Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011312.1 Corchorus capsularis cultivar CVL-1 contig11333, 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: 9087
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Found at i:106 original size:19 final size:20
Alignment explanation
Indices: 79--116 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
69 TACTATTAGT
79 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
99 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
117 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:397 original size:66 final size:66
Alignment explanation
Indices: 281--411 Score: 156
Period size: 66 Copynumber: 2.0 Consensus size: 66
271 TTGTCGCTAT
* ** * * *
281 GTGGTTATCAAAATTTCATAAGATGGTTACTATAATTTCATGAGGAGGTTATCGAAATTCCATAG
1 GTGGTTACCAAAATTTCATAAGAAAGTTACTAAAATTTCATGAGGAGGTTACCAAAATTCCATAG
346 C
66 C
* * * *
347 GTGGTTACCAAAATTTCATATGAAAGTTATTAAAATTTCAT-AGTGTGGTTACCAAAATTTCATA
1 GTGGTTACCAAAATTTCATAAGAAAGTTACTAAAATTTCATGAG-GAGGTTACCAAAATTCCATA
411 G
65 G
412 GATCAGGTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 2 0.04
66 52 0.96
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (66 bp):
GTGGTTACCAAAATTTCATAAGAAAGTTACTAAAATTTCATGAGGAGGTTACCAAAATTCCATAG
C
Found at i:463 original size:22 final size:22
Alignment explanation
Indices: 281--465 Score: 131
Period size: 22 Copynumber: 8.3 Consensus size: 22
271 TTGTCGCTAT
*
281 GTGGTTATCAAAATTTCATAAG
1 GTGGTTATCAAAATTTCATAGG
* *
303 ATGGTTA-CTATAATTTCAT-GAG
1 GTGGTTATC-AAAATTTCATAG-G
* * * *
325 GAGGTTATCGAAATTCCATAGC
1 GTGGTTATCAAAATTTCATAGG
* *
347 GTGGTTACCAAAATTTCATATG
1 GTGGTTATCAAAATTTCATAGG
*** * *
369 AAAGTTATTAAAATTTCATAGT
1 GTGGTTATCAAAATTTCATAGG
*
391 GTGGTTACCAAAATTTCATAGG
1 GTGGTTATCAAAATTTCATAGG
* * *
413 ATCAGGTTATTAAAATTTCTTAGG
1 GT--GGTTATCAAAATTTCATAGG
* **
437 TTGGTTATTGAAATTTCATAGG
1 GTGGTTATCAAAATTTCATAGG
459 GTGGTTA
1 GTGGTTA
466 ATTTTCACAA
Statistics
Matches: 121, Mismatches: 36, Indels: 12
0.72 0.21 0.07
Matches are distributed among these distances:
21 1 0.01
22 100 0.83
23 2 0.02
24 18 0.15
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (22 bp):
GTGGTTATCAAAATTTCATAGG
Found at i:531 original size:22 final size:21
Alignment explanation
Indices: 501--640 Score: 104
Period size: 22 Copynumber: 6.4 Consensus size: 21
491 ATCAAAAAGA
* *
501 TTATCAAAATGTCATAGCGAGG
1 TTATAAAAATTTCATAG-GAGG
*
523 TTATAAAAATTTCATAGTGTGG
1 TTATAAAAATTTCATAG-GAGG
545 TTA-ACAAAATTTCATTAGGAGG
1 TTATA-AAAATTTCA-TAGGAGG
* *
567 TTACT-AATATTTCATGGGGAGG
1 TTA-TAAAAATTTCAT-AGGAGG
* * *
589 TTATCAAAATTTTATAGCGTGG
1 TTATAAAAATTTCATAG-GAGG
* *
611 TTATCAAAATTTCATATGAAGG
1 TTATAAAAATTTCATA-GGAGG
633 TTATAAAA
1 TTATAAAA
641 GTCTCAATTT
Statistics
Matches: 95, Mismatches: 15, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
21 4 0.04
22 87 0.92
23 4 0.04
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.36
Consensus pattern (21 bp):
TTATAAAAATTTCATAGGAGG
Found at i:636 original size:44 final size:43
Alignment explanation
Indices: 278--893 Score: 160
Period size: 44 Copynumber: 14.0 Consensus size: 43
268 TTCTTGTCGC
* * *
278 TATGTGGTTATCAAAATTTCATA-AGATGGTTA-CTATAATTTCA
1 TATGAGGTTATCAAAATTTCATAGCGA-GGTTATC-AAAATTTCA
* * * * *
321 TGAGGAGGTTATCGAAATTCCATAGCGTGGTTACCAAAATTTCA
1 T-ATGAGGTTATCAAAATTTCATAGCGAGGTTATCAAAATTTCA
* * * * *
365 TATGAAAGTTATTAAAATTTCATAGTGTGGTTACCAAAATTTCA
1 TATG-AGGTTATCAAAATTTCATAGCGAGGTTATCAAAATTTCA
* * * * **
409 TAGGATCAGGTTATTAAAATTTCTTAG-GTTGGTTATTGAAATTTCA
1 T---ATGAGGTTATCAAAATTTCATAGCG-AGGTTATCAAAATTTCA
* * * * ** *
455 TAGGGTGGTTAATTTTCACAATTTTATAGAAATGTTATC-AAA----A
1 TA-TGAGGTT-A---TCAAAATTTCATAGCGAGGTTATCAAAATTTCA
* *
498 -A-GA--TTATCAAAATGTCATAGCGAGGTTATAAAAATTTCA
1 TATGAGGTTATCAAAATTTCATAGCGAGGTTATCAAAATTTCA
* * *
537 TAGTGTGGTTAACAAAATTTCATTAG-GAGGTTA-CTAATATTTCA
1 TA-TGAGGTTATCAAAATTTCA-TAGCGAGGTTATC-AAAATTTCA
** * *
581 TGGGGAGGTTATCAAAATTTTATAGCGTGGTTATCAAAATTTCA
1 T-ATGAGGTTATCAAAATTTCATAGCGAGGTTATCAAAATTTCA
* * *
625 TATGAAGGTTATAAAAGTCTCAATTTCATAAG-GA-G-TACCAAAAATTTGA
1 TATG-AGGTTAT-CAA-----AATTTCAT-AGCGAGGTTATC-AAAATTTCA
* * * * * *
674 TA-GAAGGTTATC-AAATCTCATAGAGTGATTATCGAAATTCCA
1 TATG-AGGTTATCAAAATTTCATAGCGAGGTTATCAAAATTTCA
* *
716 TA-GAGATCAAATTATCAAAATTT-ATAG-GAAGATTATCAAAATTTCA
1 TATGAG-----GTTATCAAAATTTCATAGCG-AGGTTATCAAAATTTCA
** * * *
762 TAATGTTGTTATCAAAATTCCAAAGCGAGGTTATCAAAATTACA
1 T-ATGAGGTTATCAAAATTTCATAGCGAGGTTATCAAAATTTCA
* * * * * * * *
806 TAATGTGATTATCAGAATTTCATAGAGGGGATCAACAAAATTTTA
1 T-ATGAGGTTATCAAAATTTCATAGCGAGG-TTATCAAAATTTCA
* * * ** *
851 TAAAGAGGTTATTAAAATTTCAGAAAGAGGTTATCAAATTTTC
1 T-ATGAGGTTATCAAAATTTCATAGCGAGGTTATCAAAATTTC
894 TAGAATGTGA
Statistics
Matches: 420, Mismatches: 100, Indels: 105
0.67 0.16 0.17
Matches are distributed among these distances:
34 17 0.04
35 3 0.01
37 1 0.00
38 2 0.00
39 1 0.00
40 4 0.01
41 10 0.02
42 11 0.03
43 23 0.05
44 186 0.44
45 44 0.10
46 58 0.14
47 11 0.03
48 28 0.07
49 11 0.03
50 8 0.02
51 2 0.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (43 bp):
TATGAGGTTATCAAAATTTCATAGCGAGGTTATCAAAATTTCA
Found at i:776 original size:22 final size:21
Alignment explanation
Indices: 748--829 Score: 76
Period size: 22 Copynumber: 3.8 Consensus size: 21
738 TATAGGAAGA
748 TTATCAAAATTTCATAATGTTG
1 TTATCAAAATTTCATAATG-TG
* * *
770 TTATCAAAATTCCA-AAGCGAGG
1 TTATCAAAATTTCATAA-TG-TG
*
792 TTATCAAAATTACATAATGTG
1 TTATCAAAATTTCATAATGTG
*
813 ATTATCAGAATTTCATA
1 -TTATCAAAATTTCATA
830 GAGGGGATCA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
21 3 0.06
22 43 0.90
23 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (21 bp):
TTATCAAAATTTCATAATGTG
Found at i:893 original size:22 final size:22
Alignment explanation
Indices: 843--898 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
833 GGGATCAACA
* *
843 AAATTTT-ATAAAGAGGTTATT
1 AAATTTTCAGAAAGAGGTTATC
*
864 AAAATTTCAGAAAGAGGTTATC
1 AAATTTTCAGAAAGAGGTTATC
886 AAATTTTCTAGAA
1 AAATTTTC-AGAA
899 TGTGATTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 6 0.21
22 19 0.66
23 4 0.14
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (22 bp):
AAATTTTCAGAAAGAGGTTATC
Found at i:1302 original size:22 final size:22
Alignment explanation
Indices: 1021--1304 Score: 131
Period size: 22 Copynumber: 13.1 Consensus size: 22
1011 TCAGGGAGGA
* *
1021 TATCAAAATTTTATAGT-TTAGT
1 TATCAAAATTTCATAGTGTGA-T
* * *
1043 TTTCAAAATTTCATAAGAG-GGT
1 TATCAAAATTTCAT-AGTGTGAT
*
1065 TATCAAAATTTCATAGTATGCA-
1 TATCAAAATTTCATAGTGTG-AT
* * *
1087 GATCAAAATTTCATAGGGAGAT
1 TATCAAAATTTCATAGTGTGAT
* * * *
1109 TAACAAAATTTCATAATGAGGT
1 TATCAAAATTTCATAGTGTGAT
** * * *
1131 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAGTGTGAT
*
1153 TATCAAAA-TT--T-GT-AG-T
1 TATCAAAATTTCATAGTGTGAT
* * **
1169 TATCAAGATTTCATA-AGAAAGT
1 TATCAAAATTTCATAGTGTGA-T
* * **
1191 TGTCAAAATTTTTATAAG-AAGATT
1 TATCAAAA-TTTCAT-AGTGTGA-T
** * *
1215 TATCAAAATTTCATAACGAGGT
1 TATCAAAATTTCATAGTGTGAT
1237 TATCAAAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
1259 TATCAAAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
* *
1281 TATCAAAATTTCAGAGTATGAT
1 TATCAAAATTTCATAGTGTGAT
1303 TA
1 TA
1305 CTAACAATTC
Statistics
Matches: 201, Mismatches: 45, Indels: 32
0.72 0.16 0.12
Matches are distributed among these distances:
16 8 0.04
17 4 0.02
18 1 0.00
19 2 0.01
20 1 0.00
21 4 0.02
22 156 0.78
23 14 0.07
24 11 0.05
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGTGAT
Found at i:1303 original size:44 final size:44
Alignment explanation
Indices: 1045--1304 Score: 148
Period size: 44 Copynumber: 6.0 Consensus size: 44
1035 AGTTTAGTTT
* * *
1045 TCAAAATTTCATAA-GAGGGTTATCAAAATTTCATAGTATGCA-GA
1 TCAAAATTTCATAACGA-GATTATCAAAATTTCAGAGTATG-ATTA
** * *
1089 TCAAAATTTCATAGGGAGATTAACAAAATTTCATA--ATGAGGTTA
1 TCAAAATTTCATAACGAGATTATCAAAATTTCAGAGTATGA--TTA
** ** *
1133 TCAAAAAATCATAGGGAGGTTATCAAAATTT----GTA-G-TTA
1 TCAAAATTTCATAACGAGATTATCAAAATTTCAGAGTATGATTA
* * * * * *
1171 TCAAGATTTCATAA-GAAAGTTGTCAAAATTTTTATAAG-AAGATTTA
1 TCAAAATTTCATAACGAGA-TTATCAAAA-TTTCA-GAGTATGA-TTA
* * *
1217 TCAAAATTTCATAACGAGGTTATCAAAATTTCATAGTGTGATTA
1 TCAAAATTTCATAACGAGATTATCAAAATTTCAGAGTATGATTA
** *
1261 TCAAAATTTCATAGTGTGATTATCAAAATTTCAGAGTATGATTA
1 TCAAAATTTCATAACGAGATTATCAAAATTTCAGAGTATGATTA
1305 CTAACAATTC
Statistics
Matches: 169, Mismatches: 29, Indels: 36
0.72 0.12 0.15
Matches are distributed among these distances:
37 2 0.01
38 21 0.12
39 3 0.02
41 2 0.01
42 4 0.02
43 1 0.01
44 102 0.60
45 8 0.05
46 24 0.14
47 2 0.01
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (44 bp):
TCAAAATTTCATAACGAGATTATCAAAATTTCAGAGTATGATTA
Found at i:1412 original size:23 final size:22
Alignment explanation
Indices: 1372--1435 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
1362 TGGACTATGG
* * *
1372 AAGTTATCAACATCTCATAGTGT
1 AAGTTATCAAAATTTCATAG-GA
* *
1395 TAGTTATCAAAATTTCATTGGA
1 AAGTTATCAAAATTTCATAGGA
1417 AAGTTATCAAAATTTCATA
1 AAGTTATCAAAATTTCATA
1436 CTGAGATCTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 18 0.53
23 16 0.47
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (22 bp):
AAGTTATCAAAATTTCATAGGA
Found at i:1501 original size:21 final size:22
Alignment explanation
Indices: 1461--1506 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1451 TTCCTTAGGG
* * *
1461 AGGTTAAGAAAATTTCATAAGA
1 AGGTTAAAAAAAATTCATAAAA
1483 AGGTTAAAAAAAATT-ATAAAA
1 AGGTTAAAAAAAATTCATAAAA
1504 AGG
1 AGG
1507 CTCTCAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.57, C:0.02, G:0.17, T:0.24
Consensus pattern (22 bp):
AGGTTAAAAAAAATTCATAAAA
Found at i:8664 original size:37 final size:37
Alignment explanation
Indices: 8613--8688 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
8603 CTGCTCATCG
* *
8613 GTCGGTATCGGTTTTTTCGGTTTTTATTTTGGTATAT
1 GTCGGTATCAGTTTTTTCGGTTTTTATTTTAGTATAT
8650 GTCGGTATCAGTTTTTTCGGTTTTTATTTTAGTATAT
1 GTCGGTATCAGTTTTTTCGGTTTTTATTTTAGTATAT
8687 GT
1 GT
8689 ATAAGTGACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.13, C:0.08, G:0.22, T:0.57
Consensus pattern (37 bp):
GTCGGTATCAGTTTTTTCGGTTTTTATTTTAGTATAT
Done.