Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013092.1 Corchorus olitorius cultivar O-4 contig13125, 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: 3749
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:879 original size:14 final size:14
Alignment explanation
Indices: 860--894 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
850 AAAATGCAAA
860 TTTTGAATTTTGAC
1 TTTTGAATTTTGAC
*
874 TTTTGACTTTTGAC
1 TTTTGAATTTTGAC
888 TTTTGAA
1 TTTTGAA
895 GAATGAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.20, C:0.09, G:0.14, T:0.57
Consensus pattern (14 bp):
TTTTGAATTTTGAC
Found at i:953 original size:7 final size:7
Alignment explanation
Indices: 943--1032 Score: 128
Period size: 7 Copynumber: 12.9 Consensus size: 7
933 TTGAGCCATA
943 AATTTTG
1 AATTTTG
950 AATTTTG
1 AATTTTG
957 AATTTTG
1 AATTTTG
964 AATTTTG
1 AATTTTG
971 AATTTTG
1 AATTTTG
*
978 AGTTTTG
1 AATTTTG
*
985 AGTTTTG
1 AATTTTG
*
992 AGTTTT-
1 AATTTTG
998 AAGTTTTG
1 AA-TTTTG
1006 AATTTTG
1 AATTTTG
*
1013 AGTTTTG
1 AATTTTG
1020 AATTTTG
1 AATTTTG
1027 AATTTT
1 AATTTT
1033 AAGCAATGAA
Statistics
Matches: 77, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
6 1 0.01
7 74 0.96
8 2 0.03
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (7 bp):
AATTTTG
Found at i:1212 original size:33 final size:33
Alignment explanation
Indices: 1170--1247 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
1160 AGAAACTGTG
* * *
1170 GATTTTGAACTTTGAGTTTTGATATGATATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
1203 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
*
1236 AATTTTGAACTT
1 GATTTTGAACTT
1248 CTTAATTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (33 bp):
GATTTTGAACTTTGAATTTTGAAATGAAATGCA
Found at i:1409 original size:54 final size:54
Alignment explanation
Indices: 1351--1881 Score: 778
Period size: 54 Copynumber: 9.8 Consensus size: 54
1341 TGATCATCGT
* * * * *
1351 AAACTTCT-TGGAATGACCACACTGGATCAACTTAAGATCAACTTAGATTTTTGA
1 AAACTTCTAT-GAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGA
* ** * *
1405 AAACTTCTATGGAAGACCACACAAGGTCATCTGAAGATCAACTTAGACCTCT-A
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGA
*
1458 AAAGCTTCTATGAAAGACCACACTGGGTCATCTGAAGATCAACTTAGATCTCTGA
1 AAA-CTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGA
*
1513 AAACTTCTATAAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGA
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGA
* * *
1567 AAAATTTTATAAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGA
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGA
* * * * *
1621 AAACTTCAATGAAAGACCGCACTGGGTCATCTTAAAATCGACTTAGATCTCTAA
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGA
*
1675 AAACTTCTATGAAAGACCACACTGGGTCAACTTAAGATCAACTTAGATCTCTGA
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGA
* * * *
1729 AAACTTTTATGAAAGACCACACTAGGTCAACTTAAGATCAACTTAGATCTCTAA
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGA
* *
1783 AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGA
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGA
*
1837 AAACTTCTATGAAAGACCACACTAGGTCATCTTAAGATCAACTTA
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTA
1882 CTAGAGAGAC
Statistics
Matches: 432, Mismatches: 42, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
53 4 0.01
54 423 0.98
55 5 0.01
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (54 bp):
AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGA
Found at i:2040 original size:75 final size:74
Alignment explanation
Indices: 1912--2618 Score: 958
Period size: 75 Copynumber: 9.5 Consensus size: 74
1902 CCTTTTAAAC
* * * **
1912 ACCTAAACAGGGAGT-TTGAACAAGAATTTT-ATGGGAAACCTAAACAGTCACCTTAAATAAGGA
1 ACCTAAACA-GGAATCTTGAACAAG-ATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA
1975 TTTGATAAGAAA
64 TTTGATAAG-AA
* *
1987 ACCTAAACAAGAATTTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
*
2052 TAATAAGAAA
66 TGATAAG-AA
* * * * * * * *
2062 AAC-AAACAGGGATCTTAAACAAAAATTTTG-TCAAGAAACCTAAACAGGCATCTTAAATAAGGA
1 ACCTAAACAGGAATCTTGAAC-AAGATTTTGAT-GAGACACCTAAACAGGGACCTTAAATAAGGA
2125 TTTGATAAGAA
64 TTTGATAAGAA
* *
2136 ACCTAAACAGGGATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA-T
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
* *
2200 TAATGAGAA
66 TGATAAGAA
2209 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA-T
2274 TTGATAAGAA
65 TTGATAAGAA
* * *
2284 AGCTAAACAGGAATCTTGAACAAAAATTTTGATGAGACACGTAAACAGGGACCTTAAATAAGGAT
1 ACCTAAACAGGAATCTTGAAC-AAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGAT
2349 TTGATAAGAA
65 TTGATAAGAA
* * *
2359 ACCTAACCAGGAATCTTGAACAAGGTTTTGATGAGACACCTATACAGGGACCTTAAATAAGGATT
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
*
2424 TGACAAGAAA
66 TGATAAG-AA
* * *
2434 ACCTAAACAGGAATCTTGAACAAGGTTTTGATGAGACACCTAAATAGGGATCTTAAATAAGGATT
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
2499 TGATAAGAA
66 TGATAAGAA
* *
2508 ATCTAAACA-GAGATCTTGAACAAGGTTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGAT
1 ACCTAAACAGGA-ATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGAT
*
2572 TTGATAAGTA
65 TTGATAAGAA
* * *
2582 ACCTAATCAGAAATCTTGAACAAGGTTTTGATGAGAC
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGAC
2619 TGAATTTTGT
Statistics
Matches: 568, Mismatches: 52, Indels: 25
0.88 0.08 0.04
Matches are distributed among these distances:
73 71 0.12
74 208 0.37
75 249 0.44
76 40 0.07
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (74 bp):
ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
TGATAAGAA
Found at i:2186 original size:149 final size:148
Alignment explanation
Indices: 1912--2618 Score: 958
Period size: 149 Copynumber: 4.8 Consensus size: 148
1902 CCTTTTAAAC
* * * **
1912 ACCTAAACAGGGAGT-TTGAACAAGAATTTT-ATGGGAAACCTAAACAGTCACCTTAAATAAGGA
1 ACCTAAACA-GGAATCTTGAACAAG-ATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA
* *
1975 TTTGATAAGAAAACCTAAACAAGAATTTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCT
64 TTTGATAAG-AAACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCT
2040 TAAATAAGGATTTAATAAGAAA
128 TAAATAAGGATTTAATAAG-AA
* * * * * * * *
2062 AAC-AAACAGGGATCTTAAACAAAAATTTTG-TCAAGAAACCTAAACAGGCATCTTAAATAAGGA
1 ACCTAAACAGGAATCTTGAAC-AAGATTTTGAT-GAGACACCTAAACAGGGACCTTAAATAAGGA
* *
2125 TTTGATAAGAAACCTAAACAGGGATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTT
64 TTTGATAAGAAACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTT
*
2190 AAATAAGGA-TTAATGAGAA
129 AAATAAGGATTTAATAAGAA
2209 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA-T
* * *
2274 TTGATAAGAAAGCTAAACAGGAATCTTGAACAAAAATTTTGATGAGACACGTAAACAGGGACCTT
65 TTGATAAGAAACCTAAACAGGAATCTTGAAC-AAGATTTTGATGAGACACCTAAACAGGGACCTT
*
2339 AAATAAGGATTTGATAAGAA
129 AAATAAGGATTTAATAAGAA
* * *
2359 ACCTAACCAGGAATCTTGAACAAGGTTTTGATGAGACACCTATACAGGGACCTTAAATAAGGATT
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
* * * *
2424 TGACAAGAAAACCTAAACAGGAATCTTGAACAAGGTTTTGATGAGACACCTAAATAGGGATCTTA
66 TGATAAG-AAACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTA
*
2489 AATAAGGATTTGATAAGAA
130 AATAAGGATTTAATAAGAA
* *
2508 ATCTAAACA-GAGATCTTGAACAAGGTTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGAT
1 ACCTAAACAGGA-ATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGAT
* * * *
2572 TTGATAAGTAACCTAATCAGAAATCTTGAACAAGGTTTTGATGAGAC
65 TTGATAAGAAACCTAAACAGGAATCTTGAACAAGATTTTGATGAGAC
2619 TGAATTTTGT
Statistics
Matches: 500, Mismatches: 46, Indels: 24
0.88 0.08 0.04
Matches are distributed among these distances:
147 39 0.08
148 93 0.19
149 238 0.48
150 130 0.26
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (148 bp):
ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
TGATAAGAAACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAA
ATAAGGATTTAATAAGAA
Found at i:2612 original size:37 final size:36
Alignment explanation
Indices: 1912--2613 Score: 433
Period size: 37 Copynumber: 18.9 Consensus size: 36
1902 CCTTTTAAAC
* **
1912 ACCTAAACAGGGAGT-TTGAACAAGAATTTT-ATGGGAA
1 ACCTAAACAGGGA-TCTTGAACAAG-GTTTTGATAAG-A
** * * * *
1949 ACCTAAACAGTCACCTTAAATAAGGATTTGATAAGAAA
1 ACCTAAACAGGGATCTTGAACAAGGTTTTGATAAG--A
* * * * *
1987 ACCTAAACAAGAATTTTGAACAAGATTTTGATGAGA
1 ACCTAAACAGGGATCTTGAACAAGGTTTTGATAAGA
* * * * *
2023 CACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAA
1 -ACCTAAACAGGGATCTTGAACAAGGTTTTGATAAG--A
* * **
2062 AAC-AAACAGGGATCTTAAACAAAAATTTTG-TCAAGAA
1 ACCTAAACAGGGATCTTGAAC-AAGGTTTTGAT-AAG-A
* * * *
2099 ACCTAAACAGGCATCTTAAATAAGGATTTGATAAGAA
1 ACCTAAACAGGGATCTTGAACAAGGTTTTGATAAG-A
* * *
2136 ACCTAAACAGGGATCTTAAACAAGATTTTGATGAGA
1 ACCTAAACAGGGATCTTGAACAAGGTTTTGATAAGA
* * * * * *
2172 CACCTAAACAGGGACCTTAAATAAGG-ATTAATGAGAA
1 -ACCTAAACAGGGATCTTGAACAAGGTTTTGATAAG-A
* * *
2209 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGA
1 ACCTAAACAGGGATCTTGAACAAGGTTTTGATAAGA
* * *
2245 CACCTAAACAGGGACCTTAAATAAGGATTTTGATAAGAA
1 -ACCTAAACAGGGATCTTGAACAAGG-TTTTGATAAG-A
* * ** *
2284 AGCTAAACAGGAATCTTGAACAAAAATTTTGATGAGA
1 ACCTAAACAGGGATCTTGAAC-AAGGTTTTGATAAGA
* * * * *
2321 CACGTAAACAGGGACCTTAAATAAGGATTTGATAAGAA
1 -ACCTAAACAGGGATCTTGAACAAGGTTTTGATAAG-A
* * *
2359 ACCTAACCAGGAATCTTGAACAAGGTTTTGATGAGA
1 ACCTAAACAGGGATCTTGAACAAGGTTTTGATAAGA
* * * * * *
2395 CACCTATACAGGGACCTTAAATAAGGATTTGACAAGAAA
1 -ACCTAAACAGGGATCTTGAACAAGGTTTTGATAAG--A
* *
2434 ACCTAAACAGGAATCTTGAACAAGGTTTTGATGAGA
1 ACCTAAACAGGGATCTTGAACAAGGTTTTGATAAGA
* * * *
2470 CACCTAAATAGGGATCTTAAATAAGGATTTGATAAGAA
1 -ACCTAAACAGGGATCTTGAACAAGGTTTTGATAAG-A
* * *
2508 ATCTAAACAGAGATCTTGAACAAGGTTTTGATGAGA
1 ACCTAAACAGGGATCTTGAACAAGGTTTTGATAAGA
* * * *
2544 CACCTAAACAGGGACCTTAAATAAGGATTTGATAAGTA
1 -ACCTAAACAGGGATCTTGAACAAGGTTTTGATAAG-A
* **
2582 ACCTAATCAGAAATCTTGAACAAGGTTTTGAT
1 ACCTAAACAGGGATCTTGAACAAGGTTTTGAT
2614 GAGACTGAAT
Statistics
Matches: 504, Mismatches: 135, Indels: 52
0.73 0.20 0.08
Matches are distributed among these distances:
36 36 0.07
37 331 0.66
38 132 0.26
39 5 0.01
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (36 bp):
ACCTAAACAGGGATCTTGAACAAGGTTTTGATAAGA
Found at i:3558 original size:87 final size:88
Alignment explanation
Indices: 3393--3563 Score: 254
Period size: 87 Copynumber: 2.0 Consensus size: 88
3383 TGATTGATGC
* * *
3393 CCCAAACCTTCTTCCAATTTGGTCATGTATTGATATTTCCCAACTCAACTGATGGTTCTGGATCA
1 CCCAAACCTTCCTCCAATTTGATCATGCATTGATATTTCCCAACTCAACTGATGGTTCTGGATCA
3458 ACTTCCCACCTTAAGAAATATTT
66 ACTTCCCACCTTAAGAAATATTT
* * *
3481 CCCAAATCTTCCTCCAATTTGATCATGCATTGATA-TTCCCAACTCAATTGATGTTTCTGGATCA
1 CCCAAACCTTCCTCCAATTTGATCATGCATTGATATTTCCCAACTCAACTGATGGTTCTGGATCA
* * *
3545 ATTTCTCATCTTAAGAAAT
66 ACTTCCCACCTTAAGAAAT
3564 GTTCAAACAT
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
87 43 0.58
88 31 0.42
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (88 bp):
CCCAAACCTTCCTCCAATTTGATCATGCATTGATATTTCCCAACTCAACTGATGGTTCTGGATCA
ACTTCCCACCTTAAGAAATATTT
Found at i:3709 original size:4 final size:4
Alignment explanation
Indices: 3696--3749 Score: 101
Period size: 4 Copynumber: 13.8 Consensus size: 4
3686 TCCTTTTGAT
3696 TTTC -TTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
3743 TTTC TTT
1 TTTC TTT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 3 0.06
4 46 0.94
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Done.