Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005327.1 Corchorus capsularis cultivar CVL-1 contig05345, 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: 2517
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Found at i:1294 original size:58 final size:58
Alignment explanation
Indices: 1166--1315 Score: 169
Period size: 58 Copynumber: 2.6 Consensus size: 58
1156 GATGAAATAC
* * *
1166 TGAAATTGAAGCATTTGAATAATTGAAATTGGAACATCGAAGGATTGAATTTGAAGAAA
1 TGAAATTGAAGCA-TTGAAGAATTGAAATTGGAACTTCGAAGGACTGAATTTGAAGAAA
* * * * * * * *
1225 AGCAATAGAAGCGTTGAAGAATTGAAATTGAAACTTTGAAGTACTGAATTTGAAGAAT
1 TGAAATTGAAGCATTGAAGAATTGAAATTGGAACTTCGAAGGACTGAATTTGAAGAAA
*
1283 TGAAATTGAAGCATTG--GAAATGAAATTGGAACT
1 TGAAATTGAAGCATTGAAGAATTGAAATTGGAACT
1316 AAAACATTGA
Statistics
Matches: 74, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
56 15 0.20
58 50 0.68
59 9 0.12
ACGTcount: A:0.43, C:0.06, G:0.23, T:0.28
Consensus pattern (58 bp):
TGAAATTGAAGCATTGAAGAATTGAAATTGGAACTTCGAAGGACTGAATTTGAAGAAA
Found at i:1332 original size:22 final size:22
Alignment explanation
Indices: 1307--1354 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1297 TGGAAATGAA
* *
1307 ATTGGAACTAAAACATTGAAGG
1 ATTGCAACTAAAACATCGAAGG
* *
1329 ATTGCAATTGAAACATCGAAGG
1 ATTGCAACTAAAACATCGAAGG
1351 ATTG
1 ATTG
1355 AATTTGAAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (22 bp):
ATTGCAACTAAAACATCGAAGG
Found at i:1362 original size:22 final size:22
Alignment explanation
Indices: 1317--1358 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1307 ATTGGAACTA
*
1317 AAACATTGAAGGATTGCAATTG
1 AAACATCGAAGGATTGCAATTG
1339 AAACATCGAAGGATTG-AATT
1 AAACATCGAAGGATTGCAATT
1359 TGAAGAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (22 bp):
AAACATCGAAGGATTGCAATTG
Found at i:1363 original size:36 final size:36
Alignment explanation
Indices: 1322--1412 Score: 110
Period size: 36 Copynumber: 2.5 Consensus size: 36
1312 AACTAAAACA
*
1322 TTGAAGGATTGCAATTGAAACATCGAAGGATTGAAT
1 TTGAAGAATTGCAATTGAAACATCGAAGGATTGAAT
* * * *
1358 TTGAAGAATTGGAATTGGAGCATTGAAGGATTGAAT
1 TTGAAGAATTGCAATTGAAACATCGAAGGATTGAAT
* * *
1394 TTGGAGAAGTGAAATTGAA
1 TTGAAGAATTGCAATTGAA
1413 GCGTCATTGA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.38, C:0.04, G:0.29, T:0.29
Consensus pattern (36 bp):
TTGAAGAATTGCAATTGAAACATCGAAGGATTGAAT
Found at i:1383 original size:22 final size:22
Alignment explanation
Indices: 1358--1399 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1348 AGGATTGAAT
1358 TTGAAGAATTGGAA-TTGGAGCA
1 TTGAAGAATT-GAATTTGGAGCA
*
1380 TTGAAGGATTGAATTTGGAG
1 TTGAAGAATTGAATTTGGAG
1400 AAGTGAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.33, C:0.02, G:0.33, T:0.31
Consensus pattern (22 bp):
TTGAAGAATTGAATTTGGAGCA
Found at i:1406 original size:22 final size:22
Alignment explanation
Indices: 1359--1406 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
1349 GGATTGAATT
* *
1359 TGAAGAATTGGAATTGGAGCAT
1 TGAAGAATTGGAATTGGAGAAG
*
1381 TGAAGGATT-GAATTTGGAGAAG
1 TGAAGAATTGGAA-TTGGAGAAG
1403 TGAA
1 TGAA
1407 ATTGAAGCGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.38, C:0.02, G:0.33, T:0.27
Consensus pattern (22 bp):
TGAAGAATTGGAATTGGAGAAG
Found at i:1479 original size:16 final size:16
Alignment explanation
Indices: 1458--1493 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1448 ATCTTGGGTC
*
1458 ATTGAAGCATTGAATA
1 ATTGAAGCATTGAAGA
*
1474 ATTGAAGGATTGAAGA
1 ATTGAAGCATTGAAGA
1490 ATTG
1 ATTG
1494 CATTTGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.31
Consensus pattern (16 bp):
ATTGAAGCATTGAAGA
Found at i:1544 original size:21 final size:21
Alignment explanation
Indices: 1512--1565 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1502 AAATTGGAAA
1512 TGAAACATTGAAATTAAAGCAT
1 TGAAA-ATTGAAATTAAAGCAT
* *
1534 TGAAAATTGAAATTGAGGCAT
1 TGAAAATTGAAATTAAAGCAT
1555 TGAATAATTGA
1 TGAA-AATTGA
1566 GGAACGGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.30
Consensus pattern (21 bp):
TGAAAATTGAAATTAAAGCAT
Found at i:1655 original size:58 final size:59
Alignment explanation
Indices: 1544--1675 Score: 160
Period size: 58 Copynumber: 2.3 Consensus size: 59
1534 TGAAAATTGA
* * * *
1544 AATTGAGGCATTGAATAATTGAGGAACGGAAGAAAGACCACCATGTATTATTG-AAGCC
1 AATTGAAGCATTGAATAATTGAGAAACGGAAGAAAGACCACCATGGATCATTGAAAGCC
* * **
1602 AATTGAAGCATTGAATAATTGAAGAAAC-GAAGAAAGACCACCCTGGGTCATTGAAAGTG
1 AATTGAAGCATTGAATAATTG-AGAAACGGAAGAAAGACCACCATGGATCATTGAAAGCC
*
1661 AATTGAAGAATTGAA
1 AATTGAAGCATTGAA
1676 GCATTGAGTA
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
58 41 0.65
59 22 0.35
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.22
Consensus pattern (59 bp):
AATTGAAGCATTGAATAATTGAGAAACGGAAGAAAGACCACCATGGATCATTGAAAGCC
Found at i:1673 original size:8 final size:8
Alignment explanation
Indices: 1660--1840 Score: 104
Period size: 8 Copynumber: 22.1 Consensus size: 8
1650 CATTGAAAGT
1660 GAATTGAA
1 GAATTGAA
1668 GAATTGAA
1 GAATTGAA
*
1676 GCATTG-A
1 GAATTGAA
1683 GTAATTGAA
1 G-AATTGAA
1692 GAATTGAA
1 GAATTGAA
1700 GCAA-T-AA
1 G-AATTGAA
1707 GTAATTGAA
1 G-AATTGAA
*
1716 GAATGGAA
1 GAATTGAA
*
1724 GAAAT--A
1 GAATTGAA
1730 -AATTGAA
1 GAATTGAA
*
1737 GTATTGAA
1 GAATTGAA
1745 GAATTGAA
1 GAATTGAA
* *
1753 TAATTAAA
1 GAATTGAA
* *
1761 GAGTCGAAGA
1 GAATTG-A-A
1771 GATAATTTGAA
1 G--AA-TTGAA
*
1782 GTATTGAA
1 GAATTGAA
*
1790 GAATAGAA
1 GAATTGAA
*
1798 TAATTGAA
1 GAATTGAA
1806 GAAAATTGAA
1 G--AATTGAA
*
1816 GCATTGAA
1 GAATTGAA
*
1824 GGATTGAA
1 GAATTGAA
*
1832 AAATTGAA
1 GAATTGAA
1840 G
1 G
1841 CTACTTGAAA
Statistics
Matches: 130, Mismatches: 28, Indels: 30
0.69 0.15 0.16
Matches are distributed among these distances:
5 3 0.02
6 1 0.01
7 8 0.06
8 93 0.72
9 9 0.07
10 10 0.08
11 2 0.02
12 2 0.02
13 2 0.02
ACGTcount: A:0.49, C:0.02, G:0.23, T:0.26
Consensus pattern (8 bp):
GAATTGAA
Found at i:1690 original size:24 final size:24
Alignment explanation
Indices: 1661--1841 Score: 117
Period size: 24 Copynumber: 7.7 Consensus size: 24
1651 ATTGAAAGTG
1661 AATTGAAGAATTGAAGCATTGAGT
1 AATTGAAGAATTGAAGCATTGAGT
* *
1685 AATTGAAGAATTGAAGCAATAAGT
1 AATTGAAGAATTGAAGCATTGAGT
* * *
1709 AATTGAAGAATGGAAGAAAT-A--
1 AATTGAAGAATTGAAGCATTGAGT
* * *
1730 AATTGAAGTATTGAAGAATTGAAT
1 AATTGAAGAATTGAAGCATTGAGT
* * *
1754 AATTAAAGAGTCGAAG-A--GA-T
1 AATTGAAGAATTGAAGCATTGAGT
* * * *
1774 AATTTGAAGTATTGAAGAATAGAAT
1 AA-TTGAAGAATTGAAGCATTGAGT
1799 AATTGAAGAAAATTGAAGCATTGAAG-
1 AATTGAAG--AATTGAAGCATTG-AGT
* *
1825 GATTGAAAAATTGAAGC
1 AATTGAAGAATTGAAGC
1842 TACTTGAAAA
Statistics
Matches: 125, Mismatches: 21, Indels: 22
0.74 0.12 0.13
Matches are distributed among these distances:
20 3 0.02
21 29 0.23
22 2 0.02
23 2 0.02
24 69 0.55
25 3 0.02
26 16 0.13
27 1 0.01
ACGTcount: A:0.49, C:0.03, G:0.23, T:0.26
Consensus pattern (24 bp):
AATTGAAGAATTGAAGCATTGAGT
Found at i:1743 original size:45 final size:43
Alignment explanation
Indices: 1685--1808 Score: 140
Period size: 45 Copynumber: 2.7 Consensus size: 43
1675 AGCATTGAGT
* *
1685 AATTGAAGAATTGAAGCAATAAGTAATTGAAGAATGGAAGAAATA
1 AATTGAAGTATTGAAG-AATAA-TAATTGAAGAATCGAAGAAATA
* * *
1730 AATTGAAGTATTGAAGAATTGAATAATTAAAGAGTCGAAGAGATA
1 AATTGAAGTATTGAAGAA-T-AATAATTGAAGAATCGAAGAAATA
*
1775 ATTTGAAGTATTGAAGAATAGAATAATTGAAGAA
1 AATTGAAGTATTGAAGAAT--AATAATTGAAGAA
1809 AATTGAAGCA
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
44 3 0.04
45 63 0.93
46 2 0.03
ACGTcount: A:0.51, C:0.02, G:0.22, T:0.26
Consensus pattern (43 bp):
AATTGAAGTATTGAAGAATAATAATTGAAGAATCGAAGAAATA
Done.