Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013748.1 Corchorus olitorius cultivar O-4 contig13781, 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: 34337
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Found at i:1245 original size:68 final size:68
Alignment explanation
Indices: 1099--1735 Score: 664
Period size: 68 Copynumber: 9.5 Consensus size: 68
1089 CTCTATTTGC
* * *
1099 TATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTT-TTGCATTTAAGTTTAGTATT
1 TATTTCCAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTTGCATTTAAGTTTAGTGTT
1163 TTA
66 TTA
* *
1166 TATTTCAAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTCGCATTTAAGTTTAGTGTT
1 TATTTCCAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTTGCATTTAAGTTTAGTGTT
1231 TTA
66 TTA
*
1234 TATTTCCAAAAATACCCTTTCGGTCGAAGGGTTGTTTTTGTCTTCTTGCATTTAAGTTTAGTGTT
1 TATTTCCAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTTGCATTTAAGTTTAGTGTT
1299 TTA
66 TTA
*
1302 TATTTCCAAAAATACCCTTTCGGTCGAAGGGTTGTTTTTGTCTTCTTGCATTTAAGTTTAGTGTT
1 TATTTCCAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTTGCATTTAAGTTTAGTGTT
1367 TTA
66 TTA
* * *
1370 TATTTCCAAAAATACCCTTTCGGTCGAAGGGTTGTTTTTGTCTTCTTGCATTTAAGTATAGTATT
1 TATTTCCAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTTGCATTTAAGTTTAGTGTT
*
1435 TTC
66 TTA
* * * * *
1438 TATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCGTTTTAGTTTAGTG--
1 TATTTCCAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTTGCATTTAAGTTTAGTGTT
1501 ---
66 TTA
* * ** * * ** *
1501 --TTTCCAAAAATGCCCTTTCGGTCGAAAGGTCGTTTTCATCTTTTTGTA-CCAAGTTTAGTACT
1 TATTTCCAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTTGCATTTAAGTTTAGT-GT
**
1563 TTCC
65 TTTA
* ** ** *** *
1567 TTTTTCCAAAAATGTCCTTTCGGTCGAAGGGTCAATTTCAACTT-TTCCATGTCTAAG-TTA--G
1 TATTTCCAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTTGCAT-T-TAAGTTTAGTG
1628 -TTTA
64 TTTTA
* * * * * * * * *
1632 CT-TTTCCCAAAATGCCCTTTCGATCAAATGGTCGATTCTGTCATTCTTGCATTTGAGTTTA--C
1 -TATTTCCAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTC-TTCTTGCATTTAAGTTTAGTG
1694 TTTT-
64 TTTTA
*
1698 GATTTCCAAAAATACCCTTTCGGT-GAAAGGGTCAGTTT
1 TATTTCCAAAAATACCCTTTCGGTCG-AAGGGTC-GTTT
1736 CATCATTCTC
Statistics
Matches: 489, Mismatches: 61, Indels: 40
0.83 0.10 0.07
Matches are distributed among these distances:
60 8 0.02
61 42 0.09
65 35 0.07
66 32 0.07
67 55 0.11
68 311 0.64
69 3 0.01
70 3 0.01
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.44
Consensus pattern (68 bp):
TATTTCCAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTTGCATTTAAGTTTAGTGTT
TTA
Found at i:1566 original size:61 final size:60
Alignment explanation
Indices: 1440--1566 Score: 148
Period size: 61 Copynumber: 2.1 Consensus size: 60
1430 GTATTTTCTA
* * *** *
1440 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCGTTTTAGTTTAGTG
1 TTTCCAAAAATACCCTTTCGGTCGAAAGGTCATTTTCATCTTTTT-CGTCCAAGTTTAGTC
* *
1501 TTTCCAAAAATGCCCTTTCGGTCGAAAGGTCGTTTTCATCTTTTT-GTACCAAGTTTAGTAC
1 TTTCCAAAAATACCCTTTCGGTCGAAAGGTCATTTTCATCTTTTTCGT-CCAAGTTTAGT-C
1562 TTTCC
1 TTTCC
1567 TTTTTCCAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 2 0.04
60 8 0.14
61 46 0.82
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (60 bp):
TTTCCAAAAATACCCTTTCGGTCGAAAGGTCATTTTCATCTTTTTCGTCCAAGTTTAGTC
Found at i:5108 original size:1 final size:1
Alignment explanation
Indices: 5102--5130 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
5092 TTTAACCCTT
5102 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5131 GACCAACATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:6573 original size:68 final size:68
Alignment explanation
Indices: 6345--6988 Score: 664
Period size: 68 Copynumber: 9.7 Consensus size: 68
6335 AGTAAAGCTC
* * *
6345 TATTTTCTATTTCTAAAAATACCCTTTCGGTCGAAGGATCATTTTCGTCTT-TTGCATTTAAGTT
1 TATTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
6409 TAG
66 TAG
*
6412 TATTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTT-TTACATTTAAGTT
1 TATTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
6476 TAG
66 TAG
* * * *
6479 TATTTTATATTTCCAAAAATACCCTTTCAGTCGAAGGGTCGTTTTTGTCTTCTCGCATTTAAGTT
1 TATTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
6544 TAG
66 TAG
* * *
6547 TGTTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTTGCATTTAAGTT
1 TATTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
6612 TAG
66 TAG
* ** * *
6615 TGTTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTTGTTTTTGTCTTCTTGCATTTAAGTA
1 TATTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
6680 TAG
66 TAG
* * * *
6683 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCGTTTTAGTT
1 TATTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
6748 TAG
66 TAG
* * * * * * **
6751 -------TGTTTCCAAAAATGCCCTTTCGGTCGAAGGGTCGTTTTCATCTTTTTGTA-CCAAGTT
1 TATTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
6808 TAG
66 TAG
** * * * ** *
6811 TACTTTCCTTTTTCCAAAAATGCCCTTTCGGTCGAAGGGTCAATTTCAACTT-TTCCATGTCTAA
1 TA-TTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCAT-T-TAA
6875 G-TTAG
63 GTTTAG
* * * * * *
6880 ---TTTACT-TTTCCCAAAATGCCCTTTCGATCAAAGGGTCGATTCT-GTCATTCTTGCATTTGA
1 TATTTTA-TATTTCCAAAAATACCCTTTCGGTCGAAGGGTC-ATTTTCGTC-TTCTTGCATTTAA
6940 GTTTA-
63 GTTTAG
* * * *
6945 -CTTTT-GATTTCCAAAACTACCCTTTCGGT-GAAAGGGTCAGTTTC
1 TATTTTATATTTCCAAAAATACCCTTTCGGTCG-AAGGGTCATTTTC
6989 ATCATTCTCG
Statistics
Matches: 496, Mismatches: 59, Indels: 45
0.83 0.10 0.08
Matches are distributed among these distances:
60 7 0.01
61 44 0.09
65 37 0.07
66 35 0.07
67 122 0.25
68 244 0.49
69 4 0.01
70 3 0.01
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.43
Consensus pattern (68 bp):
TATTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
TAG
Found at i:6959 original size:65 final size:65
Alignment explanation
Indices: 6821--7045 Score: 163
Period size: 66 Copynumber: 3.4 Consensus size: 65
6811 TACTTTCCTT
* * * * * *
6821 TTTCCAAAAATGCCCTTTCGGTCGAAGGGTCA-ATTTCAAC-TTTTC-CATGTCTAAG-TTAGTT
1 TTTCC-AAAATGCCCTTTCGGTCAAAGGGTCAGA-TTCATCATTCTCGCA--TCTGAGTTTACTC
*
6882 TACT
62 TACA
* * * * * *
6886 TTTCCCAAAATGCCCTTTCGATCAAAGGGTC-GATTCTGTCATTCTTGCATTTGAGTTTACTTTT
1 TTT-CCAAAATGCCCTTTCGGTCAAAGGGTCAGATTC-ATCATTCTCGCATCTGAGTTTACTCTA
*
6950 GA
64 CA
* * * *
6952 TTTCCAAAACTACCCTTTCGGTGAAAGGGTCAGTTTCATCATTCTCGCATCTGGGTTTACTCTAC
1 TTTCCAAAA-TGCCCTTTCGGTCAAAGGGTCAGATTCATCATTCTCGCATCTGAGTTTACTCTAC
*
7017 T
65 A
* *
7018 TTTCAAAAATGCCCTTCCGGTCAAAGGG
1 TTTCCAAAATGCCCTTTCGGTCAAAGGG
7046 CGAACTTCGT
Statistics
Matches: 124, Mismatches: 28, Indels: 16
0.74 0.17 0.10
Matches are distributed among these distances:
64 3 0.02
65 54 0.44
66 61 0.49
67 6 0.05
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (65 bp):
TTTCCAAAATGCCCTTTCGGTCAAAGGGTCAGATTCATCATTCTCGCATCTGAGTTTACTCTACA
Found at i:17976 original size:16 final size:15
Alignment explanation
Indices: 17949--17982 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
17939 TTTGGGAATG
17949 AGGAAAGAAATAGAA
1 AGGAAAGAAATAGAA
*
17964 AGGAAATGAAATAGCA
1 AGGAAA-GAAATAGAA
17980 AGG
1 AGG
17983 GAAGGGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.59, C:0.03, G:0.29, T:0.09
Consensus pattern (15 bp):
AGGAAAGAAATAGAA
Found at i:17991 original size:17 final size:16
Alignment explanation
Indices: 17955--18007 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
17945 AATGAGGAAA
* **
17955 GAAATAGAAAGGAAAT
1 GAAATAGCAAGGAAGG
17971 GAAATAGCAAGGGAAGG
1 GAAATAGCAA-GGAAGG
**
17988 GAAATAGGGAGGAAGG
1 GAAATAGCAAGGAAGG
18004 GAAA
1 GAAA
18008 GGAAGTTACA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 19 0.61
17 12 0.39
ACGTcount: A:0.53, C:0.02, G:0.38, T:0.08
Consensus pattern (16 bp):
GAAATAGCAAGGAAGG
Found at i:18999 original size:3 final size:3
Alignment explanation
Indices: 18986--19021 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
18976 TCGTATCTGA
18986 AAG AA- AAG AAG AAG AAG AAG AAG AAAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG
19022 CAAAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:20945 original size:15 final size:16
Alignment explanation
Indices: 20907--20950 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
20897 AACAAAAGAA
* *
20907 CCATCTTCCTTCCTTC
1 CCATCTTCTTTCCTCC
20923 CCAT-TTCTTTCC-CC
1 CCATCTTCTTTCCTCC
20937 CCATCTTCTTTCCT
1 CCATCTTCTTTCCT
20951 TCCTATTTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 5 0.21
15 15 0.62
16 4 0.17
ACGTcount: A:0.07, C:0.48, G:0.00, T:0.45
Consensus pattern (16 bp):
CCATCTTCTTTCCTCC
Found at i:21543 original size:17 final size:17
Alignment explanation
Indices: 21521--21578 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
21511 TTTTTTCTTC
21521 TCTCTCGTCTGCTCCCA
1 TCTCTCGTCTGCTCCCA
* * * *
21538 TCTCTCATGTCCTCCTCC
1 TCTCTCGTCTGCTCC-CA
* *
21556 TCTCACGTTTGCTCCCA
1 TCTCTCGTCTGCTCCCA
21573 TCTCTC
1 TCTCTC
21579 ATGTCCTCCT
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.07, C:0.47, G:0.09, T:0.38
Consensus pattern (17 bp):
TCTCTCGTCTGCTCCCA
Found at i:21569 original size:35 final size:35
Alignment explanation
Indices: 21520--21588 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
21510 CTTTTTTCTT
*
21520 CTCTCTCGTCTGCTCCCATCTCTCATGTCCTCCTC
1 CTCTCACGTCTGCTCCCATCTCTCATGTCCTCCTC
*
21555 CTCTCACGTTTGCTCCCATCTCTCATGTCCTCCT
1 CTCTCACGTCTGCTCCCATCTCTCATGTCCTCCT
21589 TCCCTTCATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.07, C:0.46, G:0.09, T:0.38
Consensus pattern (35 bp):
CTCTCACGTCTGCTCCCATCTCTCATGTCCTCCTC
Found at i:21587 original size:17 final size:17
Alignment explanation
Indices: 21532--21587 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
21522 CTCTCGTCTG
21532 CTCCCATCTCTCATGTC
1 CTCCCATCTCTCATGTC
* * * * *
21549 CTCCTCCTCTCACGTTTG
1 CTCC-CATCTCTCATGTC
21567 CTCCCATCTCTCATGTC
1 CTCCCATCTCTCATGTC
21584 CTCC
1 CTCC
21588 TTCCCTTCAT
Statistics
Matches: 28, Mismatches: 10, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.09, C:0.48, G:0.07, T:0.36
Consensus pattern (17 bp):
CTCCCATCTCTCATGTC
Found at i:27270 original size:2 final size:2
Alignment explanation
Indices: 27263--27302 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
27253 AAGTAATTAT
*
27263 TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA AA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27302 T
1 T
27303 TAATACAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27295 original size:16 final size:18
Alignment explanation
Indices: 27260--27298 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
27250 ATTAAGTAAT
27260 TATTATATATATATATATA
1 TATTATAT-TATATATATA
*
27279 TATTATATTATAAATATA
1 TATTATATTATATATATA
27297 TA
1 TA
27299 ATATTAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTATATTATATATATA
Found at i:27374 original size:12 final size:12
Alignment explanation
Indices: 27357--27382 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27347 TTATCGATGC
27357 ATTAATTTGTAA
1 ATTAATTTGTAA
27369 ATTAATTTGTAA
1 ATTAATTTGTAA
27381 AT
1 AT
27383 AACGGTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
ATTAATTTGTAA
Found at i:31748 original size:28 final size:28
Alignment explanation
Indices: 31717--31773 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
31707 GAAATTACGG
31717 GTATTAAAAATGATGAGGGGAATTGGGT
1 GTATTAAAAATGATGAGGGGAATTGGGT
31745 GTATTAAAAATGATGAGGGGAATTGGGT
1 GTATTAAAAATGATGAGGGGAATTGGGT
31773 G
1 G
31774 ACAGATTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.28
Consensus pattern (28 bp):
GTATTAAAAATGATGAGGGGAATTGGGT
Done.