Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1176
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: 35179
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:334 original size:117 final size:120
Alignment explanation
Indices: 136--366 Score: 328
Period size: 117 Copynumber: 1.9 Consensus size: 120
126 TAATAGTGGG
** * *
136 AAATCGCTCTACCAGGATGCTATTTTAAGAAGAAATTGGTGAATAGTGGCCTCGTGGACGCGATT
1 AAATCGCTAAACCAGGATGCTATTATAAGAAGAAATTGGTGAATAGTGCCCTCGTGGACGCGATT
201 TCGGCTACAGTGGTCATGTAAGAAATAATTTTTTGACGTTTCCTGAGCAAAATATA
66 TCGGCTACAGTGGTCATGTAAGAAATAATTTTTTGACGTTT-CTGAGCAAAATATA
* *
257 AAATCGCTAAACCAGGATGCTA-TATGAGAAG-AATT-GTGAATCG-GCCCTCGTGGACGCGATT
1 AAATCGCTAAACCAGGATGCTATTATAAGAAGAAATTGGTGAATAGTGCCCTCGTGGACGCGA-T
* * *
318 TTC-GCTACAGTTGTCATGTAGGAAATATTTTTTTGACGTTTCTGAGCAA
65 TTCGGCTACAGTGGTCATGTAAGAAATAATTTTTTGACGTTTCTGAGCAA
367 TAGTGTCAAA
Statistics
Matches: 100, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
116 8 0.08
117 50 0.50
118 11 0.11
119 4 0.04
120 7 0.07
121 20 0.20
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.31
Consensus pattern (120 bp):
AAATCGCTAAACCAGGATGCTATTATAAGAAGAAATTGGTGAATAGTGCCCTCGTGGACGCGATT
TCGGCTACAGTGGTCATGTAAGAAATAATTTTTTGACGTTTCTGAGCAAAATATA
Found at i:2901 original size:28 final size:28
Alignment explanation
Indices: 2836--3490 Score: 452
Period size: 23 Copynumber: 25.2 Consensus size: 28
2826 TACACTTGCG
2836 ATTAAATTAGGTTAGGGTTAGGGATTTTA
1 ATTAAATTAGGTTAGGGTTAGGG-TTTTA
* *
2865 ATTAAAATAGGTTAGGGTTAGGGTTTTC
1 ATTAAATTAGGTTAGGGTTAGGGTTTTA
*
2893 ATGTAAA-TAGGTTAGGGTTGGGGTTTTTA
1 AT-TAAATTAGGTTAGGGTTAGGG-TTTTA
* *
2922 ATTAAATTAGGTTA-GGTTAAGGATTTCA
1 ATTAAATTAGGTTAGGGTT-AGGGTTTTA
2950 ATTAAATTAGGTTAGGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGG-TTTTA
** *
2979 ATTAAATTAAATTA-GCTTAGGG-TTT-
1 ATTAAATTAGGTTAGGGTTAGGGTTTTA
* * *
3004 -TT-AATTAAGTTA-TGTTATGGTTTTTA
1 ATTAAATTAGGTTAGGGTTA-GGGTTTTA
*
3030 ATT--A--A-GTTA-TGTTAGGGTTTTCA
1 ATTAAATTAGGTTAGGGTTAGGGTTTT-A
3053 ATTAAATTAGGTTAGGG-T----TTTTA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTA
*
3076 ATTAAATTAGGTTA-----AGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTA
3099 ATTAAATTAGGTTAGGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGG-TTTTA
*
3128 ATTAAGTTAGGTTA-GGTT----TTTTA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTA
* *
3151 ATTAAGTTATGTTAGGG-T----TTTTA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTA
3174 ATTAAATTAGGTTAGGGTTAGGG-TTT-
1 ATTAAATTAGGTTAGGGTTAGGGTTTTA
*
3200 -TT-AATTAAG-TAGGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGG-TTTTA
3226 ATTAAATTAGGTTAGGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGG-TTTTA
* *
3255 ATTTAATTAAGTTA-GGTTA-GGTTTT-
1 ATTAAATTAGGTTAGGGTTAGGGTTTTA
* *
3280 -TT-AATTAAGTTA-TGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGG-TTTTA
3306 ATTAAATTAGGTTAGGG-T----TTTTA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTA
*
3329 ATTAAATTATGTTAGGG-T----TTTTA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTA
* *
3352 ATTTAATTAAGTTA-GGTTA-GGTTTT-
1 ATTAAATTAGGTTAGGGTTAGGGTTTTA
* * *
3377 -TTAATT-AAGTTA-TGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGG-TTTTA
*
3403 ATTAAATTAGGTTAGGGTTAAGG-TTT-
1 ATTAAATTAGGTTAGGGTTAGGGTTTTA
*
3429 -TT-AATTAAG-TAGGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGG-TTTTA
3455 ATTAAATTAGGTTAGGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGG-TTTTA
*
3484 ATCAAAT
1 ATTAAAT
3491 AATGTCAAAA
Statistics
Matches: 521, Mismatches: 44, Indels: 122
0.76 0.06 0.18
Matches are distributed among these distances:
22 8 0.02
23 183 0.35
24 34 0.07
25 22 0.04
26 12 0.02
27 22 0.04
28 101 0.19
29 139 0.27
ACGTcount: A:0.29, C:0.01, G:0.24, T:0.47
Consensus pattern (28 bp):
ATTAAATTAGGTTAGGGTTAGGGTTTTA
Found at i:2933 original size:57 final size:54
Alignment explanation
Indices: 2836--3490 Score: 422
Period size: 52 Copynumber: 12.6 Consensus size: 54
2826 TACACTTGCG
* * *
2836 ATTAAATTAGGTTAGGGTTAGGGATTTTAATTAAAATAGGTTAGGGTTAGGGTTTT
1 ATTAAA-TAAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTA-GGTTAGGGTTTT
* * * *
2892 CATGTAAATAGGTTAGGGTTGGGGTTTTTAATTAAATTAGGTTAGGTTAAGGATTTCA
1 -AT-TAAATAAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGTT-AGGGTTT-T
* ** *
2950 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTAGCTTAGGG-TTT
1 ATTAAA-TAAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTTT
* * * *
3004 -TTAATTAAGTTA-TGTTATGGTTTTTAATT--A--A-GTTATGTTAGGG-TTT
1 ATTAAATAAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTTT
* * * *
3050 -TCAATTAAATTA-GGTTAGGGTTTTTAATTAAATTAGGTTAAGGTT----TTTA
1 ATTAAATAAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTT-AGGTTAGGGTTTT
*
3099 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATT--A--A-GTTAGGTTA-GGTTTT
1 ATTAAA-TAAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTTT
* *
3148 -TTAATTAAGTTA-TGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGG-TTT
1 ATTAAATAAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTA-GGTTAGGGTTTT
*
3200 -TTAATTAAG-TAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTT
1 ATTAAATAAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTA-GGTTAGGG-TTTT
* * *
3254 AATTTAATTAAGTTA-GGTTA-GG-TTTT--TT-AATTAAGTTATGTTAGGG-TTT
1 -A-TTAAATAAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTTT
* *
3303 -TTAATTAAATTA-GGTTAGGGTTTTTAATTAAATTA---T--GTTAGGGTTTTT
1 ATTAAATAAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGG-TTTT
* * *
3351 AATTTAATTAAGTTA-GGTTA-GG-TTTT--TT-AATTAAGTTATGTTAGGGTTTTT
1 -A-TTAAATAAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGG-TTTT
* * *
3402 AATTAAATTAGGTTAGGGTTAAGGTTTTTAATT-AAGTA-G---GGTTAGGGTTTTT
1 -ATTAAA-TAAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGG-TTTT
* *
3454 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATCAAAT
1 -ATTAAA-TAAGTTAGGGTTAGGGTTTTTAATTAAAT
3491 AATGTCAAAA
Statistics
Matches: 501, Mismatches: 44, Indels: 110
0.76 0.07 0.17
Matches are distributed among these distances:
46 86 0.17
47 14 0.03
48 15 0.03
49 14 0.03
50 14 0.03
51 77 0.15
52 137 0.27
53 12 0.02
54 7 0.01
55 7 0.01
56 19 0.04
57 93 0.19
58 6 0.01
ACGTcount: A:0.29, C:0.01, G:0.24, T:0.47
Consensus pattern (54 bp):
ATTAAATAAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTTT
Found at i:3128 original size:52 final size:52
Alignment explanation
Indices: 2836--3490 Score: 566
Period size: 46 Copynumber: 12.7 Consensus size: 52
2826 TACACTTGCG
* * *
2836 ATTAAATTAGGTTAGGGTTAGGGATTTTAATTAAAATAGGTTAGGGTTAGGGTTTTC
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG-T----TTTTA
*
2893 ATGTAAA-TAGGTTAGGGTTGGGGTTTTTAATTAAATTAGGTTA-GGTTAAGGATTTCA
1 AT-TAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT-----TTT-A
*
2950 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTAGCTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGG--TTT--TT-AATTAAATTAGGTTAGGGTTTTTA
* * * * *
3007 ATT--A--A-GTTA-TGTTATGGTTTTTAATTAAGTTATGTTAGGGTTTTCA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTA
*
3053 ATT-AA--A--TTA-GGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTA
*
3099 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTA-GG-TTTT-
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTA
* *
3148 -TT-AATTAAGTTA-TGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTT-
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT----TTTA
*
3200 -TT-AATTAAG-TAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGTTTTTA
* * * * *
3255 ATTTAATTAAGTTA-GGTTAGGTTTTTTAATTAAGTTATGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTA
*
3306 ATT-AA--A--TTA-GGTTAGGGTTTTTAATTAAATTATGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTA
* * * * *
3352 ATTTAATTAAGTTA-GGTTAGGTTTTTTAATTAAGTTATGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTA
* *
3403 ATTAAATTAGGTTAGGGTTAAGGTTTTTAATT-AAGTAGGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTA-GGTTAGGGTTTTTA
*
3455 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATCAAAT
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAT
3491 AATGTCAAAA
Statistics
Matches: 512, Mismatches: 40, Indels: 96
0.79 0.06 0.15
Matches are distributed among these distances:
46 127 0.25
47 19 0.04
48 4 0.01
49 5 0.01
50 6 0.01
51 83 0.16
52 120 0.23
53 5 0.01
54 3 0.01
55 3 0.01
56 13 0.03
57 82 0.16
58 19 0.04
59 3 0.01
61 2 0.00
62 14 0.03
63 4 0.01
ACGTcount: A:0.29, C:0.01, G:0.24, T:0.47
Consensus pattern (52 bp):
ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTA
Found at i:5635 original size:14 final size:15
Alignment explanation
Indices: 5618--5651 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5608 AATAAATATC
5618 TAAAAATAT-ATAAA
1 TAAAAATATCATAAA
*
5632 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
5647 TAAAA
1 TAAAA
5652 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:5784 original size:29 final size:30
Alignment explanation
Indices: 5750--5807 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
5740 TGAAAATATT
5750 AAAAATGTTAAAATTAT-TTTAAAAAAATA
1 AAAAATGTTAAAATTATCTTTAAAAAAATA
* *
5779 AAAAATTTTAAAATTTTCTTTAAAAAAAT
1 AAAAATGTTAAAATTATCTTTAAAAAAAT
5808 GAAATTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (30 bp):
AAAAATGTTAAAATTATCTTTAAAAAAATA
Found at i:5879 original size:22 final size:22
Alignment explanation
Indices: 5849--5890 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5839 ATTTGGAGAT
*
5849 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
5871 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
5891 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:5898 original size:30 final size:30
Alignment explanation
Indices: 5862--5920 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
5852 TTGAAGGAAA
* *
5862 TTGAGAGGATTTTGGAAGGAATTTGAGAGT
1 TTGAGAGAATTTTGGAAGGAAATTGAGAGT
5892 TTGAGAGAATTTTGGAAGGAAATTGAGAG
1 TTGAGAGAATTTTGGAAGGAAATTGAGAG
5921 AAATTTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.36, T:0.31
Consensus pattern (30 bp):
TTGAGAGAATTTTGGAAGGAAATTGAGAGT
Found at i:5911 original size:52 final size:51
Alignment explanation
Indices: 5840--5942 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 51
5830 TTAATATGGA
* * *
5840 TTTGGAGATTTTTTGAAGGAAATTGAGAG-GATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTT-GAAGGGAA-TTGAGAG
5891 TTTGAGAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
5943 AATTTTTGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
51 4 0.09
52 33 0.72
53 9 0.20
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.32
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
Found at i:5917 original size:22 final size:22
Alignment explanation
Indices: 5892--5983 Score: 125
Period size: 22 Copynumber: 4.2 Consensus size: 22
5882 ATTTGAGAGT
5892 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
*
5914 TTGAGAGAAATTTT-GAAGGGAA
1 TTGAGAG-AATTTTGGAAGGAAA
*
5936 TTGAGAGAATTTTTGAAAGG-AA
1 TTGAGAGAA-TTTTGGAAGGAAA
*
5958 TTGAGAGAATTTTTGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
5980 TTGA
1 TTGA
5984 TATTGAATTT
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
21 10 0.16
22 42 0.68
23 10 0.16
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.30
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:5941 original size:44 final size:44
Alignment explanation
Indices: 5892--5983 Score: 141
Period size: 44 Copynumber: 2.1 Consensus size: 44
5882 ATTTGAGAGT
* *
5892 TTGAGAGAA-TTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAA
1 TTGAGAGAATTTTTGAAAGG-AATTGAGAGAAATTTTGAAGGAAA
*
5936 TTGAGAGAATTTTTGAAAGGAATTGAGAGAATTTTTGAAGGAAA
1 TTGAGAGAATTTTTGAAAGGAATTGAGAGAAATTTTGAAGGAAA
5980 TTGA
1 TTGA
5984 TATTGAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 35 0.80
45 9 0.20
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.30
Consensus pattern (44 bp):
TTGAGAGAATTTTTGAAAGGAATTGAGAGAAATTTTGAAGGAAA
Found at i:7137 original size:11 final size:11
Alignment explanation
Indices: 7121--7145 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
7111 ACATGGCATA
7121 AATGATGTCAT
1 AATGATGTCAT
7132 AATGATGTCAT
1 AATGATGTCAT
7143 AAT
1 AAT
7146 CTAATTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (11 bp):
AATGATGTCAT
Found at i:8779 original size:7 final size:7
Alignment explanation
Indices: 8767--8792 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
8757 TAGTCGATTG
8767 GTATTTA
1 GTATTTA
8774 GTATTTA
1 GTATTTA
8781 GTATTTA
1 GTATTTA
8788 GTATT
1 GTATT
8793 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:10060 original size:27 final size:26
Alignment explanation
Indices: 10025--10137 Score: 106
Period size: 27 Copynumber: 4.1 Consensus size: 26
10015 AATTGACAAG
10025 CCCTAAACCCTTAACTTAAAAACCCTAA
1 CCCTAAACCCTTAACTT--AAACCCTAA
10053 CCCT-AACCCTTAACTTAAAAACCTACTAA
1 CCCTAAACCCTTAACTT--AAACC--CTAA
*
10082 CCTTAAAACCC-TAACCTT-AACCCTAA
1 CCCT-AAACCCTTAA-CTTAAACCCTAA
10108 CCCTAAAACCCTTAACTCTAAACCCTAA
1 CCCT-AAACCCTTAACT-TAAACCCTAA
10136 CC
1 CC
10138 TTTAACTTAA
Statistics
Matches: 75, Mismatches: 2, Indels: 16
0.81 0.02 0.17
Matches are distributed among these distances:
26 16 0.21
27 23 0.31
28 18 0.24
29 7 0.09
30 3 0.04
31 8 0.11
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.22
Consensus pattern (26 bp):
CCCTAAACCCTTAACTTAAACCCTAA
Found at i:10088 original size:17 final size:15
Alignment explanation
Indices: 10029--10101 Score: 59
Period size: 15 Copynumber: 5.0 Consensus size: 15
10019 GACAAGCCCT
10029 AAACCCTTAA-CTTAA
1 AAACCC-TAACCTTAA
*
10044 AAACCCTAACCCT--
1 AAACCCTAACCTTAA
10057 -AACCCTTAA-CTTAA
1 AAACCC-TAACCTTAA
10071 AAACCTACTAACCTT-A
1 AAACC--CTAACCTTAA
10087 AAACCCTAACCTTAA
1 AAACCCTAACCTTAA
10102 CCCTAACCCT
Statistics
Matches: 47, Mismatches: 2, Indels: 18
0.70 0.03 0.27
Matches are distributed among these distances:
12 7 0.15
13 3 0.06
14 11 0.23
15 13 0.28
16 9 0.19
17 4 0.09
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (15 bp):
AAACCCTAACCTTAA
Found at i:10097 original size:14 final size:14
Alignment explanation
Indices: 10029--10139 Score: 76
Period size: 14 Copynumber: 7.9 Consensus size: 14
10019 GACAAGCCCT
10029 AAACCCTTAA-CTTAA
1 AAACCC-TAACCTT-A
*
10044 AAACCCTAACCCT-
1 AAACCCTAACCTTA
10057 -AACCCTTAA-CTTAA
1 AAACCC-TAACCTT-A
10071 AAACCTACTAACCTTA
1 AAACC--CTAACCTTA
10087 AAACCCTAACCTT-
1 AAACCCTAACCTTA
*
10100 -AACCCTAACCCTA
1 AAACCCTAACCTTA
10113 AAACCCTTAA-CTCT-
1 AAACCC-TAACCT-TA
10127 AAACCCTAACCTT
1 AAACCCTAACCTT
10140 TAACTTAAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 28
0.71 0.04 0.25
Matches are distributed among these distances:
12 18 0.23
13 7 0.09
14 25 0.32
15 16 0.20
16 9 0.11
17 4 0.05
ACGTcount: A:0.41, C:0.36, G:0.00, T:0.23
Consensus pattern (14 bp):
AAACCCTAACCTTA
Found at i:10115 original size:43 final size:41
Alignment explanation
Indices: 10033--10139 Score: 114
Period size: 43 Copynumber: 2.6 Consensus size: 41
10023 AGCCCTAAAC
* *
10033 CCTTAACT-TAAAAACCCTAACCCTAACCCTTAACTTAAAAA
1 CCTTAACTCT-AAAACCCTAACCTTAACCCTTAACCTAAAAA
*
10074 CCTACTAAC-CTTAAAACCCTAACCTTAACCC-TAACCCTAAAAC
1 CCT--TAACTC-TAAAACCCTAACCTTAACCCTTAA-CCTAAAAA
10117 CCTTAACTCT-AAACCCTAACCTT
1 CCTTAACTCTAAAACCCTAACCTT
10140 TAACTTAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
40 13 0.23
41 8 0.14
42 4 0.07
43 31 0.54
44 1 0.02
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.24
Consensus pattern (41 bp):
CCTTAACTCTAAAACCCTAACCTTAACCCTTAACCTAAAAA
Found at i:12233 original size:359 final size:359
Alignment explanation
Indices: 11574--12263 Score: 1139
Period size: 359 Copynumber: 1.9 Consensus size: 359
11564 CTTGTAGTAT
*
11574 GGAAATGTGTCTCGGCATTGCTTAAAGGTCCAAAACAGGCATTTGAACACTTAGCATCCACGTAG
1 GGAAATGCGTCTCGGCATTGCTTAAAGGTCCAAAACAGGCATTTGAACACTTAGCATCCACGTAG
* * *
11639 CAATCAGCCGTTATAGTACGCAAGTTCTGTTTCAAGGTCTGTGATGGCACCTAGGACGTATCTCT
66 CAATCAGCCGTTATAGTACGCAAGTTCCGTTTCAAGGTCTGTGATAGCACCTAGGACATATCTCT
* * *
11704 TTAGCACTTGACACCACTGCCATATTTCATTATATGAAGCGTCCCACCCACTATGCATCTTCTCC
131 CTAGCACTTGACACCACTACCATATTTCATTATATGAAGCATCCCACCCACTATGCATCTTCTCC
* *
11769 AACGCCTTCTGCTTAGCTATCCAAGCATTGCGGTAAGAGGGTGTGTACCTCATTTGGCTACGAAT
196 AACGCCTTCTGCTTAGCTATCCAAGCATTGCGGTAAGAGGGCGTGTACCCCATTTGGCTACGAAT
* * * * ***
11834 ATTGGTAATTAAGACTGGCACTGAAGTTTTGGGATCTGCCTTCACCGTGGGTAGTATCAAGCTAG
261 ATTAGCAATTAAGACAGGCACTAAAGCCCTGGGATCTGCCTTCACCGTGGGTAGTATCAAGCTAG
11899 CTAACAGTATGGAAATACGTATGGAAATGTGTAC
326 CTAACAGTATGGAAATACGTATGGAAATGTGTAC
* * * *
11933 GGAAATGCGTCTCGGTATTGCTTAAAGGTCCAAAACAGGCTTTTGAACACTTGGCATCCATGTAG
1 GGAAATGCGTCTCGGCATTGCTTAAAGGTCCAAAACAGGCATTTGAACACTTAGCATCCACGTAG
* * * *
11998 CAATCAGCCGTTGTAGTACGTATGTTCCGTTTCAAGGTCTGTGATAGCATCT-GGAACATATCTC
66 CAATCAGCCGTTATAGTACGCAAGTTCCGTTTCAAGGTCTGTGATAGCACCTAGG-ACATATCTC
12062 TCTAGCACTTGACACCACTACCATATTTCATTATATGAAGCATCCCACCCACTATGCATCTTCTC
130 TCTAGCACTTGACACCACTACCATATTTCATTATATGAAGCATCCCACCCACTATGCATCTTCTC
*
12127 CAACGCCTTCTGCTTAGCTATCCAAGCCTTGCGGTAAGAGGGCGTGTACCCCATTTGGCTACGAA
195 CAACGCCTTCTGCTTAGCTATCCAAGCATTGCGGTAAGAGGGCGTGTACCCCATTTGGCTACGAA
12192 TATTAGCAATTAAGACAGGCACTAAAGCCCTGGGATCTGCCTTCACCGTGGGTAGTATCAAGCTA
260 TATTAGCAATTAAGACAGGCACTAAAGCCCTGGGATCTGCCTTCACCGTGGGTAGTATCAAGCTA
12257 GCTAACA
325 GCTAACA
12264 TAGCTGAATC
Statistics
Matches: 305, Mismatches: 25, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
358 2 0.01
359 303 0.99
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.28
Consensus pattern (359 bp):
GGAAATGCGTCTCGGCATTGCTTAAAGGTCCAAAACAGGCATTTGAACACTTAGCATCCACGTAG
CAATCAGCCGTTATAGTACGCAAGTTCCGTTTCAAGGTCTGTGATAGCACCTAGGACATATCTCT
CTAGCACTTGACACCACTACCATATTTCATTATATGAAGCATCCCACCCACTATGCATCTTCTCC
AACGCCTTCTGCTTAGCTATCCAAGCATTGCGGTAAGAGGGCGTGTACCCCATTTGGCTACGAAT
ATTAGCAATTAAGACAGGCACTAAAGCCCTGGGATCTGCCTTCACCGTGGGTAGTATCAAGCTAG
CTAACAGTATGGAAATACGTATGGAAATGTGTAC
Found at i:13824 original size:125 final size:125
Alignment explanation
Indices: 13581--13898 Score: 444
Period size: 125 Copynumber: 2.5 Consensus size: 125
13571 CCCAAACATG
*
13581 CTACTGTAGCAAAAAGCGCGTCCAC-ATGGGAGCGATTTCACAAATTCTTCTGATAAAGCATCCT
1 CTACTGTAGC-AAAAGCGCGTCCACGA-GGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCT
* *
13645 GCTTGAAGCATTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCCAGGAC
64 GCTTGAAGCATTTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTTTTCCAGAAC
* * *
13707 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCAATTTCACAAATTCTTCTCAGAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
** *
13772 TTGAAGCATTTTTTTTACTATTTTCTCAAAAACGTCAACTCAAAATTATTTTTGT--AGAAC
66 TTGAAGCA-TTTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTTT-TCCAGAAC
* * ** * *
13832 CTACTGTAGCAAAAGCGTGTACACGTCGGCGCGACTTCAAAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
13897 TT
66 TT
13899 CAATTTTATC
Statistics
Matches: 171, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
125 119 0.70
126 51 0.30
127 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCATTTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTTTTCCAGAAC
Found at i:14201 original size:5 final size:5
Alignment explanation
Indices: 14191--14216 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
14181 TTGAACAATG
14191 AAAGA AAAGA AAAGA AAAGA AAAGA A
1 AAAGA AAAGA AAAGA AAAGA AAAGA A
14217 TTTAAAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:15690 original size:5 final size:6
Alignment explanation
Indices: 15674--15716 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
15664 TAATTTAGCC
* * * *
15674 ATTTTT ATTTTT ATTTTT GTTTTT GTTTTT AGTTTA ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
15717 CATTCTAAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (6 bp):
ATTTTT
Found at i:19551 original size:15 final size:16
Alignment explanation
Indices: 19531--19570 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
19521 TTCTTATTAC
*
19531 TTTATTTTAGTTTCT-
1 TTTATTTTAGTATCTA
19546 TTTATTTTAGTATCTA
1 TTTATTTTAGTATCTA
19562 TATTATTTT
1 T-TTATTTT
19571 CTTGTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 1 0.05
17 7 0.32
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (16 bp):
TTTATTTTAGTATCTA
Found at i:30322 original size:20 final size:21
Alignment explanation
Indices: 30297--30335 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
30287 AAAAAATTAA
*
30297 TTTAAATGAAT-AAATTTACG
1 TTTAAAAGAATAAAATTTACG
30317 TTTAAAAGAATAAAATTTA
1 TTTAAAAGAATAAAATTTA
30336 ATTAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (21 bp):
TTTAAAAGAATAAAATTTACG
Found at i:30343 original size:20 final size:20
Alignment explanation
Indices: 30288--30342 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
30278 AATTTAATTA
* *
30288 AAAAATTAATTTAAATGAAT
1 AAAATTTAATTTAAAAGAAT
*
30308 -AAATTTACGTTTAAAAGAAT
1 AAAATTTA-ATTTAAAAGAAT
30328 AAAATTTAA-TTAAAA
1 AAAATTTAATTTAAAA
30343 ATAATTAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 12 0.41
20 10 0.34
21 7 0.24
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (20 bp):
AAAATTTAATTTAAAAGAAT
Found at i:30432 original size:135 final size:137
Alignment explanation
Indices: 30278--30540 Score: 379
Period size: 135 Copynumber: 1.9 Consensus size: 137
30268 TCGATAATCA
* * **
30278 AATTTAATTAAAAAATTAATTTAAATGAATAAATTTACGTTTAAAAGAATAAAATTTAATT-AAA
1 AATTTAATTAAAAAATTAATATAAAGGAATAAATTTAAATTTAAAAGAATAAAATTTAATTAAAA
* * * *
30342 -AATAATTAAAGAA-ATAAACTAAGTAAAGAAATATTTCAAGAAATAAAAAAAATTTAAAAAATA
66 GAATAATTAAAGAATA-AAACTAAATAAAGAAATATTTAAAGAAACAAAAAAAAATTAAAAAATA
30405 AACCATAG
130 AACCATAG
* *
30413 AATTTAATTAAAATATTAATATAAAGGAATAAATTTAAATTTAAAAGATTAAAATTTAATTAAAA
1 AATTTAATTAAAAAATTAATATAAAGGAATAAATTTAAATTTAAAAGAATAAAATTTAATT--AA
*
30478 AAGAATGATTAAAGAATAAAACTAAATAAAGAAATATTTAAAGAAACAAAAAAAAATTAAAAA
64 AAGAATAATTAAAGAATAAAACTAAATAAAGAAATATTTAAAGAAACAAAAAAAAATTAAAAA
30541 CTTGATTGGC
Statistics
Matches: 112, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
135 55 0.49
138 3 0.03
139 53 0.47
140 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (137 bp):
AATTTAATTAAAAAATTAATATAAAGGAATAAATTTAAATTTAAAAGAATAAAATTTAATTAAAA
GAATAATTAAAGAATAAAACTAAATAAAGAAATATTTAAAGAAACAAAAAAAAATTAAAAAATAA
ACCATAG
Found at i:30473 original size:20 final size:20
Alignment explanation
Indices: 30419--30477 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
30409 ATAGAATTTA
* *
30419 ATTAAAATATTAATATAAAGG
1 ATTAAAAT-TTAATTTAAAAG
*
30440 AAT-AAATTTAAATTTAAAAG
1 ATTAAAATTT-AATTTAAAAG
30460 ATTAAAATTTAA-TTAAAA
1 ATTAAAATTTAATTTAAAA
30478 AAGAATGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
19 8 0.25
20 16 0.50
21 8 0.25
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (20 bp):
ATTAAAATTTAATTTAAAAG
Found at i:31083 original size:25 final size:26
Alignment explanation
Indices: 31032--31093 Score: 108
Period size: 25 Copynumber: 2.4 Consensus size: 26
31022 ATAAAAAATA
31032 ACCAAAATATTATAACTTTTTTTATTT
1 ACCAAAATATTATAAC-TTTTTTATTT
31059 ACCAAAATATTATAA-TTTTTTATTT
1 ACCAAAATATTATAACTTTTTTATTT
31084 ACCAAAATAT
1 ACCAAAATAT
31094 ACCAAAAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 20 0.57
27 15 0.43
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (26 bp):
ACCAAAATATTATAACTTTTTTATTT
Found at i:31184 original size:27 final size:27
Alignment explanation
Indices: 31154--31232 Score: 122
Period size: 27 Copynumber: 2.9 Consensus size: 27
31144 GGCCAATCAC
*
31154 ATTGGCGGCACCAAAGGTGCCAAAGAG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
* *
31181 ATTGGCGGCACCAATGGTGCCAATGTG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
*
31208 ATTGGCAGCACCAATGGTGCCAAAG
1 ATTGGCGGCACCAATGGTGCCAAAG
31233 GACTAAAATG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.29, C:0.23, G:0.32, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGAG
Found at i:31832 original size:41 final size:41
Alignment explanation
Indices: 31786--31867 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
31776 TAATTAAGAT
31786 ACTTAGAATTCTAATTAAGTAATAACTCTATTTTAATTTAA
1 ACTTAGAATTCTAATTAAGTAATAACTCTATTTTAATTTAA
31827 ACTTAGAATTCTAATTAAGTAATAACTCTATTTTAATTTAA
1 ACTTAGAATTCTAATTAAGTAATAACTCTATTTTAATTTAA
31868 TAAACTATTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (41 bp):
ACTTAGAATTCTAATTAAGTAATAACTCTATTTTAATTTAA
Found at i:31853 original size:24 final size:24
Alignment explanation
Indices: 31786--31853 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 24
31776 TAATTAAGAT
31786 ACTTAGAATTCTAATTAAGTAATA
1 ACTTAGAATTCTAATTAAGTAATA
*
31810 ACTCT---ATTTTAATT---T-A-A
1 ACT-TAGAATTCTAATTAAGTAATA
31827 ACTTAGAATTCTAATTAAGTAATA
1 ACTTAGAATTCTAATTAAGTAATA
31851 ACT
1 ACT
31854 CTATTTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 18
0.62 0.04 0.34
Matches are distributed among these distances:
16 1 0.03
17 4 0.12
18 1 0.03
19 9 0.27
22 9 0.27
23 1 0.03
24 7 0.21
25 1 0.03
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (24 bp):
ACTTAGAATTCTAATTAAGTAATA
Found at i:31863 original size:22 final size:22
Alignment explanation
Indices: 31797--31864 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
31787 CTTAGAATTC
31797 TAATTAAGTAATAACTCTATTT
1 TAATTAAGTAATAACTCTATTT
*
31819 TAATT---T-A-AACT-TAGAATTC
1 TAATTAAGTAATAACTCT---ATTT
31838 TAATTAAGTAATAACTCTATTT
1 TAATTAAGTAATAACTCTATTT
31860 TAATT
1 TAATT
31865 TAATAAACTA
Statistics
Matches: 35, Mismatches: 2, Indels: 18
0.64 0.04 0.33
Matches are distributed among these distances:
16 1 0.03
17 4 0.11
18 1 0.03
19 9 0.26
22 14 0.40
23 1 0.03
24 4 0.11
25 1 0.03
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (22 bp):
TAATTAAGTAATAACTCTATTT
Found at i:31870 original size:19 final size:19
Alignment explanation
Indices: 31846--31904 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
31836 TCTAATTAAG
*
31846 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTCATT
* *
31865 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTCATT
31883 TAATAACTCTATTTTCATT
1 TAATAACTCTATTTTCATT
31902 TAA
1 TAA
31905 AATATAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 15 0.44
19 19 0.56
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATAACTCTATTTTCATT
Found at i:32167 original size:18 final size:19
Alignment explanation
Indices: 32134--32193 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
32124 ATTTTTAATC
32134 TAAAATAGAGTTATTAAAT
1 TAAAATAGAGTTATTAAAT
* * *
32153 TAGAATAG-TTTATTATAT
1 TAAAATAGAGTTATTAAAT
32171 TAAAATAGAGTTATTAAAT
1 TAAAATAGAGTTATTAAAT
32190 TAAA
1 TAAA
32194 CTATTTTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 15 0.44
19 19 0.56
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (19 bp):
TAAAATAGAGTTATTAAAT
Done.