Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024333.1 Corchorus olitorius cultivar O-4 contig24366, 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: 48021
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:3336 original size:4 final size:4
Alignment explanation
Indices: 3329--3355 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3319 ATATATTTAA
3329 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
3356 AATATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:3606 original size:2 final size:2
Alignment explanation
Indices: 3601--3630 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3591 TACACATTCA
3601 AT AT 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 AT AT
3631 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4548 original size:31 final size:27
Alignment explanation
Indices: 4512--4585 Score: 76
Period size: 31 Copynumber: 2.5 Consensus size: 27
4502 GGCTAATTGT
*
4512 TTAATTTAGGGCAAAACGTTTCAATTTAGA
1 TTAATTT-GGG-AAAACCTTTCAATTT-GA
*
4542 TCTAATTTGGGATAAAACCTTTTAATTTGA
1 T-TAATTTGGG--AAAACCTTTCAATTTGA
4572 TTAATTTGGGAAAA
1 TTAATTTGGGAAAA
4586 TATTTTCCGA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 4 0.10
29 9 0.23
30 7 0.18
31 19 0.49
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.39
Consensus pattern (27 bp):
TTAATTTGGGAAAACCTTTCAATTTGA
Found at i:4582 original size:29 final size:31
Alignment explanation
Indices: 4524--4582 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
4514 AATTTAGGGC
*
4524 AAAACGTTTCAATTTAGATCTAATTTGGGAT
1 AAAACCTTTCAATTTAGATCTAATTTGGGAT
*
4555 AAAACCTTTTAATTT-GAT-TAATTTGGGA
1 AAAACCTTTCAATTTAGATCTAATTTGGGA
4583 AAATATTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 10 0.38
30 3 0.12
31 13 0.50
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (31 bp):
AAAACCTTTCAATTTAGATCTAATTTGGGAT
Found at i:7024 original size:21 final size:20
Alignment explanation
Indices: 6995--7034 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
6985 TCATATGAAA
*
6995 TTTTGTAACGTTCCTATGAT
1 TTTTGTAACCTTCCTATGAT
7015 TTTTGATAACCTTCCTATGA
1 TTTTG-TAACCTTCCTATGA
7035 GATTTTGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTTGTAACCTTCCTATGAT
Found at i:9113 original size:2 final size:2
Alignment explanation
Indices: 9106--9141 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
9096 TTCATACTTT
9106 TA TA TA TA GTA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9142 CAATTCAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9407 original size:51 final size:51
Alignment explanation
Indices: 9331--9439 Score: 200
Period size: 51 Copynumber: 2.1 Consensus size: 51
9321 TATCATGGAC
*
9331 TGTGTATGATTTAGAACAAACCAATAAAACAATTAACGACTTAATGTGTAT
1 TGTGTATGATTTAGAACAAACCAATAAAACAATTAACGACTTAATGTATAT
9382 TGTGTATGATTTAGAACAAACCAATAAAACAATTAACGACTTAATGTATAT
1 TGTGTATGATTTAGAACAAACCAATAAAACAATTAACGACTTAATGTATAT
*
9433 GGTGTAT
1 TGTGTAT
9440 CAAATAGAAG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (51 bp):
TGTGTATGATTTAGAACAAACCAATAAAACAATTAACGACTTAATGTATAT
Found at i:10086 original size:32 final size:32
Alignment explanation
Indices: 10050--10117 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
10040 AAATATATTA
10050 TTATTTTTAAAATTATAGATCAAAAACCCAAG
1 TTATTTTTAAAATTATAGATCAAAAACCCAAG
10082 TTATTTTTAAAATTATAGATCAAAAACCCAAG
1 TTATTTTTAAAATTATAGATCAAAAACCCAAG
10114 TTAT
1 TTAT
10118 ACAACTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.37
Consensus pattern (32 bp):
TTATTTTTAAAATTATAGATCAAAAACCCAAG
Found at i:17968 original size:59 final size:56
Alignment explanation
Indices: 17871--17987 Score: 189
Period size: 59 Copynumber: 2.0 Consensus size: 56
17861 TATCCGTTTC
17871 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAAATATT
1 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAAATATT
* *
17927 CTTTCACACAATAAATGTTAGTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATG-T--TATAATAAATCATATCCCCCTATCTCTACTTAAATATT
17986 CT
1 CT
17988 GAAAAATAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
56 17 0.30
57 1 0.02
59 38 0.68
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAAATATT
Found at i:19023 original size:14 final size:13
Alignment explanation
Indices: 18987--19029 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
18977 ATCATTTAAA
18987 ATATATATATATAT
1 ATATATATATAT-T
19001 ATATATATATATT
1 ATATATATATATT
*
19014 ATATGCTATATATT
1 ATAT-ATATATATT
19028 AT
1 AT
19030 TTTTAGTGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 5 0.19
14 22 0.81
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (13 bp):
ATATATATATATT
Found at i:19026 original size:2 final size:2
Alignment explanation
Indices: 18987--19017 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
18977 ATCATTTAAA
18987 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19018 GCTATATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:31929 original size:27 final size:27
Alignment explanation
Indices: 31891--31945 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
31881 CTGAGAAAAA
31891 TAATCAATATTATTATCAGAGTCATCT
1 TAATCAATATTATTATCAGAGTCATCT
31918 TAATCAATATTATTATCAGAGTCATCT
1 TAATCAATATTATTATCAGAGTCATCT
31945 T
1 T
31946 TTTTCTAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (27 bp):
TAATCAATATTATTATCAGAGTCATCT
Found at i:32104 original size:3 final size:3
Alignment explanation
Indices: 32096--32128 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
32086 TATCAACATT
32096 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
32129 AAAAAAATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:35458 original size:2 final size:2
Alignment explanation
Indices: 35451--35477 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35441 TTTATCCCTC
35451 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
35478 AAAGAGGGAT
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:39026 original size:42 final size:43
Alignment explanation
Indices: 38979--39068 Score: 128
Period size: 45 Copynumber: 2.1 Consensus size: 43
38969 CATTACGTAA
*
38979 ATTCTA-CTCCATCTCTAGGCAATTCATCAAAATAAAGCTAAT
1 ATTCTACCTCCATCTCTAGACAATTCATCAAAATAAAGCTAAT
* *
39021 ATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTACT
1 ATTCTA--CCTCCATCTCTAGACAATTCATCAAAATAAAGCTAAT
39066 ATT
1 ATT
39069 AATTGTTGCT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
42 6 0.14
45 36 0.86
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (43 bp):
ATTCTACCTCCATCTCTAGACAATTCATCAAAATAAAGCTAAT
Found at i:40269 original size:23 final size:23
Alignment explanation
Indices: 40220--40271 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
40210 TTTGGGTATT
* * *
40220 TTCGGGTTCGATCTCGGGTAGGG
1 TTCGGGTTCGAGCTCGGATAGGA
* *
40243 TTCGGGTTCGGGCTCGGATCGGA
1 TTCGGGTTCGAGCTCGGATAGGA
40266 TTCGGG
1 TTCGGG
40272 CTAGGGTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.08, C:0.19, G:0.44, T:0.29
Consensus pattern (23 bp):
TTCGGGTTCGAGCTCGGATAGGA
Found at i:40427 original size:13 final size:13
Alignment explanation
Indices: 40403--40452 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
40393 AAGTTTATTG
40403 ATAATA-TATAAT
1 ATAATATTATAAT
40415 ATAATATTATAAT
1 ATAATATTATAAT
* *
40428 ATAACATTATTAT
1 ATAATATTATAAT
40441 -TAATATATATAA
1 ATAATAT-TATAA
40453 AGATTGGATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
12 11 0.34
13 21 0.66
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAATATTATAAT
Found at i:41017 original size:2 final size:2
Alignment explanation
Indices: 41012--41045 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
41002 TTATATAAGT
41012 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41046 GTAGTTTAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41258 original size:23 final size:23
Alignment explanation
Indices: 41225--41281 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
41215 TTTAAATTAT
*
41225 TTCGGGTTCGGGCTCGAGTCGGGA
1 TTCGGGCTCGGGCTCGAGTC-GGA
* *
41249 -TCGGGCTCGGTCTCGGGTCGGA
1 TTCGGGCTCGGGCTCGAGTCGGA
41271 TTCGGGCTCGG
1 TTCGGGCTCGG
41282 ACTGCCTCGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.10
23 26 0.90
ACGTcount: A:0.05, C:0.25, G:0.46, T:0.25
Consensus pattern (23 bp):
TTCGGGCTCGGGCTCGAGTCGGA
Found at i:41307 original size:16 final size:16
Alignment explanation
Indices: 41288--41331 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
41278 TCGGACTGCC
41288 TCGGGTTCGGGTAATT
1 TCGGGTTCGGGTAATT
*
41304 TCGGGCTCGGGTAATT
1 TCGGGTTCGGGTAATT
*
41320 TCGGATTCGGGT
1 TCGGGTTCGGGT
41332 TCGGGACGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.11, C:0.16, G:0.39, T:0.34
Consensus pattern (16 bp):
TCGGGTTCGGGTAATT
Done.