Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007981.1 Corchorus capsularis cultivar CVL-1 contig08002, 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: 13140
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:845 original size:6 final size:6
Alignment explanation
Indices: 834--925 Score: 51
Period size: 6 Copynumber: 13.3 Consensus size: 6
824 GGCTTTGAAG
*
834 AATTGA AATTGA AGCATTGA AATTG- AATTCGAA GAATTGA AATTGA AGCATGGAA
1 AATTGA AATTGA A--ATTGA AATTGA AATT-G-A -AATTGA AATTGA A--ATTG-A
889 GAATTGA AATTGA AGCATTGA CATATTGA AATTGA AA
1 -AATTGA AATTGA A--ATTGA -A-ATTGA AATTGA AA
926 CATTAGTATT
Statistics
Matches: 70, Mismatches: 3, Indels: 26
0.71 0.03 0.26
Matches are distributed among these distances:
5 4 0.06
6 33 0.47
7 3 0.04
8 23 0.33
9 6 0.09
10 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.21, T:0.28
Consensus pattern (6 bp):
AATTGA
Found at i:892 original size:22 final size:22
Alignment explanation
Indices: 864--924 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
854 AATTGAATTC
864 GAAGAATTGAAATTGAAGCATG
1 GAAGAATTGAAATTGAAGCATG
*
886 GAAGAATTGAAATTGAAGCATT
1 GAAGAATTGAAATTGAAGCATG
*
908 GACA-TATTGAAATTGAA
1 GA-AGAATTGAAATTGAA
925 ACATTAGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 35 0.97
23 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.23, T:0.26
Consensus pattern (22 bp):
GAAGAATTGAAATTGAAGCATG
Found at i:909 original size:14 final size:14
Alignment explanation
Indices: 828--860 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
818 GAAGGAGGCT
828 TTGAAGAATTGAAA
1 TTGAAGAATTGAAA
*
842 TTGAAGCATTGAAA
1 TTGAAGAATTGAAA
856 TTGAA
1 TTGAA
861 TTCGAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.30
Consensus pattern (14 bp):
TTGAAGAATTGAAA
Found at i:1033 original size:14 final size:14
Alignment explanation
Indices: 1016--1049 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1006 CATTTGGAAT
1016 TTGAAGAATTGAAA
1 TTGAAGAATTGAAA
* *
1030 TTGAAGTATTGAAG
1 TTGAAGAATTGAAA
1044 TTGAAG
1 TTGAAG
1050 CGTTCGAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.26, T:0.32
Consensus pattern (14 bp):
TTGAAGAATTGAAA
Found at i:1091 original size:29 final size:29
Alignment explanation
Indices: 1059--1117 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1049 GCGTTCGAAG
* *
1059 AATTGAAATTGAGGCATTAAAGAATTGAA
1 AATTGAAATTGAAGCATCAAAGAATTGAA
* *
1088 AATTGAAATTGAAGCGTCAAAGATTTGAA
1 AATTGAAATTGAAGCATCAAAGAATTGAA
1117 A
1 A
1118 TGGAGGCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.27
Consensus pattern (29 bp):
AATTGAAATTGAAGCATCAAAGAATTGAA
Found at i:1127 original size:51 final size:52
Alignment explanation
Indices: 1028--1146 Score: 141
Period size: 51 Copynumber: 2.3 Consensus size: 52
1018 GAAGAATTGA
* * * *
1028 AATTGAAGTATTGAAGTTGAAGCGTTCGAAGAATTGAAATTGAGGCATTAAAG
1 AATTGAA-AATTGAAATTGAAGCGTTCAAAGAATTGAAATGGAGGCATTAAAG
* * *
1081 AATTGAAAATTGAAATTGAAGCG-TCAAAGATTTGAAATGGAGGCATTGAAT
1 AATTGAAAATTGAAATTGAAGCGTTCAAAGAATTGAAATGGAGGCATTAAAG
*
1132 AATTGAGGAATTGAA
1 AATTGA-AAATTGAA
1147 GCATTTAATG
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
51 29 0.51
52 21 0.37
53 7 0.12
ACGTcount: A:0.42, C:0.05, G:0.25, T:0.28
Consensus pattern (52 bp):
AATTGAAAATTGAAATTGAAGCGTTCAAAGAATTGAAATGGAGGCATTAAAG
Found at i:1150 original size:24 final size:24
Alignment explanation
Indices: 1123--1171 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1113 TGAAATGGAG
*
1123 GCATTGAATAATTGAGGAATTGAA
1 GCATTGAATAATTGAAGAATTGAA
* *
1147 GCATTTAATGATTGAAGAATTGAA
1 GCATTGAATAATTGAAGAATTGAA
1171 G
1 G
1172 AAAGACCACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.31
Consensus pattern (24 bp):
GCATTGAATAATTGAAGAATTGAA
Found at i:1257 original size:22 final size:22
Alignment explanation
Indices: 1229--1407 Score: 118
Period size: 22 Copynumber: 8.2 Consensus size: 22
1219 CCACCCCGGG
* *
1229 TCATTGAAGTACTGAAGTTGAA
1 TCATTGAAGAATTGAAGTTGAA
1251 TCATTGAAGAATTGCAA-TTGAA
1 TCATTGAAGAATTG-AAGTTGAA
*
1273 ACATTGAAGAATTGAAGTTGAA
1 TCATTGAAGAATTGAAGTTGAA
* * * *
1295 GCATCGGAA-TATTGAAATTGAA
1 TCAT-TGAAGAATTGAAGTTGAA
* * *
1317 ACATTGATGAATTGAATTTGAA
1 TCATTGAAGAATTGAAGTTGAA
** *
1339 GAATTGAA-ATATTGAAATTGAA
1 TCATTGAAGA-ATTGAAGTTGAA
* *
1361 ACATT-AAGGAATTGAA--AGAA
1 TCATTGAA-GAATTGAAGTTGAA
* *
1381 ACATTGAAGAATTGAAATTGAA
1 TCATTGAAGAATTGAAGTTGAA
*
1403 GCATT
1 TCATT
1408 AAAAATTTGG
Statistics
Matches: 126, Mismatches: 21, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
20 16 0.13
21 9 0.07
22 95 0.75
23 6 0.05
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (22 bp):
TCATTGAAGAATTGAAGTTGAA
Found at i:1289 original size:44 final size:43
Alignment explanation
Indices: 1230--1437 Score: 183
Period size: 44 Copynumber: 4.8 Consensus size: 43
1220 CACCCCGGGT
* * * *
1230 CATTGAAGTACTGAAGTTGAATCATTGAAGAATTGCAATTGAAA
1 CATTGAAGAATTGAAGTTGAAGCATTGAA-AATTGAAATTGAAA
* *
1274 CATTGAAGAATTGAAGTTGAAGCATCGGAATATTGAAATTGAAA
1 CATTGAAGAATTGAAGTTGAAGCAT-TGAAAATTGAAATTGAAA
* * *
1318 CATTGATGAATTGAATTTGAAGAATTGAAATATTGAAATTGAAA
1 CATTGAAGAATTGAAGTTGAAGCATTGAAA-ATTGAAATTGAAA
* * *
1362 CATT-AAGGAATTGAA--AGAAACATTGAAGAATTGAAATTGAAG
1 CATTGAA-GAATTGAAGTTGAAGCATTGAA-AATTGAAATTGAAA
* *
1404 CATT-AAAAATTTGGAA-TTGAGGCATTGAATAATT
1 CATTGAAGAA-TT-GAAGTTGAAGCATTGAA-AATT
1438 AGGGAATGGA
Statistics
Matches: 136, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
41 2 0.01
42 29 0.21
43 8 0.06
44 94 0.69
45 3 0.02
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (43 bp):
CATTGAAGAATTGAAGTTGAAGCATTGAAAATTGAAATTGAAA
Found at i:1357 original size:14 final size:15
Alignment explanation
Indices: 1302--1377 Score: 70
Period size: 14 Copynumber: 5.1 Consensus size: 15
1292 GAAGCATCGG
1302 AATATTGA-AATTGA
1 AATATTGAGAATTGA
*
1316 AACATTGATGAATTG-
1 AATATTGA-GAATTGA
1331 AAT-TTGAAGAATTGA
1 AATATTG-AGAATTGA
1346 AATATTGA-AATTGA
1 AATATTGAGAATTGA
* *
1360 AACATTAAGGAATTGA
1 AATATTGA-GAATTGA
1376 AA
1 AA
1378 GAAACATTGA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
14 28 0.55
15 7 0.14
16 16 0.31
ACGTcount: A:0.49, C:0.03, G:0.17, T:0.32
Consensus pattern (15 bp):
AATATTGAGAATTGA
Found at i:1546 original size:8 final size:8
Alignment explanation
Indices: 1533--1622 Score: 53
Period size: 8 Copynumber: 11.2 Consensus size: 8
1523 TCATTGAAGT
1533 GAATTGAA
1 GAATTGAA
1541 GAATTGAA
1 GAATTGAA
*
1549 GCATTG-A
1 GAATTGAA
1556 GCAATTG-A
1 G-AATTGAA
1564 GAAATTGAA
1 G-AATTGAA
1573 GCAA-T-AA
1 G-AATTGAA
**
1580 GTAATCAAA
1 G-AATTGAA
1589 GAATTGAA
1 GAATTGAA
**
1597 GTGTTGAA
1 GAATTGAA
*
1605 TAATTGAA
1 GAATTGAA
*
1613 GAATGGAA
1 GAATTGAA
1621 GA
1 GA
1623 GTTGGATCAT
Statistics
Matches: 63, Mismatches: 15, Indels: 8
0.73 0.17 0.09
Matches are distributed among these distances:
7 7 0.11
8 49 0.78
9 7 0.11
ACGTcount: A:0.47, C:0.04, G:0.24, T:0.24
Consensus pattern (8 bp):
GAATTGAA
Found at i:1563 original size:24 final size:24
Alignment explanation
Indices: 1524--1621 Score: 81
Period size: 24 Copynumber: 4.0 Consensus size: 24
1514 CGCCCTGGGT
1524 CATTGAAGTGAATTGAAGAATTGAAG
1 CATTG-AGT-AATTGAAGAATTGAAG
*
1550 CATTGAGCAATTG-AGAAATTGAAG
1 CATTGAGTAATTGAAG-AATTGAAG
* * **
1574 CAATAAGTAATCAAAGAATTGAAG
1 CATTGAGTAATTGAAGAATTGAAG
** * *
1598 TGTTGAATAATTGAAGAATGGAAG
1 CATTGAGTAATTGAAGAATTGAAG
1622 AGTTGGATCA
Statistics
Matches: 56, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
23 2 0.04
24 45 0.80
25 4 0.07
26 5 0.09
ACGTcount: A:0.45, C:0.05, G:0.24, T:0.26
Consensus pattern (24 bp):
CATTGAGTAATTGAAGAATTGAAG
Found at i:1626 original size:24 final size:24
Alignment explanation
Indices: 1587--1639 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1577 TAAGTAATCA
* *
1587 AAGAATTGAAGTGTTGAATAATTG
1 AAGAATGGAAGAGTTGAATAATTG
* *
1611 AAGAATGGAAGAGTTGGATCATTG
1 AAGAATGGAAGAGTTGAATAATTG
1635 AAGAA
1 AAGAA
1640 AGAGATCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.28, T:0.26
Consensus pattern (24 bp):
AAGAATGGAAGAGTTGAATAATTG
Found at i:2638 original size:8 final size:8
Alignment explanation
Indices: 2606--2647 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
2596 CTCTTTTCCA
2606 TTCATTTT
1 TTCATTTT
*
2614 CTCATTTT
1 TTCATTTT
*
2622 TTTA-TTT
1 TTCATTTT
2629 TTCATTTTT
1 TTCA-TTTT
2638 TTCATTTT
1 TTCATTTT
2646 TT
1 TT
2648 TTCTTTGCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 6 0.21
8 15 0.54
9 7 0.25
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCATTTT
Found at i:2988 original size:6 final size:6
Alignment explanation
Indices: 2979--3015 Score: 53
Period size: 5 Copynumber: 6.7 Consensus size: 6
2969 TCACTTTCAT
2979 TTTTGA TTTTGA TTTTGA -TTTGA -TTTGA -TTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
3016 TTTTTTGCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 15 0.50
6 15 0.50
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (6 bp):
TTTTGA
Found at i:3350 original size:16 final size:15
Alignment explanation
Indices: 3325--3358 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3315 GTTTCAAAAA
*
3325 TTATTTTTATTTTATT
1 TTATTATTA-TTTATT
3341 TTATTATTATTTATT
1 TTATTATTATTTATT
3356 TTA
1 TTA
3359 ATTTGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATTATTATTTATT
Found at i:3414 original size:33 final size:33
Alignment explanation
Indices: 3372--3436 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
3362 TGAAAATCAT
**
3372 TTTTAAAAAACATTTTTGAAAGTCATGACTCTC
1 TTTTAAAAAACATTTTTGAAAACCATGACTCTC
* *
3405 TTTTGAAAAATATTTTTGAAAACCATGACTCT
1 TTTTAAAAAACATTTTTGAAAACCATGACTCT
3437 ACTATTCCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (33 bp):
TTTTAAAAAACATTTTTGAAAACCATGACTCTC
Found at i:3486 original size:9 final size:10
Alignment explanation
Indices: 3459--3483 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3449 GCCTTTATTT
3459 ATTTTTCATC
1 ATTTTTCATC
3469 ATTTTTCATC
1 ATTTTTCATC
3479 ATTTT
1 ATTTT
3484 CATTTTTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTTTTCATC
Found at i:6472 original size:28 final size:27
Alignment explanation
Indices: 6420--6480 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
6410 TTTGCTTTAA
6420 TTAATTTGCTTTAGATTTAGATTTAGAT
1 TTAATTTGCTTTAGATTTAGATTTAG-T
*
6448 TTAATTTGCTTT-GCTTT-GATTTTTAGT
1 TTAATTTGCTTTAGATTTAGA--TTTAGT
6475 TTAATT
1 TTAATT
6481 GTTTTCTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 2 0.07
27 11 0.37
28 17 0.57
ACGTcount: A:0.23, C:0.05, G:0.13, T:0.59
Consensus pattern (27 bp):
TTAATTTGCTTTAGATTTAGATTTAGT
Done.