Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015111.1 Corchorus olitorius cultivar O-4 contig15144, 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: 20653
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Found at i:835 original size:13 final size:12
Alignment explanation
Indices: 799--845 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
789 TCAATTTTTA
*
799 TATATATTGATAA
1 TATATATT-ATAT
*
812 TA-ATGTTATAT
1 TATATATTATAT
823 TATATTATTATAT
1 TATA-TATTATAT
836 TATATATTAT
1 TATATATTAT
846 CAATAAACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:992 original size:17 final size:17
Alignment explanation
Indices: 970--1002 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
960 TCGAAATCAA
*
970 ACCCGAGCCCGAACCCT
1 ACCCGAGACCGAACCCT
987 ACCCGAGACCGAACCC
1 ACCCGAGACCGAACCC
1003 GAAAATACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.52, G:0.18, T:0.03
Consensus pattern (17 bp):
ACCCGAGACCGAACCCT
Found at i:1020 original size:16 final size:16
Alignment explanation
Indices: 995--1087 Score: 102
Period size: 16 Copynumber: 5.8 Consensus size: 16
985 CTACCCGAGA
995 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
1011 CCGAATCCGACATAAT--
1 CCGAACCCGA-A-AATAC
1027 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
**
1043 CCGAACCCG-ACTTAAC
1 CCGAACCCGAAAAT-AC
*
1059 CCGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
1075 CCGAACCCGAAAA
1 CCGAACCCGAAAA
1088 AGGCCAAACC
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
14 3 0.05
15 3 0.05
16 51 0.81
17 3 0.05
18 3 0.05
ACGTcount: A:0.40, C:0.38, G:0.14, T:0.09
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:1033 original size:32 final size:32
Alignment explanation
Indices: 995--1084 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
985 CTACCCGAGA
* *
995 CCGAACCCGAAAATACCCGAATCCGACATAAT
1 CCGAACCCGAAAATACCCGAACCCGACATAAC
*
1027 CCGAACCCGAAAATACCCGAACCCGACTTAAC
1 CCGAACCCGAAAATACCCGAACCCGACATAAC
*
1059 CCGAGCCCGAAAATACCCGAACCCGA
1 CCGAACCCGAAAATACCCGAACCCGA
1085 AAAAGGCCAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.38, C:0.39, G:0.14, T:0.09
Consensus pattern (32 bp):
CCGAACCCGAAAATACCCGAACCCGACATAAC
Found at i:3298 original size:17 final size:16
Alignment explanation
Indices: 3276--3321 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 16
3266 GCATTGTTAT
3276 TTTATAGAGATTATTAA
1 TTTATAGAG-TTATTAA
*
3293 TTTATAGAG-TATTAT
1 TTTATAGAGTTATTAA
3308 TTTATAGAGGTTAT
1 TTTATAGA-GTTAT
3322 ATCGTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 13 0.50
16 1 0.04
17 12 0.46
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (16 bp):
TTTATAGAGTTATTAA
Found at i:3311 original size:15 final size:16
Alignment explanation
Indices: 3272--3316 Score: 65
Period size: 15 Copynumber: 2.8 Consensus size: 16
3262 GTGTGCATTG
3272 TTATTTTATAGAGATTA
1 TTATTTTATAGAGA-TA
*
3289 TTAATTTATAGAG-TA
1 TTATTTTATAGAGATA
3304 TTATTTTATAGAG
1 TTATTTTATAGAG
3317 GTTATATCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 14 0.54
17 12 0.46
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (16 bp):
TTATTTTATAGAGATA
Found at i:4359 original size:22 final size:22
Alignment explanation
Indices: 4312--4360 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
4302 TATTTTTATG
** * *
4312 AAATTTTGATAATTACCCTATT
1 AAATTTTGATAACCACCATATA
4334 AAATTTTGATAACCACCATATA
1 AAATTTTGATAACCACCATATA
4356 AAATT
1 AAATT
4361 GTGACAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.14, G:0.04, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAACCACCATATA
Found at i:7239 original size:43 final size:43
Alignment explanation
Indices: 7106--7426 Score: 424
Period size: 41 Copynumber: 7.6 Consensus size: 43
7096 CCAATAACCA
* *
7106 AAAGTCCCCAAACACATATATAACACAGGGGCATCTTTATTCC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
* * * *
7149 AAAAGTCCTCAAACACATATATAACACAGAGACATCTATATT-C
1 -AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
*
7192 -AAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
* *
7234 AAAGTCCTCAAACACATATATAACACAGAGGCATC-C-A-TATC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTA-C
* *
7275 AAAGTCCCCAAACACATATATAACACAGGAGCAACTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
* * *
7318 AAAGTCCTCAAACACATATATAAAACAGAGGCAT-T-TA-TATC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTA-C
7359 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
*
7402 AAAGTCCTCAAACACATATATAACA
1 AAAGTCCCCAAACACATATATAACA
7427 TATATGCATT
Statistics
Matches: 242, Mismatches: 25, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
40 4 0.02
41 102 0.42
42 5 0.02
43 90 0.37
44 41 0.17
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
Found at i:7437 original size:84 final size:84
Alignment explanation
Indices: 7106--7426 Score: 536
Period size: 84 Copynumber: 3.8 Consensus size: 84
7096 CCAATAACCA
* *
7106 AAAGTCCCCAAACACATATATAACACAGGGGCATCTTTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC-AAAGTCCTCAAACACATATAT
*
7171 AACACAGAGACATCTATATTC
65 AACACAGAGGCATCTATA-TC
*
7192 -AAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
*
7256 ACACAGAGGCATCCATATC
66 ACACAGAGGCATCTATATC
* *
7275 AAAGTCCCCAAACACATATATAACACAGGAGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
* *
7340 AAACAGAGGCATTTATATC
66 ACACAGAGGCATCTATATC
7359 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
7424 ACA
66 ACA
7427 TATATGCATT
Statistics
Matches: 221, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
83 2 0.01
84 180 0.81
85 39 0.18
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Found at i:18434 original size:34 final size:35
Alignment explanation
Indices: 18351--18436 Score: 102
Period size: 35 Copynumber: 2.5 Consensus size: 35
18341 AAGATTAAAG
* * **
18351 CTCCTTCCTCATTCAACACTTGGGGGCTCTGGCAA
1 CTCCTTCATCATTCAACACTTCGGGGCTCCAGCAA
*
18386 CCCCTTTCATCATTCAACA-TTCGGGGCTCCAGCAA
1 CTCC-TTCATCATTCAACACTTCGGGGCTCCAGCAA
*
18421 TTCCTTCATCATTCAA
1 CTCCTTCATCATTCAA
18437 TGCTTGGGGG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
34 12 0.28
35 18 0.42
36 13 0.30
ACGTcount: A:0.21, C:0.35, G:0.14, T:0.30
Consensus pattern (35 bp):
CTCCTTCATCATTCAACACTTCGGGGCTCCAGCAA
Found at i:18447 original size:35 final size:33
Alignment explanation
Indices: 18351--18448 Score: 88
Period size: 35 Copynumber: 2.8 Consensus size: 33
18341 AAGATTAAAG
* **
18351 CTCCTTCCTCATTCAACACTTGGGGGCTCTGGCAA
1 CTCCTTCATCATTC-A-ACTTGGGGGCTCCAGCAA
* *
18386 CCCCTTTCATCATTCAACATTCGGGGCTCCAGCAA
1 CTCC-TTCATCATTCAAC-TTGGGGGCTCCAGCAA
*
18421 TTCCTTCATCATTCAATGCTTGGGGGCT
1 CTCCTTCATCATTCAA--CTTGGGGGCT
18449 ATGTCATACT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
34 14 0.27
35 27 0.53
36 10 0.20
ACGTcount: A:0.18, C:0.33, G:0.18, T:0.31
Consensus pattern (33 bp):
CTCCTTCATCATTCAACTTGGGGGCTCCAGCAA
Found at i:18807 original size:72 final size:72
Alignment explanation
Indices: 18724--19065 Score: 481
Period size: 72 Copynumber: 4.8 Consensus size: 72
18714 CCTCTTCTTC
* * *
18724 ATTGCGATTGTAGCCGAGGCAGTTCCCAGATTTGGCAGTCCTTCACACAATCCTTACGTGATAAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAAT
18789 CTTCCAT
66 CTTCCAT
* * **
18796 ATTGCGGTTGTAGCCGAGGTAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTTT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAAT
* *
18861 CTTTCGT
66 CTTCCAT
* * * *
18868 ATTGCGGTTGTAGCCGAGGCAGTTCCAACATTTGGCAGTTCTTCGCGCAATCCTTACATGATAAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAAT
18933 CTTCCAT
66 CTTCCAT
* * *
18940 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCTTTCGCACAATCCTTATGTGATTAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAAT
*
19005 C-TCCCT
66 CTTCCAT
* * *
19011 CATTGCGATTGTAGCAGAGGCAGTTCCCACA-TTGGCAGTCCTTCGCGCAATCCTT
1 -ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTT
19066 GCTAGTAATC
Statistics
Matches: 238, Mismatches: 31, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
71 26 0.11
72 212 0.89
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.32
Consensus pattern (72 bp):
ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAAT
CTTCCAT
Found at i:18985 original size:144 final size:144
Alignment explanation
Indices: 18722--19065 Score: 548
Period size: 144 Copynumber: 2.4 Consensus size: 144
18712 GTCCTCTTCT
* * * *
18722 TCATTGCGATTGTAGCCGAGGCAGTTCCCAGATTTGGCAGTCCTTCACACAATCCTTACGTGATA
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCGCAATCCTTACATGATA
*
18787 ATCTTCCATATTGCGGTTGTAGCCGAGGTAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
66 ATCTTCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
* * *
18852 TGTGATTTTCTTTCG
131 TGTGATTATC-TCCC
* * *
18867 T-ATTGCGGTTGTAGCCGAGGCAGTTCCAACATTTGGCAGTTCTTCGCGCAATCCTTACATGATA
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCGCAATCCTTACATGATA
*
18931 ATCTTCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCTTTCGCACAATCCTTA
66 ATCTTCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
18996 TGTGATTATCTCCC
131 TGTGATTATCTCCC
*
19010 TCATTGCGATTGTAGCAGAGGCAGTTCCCACA-TTGGCAGTCCTTCGCGCAATCCTT
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCGCAATCCTT
19066 GCTAGTAATC
Statistics
Matches: 182, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
143 26 0.14
144 155 0.85
145 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.33
Consensus pattern (144 bp):
TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCGCAATCCTTACATGATA
ATCTTCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
TGTGATTATCTCCC
Found at i:19727 original size:16 final size:16
Alignment explanation
Indices: 19702--19734 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
19692 CTGCAAAATC
19702 TTGCCACAACAGAATG
1 TTGCCACAACAGAATG
*
19718 TTGCCGCAACAGAATG
1 TTGCCACAACAGAATG
19734 T
1 T
19735 CCCCTGTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.21
Consensus pattern (16 bp):
TTGCCACAACAGAATG
Found at i:20598 original size:43 final size:43
Alignment explanation
Indices: 20270--20598 Score: 415
Period size: 41 Copynumber: 7.8 Consensus size: 43
20260 CCAATAACCA
* *
20270 AAAGTCCCCAAACACATATATAACACA-AGGGCATCTTTATTCC
1 AAAGTCCCCAAACACATATATAACACAGA-GGCATCTCTATTAC
* * * *
20313 AAAAGTCCTCAAACACATATATAACACAGAGGTACCTATATT-C
1 -AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
20356 -AAGTCCCCAAACACATATATAACACAG-GGCACCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* * * *
20397 AAAGTCCTCAAGCACATATATAACATAGAGGCATCTATA-T-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* *
20438 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* *
20481 AAAGTCCTCAAACACATATATAAAACAGAGGCAT-T-TA-TATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTA-C
*
20522 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
20565 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGAGGCAT
20599 TTCTCCTTAT
Statistics
Matches: 248, Mismatches: 27, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
40 12 0.05
41 95 0.38
42 28 0.11
43 75 0.30
44 37 0.15
45 1 0.00
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.22
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
Found at i:20600 original size:84 final size:84
Alignment explanation
Indices: 20270--20598 Score: 527
Period size: 84 Copynumber: 3.9 Consensus size: 84
20260 CCAATAACCA
* * *
20270 AAAGTCCCCAAACACATATATAACACAAGGGCATCTTTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC-AAAGTCCTCAAACACATATAT
* *
20335 AACACAGAGGTACCTATATTC
65 AACACAGAGGCATCTATA-TC
* *
20356 -AAGTCCCCAAACACATATATAACACA-GGGCACCTCTATTACAAAGTCCTCAAGCACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
*
20419 ACATAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
*
20438 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
* *
20503 AAACAGAGGCATTTATATC
66 ACACAGAGGCATCTATATC
20522 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
20587 ACACAGAGGCAT
66 ACACAGAGGCAT
20599 TTCTCCTTAT
Statistics
Matches: 227, Mismatches: 14, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
82 2 0.01
83 61 0.27
84 138 0.61
85 26 0.11
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.22
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Done.