Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019954.1 Corchorus olitorius cultivar O-4 contig19987, 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: 47766
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:977 original size:2 final size:2
Alignment explanation
Indices: 970--1002 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
960 TGGTGTTGGG
970 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
1003 ATTGTGCCAT
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:2396 original size:19 final size:19
Alignment explanation
Indices: 2339--2410 Score: 75
Period size: 19 Copynumber: 4.1 Consensus size: 19
2329 TTTGATATTT
*
2339 AAACTCTCAAAACTCCTTC
1 AAACTCTCAAAACTTCTTC
2358 AAACT-TC---A-TT-TTC
1 AAACTCTCAAAACTTCTTC
*
2371 TAACTCTCAAAACTTCTTC
1 AAACTCTCAAAACTTCTTC
*
2390 AAACTCTCTAAACTTCTTC
1 AAACTCTCAAAACTTCTTC
2409 AA
1 AA
2411 GGACATCATG
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
13 7 0.16
14 3 0.07
15 1 0.02
17 1 0.02
18 4 0.09
19 27 0.63
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (19 bp):
AAACTCTCAAAACTTCTTC
Found at i:2795 original size:17 final size:18
Alignment explanation
Indices: 2765--2805 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
2755 TAGTTATTTT
2765 ATTATTTGACTATAATTA
1 ATTATTTGACTATAATTA
2783 ATTATTT-ACTATAATTA
1 ATTATTTGACTATAATTA
*
2800 TTTATT
1 ATTATT
2806 ATTGTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTATTTGACTATAATTA
Found at i:3281 original size:9 final size:9
Alignment explanation
Indices: 3267--3293 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
3257 TTTAGCGTTG
3267 AATAAATTA
1 AATAAATTA
3276 AATAAATTA
1 AATAAATTA
3285 AATAAATTA
1 AATAAATTA
3294 TTTCTGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AATAAATTA
Found at i:7197 original size:26 final size:26
Alignment explanation
Indices: 7168--7226 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
7158 CACCTGCGGA
*
7168 AATAATAAATGAATAC-ATTAATAAAT
1 AATAATAAAT-AATACGACTAATAAAT
*
7194 AATAATAAATATTACGACTAATAAAT
1 AATAATAAATAATACGACTAATAAAT
7220 AATAATA
1 AATAATA
7227 CCACCTGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 4 0.13
26 26 0.87
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (26 bp):
AATAATAAATAATACGACTAATAAAT
Found at i:9952 original size:85 final size:84
Alignment explanation
Indices: 9810--9977 Score: 291
Period size: 85 Copynumber: 2.0 Consensus size: 84
9800 AAAAAAATTG
* *
9810 GGATCCTACTAGAAACGCAATAACTAAATCCAACTAGAAGCAATCTTTCTAATACAAGCCATTTT
1 GGATCCAACTAGAAACGCAATAACTAAATCCAACTAGAAGCAATCTTTCTAATACAAGCCATTTA
9875 CATACCATGAATGAATAAC
66 CATACCATGAATGAATAAC
* *
9894 GGATCCAACTAGAAGCGCAATATACTAAATCCAACTGGAAGCAATCTTTCTAATACAAGCCATTT
1 GGATCCAACTAGAAACGCAATA-ACTAAATCCAACTAGAAGCAATCTTTCTAATACAAGCCATTT
9959 ACATACCATGAATGAATAA
65 ACATACCATGAATGAATAA
9978 ATACCCTATG
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
84 20 0.25
85 59 0.75
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.24
Consensus pattern (84 bp):
GGATCCAACTAGAAACGCAATAACTAAATCCAACTAGAAGCAATCTTTCTAATACAAGCCATTTA
CATACCATGAATGAATAAC
Found at i:22746 original size:18 final size:18
Alignment explanation
Indices: 22711--22753 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
22701 AGTAACAGAC
*
22711 CTCCAAAGCCCCATCCAA
1 CTCCAAAGCCCCAACCAA
* *
22729 CTCCGAAGCCGCAACCAA
1 CTCCAAAGCCCCAACCAA
*
22747 CACCAAA
1 CTCCAAA
22754 ACCTGACGGC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.47, G:0.09, T:0.07
Consensus pattern (18 bp):
CTCCAAAGCCCCAACCAA
Found at i:23730 original size:20 final size:21
Alignment explanation
Indices: 23699--23740 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
23689 TTAATTAATA
*
23699 TATACTAATTATGGTTATTAT
1 TATACTAATTATGATTATTAT
*
23720 TATAC-AATTATTATTATTAT
1 TATACTAATTATGATTATTAT
23740 T
1 T
23741 GCTATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (21 bp):
TATACTAATTATGATTATTAT
Found at i:32856 original size:28 final size:27
Alignment explanation
Indices: 32808--32860 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
32798 AAAAATATTG
*
32808 TTAGGAGAGTTTATCACCATAGTAGAC
1 TTAGGAGAGTTTACCACCATAGTAGAC
*
32835 TTAGGAGAGCTTTACCCCCATAGTAG
1 TTAGGAGAG-TTTACCACCATAGTAG
32861 TTGACCCCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
TTAGGAGAGTTTACCACCATAGTAGAC
Found at i:33667 original size:178 final size:177
Alignment explanation
Indices: 33302--33679 Score: 449
Period size: 178 Copynumber: 2.1 Consensus size: 177
33292 TCATAAACAC
* ** *
33302 AAATTATGTAATATTAAATAGATCGTCTATTTTCGTTAACCGAAACAACTAATTCTTTGGAAGCA
1 AAATTATATAATATTAAATAGATCGTCTATTCCCGTTAACCGAAACAACAAATTCTTTGGAAGCA
**
33367 TTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATAGAAC
66 TTTTGGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATAGAAC
* * * * *
33432 AACCTTTCAAGAGACACTTGAATCATCTCAATAAGACATCTAGAGCA
131 AACCTTTCAAGAGACACTTAAATCACCTCAATAAGAAACCGAGAGCA
* * * *
33479 AAAGTTATATAATATTAAGTGGA-CAGTCTATTCCCGTTAATCGAAACAACAAATT-TTTCGTAA
1 AAA-TTATATAATATTAAATAGATC-GTCTATTCCCGTTAACCGAAACAACAAATTCTTT-GGAA
* *
33542 GTATTTTGGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATG
63 GCATTTTGGATACCTTG-AACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATA
* * * * **
33606 GAACAATCTTTTAATAGACACTTAAATCACCTTAATCGGATAACCGGAGAG-A
127 GAACAACCTTTCAAGAGACACTTAAATCACCTCAATAAGA-AACC-GAGAGCA
* *
33658 AAATTATATAATGTCAAATAGA
1 AAATTATATAATATTAAATAGA
33680 CCATTTAGTC
Statistics
Matches: 168, Mismatches: 27, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
177 11 0.07
178 147 0.88
179 6 0.04
180 4 0.02
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (177 bp):
AAATTATATAATATTAAATAGATCGTCTATTCCCGTTAACCGAAACAACAAATTCTTTGGAAGCA
TTTTGGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATAGAAC
AACCTTTCAAGAGACACTTAAATCACCTCAATAAGAAACCGAGAGCA
Found at i:33890 original size:10 final size:10
Alignment explanation
Indices: 33877--33907 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
33867 ATAATTATTG
33877 TTTTTTATAA
1 TTTTTTATAA
33887 TTTTTTATAA
1 TTTTTTATAA
33897 TTTTTTATAA
1 TTTTTTATAA
33907 T
1 T
33908 ATATATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:38523 original size:25 final size:25
Alignment explanation
Indices: 38492--38541 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
38482 AATGTTTTCC
* * *
38492 TTTTCTCTGCTTCGCTCTCACTCCT
1 TTTTCTCTACTTCCCTCCCACTCCT
38517 TTTTCTCTACTTCCCTCCCACTCCT
1 TTTTCTCTACTTCCCTCCCACTCCT
38542 CTCTCACATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.06, C:0.44, G:0.04, T:0.46
Consensus pattern (25 bp):
TTTTCTCTACTTCCCTCCCACTCCT
Found at i:39518 original size:2 final size:2
Alignment explanation
Indices: 39511--39535 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39501 TGATTGAATA
39511 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 A
39536 AATTGTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39660 original size:2 final size:2
Alignment explanation
Indices: 39615--39644 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39605 CAGTACAAAC
39615 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
39645 CTTTCGAATA
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):
TA
Found at i:40670 original size:29 final size:30
Alignment explanation
Indices: 40594--40670 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 30
40584 CTTTTGAAAA
* *
40594 GGGGCAAACCGTCCAAAATTGAGAGTTTTGG
1 GGGGCAAAACGTCCAAAATTGAGAGTTAT-G
** *
40625 GGGGCAAAATATACAAAATTGA-AGTTCAT-
1 GGGGCAAAACGTCCAAAATTGAGAGTT-ATG
40654 GGGGCAAAACGTCCAAA
1 GGGGCAAAACGTCCAAA
40671 CGCTACACGT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
29 14 0.38
30 4 0.11
31 19 0.51
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.19
Consensus pattern (30 bp):
GGGGCAAAACGTCCAAAATTGAGAGTTATG
Found at i:41886 original size:2 final size:2
Alignment explanation
Indices: 41879--41903 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41869 AGAACTCAAG
41879 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 A
41904 AATCAGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44792 original size:11 final size:11
Alignment explanation
Indices: 44766--44806 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
44756 CATGGGATTT
44766 TTAA-TAATAA
1 TTAATTAATAA
* *
44776 TTAATTATTAT
1 TTAATTAATAA
44787 TTAATTAATAA
1 TTAATTAATAA
44798 TTAATTAAT
1 TTAATTAAT
44807 TTCAGCCCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 4 0.15
11 22 0.85
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TTAATTAATAA
Found at i:44793 original size:15 final size:15
Alignment explanation
Indices: 44773--44807 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
44763 TTTTTAATAA
* *
44773 TAATTAATTATTATT
1 TAATTAATAATTAAT
44788 TAATTAATAATTAAT
1 TAATTAATAATTAAT
44803 TAATT
1 TAATT
44808 TCAGCCCTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATTAATAATTAAT
Found at i:45178 original size:13 final size:13
Alignment explanation
Indices: 45157--45187 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
45147 AGTTCAAGGT
*
45157 ATCAACAAAAATC
1 ATCACCAAAAATC
45170 ATCACCAAAAATC
1 ATCACCAAAAATC
45183 ATCAC
1 ATCAC
45188 TCATGCCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.29, G:0.00, T:0.16
Consensus pattern (13 bp):
ATCACCAAAAATC
Done.