Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014057.1 Corchorus capsularis cultivar CVL-1 contig14078, 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: 19024
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:6899 original size:28 final size:26
Alignment explanation
Indices: 6868--6928 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 26
6858 TTATTTTAGA
6868 CAAACTCTTAACCAATTTTAATCTCAAC
1 CAAACTCTT-A-CAATTTTAATCTCAAC
6896 CAAACTC--ACAATTTTAATCTCAAC
1 CAAACTCTTACAATTTTAATCTCAAC
*
6920 CAACCTCTT
1 CAAACTCTT
6929 CAAGATTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 22 0.73
25 1 0.03
28 7 0.23
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (26 bp):
CAAACTCTTACAATTTTAATCTCAAC
Found at i:7038 original size:34 final size:33
Alignment explanation
Indices: 6994--7101 Score: 126
Period size: 34 Copynumber: 3.1 Consensus size: 33
6984 ATATCCACTT
6994 AACCCGTAATATATAATTAGAATTGGACTAAGAA
1 AACCCGTAATATATAATTAGAATTGGACTAA-AA
* *
7028 AACCCATAATATATAATTTGAATTGGACTAATAAAA
1 AACCCGTAATATATAATTAGAATTGGAC---TAAAA
*
7064 TTCAACCCGTAATATATAATTGGAATTGGACTAAAA
1 ---AACCCGTAATATATAATTAGAATTGGACTAAAA
7100 AA
1 AA
7102 TTCAATTTGA
Statistics
Matches: 64, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
33 2 0.03
34 26 0.41
36 7 0.11
37 3 0.05
39 26 0.41
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (33 bp):
AACCCGTAATATATAATTAGAATTGGACTAAAA
Found at i:7071 original size:39 final size:38
Alignment explanation
Indices: 6994--7106 Score: 153
Period size: 39 Copynumber: 3.1 Consensus size: 38
6984 ATATCCACTT
*
6994 AACCCGTAATATATAATTAGAATTGGACT-AAGAA---
1 AACCCGTAATATATAATTAGAATTGGACTAAAAAATTC
* *
7028 AACCCATAATATATAATTTGAATTGGACTAATAAAATTC
1 AACCCGTAATATATAATTAGAATTGGACTAA-AAAATTC
*
7067 AACCCGTAATATATAATTGGAATTGGACTAAAAAATTC
1 AACCCGTAATATATAATTAGAATTGGACTAAAAAATTC
7105 AA
1 AA
7107 TTTGATTACT
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
34 27 0.39
35 1 0.01
36 3 0.04
38 9 0.13
39 29 0.42
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (38 bp):
AACCCGTAATATATAATTAGAATTGGACTAAAAAATTC
Found at i:11019 original size:2 final size:2
Alignment explanation
Indices: 11005--11104 Score: 58
Period size: 2 Copynumber: 54.0 Consensus size: 2
10995 CCCATATTAC
* * *
11005 TA TA TA T- TA -A TA TA TA TA TA TA T- TA TG TA -A TA CA TA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
11043 TT TA T- TA TT TCA -A TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
11083 TA -A CA TCA TA -A TA TA TA T- TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA
11105 CTAAATAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 24
0.69 0.09 0.22
Matches are distributed among these distances:
1 10 0.13
2 64 0.84
3 2 0.03
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:11102 original size:53 final size:51
Alignment explanation
Indices: 11005--11103 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
10995 CCCATATTAC
* * * *
11005 TATATATTAATATATATATATATTATGTAATACATATCTTTATTATTTCAA
1 TATATATTAATATATATATATATTATATAACACATATATATATTATTTCAA
11056 TATATA-TATATATATATATATATTATATAACATCATAATATATATTAT
1 TATATATTA-ATATATATATATATTATATAACA-CAT-ATATATATTAT
11104 ACTAAATAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
50 2 0.05
51 27 0.66
52 3 0.07
53 9 0.22
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.49
Consensus pattern (51 bp):
TATATATTAATATATATATATATTATATAACACATATATATATTATTTCAA
Found at i:11151 original size:25 final size:24
Alignment explanation
Indices: 11105--11151 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
11095 ATATATTATA
*
11105 CTAAATAAATATTTTTATAAATCC
1 CTAAATAAATATTTTTAAAAATCC
11129 CTAAA-AAATATATTTATAAAAAT
1 CTAAATAAATAT-TTT-TAAAAAT
11152 TATGGTTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 8 0.40
25 6 0.30
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (24 bp):
CTAAATAAATATTTTTAAAAATCC
Found at i:11773 original size:4 final size:4
Alignment explanation
Indices: 11766--11797 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
11756 TATAATTCTC
11766 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
11798 TTTTTTCCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:12247 original size:13 final size:13
Alignment explanation
Indices: 12225--12264 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
12215 CAGAGAATAT
12225 TATCAACAGAAGA
1 TATCAACAGAAGA
*
12238 TATCATCAGAAGA
1 TATCAACAGAAGA
* *
12251 TTTCAACTGAAGA
1 TATCAACAGAAGA
12264 T
1 T
12265 TATATGGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (13 bp):
TATCAACAGAAGA
Found at i:12298 original size:21 final size:22
Alignment explanation
Indices: 12257--12299 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
12247 AAGATTTCAA
*
12257 CTGAAGATTATATGGAGATTAT
1 CTGAAGATTATAAGGAGATTAT
*
12279 CTGAAGATT-TAAGTAGATTAT
1 CTGAAGATTATAAGGAGATTAT
12300 ATTTAGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (22 bp):
CTGAAGATTATAAGGAGATTAT
Found at i:12684 original size:41 final size:41
Alignment explanation
Indices: 12627--12824 Score: 231
Period size: 41 Copynumber: 4.8 Consensus size: 41
12617 AATAATATTG
*
12627 AAAATTACCT-TTGACACCAGAAGTTGTCATTTTGGTAAATT
1 AAAATTA-CTATTGACACCAGAAGTTGTCACTTTGGTAAATT
* * * *
12668 AAAATTACTACTGACACTAGAAGTTATCACCTTGGTAAATT
1 AAAATTACTATTGACACCAGAAGTTGTCACTTTGGTAAATT
* *
12709 AAAATTACTTTTGACACCAGAAGTTGACACTTTGGTAAATT
1 AAAATTACTATTGACACCAGAAGTTGTCACTTTGGTAAATT
* ***
12750 AAAATTATCT-TTGACACCAGAAG-TGTTACTCCAGTAAATT
1 AAAATTA-CTATTGACACCAGAAGTTGTCACTTTGGTAAATT
* *
12790 ATAATTACTATTGACACCAGAAATTGTCACCTTTG
1 AAAATTACTATTGACACCAGAAGTTGTCA-CTTTG
12825 AATTTCCCCC
Statistics
Matches: 130, Mismatches: 22, Indels: 9
0.81 0.14 0.06
Matches are distributed among these distances:
39 2 0.02
40 32 0.25
41 92 0.71
42 4 0.03
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (41 bp):
AAAATTACTATTGACACCAGAAGTTGTCACTTTGGTAAATT
Found at i:14146 original size:50 final size:50
Alignment explanation
Indices: 14071--14172 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
14061 TGTCAACATC
*
14071 AACATTTGAGAAATTACTTTATGGCTTTGGTATATGTGGCGAGTTAGTAA
1 AACATTTGAGAAATTACTTTATGGCTTTGGTATATGTGGCGAGCTAGTAA
14121 AACATTTGAGAAATTACTTTATGGCTTTGGTATATGTGGCGAGCTAGTAA
1 AACATTTGAGAAATTACTTTATGGCTTTGGTATATGTGGCGAGCTAGTAA
14171 AA
1 AA
14173 TGCAAGATTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.36
Consensus pattern (50 bp):
AACATTTGAGAAATTACTTTATGGCTTTGGTATATGTGGCGAGCTAGTAA
Found at i:14712 original size:34 final size:35
Alignment explanation
Indices: 14674--14749 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
14664 TTATCTGGAG
* *
14674 ATTATCTGAATATTTAA-GTAGATTAT-ATTTAGAT
1 ATTATCTGAATATGTAATCTAGATT-TGATTTAGAT
* *
14708 ATTATTTGATTATGTAATCTAGATTTGATTTAGAT
1 ATTATCTGAATATGTAATCTAGATTTGATTTAGAT
*
14743 TTTATCT
1 ATTATCT
14750 CTTCAGATGA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
34 15 0.44
35 19 0.56
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (35 bp):
ATTATCTGAATATGTAATCTAGATTTGATTTAGAT
Found at i:16505 original size:69 final size:69
Alignment explanation
Indices: 16394--16531 Score: 267
Period size: 69 Copynumber: 2.0 Consensus size: 69
16384 CAGGACCTAA
*
16394 GTTACTTATTCATAATTAATTGTTTATTACTTTTCTCAAGAGTGAGTTCTTGTTTAGAAGGAATT
1 GTTACTTATTCATAATTAATTGTTTATTACTTTTCTCAAGAGTGAGTTCTTGCTTAGAAGGAATT
16459 ATAT
66 ATAT
16463 GTTACTTATTCATAATTAATTGTTTATTACTTTTCTCAAGAGTGAGTTCTTGCTTAGAAGGAATT
1 GTTACTTATTCATAATTAATTGTTTATTACTTTTCTCAAGAGTGAGTTCTTGCTTAGAAGGAATT
16528 ATAT
66 ATAT
16532 TTAGAGTTTA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.47
Consensus pattern (69 bp):
GTTACTTATTCATAATTAATTGTTTATTACTTTTCTCAAGAGTGAGTTCTTGCTTAGAAGGAATT
ATAT
Found at i:17468 original size:19 final size:19
Alignment explanation
Indices: 17444--17484 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
17434 ACTGTCAGTG
17444 TATCAAATATAAACTCTTA
1 TATCAAATATAAACTCTTA
17463 TATCAAATATAAACTCTTA
1 TATCAAATATAAACTCTTA
17482 TAT
1 TAT
17485 TTATGTTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (19 bp):
TATCAAATATAAACTCTTA
Found at i:17802 original size:27 final size:27
Alignment explanation
Indices: 17764--17818 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
17754 TACATTATAA
*
17764 TCTGTGTTTTTCTTAACTATTCATAGT
1 TCTGTGTGTTTCTTAACTATTCATAGT
17791 TCTGTGTGTTTCTTAACTATTCATAGT
1 TCTGTGTGTTTCTTAACTATTCATAGT
17818 T
1 T
17819 TTGGATTGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.18, C:0.15, G:0.13, T:0.55
Consensus pattern (27 bp):
TCTGTGTGTTTCTTAACTATTCATAGT
Done.