAAAAGATTGACAGG-TTTTTACATCATATCGTTTTCCCATTTTTTT
* **
7822 CCGAATAAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAAC-AATTTTTTATATC
305 CCGAATAAATTTATAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTT-TA-C
** *
7886 -CAATGTGGCTGAAATTTGGTTAGATGAAT-TCAGATATTTTGAGGATTCTTTCTGCCAAAAATC
368 GCAATGTGGCTGAAATTTGGTTAGATGAATAT-AGATATTTCAAGGAGTCTTTCTGCCAAAAATC
*
7949 ACACAAAACTGAGTCAT-GGCCCCGAAACACGTTTTTAGCAAAAAAAAAAAACAGTGATGAGTAC
432 ACACAAAACTGA-AC-TGGGCCCCGAAACACGTTTTTAGC------AAAAAACAGTGAT---T-C
*** * *
8013 ACGACTT-CA-ACT-AAAAACTGACCAT-AATTTTTTTTTTCTGAATTTTTTAACACAATACTCA
485 A--ACTTACATACTCAAAAACTGACC-TGAA-AAATTTTTCCTCAATTTTTTAACACAATACTCA
* * * * * ** **
8074 -TAAAAATATATAATTCATTGCCAAAAAGATTGACGGGCTATTCACGCTTCTAATATTGTTTTTC
546 GAAAAAATACATAATTCAATGCCAAAAAAATTGA-AGAATATTCACGCTTCTAATATCATTTTTC
**
8138 CATTTTTTC
610 CATTTTCCC
* *
8147 CGAATTAATTTCTAATTAAATCAAAACAAGATTCAAATTCTCGTAAAAACAAATCCTTTTACGCA
1 CGAATTAATTTCTAATTAAATCAAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTATAC-CA
* ** * *
8212 ATGTGGCTGAAATTTGGTTGGATGCATATAAATATTTAAAGGAGTCTTTCTGCCAAAAATCATGC
65 ATGTGGCTGAGATTTGGTTACATGAATATAGATATTTAAAGGAGTCTTTCTGCCAAAAATCATGC
*
8277 AAAATTGAGCAGGACTCCCGAAACACGTTTTTAGC
130 AAAACTGAGC-GGACTCCCGAAACACGTTTTTAGC
8312 AAGAATTACA
Statistics
Matches: 653, Mismatches: 110, Indels: 73
0.78 0.13 0.09
Matches are distributed among these distances:
624 91 0.14
625 35 0.05
626 11 0.02
630 2 0.00
633 8 0.01
634 135 0.21
635 25 0.04
636 1 0.00
637 20 0.03
640 4 0.01
641 44 0.07
642 35 0.05
643 46 0.07
644 187 0.29
645 3 0.00
646 2 0.00
647 4 0.01
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (618 bp):
CGAATTAATTTCTAATTAAATCAAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTATACCAA
TGTGGCTGAGATTTGGTTACATGAATATAGATATTTAAAGGAGTCTTTCTGCCAAAAATCATGCA
AAACTGAGCGGACTCCCGAAACACGTTTTTAGCCCAAAAACCGTGACGATTCCGGCAAAAAACTG
ACCCGATATTTTTTTTTGAATTTTTCAACACAATACTCAGAAAAAAATATATAATTCAACCCAAA
AAAGATTGACAGGTTTTTACATCATATCGTTTTCCCATTTTTTTCCGAATAAATTTATAATTAAA
TCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTTTACGCAATGTGGCTGAAATTTGGTTA
GATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCACACAAAACTGAACTGGGCCCCGA
AACACGTTTTTAGCAAAAAACAGTGATTCAACTTACATACTCAAAAACTGACCTGAAAAATTTTT
CCTCAATTTTTTAACACAATACTCAGAAAAAATACATAATTCAATGCCAAAAAAATTGAAGAATA
TTCACGCTTCTAATATCATTTTTCCATTTTCCC
Found at i:19662 original size:33 final size:33
Alignment explanation
Indices: 19607--19722 Score: 103
Period size: 33 Copynumber: 3.5 Consensus size: 33
19597 GGCGAAACCA
* *
19607 CCCCACTTGGGAGGC-TCAACCAT-GGCGAAGCCG
1 CCCCACTGGGGCGGCTTC-ACCATGGGC-AAGCCG
** * *
19640 TTCCACTGGGGCGGTTTCACCATGGGCAGGCCG
1 CCCCACTGGGGCGGCTTCACCATGGGCAAGCCG
** *
19673 CCCCACTGGGGCGGCTTCACCAT-GAAAAGGTCG
1 CCCCACTGGGGCGGCTTCACCATGGGCAA-GCCG
19706 CCCCACTGGGGCGGCTT
1 CCCCACTGGGGCGGCTT
19723 AGCCACGGCA
Statistics
Matches: 67, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
32 2 0.03
33 60 0.90
34 5 0.07
ACGTcount: A:0.16, C:0.34, G:0.33, T:0.16
Consensus pattern (33 bp):
CCCCACTGGGGCGGCTTCACCATGGGCAAGCCG
Done.