Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023981.1 Corchorus olitorius cultivar O-4 contig24014, 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: 18972
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:792 original size:26 final size:26
Alignment explanation
Indices: 748--797 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
738 TGAAAGAAGA
*
748 TTTTGGAAATTAATAAAATTGGTAAGT
1 TTTTGGAAATAAATAAAA-TGGTAAGT
*
775 TTTTGGAAA-AAATCAAATGGTAA
1 TTTTGGAAATAAATAAAATGGTAA
798 AAAGTTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 6 0.29
27 9 0.43
ACGTcount: A:0.44, C:0.02, G:0.18, T:0.36
Consensus pattern (26 bp):
TTTTGGAAATAAATAAAATGGTAAGT
Found at i:2911 original size:67 final size:67
Alignment explanation
Indices: 2838--3268 Score: 618
Period size: 67 Copynumber: 6.4 Consensus size: 67
2828 CTCTTCCCAG
*
2838 AAATACCCTTTCGGTCAAAGGGTCAGTCTT-GTCTTTTTACATTCAAGTTTAGTATTTTCATTTC
1 AAATACCCTTTCGGTCGAAGGGTCAGT-TTCGTCTTTTTACATTCAAGTTTAGTATTTTCATTTC
2902 CAA
65 CAA
2905 AAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTACATTCAAGTTTAGTATTTTCATTTCC
1 AAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTACATTCAAGTTTAGTATTTTCATTTCC
2970 AAA
66 -AA
* * ** *
2973 AAATACCCTTTTGGTCGAAGGGTCAGTTTCGTCTTTTTACGTTCTGGTTTAGTATTTTCGTTTCC
1 AAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTACATTCAAGTTTAGTATTTTCATTTCC
*
3038 GA
66 AA
* * * *
3040 AAATACCCTTTCAGTAGAAGGGTCAGTTTTGTCTTTTTACATTCAAGTTTAGTATATTCATTTCC
1 AAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTACATTCAAGTTTAGTATTTTCATTTCC
3105 AA
66 AA
* * *
3107 AAATACCCTTTCGGTCGGAGGGTTAGTTTCGTCTTTTTACATTCAAGTTCAGTATTTTCATTTCC
1 AAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTACATTCAAGTTTAGTATTTTCATTTCC
3172 AA
66 AA
* * * * *
3174 AAATACCCTTTCGGTCGAACGGTC-GATTTCGTCTTTCTGCATTCAGGTTTAGT-TTTAC-TTTC
1 AAATACCCTTTCGGTCGAAGGGTCAG-TTTCGTCTTTTTACATTCAAGTTTAGTATTTTCATTTC
3236 CAA
65 CAA
* *
3239 AAATACCCTTCCGGTCGACGGGTCAGTTTC
1 AAATACCCTTTCGGTCGAAGGGTCAGTTTC
3269 ATCAGGATGA
Statistics
Matches: 325, Mismatches: 35, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
65 32 0.10
66 8 0.02
67 223 0.69
68 62 0.19
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (67 bp):
AAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTACATTCAAGTTTAGTATTTTCATTTCC
AA
Found at i:3064 original size:135 final size:134
Alignment explanation
Indices: 2838--3268 Score: 618
Period size: 135 Copynumber: 3.2 Consensus size: 134
2828 CTCTTCCCAG
*
2838 AAATACCCTTTCGGTCAAAGGGTCAGTCTT-GTCTTTTTACATTCAAGTTTAGTATTTTCATTTC
1 AAATACCCTTTCGGTCGAAGGGTCAGT-TTCGTCTTTTTACATTCAAGTTTAGTATTTTCATTTC
2902 CAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTACATTCAAGTTTAGTATTTTCATT
65 CAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTACATTCAAGTTTAGTATTTTCATT
2967 TCCAAA
130 TCC-AA
* * ** *
2973 AAATACCCTTTTGGTCGAAGGGTCAGTTTCGTCTTTTTACGTTCTGGTTTAGTATTTTCGTTTCC
1 AAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTACATTCAAGTTTAGTATTTTCATTTCC
* * * * *
3038 GAAAATACCCTTTCAGTAGAAGGGTCAGTTTTGTCTTTTTACATTCAAGTTTAGTATATTCATTT
66 AAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTACATTCAAGTTTAGTATTTTCATTT
3103 CCAA
131 CCAA
* * *
3107 AAATACCCTTTCGGTCGGAGGGTTAGTTTCGTCTTTTTACATTCAAGTTCAGTATTTTCATTTCC
1 AAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTACATTCAAGTTTAGTATTTTCATTTCC
* * * * *
3172 AAAAATACCCTTTCGGTCGAACGGTC-GATTTCGTCTTTCTGCATTCAGGTTTAGT-TTTAC-TT
66 AAAAATACCCTTTCGGTCGAAGGGTCAG-TTTCGTCTTTTTACATTCAAGTTTAGTATTTTCATT
3234 TCCAA
130 TCCAA
* *
3239 AAATACCCTTCCGGTCGACGGGTCAGTTTC
1 AAATACCCTTTCGGTCGAAGGGTCAGTTTC
3269 ATCAGGATGA
Statistics
Matches: 261, Mismatches: 33, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
132 33 0.13
133 4 0.02
134 106 0.41
135 118 0.45
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (134 bp):
AAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTACATTCAAGTTTAGTATTTTCATTTCC
AAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTACATTCAAGTTTAGTATTTTCATTT
CCAA
Found at i:3463 original size:65 final size:66
Alignment explanation
Indices: 2838--3463 Score: 285
Period size: 67 Copynumber: 9.4 Consensus size: 66
2828 CTCTTCCCAG
* * * * * * *
2838 AAATACCCTTTCGGTCAAAGGGTCAGTCTT-GTC-TTTTTACATTCAAGTTTAGTATTTTCATTT
1 AAATACCCTTTCGGTCAAAGGGTCAGT-TTCATCATTTCTGCATTTAAGTTTACT-TCTAC-TTT
2901 CCAA
63 CCAA
* * * * * * * *
2905 AAATACCCTTTCGGTCGAAGGGTCAGTTTCGTC-TTTTTACATTCAAGTTTAGTATTTTCATTTC
1 AAATACCCTTTCGGTCAAAGGGTCAGTTTCATCATTTCTGCATTTAAGTTTACT-TCTAC-TTTC
2969 CAAA
64 C-AA
* * * * * * * * * *
2973 AAATACCCTTTTGGTCGAAGGGTCAGTTTCGTC-TTTTTACGTTCT-GGTTTAGTATTTTCGTTT
1 AAATACCCTTTCGGTCAAAGGGTCAGTTTCATCATTTCTGCATT-TAAGTTTACT-TCTAC-TTT
*
3036 CCGA
63 CCAA
* ** * * * * * *
3040 AAATACCCTTTCAGT-AGAAGGGTCAGTTTTGTC-TTTTTACATTCAAGTTTAGTATATTCATTT
1 AAATACCCTTTCGGTCA-AAGGGTCAGTTTCATCATTTCTGCATTTAAGTTTACT-TCTAC-TTT
3103 CCAA
63 CCAA
** * * * * * * * * *
3107 AAATACCCTTTCGGTCGGAGGGTTAGTTTCGTC-TTTTTACATTCAAGTTCAGTATTTTCATTTC
1 AAATACCCTTTCGGTCAAAGGGTCAGTTTCATCATTTCTGCATTTAAGTTTACT-TCTAC-TTTC
3171 CAA
64 CAA
* * * * * * *
3174 AAATACCCTTTCGGTCGAACGGTC-GATTTCGTC-TTTCTGCATTCAGGTTTAGTTTTACTTTCC
1 AAATACCCTTTCGGTCAAAGGGTCAG-TTTCATCATTTCTGCATTTAAGTTTACTTCTACTTTCC
3237 AA
65 AA
* * * * ** *
3239 AAATACCCTTCCGGTCGACGGGTCAGTTTCATCAGGATGATGCATTTAAGTCTAGTCTT-T-CTT
1 AAATACCCTTTCGGTCAAAGGGTCAGTTTCATCA--TTTCTGCATTTAAGTTTA--CTTCTACTT
3302 TCCAA
62 TCCAA
* * * * *
3307 AGAATACCCTTTCGGTCAAAGGGTCAATTTCATCA-TTCTTGCATTTGAGTTCACTTTTGA-TAT
1 A-AATACCCTTTCGGTCAAAGGGTCAGTTTCATCATTTC-TGCATTTAAGTTTACTTCT-ACTTT
3370 CCAAA
63 CC-AA
* * * * *
3375 AAATA-CCTTTCGGTGAAAAGGTCAGTTTCGTCATTTCCGCATTTTAGTTTA-TTCTACTTTCCA
1 AAATACCCTTTCGGTCAAAGGGTCAGTTTCATCATTTCTGCATTTAAGTTTACTTCTACTTTCCA
3438 A
66 A
* *
3439 AAATGCCCTCTCGGTCAAAGGGTCA
1 AAATACCCTTTCGGTCAAAGGGTCA
3464 AGCTTGTCGT
Statistics
Matches: 471, Mismatches: 66, Indels: 46
0.81 0.11 0.08
Matches are distributed among these distances:
64 7 0.01
65 60 0.13
66 45 0.10
67 242 0.51
68 85 0.18
69 30 0.06
70 2 0.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.39
Consensus pattern (66 bp):
AAATACCCTTTCGGTCAAAGGGTCAGTTTCATCATTTCTGCATTTAAGTTTACTTCTACTTTCCA
A
Found at i:9807 original size:6 final size:6
Alignment explanation
Indices: 9796--9830 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
9786 ATACATAAAT
9796 ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
9831 TATAGGCTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:10905 original size:72 final size:73
Alignment explanation
Indices: 10787--10929 Score: 270
Period size: 72 Copynumber: 2.0 Consensus size: 73
10777 GATGAAGATA
10787 AAAATTTTTTTCTAAAGGTTGCTCTCAAACACTAAATTCTTATAGATGTGTATCCTTATTTTCTT
1 AAAATTTTTTTCTAAAGGTTGCTCTCAAACACTAAATTCTTATAGATGTGTATCCTTATTTTCTT
10852 GACAATGC
66 GACAATGC
*
10860 AAAA-TTTTTTCTAAAGGTTGCTCTCAAACACTAAATTCTTATAGATGTGTATCCTTCTTTTCTT
1 AAAATTTTTTTCTAAAGGTTGCTCTCAAACACTAAATTCTTATAGATGTGTATCCTTATTTTCTT
10924 GACAAT
66 GACAAT
10930 ACGATTTTAG
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
72 65 0.94
73 4 0.06
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (73 bp):
AAAATTTTTTTCTAAAGGTTGCTCTCAAACACTAAATTCTTATAGATGTGTATCCTTATTTTCTT
GACAATGC
Found at i:11253 original size:20 final size:21
Alignment explanation
Indices: 11230--11272 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
11220 ATCTTGAAGA
11230 ATTTAAAG-CCATCGGAGATC
1 ATTTAAAGCCCATCGGAGATC
* *
11250 ATTTGAAGCCCATTGGAGATC
1 ATTTAAAGCCCATCGGAGATC
11271 AT
1 AT
11273 CAACAAAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (21 bp):
ATTTAAAGCCCATCGGAGATC
Found at i:12705 original size:2 final size:2
Alignment explanation
Indices: 12698--12733 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
12688 GGAGCCAAGA
12698 AT AT AT AT AT AT AT AT AT GAT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT A
12734 AAGCTACAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12722 original size:17 final size:17
Alignment explanation
Indices: 12700--12732 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
12690 AGCCAAGAAT
12700 ATATATATATATATATG
1 ATATATATATATATATG
12717 ATATATATATATATAT
1 ATATATATATATATAT
12733 AAAGCTACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
ATATATATATATATATG
Found at i:12861 original size:35 final size:35
Alignment explanation
Indices: 12815--12884 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
12805 CCGCTGCTAA
12815 CACTTGTAATGATATAGTTAAAAGTGAATTACATC
1 CACTTGTAATGATATAGTTAAAAGTGAATTACATC
12850 CACTTGTAATGATATAGTTAAAAGTGAATTACATC
1 CACTTGTAATGATATAGTTAAAAGTGAATTACATC
12885 TAGATAGGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.34
Consensus pattern (35 bp):
CACTTGTAATGATATAGTTAAAAGTGAATTACATC
Found at i:18032 original size:21 final size:21
Alignment explanation
Indices: 17985--18032 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
17975 TTTTCATATC
* *
17985 TAAGATTAGTAAAAAAAGTTA
1 TAAGATTAGTAAAAAAAATAA
18006 TGAAGATTA-TAAAAAAAAATAA
1 T-AAGATTAGT-AAAAAAAATAA
18028 TAAGA
1 TAAGA
18033 AGCTATAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (21 bp):
TAAGATTAGTAAAAAAAATAA
Done.