Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012140.1 Corchorus olitorius cultivar O-4 contig12173, 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: 53213
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2927 original size:23 final size:22
Alignment explanation
Indices: 2883--3072 Score: 83
Period size: 22 Copynumber: 8.6 Consensus size: 22
2873 ATATAATATG
* *
2883 GAGGTTATAAAACATCTCATAGT
1 GAGGTTATCAAA-ATTTCATAGT
*
2906 GTTGGTTATCAAAATTTCATAGT
1 G-AGGTTATCAAAATTTCATAGT
*
2929 GAGGTGT-TCAAAATTTCTTAG-
1 GAGGT-TATCAAAATTTCATAGT
*
2950 GAAGGTTAACAAAATTTCATAAG-
1 G-AGGTTATCAAAATTTCAT-AGT
* ** *
2973 AAGGTTAAAAAAAATTT-AT-GAA
1 GAGGTT-ATCAAAATTTCATAG-T
* * *
2995 AAGGTTCTCGAAATTTCATAGT
1 GAGGTTATCAAAATTTCATAGT
* *
3017 -ATTGTTATTAAAATTTCATAAG-
1 GA-GGTTATCAAAATTTCAT-AGT
*
3039 AAGGTTATC-AAATTTCATAAG-
1 GAGGTTATCAAAATTTCAT-AGT
*
3060 GAGGTCATCAAAA
1 GAGGTTATCAAAA
3073 ATAGTGTAAT
Statistics
Matches: 131, Mismatches: 22, Indels: 29
0.72 0.12 0.16
Matches are distributed among these distances:
20 1 0.01
21 28 0.21
22 66 0.50
23 27 0.21
24 9 0.07
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.34
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAGT
Found at i:2942 original size:22 final size:22
Alignment explanation
Indices: 2909--3072 Score: 115
Period size: 22 Copynumber: 7.5 Consensus size: 22
2899 TCATAGTGTT
2909 GGTTATCAAAATTTCATAGTG-A
1 GGTTATCAAAATTTCATAG-GAA
*
2931 GGTGT-TCAAAATTTCTTAGGAA
1 GGT-TATCAAAATTTCATAGGAA
* *
2953 GGTTAACAAAATTTCATAAGAA
1 GGTTATCAAAATTTCATAGGAA
** *
2975 GGTTAAAAAAAATTT-AT-GAAAA
1 GGTT-ATCAAAATTTCATAG-GAA
* * * *
2997 GGTTCTCGAAATTTCATAGTAT
1 GGTTATCAAAATTTCATAGGAA
* * *
3019 TGTTATTAAAATTTCATAAGAA
1 GGTTATCAAAATTTCATAGGAA
3041 GGTTATC-AAATTTCATAAGG-A
1 GGTTATCAAAATTTCAT-AGGAA
*
3062 GGTCATCAAAA
1 GGTTATCAAAA
3073 ATAGTGTAAT
Statistics
Matches: 109, Mismatches: 24, Indels: 18
0.72 0.16 0.12
Matches are distributed among these distances:
21 24 0.22
22 74 0.68
23 11 0.10
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGGAA
Found at i:10982 original size:11 final size:10
Alignment explanation
Indices: 10975--11036 Score: 70
Period size: 11 Copynumber: 5.9 Consensus size: 10
10965 TGGCCGGGTT
10975 CGGGCCGGGC
1 CGGGCCGGGC
*
10985 CGGGTTCGGGC
1 CGGG-CCGGGC
*
10996 CGGGCCGGGTT
1 CGGGCCGGG-C
11007 CGGGCCGGGC
1 CGGGCCGGGC
*
11017 CGGGTTCGGGC
1 CGGG-CCGGGC
11028 CGGGCCGGG
1 CGGGCCGGG
11037 TTCGGAGATT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
10 16 0.37
11 27 0.63
ACGTcount: A:0.00, C:0.32, G:0.58, T:0.10
Consensus pattern (10 bp):
CGGGCCGGGC
Found at i:10985 original size:5 final size:5
Alignment explanation
Indices: 10975--11036 Score: 70
Period size: 5 Copynumber: 11.8 Consensus size: 5
10965 TGGCCGGGTT
* * *
10975 CGGGC CGGGC CGGGTT CGGGC CGGGC CGGGTT CGGGC CGGGC CGGGTT
1 CGGGC CGGGC CGGG-C CGGGC CGGGC CGGG-C CGGGC CGGGC CGGG-C
11023 CGGGC CGGGC CGGG
1 CGGGC CGGGC CGGG
11037 TTCGGAGATT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
5 36 0.75
6 12 0.25
ACGTcount: A:0.00, C:0.32, G:0.58, T:0.10
Consensus pattern (5 bp):
CGGGC
Found at i:10987 original size:16 final size:16
Alignment explanation
Indices: 10966--11041 Score: 152
Period size: 16 Copynumber: 4.8 Consensus size: 16
10956 ACCTGTTCAT
10966 GGCCGGGTTCGGGCCG
1 GGCCGGGTTCGGGCCG
10982 GGCCGGGTTCGGGCCG
1 GGCCGGGTTCGGGCCG
10998 GGCCGGGTTCGGGCCG
1 GGCCGGGTTCGGGCCG
11014 GGCCGGGTTCGGGCCG
1 GGCCGGGTTCGGGCCG
11030 GGCCGGGTTCGG
1 GGCCGGGTTCGG
11042 AGATTAAGAC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 60 1.00
ACGTcount: A:0.00, C:0.30, G:0.57, T:0.13
Consensus pattern (16 bp):
GGCCGGGTTCGGGCCG
Found at i:12119 original size:27 final size:27
Alignment explanation
Indices: 12089--12150 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
12079 ATGGAAAAGA
*
12089 TTAATTTTGCTT-AAGTATAAAGCTGGT
1 TTAATTTTGCTTGAAATA-AAAGCTGGT
**
12116 TTAATTTTTTTTTGAAATAAAAGCTGGT
1 TTAA-TTTTGCTTGAAATAAAAGCTGGT
12144 TTAATTT
1 TTAATTT
12151 AAGCGATCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 7 0.23
28 19 0.63
29 4 0.13
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.50
Consensus pattern (27 bp):
TTAATTTTGCTTGAAATAAAAGCTGGT
Found at i:12825 original size:11 final size:11
Alignment explanation
Indices: 12811--12843 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
12801 ATTCATAACA
12811 AATTTATAATT
1 AATTTATAATT
12822 AATTTATAATT
1 AATTTATAATT
12833 -ATTTGATAATT
1 AATTT-ATAATT
12844 TTTTTCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
AATTTATAATT
Found at i:15929 original size:11 final size:11
Alignment explanation
Indices: 15902--15934 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
15892 TCGTTCATTC
15902 TCTTTCTATCTT
1 TCTTTCT-TCTT
15914 T-TTTCTTCTT
1 TCTTTCTTCTT
15924 TCTTTCTTCTT
1 TCTTTCTTCTT
15935 CTGTGTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.25
11 14 0.70
12 1 0.05
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (11 bp):
TCTTTCTTCTT
Found at i:27919 original size:20 final size:20
Alignment explanation
Indices: 27896--27937 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
27886 TTGAATAATA
* *
27896 ATAATTATTTTATAATTATT
1 ATAATCATTTTATAATCATT
27916 ATAATCATTTTATAATCATT
1 ATAATCATTTTATAATCATT
27936 AT
1 AT
27938 TATTTCAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
ATAATCATTTTATAATCATT
Found at i:30586 original size:19 final size:19
Alignment explanation
Indices: 30548--30586 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
30538 CGTGTATCTG
*
30548 TAATCGTTTCACCACTGTT
1 TAATCGTTTCACCACCGTT
*
30567 TAATCGTTTCATCACCGTT
1 TAATCGTTTCACCACCGTT
30586 T
1 T
30587 TGAGACCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.10, T:0.44
Consensus pattern (19 bp):
TAATCGTTTCACCACCGTT
Found at i:30661 original size:21 final size:20
Alignment explanation
Indices: 30637--30695 Score: 84
Period size: 19 Copynumber: 3.0 Consensus size: 20
30627 GCTGCTCTAA
*
30637 TAATTTCATCTGTACAGTTG
1 TAATCTCATCTGTACAGTTG
*
30657 CTAATCTAATCTGTACAG-TG
1 -TAATCTCATCTGTACAGTTG
30677 TAATCTCATCTGTACAGTT
1 TAATCTCATCTGTACAGTT
30696 ACTAGACAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 16 0.47
20 3 0.09
21 15 0.44
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTTG
Found at i:35087 original size:2 final size:2
Alignment explanation
Indices: 35080--35106 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35070 TATGTAATGG
35080 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
35107 CTAAATCTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49215 original size:23 final size:23
Alignment explanation
Indices: 49175--49228 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
49165 TAAAATAATT
**
49175 ATAAAAATATTGAATTTAACTA-A
1 ATAAAAATAGAGAATTT-ACTACA
* *
49198 ATAAAAATAGAGATTTTAGTACA
1 ATAAAAATAGAGAATTTACTACA
49221 ATAAAAAT
1 ATAAAAAT
49229 TTAAAAGTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.31
Consensus pattern (23 bp):
ATAAAAATAGAGAATTTACTACA
Found at i:50321 original size:12 final size:12
Alignment explanation
Indices: 50306--50330 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50296 AATAACAAAA
50306 TAAATATATAAT
1 TAAATATATAAT
50318 TAAATATATAAT
1 TAAATATATAAT
50330 T
1 T
50331 TTTTTCTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAATATATAAT
Found at i:51270 original size:17 final size:17
Alignment explanation
Indices: 51248--51280 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
51238 AATTCATAGT
51248 TAATCTTAACTCTTAAA
1 TAATCTTAACTCTTAAA
51265 TAATCTTAACTCTTAA
1 TAATCTTAACTCTTAA
51281 TAACTAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATCTTAACTCTTAAA
Done.