Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018891.1 Corchorus olitorius cultivar O-4 contig18924, 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: 59095
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:2281 original size:33 final size:33
Alignment explanation
Indices: 2223--2292 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 33
2213 ACAGAAAATA
*
2223 AAGAAAATATTTTTTTTTCTAAAAACGCAGGAAC
1 AAGAAAATATTTTTTTTTCTAAAAACGCA-AAAC
*
2257 AAGAAATTA-TTTTTTTT-TAGAAAACGCAAAAC
1 AAGAAAATATTTTTTTTTCTA-AAAACGCAAAAC
2289 AAGA
1 AAGA
2293 TTTTTTTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 9 0.27
33 16 0.48
34 8 0.24
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.31
Consensus pattern (33 bp):
AAGAAAATATTTTTTTTTCTAAAAACGCAAAAC
Found at i:7300 original size:15 final size:16
Alignment explanation
Indices: 7280--7312 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
7270 AGCTTCCTAG
7280 AAAAACTCAAAA-AAA
1 AAAAACTCAAAAGAAA
7295 AAAAACTCAAAAGAAA
1 AAAAACTCAAAAGAAA
7311 AA
1 AA
7313 TTTGTTAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.79, C:0.12, G:0.03, T:0.06
Consensus pattern (16 bp):
AAAAACTCAAAAGAAA
Found at i:7480 original size:23 final size:24
Alignment explanation
Indices: 7442--7504 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 24
7432 TAGAAAAACT
*
7442 CAAAAAC-T-TTTTTTTTATGATG
1 CAAAAACATATTTTTTTTATGACG
*
7464 CAGAAACA-ATTTTTTTTATGACG
1 CAAAAACATATTTTTTTTATGACG
*
7487 CAAAAATATATTTTTTTT
1 CAAAAACATATTTTTTTT
7505 CCTACGCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 6 0.18
23 19 0.56
24 9 0.26
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.48
Consensus pattern (24 bp):
CAAAAACATATTTTTTTTATGACG
Found at i:7967 original size:15 final size:16
Alignment explanation
Indices: 7943--7982 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
7933 AGAGATTGAC
*
7943 AGAAAGCAATTAAA-T
1 AGAAAACAATTAAACT
7958 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
7974 AGAAAACAA
1 AGAAAACAA
7983 AGCAAAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:26353 original size:24 final size:26
Alignment explanation
Indices: 26307--26361 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
26297 ATTGGAGTAT
*
26307 TTATTTATCTTGTTGCTTAA-TTTTA
1 TTATTTATCTTGTTGATTAATTTTTA
* *
26332 TTATTT-TCTTGTTTATTTATTTTTA
1 TTATTTATCTTGTTGATTAATTTTTA
26357 TTATT
1 TTATT
26362 CACTTAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (26 bp):
TTATTTATCTTGTTGATTAATTTTTA
Found at i:26572 original size:8 final size:8
Alignment explanation
Indices: 26561--26594 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
26551 CTCTACTTTA
26561 TTTTTTTG
1 TTTTTTTG
26569 TTTTTTTG
1 TTTTTTTG
*
26577 TTTTTGTG
1 TTTTTTTG
26585 TTCTTTTTG
1 TT-TTTTTG
26594 T
1 T
26595 AACTTTGCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 17 0.74
9 6 0.26
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (8 bp):
TTTTTTTG
Found at i:27135 original size:21 final size:21
Alignment explanation
Indices: 27109--27158 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
27099 TGCTAGGAGA
27109 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
27130 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
27151 TCATTGGA
1 TCATTGGA
27159 ATTGCCTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:27300 original size:21 final size:21
Alignment explanation
Indices: 27274--27315 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
27264 TCTTGACGAG
*
27274 TTGAAGGCCATTGGAGATCAT
1 TTGAAGCCCATTGGAGATCAT
27295 TTGAAGCCCATTGGAGATCAT
1 TTGAAGCCCATTGGAGATCAT
27316 CACCAAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (21 bp):
TTGAAGCCCATTGGAGATCAT
Found at i:27918 original size:26 final size:23
Alignment explanation
Indices: 27869--27918 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 23
27859 CTATCCTTCT
27869 ATTCATCTATCATCAAGTTTTTC
1 ATTCATCTATCATCAAGTTTTTC
27892 ATTCATCTCATCCATCAAAGTTTTTC
1 ATTCATCT-AT-CATC-AAGTTTTTC
27918 A
1 A
27919 AATTTTCTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 8 0.33
24 2 0.08
25 4 0.17
26 10 0.42
ACGTcount: A:0.28, C:0.24, G:0.04, T:0.44
Consensus pattern (23 bp):
ATTCATCTATCATCAAGTTTTTC
Found at i:33331 original size:21 final size:21
Alignment explanation
Indices: 33305--33354 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
33295 TGCTAGGAGA
33305 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
33326 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
33347 TCATTGGA
1 TCATTGGA
33355 ATTACCTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:34297 original size:22 final size:22
Alignment explanation
Indices: 34269--34314 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
34259 AAAATCTCCT
34269 AATTCAACCTGT-GGAGAGGTCG
1 AATTCAACCT-TCGGAGAGGTCG
*
34291 AATTCAACCTTCGTAGAGGTCG
1 AATTCAACCTTCGGAGAGGTCG
34313 AA
1 AA
34315 ACAACAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (22 bp):
AATTCAACCTTCGGAGAGGTCG
Found at i:35032 original size:21 final size:21
Alignment explanation
Indices: 34994--35062 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
34984 GCGGCAAGGC
*
34994 CCCCTTGACGAGAACGGGGAG
1 CCCCTTGACGAGAGCGGGGAG
* * *
35015 CCCCTTGATGCGAGCGGGAAGG
1 CCCCTTGACGAGAGCGGGGA-G
* *
35037 TCACCTTGACGTGAGCGGGGAG
1 -CCCCTTGACGAGAGCGGGGAG
35059 CCCC
1 CCCC
35063 ATATCCTTCG
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
21 19 0.51
22 2 0.05
23 16 0.43
ACGTcount: A:0.19, C:0.30, G:0.38, T:0.13
Consensus pattern (21 bp):
CCCCTTGACGAGAGCGGGGAG
Found at i:39108 original size:18 final size:21
Alignment explanation
Indices: 39080--39132 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 21
39070 AATGAAATTT
*
39080 TAGAATTAGTTTAATT-TC-A
1 TAGATTTAGTTTAATTATCAA
39099 TAG-TTTAGTTTAATTATCAA
1 TAGATTTAGTTTAATTATCAA
*
39119 TAGATTAAGTTTAA
1 TAGATTTAGTTTAA
39133 ATAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 11 0.38
19 5 0.17
20 4 0.14
21 9 0.31
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (21 bp):
TAGATTTAGTTTAATTATCAA
Found at i:39703 original size:36 final size:34
Alignment explanation
Indices: 39656--39753 Score: 135
Period size: 34 Copynumber: 2.8 Consensus size: 34
39646 ATCAAGAATC
39656 AGTTTTCAAATTGGGAAAGTTCCCATCA-CTCAATTA
1 AGTTTTCAAATTGGGAAAGTTCCCATCAGCT---TTA
* * *
39692 AGTTTTCAAATTGGGAAAGTTCCCACCAGGTTTT
1 AGTTTTCAAATTGGGAAAGTTCCCATCAGCTTTA
39726 AGTTTTCAAATTGGGAAAGTTCCCATCA
1 AGTTTTCAAATTGGGAAAGTTCCCATCA
39754 ATTTTCAATT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
34 29 0.51
36 27 0.47
37 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (34 bp):
AGTTTTCAAATTGGGAAAGTTCCCATCAGCTTTA
Found at i:39784 original size:27 final size:27
Alignment explanation
Indices: 39728--39786 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
39718 CAGGTTTTAG
39728 TTTTCAAATTGGGAAAGTTCCCATCAA
1 TTTTCAAATTGGGAAAGTTCCCATCAA
* *
39755 TTTTCAATTTAGGGAAAGTTCCCGTC-A
1 TTTTCAAATT-GGGAAAGTTCCCATCAA
39782 TTTTC
1 TTTTC
39787 GGTCCTAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (27 bp):
TTTTCAAATTGGGAAAGTTCCCATCAA
Done.