Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006114.1 Corchorus olitorius cultivar O-4 contig06139, 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, 801
Length: 1336
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.32
Found at i:645 original size:19 final size:19
Alignment explanation
Indices: 621--990 Score: 101
Period size: 19 Copynumber: 17.6 Consensus size: 19
611 AGAGAAAGAC
621 TTGGTAACTAAAAAAGAAT
1 TTGGTAACTAAAAAAGAAT
* *
640 TTGGTAATTAAAGTGTAAAAGTAAGA
1 TTGGTAACT-AA----AAAAG-AA-T
666 TTGGTAACTAAAAAAGAAT
1 TTGGTAACTAAAAAAGAAT
* * *
685 TTTGTAATTAAAGAGTAAAAGTAAGA
1 TTGGTAACT--A-A--AAAAG-AA-T
711 TTGGTAACTAAAAAAGAAT
1 TTGGTAACTAAAAAAGAAT
730 TTGGTAA-TCAAAAAGAGTAATAGT
1 TTGGTAACT-AAAAA-AG--A-A-T
754 AAAATTGGTAACTAAAAAAGAAT
1 ----TTGGTAACTAAAAAAGAAT
* *
777 TTGGTAATTAAAGAGTAAAAGTAAAA
1 TTGGTAACT--A-A--AAAAG--AAT
803 TTGGTAACTAAAAAAAGAAT
1 TTGGTAACT-AAAAAAGAAT
*
823 TTGGTAATTAGAGAGTAAAAGTAAAT
1 TTGGTAACT--A-A--AAAAG--AAT
*
849 TTGGTAA-TTAAAAAGAA-
1 TTGGTAACTAAAAAAGAAT
*
866 TCGGTAACTATAAAAAGAA-
1 TTGGTAACTA-AAAAAGAAT
* *
885 TTAGTAAAGT-AAAAAGAAT
1 TTGGT-AACTAAAAAAGAAT
* * *
904 TTGATAAAGT-AAAAGGAAT
1 TTGGT-AACTAAAAAAGAAT
*
923 TTGGTAAAGT-AAAAAGAAT
1 TTGGT-AACTAAAAAAGAAT
* *
942 TTGGTAA-TTAAAAGGAAT
1 TTGGTAACTAAAAAAGAAT
*
960 TTGGTAAAGT-AAAAAGAAT
1 TTGGT-AACTAAAAAAGAAT
*
979 TTGGTAATTAAA
1 TTGGTAACTAAA
991 GAATGAAAAT
Statistics
Matches: 275, Mismatches: 30, Indels: 92
0.69 0.08 0.23
Matches are distributed among these distances:
17 7 0.03
18 30 0.11
19 101 0.37
20 27 0.10
21 13 0.05
22 10 0.04
23 3 0.01
24 24 0.09
25 10 0.04
26 35 0.13
27 2 0.01
28 12 0.04
29 1 0.00
ACGTcount: A:0.51, C:0.02, G:0.19, T:0.28
Consensus pattern (19 bp):
TTGGTAACTAAAAAAGAAT
Found at i:669 original size:26 final size:25
Alignment explanation
Indices: 640--814 Score: 71
Period size: 26 Copynumber: 7.5 Consensus size: 25
630 AAAAAAGAAT
*
640 TTGGTAATTAAAGTGTAAAAGTAAGA
1 TTGGTAACTAAAG-GTAAAAGTAAGA
*
666 TTGGTAACT-AA---AAAAG-AA-T
1 TTGGTAACTAAAGGTAAAAGTAAGA
* *
685 TTTGTAATTAAAGAGTAAAAGTAAGA
1 TTGGTAACTAAAG-GTAAAAGTAAGA
*
711 TTGGTAACT-AA---AAAAG-AA-T
1 TTGGTAACTAAAGGTAAAAGTAAGA
* * *
730 TTGGTAATCAAAAAGAGTAATAGTAAAA
1 TTGGTAA-C-TAAAG-GTAAAAGTAAGA
*
758 TTGGTAACT-AA---AAAAG-AA-T
1 TTGGTAACTAAAGGTAAAAGTAAGA
* *
777 TTGGTAATTAAAGAGTAAAAGTAAAA
1 TTGGTAACTAAAG-GTAAAAGTAAGA
803 TTGGTAACTAAA
1 TTGGTAACTAAA
815 AAAAGAATTT
Statistics
Matches: 109, Mismatches: 17, Indels: 46
0.63 0.10 0.27
Matches are distributed among these distances:
19 22 0.20
20 11 0.10
21 14 0.13
22 2 0.02
24 10 0.09
25 10 0.09
26 30 0.28
27 3 0.03
28 7 0.06
ACGTcount: A:0.51, C:0.03, G:0.18, T:0.28
Consensus pattern (25 bp):
TTGGTAACTAAAGGTAAAAGTAAGA
Found at i:670 original size:45 final size:45
Alignment explanation
Indices: 616--866 Score: 371
Period size: 45 Copynumber: 5.5 Consensus size: 45
606 AAAAGAGAGA
*
616 AAGACTTGGTAACTAAAAAAGAATTTGGTAATTAAAGTGTAAAAGT
1 AAGA-TTGGTAACTAAAAAAGAATTTGGTAATTAAAGAGTAAAAGT
*
662 AAGATTGGTAACTAAAAAAGAATTTTGTAATTAAAGAGTAAAAGT
1 AAGATTGGTAACTAAAAAAGAATTTGGTAATTAAAGAGTAAAAGT
* *
707 AAGATTGGTAACTAAAAAAGAATTTGGTAATCAAAAAGAGTAATAGT
1 AAGATTGGTAACTAAAAAAGAATTTGGTAAT--TAAAGAGTAAAAGT
*
754 AAAATTGGTAACTAAAAAAGAATTTGGTAATTAAAGAGTAAAAGT
1 AAGATTGGTAACTAAAAAAGAATTTGGTAATTAAAGAGTAAAAGT
* *
799 AAAATTGGTAACTAAAAAAAGAATTTGGTAATTAGAGAGTAAAAGT
1 AAGATTGGTAACT-AAAAAAGAATTTGGTAATTAAAGAGTAAAAGT
*
845 AA-ATTTGGTAA-TTAAAAAGAAT
1 AAGA-TTGGTAACTAAAAAAGAAT
867 CGGTAACTAT
Statistics
Matches: 191, Mismatches: 10, Indels: 10
0.91 0.05 0.05
Matches are distributed among these distances:
44 9 0.05
45 96 0.50
46 44 0.23
47 42 0.22
ACGTcount: A:0.51, C:0.03, G:0.18, T:0.27
Consensus pattern (45 bp):
AAGATTGGTAACTAAAAAAGAATTTGGTAATTAAAGAGTAAAAGT
Found at i:778 original size:92 final size:90
Alignment explanation
Indices: 616--866 Score: 378
Period size: 92 Copynumber: 2.8 Consensus size: 90
606 AAAAGAGAGA
* *
616 AAGACTTGGTAACTAAAAAAGAATTTGGTAATTAAAGTGTAAAAGTAAGATTGGTAACTAAAAAA
1 AAGA-TTGGTAACTAAAAAAGAATTTGGTAATTAAAGAGTAAAAGTAAAATTGGTAACTAAAAAA
*
681 GAATTTTGTAATTAAAGAGTAAAAGT
65 GAATTTGGTAATTAAAGAGTAAAAGT
* *
707 AAGATTGGTAACTAAAAAAGAATTTGGTAATCAAAAAGAGTAATAGTAAAATTGGTAACTAAAAA
1 AAGATTGGTAACTAAAAAAGAATTTGGTAAT--TAAAGAGTAAAAGTAAAATTGGTAACTAAAAA
772 AGAATTTGGTAATTAAAGAGTAAAAGT
64 AGAATTTGGTAATTAAAGAGTAAAAGT
* * * *
799 AAAATTGGTAACTAAAAAAAGAATTTGGTAATTAGAGAGTAAAAGTAAATTTGGTAA-TTAAAAA
1 AAGATTGGTAACT-AAAAAAGAATTTGGTAATTAAAGAGTAAAAGTAAAATTGGTAACTAAAAAA
863 GAAT
65 GAAT
867 CGGTAACTAT
Statistics
Matches: 146, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
90 37 0.25
91 25 0.17
92 66 0.45
93 18 0.12
ACGTcount: A:0.51, C:0.03, G:0.18, T:0.27
Consensus pattern (90 bp):
AAGATTGGTAACTAAAAAAGAATTTGGTAATTAAAGAGTAAAAGTAAAATTGGTAACTAAAAAAG
AATTTGGTAATTAAAGAGTAAAAGT
Found at i:849 original size:26 final size:25
Alignment explanation
Indices: 774--859 Score: 101
Period size: 26 Copynumber: 3.6 Consensus size: 25
764 ACTAAAAAAG
774 AATTTGGTAATTAAAGAGTAAAAGTA
1 AATTTGGTAATT-AAGAGTAAAAGTA
* *
800 AAATTGGTAACTAA-A--AAAAG--
1 AATTTGGTAATTAAGAGTAAAAGTA
820 AATTTGGTAATTAGAGAGTAAAAGTA
1 AATTTGGTAATTA-AGAGTAAAAGTA
846 AATTTGGTAATTAA
1 AATTTGGTAATTAA
860 AAAGAATCGG
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
20 11 0.22
21 1 0.02
22 6 0.12
24 6 0.12
25 3 0.06
26 23 0.46
ACGTcount: A:0.50, C:0.01, G:0.19, T:0.30
Consensus pattern (25 bp):
AATTTGGTAATTAAGAGTAAAAGTA
Found at i:898 original size:37 final size:38
Alignment explanation
Indices: 846--990 Score: 185
Period size: 37 Copynumber: 3.9 Consensus size: 38
836 AGTAAAAGTA
* * *
846 AATTTGGT-AATTAAAAAGAA-TCGGTAACTATAAAAAG
1 AATTTGGTAAAGTAAAAAGAATTTGGTAA-TATAAAAGG
* *
883 AA-TTAGTAAAGTAAAAAGAATTTGATAA-AGTAAAAGG
1 AATTTGGTAAAGTAAAAAGAATTTGGTAATA-TAAAAGG
920 AATTTGGTAAAGTAAAAAGAATTTGGTAAT-TAAAAGG
1 AATTTGGTAAAGTAAAAAGAATTTGGTAATATAAAAGG
957 AATTTGGTAAAGTAAAAAGAATTTGGTAAT-TAAA
1 AATTTGGTAAAGTAAAAAGAATTTGGTAATATAAA
991 GAATGAAAAT
Statistics
Matches: 96, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
36 5 0.05
37 62 0.65
38 29 0.30
ACGTcount: A:0.52, C:0.01, G:0.19, T:0.28
Consensus pattern (38 bp):
AATTTGGTAAAGTAAAAAGAATTTGGTAATATAAAAGG
Found at i:979 original size:56 final size:56
Alignment explanation
Indices: 846--985 Score: 162
Period size: 56 Copynumber: 2.5 Consensus size: 56
836 AGTAAAAGTA
* *
846 AATTTGGT-AATTAAAAAGAA-TCGGTAACTATAAAAAGAATTAGTAAAGTAAAAAG
1 AATTTGGTAAAGTAAAAAGAATTTGGTAAC-ATAAAAAGAATTAGTAAAGTAAAAAG
* * * * *
901 AATTTGATAAAGTAAAAGGAATTTGGTAA-AGTAAAAAGAATTTGGT-AATTAAAAGG
1 AATTTGGTAAAGTAAAAAGAATTTGGTAACA-TAAAAAGAA-TTAGTAAAGTAAAAAG
957 AATTTGGTAAAGTAAAAAGAATTTGGTAA
1 AATTTGGTAAAGTAAAAAGAATTTGGTAA
986 TTAAAGAATG
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
55 8 0.11
56 54 0.75
57 10 0.14
ACGTcount: A:0.51, C:0.01, G:0.19, T:0.28
Consensus pattern (56 bp):
AATTTGGTAAAGTAAAAAGAATTTGGTAACATAAAAAGAATTAGTAAAGTAAAAAG
Found at i:1005 original size:37 final size:38
Alignment explanation
Indices: 888--1031 Score: 120
Period size: 37 Copynumber: 3.8 Consensus size: 38
878 AAAAGAATTA
* * **
888 GTAAAGTAAAAAGAATTTGATAAAGT-AA-AAGGAATTT
1 GTAAAGTAAAAAGAATTTGGT-AATTAAAGAAGGAAAAT
**
925 GGTAAAGTAAAAAGAATTTGGTAATT-AA-AAGGAATTT
1 -GTAAAGTAAAAAGAATTTGGTAATTAAAGAAGGAAAAT
*
962 GGTAAAGTAAAAAGAATTTGGTAATTAAAGAATGAAAAT
1 -GTAAAGTAAAAAGAATTTGGTAATTAAAGAAGGAAAAT
*
1001 -TAAAGAGTAAAATGAA-TTGGATAATTAAAGA
1 GT-AA-AGTAAAAAGAATTTGG-TAATTAAAGA
1032 GTAATTGGTA
Statistics
Matches: 95, Mismatches: 6, Indels: 9
0.86 0.05 0.08
Matches are distributed among these distances:
37 41 0.43
38 28 0.29
39 26 0.27
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (38 bp):
GTAAAGTAAAAAGAATTTGGTAATTAAAGAAGGAAAAT
Found at i:1010 original size:25 final size:27
Alignment explanation
Indices: 982--1143 Score: 80
Period size: 25 Copynumber: 6.2 Consensus size: 27
972 AAAGAATTTG
982 GTAATTAAAGAA-T-GAAAATTAAAGA
1 GTAATTAAAGAATTGGAAAATTAAAGA
* *
1007 GTAA--AATGAATTGGATAATTAAAGA
1 GTAATTAAAGAATTGGAAAATTAAAGA
* *
1032 GTAATTGGTAAA-ATTTGG-TAATTAAAGA
1 GTAA-T--TAAAGAATTGGAAAATTAAAGA
*
1060 GTAAATT---GAATTGGATAATTAAAGA
1 GT-AATTAAAGAATTGGAAAATTAAAGA
* *
1085 GTAATTGCTAAA-ATTTGG-TAATTAAAGA
1 GTAA-T--TAAAGAATTGGAAAATTAAAGA
* * *
1113 GTAA--AATGAAATGGATAATTAAAGA
1 GTAATTAAAGAATTGGAAAATTAAAGA
1138 GTAATT
1 GTAATT
1144 GGTAAAATTT
Statistics
Matches: 108, Mismatches: 9, Indels: 38
0.70 0.06 0.25
Matches are distributed among these distances:
23 7 0.06
24 12 0.11
25 46 0.43
26 1 0.01
27 1 0.01
28 27 0.25
29 12 0.11
30 2 0.02
ACGTcount: A:0.49, C:0.01, G:0.19, T:0.31
Consensus pattern (27 bp):
GTAATTAAAGAATTGGAAAATTAAAGA
Found at i:1055 original size:28 final size:29
Alignment explanation
Indices: 1017--1162 Score: 165
Period size: 28 Copynumber: 5.4 Consensus size: 29
1007 GTAAAATGAA
1017 TTGGATAATTAAAGAGTAATTGGTAAAAT
1 TTGGATAATTAAAGAGTAATTGGTAAAAT
1046 TTGG-TAATTAAAGAGTAAATT-G---AA-
1 TTGGATAATTAAAGAGT-AATTGGTAAAAT
*
1070 TTGGATAATTAAAGAGTAATTGCTAAAAT
1 TTGGATAATTAAAGAGTAATTGGTAAAAT
*
1099 TTGG-TAATTAAAGAGTAAAAT-G--AAA-
1 TTGGATAATTAAAGAGT-AATTGGTAAAAT
1124 -TGGATAATTAAAGAGTAATTGGTAAAAT
1 TTGGATAATTAAAGAGTAATTGGTAAAAT
1152 TTGGA-AATTAA
1 TTGGATAATTAA
1163 GAAGTAAAAT
Statistics
Matches: 99, Mismatches: 4, Indels: 29
0.75 0.03 0.22
Matches are distributed among these distances:
24 14 0.14
25 27 0.27
26 3 0.03
27 3 0.03
28 33 0.33
29 19 0.19
ACGTcount: A:0.47, C:0.01, G:0.20, T:0.33
Consensus pattern (29 bp):
TTGGATAATTAAAGAGTAATTGGTAAAAT
Found at i:1060 original size:53 final size:53
Alignment explanation
Indices: 998--1177 Score: 308
Period size: 53 Copynumber: 3.4 Consensus size: 53
988 AAAGAATGAA
998 AATTAAAGAGTAAAATGAATTGGATAATTAAAGAGTAATTGGTAAAATTTGGT
1 AATTAAAGAGTAAAATGAATTGGATAATTAAAGAGTAATTGGTAAAATTTGGT
* *
1051 AATTAAAGAGTAAATTGAATTGGATAATTAAAGAGTAATTGCTAAAATTTGGT
1 AATTAAAGAGTAAAATGAATTGGATAATTAAAGAGTAATTGGTAAAATTTGGT
* *
1104 AATTAAAGAGTAAAATGAAATGGATAATTAAAGAGTAATTGGTAAAATTTGGA
1 AATTAAAGAGTAAAATGAATTGGATAATTAAAGAGTAATTGGTAAAATTTGGT
1157 AATT-AAGAAGTAAAATGAATT
1 AATTAAAG-AGTAAAATGAATT
1178 AATTAAAAGT
Statistics
Matches: 119, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
52 3 0.03
53 116 0.97
ACGTcount: A:0.49, C:0.01, G:0.19, T:0.31
Consensus pattern (53 bp):
AATTAAAGAGTAAAATGAATTGGATAATTAAAGAGTAATTGGTAAAATTTGGT
Found at i:1189 original size:20 final size:21
Alignment explanation
Indices: 1157--1197 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
1147 AAAATTTGGA
1157 AATTAAGAAGTAAAATGAATT
1 AATTAAGAAGTAAAATGAATT
1178 AATTAA-AAGTAAAATGAATT
1 AATTAAGAAGTAAAATGAATT
1198 TGGAAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (21 bp):
AATTAAGAAGTAAAATGAATT
Found at i:1325 original size:28 final size:28
Alignment explanation
Indices: 1274--1336 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
1264 AAAGAGTAAG
**
1274 AAAGAGTAAAAGGAAAATTTGGTTAATT
1 AAAGAGTAAAAGGAAAATCCGGTTAATT
*
1302 AAGAGAGTAAGA-GAAAATCCGGTTAATT
1 AA-AGAGTAAAAGGAAAATCCGGTTAATT
1330 AAAGAGT
1 AAAGAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 5 0.16
28 18 0.58
29 8 0.26
ACGTcount: A:0.49, C:0.03, G:0.24, T:0.24
Consensus pattern (28 bp):
AAAGAGTAAAAGGAAAATCCGGTTAATT
Done.