Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019183.1 Corchorus olitorius cultivar O-4 contig19216, 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: 27019
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Found at i:8928 original size:14 final size:15
Alignment explanation
Indices: 8911--8941 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
8901 TAATTATAGA
8911 ATAATAATAATT-TT
1 ATAATAATAATTATT
8925 ATAATAATAATTATT
1 ATAATAATAATTATT
8940 AT
1 AT
8942 GATTATTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAATAATAATTATT
Found at i:12468 original size:23 final size:23
Alignment explanation
Indices: 12440--12513 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 23
12430 TTTAATTAAA
12440 TAAAAATAGAGTTTTTATTGAATT
1 TAAAAATAGAGTTTTTATTGAA-T
* * *
12464 TAAAATATTGA-ATTTAATT-AAT
1 TAAAA-ATAGAGTTTTTATTGAAT
*
12486 TAAAAATATAGTTTTTAGTTGAA-
1 TAAAAATAGAGTTTTTA-TTGAAT
12509 TAAAA
1 TAAAA
12514 CTGTGAAAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
21 3 0.08
22 10 0.26
23 9 0.23
24 13 0.33
25 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.43
Consensus pattern (23 bp):
TAAAAATAGAGTTTTTATTGAAT
Found at i:12786 original size:78 final size:78
Alignment explanation
Indices: 12704--12852 Score: 271
Period size: 78 Copynumber: 1.9 Consensus size: 78
12694 AAGGTTTTTT
12704 TTTTTGGAAACAATAAAACTGTAAAAGTTTAAACAATGTCATTTAAGAAATATATGTAAAAATTC
1 TTTTTGGAAACAATAAAACTGTAAAAGTTTAAACAATGTCATTTAAGAAATATATGTAAAAATTC
12769 TAATAATAAATTA
66 TAATAATAAATTA
* **
12782 TTTTTGGCAACGGTAAAACTGTAAAAGTTTAAACAATGTCATTTAAGAAATATATGTAAAAATTC
1 TTTTTGGAAACAATAAAACTGTAAAAGTTTAAACAATGTCATTTAAGAAATATATGTAAAAATTC
12847 TAATAA
66 TAATAA
12853 ATCTAATTTT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 68 1.00
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.34
Consensus pattern (78 bp):
TTTTTGGAAACAATAAAACTGTAAAAGTTTAAACAATGTCATTTAAGAAATATATGTAAAAATTC
TAATAATAAATTA
Found at i:13629 original size:2 final size:2
Alignment explanation
Indices: 13624--13673 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
13614 GTGTGTGTAT
* * *
13624 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA -A AA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13665 TA TA TA TA T
1 TA TA TA TA T
13674 TCGCATGCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:14138 original size:69 final size:72
Alignment explanation
Indices: 14054--14256 Score: 250
Period size: 69 Copynumber: 2.7 Consensus size: 72
14044 GAAGGAACGT
* * *
14054 TCATTTGCTAAAGATTTCGAACCCAAGCCCAACCTTTCGGCTTATGGTGATGAAGGTG-AAG-AG
1 TCATTTGCTAAAGATTTTGAACCCAGGCCAAACCTTTCGGCTTATGGTGATGAAGGTGTAAGAAG
14117 A-AAAAA
66 AGAAAAA
* *
14123 TCATTTGCTATAGATTTTGAACCCAGGCCAAACCTTTCGGCTTATGGTGATGATGGTGATCTTAA
1 TCATTTGCTAAAGATTTTGAACCCAGGCCAAACCTTTCGGCTTATGGTGATGAAGGTG----T-A
14188 AGAAGAGGAAAAA
61 AGAAGA-GAAAAA
*
14201 TCATCCTTTGCTAAAGATTTTGAACCCAGGCCTAACCTTTCGGCTTATGGTGATGA
1 TCA---TTTGCTAAAGATTTTGAACCCAGGCCAAACCTTTCGGCTTATGGTGATGA
14257 TTGTTATCTG
Statistics
Matches: 115, Mismatches: 7, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
69 53 0.46
75 3 0.03
76 3 0.03
78 8 0.07
81 48 0.42
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (72 bp):
TCATTTGCTAAAGATTTTGAACCCAGGCCAAACCTTTCGGCTTATGGTGATGAAGGTGTAAGAAG
AGAAAAA
Found at i:14230 original size:81 final size:81
Alignment explanation
Indices: 14111--14311 Score: 252
Period size: 81 Copynumber: 2.5 Consensus size: 81
14101 TGATGAAGGT
*
14111 GAAGA-GAAAAA--ATCATTTGCTATAGATTTTGAACCCAGGCCAAACCTTTCGGCTTATGGTGA
1 GAAGAGGAAAAATCATCATTTGCTAAAGATTTTGAACCCAGGCCAAACCTTTCGGCTTATGGTGA
*
14173 TGATGGTGATCTTAAA
66 TGATGGTGATCTGAAA
* *
14189 GAAGAGGAAAAATCATCCTTTGCTAAAGATTTTGAACCCAGGCCTAACCTTTCGGCTTATGGTGA
1 GAAGAGGAAAAATCATCATTTGCTAAAGATTTTGAACCCAGGCCAAACCTTTCGGCTTATGGTGA
* *
14254 TGATTGTTATCTGAAA
66 TGATGGTGATCTGAAA
* * * * *
14270 GGAGA-GAAAAA-AATCATTTCCTAGTA-ATTTTGAACCGAGGCC
1 GAAGAGGAAAAATCATCATTTGCTA-AAGATTTTGAACCCAGGCC
14312 CAATACGTCT
Statistics
Matches: 107, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
78 5 0.05
79 30 0.28
80 7 0.07
81 65 0.61
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.29
Consensus pattern (81 bp):
GAAGAGGAAAAATCATCATTTGCTAAAGATTTTGAACCCAGGCCAAACCTTTCGGCTTATGGTGA
TGATGGTGATCTGAAA
Found at i:16260 original size:12 final size:12
Alignment explanation
Indices: 16230--16302 Score: 110
Period size: 12 Copynumber: 5.9 Consensus size: 12
16220 AGGTATTTAT
16230 GGATATATCGAAC
1 GGATATATCG-AC
*
16243 GGATATATCGAT
1 GGATATATCGAC
16255 GGATATATCGAAC
1 GGATATATCG-AC
*
16268 GGATATATCGAT
1 GGATATATCGAC
16280 GGATATATCGAC
1 GGATATATCGAC
16292 GGATATATCGA
1 GGATATATCGA
16303 GGTATCGATG
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
12 34 0.62
13 21 0.38
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (12 bp):
GGATATATCGAC
Found at i:16262 original size:25 final size:25
Alignment explanation
Indices: 16228--16302 Score: 143
Period size: 25 Copynumber: 3.0 Consensus size: 25
16218 ACAGGTATTT
16228 ATGGATATATCGAACGGATATATCG
1 ATGGATATATCGAACGGATATATCG
16253 ATGGATATATCGAACGGATATATCG
1 ATGGATATATCGAACGGATATATCG
16278 ATGGATATATCG-ACGGATATATCG
1 ATGGATATATCGAACGGATATATCG
16302 A
1 A
16303 GGTATCGATG
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
24 13 0.26
25 37 0.74
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (25 bp):
ATGGATATATCGAACGGATATATCG
Found at i:16290 original size:37 final size:38
Alignment explanation
Indices: 16230--16302 Score: 121
Period size: 37 Copynumber: 1.9 Consensus size: 38
16220 AGGTATTTAT
*
16230 GGATATATCGAACGGATATATCGATGGATATATCGAAC
1 GGATATATCGAACGGATATATCGACGGATATATCGAAC
*
16268 GGATATATCG-ATGGATATATCGACGGATATATCGA
1 GGATATATCGAACGGATATATCGACGGATATATCGA
16303 GGTATCGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 23 0.70
38 10 0.30
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (38 bp):
GGATATATCGAACGGATATATCGACGGATATATCGAAC
Found at i:17306 original size:10 final size:10
Alignment explanation
Indices: 17291--17316 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
17281 AATTTAATAT
17291 GGATATTTAC
1 GGATATTTAC
17301 GGATATTTAC
1 GGATATTTAC
17311 GGATAT
1 GGATAT
17317 ATCGAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (10 bp):
GGATATTTAC
Found at i:17465 original size:20 final size:21
Alignment explanation
Indices: 17424--17466 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
17414 AGAGGTACAG
*
17424 ATATCGGATATATCGACGGAT
1 ATATCGGATATATCGACAGAT
17445 ATATCGAGATAT-T-GACAGAT
1 ATATCG-GATATATCGACAGAT
17465 AT
1 AT
17467 TTAATTCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 8 0.40
21 7 0.35
22 5 0.25
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (21 bp):
ATATCGGATATATCGACAGAT
Found at i:18177 original size:24 final size:24
Alignment explanation
Indices: 18145--18194 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
18135 AACCACATTG
*
18145 AAGCTCAAAGTTTGAATGCTGATT
1 AAGCTCAAAGTTTGAAAGCTGATT
18169 AAGCTCAAAGTTTGAAAGCTGATT
1 AAGCTCAAAGTTTGAAAGCTGATT
18193 AA
1 AA
18195 TAGTACATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (24 bp):
AAGCTCAAAGTTTGAAAGCTGATT
Found at i:19165 original size:40 final size:40
Alignment explanation
Indices: 19105--19185 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
19095 TTACATAGGA
*
19105 AGGTTATTAAAATTTCATAGTGTAATTACCAAAATTTCAT
1 AGGTTATCAAAATTTCATAGTGTAATTACCAAAATTTCAT
* * *
19145 AGGTTATCAAAACTTT-ATAGTGTAGTTATCAGAATTTCAT
1 AGGTTATCAAAA-TTTCATAGTGTAATTACCAAAATTTCAT
19185 A
1 A
19186 CAAAGGTTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
40 33 0.92
41 3 0.08
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (40 bp):
AGGTTATCAAAATTTCATAGTGTAATTACCAAAATTTCAT
Found at i:19194 original size:22 final size:22
Alignment explanation
Indices: 19169--19295 Score: 119
Period size: 22 Copynumber: 5.8 Consensus size: 22
19159 TTATAGTGTA
*
19169 GTTATCAGAATTTCATACAAAG
1 GTTATCAAAATTTCATACAAAG
* * * *
19191 GTTACCAAAATTTCACATAATG
1 GTTATCAAAATTTCATACAAAG
* * *
19213 GTTATCAAAATTTCTTAGAGAG
1 GTTATCAAAATTTCATACAAAG
* *
19235 GTTAACAAAATTTCATACGAAG
1 GTTATCAAAATTTCATACAAAG
* ****
19257 GTTATCAAAATTTTATAGTGTG
1 GTTATCAAAATTTCATACAAAG
19279 GTTATCAAAATTTCATA
1 GTTATCAAAATTTCATA
19296 AGAAAGCAAA
Statistics
Matches: 82, Mismatches: 23, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 82 1.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.35
Consensus pattern (22 bp):
GTTATCAAAATTTCATACAAAG
Found at i:19260 original size:44 final size:43
Alignment explanation
Indices: 19169--19323 Score: 148
Period size: 44 Copynumber: 3.5 Consensus size: 43
19159 TTATAGTGTA
* * * * * *
19169 GTTATCAGAATTTCATACAAAGGTTACCAAAATTTCACATAATG
1 GTTATCAAAATTTCATAGAGAGGTTAACAAAATTTCATAGAA-G
*
19213 GTTATCAAAATTTCTTAGAGAGGTTAACAAAATTTCATACGAAG
1 GTTATCAAAATTTCATAGAGAGGTTAACAAAATTTCATA-GAAG
* * * * *
19257 GTTATCAAAATTTTATAGTGTGGTTATCAAAATTTCATAAGAAA
1 GTTATCAAAATTTCATAGAGAGGTTAACAAAATTTCAT-AGAAG
** *
19301 GCAAACAAAATTTCATAGAGAGG
1 GTTATCAAAATTTCATAGAGAGG
19324 GAGGTTATCA
Statistics
Matches: 90, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
44 87 0.97
45 3 0.03
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.32
Consensus pattern (43 bp):
GTTATCAAAATTTCATAGAGAGGTTAACAAAATTTCATAGAAG
Found at i:19308 original size:66 final size:66
Alignment explanation
Indices: 19177--19317 Score: 169
Period size: 66 Copynumber: 2.1 Consensus size: 66
19167 TAGTTATCAG
* * **
19177 AATTTCATACAAAGGTTACCAAAATTTCACATAATGGTTATCAAAATTTCTTAGAGAGGTTAACA
1 AATTTCATACAAAGGTTACCAAAATTTCACATAATGGTTATCAAAATTTCTAAGAGAAGCAAACA
19242 A
66 A
* * * * *
19243 AATTTCATACGAAGGTTATCAAAATTTTATAGT-GTGGTTATCAAAATTTCATAAGA-AAGCAAA
1 AATTTCATACAAAGGTTACCAAAATTTCACA-TAATGGTTATCAAAATTTC-TAAGAGAAGCAAA
19306 CAA
64 CAA
19309 AATTTCATA
1 AATTTCATA
19318 GAGAGGGAGG
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
66 59 0.92
67 5 0.08
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (66 bp):
AATTTCATACAAAGGTTACCAAAATTTCACATAATGGTTATCAAAATTTCTAAGAGAAGCAAACA
A
Found at i:19557 original size:21 final size:22
Alignment explanation
Indices: 19525--19669 Score: 130
Period size: 22 Copynumber: 6.6 Consensus size: 22
19515 ATTTTATAGA
* *
19525 TTATCAAAAATTCACATTGAT-G
1 TTATCAAAATTTCACAGTG-TGG
*
19547 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCACAGTGTGG
19569 TTATCAAAATTTCACAGTGTGG
1 TTATCAAAATTTCACAGTGTGG
* * * *
19591 TTATCAAATTTTCATAATGAGG
1 TTATCAAAATTTCACAGTGTGG
** * * * *
19613 TTATCGGAATTTTATAATGAGG
1 TTATCAAAATTTCACAGTGTGG
* *
19635 TTATCAAATTTTCACAATGTGG
1 TTATCAAAATTTCACAGTGTGG
*
19657 TTATCAATATTTC
1 TTATCAAAATTTC
19670 TACGTTGGAG
Statistics
Matches: 102, Mismatches: 20, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
21 1 0.01
22 101 0.99
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTTCACAGTGTGG
Found at i:19576 original size:44 final size:44
Alignment explanation
Indices: 19525--19669 Score: 157
Period size: 44 Copynumber: 3.3 Consensus size: 44
19515 ATTTTATAGA
* * * *
19525 TTATCAAAAATTCACATTGATGTTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCACAATGATGTTATCAAATTTTCATAATGTGG
* *
19569 TTATCAAAATTTCACAGTG-TGGTTATCAAATTTTCATAATGAGG
1 TTATCAAAATTTCACAATGAT-GTTATCAAATTTTCATAATGTGG
** * * * *
19613 TTATCGGAATTTTATAATGAGGTTATCAAATTTTCACAATGTGG
1 TTATCAAAATTTCACAATGATGTTATCAAATTTTCATAATGTGG
*
19657 TTATCAATATTTC
1 TTATCAAAATTTC
19670 TACGTTGGAG
Statistics
Matches: 82, Mismatches: 17, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
43 1 0.01
44 81 0.99
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (44 bp):
TTATCAAAATTTCACAATGATGTTATCAAATTTTCATAATGTGG
Found at i:21056 original size:17 final size:16
Alignment explanation
Indices: 21030--21069 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
21020 AAAGTACTAG
21030 TATAAT-TATAATATA
1 TATAATATATAATATA
*
21045 TATATATATATAATCTA
1 TATA-ATATATAATATA
21062 TATAATAT
1 TATAATAT
21070 CTGTAACTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 6 0.27
17 12 0.55
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATATATAATATA
Done.