Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014184.1 Corchorus olitorius cultivar O-4 contig14217, 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: 3435
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Found at i:747 original size:21 final size:22
Alignment explanation
Indices: 730--1382 Score: 291
Period size: 22 Copynumber: 30.0 Consensus size: 22
720 ATTTTTTATT
*
730 ACCTTCTTATGAAATTTTGATA
1 ACCTTCCTATGAAATTTTGATA
**
752 ACCTTCCTATGAAATTTCAATA
1 ACCTTCCTATGAAATTTTGATA
* * * * *
774 A-CATACTATGGAATTTCGAGA
1 ACCTTCCTATGAAATTTTGATA
** **
795 ACCTTTTTAT-AAATTTTTTTTA
1 ACCTTCCTATGAAA-TTTTGATA
* *
817 ACCTTCTTATGAAATTTTGTTA
1 ACCTTCCTATGAAATTTTGATA
*
839 ACC-TCTCTAAGAAATTTTGA-A
1 ACCTTC-CTATGAAATTTTGATA
*
860 GACC-TCATTATGAAATTTTGATA
1 -ACCTTC-CTATGAAATTTTGATA
*
883 A-CTTCCCATTGAAATTTTGATA
1 ACCTTCCTA-TGAAATTTTGATA
** *
905 ACCAACACTATGAAATGTTGATA
1 ACCTTC-CTATGAAATTTTGATA
* * *
928 ACC-TCTATATGATATATTGATA
1 ACCTTC-CTATGAAATTTTGATA
* * * * *
950 ACC-ACGTTATGAAAATTTAAAA
1 ACCTTC-CTATGAAATTTTGATA
*
972 ACC-TCCATATG-AATTGTTAATA
1 ACCTTCC-TATGAAATT-TTGATA
* * * *
994 ATC-ACACTCTGAAATGTTGATA
1 ACCTTC-CTATGAAATTTTGATA
* * **
1016 ATC-ACACTATGAAATTGCGATA
1 ACCTTC-CTATGAAATTTTGATA
1038 ACC-TCTCTATGAAATTTTGATAA
1 ACCTTC-CTATGAAATTTTGAT-A
* *
1061 ACATTCCTATAAAATTTTGATAA
1 ACCTTCCTATGAAATTTTGAT-A
* *
1084 ACCTCCCTATAAAATTTTGATA
1 ACCTTCCTATGAAATTTTGATA
*
1106 ACC-TCCTTATGAAATCTTGATA
1 ACCTTCC-TATGAAATTTTGATA
* *
1128 A-----CTA-CAAATTTTTATA
1 ACCTTCCTATGAAATTTTGATA
* ** *
1144 ACCTCCCTATGATTTTTTTATA
1 ACCTTCCTATGAAATTTTGATA
* *
1166 ACC-TCATTATGAAATTTTGTTA
1 ACCTTC-CTATGAAATTTTGATA
* *
1188 ATCTCCCTATGAAATTTTGATA
1 ACCTTCCTATGAAATTTTGATA
*
1210 ATCC-TCTTATGAAATTTTGA-A
1 A-CCTTCCTATGAAATTTTGATA
* **
1231 AACTAAGCTATGAAATTTTGATA
1 ACCT-TCCTATGAAATTTTGATA
* *
1254 ACCTTCATATGAAATTTTGATCT
1 ACCTTCCTATGAAATTTTGAT-A
* * *
1277 A-CATACTATAAAATTTTGATA
1 ACCTTCCTATGAAATTTTGATA
* *
1298 ACCCTCTTATGAAATTTTGA-A
1 ACCTTCCTATGAAATTTTGATA
* **
1319 TA-GTAAACTATGAAATTTTGATA
1 -ACCT-TCCTATGAAATTTTGATA
*
1342 ACCTTCATATGAAATTTTGATA
1 ACCTTCCTATGAAATTTTGATA
* *
1364 TCC-TCC-CTGAAATTTTGAT
1 ACCTTCCTATGAAATTTTGAT
1383 TACTCCATAA
Statistics
Matches: 479, Mismatches: 117, Indels: 72
0.72 0.18 0.11
Matches are distributed among these distances:
16 10 0.02
17 2 0.00
18 1 0.00
20 13 0.03
21 38 0.08
22 339 0.71
23 72 0.15
24 4 0.01
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
ACCTTCCTATGAAATTTTGATA
Found at i:932 original size:67 final size:66
Alignment explanation
Indices: 826--951 Score: 148
Period size: 67 Copynumber: 1.9 Consensus size: 66
816 AACCTTCTTA
* * * * *
826 TGAAATTTTGTTAACCTCTCTAAGAAATTTTGAAGACCTC-ATTATGAAATTTTGATAACTTCCC
1 TGAAATTTTGATAACCACACTAAGAAATGTTGAAGACCTCTA-TATGAAATATTGATAACTTCCC
890 AT
65 AT
* *
892 TGAAATTTTGATAACCAACACTATGAAATGTTGATA-ACCTCTATATGATATATTGATAAC
1 TGAAATTTTGATAACC-ACACTAAGAAATGTTGA-AGACCTCTATATGAAATATTGATAAC
952 CACGTTATGA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
66 15 0.30
67 33 0.66
68 2 0.04
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (66 bp):
TGAAATTTTGATAACCACACTAAGAAATGTTGAAGACCTCTATATGAAATATTGATAACTTCCCA
T
Found at i:948 original size:45 final size:45
Alignment explanation
Indices: 868--953 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
858 AAGACCTCAT
* * *
868 TATGAAATTTTGATAACTTCCCATTGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAACCTCCCATTGAAATATTGATAACCAACAC
* *
913 TATGAAATGTTGATAACCT-CTATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCCAT-TGAAATATTGATAACCA
954 CGTTATGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 3 0.09
45 32 0.91
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCCATTGAAATATTGATAACCAACAC
Found at i:1632 original size:89 final size:88
Alignment explanation
Indices: 1472--1634 Score: 193
Period size: 89 Copynumber: 1.8 Consensus size: 88
1462 TACCACTATG
* * * * ** *
1472 AAATTTTGGTAATGACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTCTAT
1 AAATTTTGATAATCACATTATGAAAATTTGATAACCTCTTTA-GAAATTTTCATAACAACACTAT
1537 AAAATTTTGTTGACCCCTCTATTA
65 AAAATTTTGTTGACCCCTCTATTA
* *
1561 AAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTTTA-AAATTTTCATAACAACACTA
1 AAATTTTGATAATCACATTATGAAAATTTGATAACCT--CTTTAGAAATTTTCATAACAACACTA
**
1625 TGGAATTTTG
64 TAAAATTTTG
1635 ATAATCTTCC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
89 56 0.92
91 5 0.08
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (88 bp):
AAATTTTGATAATCACATTATGAAAATTTGATAACCTCTTTAGAAATTTTCATAACAACACTATA
AAATTTTGTTGACCCCTCTATTA
Found at i:1689 original size:20 final size:19
Alignment explanation
Indices: 1664--1703 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1654 TGATAATCCG
1664 ATCTCTATGAAATTTCGATA
1 ATCTCTATGAAATTT-GATA
*
1684 ATCTCTATGAGATTTGATA
1 ATCTCTATGAAATTTGATA
1703 A
1 A
1704 CCTTCTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (19 bp):
ATCTCTATGAAATTTGATA
Found at i:1847 original size:22 final size:21
Alignment explanation
Indices: 1492--1860 Score: 149
Period size: 22 Copynumber: 16.7 Consensus size: 21
1482 AATGACATTT
* *
1492 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTC-CTA
1514 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTC-CTA
* * * *
1536 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTC-CTA
* * * *
1558 TTAAAATTTTGATAATCACATTA
1 -TGAAATTTTGATAACCTC-CTA
* *
1581 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCTC-CTA
* * **
1603 TAAAATTTTCATAACAACACTA
1 TGAAATTTTGATAACCTC-CTA
* *
1625 TGGAATTTTGATAATCTTCCTA
1 TGAAATTTTGATAA-CCTCCTA
1647 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TC-CTA
* *
1671 TGAAATTTCGATAATCT-CTA
1 TGAAATTTTGATAACCTCCTA
* * *
1691 TGAGA-TTTGATAACCTTCTT
1 TGAAATTTTGATAACCTCCTA
* *
1711 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCTCC-TA
* *
1731 TGAAATTGAGACTTTTATAACCTTCTTA
1 TGAAA-T-----TTTGATAACC-TCCTA
* *
1759 TGAAATTTTGAAAACCTCCCCA
1 TGAAATTTTGATAACCT-CCTA
*
1781 TGAAATATT-AGTAACCTCCTTA
1 TGAAATTTTGA-TAACCTCC-TA
* *
1803 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTC-CTA
1825 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCTC-CTA
**
1847 TGGCATTTTGATAA
1 TGAAATTTTGATAA
1861 TCTCTTTGAT
Statistics
Matches: 259, Mismatches: 63, Indels: 50
0.70 0.17 0.13
Matches are distributed among these distances:
19 12 0.05
20 18 0.07
21 25 0.10
22 149 0.58
23 23 0.09
24 5 0.02
25 11 0.04
26 4 0.02
27 2 0.01
28 8 0.03
29 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (21 bp):
TGAAATTTTGATAACCTCCTA
Found at i:1981 original size:22 final size:22
Alignment explanation
Indices: 1890--2101 Score: 141
Period size: 22 Copynumber: 9.5 Consensus size: 22
1880 ATAAAGTTTG
1890 TGATAACCACACTATGAAATTT
1 TGATAACCACACTATGAAATTT
** * *
1912 CAATAACCTTC-CTAAGAAATTT
1 TGATAACC-ACACTATGAAATTT
* *
1934 TAATAACCTGATC-CTATTAAATTT
1 TGATAACC--A-CACTATGAAATTT
* * *
1958 TGGTAACCACATTATGGAATTT
1 TGATAACCACACTATGAAATTT
* *
1980 TGATAACCTTC-CCATGAAATTT
1 TGATAACC-ACACTATGAAATTT
2002 TGATAACTTC-CA-TATGAAATTT
1 TGATAAC--CACACTATGAAATTT
* *
2024 TGGTAACCACACTATGGAATTT
1 TGATAACCACACTATGAAATTT
* *
2046 TGATAACCTC-CTCATGAAATTA
1 TGATAACCACACT-ATGAAATTT
* *
2068 TAATAACCATC-TTATGAAATTT
1 TGATAACCA-CACTATGAAATTT
2090 TGATAACCACAC
1 TGATAACCACAC
2102 AGAGACAAGA
Statistics
Matches: 145, Mismatches: 32, Indels: 26
0.71 0.16 0.13
Matches are distributed among these distances:
20 1 0.01
21 6 0.04
22 117 0.81
23 4 0.03
24 17 0.12
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (22 bp):
TGATAACCACACTATGAAATTT
Found at i:2046 original size:66 final size:66
Alignment explanation
Indices: 1869--2101 Score: 265
Period size: 66 Copynumber: 3.5 Consensus size: 66
1859 AATCTCTTTG
* * * ** * *
1869 ATAACCTTTCTAT-AAAGTTTGTGATAACCACACTATGAAATTTCAATAACCTTCCTAAGAAATT
1 ATAACCTTCCTATGAAA-TTT-TGGTAACCACACTATGGAATTTTGATAACCTTCCCATGAAATT
1933 TTA
64 TTA
* *
1936 ATAACCTGATCCTATTAAATTTTGGTAACCACATTATGGAATTTTGATAACCTTCCCATGAAATT
1 ATAACCT--TCCTATGAAATTTTGGTAACCACACTATGGAATTTTGATAACCTTCCCATGAAATT
*
2001 TTG
64 TTA
2004 ATAA-CTTCCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACC-TCCTCATGAAATT
1 ATAACCTTCC-TATGAAATTTTGGTAACCACACTATGGAATTTTGATAACCTTCC-CATGAAATT
*
2067 ATA
64 TTA
* * *
2070 ATAACCATCTTATGAAATTTTGATAACCACAC
1 ATAACCTTCCTATGAAATTTTGGTAACCACAC
2102 AGAGACAAGA
Statistics
Matches: 144, Mismatches: 16, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
65 6 0.04
66 73 0.51
67 12 0.08
68 42 0.29
69 8 0.06
70 3 0.02
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (66 bp):
ATAACCTTCCTATGAAATTTTGGTAACCACACTATGGAATTTTGATAACCTTCCCATGAAATTTT
A
Found at i:2097 original size:44 final size:43
Alignment explanation
Indices: 1865--2097 Score: 175
Period size: 44 Copynumber: 5.2 Consensus size: 43
1855 TGATAATCTC
* *
1865 TTTGATAACCTTTCTAT-AAAGTTTGTGATAACCA-CACTATGAAAT
1 TTTGATAACC-TCCTATGAAA-TTT-TAATAACCATC-CTATGAAAT
** * *
1910 TTCAATAACCTTCCTAAGAAATTTTAATAACCTGATCCTATTAAAT
1 TTTGATAACC-TCCTATGAAATTTTAATAACC--ATCCTATGAAAT
* * * * * * *
1956 TTTGGTAACCACATTATGGAATTTTGATAACCTTCCCATGAAAT
1 TTTGATAACCTC-CTATGAAATTTTAATAACCATCCTATGAAAT
* ** *
2000 TTTGATAACTTCCATATGAAATTTTGGTAACCA-CACTATGGAAT
1 TTTGATAACCTCC-TATGAAATTTTAATAACCATC-CTATGAAAT
* *
2044 TTTGATAACCTCCTCATGAAATTATAATAACCATCTTATGAAAT
1 TTTGATAACCTCCT-ATGAAATTTTAATAACCATCCTATGAAAT
2088 TTTGATAACC
1 TTTGATAACC
2098 ACACAGAGAC
Statistics
Matches: 147, Mismatches: 32, Indels: 19
0.74 0.16 0.10
Matches are distributed among these distances:
43 2 0.01
44 92 0.63
45 18 0.12
46 34 0.23
47 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.37
Consensus pattern (43 bp):
TTTGATAACCTCCTATGAAATTTTAATAACCATCCTATGAAAT
Found at i:3131 original size:18 final size:18
Alignment explanation
Indices: 3108--3142 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3098 ACAAAAATTG
3108 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
3126 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
3143 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:3291 original size:19 final size:19
Alignment explanation
Indices: 3267--3314 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
3257 TTTATAATTT
* *
3267 TTATTAATAATATATATTA
1 TTATTAATAATATAAATAA
3286 TTATTAAT-ATATAAATAA
1 TTATTAATAATATAAATAA
3304 TTATATAATAA
1 TTAT-TAATAA
3315 ATGAACGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 12 0.48
19 12 0.48
20 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTATTAATAATATAAATAA
Found at i:3401 original size:35 final size:36
Alignment explanation
Indices: 3341--3410 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 36
3331 TTATATAAAC
*
3341 GAACACTTAAATGAAACAATAAACGAGTCTGTTCGT
1 GAACACTTAAATGAAACAATAAACGAGGCTGTTCGT
3377 GAACACTTAAATG-AACAATAAACGAGGCTGTTCG
1 GAACACTTAAATGAAACAATAAACGAGGCTGTTCG
3411 GAAACATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.61
36 13 0.39
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (36 bp):
GAACACTTAAATGAAACAATAAACGAGGCTGTTCGT
Done.