Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011701.1 Corchorus capsularis cultivar CVL-1 contig11722, 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: 74715
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:914 original size:6 final size:6
Alignment explanation
Indices: 903--941 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
893 AAAGCAAAGC
903 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA
942 GCAGAATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATCT
Found at i:953 original size:18 final size:18
Alignment explanation
Indices: 907--953 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
897 CAAAGCAAAT
* *
907 CTAAATCTAAATCTAAAT
1 CTAAATATAAATCTAAAG
*
925 CTAAATCTAAATCTAAAG
1 CTAAATATAAATCTAAAG
943 C-AGAATATAAA
1 CTA-AATATAAA
954 GCAAACAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.53, C:0.15, G:0.04, T:0.28
Consensus pattern (18 bp):
CTAAATATAAATCTAAAG
Found at i:1886 original size:10 final size:10
Alignment explanation
Indices: 1871--1896 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1861 GAGGACTCTA
1871 GAATTTTCTG
1 GAATTTTCTG
1881 GAATTTTCTG
1 GAATTTTCTG
1891 GAATTT
1 GAATTT
1897 GGCAGCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:3832 original size:15 final size:14
Alignment explanation
Indices: 3806--3839 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
3796 GGAAAATCCT
3806 AAAA-AAGAAAAGA
1 AAAATAAGAAAAGA
3819 AAAATAAGACAAAGA
1 AAAATAAGA-AAAGA
3834 AAAATA
1 AAAATA
3840 TTATGGGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.21
14 4 0.21
15 11 0.58
ACGTcount: A:0.79, C:0.03, G:0.12, T:0.06
Consensus pattern (14 bp):
AAAATAAGAAAAGA
Found at i:4122 original size:21 final size:22
Alignment explanation
Indices: 4076--4122 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
4066 GTGACTTGGC
*
4076 ATGGCGCGGCATAGGCTCGTGG
1 ATGGCGCGGCATAGGCTCGCGG
4098 -TGGCGCGGCAT-GG-TACGCGG
1 ATGGCGCGGCATAGGCT-CGCGG
4118 ATGGC
1 ATGGC
4123 TTGGCAAGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 1 0.05
20 6 0.27
21 15 0.68
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (22 bp):
ATGGCGCGGCATAGGCTCGCGG
Found at i:7743 original size:23 final size:23
Alignment explanation
Indices: 7687--7747 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
7677 GAAAAACGGA
7687 AAAAACTTTTTTTTTATCGACGC
1 AAAAACTTTTTTTTTATCGACGC
*
7710 AAAAACATTTTTTTTATCGACGC
1 AAAAACTTTTTTTTTATCGACGC
**
7733 -AATTCTTTTTTTTTA
1 AAAAACTTTTTTTTTA
7748 GAAAAAACGG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 12 0.35
23 22 0.65
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.49
Consensus pattern (23 bp):
AAAAACTTTTTTTTTATCGACGC
Found at i:8065 original size:6 final size:6
Alignment explanation
Indices: 8050--8081 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
8040 AAAGCAAAGC
8050 AAAT-T AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
8082 GCAGAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATCT
Found at i:8093 original size:18 final size:16
Alignment explanation
Indices: 8045--8084 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
8035 AAATCAAAGC
8045 AAAGCAAATTAAATCT
1 AAAGCAAATTAAATCT
*
8061 AAATCTAAATCTAAATCT
1 AAAGC-AAAT-TAAATCT
8079 AAAGCA
1 AAAGCA
8085 GAATATAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 4 0.20
17 5 0.25
18 11 0.55
ACGTcount: A:0.55, C:0.15, G:0.05, T:0.25
Consensus pattern (16 bp):
AAAGCAAATTAAATCT
Found at i:20871 original size:2 final size:2
Alignment explanation
Indices: 20864--20889 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20854 ATTCATTGTC
20864 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
20890 GTAGAGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21888 original size:2 final size:2
Alignment explanation
Indices: 21881--21909 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21871 TTGACTTCTT
21881 TA 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 TA T
21910 TAATGTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22225 original size:20 final size:20
Alignment explanation
Indices: 22200--22239 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
22190 CTATGGAAAA
*
22200 TTAATTATTATTTAATTTTG
1 TTAATTATTATTAAATTTTG
*
22220 TTAATTTTTATTAAATTTTG
1 TTAATTATTATTAAATTTTG
22240 GGAAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (20 bp):
TTAATTATTATTAAATTTTG
Found at i:23557 original size:2 final size:2
Alignment explanation
Indices: 23550--23582 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
23540 TTGACTTCTT
23550 TA TA TA 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 TA TA TA T
23583 TAATGCTGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24496 original size:2 final size:2
Alignment explanation
Indices: 24489--24521 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
24479 AGGTAATGGT
24489 TA TA TA 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 TA TA TA T
24522 GCCCATGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25805 original size:13 final size:13
Alignment explanation
Indices: 25784--25818 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
25774 TATAATTATA
*
25784 TATATATATAAAT
1 TATAAATATAAAT
*
25797 TATAAATATCAAT
1 TATAAATATAAAT
25810 TATAAATAT
1 TATAAATAT
25819 TCTCTTCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (13 bp):
TATAAATATAAAT
Found at i:28135 original size:2 final size:2
Alignment explanation
Indices: 28128--28158 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28118 GAATGGTATG
28128 TA TA 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 TA TA T
28159 TTGTATGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43637 original size:22 final size:22
Alignment explanation
Indices: 43607--43666 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
43597 AATAAAGATT
*
43607 GTGGTCGTGAGATTCGGCCATG
1 GTGGTCGTGAGATTCGGCCATA
*
43629 GTGGCCGTGAGATTCGGCCATA
1 GTGGTCGTGAGATTCGGCCATA
*
43651 GTGGTCATGAGATTCG
1 GTGGTCGTGAGATTCG
43667 ACCACATGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.17, C:0.18, G:0.38, T:0.27
Consensus pattern (22 bp):
GTGGTCGTGAGATTCGGCCATA
Found at i:46595 original size:42 final size:42
Alignment explanation
Indices: 46532--46615 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
46522 TCAAAAAAGT
*
46532 GCACCAATATAATTACATTAATAATGTCATGACAGTTACATA
1 GCACCAATATAATTACATTAATAATGTCATGACAGTCACATA
*
46574 GCACCAATATAATTACGTTAATAATGTCATGACAGTCACATA
1 GCACCAATATAATTACATTAATAATGTCATGACAGTCACATA
46616 TAGAAACATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.30
Consensus pattern (42 bp):
GCACCAATATAATTACATTAATAATGTCATGACAGTCACATA
Found at i:48933 original size:15 final size:14
Alignment explanation
Indices: 48878--48959 Score: 50
Period size: 14 Copynumber: 6.0 Consensus size: 14
48868 TAGTTTATGA
48878 TTAGTTTTAATTAG-
1 TTAG-TTTAATTAGT
* *
48892 TTAATTAAAATTA-T
1 TTAGTT-TAATTAGT
48906 TTAGTTT-ATTAGT
1 TTAGTTTAATTAGT
48919 TTATGTTTAATTAG-
1 TTA-GTTTAATTAGT
*
48933 -TA-TCTAATTAGT
1 TTAGTTTAATTAGT
*
48945 TTATTATTAATTAGT
1 TTAGT-TTAATTAGT
48960 ATTTAATCAG
Statistics
Matches: 53, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
11 8 0.15
12 4 0.08
13 10 0.19
14 18 0.34
15 13 0.25
ACGTcount: A:0.33, C:0.01, G:0.10, T:0.56
Consensus pattern (14 bp):
TTAGTTTAATTAGT
Found at i:48942 original size:26 final size:26
Alignment explanation
Indices: 48913--48980 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
48903 TATTTAGTTT
48913 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
48939 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
* *
48965 ATCAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
48981 AATGAAGGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 1 0.03
26 36 0.97
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.53
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:49024 original size:24 final size:25
Alignment explanation
Indices: 48989--49048 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
48979 AAAATGAAGG
*
48989 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
*
49012 GAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
49037 AAAATGAAGTTT
1 AAAATGAAGTTT
49049 AGGGTTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 7 0.22
24 7 0.22
25 18 0.56
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:56114 original size:2 final size:2
Alignment explanation
Indices: 56107--56138 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
56097 AACCTATAAC
*
56107 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56139 TTGACTCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:56120 original size:10 final size:10
Alignment explanation
Indices: 56101--56135 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
56091 TTAATAAACC
56101 TATA-ACATA
1 TATATACATA
56110 TATATACATA
1 TATATACATA
*
56120 TATATATATA
1 TATATACATA
56130 TATATA
1 TATATA
56136 TATTTGACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 4 0.17
10 20 0.83
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (10 bp):
TATATACATA
Found at i:57216 original size:3 final size:3
Alignment explanation
Indices: 57208--57243 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
57198 ATTGGCAGTA
57208 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
57244 ATATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:59609 original size:58 final size:58
Alignment explanation
Indices: 59517--59631 Score: 185
Period size: 58 Copynumber: 2.0 Consensus size: 58
59507 ATACTTTTTT
*
59517 TTCTACATTTTTTAAAAAGCAAAGATGTGATGCAATATTTGTAGTAGTGTACATGTTA
1 TTCTACATTTTTTAAAAAGCAAAGATATGATGCAATATTTGTAGTAGTGTACATGTTA
** * *
59575 TTCTACATTTTTTTTAAAGCAAAGATATGGTGCAATATTTGTAGTATTGTACATGTT
1 TTCTACATTTTTTAAAAAGCAAAGATATGATGCAATATTTGTAGTAGTGTACATGTT
59632 TCCATTGGGA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.43
Consensus pattern (58 bp):
TTCTACATTTTTTAAAAAGCAAAGATATGATGCAATATTTGTAGTAGTGTACATGTTA
Found at i:62699 original size:2 final size:2
Alignment explanation
Indices: 62692--62726 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
62682 ACATACCTAG
*
62692 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
62727 TCCTCTCTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:62998 original size:57 final size:58
Alignment explanation
Indices: 62897--63006 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 58
62887 TGCAGACATT
* * *
62897 TTGCAGAGATTCTTTTCATGGTGAGGATAACTTTGCAGAGCATTATTTTCTTCTTTTG
1 TTGCAGAGATTCTCTTCATGATGAGGATAACTTTGCAGAACATTATTTTCTTCTTTTG
*
62955 TTGCAGAGATTC-CTTCATGATGATGATAACTTTGCAGAACATTATTTTCTTC
1 TTGCAGAGATTCTCTTCATGATGAGGATAACTTTGCAGAACATTATTTTCTTC
63007 AACTTTTGAC
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
57 36 0.75
58 12 0.25
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (58 bp):
TTGCAGAGATTCTCTTCATGATGAGGATAACTTTGCAGAACATTATTTTCTTCTTTTG
Found at i:70634 original size:13 final size:13
Alignment explanation
Indices: 70611--70641 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
70601 TTAATACAGG
70611 TATCG-ACGGATA
1 TATCGAACGGATA
70623 TATCGAACGGATA
1 TATCGAACGGATA
70636 TATCGA
1 TATCGA
70642 GGTATCGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (13 bp):
TATCGAACGGATA
Found at i:71852 original size:18 final size:18
Alignment explanation
Indices: 71829--71863 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
71819 ATTTACGGAT
* *
71829 ATTTATGGATATATCGAG
1 ATTTATCGAGATATCGAG
71847 ATTTATCGAGATATCGA
1 ATTTATCGAGATATCGA
71864 TAAATATCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (18 bp):
ATTTATCGAGATATCGAG
Done.