Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000243.1 Corchorus capsularis cultivar CVL-1 contig00243, 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, 752
Length: 1254
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.39
Found at i:220 original size:19 final size:20
Alignment explanation
Indices: 193--230 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
183 TACTATTATT
193 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
213 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
231 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:481 original size:22 final size:22
Alignment explanation
Indices: 456--595 Score: 119
Period size: 22 Copynumber: 6.4 Consensus size: 22
446 ATCAAAGAGA
* *
456 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
478 TTAT-AAGAATTTCATGGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
*
500 TTAACAAAATTTCATTAG-GAGG
1 TTATCAAAATTTCA-TAGTGAGG
* * *
522 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
* *
544 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
566 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
588 TTAT-AAAA
1 TTATCAAAA
596 GTCCCAATTT
Statistics
Matches: 95, Mismatches: 16, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
21 11 0.12
22 79 0.83
23 5 0.05
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:894 original size:22 final size:22
Alignment explanation
Indices: 847--1160 Score: 141
Period size: 22 Copynumber: 14.5 Consensus size: 22
837 TTACGGAGTA
* *
847 ATCAAAATTTC--ATGGAGGAT
1 ATCAAAATTTCATATGAAGGTT
867 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
**
889 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATA-TGAAGGTT
* * * *
911 TTCAAAATTTCACAAGAGGGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
933 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATGAAGGT-T
* * * *
955 ATCAAGATTTCATAGGGAGATT
1 ATCAAAATTTCATATGAAGGTT
* *
977 AACAAAATTTCATAATTAA-GTT
1 ATCAAAATTTCAT-ATGAAGGTT
** ** *
999 ATCAAAAAATCATCGGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
*
1021 ATCAAAA--T--T-TGTA-GTT
1 ATCAAAATTTCATATGAAGGTT
* * **
1037 ATCAAGATTTCATAAGAAATTT
1 ATCAAAATTTCATATGAAGGTT
* * *
1059 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATATGAAGG-TT
* * *
1082 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATATGAAG-GTT
*
1105 ATCAAAATTTCATA-GCGAGGTT
1 ATCAAAATTTCATATG-AAGGTT
* * *
1127 ATCACAATTTCATAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
1149 ATCAAAATTTCA
1 ATCAAAATTTCA
1161 GAGTGTGATT
Statistics
Matches: 220, Mismatches: 55, Indels: 36
0.71 0.18 0.12
Matches are distributed among these distances:
16 9 0.04
17 2 0.01
18 2 0.01
20 13 0.06
21 6 0.03
22 143 0.65
23 44 0.20
24 1 0.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTT
Found at i:1085 original size:23 final size:23
Alignment explanation
Indices: 1056--1160 Score: 115
Period size: 23 Copynumber: 4.7 Consensus size: 23
1046 TCATAAGAAA
*
1056 TTTATCAAAATTTTATAGGGAGG
1 TTTATCAAAATTTCATAGGGAGG
* * *
1079 TTTATCAAAATTTTATAGGAAGA
1 TTTATCAAAATTTCATAGGGAGG
*
1102 TTTATCAAAATTTCATAGCGAGG
1 TTTATCAAAATTTCATAGGGAGG
* * *
1125 -TTATCACAATTTCATAGTG-TG
1 TTTATCAAAATTTCATAGGGAGG
*
1146 ATTATCAAAATTTCA
1 TTTATCAAAATTTCA
1161 GAGTGTGATT
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
21 1 0.01
22 30 0.42
23 40 0.56
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (23 bp):
TTTATCAAAATTTCATAGGGAGG
Found at i:1129 original size:45 final size:45
Alignment explanation
Indices: 847--1160 Score: 176
Period size: 44 Copynumber: 7.3 Consensus size: 45
837 TTACGGAGTA
* * *
847 ATCAAAATTTCAT-G-GAGGATATCAAAATTTCATATGAAG-GTT
1 ATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAGGAAGATTT
** * * * **
889 ATCAAAATTTCATAGTTTA-GTTTTCAAAATTTCACAAG-AGGGTT
1 ATCAAAATTTCATAG-CGAGGTTATCAAAATTTCATAGGAAGATTT
* * * * *
933 ATCAAAATTTCATAG-TATGTAGATCAAGATTTCATAGGGAGA-TT
1 ATCAAAATTTCATAGCGAGGT-TATCAAAATTTCATAGGAAGATTT
* *** * ** * * *
977 AACAAAATTTCATAATTAAGTTATCAAAAAATCATCGGGAG-GTT
1 ATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAGGAAGATTT
* * *
1021 ATCAAAA-TT--T-G-TA-GTTATCAAGATTTCATAAGAA-ATTT
1 ATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAGGAAGATTT
* * *
1059 ATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGCGAGG-TTATCAAAATTTCATAGGAAGATTT
* *
1105 ATCAAAATTTCATAGCGAGGTTATCACAATTTCATAGTG-TGA-TT
1 ATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAG-GAAGATTT
1149 ATCAAAATTTCA
1 ATCAAAATTTCA
1161 GAGTGTGATT
Statistics
Matches: 216, Mismatches: 37, Indels: 36
0.75 0.13 0.12
Matches are distributed among these distances:
38 24 0.11
39 4 0.02
41 2 0.01
42 16 0.07
43 8 0.04
44 98 0.45
45 41 0.19
46 23 0.11
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36
Consensus pattern (45 bp):
ATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAGGAAGATTT
Done.