Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021929.1 Corchorus olitorius cultivar O-4 contig21962, 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: 18268
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3128 original size:41 final size:41
Alignment explanation
Indices: 3074--3192 Score: 159
Period size: 41 Copynumber: 2.9 Consensus size: 41
3064 AAAAAAAATT
*
3074 TCTAAATCCGGGACAAAATTGAATCAATAAATAAATATTAC
1 TCTAAATCAGGGACAAAATTGAATCAATAAATAAATATTAC
* * *
3115 TCTAAATTAGGGACAAAATTGAATCAATTAACAAATATTAC
1 TCTAAATCAGGGACAAAATTGAATCAATAAATAAATATTAC
* * *
3156 -CTTAGATCAGGGAAAAAATTGAATCAATGAATAAATA
1 TC-TAAATCAGGGACAAAATTGAATCAATAAATAAATA
3193 ACAGCCTAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 1 0.01
41 67 0.99
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.27
Consensus pattern (41 bp):
TCTAAATCAGGGACAAAATTGAATCAATAAATAAATATTAC
Found at i:3379 original size:22 final size:23
Alignment explanation
Indices: 3340--3382 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3330 ATTAATTAAC
* *
3340 AAATTGAAGGATTTAATTGAATT
1 AAATTGAAGGACTCAATTGAATT
3363 AAATTG-AGGACTCAATTGAA
1 AAATTGAAGGACTCAATTGAA
3383 AGAAATTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.33
Consensus pattern (23 bp):
AAATTGAAGGACTCAATTGAATT
Found at i:3388 original size:22 final size:23
Alignment explanation
Indices: 3340--3394 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
3330 ATTAATTAAC
* * **
3340 AAATTGAAGGATTTAATTGAATT
1 AAATTGAAGGACTCAATTGAAAG
3363 AAATTG-AGGACTCAATTGAAAG
1 AAATTGAAGGACTCAATTGAAAG
3385 AAATTAGAAG
1 AAATT-GAAG
3395 TTTTACCTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 17 0.65
23 7 0.27
24 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.20, T:0.29
Consensus pattern (23 bp):
AAATTGAAGGACTCAATTGAAAG
Found at i:5812 original size:27 final size:27
Alignment explanation
Indices: 5772--5869 Score: 90
Period size: 27 Copynumber: 3.7 Consensus size: 27
5762 TGGACTTAAC
** *
5772 ATGACCAACGTGCCCCTGAATATGCAA
1 ATGACCAAAATGCCCCTGAATATGAAA
* * * *
5799 ATGACCAAAATG-CCCTTAGTGTAAAA
1 ATGACCAAAATGCCCCTGAATATGAAA
* * **
5825 ATGACCAAAATACCCCTGAACATGTGA
1 ATGACCAAAATGCCCCTGAATATGAAA
5852 ATGACCAAAATGCCCCTG
1 ATGACCAAAATGCCCCTG
5870 GGTGACCCTA
Statistics
Matches: 54, Mismatches: 16, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
26 20 0.37
27 34 0.63
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.19
Consensus pattern (27 bp):
ATGACCAAAATGCCCCTGAATATGAAA
Found at i:6144 original size:27 final size:27
Alignment explanation
Indices: 6114--6186 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 27
6104 CAGCTTCTTT
*
6114 GAATTGTCTTCCAATTCAATCTTCAGG
1 GAATTGTCTTCCAATTCAATCTTCACG
* * *
6141 GAATCGTCTTCCGAA-TCAA-CTTCTCT
1 GAATTGTCTTCC-AATTCAATCTTCACG
*
6167 GAATTGTCTTCCAATCCAAT
1 GAATTGTCTTCCAATTCAAT
6187 ATTAAAAGGA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
25 2 0.05
26 18 0.49
27 15 0.41
28 2 0.05
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (27 bp):
GAATTGTCTTCCAATTCAATCTTCACG
Found at i:6202 original size:53 final size:52
Alignment explanation
Indices: 6093--6206 Score: 140
Period size: 53 Copynumber: 2.2 Consensus size: 52
6083 CGAAATGGAT
* * * * * * *
6093 CGTCTTCCGATCAGCTTCTTTGAATTGTCTTCCAATTCAATCTTCAGGGAAT
1 CGTCTTCCGATCAACTTCTCTGAATTGTCTTCCAATCCAATATTAAAGGAAC
6145 CGTCTTCCGAATCAACTTCTCTGAATTGTCTTCCAATCCAATATTAAAAGG-AC
1 CGTCTTCCG-ATCAACTTCTCTGAATTGTCTTCCAATCCAATATT-AAAGGAAC
6198 CGTCTTCCG
1 CGTCTTCCG
6207 CTTATCCTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
52 9 0.17
53 41 0.77
54 3 0.06
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (52 bp):
CGTCTTCCGATCAACTTCTCTGAATTGTCTTCCAATCCAATATTAAAGGAAC
Found at i:6853 original size:193 final size:192
Alignment explanation
Indices: 6489--6864 Score: 502
Period size: 193 Copynumber: 2.0 Consensus size: 192
6479 CATCTTCTGA
* * * *
6489 TCAACTTCTGAAAATTTTTGAGAAACCATCTTCTGGCATACTTTTTGACAAGATCCTCTTCCGAT
1 TCAACTTCTGAAAACTGTTGAGAAACAATCTTCTGGCATACTTCTTGACAAGATCCTCTTCCGAT
* * * *
6554 CAACTTCTGAAAACTCTTGAGAAAACATCTTCTGGTGTACTTTTTTATAGGATCATCTTCCAATC
66 CAACTTCTGAAAACTCTTGAGAAAACATCTTCTGGTGTACTTCTTGACAAGATCATCTTCCAATC
* *
6619 AACATCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTCGACAAGATCAGCTTCCGG
131 AACATCTGAAAACTCTTGAGAAACCATCTTCCGGAGTACTTCTCGACAAGATCAGCTTCCGG
** **
6681 TCAACATT-TGAAAACTGTTGAGAAAACAATCTTCTGGTGTACTTCTTGACAAGATTGTCTTCCG
1 TCAAC-TTCTGAAAACTGTTGAG-AAACAATCTTCTGGCATACTTCTTGACAAGATCCTCTTCCG
* * * * * *
6745 ATCATCTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGA
64 ATCAACTTCTGAAAACTCTTGAGAAAACATCTTCTGGTGTACTTCTTGACAAGATCATCTTCCAA
* * * * *
6810 TCATCTTCTGAAAATTGTTGAGAAACCATCTTCCGGAGTACTTCTTGACAAGATC
129 TCAACATCTGAAAACTCTTGAGAAACCATCTTCCGGAGTACTTCTCGACAAGATC
6865 GTCTTCCAAT
Statistics
Matches: 157, Mismatches: 25, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
192 17 0.11
193 140 0.89
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.34
Consensus pattern (192 bp):
TCAACTTCTGAAAACTGTTGAGAAACAATCTTCTGGCATACTTCTTGACAAGATCCTCTTCCGAT
CAACTTCTGAAAACTCTTGAGAAAACATCTTCTGGTGTACTTCTTGACAAGATCATCTTCCAATC
AACATCTGAAAACTCTTGAGAAACCATCTTCCGGAGTACTTCTCGACAAGATCAGCTTCCGG
Found at i:6879 original size:64 final size:64
Alignment explanation
Indices: 6467--6876 Score: 500
Period size: 64 Copynumber: 6.4 Consensus size: 64
6457 CCGATGCATC
* * * * * * **
6467 TCTTAACAAGACCATCTTCTGATCAACTTCTGAAAATTTTTGAGAAACCATCTTCTGGCATACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT
* * * *
6531 TTTTGACAAGATCCTCTTCCGATCAACTTCTGAAAACTCTTGAGAAAACATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT
* * * * * * * *
6595 TTTTTATAGGATCATCTTCCAATCAACATCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT
* * *
6659 TCTCGACAAGATCAG-CTTCCGGTCAACATT-TGAAAACTGTTGAGAAAACAATCTTCTGGTGTA
1 TCTTGACAAGATC-GTCTTCCGATCAAC-TTCTGAAAACTGTTGAG-AAACCATCTTCTGGTGTA
6722 CT
63 CT
* * *
6724 TCTTGACAAGATTGTCTTCCGATCATCTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT
* * * *
6788 TCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAATTGTTGAGAAACCATCTTCCGGAGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT
*
6852 TCTTGACAAGATCGTCTTCCAATCA
1 TCTTGACAAGATCGTCTTCCGATCA
6877 TCTGACAATT
Statistics
Matches: 303, Mismatches: 38, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
64 249 0.82
65 54 0.18
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.34
Consensus pattern (64 bp):
TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT
Found at i:6921 original size:128 final size:125
Alignment explanation
Indices: 6506--6889 Score: 443
Period size: 129 Copynumber: 3.0 Consensus size: 125
6496 CTGAAAATTT
** * * *
6506 TTGAGAAACCATCTTCTGGCATACTTTTTGACAAGATCCTCTTCCGATCAACTTCTGAAAACTCT
1 TTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGT
* * * * * * *
6571 TGAGAAAACATCTTCTGGTGTACTTTTTTATAGGATCATCTTCCAATCAACATCTGAAAACTC
66 TGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCAAT---CATCTGAAATCTC
* *
6634 TTGAGAAACCATCTTCTGGTGTACTTCTCGACAAGATCAG-CTTCCGGTCAACATT-TGAAAACT
1 TTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATC-GTCTTCCGATCAAC-TTCTGAAAACT
* * *
6697 GTTGAGAAAACAATCTTCTGGTGTACTTCTTGACAAGATTGTCTTCCGATCATCTTCTGAAAAT-
64 GTTGAG-AAACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCC-A--ATCATCTG-AAATC
*
6761 TG
124 TC
* *
6763 TTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAATTGT
1 TTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGT
* *
6828 TGAGAAACCATCTTCCGGAGTACTTCTTGACAAGATCGTCTTCCAATCATCTGACAAT-TC
66 TGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCAATCATCTGA-AATCTC
6888 TT
1 TT
6890 TCTGGTAAAC
Statistics
Matches: 218, Mismatches: 28, Indels: 23
0.81 0.10 0.09
Matches are distributed among these distances:
124 1 0.00
125 13 0.06
127 1 0.00
128 97 0.44
129 100 0.46
130 4 0.02
132 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (125 bp):
TTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGT
TGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCAATCATCTGAAATCTC
Found at i:6953 original size:193 final size:191
Alignment explanation
Indices: 6490--6957 Score: 428
Period size: 193 Copynumber: 2.4 Consensus size: 191
6480 ATCTTCTGAT
* * * * *** * ** *
6490 CAACTTCTGAAAATTTTTGAG-AAACCATCTTCTGGCATACTTTTTGACAAGATCCTCTTCCGAT
1 CAACATCTGAAAACTGTTGAGAAAACAATCTTCTGATGTACTTCTTGACAAGATTGTCTTCCAAT
* * * * * * *
6554 CAACTTCTGAAAACTCTTGAGAAAACATCTTCTGGTGTACTTTTTTATAGGATCATCTTCCAATC
66 CATCATCTGAAAATTCTTGAGAAAACATCTTCTGGTGTACTTCTTGACAAGATCATCTTCCAATC
* *
6619 AACATCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTCGACAAGATCAGCTTCCGG
131 AACATCTGAAAACTCTTGAGAAACCATCTTCCGGAGTACTTCTCGACAAGATCAGCTTCC-G
* * *
6681 TCAACATTTGAAAACTGTTGAGAAAACAATCTTCTGGTGTACTTCTTGACAAGATTGTCTTCCGA
1 -CAACATCTGAAAACTGTTGAGAAAACAATCTTCTGATGTACTTCTTGACAAGATTGTCTTCCAA
* * * * *
6746 TCATCTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGAT
65 TCATCATCTGAAAATTCTTGAGAAAACATCTTCTGGTGTACTTCTTGACAAGATCATCTTCCAAT
* * * * *
6811 CATCTTCTGAAAATTGTTGAGAAACCATCTTCCGGAGTACTTCTTGACAAGATC-GTCTT-C-
130 CAACATCTGAAAACTCTTGAGAAACCATCTTCCGGAGTACTTCTCGACAAGATCAG-CTTCCG
* * * ** **
6871 CAATCATCTGACAATTCTTTCTG-GTAAACCGTCTTCTGATGTA-TTCCTTGATGAGATTGTCTT
1 CAA-CATCTGA-AA-ACTGT-TGAGAAAACAATCTTCTGATGTACTT-CTTGACAAGATTGTCTT
*
6934 CCAATTTACTCAT-TGAAAATTCTT
61 CCAA-TCA-TCATCTGAAAATTCTT
6958 TCTAGCAAGC
Statistics
Matches: 227, Mismatches: 40, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
189 3 0.01
190 6 0.03
191 4 0.02
192 56 0.25
193 155 0.68
194 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (191 bp):
CAACATCTGAAAACTGTTGAGAAAACAATCTTCTGATGTACTTCTTGACAAGATTGTCTTCCAAT
CATCATCTGAAAATTCTTGAGAAAACATCTTCTGGTGTACTTCTTGACAAGATCATCTTCCAATC
AACATCTGAAAACTCTTGAGAAACCATCTTCCGGAGTACTTCTCGACAAGATCAGCTTCCG
Found at i:7242 original size:67 final size:67
Alignment explanation
Indices: 6883--7248 Score: 518
Period size: 67 Copynumber: 5.4 Consensus size: 67
6873 ATCATCTGAC
* * * * **
6883 AATTCTTTCTGGTAAACCGTCTTCTGATGTATTCCTTGATGAGATTGTCTTCCAATTTAC-TCAT
1 AATTCTTTCTAGCAAACCGTCTTCCGATGTATTCCTTAATGAGATTGTCTTCCAATCAACAT--T
6947 TGAA
64 TGAA
* * * *
6951 AATTCTTTCTAGCAAGCCGTCTTCTGGTGTATTCTTTAATGAGATTGTCTTCCAATCAACATTTG
1 AATTCTTTCTAGCAAACCGTCTTCCGATGTATTCCTTAATGAGATTGTCTTCCAATCAACATTTG
7016 AA
66 AA
* * * *
7018 AAGTCTTTCTAGCAAACCGTCTTTCGGTGTATTCTTTAATGAGATTGTCTTCCAATCAACATTTG
1 AATTCTTTCTAGCAAACCGTCTTCCGATGTATTCCTTAATGAGATTGTCTTCCAATCAACATTTG
7083 AA
66 AA
* * * * *
7085 TATTCTTTCTAGCAAACCGTCTTCCGGTTTACTCCTTAATGAGATTGTCTTCCAATCAACATTAG
1 AATTCTTTCTAGCAAACCGTCTTCCGATGTATTCCTTAATGAGATTGTCTTCCAATCAACATTTG
7150 AA
66 AA
* *
7152 AATTCTTTCTTGCAAACCGTCTTCCTATGTATTCCTTAATGAGATTGTCTTCCAATCAACATTTG
1 AATTCTTTCTAGCAAACCGTCTTCCGATGTATTCCTTAATGAGATTGTCTTCCAATCAACATTTG
7217 AA
66 AA
7219 AATTCTTTCTAGCAAACCGTCTTCCGATGT
1 AATTCTTTCTAGCAAACCGTCTTCCGATGT
7249 TATTTCTAAA
Statistics
Matches: 269, Mismatches: 28, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
67 216 0.80
68 52 0.19
69 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (67 bp):
AATTCTTTCTAGCAAACCGTCTTCCGATGTATTCCTTAATGAGATTGTCTTCCAATCAACATTTG
AA
Found at i:10585 original size:21 final size:22
Alignment explanation
Indices: 10542--10586 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
10532 CATCCAATCA
10542 ATTAATTCAAGCAATTCAAAGC
1 ATTAATTCAAGCAATTCAAAGC
*
10564 ATTAA-TCAAAGCAA-TCATAGC
1 ATTAATTC-AAGCAATTCAAAGC
10585 AT
1 AT
10587 AAGTCATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.47, C:0.18, G:0.09, T:0.27
Consensus pattern (22 bp):
ATTAATTCAAGCAATTCAAAGC
Done.