Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007429.1 Corchorus capsularis cultivar CVL-1 contig07450, 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: 22620
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Found at i:572 original size:24 final size:26
Alignment explanation
Indices: 545--597 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
535 GAAATCGACA
*
545 AATTTTGT-A-AATAAAAAACATTAG
1 AATTTTGTGAGAATAAAAAACAGTAG
*
569 AATTTTTTGAGAATAAAAAACAGTAG
1 AATTTTGTGAGAATAAAAAACAGTAG
595 AAT
1 AAT
598 AAAAACTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.28
25 1 0.04
26 17 0.68
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.32
Consensus pattern (26 bp):
AATTTTGTGAGAATAAAAAACAGTAG
Found at i:2298 original size:16 final size:16
Alignment explanation
Indices: 2273--2314 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2263 AACAGAAACT
2273 TATAAT-ATAAT-ATA
1 TATAATAATAATAATA
2287 TATAATATATAATAATA
1 TATAATA-ATAATAATA
2304 -ATAATAATAAT
1 TATAATAATAAT
2315 GTTTAAGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.24
15 5 0.20
16 11 0.44
17 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TATAATAATAATAATA
Found at i:2303 original size:3 final size:3
Alignment explanation
Indices: 2274--2314 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
2264 ACAGAAACTT
2274 ATA AT- ATA AT- ATA TATA ATA TATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA -ATA ATA -ATA ATA ATA ATA ATA ATA AT
2315 GTTTAAGAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 4 0.12
3 24 0.71
4 6 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:9353 original size:21 final size:22
Alignment explanation
Indices: 9329--9384 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
9319 TTTTTAACTC
9329 ATTTTTTATTATTTAA-AATAT
1 ATTTTTTATTATTTAATAATAT
*
9350 ATTTATTATTTATTTAATAATAT
1 ATTTTTTA-TTATTTAATAATAT
* *
9373 ATATTATATTAT
1 ATTTTTTATTAT
9385 ATCTAATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 7 0.24
22 12 0.41
23 10 0.34
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTTTTATTATTTAATAATAT
Found at i:11693 original size:39 final size:42
Alignment explanation
Indices: 11599--11696 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 42
11589 CTCTCTCCCC
* * * *
11599 AAAGTCCCCAAACACATATAATACATGGACAATTCTCCTTCT
1 AAAGTCCCTAAACACATATAACACATGGACAATTCTCATACT
11641 AAAGT-CCTCAAACACATATAACACA-GAGAC-A-TCT-ATACT
1 AAAGTCCCT-AAACACATATAACACATG-GACAATTCTCATACT
11680 AAAGTCCCTAAACACAT
1 AAAGTCCCTAAACACAT
11697 GCAGCACAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
39 16 0.33
40 6 0.12
41 4 0.08
42 23 0.47
ACGTcount: A:0.43, C:0.28, G:0.07, T:0.22
Consensus pattern (42 bp):
AAAGTCCCTAAACACATATAACACATGGACAATTCTCATACT
Found at i:14196 original size:40 final size:40
Alignment explanation
Indices: 14140--14219 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
14130 CCACTCCAAC
14140 TTCCTGCTGTAAAAGTCGACACTCTTT-TCAATCAATGGGT
1 TTCCTGCTGTAAAAGTCGACACT-TTTCTCAATCAATGGGT
* *
14180 TTCCTGCTGTAGAAGTCGACGCTTTTCTCAATCAATGGGT
1 TTCCTGCTGTAAAAGTCGACACTTTTCTCAATCAATGGGT
14220 GGTAGAGAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 3 0.08
40 34 0.92
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.35
Consensus pattern (40 bp):
TTCCTGCTGTAAAAGTCGACACTTTTCTCAATCAATGGGT
Found at i:15114 original size:26 final size:25
Alignment explanation
Indices: 15077--15299 Score: 85
Period size: 26 Copynumber: 7.9 Consensus size: 25
15067 TTCTCTTCAA
15077 AAGTCCTCAAACACAAAGGCAGTCAT
1 AAGTCCTCAAACACAAAGGCA-TCAT
*
15103 AAGTCC-CTAAACACAGAGGCATCTATACT
1 AAGTCCTC-AAACACAAAGGCATC---A-T
*
15132 AAAAAGTCCTCAAACACAAGGGCATTCAT
1 ---AAGTCCTCAAACACAAAGGCA-TCAT
*
15161 AAGTCC-CTAAACACAGAGGCATCTATACT
1 AAGTCCTC-AAACACAAAGGCATC---A-T
*
15190 AAAAAGTCCTCAAACACAAGGGCATTCAT
1 ---AAGTCCTCAAACACAAAGGCA-TCAT
* *
15219 AAATCC-CTAAACACAGAGGCATCTATACT
1 AAGTCCTC-AAACACAAAGGCATC---A-T
*
15248 AAAAAGTCCTCAAACACAAGGGCATTCAT
1 ---AAGTCCTCAAACACAAAGGCA-TCAT
*
15277 AAGTCC-CTAAACACAGAGGCATC
1 AAGTCCTC-AAACACAAAGGCATC
15300 TATATCAAAG
Statistics
Matches: 151, Mismatches: 15, Indels: 63
0.66 0.07 0.28
Matches are distributed among these distances:
25 12 0.08
26 68 0.45
28 3 0.02
29 6 0.04
30 3 0.02
32 50 0.33
33 9 0.06
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.18
Consensus pattern (25 bp):
AAGTCCTCAAACACAAAGGCATCAT
Found at i:15145 original size:58 final size:58
Alignment explanation
Indices: 15075--15303 Score: 431
Period size: 58 Copynumber: 3.9 Consensus size: 58
15065 TATTCTCTTC
* *
15075 AAAAGTCCTCAAACACAAAGGCAGTCATAAGTCCCTAAACACAGAGGCATCTATACTA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
15133 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
*
15191 AAAAGTCCTCAAACACAAGGGCATTCATAAATCCCTAAACACAGAGGCATCTATACTA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
15249 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATA
15304 TCAAAGTCCC
Statistics
Matches: 167, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 167 1.00
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.18
Consensus pattern (58 bp):
AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
Found at i:16222 original size:35 final size:35
Alignment explanation
Indices: 16129--16224 Score: 93
Period size: 35 Copynumber: 2.7 Consensus size: 35
16119 ATTTCATCAG
* * * *
16129 ATTCAGCACTTGGGGGCTGCAGAAACCCCTTCATC
1 ATTCAACACTTGGGGGCTCCAGCAACCCATTCATC
* ** * *
16164 ATTCAACAATTGGGTACTCCAGCAACTCATTCTTC
1 ATTCAACACTTGGGGGCTCCAGCAACCCATTCATC
* *
16199 ATTCAATACTTGGGGGCTTCAGCAAC
1 ATTCAACACTTGGGGGCTCCAGCAAC
16225 AAAAATTTCA
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (35 bp):
ATTCAACACTTGGGGGCTCCAGCAACCCATTCATC
Found at i:16680 original size:72 final size:72
Alignment explanation
Indices: 16573--16990 Score: 531
Period size: 72 Copynumber: 5.8 Consensus size: 72
16563 ACATGGTCCC
*
16573 CTTCTTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACA
1 CTTCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACA
* *
16638 TGATCCC
66 TGATACT
* ** * * *
16645 CTTCTTCATTGCGATTGTAGCTAAGACAGTTCCCACAATTGGCAGTTCTTCGCACAATCCTTACA
1 CTTCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACA
16710 TGATACT
66 TGATACT
* * * *
16717 CTTCAT-ATTGCGGTTGTAGCCGAGGCAGTTCCTACATGTGGCAGTCCTTCACACAATCCTTACA
1 CTTCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACA
*
16781 TGATAGT
66 TGATACT
* * * * *
16788 CTTCCAT-ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCATTTGCACAACCCTTAT
1 CTT-CATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
**
16852 GCGATTA-T
65 ATGA-TACT
* * **
16860 ATTCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATACTTATG
1 CTTCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACA
16925 TGATTA-T
66 TGA-TACT
* *
16932 CTTCCTCATTGTGATTGTAGCCGAGGCAGTTCCCACA-TTGGCAGTCCTTCGCACAATCC
1 CTTCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCC
16991 ATGCTACTAC
Statistics
Matches: 305, Mismatches: 38, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
71 82 0.27
72 221 0.72
73 2 0.01
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.32
Consensus pattern (72 bp):
CTTCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACA
TGATACT
Found at i:16760 original size:143 final size:144
Alignment explanation
Indices: 16578--16990 Score: 521
Period size: 143 Copynumber: 2.9 Consensus size: 144
16568 GTCCCCTTCT
*
16578 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATC
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
** * ** *
16643 CCCTTCTTCATTGCGATTGTAGCTAAGACAGTTCCCACAATTGGCAGTTCTTCGCACAATCCTTA
66 ATCTTCATCATTGCGATTGTAGCCGAGGCAGTTCCCACAATTGGCAGTTCTTCGCACAATCCTTA
* *
16708 CATGA-TACTCTTCA
131 CACGATTA-TATTCA
* * * *
16722 T-ATTGCGGTTGTAGCCGAGGCAGTTCCTACATGTGGCAGTCCTTCACACAATCCTTACATGATA
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
* * * * *
16786 GTCTTCCAT-ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAG-TCATTTGCACAACCCT
66 ATCTT-CATCATTGCGATTGTAGCCGAGGCAGTTCCCACAATTGGCAGTTC-TTCGCACAATCCT
**
16849 TATGCGATTATATTCA
129 TACACGATTATATTCA
* ** *
16865 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATACTTATGTGATT
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
* * *
16930 ATCTTCCTCATTGTGATTGTAGCCGAGGCAGTTCCCAC-ATTGGCAGTCCTTCGCACAATCC
66 ATCTTCATCATTGCGATTGTAGCCGAGGCAGTTCCCACAATTGGCAGTTCTTCGCACAATCC
16991 ATGCTACTAC
Statistics
Matches: 228, Mismatches: 35, Indels: 13
0.83 0.13 0.05
Matches are distributed among these distances:
142 2 0.01
143 134 0.59
144 92 0.40
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.31
Consensus pattern (144 bp):
TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
ATCTTCATCATTGCGATTGTAGCCGAGGCAGTTCCCACAATTGGCAGTTCTTCGCACAATCCTTA
CACGATTATATTCA
Found at i:16976 original size:215 final size:215
Alignment explanation
Indices: 16580--16990 Score: 565
Period size: 215 Copynumber: 1.9 Consensus size: 215
16570 CCCCTTCTTC
* * * *
16580 ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATCCC
1 ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCATTCGCACAACCCTTACACGATCAC
* * * * *
16645 CTTCTTCATTGCGATTGTAGCTAAGACAGTTCCCACAATTGGCAGTTCTTCGCACAATCCTTACA
66 ATTCATCATTGCGATTGTAGCCAAGACAGTTCCCACAATTGGCAGTCCTTCGCACAATACTTACA
* *
16710 TGATACTCTTCATATTGCGGTTGTAGCCGAGGCAGTTCCTACATGTGGCAGTCCTTCACACAATC
131 TGATACTCTTCATATTGCGATTGTAGCCGAGGCAGTTCCCACATGTGGCAGTCCTTCACACAATC
16775 CTTACATGATAGTCTTCCAT
196 CTTACATGATAGTCTTCCAT
* * ** * *
16795 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCATTTGCACAACCCTTATGCGATTAT
1 ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCATTCGCACAACCCTTACACGATCAC
* * * **
16860 ATTCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATACTTATG
66 ATTCATCATTGCGATTGTAGCCAAGACAGTTCCCACAATTGGCAGTCCTTCGCACAATACTTACA
* * *
16925 TGATTA-TCTTCCTCATTGTGATTGTAGCCGAGGCAGTTCCCACAT-TGGCAGTCCTTCGCACAA
131 TGA-TACTCTTCAT-ATTGCGATTGTAGCCGAGGCAGTTCCCACATGTGGCAGTCCTTCACACAA
16988 TCC
194 TCC
16991 ATGCTACTAC
Statistics
Matches: 169, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
215 139 0.82
216 30 0.18
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.31
Consensus pattern (215 bp):
ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCATTCGCACAACCCTTACACGATCAC
ATTCATCATTGCGATTGTAGCCAAGACAGTTCCCACAATTGGCAGTCCTTCGCACAATACTTACA
TGATACTCTTCATATTGCGATTGTAGCCGAGGCAGTTCCCACATGTGGCAGTCCTTCACACAATC
CTTACATGATAGTCTTCCAT
Found at i:17665 original size:16 final size:16
Alignment explanation
Indices: 17644--17674 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17634 AACGGAAGGT
*
17644 TACCGCAGTAGAATGG
1 TACCGCAGCAGAATGG
17660 TACCGCAGCAGAATG
1 TACCGCAGCAGAATG
17675 TCGCCGCATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.23, G:0.29, T:0.16
Consensus pattern (16 bp):
TACCGCAGCAGAATGG
Done.