Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013131.1 Corchorus olitorius cultivar O-4 contig13164, 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: 27710
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:582 original size:22 final size:22
Alignment explanation
Indices: 557--608 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
547 TTCACATAAT
557 TGCGACAAGCATATTTCCTATA
1 TGCGACAAGCATATTTCCTATA
579 TGCGACAAGCATATTTCCTATA
1 TGCGACAAGCATATTTCCTATA
601 TGCGACAA
1 TGCGACAA
609 CCAGCAACGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (22 bp):
TGCGACAAGCATATTTCCTATA
Found at i:1523 original size:30 final size:29
Alignment explanation
Indices: 1455--1530 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 29
1445 GGTATTACAA
1455 AAAT-TGTTATAGTTTGGGAAATAAGTTT
1 AAATATGTTATAGTTTGGGAAATAAGTTT
1483 AAATATGTTATA-TATTGGGAAATAAGTTTT
1 AAATATGTTATAGT-TTGGGAAATAAG-TTT
*
1513 CTAA-ATGTTATAGTTTGG
1 -AAATATGTTATAGTTTGG
1531 TAAAAAATCT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
28 5 0.12
29 19 0.45
30 15 0.36
31 3 0.07
ACGTcount: A:0.36, C:0.01, G:0.20, T:0.43
Consensus pattern (29 bp):
AAATATGTTATAGTTTGGGAAATAAGTTT
Found at i:10719 original size:15 final size:15
Alignment explanation
Indices: 10699--10727 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10689 GTTTGGCTAG
10699 GAAGAAGAAGAAAAA
1 GAAGAAGAAGAAAAA
10714 GAAGAAGAAGAAAA
1 GAAGAAGAAGAAAA
10728 TGTAATAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAGAAAAA
Found at i:10986 original size:41 final size:42
Alignment explanation
Indices: 10904--11009 Score: 144
Period size: 41 Copynumber: 2.6 Consensus size: 42
10894 AGTACTGTTT
* *
10904 ATTCAATTTTGTCCCTGATCTA-AGGTAACATTTGTTAATTG
1 ATTCAATTTTGTCCCTGATTTAGAGGTAACATTTATTAATTG
* * *
10945 ATTCAATTTTGTCCCTAATTTAGA-GTAATATTTATTTATTG
1 ATTCAATTTTGTCCCTGATTTAGAGGTAACATTTATTAATTG
*
10986 ATTCAATTTTATCCCTGATTTAGA
1 ATTCAATTTTGTCCCTGATTTAGA
11010 ATTTTATTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 56 0.98
42 1 0.02
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.47
Consensus pattern (42 bp):
ATTCAATTTTGTCCCTGATTTAGAGGTAACATTTATTAATTG
Found at i:14647 original size:16 final size:15
Alignment explanation
Indices: 14629--14664 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
14619 CAAGACATGT
14629 TTTTCAAGAAAATTG
1 TTTTCAAGAAAATTG
*
14644 TTTTCAAGAAAA-GG
1 TTTTCAAGAAAATTG
14658 TTTTCAA
1 TTTTCAA
14665 AAATAGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (15 bp):
TTTTCAAGAAAATTG
Found at i:14662 original size:14 final size:14
Alignment explanation
Indices: 14629--14678 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
14619 CAAGACATGT
*
14629 TTTTCAAGAAAATTG
1 TTTTCAAGAAAA-GG
14644 TTTTCAAGAAAAGG
1 TTTTCAAGAAAAGG
14658 TTTTCAA-AAATAGG
1 TTTTCAAGAAA-AGG
14672 TTTTCAA
1 TTTTCAA
14679 AATGGTTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
13 3 0.09
14 18 0.55
15 12 0.36
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (14 bp):
TTTTCAAGAAAAGG
Found at i:17878 original size:68 final size:67
Alignment explanation
Indices: 17595--17922 Score: 507
Period size: 67 Copynumber: 4.9 Consensus size: 67
17585 GAATTTTAGA
*
17595 AGTACACCGAAAGAAGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAA
1 AGTACACCGAAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAA
17660 GG
66 GG
*
17662 AGTACACCGAAAGACGGTTTACTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAA
1 AGTACACCGAAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAA
17727 GG
66 GG
* *
17729 AGTACGCCGAAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAA
1 AGTACACCGAAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAA
17794 GG
66 GG
*
17796 AGTACACCGAAAGACAGTTTGCTAGAAAGAATTTTCAAATGGTTGATTGGAAGACAATCTCATTA
1 AGTACACCGAAAGACGGTTTGCTAGAAAGAATTTTCAAAT-GTTGATTGGAAGACAATCTCATTA
*
17861 AGC
65 AGG
* * * * * *
17864 AATACATC-AGAAGACGGTTTGCTAGAAAGAGTTTTCAGAA-ATTGATCGGAAGACGATCT
1 AGTACACCGA-AAGACGGTTTGCTAGAAAGAATTTTCA-AATGTTGATTGGAAGACAATCT
17923 TGTCAAGAAG
Statistics
Matches: 242, Mismatches: 16, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
67 183 0.76
68 57 0.24
69 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (67 bp):
AGTACACCGAAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAA
GG
Found at i:17950 original size:67 final size:66
Alignment explanation
Indices: 17592--18249 Score: 483
Period size: 64 Copynumber: 10.0 Consensus size: 66
17582 GAAGAATTTT
* * * **
17592 AGAAGTACACC-GAAAGAAGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCA
1 AGAAGTACACCAG-AAGATGGTTT-CTAGAAAGAATTTTCAAATGTTGATCGGAAGACGATCTTG
17656 TTA
64 TTA
* * * * **
17659 AGGAGTACACC-GAAAGACGGTTTACTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCA
1 AGAAGTACACCAG-AAGATGGTTT-CTAGAAAGAATTTTCAAATGTTGATCGGAAGACGATCTTG
17723 TTA
64 TTA
* * * * * * **
17726 AGGAGTACGCC-GAAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCA
1 AGAAGTACACCAG-AAGATGGTTT-CTAGAAAGAATTTTCAAATGTTGATCGGAAGACGATCTTG
17790 TTA
64 TTA
* ** * * *
17793 AGGAGTACACC-GAAAGACAGTTTGCTAGAAAGAATTTTCAAATGGTTGATTGGAAGACAATCTC
1 AGAAGTACACCAG-AAGATGGTTT-CTAGAAAGAATTTTCAAAT-GTTGATCGGAAGACGATCTT
*
17857 ATTA
63 GTTA
* * * *
17861 AGCAA-TACATCAGAAGACGGTTTGCTAGAAAGAGTTTTCAGAA-ATTGATCGGAAGACGATCTT
1 AG-AAGTACACCAGAAGATGGTTT-CTAGAAAGAATTTTCA-AATGTTGATCGGAAGACGATCTT
*
17924 GTCA
63 GTTA
* * * *
17928 AGAAGTACACCAGAAGATGGTTTCT--CAACAATTTTCAGAA-GATGAACGGAAGACGATCTTGT
1 AGAAGTACACCAGAAGATGGTTTCTAGAAAGAATTTTCA-AATGTTGATCGGAAGACGATCTTGT
*
17990 CA
65 TA
* * *
17992 AGAAGTACACCAGAAGATGGTTTCT--CAATAATTTTCAGAA-GATGATCGGAAGACGATCTTGT
1 AGAAGTACACCAGAAGATGGTTTCTAGAAAGAATTTTCA-AATGTTGATCGGAAGACGATCTTGT
*
18054 CA
65 TA
* * * * ** *
18056 AGAAGTACACCAGAAGGTGGTTTCT--CAAGAGTTTTCAGGA-GTAAATCGGAAGATGATCTTGT
1 AGAAGTACACCAGAAGATGGTTTCTAGAAAGAATTTTCA-AATGTTGATCGGAAGACGATCTTGT
18118 TA
65 TA
* * * * * * *
18120 AGAAGCACGCAAGAAGATGGTTTCT-CAAA-AATTTTTAAAAGTTGGTCGGAAGACGATCTTGTT
1 AGAAGTACACCAGAAGATGGTTTCTAGAAAGAATTTTCAAATGTTGATCGGAAGACGATCTTGTT
18183 A
66 A
* * * * * *
18184 AAAAGTACACCAGAAGATAGTTTCTCGAAA-AGGTTTT-AGAA-GCTGATCGAAAGACGATCTTG
1 AGAAGTACACCAGAAGATGGTTTCTAGAAAGA-ATTTTCA-AATGTTGATCGGAAGACGATCTTG
18246 TTA
64 TTA
18249 A
1 A
18250 AAGATGCACC
Statistics
Matches: 521, Mismatches: 60, Indels: 22
0.86 0.10 0.04
Matches are distributed among these distances:
63 1 0.00
64 217 0.42
65 29 0.06
66 10 0.02
67 204 0.39
68 56 0.11
69 4 0.01
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.27
Consensus pattern (66 bp):
AGAAGTACACCAGAAGATGGTTTCTAGAAAGAATTTTCAAATGTTGATCGGAAGACGATCTTGTT
A
Found at i:18417 original size:50 final size:50
Alignment explanation
Indices: 18340--18605 Score: 435
Period size: 50 Copynumber: 5.3 Consensus size: 50
18330 GAAGCCAATG
*
18340 GGAAGACAGTTCAAAGGATAAGTGGAAGACGGTCCTTTTAAGATTGAATT
1 GGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAATT
*
18390 GGAAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTAAGATTGAATT
1 GGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAATT
*
18440 GGAAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTAAGATTGAATT
1 GGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAATT
* * *
18490 GGAAGACAGTTCAAAAGATAAGCAGAAGACAGTCCTTTTAAGATTGAATT
1 GGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAATT
* *
18540 GGAAGACAGTTCAAAGCATAAGCGGAAGACGGTCCTTTTAATG-TTGGATT
1 GGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAA-GATTGAATT
*
18590 GGAAGACAATTCAAAG
1 GGAAGACAGTTCAAAG
18606 AAGTTGTTTC
Statistics
Matches: 203, Mismatches: 12, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
50 202 1.00
51 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (50 bp):
GGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAATT
Found at i:18661 original size:27 final size:26
Alignment explanation
Indices: 18582--18665 Score: 89
Period size: 26 Copynumber: 3.2 Consensus size: 26
18572 TCCTTTTAAT
*
18582 GTTGGATTGGAAGACAATTCAAAGAA
1 GTTGAATTGGAAGACAATTCAAAGAA
* * ***
18608 GTTG-TTTCGGAAGACGATTCCCCGAA
1 GTTGAATT-GGAAGACAATTCAAAGAA
18634 GATTGAATTGGAAGACAATTCAAAGAA
1 G-TTGAATTGGAAGACAATTCAAAGAA
18661 GTTGA
1 GTTGA
18666 TCGGGAGATG
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
25 2 0.04
26 23 0.51
27 18 0.40
28 2 0.04
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.25
Consensus pattern (26 bp):
GTTGAATTGGAAGACAATTCAAAGAA
Found at i:24322 original size:15 final size:15
Alignment explanation
Indices: 24302--24338 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
24292 ATTGGGGAAT
24302 AATCAATCCAAAAAC
1 AATCAATCCAAAAAC
*
24317 AATCAATTCAAAAAC
1 AATCAATCCAAAAAC
*
24332 AAACAAT
1 AATCAAT
24339 TTTCTATCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.62, C:0.22, G:0.00, T:0.16
Consensus pattern (15 bp):
AATCAATCCAAAAAC
Done.