Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016792.1 Corchorus olitorius cultivar O-4 contig16825, 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: 44241
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1358 original size:34 final size:32
Alignment explanation
Indices: 1256--1456 Score: 212
Period size: 28 Copynumber: 6.5 Consensus size: 32
1246 TTTCCTCAGC
1256 ATGACAACTTCTGGTGTCAAGATAATAATTTT
1 ATGACAACTTCTGGTGTCAAGATAATAATTTT
*
1288 ATGACAACTTCTGGT-T----TTAATAATTTT
1 ATGACAACTTCTGGTGTCAAGATAATAATTTT
*
1315 CATGACAACTCCTGGTGTCAAGATAATAATTTGAT
1 -ATGACAACTTCTGGTGTCAAGATAATAATTT--T
*
1350 ATGACAACTTCTGGTGTC-A-ATAAT--TTTC
1 ATGACAACTTCTGGTGTCAAGATAATAATTTT
*
1378 ATGACAACTTCTGGTGTCAAGATAATAATATAAT
1 ATGACAACTTCTGGTGTCAAGATAATAAT-T-TT
* *
1412 ATGACAACTTCTGGTGTC-A-AT-A-ACTTCT
1 ATGACAACTTCTGGTGTCAAGATAATAATTTT
1440 ATGACAACTTCTGGTGT
1 ATGACAACTTCTGGTGT
1457 TAATTAAATT
Statistics
Matches: 146, Mismatches: 9, Indels: 32
0.78 0.05 0.17
Matches are distributed among these distances:
27 10 0.07
28 50 0.34
29 3 0.02
30 10 0.07
31 2 0.01
32 23 0.16
33 12 0.08
34 35 0.24
35 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (32 bp):
ATGACAACTTCTGGTGTCAAGATAATAATTTT
Found at i:1382 original size:62 final size:61
Alignment explanation
Indices: 1223--1456 Score: 337
Period size: 62 Copynumber: 3.7 Consensus size: 61
1213 CAATCTTAGG
1223 ATGACAACTTCTGGTGTCAATAATTTCCTCAGCATGACAACTTCTGGTGTCAAGATAATAATTT-
1 ATGACAACTTCTGGTGTCAATAATTT--T---CATGACAACTTCTGGTGTCAAGATAATAATTTA
1287 T
61 T
* * *
1288 ATGACAACTTCTGGTTTTAATAATTTTCATGACAACTCCTGGTGTCAAGATAATAATTTGAT
1 ATGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTT-AT
*
1350 ATGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATAATATAAT
1 ATGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATAAT-TTAT
*
1412 ATGACAACTTCTGGTGTCAATAA-CTTCTATGACAACTTCTGGTGT
1 ATGACAACTTCTGGTGTCAATAATTTTC-ATGACAACTTCTGGTGT
1457 TAATTAAATT
Statistics
Matches: 157, Mismatches: 8, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
60 31 0.20
61 3 0.02
62 97 0.62
63 2 0.01
65 24 0.15
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (61 bp):
ATGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTAT
Found at i:1850 original size:22 final size:24
Alignment explanation
Indices: 1815--1868 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
1805 ACAAATGTTG
* *
1815 CTGATAA-TCTTCT-CTTTTATCT
1 CTGATAATTCTTCTCCATTTATCA
1837 CTGATAATTC-TCTCCATTTATCA
1 CTGATAATTCTTCTCCATTTATCA
1860 CTTGATAAT
1 C-TGATAAT
1869 ATCTAGCCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 10 0.37
23 10 0.37
24 7 0.26
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.48
Consensus pattern (24 bp):
CTGATAATTCTTCTCCATTTATCA
Found at i:3569 original size:49 final size:50
Alignment explanation
Indices: 3452--3589 Score: 185
Period size: 50 Copynumber: 2.8 Consensus size: 50
3442 AGCGTCCCAA
* * *
3452 TCAATTTTGTTATAAAAATTGATAAAAA-GTGC-AGG-AACTGTAAATGT
1 TCAATTTTGTTATAAAAATTGAGAAAAAGGTGCAAGGAAAATGTAAAGGT
*
3499 TCAATTTTGTCAATAAAAATTGAGAAAAAGGTGCAAGGAAAAT-TAAAGGT
1 TCAATTTTGT-TATAAAAATTGAGAAAAAGGTGCAAGGAAAATGTAAAGGT
*
3549 TCAATTTTGTTGTAAAAATTGAGAAAAAAGGTGCAAGGAAA
1 TCAATTTTGTTATAAAAATTGAG-AAAAAGGTGCAAGGAAA
3590 CTAAAAGTAA
Statistics
Matches: 80, Mismatches: 6, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
47 10 0.12
48 16 0.20
49 15 0.19
50 36 0.45
51 3 0.04
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.29
Consensus pattern (50 bp):
TCAATTTTGTTATAAAAATTGAGAAAAAGGTGCAAGGAAAATGTAAAGGT
Found at i:6960 original size:20 final size:20
Alignment explanation
Indices: 6935--7018 Score: 109
Period size: 20 Copynumber: 4.2 Consensus size: 20
6925 TGCCTTAGTT
6935 GTTTATTGT-GTTAGCAGCAA
1 GTTTATT-TCGTTAGCAGCAA
6955 GTTTATTAT-GTTAGCAGCAA
1 GTTTATT-TCGTTAGCAGCAA
* *
6975 GTTTGTTTCGTTAGGAGCAA
1 GTTTATTTCGTTAGCAGCAA
*
6995 ATTTATTTCGTTAGCAGCAA
1 GTTTATTTCGTTAGCAGCAA
7015 GTTT
1 GTTT
7019 GTGATTTCTG
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
19 1 0.02
20 55 0.98
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.42
Consensus pattern (20 bp):
GTTTATTTCGTTAGCAGCAA
Found at i:6994 original size:40 final size:40
Alignment explanation
Indices: 6944--7020 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
6934 TGTTTATTGT
*
6944 GTTAGCAGCAAGTTTATTAT-GTTAGCAGCAAGTTTGTTTC
1 GTTAGCAGCAAATTTATT-TCGTTAGCAGCAAGTTTGTTTC
*
6984 GTTAGGAGCAAATTTATTTCGTTAGCAGCAAGTTTGT
1 GTTAGCAGCAAATTTATTTCGTTAGCAGCAAGTTTGT
7021 GATTTCTGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 1 0.03
40 33 0.97
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (40 bp):
GTTAGCAGCAAATTTATTTCGTTAGCAGCAAGTTTGTTTC
Found at i:11706 original size:20 final size:20
Alignment explanation
Indices: 11681--11764 Score: 109
Period size: 20 Copynumber: 4.2 Consensus size: 20
11671 TACCTTGGTT
*
11681 GTTTATTGT-GTTAGCAACAA
1 GTTTATT-TCGTTAGCAGCAA
11701 GTTTATTGT-GTTAGCAGCAA
1 GTTTATT-TCGTTAGCAGCAA
* *
11721 GTTTGTTTCGTTAGGAGCAA
1 GTTTATTTCGTTAGCAGCAA
11741 GTTTATTTCGTTAGCAGCAA
1 GTTTATTTCGTTAGCAGCAA
11761 GTTT
1 GTTT
11765 GTGATTTCTG
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
19 1 0.02
20 57 0.98
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.42
Consensus pattern (20 bp):
GTTTATTTCGTTAGCAGCAA
Found at i:24965 original size:28 final size:27
Alignment explanation
Indices: 24865--24964 Score: 128
Period size: 27 Copynumber: 3.7 Consensus size: 27
24855 GGTCACCTAG
*
24865 GGGGCATTTTAGTCATTTGCATGTTCA
1 GGGGCATTTTAGTCATTTGCACGTTCA
*
24892 GGGGCATTTTAGTCATTTGCACGTCCA
1 GGGGCATTTTAGTCATTTGCACGTTCA
* *
24919 GGGGCATTTTGGTCATTTTGCACATTCA
1 GGGGCATTTTAGTCA-TTTGCACGTTCA
* * *
24947 AGGGCATGTTGGTCATTT
1 GGGGCATTTTAGTCATTT
24965 TAAGTTCGCT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 42 0.65
28 23 0.35
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.38
Consensus pattern (27 bp):
GGGGCATTTTAGTCATTTGCACGTTCA
Found at i:27933 original size:16 final size:17
Alignment explanation
Indices: 27914--27946 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
27904 TTATGGATAC
27914 TTAT-ATTTTAATTAAT
1 TTATAATTTTAATTAAT
27930 TTATAATTTTAATTAAT
1 TTATAATTTTAATTAAT
27947 GTTACGAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATAATTTTAATTAAT
Found at i:33696 original size:18 final size:17
Alignment explanation
Indices: 33682--33728 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
33672 GCATACATAT
33682 ATACATACACATACATGC
1 ATACATACACATACAT-C
* * *
33700 ATGCATATACATACATG
1 ATACATACACATACATC
33717 ATACATACACAT
1 ATACATACACAT
33729 CGTATGAGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.45, C:0.23, G:0.06, T:0.26
Consensus pattern (17 bp):
ATACATACACATACATC
Found at i:38631 original size:23 final size:23
Alignment explanation
Indices: 38600--38643 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
38590 CTTCAAGTCC
*
38600 TAATTACTTATAAGTCCTAATTA
1 TAATCACTTATAAGTCCTAATTA
38623 TAATCACTTATAAGTCCTAAT
1 TAATCACTTATAAGTCCTAAT
38644 CAACCGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.41
Consensus pattern (23 bp):
TAATCACTTATAAGTCCTAATTA
Found at i:39439 original size:31 final size:30
Alignment explanation
Indices: 39379--39452 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
39369 TGGGCAATTG
*
39379 AGGACTCAATTGACCCAATATTATGAGTAT
1 AGGACTAAATTGACCCAATATTATGAGTAT
* * * *
39409 ATGGACTAAATTGGCCCAATCTTGTTAGTAT
1 A-GGACTAAATTGACCCAATATTATGAGTAT
39440 AGAGACT-AATTGA
1 AG-GACTAAATTGA
39453 TCGCTTATTG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
30 7 0.19
31 29 0.81
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (30 bp):
AGGACTAAATTGACCCAATATTATGAGTAT
Found at i:39986 original size:37 final size:37
Alignment explanation
Indices: 39936--40023 Score: 142
Period size: 37 Copynumber: 2.4 Consensus size: 37
39926 AGCACAGTCA
39936 TAAGAACCAACAGAACATATACCAACTAAACAACAGC
1 TAAGAACCAACAGAACATATACCAACTAAACAACAGC
*
39973 TAAGAACCAACAGAACATATGCCAACTAAACAACAGC
1 TAAGAACCAACAGAACATATACCAACTAAACAACAGC
* *
40010 AAAGAATCAA-AGAA
1 TAAGAACCAACAGAA
40024 AAAAAACAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
36 4 0.08
37 44 0.92
ACGTcount: A:0.56, C:0.24, G:0.10, T:0.10
Consensus pattern (37 bp):
TAAGAACCAACAGAACATATACCAACTAAACAACAGC
Found at i:40047 original size:2 final size:2
Alignment explanation
Indices: 40042--40068 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40032 AGGGATGTTT
40042 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
40069 TCTCTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.