Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018854.1 Corchorus olitorius cultivar O-4 contig18887, 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: 48106
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Found at i:16214 original size:4 final size:4
Alignment explanation
Indices: 16205--16253 Score: 55
Period size: 4 Copynumber: 11.8 Consensus size: 4
16195 TATATAATAA
*
16205 AAAT AAAT AAAT -TAT AAAT AAAT AAAT AAAT AAATT ACCAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T A--AAT AAAT AAA
16254 CGAAGTGCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 2 0.05
4 31 0.79
5 2 0.05
6 2 0.05
7 2 0.05
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:16235 original size:23 final size:23
Alignment explanation
Indices: 16193--16253 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
16183 CAGTTCTTTT
16193 ATTATATAAT-AA-AAATAAATAA
1 ATTATA-AATAAATAAATAAATAA
16215 ATTATAAATAAATAAATAAATAA
1 ATTATAAATAAATAAATAAATAA
**
16238 ATTACCAATAAATAAA
1 ATTATAAATAAATAAA
16254 CGAAGTGCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 3 0.09
22 8 0.23
23 24 0.69
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (23 bp):
ATTATAAATAAATAAATAAATAA
Found at i:17897 original size:18 final size:18
Alignment explanation
Indices: 17874--17931 Score: 107
Period size: 18 Copynumber: 3.2 Consensus size: 18
17864 GCTTCTCCTA
17874 CTCGCCGCAGCCCTAGTC
1 CTCGCCGCAGCCCTAGTC
*
17892 CTCGCCGCAGCCATAGTC
1 CTCGCCGCAGCCCTAGTC
17910 CTCGCCGCAGCCCTAGTC
1 CTCGCCGCAGCCCTAGTC
17928 CTCG
1 CTCG
17932 GAAAAGTCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.12, C:0.48, G:0.22, T:0.17
Consensus pattern (18 bp):
CTCGCCGCAGCCCTAGTC
Found at i:28589 original size:52 final size:52
Alignment explanation
Indices: 28476--28580 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
28466 TTCTCATTTA
28476 GATGTTTGGGCATAGAGATTTATTTGAAATGTAATGAGATTTCACTGGGTTT
1 GATGTTTGGGCATAGAGATTTATTTGAAATGTAATGAGATTTCACTGGGTTT
28528 GATGTTTGGGCATAGAGATTTATTTGAAATGTAATGAGATTTCACTGGGTTT
1 GATGTTTGGGCATAGAGATTTATTTGAAATGTAATGAGATTTCACTGGGTTT
28580 G
1 G
28581 TTTGTTGGGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.27, C:0.06, G:0.28, T:0.40
Consensus pattern (52 bp):
GATGTTTGGGCATAGAGATTTATTTGAAATGTAATGAGATTTCACTGGGTTT
Found at i:29627 original size:22 final size:21
Alignment explanation
Indices: 29579--29629 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
29569 TATCAGTCAA
*
29579 CATCCATATCGTTTTTACCAG
1 CATCCATATCGCTTTTACCAG
29600 CATCCATATCGCTTTTACCAG
1 CATCCATATCGCTTTTACCAG
29621 CAGTCCATA
1 CA-TCCATA
29630 GCTTTATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.25, C:0.31, G:0.10, T:0.33
Consensus pattern (21 bp):
CATCCATATCGCTTTTACCAG
Found at i:35736 original size:16 final size:16
Alignment explanation
Indices: 35696--35744 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
35686 CTTTTAATCT
35696 TTTATTTATATT--T-
1 TTTATTTATATTGATG
* *
35709 TTAATTTGTATTGATG
1 TTTATTTATATTGATG
35725 TTTATTTATATTGATTG
1 TTTATTTATATTGA-TG
35742 TTT
1 TTT
35745 CATAAGAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 10 0.36
15 1 0.04
16 12 0.43
17 5 0.18
ACGTcount: A:0.22, C:0.00, G:0.10, T:0.67
Consensus pattern (16 bp):
TTTATTTATATTGATG
Found at i:36378 original size:2 final size:2
Alignment explanation
Indices: 36371--36403 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
36361 TGTGATTTGG
36371 AT AT AT 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 AT AT AT A
36404 ACTATCTGTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38868 original size:26 final size:26
Alignment explanation
Indices: 38834--38885 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
38824 TAATGAAAAA
*
38834 CAAATCAATCACAATAACTAAATTTT
1 CAAACCAATCACAATAACTAAATTTT
38860 CAAACCAATCACAATAACTAAATTTT
1 CAAACCAATCACAATAACTAAATTTT
38886 ACTAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (26 bp):
CAAACCAATCACAATAACTAAATTTT
Found at i:45358 original size:84 final size:84
Alignment explanation
Indices: 45145--45470 Score: 475
Period size: 84 Copynumber: 3.9 Consensus size: 84
45135 ATAACCAAAA
* *
45145 AAGTCCCCAAACACATATATAACACATGGGCAATTCTATTCCAAAAGTCCTCAAACACATATATA
1 AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTAC-AAAGTCCTCAAACACATATATA
* *
45210 ACACATAGGCACCTATATCC
65 ACACAGAGGCACCTATATTC
*
45230 AAGTCCCCAAACAC--ATATAACACAGGGGCACCTT-TATTACAAAGTCCTCAAACACATATATA
1 AAGTCCCCAAACACATATATAACACAGGGGCA-ATTCTATTACAAAGTCCTCAAACACATATATA
*
45292 ACACAGAGACACCTATATTC
65 ACACAGAGGCACCTATATTC
* *
45312 AAGTCCCCAAACACATATATAACACAAGGGCAATTCTATTACAAAGTCCTCAAACACATGTATAA
1 AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAA
*
45377 CACAGAGGCA--TTTATGTC
66 CACAGAGGCACCTATAT-TC
45395 AAAGTCCCCAAACACATATATAACACAGGGGC-ATCTCTATTACAAAGTCCTCAAACACATATAT
1 -AAGTCCCCAAACACATATATAACACAGGGGCAAT-TCTATTACAAAGTCCTCAAACACATATAT
*
45459 AACATAGAGGCA
64 AACACAGAGGCA
45471 TTTCTCCTTA
Statistics
Matches: 220, Mismatches: 14, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
82 57 0.26
83 26 0.12
84 123 0.56
85 14 0.06
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.21
Consensus pattern (84 bp):
AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAA
CACAGAGGCACCTATATTC
Found at i:45471 original size:43 final size:43
Alignment explanation
Indices: 45144--45471 Score: 351
Period size: 41 Copynumber: 7.8 Consensus size: 43
45134 AATAACCAAA
*
45144 AAAGTCCCCAAACACATATATAACACATG-GGCAAT-TCTATTCC
1 AAAGTCCCCAAACACATATATAACACA-GAGGC-ATCTCTATTAC
* *
45187 AAAAGTCCTCAAACACATATATAACACATAGGCA-C-CTA-TATC
1 -AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTA-C
* * * *
45229 CAAGTCCCCAAACAC--ATATAACACAGGGGCACCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* * * *
45270 AAAGTCCTCAAACACATATATAACACAGAGACACCTATATT-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
45312 -AAGTCCCCAAACACATATATAACACA-AGGGCAAT-TCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGA-GGC-ATCTCTATTAC
* *
45354 AAAGTCCTCAAACACATGTATAACACAGAGGCAT-T-TATGT-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTAT-TAC
*
45395 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* *
45438 AAAGTCCTCAAACACATATATAACATAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGAGGCAT
45472 TTCTCCTTAT
Statistics
Matches: 242, Mismatches: 25, Indels: 35
0.80 0.08 0.12
Matches are distributed among these distances:
39 14 0.06
40 2 0.01
41 97 0.40
42 15 0.06
43 84 0.35
44 30 0.12
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
Done.