Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019163.1 Corchorus olitorius cultivar O-4 contig19196, 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: 31322
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:204 original size:58 final size:58
Alignment explanation
Indices: 105--214 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 58
95 ATTAATCAAA
*
105 TATCAAGTGACATGTTCTTTATAAGATGCATAAAAAAAGACGTTTTCGGACCAAAACT
1 TATCAAGTGACATGTTCTTTATAAGATGCATAAAAAAAGACGTTTTAGGACCAAAACT
* * * * *
163 TATCGAGTGACATATTTTTTTATTAGATGCCT-AAAAAAGACGTTTTAGGACC
1 TATCAAGTGACAT-GTTCTTTATAAGATGCATAAAAAAAGACGTTTTAGGACC
215 GAGGCATGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 31 0.69
59 14 0.31
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATAAGATGCATAAAAAAAGACGTTTTAGGACCAAAACT
Found at i:1540 original size:36 final size:36
Alignment explanation
Indices: 1493--1562 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
1483 TTCATTAACC
* *
1493 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
1529 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
1563 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:2441 original size:204 final size:203
Alignment explanation
Indices: 2091--2485 Score: 677
Period size: 204 Copynumber: 1.9 Consensus size: 203
2081 ATCGATGATG
2091 AATGTTATTAAATTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACA
1 AATGTTATTAAATTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACA
** * *
2156 TTGTTATTATATATAAATCTATACAAAAAAAAAGTAGTTGAACATTAGTGGTTGATTTATTAAAT
66 TTACTATTATATATAAAACTATACAAAAAAAAAGTAGTTAAACATTAGTGGTTGATTTATTAAAT
* *
2221 TAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCTGATTTATATA
131 TAAATTAGATCAATGTCAAACAAAATTTCAAAACTATAAAAGATATT-AAGATCCGATTTATATA
2286 TCAATGGTC
195 TCAATGGTC
2295 AATGTTATT-AA-TTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACA
1 AATGTTATTAAATTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACA
* *
2358 TTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTAAACATTAGTGGTTGATTTATTAA
66 TTACTATTATATATA-A-AACTATACAAAAAAAAAGTAGTTAAACATTAGTGGTTGATTTATTAA
2423 ATTAAATTAGATCAATGTCAAACAAAATTTCAAAACTATAAAAGATATTAAGATCCGATTTAT
129 ATTAAATTAGATCAATGTCAAACAAAATTTCAAAACTATAAAAGATATTAAGATCCGATTTAT
2486 TTATTATTAA
Statistics
Matches: 181, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
202 65 0.36
203 16 0.09
204 100 0.55
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.36
Consensus pattern (203 bp):
AATGTTATTAAATTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACA
TTACTATTATATATAAAACTATACAAAAAAAAAGTAGTTAAACATTAGTGGTTGATTTATTAAAT
TAAATTAGATCAATGTCAAACAAAATTTCAAAACTATAAAAGATATTAAGATCCGATTTATATAT
CAATGGTC
Found at i:2652 original size:38 final size:40
Alignment explanation
Indices: 2601--2680 Score: 128
Period size: 38 Copynumber: 2.0 Consensus size: 40
2591 ATACCTAAAA
*
2601 ATTTAATTAATGTAAGTATTTCAGTTA-TATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
2639 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
2679 AT
1 AT
2681 AGGAATTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 26 0.68
39 4 0.11
40 8 0.21
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.50
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:7838 original size:21 final size:22
Alignment explanation
Indices: 7814--7861 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
7804 AGCTTAGCAA
7814 ATTTTGATAG-TAAAAGTGA-CC
1 ATTTT-ATAGTTAAAAGTGAGCC
*
7835 ATTTTTTAGTTAAAAGTGAGCC
1 ATTTTATAGTTAAAAGTGAGCC
7857 ATTTT
1 ATTTT
7862 TTTGGGTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 3 0.12
21 14 0.58
22 7 0.29
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (22 bp):
ATTTTATAGTTAAAAGTGAGCC
Found at i:8284 original size:2 final size:2
Alignment explanation
Indices: 8277--8310 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
8267 AACATCTAAT
8277 TA TA TA TA TA TA TA TA TA TA TA TA T- TCA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
8311 AATTTATGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 28 0.93
3 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9978 original size:30 final size:30
Alignment explanation
Indices: 9890--9987 Score: 151
Period size: 30 Copynumber: 3.3 Consensus size: 30
9880 TTCTGAGAAT
*
9890 GATTTTGACCCGGATGAGGATCCCAAGGAG
1 GATTTTGACCCGGATGAGGATCCCGAGGAG
9920 GATTTTGACCCGGATGAGGATCCCGAGGAG
1 GATTTTGACCCGGATGAGGATCCCGAGGAG
* * *
9950 GATTTTGACCCGGACGAGGATCCTGAGGAA
1 GATTTTGACCCGGATGAGGATCCCGAGGAG
*
9980 GAATTTGA
1 GATTTTGA
9988 GGTGTCAGCC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.27, C:0.18, G:0.34, T:0.21
Consensus pattern (30 bp):
GATTTTGACCCGGATGAGGATCCCGAGGAG
Found at i:14284 original size:84 final size:85
Alignment explanation
Indices: 14141--14309 Score: 286
Period size: 84 Copynumber: 2.0 Consensus size: 85
14131 TAGCTAATGA
* * * *
14141 AACTTGGTATTTTGAGTTCAAAATAGCTTGAACCTTATCCTCTTCTAAAATTTTTTTAAGAAAAG
1 AACTTGATAATTTGAGTTCAAAATAGCTTGAACCTTAACCTCTTCTAAAATTTTCTTAAGAAAAG
14206 GC-CCTCTACCATCCCATCT
66 GCACCTCTACCATCCCATCT
*
14225 AACTTGATAATTTGAGTTCAAACTAGCTTGAACCTTAACCTCTTCTAAAATTTTCTTAAGAAAAG
1 AACTTGATAATTTGAGTTCAAAATAGCTTGAACCTTAACCTCTTCTAAAATTTTCTTAAGAAAAG
14290 GCACCTCTACCATCCCATCT
66 GCACCTCTACCATCCCATCT
14310 TCACCTCTTT
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
84 62 0.78
85 17 0.22
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (85 bp):
AACTTGATAATTTGAGTTCAAAATAGCTTGAACCTTAACCTCTTCTAAAATTTTCTTAAGAAAAG
GCACCTCTACCATCCCATCT
Found at i:19075 original size:17 final size:16
Alignment explanation
Indices: 19021--19071 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
19011 GATCACCCCC
19021 AGATCACTAGTGATCTA
1 AGATCACTAGTGATC-A
19038 AGATCA-TCAGTGATGCA
1 AGATCACT-AGTGAT-CA
*
19055 AGATCACTGGTGATCA
1 AGATCACTAGTGATCA
19071 A
1 A
19072 AGATTACATG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 4 0.13
17 24 0.80
18 2 0.07
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (16 bp):
AGATCACTAGTGATCA
Found at i:20707 original size:22 final size:21
Alignment explanation
Indices: 20683--21188 Score: 159
Period size: 22 Copynumber: 22.6 Consensus size: 21
20673 ATAACCTCAT
*
20683 TATGAAATTTCGATAACTTCC
1 TATGAAATTTTGATAACTTCC
* **
20704 TTATGAAAATTTGATAACTAGAC
1 -TATGAAATTTTGATAACT-TCC
* *
20727 TATGAAATTTTGATAACCATAC
1 TATGAAATTTTGATAA-CTTCC
*
20749 TATGAAATTTTGATAAC-CCC
1 TATGAAATTTTGATAACTTCC
* *
20769 AGTGTGAAATTTTGATAATCTCCC
1 --TATGAAATTTTGATAA-CTTCC
20793 TATGAAATTTTGATAA--TCAC
1 TATGAAATTTTGATAACTTC-C
* * *
20813 AATAT-AAA-ATTGGTAA-TCGCAC
1 --TATGAAATTTTGATAACT-TC-C
* *
20835 TCATAAAATTTTGATAACCTCC
1 T-ATGAAATTTTGATAACTTCC
* *
20857 TCATAAAATTTTGATAACCATACC
1 T-ATGAAATTTTGATAA-C-TTCC
* *
20881 -ATGAAATTTCGATAACCTGCC
1 TATGAAATTTTGATAA-CTTCC
* * *
20902 TATGAGAATGAACCTGTGATATCCTCTC
1 TATGA-AAT-----TTTGATAACTTC-C
* *
20930 TATTTAATTTTTGATAACCTCTCC
1 TA-TGAAATTTTGATAA-CT-TCC
* * *
20954 -ATAAAATTTTCATAACCTCC
1 TATGAAATTTTGATAACTTCC
* * *
20974 TATGAAATTTTTGTTAACCTCA
1 TATGAAA-TTTTGATAACTTCC
*
20996 TAAGGAAATTTTGATAACCTCCCTCCC
1 T-ATGAAATTTTGATAA-CT---T-CC
* *
21023 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAA-CTTCC
* * **
21045 TAAGAAATTTTCATAACCTTTT
1 TATGAAATTTTGATAA-CTTCC
*
21067 TATGAAATTTTGATAATCTTTGC
1 TATGAAATTTTGATAA-C-TTCC
* *
21090 -ATGAAATTTTGATAACTACAA
1 TATGAAATTTTGATAACTTC-C
*
21111 TATGAAGTTTTGATAA-TCTCC
1 TATGAAATTTTGATAACT-TCC
* * **
21132 ATATAAAATTTTGGTAACAACAC
1 -TATGAAATTTTGATAACTTC-C
21155 TATGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAA-CTTCC
*
21177 TATGTAATTTTG
1 TATGAAATTTTG
21189 GTTTGATTGC
Statistics
Matches: 364, Mismatches: 76, Indels: 88
0.69 0.14 0.17
Matches are distributed among these distances:
19 1 0.00
20 13 0.04
21 17 0.05
22 259 0.71
23 32 0.09
24 7 0.02
25 2 0.01
26 17 0.05
27 4 0.01
28 10 0.03
29 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (21 bp):
TATGAAATTTTGATAACTTCC
Found at i:20888 original size:65 final size:64
Alignment explanation
Indices: 20726--20897 Score: 157
Period size: 65 Copynumber: 2.6 Consensus size: 64
20716 GATAACTAGA
* * * * *
20726 CTATGAAATTTTGATAACCATACTATGAAATTTTGATAACCCCAGTGTGAAATTTTGATAATCTC
1 CTATAAAATTTTGATAACCATACTATGAAA--TTGATAACCCCACTATAAAATTTTGATAACCTC
20791 C
64 C
* * * * * * * *
20792 CTATGAAATTTTGATAATCACAATATAAAATTGGTAATCGCACTCATAAAATTTTGATAACCT-C
1 CTATAAAATTTTGATAACCATACTATGAAATTGATAACCCCACT-ATAAAATTTTGATAACCTCC
*
20856 CTCATAAAATTTTGATAACCATACCATGAAATTTCGATAACC
1 CT-ATAAAATTTTGATAACCATACTATGAAA-TT-GATAACC
20898 TGCCTATGAG
Statistics
Matches: 83, Mismatches: 19, Indels: 7
0.76 0.17 0.06
Matches are distributed among these distances:
64 13 0.16
65 37 0.45
66 28 0.34
67 5 0.06
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.34
Consensus pattern (64 bp):
CTATAAAATTTTGATAACCATACTATGAAATTGATAACCCCACTATAAAATTTTGATAACCTCC
Found at i:21062 original size:70 final size:66
Alignment explanation
Indices: 20938--21105 Score: 149
Period size: 70 Copynumber: 2.5 Consensus size: 66
20928 TCTATTTAAT
* **
20938 TTTTGATAACCTCTCCATAAAATTTTCATAACCTCCTATGAAATTTTTGTTAACCTCATAAGGAA
1 TTTTGATAACCTCTCCATAAAATTTTCATAACCTCCTAAGAAATTTTTCATAACCTCATAAGGAA
21003 A
66 A
* ** ** *
21004 TTTTGATAACCTCCCTCCCTATGAAATTTTGTTAACCTCCCTAAGAAA-TTTTCATAACCTTTTT
1 TTTTGATAACCT--CT-CC-ATAAAATTTTCATAACCT-CCTAAGAAATTTTTCATAACCTCATA
*
21068 ATGAAA
61 AGGAAA
* * * * *
21074 TTTTGATAATCTTTGCATGAAATTTTGATAAC
1 TTTTGATAACCTCTCCATAAAATTTTCATAAC
21106 TACAATATGA
Statistics
Matches: 83, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
66 27 0.33
67 1 0.01
68 3 0.04
69 2 0.02
70 42 0.51
71 8 0.10
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.40
Consensus pattern (66 bp):
TTTTGATAACCTCTCCATAAAATTTTCATAACCTCCTAAGAAATTTTTCATAACCTCATAAGGAA
A
Found at i:21880 original size:2 final size:2
Alignment explanation
Indices: 21873--21906 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
21863 CTGTTATAGC
21873 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
21907 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:21911 original size:2 final size:2
Alignment explanation
Indices: 21906--21940 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
21896 ACACACACAC
* *
21906 AT AT AT AT AT AT AT AT AT GT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21941 CACCATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24803 original size:74 final size:74
Alignment explanation
Indices: 24682--24830 Score: 289
Period size: 74 Copynumber: 2.0 Consensus size: 74
24672 ATTATGAATT
24682 ATTGAGTTTTCCCTTTGGTGGAACTTTATGAAGATTTATTCTCGTTATTTTGGGTTTTCTTGATT
1 ATTGAGTTTTCCCTTTGGTGGAACTTTATGAAGATTTATTCTCGTTATTTTGGGTTTTCTTGATT
24747 TGTTCATGA
66 TGTTCATGA
*
24756 ATTGAGTTTTCCCTTTGGTGGAATTTTATGAAGATTTATTCTCGTTATTTTGGGTTTTCTTGATT
1 ATTGAGTTTTCCCTTTGGTGGAACTTTATGAAGATTTATTCTCGTTATTTTGGGTTTTCTTGATT
24821 TGTTCATGA
66 TGTTCATGA
24830 A
1 A
24831 ATCCGTATTT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.18, C:0.10, G:0.20, T:0.52
Consensus pattern (74 bp):
ATTGAGTTTTCCCTTTGGTGGAACTTTATGAAGATTTATTCTCGTTATTTTGGGTTTTCTTGATT
TGTTCATGA
Found at i:28056 original size:20 final size:20
Alignment explanation
Indices: 28015--28057 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
28005 CTCTCACAAG
* *
28015 TTTCTAGCCGTTGGAGCTCT
1 TTTCTAGCCGTTAGAGCACT
*
28035 TTTCTAGCCGTTATAGCACT
1 TTTCTAGCCGTTAGAGCACT
28055 TTT
1 TTT
28058 TCCACTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTCTAGCCGTTAGAGCACT
Done.