Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007923.1 Corchorus capsularis cultivar CVL-1 contig07944, 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: 31557
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:7872 original size:40 final size:40
Alignment explanation
Indices: 7817--7895 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
7807 ACAGCTAAAA
7817 CCTTAACACAGTGTAATTAAGAAAAATTAAGAAAAGCAAG
1 CCTTAACACAGTGTAATTAAGAAAAATTAAGAAAAGCAAG
7857 CCTTAA-ATCAGTGTAATTAAGAAAAATTAAGAAAAGCAA
1 CCTTAACA-CAGTGTAATTAAGAAAAATTAAGAAAAGCAA
7896 ACACAGTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 1 0.03
40 37 0.97
ACGTcount: A:0.53, C:0.11, G:0.14, T:0.22
Consensus pattern (40 bp):
CCTTAACACAGTGTAATTAAGAAAAATTAAGAAAAGCAAG
Found at i:7927 original size:41 final size:41
Alignment explanation
Indices: 7881--7968 Score: 144
Period size: 41 Copynumber: 2.2 Consensus size: 41
7871 AATTAAGAAA
*
7881 AATTAAGAAAAGCAAACACAGTTAAAGTCTTAATTCAGGGT
1 AATTAAGAAAAGCAAACACAGTCAAAGTCTTAATTCAGGGT
*
7922 AATTAAGAAAAGCAAACACAGTCAAAGTCTTAATT--TGGT
1 AATTAAGAAAAGCAAACACAGTCAAAGTCTTAATTCAGGGT
7961 AATTAAGA
1 AATTAAGA
7969 GGAGTAAGTC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
39 11 0.24
41 34 0.76
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (41 bp):
AATTAAGAAAAGCAAACACAGTCAAAGTCTTAATTCAGGGT
Found at i:8018 original size:67 final size:70
Alignment explanation
Indices: 7905--8037 Score: 182
Period size: 67 Copynumber: 1.9 Consensus size: 70
7895 AACACAGTTA
* *
7905 AAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTCAAAGTCTTAATT-TG-GTAATTAAG
1 AAGTCTTAATT-AGGGTAATTAAGAAAAGCAAACAAAGTCAAAGTCTTAATTCAGAGTAATTAAG
7968 AGGAGT
65 AGGAGT
* * * *
7974 AAGTCTTAATT-TGGTAATTAAGAAAAGCTAACAAAGTTAGAGTCTTAATTCAGAGTAATTAAGA
1 AAGTCTTAATTAGGGTAATTAAGAAAAGCAAACAAAGTCAAAGTCTTAATTCAGAGTAATTAAGA
8038 AAAGCAAACA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
67 34 0.61
68 1 0.02
69 21 0.38
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.29
Consensus pattern (70 bp):
AAGTCTTAATTAGGGTAATTAAGAAAAGCAAACAAAGTCAAAGTCTTAATTCAGAGTAATTAAGA
GGAGT
Found at i:8037 original size:41 final size:39
Alignment explanation
Indices: 7975--8180 Score: 166
Period size: 41 Copynumber: 5.4 Consensus size: 39
7965 AAGAGGAGTA
* *
7975 AGTCTTAATTTGGTAATTAAGAAAAGCTAACAAAGTTAG
1 AGTCTTAATTTGGTAATTAAGAAAAGCAAACAAAGTCAG
* *
8014 AGTCTTAATTCAGAGTAATTAAGAAAAGCAAACACAGTCAG
1 AGTCTTAATT-TG-GTAATTAAGAAAAGCAAACAAAGTCAG
8055 AGTCTTAATTTGGTAATT-----AAG---A-AAAGT-A-
1 AGTCTTAATTTGGTAATTAAGAAAAGCAAACAAAGTCAG
* * * *
8083 AGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGCCAG
1 AGTCTTAATT--TGGTAATTAAGAAAAGCAAACAAAGTCAG
* * *
8124 AGTCTTAATTCAGGGTAATTAAGAAGAGCAAACATAGTCA-
1 AGTCTTAATT--TGGTAATTAAGAAAAGCAAACAAAGTCAG
8164 AGGTCTTAATTTGGTAA
1 A-GTCTTAATTTGGTAA
8181 GCAAGTCTTA
Statistics
Matches: 137, Mismatches: 14, Indels: 32
0.75 0.08 0.17
Matches are distributed among these distances:
28 10 0.07
29 1 0.01
30 11 0.08
31 1 0.01
34 3 0.02
35 3 0.02
38 1 0.01
39 24 0.18
40 4 0.03
41 79 0.58
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.28
Consensus pattern (39 bp):
AGTCTTAATTTGGTAATTAAGAAAAGCAAACAAAGTCAG
Found at i:8070 original size:108 final size:108
Alignment explanation
Indices: 7881--8412 Score: 516
Period size: 108 Copynumber: 4.8 Consensus size: 108
7871 AATTAAGAAA
* *
7881 AATTAAGAAAAGCAAACACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTCA
1 AATTAAGAAAAGCTAACACAGTTAGAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTC-
** *
7946 AAGTCTTAATTTGGTAATTAAGAGGAGTAAGTCTTAATT-TGGT
65 AAGTCTTAATTTGGTAATTAAGAAAAGTAAGTCTTAATTAGGGT
* *
7989 AATTAAGAAAAGCTAACAAAGTTAGAGTCTTAATTCAGAGTAATTAAGAAAAGCAAACACAGTCA
1 AATTAAGAAAAGCTAACACAGTTAGAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTCA
8054 GAGTCTTAATTTGGTAATTAAGAAAAGTAAGTCTTAATTCAGGGT
66 -AGTCTTAATTTGGTAATTAAGAAAAGTAAGTCTTAATT-AGGGT
** * *
8099 AATTAAGAAAAG-TAAACACAGCCAGAGTCTTAATTCAGGGTAATTAAGAAGAGCAAACATAGTC
1 AATTAAGAAAAGCT-AACACAGTTAGAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTC
*
8163 AAGGTCTTAATTTGG----T-----AAGCAAGTCTTAATTCAGGGT
65 AA-GTCTTAATTTGGTAATTAAGAAAAGTAAGTCTTAATT-AGGGT
*
8200 AATTAAGAAAAG-TAAACACAGTTAGAGTCTTAATTTAGGGTAATTAAG-AAAGTCAAACACAGT
1 AATTAAGAAAAGCT-AACACAGTTAGAGTCTTAATTCAGGGTAATTAAGAAAAG-CAAACACAGT
* *
8263 CAAAGTCTTAATTTAGGGTAATTAAGAAGGTCAAACACAGTTAAAGTATTAATTCATGGT
64 C-AAGTCTTAATTT--GGTAATT---AA-G---AA-A-AG-T-AAGTCTTAATT-AGGGT
* * * * * * * *
8323 AATTAAGGAGAGCAAACACAATTAAAATCTTAATTCATGGTAATTAAGAAAAGTAAACACAG-CA
1 AATTAAGAAAAGCTAACACAGTTAGAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTCA
*
8387 GAGTCTTAATTCAGGGTAATTAAGAA
66 -AGTCTTAATT--TGGTAATTAAGAA
8413 GAGCATACAC
Statistics
Matches: 358, Mismatches: 32, Indels: 61
0.79 0.07 0.14
Matches are distributed among these distances:
100 3 0.01
101 85 0.24
102 2 0.01
103 2 0.01
106 1 0.00
107 2 0.01
108 96 0.27
109 2 0.01
110 72 0.20
115 2 0.01
118 1 0.00
119 2 0.01
120 1 0.00
121 3 0.01
122 18 0.05
123 62 0.17
124 4 0.01
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.27
Consensus pattern (108 bp):
AATTAAGAAAAGCTAACACAGTTAGAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTCA
AGTCTTAATTTGGTAATTAAGAAAAGTAAGTCTTAATTAGGGT
Found at i:8087 original size:28 final size:29
Alignment explanation
Indices: 8055--8113 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 29
8045 ACACAGTCAG
*
8055 AGTCTTAATT-TGGTAATTAAGAAAAGTA
1 AGTCTTAATTAGGGTAATTAAGAAAAGTA
8083 AGTCTTAATTCAGGGTAATTAAGAAAAGTA
1 AGTCTTAATT-AGGGTAATTAAGAAAAGTA
8113 A
1 A
8114 ACACAGCCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 10 0.36
30 18 0.64
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (29 bp):
AGTCTTAATTAGGGTAATTAAGAAAAGTA
Found at i:8087 original size:69 final size:70
Alignment explanation
Indices: 8014--8148 Score: 218
Period size: 69 Copynumber: 1.9 Consensus size: 70
8004 ACAAAGTTAG
* *
8014 AGTCTTAATTCAGAGTAATTAAGAAAAGCAAACACAGTCAGAGTCTTAATT-TGGTAATTAAGAA
1 AGTCTTAATTCAGAGTAATTAAGAAAAGCAAACACAGCCAGAGTCTTAATTAGGGTAATTAAGAA
8078 AAGTA
66 AAGTA
* *
8083 AGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGCCAGAGTCTTAATTCAGGGTAATTAAGA
1 AGTCTTAATTCAGAGTAATTAAGAAAAGCAAACACAGCCAGAGTCTTAATT-AGGGTAATTAAGA
8148 A
65 A
8149 GAGCAAACAT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
69 48 0.80
71 12 0.20
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.27
Consensus pattern (70 bp):
AGTCTTAATTCAGAGTAATTAAGAAAAGCAAACACAGCCAGAGTCTTAATTAGGGTAATTAAGAA
AAGTA
Found at i:8191 original size:101 final size:101
Alignment explanation
Indices: 8082--8276 Score: 329
Period size: 101 Copynumber: 1.9 Consensus size: 101
8072 TAAGAAAAGT
8082 AAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGCCAGAGTCTTAATTCAGGGTAATTAAG
1 AAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGCCAGAGTCTTAATTCAGGGTAATTAAG
* *
8147 AAGAG-CAAACATAGTCAAGGTCTTAATTTGGTAAGC
66 AA-AGTCAAACACAGTCAAAGTCTTAATTTGGTAAGC
** *
8183 AAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTTAGAGTCTTAATTTAGGGTAATTAAG
1 AAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGCCAGAGTCTTAATTCAGGGTAATTAAG
8248 AAAGTCAAACACAGTCAAAGTCTTAATTT
66 AAAGTCAAACACAGTCAAAGTCTTAATTT
8277 AGGGTAATTA
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
100 2 0.02
101 86 0.98
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.28
Consensus pattern (101 bp):
AAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGCCAGAGTCTTAATTCAGGGTAATTAAG
AAAGTCAAACACAGTCAAAGTCTTAATTTGGTAAGC
Found at i:8241 original size:41 final size:41
Alignment explanation
Indices: 8183--8506 Score: 366
Period size: 41 Copynumber: 7.9 Consensus size: 41
8173 TTTGGTAAGC
8183 AAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTTA
1 AAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTTA
* * *
8224 GAGTCTTAATTTAGGGTAATTAAG-AAAGTCAAACACAGTCA
1 AAGTCTTAATTCAGGGTAATTAAGAAAAGT-AAACACAGTTA
* *
8265 AAGTCTTAATTTAGGGTAATTAAG-AAGGTCAAACACAGTTA
1 AAGTCTTAATTCAGGGTAATTAAGAAAAGT-AAACACAGTTA
* * * * * *
8306 AAGTATTAATTCATGGTAATTAAGGAGAGCAAACACAATTA
1 AAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTTA
* * *
8347 AAATCTTAATTCATGGTAATTAAGAAAAGTAAACACAG-CA
1 AAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTTA
* * * *
8387 GAGTCTTAATTCAGGGTAATTAAGAAGAGCATACACAGTTA
1 AAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTTA
* ** *
8428 AGGTCTTAATTCATAGAAATTAAGGAAAAGTAAACACAGTTA
1 AAGTCTTAATTCAGGGTAATTAA-GAAAAGTAAACACAGTTA
* * * *
8470 AGGTCTTAATTCACGGTAATTAAGAAAGGTAATCACA
1 AAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACA
8507 AGGCTTAATT
Statistics
Matches: 239, Mismatches: 40, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
40 38 0.16
41 164 0.69
42 37 0.15
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.27
Consensus pattern (41 bp):
AAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTTA
Found at i:8495 original size:123 final size:124
Alignment explanation
Indices: 8183--8506 Score: 417
Period size: 123 Copynumber: 2.6 Consensus size: 124
8173 TTTGGTAAGC
* * *
8183 AAGTCTTAATTCAGGGTAATTAA-GAAAAGTAAACACAGTT-AGAGTCTTAATTTAGGGTAATTA
1 AAGTCTTAATTCATGGTAATTAAGGAAAAGTAAACACAGTTAAG-GTCTTAATTCACGGTAATTA
*
8246 AG-AAAGTCAAACACAGTCAAAGTCTTAATTTAGGGTAATTAAGAAGGTCAAACACAGTTA
65 AGAAAAGT-AAACACAGTCAAAGTCTTAATTCAGGGTAATTAAGAAGGTCAAACACAGTTA
* * * * ** *
8306 AAGTATTAATTCATGGTAATTAAGG-AGAGCAAACACAATTAAAATCTTAATTCATGGTAATTAA
1 AAGTCTTAATTCATGGTAATTAAGGAAAAGTAAACACAGTTAAGGTCTTAATTCACGGTAATTAA
* *
8370 GAAAAGTAAACACAG-CAGAGTCTTAATTCAGGGTAATTAAGAAGAG-CATACACAGTTA
66 GAAAAGTAAACACAGTCAAAGTCTTAATTCAGGGTAATTAAGAAG-GTCAAACACAGTTA
* * *
8428 AGGTCTTAATTCATAGAAATTAAGGAAAAGTAAACACAGTTAAGGTCTTAATTCACGGTAATTAA
1 AAGTCTTAATTCATGGTAATTAAGGAAAAGTAAACACAGTTAAGGTCTTAATTCACGGTAATTAA
* *
8493 GAAAGGTAATCACA
66 GAAAAGTAAACACA
8507 AGGCTTAATT
Statistics
Matches: 172, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
122 59 0.34
123 106 0.62
124 7 0.04
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.27
Consensus pattern (124 bp):
AAGTCTTAATTCATGGTAATTAAGGAAAAGTAAACACAGTTAAGGTCTTAATTCACGGTAATTAA
GAAAAGTAAACACAGTCAAAGTCTTAATTCAGGGTAATTAAGAAGGTCAAACACAGTTA
Found at i:8586 original size:41 final size:41
Alignment explanation
Indices: 8541--8787 Score: 318
Period size: 41 Copynumber: 5.8 Consensus size: 41
8531 AAGAATAGTA
8541 AAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGT
1 AAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGT
*
8582 AAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGGAAATTAGGTAAAGG
1 AAAGCACAGACTTAATTTC----AAGG--A--A-GGAAATTAGGTAAAGT
* **
8632 AAAGCACACACTTAATTTCAAGGAAGGAAATTAGGTAAAAC
1 AAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGT
*
8673 AAAGTACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGT
1 AAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGT
*
8714 AAAGCATAGACTTAATTTCAAGGAAGGAAATTAGGTAAAG-
1 AAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGT
*
8754 ATATGCACAGACTTAATTTCAA-GAGAGGAAATTA
1 A-AAGCACAGACTTAATTTCAAGGA-AGGAAATTA
8788 AGTAGAGTCA
Statistics
Matches: 183, Mismatches: 12, Indels: 22
0.84 0.06 0.10
Matches are distributed among these distances:
40 3 0.02
41 135 0.74
42 1 0.01
44 1 0.01
45 4 0.02
46 4 0.02
47 1 0.01
49 1 0.01
50 33 0.18
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.22
Consensus pattern (41 bp):
AAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGT
Found at i:8943 original size:36 final size:35
Alignment explanation
Indices: 8783--8946 Score: 184
Period size: 36 Copynumber: 4.8 Consensus size: 35
8773 CAAGAGAGGA
*
8783 AATTAAGTAGAGTCAATAAA-AGGCTTAATTCAGGGT
1 AATTAAGT-GAGTCAATAAAGA-ACTTAATTCAGGGT
*
8819 AATTAAGT-AG--AATAAAGAACTTATTTCAGGGT
1 AATTAAGTGAGTCAATAAAGAACTTAATTCAGGGT
* *
8851 AATTAACTGGAGTCAATAAA-AGGCTTAATTCAGGGT
1 AATTAAGT-GAGTCAATAAAGA-ACTTAATTCAGGGT
8887 -ATTAAGTG-G--AATAAAGAACTTAATTCAGGGT
1 AATTAAGTGAGTCAATAAAGAACTTAATTCAGGGT
8918 AATTAAGTGGAGTCAATAAAGAACTTAAT
1 AATTAAGT-GAGTCAATAAAGAACTTAAT
8947 CTAAAAAGAT
Statistics
Matches: 109, Mismatches: 7, Indels: 24
0.78 0.05 0.17
Matches are distributed among these distances:
31 19 0.17
32 33 0.30
33 3 0.03
34 6 0.06
35 7 0.06
36 41 0.38
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.29
Consensus pattern (35 bp):
AATTAAGTGAGTCAATAAAGAACTTAATTCAGGGT
Found at i:8946 original size:67 final size:68
Alignment explanation
Indices: 8783--8937 Score: 267
Period size: 67 Copynumber: 2.3 Consensus size: 68
8773 CAAGAGAGGA
* *
8783 AATTAAGTAGAGTCAATAAAAGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTATTTCAG
1 AATTAAGTGGAGTCAATAAAAGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCAG
8848 GGT
66 GGT
* *
8851 AATTAACTGGAGTCAATAAAAGGCTTAATTCAGGGT-ATTAAGTGGAATAAAGAACTTAATTCAG
1 AATTAAGTGGAGTCAATAAAAGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCAG
8915 GGT
66 GGT
8918 AATTAAGTGGAGTCAATAAA
1 AATTAAGTGGAGTCAATAAA
8938 GAACTTAATC
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
67 48 0.59
68 34 0.41
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.28
Consensus pattern (68 bp):
AATTAAGTGGAGTCAATAAAAGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCAG
GGT
Found at i:30561 original size:21 final size:22
Alignment explanation
Indices: 30516--30638 Score: 82
Period size: 21 Copynumber: 5.6 Consensus size: 22
30506 TTTACTGAAT
* *
30516 TACTGATTACCATCATTA-TTT-
1 TACTGATTA-CTTCTTTACTTTG
30537 TACTGATTA-TTCTTTACTTTG
1 TACTGATTACTTCTTTACTTTG
30558 TACTGATTACTAT-TTTACTCTTG
1 TACTGATTACT-TCTTTACT-TTG
*
30581 T--TGATTACCTTC-TTACTTTT
1 TACTGATTA-CTTCTTTACTTTG
* *
30601 TACTGATTACCAT-TTTACTCTTT
1 TACTGATTA-CTTCTTTACT-TTG
30624 TACTGATTACCTTCT
1 TACTGATTA-CTTCT
30639 ACTGATTACT
Statistics
Matches: 85, Mismatches: 5, Indels: 21
0.77 0.05 0.19
Matches are distributed among these distances:
19 5 0.06
20 6 0.07
21 30 0.35
22 23 0.27
23 20 0.24
24 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.07, T:0.53
Consensus pattern (22 bp):
TACTGATTACTTCTTTACTTTG
Found at i:30609 original size:43 final size:44
Alignment explanation
Indices: 30550--30638 Score: 135
Period size: 43 Copynumber: 2.0 Consensus size: 44
30540 TGATTATTCT
*
30550 TTACTTTGTACTGATTACTATTTTACTCTTGT-TGATTACCTTC
1 TTACTTTGTACTGATTACCATTTTACTCTTGTATGATTACCTTC
* *
30593 TTACTTTTTACTGATTACCATTTTACTCTTTTACTGATTACCTTC
1 TTACTTTGTACTGATTACCATTTTACTCTTGTA-TGATTACCTTC
30638 T
1 T
30639 ACTGATTACT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 29 0.71
45 12 0.29
ACGTcount: A:0.19, C:0.20, G:0.07, T:0.54
Consensus pattern (44 bp):
TTACTTTGTACTGATTACCATTTTACTCTTGTATGATTACCTTC
Found at i:30657 original size:21 final size:22
Alignment explanation
Indices: 30633--30731 Score: 82
Period size: 21 Copynumber: 4.6 Consensus size: 22
30623 TTACTGATTA
30633 CCTTCTACTGATTACTA-TTTG
1 CCTTCTACTGATTACTATTTTG
* *
30654 CCTTTTGCTGATTACTATTTT-
1 CCTTCTACTGATTACTATTTTG
* * *
30675 AC-TCTCATTGATTACCATTTTG
1 CCTTCT-ACTGATTACTATTTTG
*
30697 -C-TCTTACTGATTACTATTTTA
1 CCTTC-TACTGATTACTATTTTG
*
30718 CCTTTTACTGATTA
1 CCTTCTACTGATTA
30732 TCATTACTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
20 2 0.03
21 44 0.72
22 14 0.23
23 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.08, T:0.51
Consensus pattern (22 bp):
CCTTCTACTGATTACTATTTTG
Found at i:30731 original size:43 final size:43
Alignment explanation
Indices: 30515--30736 Score: 146
Period size: 42 Copynumber: 5.3 Consensus size: 43
30505 TTTTACTGAA
* *
30515 TTACTGATTACCATCATTA-TTTTACTGATTA-T-TCTTTA-CTT
1 TTACTGATTACCAT-TTTACTCTTACTGATTACTAT-TTTACCTT
* ** * *
30556 TGTACTGATTACTATTTTACTCTTGTTGATTACCT-TCTTACTTT
1 T-TACTGATTACCATTTTACTCTTACTGATTA-CTATTTTACCTT
30600 TTACTGATTACCATTTTACTC-T--T--TTACTGA--TTACCTT
1 TTACTGATTACCATTTTACTCTTACTGATTACT-ATTTTACCTT
* * ** * * *
30637 CTACTGATTACTATTTGCCTTTTGCTGATTACTATTTTA-CTC
1 TTACTGATTACCATTTTACTCTTACTGATTACTATTTTACCTT
* * *
30679 TCATTGATTACCATTTTGCTCTTACTGATTACTATTTTACCTT
1 TTACTGATTACCATTTTACTCTTACTGATTACTATTTTACCTT
*
30722 TTACTGATTATCATT
1 TTACTGATTACCATT
30737 ACTTTTTTAT
Statistics
Matches: 139, Mismatches: 27, Indels: 28
0.72 0.14 0.14
Matches are distributed among these distances:
37 24 0.17
38 4 0.03
40 2 0.01
41 5 0.04
42 60 0.43
43 39 0.28
44 5 0.04
ACGTcount: A:0.21, C:0.19, G:0.07, T:0.52
Consensus pattern (43 bp):
TTACTGATTACCATTTTACTCTTACTGATTACTATTTTACCTT
Found at i:30810 original size:22 final size:21
Alignment explanation
Indices: 30769--30818 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
30759 ACTATTTCAT
* *
30769 TCTTTACTGATTATCTTTTTAC
1 TCTTTACTGATTACCCTTTT-C
*
30791 TTTTTACTGATTACCCTTTTC
1 TCTTTACTGATTACCCTTTTC
30812 TCTTTAC
1 TCTTTAC
30819 CATTCTTCCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.16, C:0.22, G:0.04, T:0.58
Consensus pattern (21 bp):
TCTTTACTGATTACCCTTTTC
Found at i:30839 original size:86 final size:86
Alignment explanation
Indices: 30748--30931 Score: 203
Period size: 86 Copynumber: 2.1 Consensus size: 86
30738 CTTTTTTATG
* ** ** *
30748 GATTACCT-TTTACTATTTCATTC-TTTACTGATTATCTTTTTACTTTTTACTGATTACCCTTTT
1 GATTACCTCTTTACTATTTCA-TCATTTACTCATTA-CTAATTACTCCTTACTGATTACCCTTTA
30811 CTCTTTACCATTCTTCCTTTACT
64 CTCTTTACCATTCTTCCTTTACT
* * * **
30834 GATTA-CTCTTTACTTTTTTATCATTTTACTCTTTACTAATTACTCCTTACTGATTATTCTTTAC
1 GATTACCTCTTTACTATTTCATCA-TTTACTCATTACTAATTACTCCTTACTGATTACCCTTTAC
*
30898 TCTTTACCATTTTTCCTTTACT
65 TCTTTACCATTCTTCCTTTACT
30920 GATTACTCTCTT
1 GATTAC-CTCTT
30932 GAATTTAATT
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
85 4 0.05
86 63 0.78
87 9 0.11
88 5 0.06
ACGTcount: A:0.18, C:0.23, G:0.03, T:0.55
Consensus pattern (86 bp):
GATTACCTCTTTACTATTTCATCATTTACTCATTACTAATTACTCCTTACTGATTACCCTTTACT
CTTTACCATTCTTCCTTTACT
Found at i:30878 original size:14 final size:14
Alignment explanation
Indices: 30859--30898 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
30849 TTTTATCATT
30859 TTACTCTTTACTAA
1 TTACTCTTTACTAA
* *
30873 TTACTCCTTACTGA
1 TTACTCTTTACTAA
*
30887 TTATTCTTTACT
1 TTACTCTTTACT
30899 CTTTACCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.53
Consensus pattern (14 bp):
TTACTCTTTACTAA
Found at i:31141 original size:26 final size:26
Alignment explanation
Indices: 31108--31197 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 26
31098 AATTATCAAT
31108 TTACTGATTACTATCTTTTTACTTAA
1 TTACTGATTACTATCTTTTTACTTAA
*
31134 TTACTGATTTACTGAT-TACTATTACCTTAA
1 TTACTGA-TTACT-ATCT--TTTTA-CTTAA
* * * *
31164 CT-CTGATTAATCTCTTTTTATTTAA
1 TTACTGATTACTATCTTTTTACTTAA
31189 TTACTGATT
1 TTACTGATT
31198 TACTGATTGC
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
25 5 0.10
26 17 0.34
27 7 0.14
28 7 0.14
29 8 0.16
30 6 0.12
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.52
Consensus pattern (26 bp):
TTACTGATTACTATCTTTTTACTTAA
Found at i:31159 original size:71 final size:71
Alignment explanation
Indices: 31018--31167 Score: 164
Period size: 71 Copynumber: 2.1 Consensus size: 71
31008 GATCAATCCA
* * * *
31018 TTGACTTTTAATTACTGATTTACTGATTACTATTTTTACCTTGACTCTTAATTACTGATTAATCT
1 TTGACTCTTAATTACTAATTTACTGATTACTATTTTTACCTTAACTCTGAATTACTGATTAATCT
*
31083 CTTACC
66 ATTACC
* *
31089 TTGACTCTTAATTA-TCAATTTACTGATTACTATCTTTTTA-CTTAATTACTGATTTACTGATT-
1 TTGACTCTTAATTACT-AATTTACTGATTACTA--TTTTTACCTTAACT-CTGAATTACTGATTA
31151 A-CTATTACC
62 ATCTATTACC
*
31160 TTAACTCT
1 TTGACTCT
31168 GATTAATCTC
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
70 1 0.01
71 42 0.63
72 6 0.09
73 18 0.27
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.49
Consensus pattern (71 bp):
TTGACTCTTAATTACTAATTTACTGATTACTATTTTTACCTTAACTCTGAATTACTGATTAATCT
ATTACC
Found at i:31172 original size:55 final size:55
Alignment explanation
Indices: 31111--31361 Score: 310
Period size: 55 Copynumber: 4.6 Consensus size: 55
31101 TATCAATTTA
* * * * *
31111 CTGATTACTATCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACCATCACCTTGACT
* * *
31166 CTGATTAATCTCTTTTTATTTAATTACTGATTTACTGATT-GC-TGCTACTTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACCAT-C-ACCTTGACT
* * *
31221 CTGATTTACCTCTTTTTACTTAATTATTGATTTACTGATTACCATCACCTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACCATCACCTTGACT
* * * * *
31276 TTGATTAATCTCTTTCTACTGATTTACTGATTGACTGATTACCATCACCTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACCATCACCTTGACT
*
31331 CTGATTAATCTCTTTTTAC-TGATTACTGATT
1 CTGATTAATCTCTTTTTACTTAATTACTGATT
31362 GCCCCTTTTT
Statistics
Matches: 165, Mismatches: 27, Indels: 9
0.82 0.13 0.04
Matches are distributed among these distances:
53 1 0.01
54 9 0.05
55 152 0.92
56 2 0.01
57 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.09, T:0.48
Consensus pattern (55 bp):
CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACCATCACCTTGACT
Done.