Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014729.1 Corchorus capsularis cultivar CVL-1 contig14750, 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: 6865
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Found at i:198 original size:14 final size:12
Alignment explanation
Indices: 142--198 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 12
132 GAGGGACTTA
* *
142 TTTTTATTACTG
1 TTTTTATAAATG
154 TTTTTAATAAATTG
1 TTTTT-ATAAA-TG
168 TTTTTATAAATG
1 TTTTTATAAATG
180 ATTTTTATTAAGATG
1 -TTTTTA-TAA-ATG
195 TTTT
1 TTTT
199 GGGTGCATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
12 7 0.18
13 14 0.37
14 14 0.37
15 3 0.08
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.61
Consensus pattern (12 bp):
TTTTTATAAATG
Found at i:1206 original size:22 final size:22
Alignment explanation
Indices: 1181--1295 Score: 74
Period size: 22 Copynumber: 5.2 Consensus size: 22
1171 TATCAAAATG
*
1181 TCATAGCGTGGTTATAAGAATT
1 TCATAGTGTGGTTATAAGAATT
*
1203 TCATAGTGTGGTTA-ACAAAATT
1 TCATAGTGTGGTTATA-AGAATT
* *
1225 TCATTAG-GAGGTTACTAA-TATT
1 TCA-TAGTGTGGTTA-TAAGAATT
* * * *
1247 TCATGGGGAGGTTATCAGAATT
1 TCATAGTGTGGTTATAAGAATT
* * * *
1269 TTATATTGTGATTATCAGAATT
1 TCATAGTGTGGTTATAAGAATT
1291 TCATA
1 TCATA
1296 TGAAGGTTAT
Statistics
Matches: 73, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
21 5 0.07
22 63 0.86
23 4 0.05
24 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (22 bp):
TCATAGTGTGGTTATAAGAATT
Found at i:1305 original size:22 final size:22
Alignment explanation
Indices: 1254--1305 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1244 ATTTCATGGG
*
1254 GAGGTTATCAGAATTTTATATT
1 GAGGTTATCAGAATTTCATATT
* *
1276 GTGATTATCAGAATTTCATA-T
1 GAGGTTATCAGAATTTCATATT
1297 GAAGGTTAT
1 G-AGGTTAT
1306 AAAAGTGTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (22 bp):
GAGGTTATCAGAATTTCATATT
Found at i:1434 original size:22 final size:21
Alignment explanation
Indices: 1406--1487 Score: 83
Period size: 22 Copynumber: 3.8 Consensus size: 21
1396 GAGATTAGAA
1406 TATCAAAATTTCATAGTGTTGT
1 TATCAAAATTTCATAGTG-TGT
* * *
1428 TATCAAAATTTCAAAGCGAAGT
1 TATCAAAATTTCATAGTG-TGT
* *
1450 TATCAAAATTACATAATGTGAT
1 TATCAAAATTTCATAGTGTG-T
*
1472 TATCAGAATTTCATAG
1 TATCAAAATTTCATAG
1488 AGGGGTCAAC
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
21 1 0.02
22 46 0.98
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (21 bp):
TATCAAAATTTCATAGTGTGT
Found at i:1503 original size:22 final size:22
Alignment explanation
Indices: 1473--1550 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
1463 TAATGTGATT
* * *
1473 ATCAGAATTTCATAGAGGGGTCA
1 ATCAAAATTTCATAAAGAGGT-A
*
1496 A-CAAAATTTTATAAAGAGGTA
1 ATCAAAATTTCATAAAGAGGTA
* *
1517 ATCAAAATTTTATAAAGAGGTT
1 ATCAAAATTTCATAAAGAGGTA
*
1539 ATCAAATTTTCA
1 ATCAAAATTTCA
1551 AAATGTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
21 2 0.04
22 44 0.94
23 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (22 bp):
ATCAAAATTTCATAAAGAGGTA
Found at i:1547 original size:21 final size:22
Alignment explanation
Indices: 1497--1548 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1487 GAGGGGTCAA
1497 CAAAATTTTATAAAGAGGTAAT
1 CAAAATTTTATAAAGAGGTAAT
*
1519 CAAAATTTTATAAAGAGGTTAT
1 CAAAATTTTATAAAGAGGTAAT
1541 C-AAATTTT
1 CAAAATTTT
1549 CAAAATGTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 7 0.24
22 22 0.76
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.37
Consensus pattern (22 bp):
CAAAATTTTATAAAGAGGTAAT
Found at i:2059 original size:23 final size:22
Alignment explanation
Indices: 1657--2126 Score: 197
Period size: 22 Copynumber: 21.6 Consensus size: 22
1647 TATGGAGTAT
* *
1657 TCAAAATTTC--AGGGAGGATA
1 TCAAAATTTCATAGTGAGGTTA
* * *
1677 TCCAAATTTCATAGTTTA-GTTT
1 TCAAAATTTCATAG-TGAGGTTA
* *
1699 TCAAAATTTGATA-AGAGGGTTA
1 TCAAAATTTCATAGTGA-GGTTA
* *
1721 TCAAAATTTCATAGT-ATGTAGA
1 TCAAAATTTCATAGTGAGGT-TA
* *
1743 TCAAAATTTCATAGGGAGATTA
1 TCAAAATTTCATAGTGAGGTTA
* *
1765 ACAAAA-TTCAATAATGAGGTTA
1 TCAAAATTTC-ATAGTGAGGTTA
** *
1787 TCAAAAAATCATAGGGAGGTTA
1 TCAAAATTTCATAGTGAGGTTA
*
1809 TCAAAA-TT--T-GT-A-GTTT
1 TCAAAATTTCATAGTGAGGTTA
* * *
1825 TCAAGATTTCATAAG-AAAGTTA
1 TCAAAATTTCAT-AGTGAGGTTA
1847 TCAAAATTTCATAG-GTAGGTTTA
1 TCAAAATTTCATAGTG-AGG-TTA
* *
1870 TCAAAATTTTATAG-GAAGATTTA
1 TCAAAATTTCATAGTG-AG-GTTA
* *
1893 TCAAAATTTCATTGCGAGGTTA
1 TCAAAATTTCATAGTGAGGTTA
* * *
1915 TCACAATTTCATAGTGTGATTA
1 TCAAAATTTCATAGTGAGGTTA
* * * * **
1937 TTAAGATTTCAGAGTGTGACTA
1 TCAAAATTTCATAGTGAGGTTA
* *
1959 -CTAATAA-TTCATA-TGTAGCTTT
1 TC-AA-AATTTCATAGTG-AGGTTA
* * * *
1981 TTAAATTTTCATAATGTGGTTA
1 TCAAAATTTCATAGTGAGGTTA
* *
2003 TCAATATATCATA-TGGAGGTTA
1 TCAAAATTTCATAGT-GAGGTTA
* * *
2025 TCAACATCTCATAGTGTTGGTTA
1 TCAAAATTTCATAGTG-AGGTTA
* * *
2048 TCAAAATTTCATTGGGAAGTTA
1 TCAAAATTTCATAGTGAGGTTA
*
2070 TCAAAATTTCATATTGAGGTCT-
1 TCAAAATTTCATAGTGAGGT-TA
* * *
2092 TCAAAATTCCTTAGGGAGGTTA
1 TCAAAATTTCATAGTGAGGTTA
*
2114 ACAAAATTTCATA
1 TCAAAATTTCATA
2127 AGAAGATTAA
Statistics
Matches: 331, Mismatches: 87, Indels: 62
0.69 0.18 0.13
Matches are distributed among these distances:
16 8 0.02
17 3 0.01
18 1 0.00
19 2 0.01
20 10 0.03
21 15 0.05
22 228 0.69
23 63 0.19
24 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (22 bp):
TCAAAATTTCATAGTGAGGTTA
Found at i:2070 original size:45 final size:44
Alignment explanation
Indices: 1989--2082 Score: 109
Period size: 45 Copynumber: 2.1 Consensus size: 44
1979 TTTTAAATTT
* * *
1989 TCATAATGTGGTTATCAATATATCATATGGAGGTTATCAACATC
1 TCATAATGTGGTTATCAAAATATCATATGGAAGTTATCAAAATC
* * *
2033 TCATAGTGTTGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATT
1 TCATAATG-TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATC
2078 TCATA
1 TCATA
2083 TTGAGGTCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
44 8 0.19
45 34 0.81
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (44 bp):
TCATAATGTGGTTATCAAAATATCATATGGAAGTTATCAAAATC
Done.