Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017245.1 Corchorus olitorius cultivar O-4 contig17278, 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: 21944
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:259 original size:133 final size:129
Alignment explanation
Indices: 1--241 Score: 395
Period size: 123 Copynumber: 1.9 Consensus size: 129
1 TAATATATATAAGTTTTTTAATTAAAAATAGTAAAATAGGTAAAAATAAAATAGGTATAAGGATA
1 TAATATATATAAGTTTTTTAATTAAAAATAGTAAAATAGGTAAAAAT---ATA-GTATAAGGATA
*
66 TTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAGTATATTTAAAAAA
62 TTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAAAA
131 TTC
127 TTC
134 TAATATATATAAGTTTTTTAATT-AAAATAGTAAAAT-GGTAAAAAT-TA-TA-AA-GATATTAG
1 TAATATATATAAGTTTTTTAATTAAAAATAGTAAAATAGGTAAAAATATAGTATAAGGATATTAG
193 ATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
66 ATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
242 TTAAACAATG
Statistics
Matches: 107, Mismatches: 1, Indels: 10
0.91 0.01 0.08
Matches are distributed among these distances:
123 56 0.52
124 2 0.02
125 2 0.02
127 2 0.02
131 9 0.08
132 13 0.12
133 23 0.21
ACGTcount: A:0.50, C:0.01, G:0.12, T:0.37
Consensus pattern (129 bp):
TAATATATATAAGTTTTTTAATTAAAAATAGTAAAATAGGTAAAAATATAGTATAAGGATATTAG
ATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAAAATTC
Found at i:1841 original size:22 final size:22
Alignment explanation
Indices: 1824--1951 Score: 89
Period size: 22 Copynumber: 5.8 Consensus size: 22
1814 TACATAGTGT
*
1824 AGTTATCAAAATTTCATACAAA
1 AGTTATCAAAATTTCATAGAAA
* * *
1846 GGTTACCAAAATTTCATAAAAA
1 AGTTATCAAAATTTCATAGAAA
* * *
1868 AGTTATAAAAATTTCTTA-AGGA
1 AGTTATCAAAATTTCATAGA-AA
* *
1890 AGTTAACAAATTTTCATA-AAA
1 AGTTATCAAAATTTCATAGAAA
* * ***
1911 AGGTTATCGAAATTTTATAGTGT
1 A-GTTATCAAAATTTCATAGAAA
*
1934 GGTTATCAAAATTTCATA
1 AGTTATCAAAATTTCATA
1952 ACAAGATTTA
Statistics
Matches: 80, Mismatches: 23, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
21 3 0.04
22 77 0.96
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (22 bp):
AGTTATCAAAATTTCATAGAAA
Found at i:1879 original size:44 final size:43
Alignment explanation
Indices: 1824--1917 Score: 109
Period size: 44 Copynumber: 2.1 Consensus size: 43
1814 TACATAGTGT
* *
1824 AGTTATCAAAATTTCATACA-AAGGTTACCAAAATTTCATAAAAA
1 AGTTATAAAAATTTCATA-AGAA-GTTAACAAAATTTCATAAAAA
* *
1868 AGTTATAAAAATTTCTTAAGGAAGTTAACAAATTTTCATAAAAA
1 AGTTATAAAAATTTCATAA-GAAGTTAACAAAATTTCATAAAAA
*
1912 GGTTAT
1 AGTTAT
1918 CGAAATTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
43 1 0.02
44 40 0.93
45 2 0.05
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (43 bp):
AGTTATAAAAATTTCATAAGAAGTTAACAAAATTTCATAAAAA
Found at i:1949 original size:44 final size:44
Alignment explanation
Indices: 1845--1952 Score: 112
Period size: 44 Copynumber: 2.5 Consensus size: 44
1835 TTTCATACAA
*
1845 AGGTTACCAAAATTTCATAAAAAAGTTATAAAAATTTCTTAAGG
1 AGGTTAACAAAATTTCATAAAAAAGTTATAAAAATTTCTTAAGG
* * * **
1889 AAGTTAACAAATTTTCATAAAAAGGTTATCGAAA-TT-TTATAGTG
1 AGGTTAACAAAATTTCATAAAAAAGTTATAAAAATTTCTTA-AG-G
* *
1933 TGGTTATCAAAATTTCATAA
1 AGGTTAACAAAATTTCATAA
1953 CAAGATTTAA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
42 3 0.06
43 4 0.08
44 45 0.87
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.35
Consensus pattern (44 bp):
AGGTTAACAAAATTTCATAAAAAAGTTATAAAAATTTCTTAAGG
Found at i:2087 original size:22 final size:21
Alignment explanation
Indices: 2001--2094 Score: 82
Period size: 22 Copynumber: 4.3 Consensus size: 21
1991 AAATTTGTGC
**
2001 TTATCAAAATTTCCTAAGGAGG
1 TTATCAAAATTTAATAA-GAGG
2023 TTAAT-AAAATTTAATAAGGAGG
1 TT-ATCAAAATTTAATAA-GAGG
* *
2045 TTATGAAAATTTTATATAGAGG
1 TTATCAAAATTTAATA-AGAGG
*
2067 TTATCAAAATTAAATAGAGAGG
1 TTATCAAAATTTAATA-AGAGG
*
2089 ATATCA
1 TTATCA
2095 CAGTTTCATT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
21 2 0.03
22 56 0.92
23 3 0.05
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.33
Consensus pattern (21 bp):
TTATCAAAATTTAATAAGAGG
Found at i:2227 original size:22 final size:22
Alignment explanation
Indices: 2202--2327 Score: 87
Period size: 22 Copynumber: 5.7 Consensus size: 22
2192 TTTACAGCGT
2202 GATTATCAAAATTTCATATGGA
1 GATTATCAAAATTTCATATGGA
* * * **
2224 GATTATCGAAATTTTAAACCGA
1 GATTATCAAAATTTCATATGGA
*
2246 GCTTATCAAAATTTCATAGTGTG-
1 GATTATCAAAATTTCATA-TG-GA
* * *
2269 G-TTATCAAATTTTCGTAAGGA
1 GATTATCAAAATTTCATATGGA
* *
2290 GATTATCGAAACTTCATAAT-GA
1 GATTATCAAAATTTCAT-ATGGA
* *
2312 GATTACCAAATTTTCA
1 GATTATCAAAATTTCA
2328 CAATGTGGTT
Statistics
Matches: 76, Mismatches: 23, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
20 1 0.01
21 2 0.03
22 70 0.92
23 2 0.03
24 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (22 bp):
GATTATCAAAATTTCATATGGA
Found at i:2274 original size:44 final size:42
Alignment explanation
Indices: 2161--2281 Score: 129
Period size: 44 Copynumber: 2.8 Consensus size: 42
2151 TATGAGAAAG
* * * *
2161 TTATCAAAATCTTCATAGTGCGGTTA-CCAATTTTACAGCGTGA
1 TTATCAAAAT-TTCATAGTG-GGTTATCAAATTTTAAACCGAGA
*
2204 TTATCAAAATTTCATA-TGGAGATTATCGAAATTTTAAACCGAGC
1 TTATCAAAATTTCATAGTGG-G-TTATC-AAATTTTAAACCGAGA
2248 TTATCAAAATTTCATAGTGTGGTTATCAAATTTT
1 TTATCAAAATTTCATAGTG-GGTTATCAAATTTT
2282 CGTAAGGAGA
Statistics
Matches: 67, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
40 1 0.01
41 3 0.04
42 9 0.13
43 18 0.27
44 32 0.48
45 3 0.04
46 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (42 bp):
TTATCAAAATTTCATAGTGGGTTATCAAATTTTAAACCGAGA
Found at i:2296 original size:44 final size:41
Alignment explanation
Indices: 2161--2325 Score: 111
Period size: 44 Copynumber: 3.8 Consensus size: 41
2151 TATGAGAAAG
* *
2161 TTATCAAAATCTTCATAGTGCGGTTA-CCAA-TTTTACAGCGTGA
1 TTATCAAAAT-TTCATAGTG-GGTTATCAAATTTTTA-AG-GAGA
* * *
2204 TTATCAAAATTTCATA-TGGAGATTATCGAAATTTTAAACCGAGC
1 TTATCAAAATTTCATAGTGG-G-TTATC-AAATTTTTAA-GGAGA
2248 TTATCAAAATTTCATAGTGTGGTTATCAAATTTTCGTAAGGAGA
1 TTATCAAAATTTCATAGTG-GGTTATCAAATTTT--TAAGGAGA
* * * * *
2292 TTATCGAAACTTCATAATGAGATTACCAAATTTT
1 TTATCAAAATTTCATAGTG-GGTTATCAAATTTT
2326 CACAATGTGG
Statistics
Matches: 98, Mismatches: 14, Indels: 19
0.75 0.11 0.15
Matches are distributed among these distances:
40 1 0.01
41 3 0.03
42 9 0.09
43 18 0.18
44 57 0.58
45 9 0.09
46 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (41 bp):
TTATCAAAATTTCATAGTGGGTTATCAAATTTTTAAGGAGA
Found at i:2327 original size:66 final size:66
Alignment explanation
Indices: 2161--2347 Score: 173
Period size: 66 Copynumber: 2.8 Consensus size: 66
2151 TATGAGAAAG
* * * * * * *
2161 TTATCAAAATCTTCATAGTGCGGTTACC-AATTTT-ACAGCGTGATTATCAAAATTTCATATGGA
1 TTATCGAAA-CTTCATAATGAGATTACCAAATTTTCACAGTGTGGTTATCAAAATTTCATAAGGA
2224 GA
65 GA
* * * * * * * * *
2226 TTATCGAAATTTTA-AACCGAGCTTATCAAAATTTCATAGTGTGGTTATCAAATTTTCGTAAGGA
1 TTATCGAAACTTCATAA-TGAGATTACCAAATTTTCACAGTGTGGTTATCAAAATTTCATAAGGA
2290 GA
65 GA
*
2292 TTATCGAAACTTCATAATGAGATTACCAAATTTTCACAATGTGGTTATCAATAATT
1 TTATCGAAACTTCATAATGAGATTACCAAATTTTCACAGTGTGGTTATCAA-AATT
2348 CTATGAAACA
Statistics
Matches: 93, Mismatches: 24, Indels: 8
0.74 0.19 0.06
Matches are distributed among these distances:
63 1 0.01
64 9 0.10
65 13 0.14
66 65 0.70
67 5 0.05
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Consensus pattern (66 bp):
TTATCGAAACTTCATAATGAGATTACCAAATTTTCACAGTGTGGTTATCAAAATTTCATAAGGAG
A
Found at i:17721 original size:15 final size:16
Alignment explanation
Indices: 17701--17730 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17691 CGTTTTGCCT
17701 ATATAATATA-ATTTG
1 ATATAATATATATTTG
17716 ATATAATATATATTT
1 ATATAATATATATTT
17731 TTAGTTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
ATATAATATATATTTG
Found at i:17742 original size:2 final size:2
Alignment explanation
Indices: 17737--17771 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
17727 ATTTTTAGTT
17737 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17772 TAACTAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21476 original size:12 final size:13
Alignment explanation
Indices: 21439--21489 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
21429 GTTTCAGGTA
21439 CAATTCTGTTTTT
1 CAATTCTGTTTTT
**
21452 CAAAACTGTTTTT
1 CAATTCTGTTTTT
21465 CAATTCTG-TTTT
1 CAATTCTGTTTTT
*
21477 GAATTTCTGTTTT
1 CAA-TTCTGTTTT
21490 ACTTTTCAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 6 0.19
13 22 0.71
14 3 0.10
ACGTcount: A:0.20, C:0.14, G:0.10, T:0.57
Consensus pattern (13 bp):
CAATTCTGTTTTT
Found at i:21496 original size:31 final size:31
Alignment explanation
Indices: 21461--21616 Score: 181
Period size: 31 Copynumber: 4.9 Consensus size: 31
21451 TCAAAACTGT
21461 TTTTCAATTCTGTTTTGAATTTCTGTTTTAC
1 TTTTCAATTCTGTTTTGAATTTCTGTTTTAC
* *
21492 TTTTCAATTATGTTTT-ACATTCCTGTTTTAC
1 TTTTCAATTCTGTTTTGA-ATTTCTGTTTTAC
21523 TTTTCAATTCTGTTTT-ACATTTCTGTTTTAC
1 TTTTCAATTCTGTTTTGA-ATTTCTGTTTTAC
*
21554 TTTTCAATTCTGTTTTGCATTTCTGTTGTTAAAC
1 TTTTCAATTCTGTTTTGAATTTCTGTT-TT--AC
**** *
21588 TGAGGAATTCTGTTTTGCATTTCTGTTTT
1 TTTTCAATTCTGTTTTGAATTTCTGTTTT
21617 GCAATTCTGT
Statistics
Matches: 111, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
30 1 0.01
31 81 0.73
32 2 0.02
33 2 0.02
34 25 0.23
ACGTcount: A:0.17, C:0.14, G:0.11, T:0.58
Consensus pattern (31 bp):
TTTTCAATTCTGTTTTGAATTTCTGTTTTAC
Found at i:21507 original size:18 final size:18
Alignment explanation
Indices: 21481--21569 Score: 81
Period size: 18 Copynumber: 5.5 Consensus size: 18
21471 TGTTTTGAAT
21481 TTCTGTTTTACTTTTCAA
1 TTCTGTTTTACTTTTCAA
* *
21499 TTATGTTTTAC-ATTC--
1 TTCTGTTTTACTTTTCAA
21514 --CTGTTTTACTTTTCAA
1 TTCTGTTTTACTTTTCAA
*
21530 TTCTGTTTTA-----CAT
1 TTCTGTTTTACTTTTCAA
21543 TTCTGTTTTACTTTTCAA
1 TTCTGTTTTACTTTTCAA
21561 TTCTGTTTT
1 TTCTGTTTT
21570 GCATTTCTGT
Statistics
Matches: 55, Mismatches: 6, Indels: 20
0.68 0.07 0.25
Matches are distributed among these distances:
13 20 0.36
14 3 0.05
17 3 0.05
18 29 0.53
ACGTcount: A:0.16, C:0.16, G:0.07, T:0.62
Consensus pattern (18 bp):
TTCTGTTTTACTTTTCAA
Found at i:21545 original size:62 final size:64
Alignment explanation
Indices: 21461--21616 Score: 201
Period size: 62 Copynumber: 2.5 Consensus size: 64
21451 TCAAAACTGT
21461 TTTTCAATTCTGTTTTGA-ATTTCTGTTTTACTTTTCAATTATGTTTTACATTCCTGTT-TT-AC
1 TTTTCAATTCTGTTTT-ACATTTCTGTTTTACTTTTCAATTATGTTTTACATTCCTGTTGTTAAC
* * *
21523 TTTTCAATTCTGTTTTACATTTCTGTTTTACTTTTCAATTCTGTTTTGCATTTCTGTTGTTAAAC
1 TTTTCAATTCTGTTTTACATTTCTGTTTTACTTTTCAATTATGTTTTACATTCCTGTTGTT-AAC
**** *
21588 TGAGGAATTCTGTTTTGCATTTCTGTTTT
1 TTTTCAATTCTGTTTTACATTTCTGTTTT
21617 GCAATTCTGT
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
61 1 0.01
62 53 0.65
63 2 0.02
65 26 0.32
ACGTcount: A:0.17, C:0.14, G:0.11, T:0.58
Consensus pattern (64 bp):
TTTTCAATTCTGTTTTACATTTCTGTTTTACTTTTCAATTATGTTTTACATTCCTGTTGTTAAC
Found at i:21613 original size:13 final size:13
Alignment explanation
Indices: 21593--21627 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
21583 TAAACTGAGG
21593 AATTCTGTTTTGC
1 AATTCTGTTTTGC
*
21606 ATTTCTGTTTTGC
1 AATTCTGTTTTGC
21619 AATTCTGTT
1 AATTCTGTT
21628 AAACTGAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (13 bp):
AATTCTGTTTTGC
Found at i:21642 original size:44 final size:45
Alignment explanation
Indices: 21561--21660 Score: 166
Period size: 44 Copynumber: 2.2 Consensus size: 45
21551 TACTTTTCAA
*
21561 TTCTGTTTTGCATTTCTGTTGTTAAACTGAGGAATTCTGTTTTGCAT
1 TTCTGTTTTGCAATTC--TTGTTAAACTGAGGAATTCTGTTTTGCAT
21608 TTCTGTTTTGCAATTC-TGTTAAACTGAGGAATTCTGTTTTGCAT
1 TTCTGTTTTGCAATTCTTGTTAAACTGAGGAATTCTGTTTTGCAT
21652 TTCTGTTTT
1 TTCTGTTTT
21661 ACATTTCAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
44 37 0.71
47 15 0.29
ACGTcount: A:0.17, C:0.13, G:0.18, T:0.52
Consensus pattern (45 bp):
TTCTGTTTTGCAATTCTTGTTAAACTGAGGAATTCTGTTTTGCAT
Found at i:21721 original size:32 final size:32
Alignment explanation
Indices: 21680--21755 Score: 152
Period size: 32 Copynumber: 2.4 Consensus size: 32
21670 TTTTGTTTAG
21680 TGTTTTGCATTTTTCAATTAGTTTTTCAATTC
1 TGTTTTGCATTTTTCAATTAGTTTTTCAATTC
21712 TGTTTTGCATTTTTCAATTAGTTTTTCAATTC
1 TGTTTTGCATTTTTCAATTAGTTTTTCAATTC
21744 TGTTTTGCATTT
1 TGTTTTGCATTT
21756 AACTCACCTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.17, C:0.12, G:0.11, T:0.61
Consensus pattern (32 bp):
TGTTTTGCATTTTTCAATTAGTTTTTCAATTC
Done.