Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014563.1 Corchorus capsularis cultivar CVL-1 contig14584, 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: 1866
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Found at i:773 original size:325 final size:322
Alignment explanation
Indices: 1--1766 Score: 2453
Period size: 321 Copynumber: 5.5 Consensus size: 322
* * * *
1 AAAATATATATTTCAATTCCAAAAATATTGACAGACTTTTCACACTTCTAATATCATTTTTCCAT
1 AAAATATATAATTCAATGCCAAAAATATTGACAGACTTTTCACGCTTCTAATATCGTTTTTCCAT
* * *
66 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGTTCG-AAAAACAAATCCCT
66 TTTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTGAGATGCTCGAAAAAACAAATCCTT
* *
130 ATATCCAATGTTGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTATG-CAAAG
131 ATATCCAATATTGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAA-
*
194 AATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTAC
195 AATCATGCAAAATTGAGCC-GGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTAC
*
259 ACAA-TTTGGACTAAAAACTGACCCGAAATTTTTTCTTTCTCAATTTTTTGCCACAATACACAGA
259 ACAATTTTGG-CTAAAAACTGACCCGAAAATTTTT-TTTCTCAATTTTTTGCCACAATACACAGA
323 A
322 A
*
324 AAAATATATAATTCAATGCCAAAAATATTGACAGACTTTACACGCTTCTAATATCGTTTTTCCAT
1 AAAATATATAATTCAATGCCAAAAATATTGACAGACTTTTCACGCTTCTAATATCGTTTTTCCAT
* * *
389 TTTTTTCCGAATTAATTTCTAATTAAATCTAAATAAGATTAAGATGCTCAAAAAAACAAATCCTT
66 TTTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTGAGATGCTCGAAAAAACAAATCCTT
* ** * *
454 ATATCCAATATTGCTGAGATTTGGTTCGATGAGTATAGGGATTTCAAGGAGTGTTTGTGCCAATA
131 ATATCCAATATTGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAA
* * *
519 ATCATGCAAAATTAAGCCGAGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGCTTAGTTCA
196 ATCATGCAAAATTGAGCCG-GGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
* *
584 CAATTTTGGCTAAAAACTGACCCGAAAATTTTTTTTCTTAATTTTTTGCCACAATACAAAGAAAA
260 CAATTTTGGCTAAAAACTGACCCGAAAATTTTTTTTCTCAATTTTTTGCCACAATACACAG--AA
* *
649 AAAATATATAATTCAATGCCAAAAATATTGACAGACCTTACACGCTTCTAATATCGTTTTTCCAT
1 AAAATATATAATTCAATGCCAAAAATATTGACAGACTTTTCACGCTTCTAATATCGTTTTTCCAT
* * * * *
714 TTTTTTCCGAATTAATTTCTATTTCAATCTAAATAAGATTAAGATGCTCAAAAAAACAAATCCTT
66 TTTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTGAGATGCTCGAAAAAACAAATCCTT
* * ** *
779 TTATCCAATATTGCTGAGATTTGGTTCGATGAGTATAGGGATTTCAAGGAGTGTTTGTGCCAAAA
131 ATATCCAATATTGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAA
* *
844 ATGATGCAAAATTAAGCCGAGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
196 ATCATGCAAAATTGAGCCG-GGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
* **
909 CAATTTTGACTAAAAACTGACCC-AAAATTTCGTTTCTCAATTTTTTGCCACAATACACAG-A
260 CAATTTTGGCTAAAAACTGACCCGAAAATTTTTTTTCTCAATTTTTTGCCACAATACACAGAA
* * *
970 AAAATATATAATTCAATGCCAAAAATATTGACGGACTTTTTACGCTTCCAATATCGTTTTTCCAT
1 AAAATATATAATTCAATGCCAAAAATATTGACAGACTTTTCACGCTTCTAATATCGTTTTTCCAT
*
1035 TTTTTTCCGAATCAATTTCTAATTAAATCGAAATAAGATTGAGATGCTCGAAAAAACAAATCCTT
66 TTTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTGAGATGCTCGAAAAAACAAATCCTT
* ** * * *
1100 TTATCCAATATTGCTGAGATTTGGTTTAAAGTATATAGATATTTCAAGGAGTCTTTGTACCAAAA
131 ATATCCAATATTGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAA
* * *
1165 ATCATGCAAAATTGAGTCGGAGCTACGGAACGCG-TTTAAGCC----ACCGTGAT-G-TAGTACA
196 ATCATGCAAAATTGAGCCGG-GCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
* * *
1223 CAATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCCTCAATTTTTTGCCACAATACGCAGAA
260 CAATTTTGGCTAAAAACTGACCCGAAAATTTTTTTTCTCAATTTTTTGCCACAATACACAGAA
** * * * * * *
1286 AAAGCATATAATTTACTGCCAGATATATTGACGGTCTTTTCACGCTTCTAATATCGTTTTTCCAT
1 AAAATATATAATTCAATGCCAAAAATATTGACAGACTTTTCACGCTTCTAATATCGTTTTTCCAT
* *
1351 TTTTTTCCGAATTAATTTTTAATTAAATCGAAATAAGATTGAGATGCTCGAAAAAACAAATCCTG
66 TTTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTGAGATGCTCGAAAAAACAAATCCTT
* * ***
1416 ATATCCAATATTGTTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTTTTTACACCAAAA
131 ATATCCAATATTGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAA
** * ** * * **
1481 ATCATGTGAAATTGAGCCGGTGCTCCGAAACGAATTTTTTGCCAAAAATCGTGATGGTTAGTGGA
196 ATCATGCAAAATTGAGCCGG-GCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
* * * * * *
1546 CAATTTTGGATAAAAACTGA-CC-AAAAATTTTTTTCTTAATTTTTTACCACAACATACAGAA
260 CAATTTTGGCTAAAAACTGACCCGAAAATTTTTTTTCTCAATTTTTTGCCACAATACACAGAA
* * * *
1607 AAAATATATAATTCAATGCCAAAAATATTGACGGATTTTTTAGGCTTCTAATATCGTTTTTCCAT
1 AAAATATATAATTCAATGCCAAAAATATTGACAGACTTTTCACGCTTCTAATATCGTTTTTCCAT
* * * * *
1672 TTTTTTCCGAATTAATTTCCAATTAAATCGAAACAAGATTTAGATGCTCGAAATAACAAATTCTT
66 TTTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTGAGATGCTCGAAAAAACAAATCCTT
* *
1737 ATATCTAATATTGCTAAGATTTGGTTCGAT
131 ATATCCAATATTGCTGAGATTTGGTTCGAT
1767 ATATATATAA
Statistics
Matches: 1295, Mismatches: 132, Indels: 34
0.89 0.09 0.02
Matches are distributed among these distances:
314 28 0.02
315 34 0.03
316 209 0.16
317 6 0.00
320 8 0.01
321 383 0.30
322 3 0.00
323 155 0.12
324 185 0.14
325 284 0.22
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (322 bp):
AAAATATATAATTCAATGCCAAAAATATTGACAGACTTTTCACGCTTCTAATATCGTTTTTCCAT
TTTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTGAGATGCTCGAAAAAACAAATCCTT
ATATCCAATATTGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAA
ATCATGCAAAATTGAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACAC
AATTTTGGCTAAAAACTGACCCGAAAATTTTTTTTCTCAATTTTTTGCCACAATACACAGAA
Found at i:1564 original size:637 final size:639
Alignment explanation
Indices: 1--1763 Score: 2459
Period size: 637 Copynumber: 2.7 Consensus size: 639
* * * * *
1 AAAATATATATTTCAATTCCAAAAATATTGACAGACTTTTCACACTTCTAATATCATTTTTCCAT
1 AAAACATATAATTCAATGCCAAAAATATTGACAGACTTTTCACGCTTCTAATATCGTTTTTCCAT
* *
66 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGTTCG-AAAAACAAATCCCT
66 TTTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTGAGATGCTCGAAAAAACAAAT-CCT
* **
130 ATATCCAATGTTGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTATGCAAAGA
130 ATATCCAATATTGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTAACCAAA-A
*
195 ATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACA
194 ATCATGCAAAATTGAGCC-GGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
*
260 CAA-TTTGGACTAAAAACTGACCCGAAATTTTTTCTTTCTCAATTTTTTGCCACAATACACAGAA
258 CAATTTTGGACTAAAAACTGACCC-AAA--ATTTCTTTCTCAATTTTTTGCCACAATACACAGAA
* **
324 AAAATATATAATTCAATGCCAAAAATATTGACAGACTTTACACGCTTCTAATATCGTTTTTCCAT
320 AAAATATATAATTCAATGCCAAAAATATTGACGGACTTTTTACGCTTCTAATATCGTTTTTCCAT
* *
389 TTTTTTCCGAATTAATTTCTAATTAAATCTAAATAAGATTAAGATGCTCAAAAAAACAAATCCTT
385 TTTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTAAGATGCTCGAAAAAACAAATCCTT
* * * * * *
454 ATATCCAATATTGCTGAGATTTGGTTCGATGAGTATAGGGATTTCAAGGAGTGTTTGTGCCAATA
450 ATATCCAATATTGCTGAGATTTGGTTCAAAGAGTATAGAGATTTCAAGGAGTCTTTGTACCAAAA
* * *
519 ATCATGCAAAATTAAGCCGAGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGCTTAGTTCA
515 ATCATGCAAAATTAAGCCGAGGCTACGGAACGCGTTTTAAGCC---AACCGTGATGC-TAGTACA
* * *
584 CAATTTTGGCTAAAAACTGACCCGAAAATTTTTTTTCTTAATTTTTTGCCACAATACAAAGAAAA
576 CAATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCCTCAATTTTTTGCCACAATACAAAG-AAA
* * *
649 AAAATATATAATTCAATGCCAAAAATATTGACAGACCTTACACGCTTCTAATATCGTTTTTCCAT
1 AAAACATATAATTCAATGCCAAAAATATTGACAGACTTTTCACGCTTCTAATATCGTTTTTCCAT
* * * * *
714 TTTTTTCCGAATTAATTTCTATTTCAATCTAAATAAGATTAAGATGCTCAAAAAAACAAATCCTT
66 TTTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTGAGATGCTCGAAAAAACAAATCC-T
* * ** * **
779 TTATCCAATATTGCTGAGATTTGGTTCGATGAGTATAGGGATTTCAAGGAGTGTTTGTGCCAAAA
130 ATATCCAATATTGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT-AACCAAAA
* *
844 ATGATGCAAAATTAAGCCGAGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
194 ATCATGCAAAATTGAGCCG-GGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
909 CAATTTT-GACTAAAAACTGACCCAAAATTTCGTTTCTCAATTTTTTGCCACAATACACAG-AAA
258 CAATTTTGGACTAAAAACTGACCCAAAATTTC-TTTCTCAATTTTTTGCCACAATACACAGAAAA
*
972 AATATATAATTCAATGCCAAAAATATTGACGGACTTTTTACGCTTCCAATATCGTTTTTCCATTT
322 AATATATAATTCAATGCCAAAAATATTGACGGACTTTTTACGCTTCTAATATCGTTTTTCCATTT
* * *
1037 TTTTCCGAATCAATTTCTAATTAAATCGAAATAAGATTGAGATGCTCGAAAAAACAAATCCTTTT
387 TTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTAAGATGCTCGAAAAAACAAATCCTTAT
* *
1102 ATCCAATATTGCTGAGATTTGGTTTAAAGTA-TATAGATATTTCAAGGAGTCTTTGTACCAAAAA
452 ATCCAATATTGCTGAGATTTGGTTCAAAG-AGTATAGAGATTTCAAGGAGTCTTTGTACCAAAAA
* *
1166 TCATGCAAAATTGAGTCG-GAGCTACGGAACGCG-TTTAAGCC-ACCGTGATG-TAGTACACAAT
516 TCATGCAAAATTAAGCCGAG-GCTACGGAACGCGTTTTAAGCCAACCGTGATGCTAGTACACAAT
**
1227 TTCGGCTAAAAACTGACCCGAAAATTTTTTTCCTCAATTTTTTGCCACAATACGCAG-AA
580 TTCGGCTAAAAACTGACCCGAAAATTTTTTTCCTCAATTTTTTGCCACAATACAAAGAAA
* * * * * * *
1286 AAAGCATATAATTTACTGCCAGATATATTGACGGTCTTTTCACGCTTCTAATATCGTTTTTCCAT
1 AAAACATATAATTCAATGCCAAAAATATTGACAGACTTTTCACGCTTCTAATATCGTTTTTCCAT
*
1351 TTTTTTCCGAATTAATTTTTAATTAAATCGAAATAAGATTGAGATGCTCGAAAAAACAAATCCTG
66 TTTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTGAGATGCTCGAAAAAACAAATCCT-
* *
1416 ATATCCAATATTGTTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTTTTTACACCAAAA
130 ATATCCAATATTGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTA-ACCAAAA
** * ** * * **
1481 ATCATGTGAAATTGAGCCGGTGCTCCGAAACGAATTTTTTGCCAAAAATCGTGATGGTTAGTGGA
194 ATCATGCAAAATTGAGCCGG-GCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
* * * * * *
1546 CAATTTTGGA-TAAAAACTGACCAAAAATTTTTTTCTTAATTTTTTACCACAACATACAGAAAAA
258 CAATTTTGGACTAAAAACTGACCCAAAATTTCTTTCTCAATTTTTTGCCACAATACACAGAAAAA
* *
1610 ATATATAATTCAATGCCAAAAATATTGACGGATTTTTTAGGCTTCTAATATCGTTTTTCCATTTT
323 ATATATAATTCAATGCCAAAAATATTGACGGACTTTTTACGCTTCTAATATCGTTTTTCCATTTT
* * * * *
1675 TTTCCGAATTAATTTCCAATTAAATCGAAACAAGATTTAGATGCTCGAAATAACAAATTCTTATA
388 TTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTAAGATGCTCGAAAAAACAAATCCTTATA
* *
1740 TCTAATATTGCTAAGATTTGGTTC
453 TCCAATATTGCTGAGATTTGGTTC
1764 GATATATATA
Statistics
Matches: 995, Mismatches: 107, Indels: 37
0.87 0.09 0.03
Matches are distributed among these distances:
636 26 0.03
637 393 0.39
638 2 0.00
639 62 0.06
641 9 0.01
645 8 0.01
646 210 0.21
647 29 0.03
648 108 0.11
649 141 0.14
650 7 0.01
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (639 bp):
AAAACATATAATTCAATGCCAAAAATATTGACAGACTTTTCACGCTTCTAATATCGTTTTTCCAT
TTTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTGAGATGCTCGAAAAAACAAATCCTA
TATCCAATATTGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTAACCAAAAAT
CATGCAAAATTGAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAA
TTTTGGACTAAAAACTGACCCAAAATTTCTTTCTCAATTTTTTGCCACAATACACAGAAAAAATA
TATAATTCAATGCCAAAAATATTGACGGACTTTTTACGCTTCTAATATCGTTTTTCCATTTTTTT
CCGAATTAATTTCTAATTAAATCGAAATAAGATTAAGATGCTCGAAAAAACAAATCCTTATATCC
AATATTGCTGAGATTTGGTTCAAAGAGTATAGAGATTTCAAGGAGTCTTTGTACCAAAAATCATG
CAAAATTAAGCCGAGGCTACGGAACGCGTTTTAAGCCAACCGTGATGCTAGTACACAATTTCGGC
TAAAAACTGACCCGAAAATTTTTTTCCTCAATTTTTTGCCACAATACAAAGAAA
Found at i:1772 original size:2 final size:2
Alignment explanation
Indices: 1765--1825 Score: 81
Period size: 2 Copynumber: 30.0 Consensus size: 2
1755 ATTTGGTTCG
1765 AT AT AT AT AT A- AGT AT AT AT AT AT ACT AT AT AT A- AGT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT A-T AT AT
1806 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1826 TTCATGGAGT
Statistics
Matches: 54, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
1 2 0.04
2 48 0.89
3 4 0.07
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1794 original size:23 final size:22
Alignment explanation
Indices: 1765--1820 Score: 103
Period size: 23 Copynumber: 2.5 Consensus size: 22
1755 ATTTGGTTCG
1765 ATATATATATAAGTATATATAT
1 ATATATATATAAGTATATATAT
1787 ATACTATATATAAGTATATATAT
1 ATA-TATATATAAGTATATATAT
1810 ATATATATATA
1 ATATATATATA
1821 TATATTTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 11 0.33
23 22 0.67
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (22 bp):
ATATATATATAAGTATATATAT
Done.