Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023326.1 Corchorus olitorius cultivar O-4 contig23359, 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: 6996
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:938 original size:39 final size:39
Alignment explanation
Indices: 891--1895 Score: 236
Period size: 40 Copynumber: 25.0 Consensus size: 39
881 AATAAGACTT
* * * *
891 TGAAATTAACTGAGAAAACAATGACCCTGAACAGGATTC
1 TGAAATTAACTGATAAAACAATGATCCTAAATAGGATTC
930 TGAAATTAACTGATAAAACAATGATCCTAAATAGGATTC
1 TGAAATTAACTGATAAAACAATGATCCTAAATAGGATTC
969 TGAAATTAACTGATAAAACAATGATCCTAAATAGGATTC
1 TGAAATTAACTGATAAAACAATGATCCTAAATAGGATTC
** * * ** *** **
1008 TGAAAACAA-TGATCCTGAATAGCATTTGAGAAAGC-AATGATCCTAAATAGGA
1 TGAAATTAACTGA---T-AA-AACA-AT--G-ATCCTAA--AT--AGGAT--TC
* * * *
1060 TGGAAATTGATTGATAAAGA-AACGATCCTGAATAGGATTC
1 T-GAAATTAACTGATAAA-ACAATGATCCTAAATAGGATTC
* * ** * *
1100 CGAAAAAGTGTCTTCG-TAAAGCAATGATCCTAAGTAGGATTC
1 TG--AAATTAAC-T-GATAAAACAATGATCCTAAATAGGATTC
* * * * **
1142 TAAAATCT-CCTTGATAAAGCAATGATCCTGAGCAGGATTC
1 TGAAAT-TAAC-TGATAAAACAATGATCCTAAATAGGATTC
* ** * * * * *
1182 TGAAATTAATTTGATAATGCGATGATTCTGAGTAGGATTG
1 TGAAATTAA-CTGATAAAACAATGATCCTAAATAGGATTC
* * * * * *
1222 TG--ATTAATTTGATAAAGCAATGATCCTGAGTAGGGTTT
1 TGAAATTAA-CTGATAAAACAATGATCCTAAATAGGATTC
* * * ** * *
1260 TGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTT
1 TGAAATTAA-CTGATAAAACAATGATCCTAAATAGGATTC
* * * * ** * *
1300 TGAAATTAATTAGACAAAGCAATGATCCTGAGCAGGGTTT
1 TGAAATTAACT-GATAAAACAATGATCCTAAATAGGATTC
* * * ** *
1340 TGAAATTAATTTGATAAAGCAGATGATCCTGAGCAGGATTT
1 TGAAATTAA-CTGATAAAACA-ATGATCCTAAATAGGATTC
* * * * ** *
1381 TGAAATTAATTTGATAAAGCAATGATCTTGAGCAGGAATC
1 TGAAATTAA-CTGATAAAACAATGATCCTAAATAGGATTC
** * * * ** * *
1421 TGAAATTGATTTGGTAAAGCAATGATCCTGAGCAGGGTTT
1 TGAAATT-AACTGATAAAACAATGATCCTAAATAGGATTC
* * ** *
1461 TGAAATTAATTTGATAAAA-AGATGATCCTGAGCAGGATTT
1 TGAAATTAA-CTGATAAAACA-ATGATCCTAAATAGGATTC
* * * * **
1501 TGAAATTAATTTGATAAAGCAATGATTCTGAGCAGGATTC
1 TGAAATTAA-CTGATAAAACAATGATCCTAAATAGGATTC
** * * **
1541 TGAAATTGATTTGATAAAGCAATGATCCTGAGCAGGATTC
1 TGAAATT-AACTGATAAAACAATGATCCTAAATAGGATTC
** * * *
1581 TGAAATTGATTTGATAAAGCAATGATCCTGATTAGGATT-
1 TGAAATT-AACTGATAAAACAATGATCCTAAATAGGATTC
* * * * *
1620 TGAAATTAATTTGACAAAGCAATGATCCTGAATAGGATTG
1 TGAAATTAA-CTGATAAAACAATGATCCTAAATAGGATTC
* * * ** * *
1660 TG--ATTGACTGGTAAAGA-AATGATCCTGAGCAGGGTTT
1 TGAAATTAACTGATAAA-ACAATGATCCTAAATAGGATTC
* * ** *
1697 TGAAATTAATTTGATAAAA-AGATGATCCTGAGCAGGATTT
1 TGAAATTAA-CTGATAAAACA-ATGATCCTAAATAGGATTC
* * * **
1737 TGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGATTC
1 TGAAATTAA-CTGATAAAACAATGATCCTAAATAGGATTC
** * * ** *
1777 TGAAATTGATTTGATAAAGCAATGATCCTGAGCAGGATTT
1 TGAAATT-AACTGATAAAACAATGATCCTAAATAGGATTC
** * * ** *
1817 TGAAATTGATTTGATAAAGCAATGATCCTGAGCAGGATTT
1 TGAAATT-AACTGATAAAACAATGATCCTAAATAGGATTC
* * *
1857 TGAAATTAATTTGATAAAGCAATGATCCTGAATAGGATT
1 TGAAATTAA-CTGATAAAACAATGATCCTAAATAGGATT
1896 GTGATTGACT
Statistics
Matches: 815, Mismatches: 103, Indels: 95
0.80 0.10 0.09
Matches are distributed among these distances:
37 23 0.03
38 41 0.05
39 129 0.16
40 509 0.62
41 53 0.07
42 26 0.03
43 4 0.00
44 3 0.00
45 2 0.00
46 5 0.01
47 2 0.00
48 2 0.00
49 2 0.00
50 4 0.00
51 1 0.00
52 1 0.00
53 5 0.01
54 3 0.00
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (39 bp):
TGAAATTAACTGATAAAACAATGATCCTAAATAGGATTC
Found at i:1013 original size:27 final size:26
Alignment explanation
Indices: 983--1060 Score: 111
Period size: 27 Copynumber: 2.9 Consensus size: 26
973 ATTAACTGAT
983 AAAACAATGATCCTAAATAGGATTCTG
1 AAAACAATGATCCTAAATAGGATT-TG
* *
1010 AAAACAATGATCCTGAATAGCATTTG
1 AAAACAATGATCCTAAATAGGATTTG
1036 AGAAAGCAATGATCCTAAATAGGAT
1 A-AAA-CAATGATCCTAAATAGGAT
1061 GGAAATTGAT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
26 3 0.07
27 25 0.56
28 17 0.38
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (26 bp):
AAAACAATGATCCTAAATAGGATTTG
Found at i:1169 original size:40 final size:40
Alignment explanation
Indices: 1116--1932 Score: 1046
Period size: 40 Copynumber: 20.6 Consensus size: 40
1106 AGTGTCTTCG
* * * * **
1116 TAAAGCAATGATCCTAAGTAGGATTCTAAAATCT-CCTTGA
1 TAAAGCAATGATCCTGAGCAGGATTTTGAAAT-TAATTTGA
*
1156 TAAAGCAATGATCCTGAGCAGGATTCTGAAATTAATTTGA
1 TAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGA
* * * * *
1196 TAATGCGATGATTCTGAGTAGGATTGTG--ATTAATTTGA
1 TAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGA
* *
1234 TAAAGCAATGATCCTGAGTAGGGTTTTGAAATTAATTTGA
1 TAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGA
* *
1274 TAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTAGA
1 TAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGA
* *
1314 CAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGA
1 TAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGA
1354 TAAAGCAGATGATCCTGAGCAGGATTTTGAAATTAATTTGA
1 TAAAGCA-ATGATCCTGAGCAGGATTTTGAAATTAATTTGA
* * * * *
1395 TAAAGCAATGATCTTGAGCAGGAATCTGAAATTGATTTGG
1 TAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGA
*
1435 TAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGA
1 TAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGA
*
1475 TAAA-AAGATGATCCTGAGCAGGATTTTGAAATTAATTTGA
1 TAAAGCA-ATGATCCTGAGCAGGATTTTGAAATTAATTTGA
* * *
1515 TAAAGCAATGATTCTGAGCAGGATTCTGAAATTGATTTGA
1 TAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGA
* *
1555 TAAAGCAATGATCCTGAGCAGGATTCTGAAATTGATTTGA
1 TAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGA
**
1595 TAAAGCAATGATCCTGATTAGGA-TTTGAAATTAATTTGA
1 TAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGA
* ** * * * *
1634 CAAAGCAATGATCCTGAATAGGATTGTG--ATTGA-CTGG
1 TAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGA
* *
1671 TAAAGAAATGATCCTGAGCAGGGTTTTGAAATTAATTTGA
1 TAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGA
*
1711 TAAA-AAGATGATCCTGAGCAGGATTTTGAAATTAATTTGA
1 TAAAGCA-ATGATCCTGAGCAGGATTTTGAAATTAATTTGA
* *
1751 TAAAGCAATGATCCTGAGCAGGATTCTGAAATTGATTTGA
1 TAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGA
*
1791 TAAAGCAATGATCCTGAGCAGGATTTTGAAATTGATTTGA
1 TAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGA
1831 TAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGA
1 TAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGA
** * * * *
1871 TAAAGCAATGATCCTGAATAGGATTGTG--ATTGA-CTGG
1 TAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGA
*
1908 TAAAGAAATGATCCTGAGCAGGATT
1 TAAAGCAATGATCCTGAGCAGGATT
1933 CTGGACTCGA
Statistics
Matches: 692, Mismatches: 73, Indels: 27
0.87 0.09 0.03
Matches are distributed among these distances:
37 48 0.07
38 41 0.06
39 43 0.06
40 519 0.75
41 41 0.06
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (40 bp):
TAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGA
Found at i:1970 original size:39 final size:37
Alignment explanation
Indices: 1870--1971 Score: 114
Period size: 39 Copynumber: 2.7 Consensus size: 37
1860 AATTAATTTG
* * *
1870 ATAAAGCAATGATCCTGAATAGGATTGTGATTGACTG
1 ATAAAGCAATGATCCTGAATAGGATTCTGATCGACTA
* * **
1907 GTAAAGAAATGATCCTGAGCAGGATTCTGGACTCGACTA
1 ATAAAGCAATGATCCTGAATAGGATTCT-GA-TCGACTA
*
1946 ATAAAGCAATGATCATGAATAGGATT
1 ATAAAGCAATGATCCTGAATAGGATT
1972 AAAACACATA
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
37 23 0.45
38 2 0.04
39 26 0.51
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (37 bp):
ATAAAGCAATGATCCTGAATAGGATTCTGATCGACTA
Found at i:2323 original size:148 final size:147
Alignment explanation
Indices: 2036--2544 Score: 791
Period size: 148 Copynumber: 3.5 Consensus size: 147
2026 AGGACATGTT
* * * * *
2036 AGAATTGACACCCAGAGGTTCCTGAAATGGTGTCCGGAGGTCTTACAAATGCAAACTCAACCTTG
1 AGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGGAGGTCTTACAAATGCAAACTCAACCTTG
* *
2101 AGCAAGAT--TTTTGAAA--T----TTAAACACAGCTTTGATTAAAAACTTGATGAAATGAAATG
66 AGCAAGGTGCTTTTGAAACTTAAACTTAAACGCAGCTTTGATTAAAAA-TTGATGAAATGAAATG
2158 ATACCCGGAGGATTTATC
130 ATACCCGGAGGATTTATC
*
2176 AGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCAACCTTG
1 AGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGGAGGTCTTACAAATGCAAACTCAACCTTG
*
2241 AGCAAGGTGCTTTTGAAACTTAAACTTAAACGCAGCTTTGATTAAACATTGGATGAAATGAAATG
66 AGCAAGGTGCTTTTGAAACTTAAACTTAAACGCAGCTTTGATTAAAAATT-GATGAAATGAAATG
*
2306 ATACCCGAAGGATTTATC
130 ATACCCGGAGGATTTATC
* * *
2324 AGAATTTATACCCGGAGGTTTTTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCAACCTTG
1 AGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGGAGGTCTTACAAATGCAAACTCAACCTTG
*
2389 AGCAAGGTGCTTTTGAAACTTAAACTTAAACGCAGCTTTGATTAAAAATTTGATGAAGTGAAATG
66 AGCAAGGTGCTTTTGAAACTTAAACTTAAACGCAGCTTTGATTAAAAA-TTGATGAAATGAAATG
2454 ATACCCGGAGGATTTATC
130 ATACCCGGAGGATTTATC
**
2472 AGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCAAAGGTCTTACAAATGCAAACTCAACCTTG
1 AGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGGAGGTCTTACAAATGCAAACTCAACCTTG
2537 AGCAAGGT
66 AGCAAGGT
2545 TTTGATTTTA
Statistics
Matches: 339, Mismatches: 20, Indels: 12
0.91 0.05 0.03
Matches are distributed among these distances:
140 66 0.19
142 8 0.02
144 1 0.00
147 2 0.01
148 260 0.77
149 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (147 bp):
AGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGGAGGTCTTACAAATGCAAACTCAACCTTG
AGCAAGGTGCTTTTGAAACTTAAACTTAAACGCAGCTTTGATTAAAAATTGATGAAATGAAATGA
TACCCGGAGGATTTATC
Found at i:3851 original size:19 final size:20
Alignment explanation
Indices: 3822--3863 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
3812 CTTATACTTT
3822 TTTCAATTTTCAATTTCCAC
1 TTTCAATTTTCAATTTCCAC
*
3842 TTTC-ATTTTCAATTTTCAC
1 TTTCAATTTTCAATTTCCAC
3861 TTT
1 TTT
3864 TTTGTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTCAATTTTCAATTTCCAC
Done.