Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015109.1 Corchorus olitorius cultivar O-4 contig15142, 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: 85636
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:96 original size:36 final size:36
Alignment explanation
Indices: 8--110 Score: 113
Period size: 36 Copynumber: 2.9 Consensus size: 36
1 TTAGTTT
* * * *
8 TTCAAATCGGGAAAGTTCCCATCAAGTCTTAAAGTC
1 TTCAAATTGGGAAAGTTCCCATCCAGTTTTAAAATC
44 TTCAAATTGGGAAAGTTCCCATCCAGTTTTCAAAAT-
1 TTCAAATTGGGAAAGTTCCCATCCAGTTTT-AAAATC
*
80 TGTCAAATTGGG-AAGTTTCCA-CCAGGTTTTA
1 T-TCAAATTGGGAAAGTTCCCATCCA-GTTTTA
111 GCTTTTTTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
35 4 0.07
36 41 0.69
37 14 0.24
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (36 bp):
TTCAAATTGGGAAAGTTCCCATCCAGTTTTAAAATC
Found at i:2972 original size:7 final size:7
Alignment explanation
Indices: 2960--2985 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2950 CCAAGTTCCT
2960 TTCTTAC
1 TTCTTAC
2967 TTCTTAC
1 TTCTTAC
2974 TTCTTAC
1 TTCTTAC
2981 TTCTT
1 TTCTT
2986 CCTTTTTTGT
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:0.12, C:0.27, G:0.00, T:0.62
Consensus pattern (7 bp):
TTCTTAC
Found at i:7616 original size:19 final size:18
Alignment explanation
Indices: 7583--7618 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7573 TTGAGATAAT
7583 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
7601 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
7619 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:9202 original size:151 final size:151
Alignment explanation
Indices: 9021--9324 Score: 608
Period size: 151 Copynumber: 2.0 Consensus size: 151
9011 AACTCCTACA
9021 AACTCATACACATATTTTCATACTCTTGATATTCTTCATTTTCTCCAGATTCTCTCTTCACAACT
1 AACTCATACACATATTTTCATACTCTTGATATTCTTCATTTTCTCCAGATTCTCTCTTCACAACT
9086 AGCTCACTTCTTCACACCCTCATCTTCTCTCATTCAACAAACAAAAAAATTTCTCTCTTGAGCTG
66 AGCTCACTTCTTCACACCCTCATCTTCTCTCATTCAACAAACAAAAAAATTTCTCTCTTGAGCTG
9151 TCTTTAACACATGATACACAC
131 TCTTTAACACATGATACACAC
9172 AACTCATACACATATTTTCATACTCTTGATATTCTTCATTTTCTCCAGATTCTCTCTTCACAACT
1 AACTCATACACATATTTTCATACTCTTGATATTCTTCATTTTCTCCAGATTCTCTCTTCACAACT
9237 AGCTCACTTCTTCACACCCTCATCTTCTCTCATTCAACAAACAAAAAAATTTCTCTCTTGAGCTG
66 AGCTCACTTCTTCACACCCTCATCTTCTCTCATTCAACAAACAAAAAAATTTCTCTCTTGAGCTG
9302 TCTTTAACACATGATACACAC
131 TCTTTAACACATGATACACAC
9323 AA
1 AA
9325 GAATTGGAGC
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
151 153 1.00
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.36
Consensus pattern (151 bp):
AACTCATACACATATTTTCATACTCTTGATATTCTTCATTTTCTCCAGATTCTCTCTTCACAACT
AGCTCACTTCTTCACACCCTCATCTTCTCTCATTCAACAAACAAAAAAATTTCTCTCTTGAGCTG
TCTTTAACACATGATACACAC
Found at i:12073 original size:18 final size:19
Alignment explanation
Indices: 12039--12074 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
12029 AAATTGCTGT
12039 TGGGCTTTGTCTTTTCTTA
1 TGGGCTTTGTCTTTTCTTA
*
12058 TGGGCTTT-TTTTTTCTT
1 TGGGCTTTGTCTTTTCTT
12075 TCTTTTGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.03, C:0.14, G:0.19, T:0.64
Consensus pattern (19 bp):
TGGGCTTTGTCTTTTCTTA
Found at i:12705 original size:34 final size:34
Alignment explanation
Indices: 12655--12930 Score: 416
Period size: 34 Copynumber: 8.2 Consensus size: 34
12645 AAAATTGAGA
*
12655 AATTAAAAAG-AAAAGTAAATTGGTTAATTTGGT
1 AATTAAAGAGTAAAAGTAAATTGGTTAATTTGGT
*
12688 AATTAAAGAGTAAAAGT-AATTCGGTTAATTTGGA
1 AATTAAAGAGTAAAAGTAAATT-GGTTAATTTGGT
*
12722 AATTAAAAAG-AAAAGTAAATTGGTTAATTTGGT
1 AATTAAAGAGTAAAAGTAAATTGGTTAATTTGGT
* *
12755 AATTAAAGAATAAGAGTAAATTGGTTAATTTGGT
1 AATTAAAGAGTAAAAGTAAATTGGTTAATTTGGT
12789 AATTAAAGAGTAAAAGTAAATTGGTTAATTTGGT
1 AATTAAAGAGTAAAAGTAAATTGGTTAATTTGGT
* *
12823 AATTAAAGAGTAAGAGTAAATTGGTTAATTTGGA
1 AATTAAAGAGTAAAAGTAAATTGGTTAATTTGGT
* *
12857 AATTAAAAAG-AAAAGTAAATTGGTTAATTTAGT
1 AATTAAAGAGTAAAAGTAAATTGGTTAATTTGGT
* *
12890 AATTAAAGAGTAAGAGTAAATTGGTAAATTTGGT
1 AATTAAAGAGTAAAAGTAAATTGGTTAATTTGGT
12924 AATTAAA
1 AATTAAA
12931 AAGAATTTGG
Statistics
Matches: 219, Mismatches: 19, Indels: 9
0.89 0.08 0.04
Matches are distributed among these distances:
33 67 0.31
34 152 0.69
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (34 bp):
AATTAAAGAGTAAAAGTAAATTGGTTAATTTGGT
Found at i:12724 original size:67 final size:67
Alignment explanation
Indices: 12653--12935 Score: 478
Period size: 67 Copynumber: 4.2 Consensus size: 67
12643 CGAAAATTGA
*
12653 GAAATTAAAAAGAAAAGTAAATTGGTTAATTTGGTAATTAAAGAGTAAAAGT-AATTCGGTTAAT
1 GAAATTAAAAAGAAAAGTAAATTGGTTAATTTGGTAATTAAAGAGTAAGAGTAAATT-GGTTAAT
12717 TTG
65 TTG
*
12720 GAAATTAAAAAGAAAAGTAAATTGGTTAATTTGGTAATTAAAGAATAAGAGTAAATTGGTTAATT
1 GAAATTAAAAAGAAAAGTAAATTGGTTAATTTGGTAATTAAAGAGTAAGAGTAAATTGGTTAATT
12785 TG
66 TG
* *
12787 GTAATTAAAGAGTAAAAGTAAATTGGTTAATTTGGTAATTAAAGAGTAAGAGTAAATTGGTTAAT
1 GAAATTAAAAAG-AAAAGTAAATTGGTTAATTTGGTAATTAAAGAGTAAGAGTAAATTGGTTAAT
12852 TTG
65 TTG
* *
12855 GAAATTAAAAAGAAAAGTAAATTGGTTAATTTAGTAATTAAAGAGTAAGAGTAAATTGGTAAATT
1 GAAATTAAAAAGAAAAGTAAATTGGTTAATTTGGTAATTAAAGAGTAAGAGTAAATTGGTTAATT
12920 TG
66 TG
*
12922 GTAATTAAAAAGAA
1 GAAATTAAAAAGAA
12936 TTTGGTAATT
Statistics
Matches: 204, Mismatches: 10, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
67 136 0.67
68 68 0.33
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (67 bp):
GAAATTAAAAAGAAAAGTAAATTGGTTAATTTGGTAATTAAAGAGTAAGAGTAAATTGGTTAATT
TG
Found at i:12829 original size:135 final size:134
Alignment explanation
Indices: 12655--12935 Score: 492
Period size: 135 Copynumber: 2.1 Consensus size: 134
12645 AAAATTGAGA
12655 AATTAAAAAGAAAAGTAAATTGGTTAATTTGGTAATTAAAGAGTAAAAGT-AATTCGGTTAATTT
1 AATTAAAAAGAAAAGTAAATTGGTTAATTTGGTAATTAAAGAGTAAAAGTAAATT-GGTTAATTT
* *
12719 GGAAATTAAAAAGAAAAGTAAATTGGTTAATTTGGTAATTAAAGAATAAGAGTAAATTGGTTAAT
65 GGAAATTAAAAAGAAAAGTAAATTGGTTAATTTAGTAATTAAAGAATAAGAGTAAATTGGTAAAT
12784 TTGGT
130 TTGGT
* *
12789 AATTAAAGAGTAAAAGTAAATTGGTTAATTTGGTAATTAAAGAGTAAGAGTAAATTGGTTAATTT
1 AATTAAAAAG-AAAAGTAAATTGGTTAATTTGGTAATTAAAGAGTAAAAGTAAATTGGTTAATTT
*
12854 GGAAATTAAAAAGAAAAGTAAATTGGTTAATTTAGTAATTAAAGAGTAAGAGTAAATTGGTAAAT
65 GGAAATTAAAAAGAAAAGTAAATTGGTTAATTTAGTAATTAAAGAATAAGAGTAAATTGGTAAAT
12919 TTGGT
130 TTGGT
12924 AATTAAAAAGAA
1 AATTAAAAAGAA
12936 TTTGGTAATT
Statistics
Matches: 139, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
134 11 0.08
135 124 0.89
136 4 0.03
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (134 bp):
AATTAAAAAGAAAAGTAAATTGGTTAATTTGGTAATTAAAGAGTAAAAGTAAATTGGTTAATTTG
GAAATTAAAAAGAAAAGTAAATTGGTTAATTTAGTAATTAAAGAATAAGAGTAAATTGGTAAATT
TGGT
Found at i:12939 original size:18 final size:18
Alignment explanation
Indices: 12916--13130 Score: 124
Period size: 18 Copynumber: 11.8 Consensus size: 18
12906 TAAATTGGTA
12916 AATTTGGTAATTAAAAAG
1 AATTTGGTAATTAAAAAG
*
12934 AATTTGGTAATTAAAGAG
1 AATTTGGTAATTAAAAAG
* ***
12952 TAA---AGTAACTT-GGTA-
1 -AATTTGGTAA-TTAAAAAG
*
12967 AATTTGGTCATTAAAAAG
1 AATTTGGTAATTAAAAAG
*
12985 AATTTGGTAATTAAAGAG
1 AATTTGGTAATTAAAAAG
** ***
13003 TAA--AAGTAAATTGGTAA-
1 -AATTTGGT-AATTAAAAAG
13020 -ATTTGGTAATTAAAAAG
1 AATTTGGTAATTAAAAAG
13037 AATTTGGTAATTAAAAAG
1 AATTTGGTAATTAAAAAG
* *
13055 AACTTAGTAATTAAAGAGTAAAAG
1 AATTTGGTAATT----A--AAAAG
*
13079 TAAATTGGTAATTAAAAAG
1 -AATTTGGTAATTAAAAAG
13098 AATTTGGTAATTAAAAAG
1 AATTTGGTAATTAAAAAG
*
13116 AACTTGGTAATTAAA
1 AATTTGGTAATTAAA
13131 GAGTAAAAGT
Statistics
Matches: 148, Mismatches: 29, Indels: 40
0.68 0.13 0.18
Matches are distributed among these distances:
14 2 0.01
15 1 0.01
16 13 0.09
17 10 0.07
18 96 0.65
19 9 0.06
21 1 0.01
22 1 0.01
24 5 0.03
25 10 0.07
ACGTcount: A:0.48, C:0.02, G:0.18, T:0.32
Consensus pattern (18 bp):
AATTTGGTAATTAAAAAG
Found at i:12980 original size:51 final size:51
Alignment explanation
Indices: 12882--13051 Score: 295
Period size: 52 Copynumber: 3.3 Consensus size: 51
12872 TAAATTGGTT
*
12882 AATTTAGTAATTAAAGAGTAAGAGTAAATTGGTAAATTTGGTAATTAAAAAG
1 AATTTGGTAATTAAAGAGTAA-AGTAAATTGGTAAATTTGGTAATTAAAAAG
* *
12934 AATTTGGTAATTAAAGAGTAAAGTAACTTGGTAAATTTGGTCATTAAAAAG
1 AATTTGGTAATTAAAGAGTAAAGTAAATTGGTAAATTTGGTAATTAAAAAG
12985 AATTTGGTAATTAAAGAGTAAAAGTAAATTGGTAAATTTGGTAATTAAAAAG
1 AATTTGGTAATTAAAGAGT-AAAGTAAATTGGTAAATTTGGTAATTAAAAAG
13037 AATTTGGTAATTAAA
1 AATTTGGTAATTAAA
13052 AAGAACTTAG
Statistics
Matches: 112, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
51 47 0.42
52 65 0.58
ACGTcount: A:0.46, C:0.01, G:0.19, T:0.34
Consensus pattern (51 bp):
AATTTGGTAATTAAAGAGTAAAGTAAATTGGTAAATTTGGTAATTAAAAAG
Found at i:12991 original size:27 final size:26
Alignment explanation
Indices: 12961--13046 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 26
12951 GTAAAGTAAC
12961 TTGGTAAATTTGGTCATTAAAAAGAAT
1 TTGGTAAATTTGGT-ATTAAAAAGAAT
** * *
12988 TTGGT-AATTAAAG-AGT-AAAAGTAAA
1 TTGGTAAATT-TGGTATTAAAAAG-AAT
13013 TTGGTAAATTTGGTAATTAAAAAGAAT
1 TTGGTAAATTTGGT-ATTAAAAAGAAT
13040 TTGGTAA
1 TTGGTAA
13047 TTAAAAAGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
24 5 0.11
25 10 0.22
26 8 0.18
27 17 0.38
28 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.20, T:0.35
Consensus pattern (26 bp):
TTGGTAAATTTGGTATTAAAAAGAAT
Found at i:13052 original size:70 final size:70
Alignment explanation
Indices: 12967--13182 Score: 315
Period size: 70 Copynumber: 3.2 Consensus size: 70
12957 TAACTTGGTA
* *
12967 AATTTGGTCATTAAAAAGAATTTGGTAATTAAAGAGTAAAAGTAAATTGGTAAATTTGGTAATTA
1 AATTTGGTAATTAAAAAGAACTTGGTAATTAAAGAGTAAAAGTAAATTGGTAAATTTGGTAATTA
13032 AAAAG
66 AAAAG
*
13037 AATTTGGTAATTAAAAAGAACTTAGTAATTAAAGAGT---A--AAA---GTAAA-TTGGTAATTA
1 AATTTGGTAATTAAAAAGAACTTGGTAATTAAAGAGTAAAAGTAAATTGGTAAATTTGGTAATTA
13093 AAAAG
66 AAAAG
*
13098 AATTTGGTAATTAAAAAGAACTTGGTAATTAAAGAGTAAAAGTAAATTGGTTAATTTGGTAATTA
1 AATTTGGTAATTAAAAAGAACTTGGTAATTAAAGAGTAAAAGTAAATTGGTAAATTTGGTAATTA
*
13163 AAATG
66 AAAAG
*
13168 AAATTGGTAATTAAA
1 AATTTGGTAATTAAA
13183 GAGTAAAAGG
Statistics
Matches: 130, Mismatches: 7, Indels: 18
0.84 0.05 0.12
Matches are distributed among these distances:
61 51 0.39
62 5 0.04
64 1 0.01
65 3 0.02
66 3 0.02
67 1 0.01
69 4 0.03
70 62 0.48
ACGTcount: A:0.49, C:0.01, G:0.18, T:0.32
Consensus pattern (70 bp):
AATTTGGTAATTAAAAAGAACTTGGTAATTAAAGAGTAAAAGTAAATTGGTAAATTTGGTAATTA
AAAAG
Found at i:13077 original size:43 final size:43
Alignment explanation
Indices: 13032--13112 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
13022 TTGGTAATTA
*
13032 AAAAG-AATTTGGTAATTAAAAAGAACTTAGTAATTAAAGAGT
1 AAAAGTAAATTGGTAATTAAAAAGAACTTAGTAATTAAAGAGT
* *
13074 AAAAGTAAATTGGTAATTAAAAAGAATTTGGTAATTAAA
1 AAAAGTAAATTGGTAATTAAAAAGAACTTAGTAATTAAA
13113 AAGAACTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 5 0.14
43 30 0.86
ACGTcount: A:0.53, C:0.01, G:0.16, T:0.30
Consensus pattern (43 bp):
AAAAGTAAATTGGTAATTAAAAAGAACTTAGTAATTAAAGAGT
Found at i:13087 original size:61 final size:61
Alignment explanation
Indices: 13016--13153 Score: 249
Period size: 61 Copynumber: 2.2 Consensus size: 61
13006 AAGTAAATTG
13016 GTAAATTTGGTAATTAAAAAGAATTTGGTAATTAAAAAGAACTTAGTAATTAAAGAGTAAAA
1 GTAAA-TTGGTAATTAAAAAGAATTTGGTAATTAAAAAGAACTTAGTAATTAAAGAGTAAAA
*
13078 GTAAATTGGTAATTAAAAAGAATTTGGTAATTAAAAAGAACTTGGTAATTAAAGAGTAAAA
1 GTAAATTGGTAATTAAAAAGAATTTGGTAATTAAAAAGAACTTAGTAATTAAAGAGTAAAA
13139 GTAAATTGGTTAATT
1 GTAAATTGG-TAATT
13154 TGGTAATTAA
Statistics
Matches: 74, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
61 64 0.86
62 10 0.14
ACGTcount: A:0.49, C:0.01, G:0.17, T:0.32
Consensus pattern (61 bp):
GTAAATTGGTAATTAAAAAGAATTTGGTAATTAAAAAGAACTTAGTAATTAAAGAGTAAAA
Found at i:13159 original size:52 final size:52
Alignment explanation
Indices: 13098--13220 Score: 194
Period size: 52 Copynumber: 2.3 Consensus size: 52
13088 AATTAAAAAG
* *
13098 AATTTGGTAATTAAAAAGAACTTGGTAATTAAAGAGTAAAA-GTAAATTGGTT
1 AATTTGGTAATTAAAAAGAAATTGGTAATTAAAGAGTAAAAGGT-AATTGGTA
*
13150 AATTTGGTAATTAAAATGAAATTGGTAATTAAAGAGTAAAAGGTAATTGGTA
1 AATTTGGTAATTAAAAAGAAATTGGTAATTAAAGAGTAAAAGGTAATTGGTA
13202 AATTTGGATAATTAAAAAG
1 AATTTGG-TAATTAAAAAG
13221 TAAAATGAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
52 53 0.82
53 12 0.18
ACGTcount: A:0.47, C:0.01, G:0.20, T:0.33
Consensus pattern (52 bp):
AATTTGGTAATTAAAAAGAAATTGGTAATTAAAGAGTAAAAGGTAATTGGTA
Found at i:13197 original size:25 final size:24
Alignment explanation
Indices: 13111--13202 Score: 71
Period size: 25 Copynumber: 3.6 Consensus size: 24
13101 TTGGTAATTA
13111 AAAAG-AACTTGGTAATTAAAGAGT
1 AAAAGTAA-TTGGTAATTAAAGAGT
** *
13135 AAAAGTAAATTGGTTAATT-TGGTAATT
1 AAAAGT-AATTGG-TAATTAAAG--AGT
*
13162 AAAATGAAATTGGTAATTAAAGAGT
1 AAAA-GTAATTGGTAATTAAAGAGT
13187 AAAAGGTAATTGGTAA
1 AAAA-GTAATTGGTAA
13203 ATTTGGATAA
Statistics
Matches: 52, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
24 5 0.10
25 21 0.40
26 12 0.23
27 13 0.25
28 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.21, T:0.30
Consensus pattern (24 bp):
AAAAGTAATTGGTAATTAAAGAGT
Found at i:13238 original size:131 final size:128
Alignment explanation
Indices: 12976--13240 Score: 293
Period size: 131 Copynumber: 2.0 Consensus size: 128
12966 AAATTTGGTC
* *
12976 ATTAAAAAGAATTTGGTAATTAAAGAGTAAAAGTAAATTGGTAAATTTGGTAATTAAAAAGAATT
1 ATTAAAAAGAACTTGGTAATTAAAGAGTAAAAGTAAATTGGTAAATTTGGTAATTAAAAAGAAAT
* * *** * **
13041 TGGTAATTAAAAAGAACTTAGTAATTAAAGAGTAAAAGTAAATTGGTAATTAAAAAGAATTTGGT
66 TGGTAATTAAAAAGAAC-AAGTAATT--AGAGTAAAAGGAAATTAAAAAGTAAAAAGAATAGGGT
13106 A
128 A
* *
13107 ATTAAAAAGAACTTGGTAATTAAAGAGTAAAAGTAAATTGGTTAATTTGGTAATTAAAATGAAAT
1 ATTAAAAAGAACTTGGTAATTAAAGAGTAAAAGTAAATTGGTAAATTTGGTAATTAAAAAGAAAT
* * *
13172 TGGTAATTAAAGAGTAA-AAGGTAATT-G-GTAAATTTGGATAATTAAAAAGTAAAATGAAATAG
66 TGGTAATTAAAAAG-AACAA-GTAATTAGAGTAAA--AGGA-AATTAAAAAGTAAAAAG-AATAG
13234 GGTA
125 GGTA
13238 ATT
1 ATT
13241 GGTAAATTTG
Statistics
Matches: 113, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
127 5 0.04
128 1 0.01
129 2 0.02
130 13 0.12
131 90 0.80
132 2 0.02
ACGTcount: A:0.49, C:0.01, G:0.18, T:0.31
Consensus pattern (128 bp):
ATTAAAAAGAACTTGGTAATTAAAGAGTAAAAGTAAATTGGTAAATTTGGTAATTAAAAAGAAAT
TGGTAATTAAAAAGAACAAGTAATTAGAGTAAAAGGAAATTAAAAAGTAAAAAGAATAGGGTA
Found at i:17019 original size:44 final size:44
Alignment explanation
Indices: 16701--17392 Score: 227
Period size: 49 Copynumber: 15.0 Consensus size: 44
16691 AAAACCAATA
* * *
16701 TGAAAACTCGAAAGACCCGTTATGAGGTCGGCTTTTAAAACTGC
1 TGAAAACTGGAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGC
** * * ** * *
16745 TGAAGTCTGACAAAAGATGACCTGTTCTGAGGCCAACTTTGATAACTGC
1 TGAAAACTG---GAA-A-GACCTGTTCTGAGGTCGGCTTTTAAAACTGC
* *
16794 TGAAAAGTAGAAAAGA-C----CTGAGGTCGGCTTTTAAAACTGC
1 TGAAAACT-GGAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGC
* * * ** * *
16834 T-AAAGTCTGAGAAAAGATGACCTGTTCTAAGGCCAACTTTGATAACTGC
1 TGAAA-ACTG-G--AA-A-GACCTGTTCTGAGGTCGGCTTTTAAAACTGC
* * *
16883 TGAAAATTGGAAAAGACCTGTTCCGAGGTCGACTTTTAAAACTGC
1 TGAAAACTGG-AAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGC
* * * ** * * *
16928 T-AAAGTCTGAGAAAAGATGGCCTGTCCTGAGGCCAACTTTGACAACTGT
1 TGAAA-ACTG-G-AAAGA---CCTGTTCTGAGGTCGGCTTTTAAAACTGC
*
16977 TGAAAACTGGAAAGACCTATTCTGAGGTCGGCTTTTAAAACTGC
1 TGAAAACTGGAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGC
* * ** * *
17021 T-AAAGTCTGAGAAAAGATGACCTGTTCTGAGGCCAACTTTGATAACTGC
1 TGAAA-ACTG-G--AA-A-GACCTGTTCTGAGGTCGGCTTTTAAAACTGC
*
17070 TGAAAAATGGAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGC
1 TGAAAACTGGAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGC
* ** * * * ** * * * **
17114 T-AAAGTCTGAGAAAAGATGAATTGTTTTCAGGCCAACTATGATAACTAT
1 TGAAA-ACTG-G--AA-A-GACCTGTTCTGAGGTCGGCTTTTAAAACTGC
* *
17163 TGAAAACTGGGAAAGACCCGTTCTAAGGTCGGCTTTTAAAACTGC
1 TGAAAACT-GGAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGC
* * *** * * * *
17208 T-AAAATCTGAGAAAAGATGACCTGTTTTGAGGCCAAATCTGATAACTGT
1 TGAAAA-CTG-G--AA-A-GACCTGTTCTGAGGTCGGCTTTTAAAACTGC
* * *
17257 TGAAAACTGGAAGGACCTGTTCTGAGGTCGACTTATAAAACTGC
1 TGAAAACTGGAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGC
* * ** **
17301 T-AAAATCTAAGAAAAGATGACCTGTTCTGAGGCCAACTTCGAAAACTGC
1 TGAAAA-CT--G-GAA-A-GACCTGTTCTGAGGTCGGCTTTTAAAACTGC
* * *
17350 TGAAGACTGAGAAAGACCTGCTCTGAGGTCGACTTTTAAAACT
1 TGAAAACTG-GAAAGACCTGTTCTGAGGTCGGCTTTTAAAACT
17393 TCTAAATCTG
Statistics
Matches: 465, Mismatches: 130, Indels: 105
0.66 0.19 0.15
Matches are distributed among these distances:
39 4 0.01
40 20 0.04
42 2 0.00
43 11 0.02
44 96 0.21
45 80 0.17
46 16 0.03
47 27 0.06
48 8 0.02
49 180 0.39
50 21 0.05
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (44 bp):
TGAAAACTGGAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGC
Found at i:17045 original size:93 final size:93
Alignment explanation
Indices: 16701--17416 Score: 976
Period size: 93 Copynumber: 7.7 Consensus size: 93
16691 AAAACCAATA
* * * * *
16701 TGAAAACTCGAAAGACCCGTTATGAGGTCGGCTTTTAAAACTGCTGAAGTCTGACAAAAGATGAC
1 TGAAAACTGGAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGCTAAAGTCTGAGAAAAGATGAC
16766 CTGTTCTGAGGCCAACTTTGATAACTGC
66 CTGTTCTGAGGCCAACTTTGATAACTGC
* *
16794 TGAAAAGTAGAAAAGA-C----CTGAGGTCGGCTTTTAAAACTGCTAAAGTCTGAGAAAAGATGA
1 TGAAAACT-GGAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGCTAAAGTCTGAGAAAAGATGA
*
16854 CCTGTTCTAAGGCCAACTTTGATAACTGC
65 CCTGTTCTGAGGCCAACTTTGATAACTGC
* * * *
16883 TGAAAATTGGAAAAGACCTGTTCCGAGGTCGACTTTTAAAACTGCTAAAGTCTGAGAAAAGATGG
1 TGAAAACTGG-AAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGCTAAAGTCTGAGAAAAGATGA
* * *
16948 CCTGTCCTGAGGCCAACTTTGACAACTGT
65 CCTGTTCTGAGGCCAACTTTGATAACTGC
*
16977 TGAAAACTGGAAAGACCTATTCTGAGGTCGGCTTTTAAAACTGCTAAAGTCTGAGAAAAGATGAC
1 TGAAAACTGGAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGCTAAAGTCTGAGAAAAGATGAC
17042 CTGTTCTGAGGCCAACTTTGATAACTGC
66 CTGTTCTGAGGCCAACTTTGATAACTGC
* *
17070 TGAAAAATGGAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGCTAAAGTCTGAGAAAAGATGAA
1 TGAAAACTGGAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGCTAAAGTCTGAGAAAAGATGAC
* * * * **
17135 TTGTTTTCAGGCCAACTATGATAACTAT
66 CTGTTCTGAGGCCAACTTTGATAACTGC
* * *
17163 TGAAAACTGGGAAAGACCCGTTCTAAGGTCGGCTTTTAAAACTGCTAAAATCTGAGAAAAGATGA
1 TGAAAACT-GGAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGCTAAAGTCTGAGAAAAGATGA
* * * *
17228 CCTGTTTTGAGGCCAAATCTGATAACTGT
65 CCTGTTCTGAGGCCAACTTTGATAACTGC
* * * * *
17257 TGAAAACTGGAAGGACCTGTTCTGAGGTCGACTTATAAAACTGCTAAAATCTAAGAAAAGATGAC
1 TGAAAACTGGAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGCTAAAGTCTGAGAAAAGATGAC
* *
17322 CTGTTCTGAGGCCAACTTCGAAAACTGC
66 CTGTTCTGAGGCCAACTTTGATAACTGC
* * * *
17350 TGAAGACTGAGAAAGACCTGCTCTGAGGTCGACTTTTAAAACTTCTAAA-TCTGAGAAAAGATGA
1 TGAAAACTG-GAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGCTAAAGTCTGAGAAAAGATGA
17414 CCT
65 CCT
17417 ATTTCAAGTC
Statistics
Matches: 553, Mismatches: 61, Indels: 18
0.88 0.10 0.03
Matches are distributed among these distances:
88 1 0.00
89 80 0.14
90 1 0.00
93 273 0.49
94 198 0.36
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (93 bp):
TGAAAACTGGAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGCTAAAGTCTGAGAAAAGATGAC
CTGTTCTGAGGCCAACTTTGATAACTGC
Found at i:17058 original size:187 final size:187
Alignment explanation
Indices: 16701--17416 Score: 962
Period size: 187 Copynumber: 3.9 Consensus size: 187
16691 AAAACCAATA
* * * * * * *
16701 TGAAAACTCGAAAGACCCGTTATGAGGTCGGCTTTTAAAACTGCTGAAGTCTGACAAAAGATGAC
1 TGAAAAATGGAAAGACCTGTTCTGAGGTCGACTTTTAAAACTGCTAAAGTCTGAGAAAAGATGAC
* *
16766 CTGTTCTGAGGCCAACTTTGATAACTGCTGAAAAGTAGAAAAGA-C----CTGAGGTCGGCTTTT
66 CTGTTCTGAGGCCAACTTTGATAACTGCTGAAAACTAGGAAAGACCTGTTCTGAGGTCGGCTTTT
*
16826 AAAACTGCTAAAGTCTGAGAAAAGATGACCTGTTCTAAGGCCAACTTTGATAACTGC
131 AAAACTGCTAAAGTCTGAGAAAAGATGACCTGTTCTGAGGCCAACTTTGATAACTGC
* * *
16883 TGAAAATTGGAAAAGACCTGTTCCGAGGTCGACTTTTAAAACTGCTAAAGTCTGAGAAAAGATGG
1 TGAAAAATGG-AAAGACCTGTTCTGAGGTCGACTTTTAAAACTGCTAAAGTCTGAGAAAAGATGA
* * * *
16948 CCTGTCCTGAGGCCAACTTTGACAACTGTTGAAAACT-GGAAAGACCTATTCTGAGGTCGGCTTT
65 CCTGTTCTGAGGCCAACTTTGATAACTGCTGAAAACTAGGAAAGACCTGTTCTGAGGTCGGCTTT
17012 TAAAACTGCTAAAGTCTGAGAAAAGATGACCTGTTCTGAGGCCAACTTTGATAACTGC
130 TAAAACTGCTAAAGTCTGAGAAAAGATGACCTGTTCTGAGGCCAACTTTGATAACTGC
* *
17070 TGAAAAATGGAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGCTAAAGTCTGAGAAAAGATGAA
1 TGAAAAATGGAAAGACCTGTTCTGAGGTCGACTTTTAAAACTGCTAAAGTCTGAGAAAAGATGAC
* * * * ** * * *
17135 TTGTTTTCAGGCCAACTATGATAACTATTGAAAACTGGGAAAGACCCGTTCTAAGGTCGGCTTTT
66 CTGTTCTGAGGCCAACTTTGATAACTGCTGAAAACTAGGAAAGACCTGTTCTGAGGTCGGCTTTT
* * * * *
17200 AAAACTGCTAAAATCTGAGAAAAGATGACCTGTTTTGAGGCCAAATCTGATAACTGT
131 AAAACTGCTAAAGTCTGAGAAAAGATGACCTGTTCTGAGGCCAACTTTGATAACTGC
* * * * *
17257 TGAAAACTGGAAGGACCTGTTCTGAGGTCGACTTATAAAACTGCTAAAATCTAAGAAAAGATGAC
1 TGAAAAATGGAAAGACCTGTTCTGAGGTCGACTTTTAAAACTGCTAAAGTCTGAGAAAAGATGAC
* * * * *
17322 CTGTTCTGAGGCCAACTTCGAAAACTGCTGAAGACT-GAGAAAGACCTGCTCTGAGGTCGACTTT
66 CTGTTCTGAGGCCAACTTTGATAACTGCTGAAAACTAG-GAAAGACCTGTTCTGAGGTCGGCTTT
*
17386 TAAAACTTCTAAA-TCTGAGAAAAGATGACCT
130 TAAAACTGCTAAAGTCTGAGAAAAGATGACCT
17417 ATTTCAAGTC
Statistics
Matches: 470, Mismatches: 56, Indels: 12
0.87 0.10 0.02
Matches are distributed among these distances:
182 14 0.03
183 81 0.17
186 99 0.21
187 276 0.59
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (187 bp):
TGAAAAATGGAAAGACCTGTTCTGAGGTCGACTTTTAAAACTGCTAAAGTCTGAGAAAAGATGAC
CTGTTCTGAGGCCAACTTTGATAACTGCTGAAAACTAGGAAAGACCTGTTCTGAGGTCGGCTTTT
AAAACTGCTAAAGTCTGAGAAAAGATGACCTGTTCTGAGGCCAACTTTGATAACTGC
Found at i:17219 original size:280 final size:279
Alignment explanation
Indices: 16701--17413 Score: 1004
Period size: 280 Copynumber: 2.6 Consensus size: 279
16691 AAAACCAATA
* * * * *
16701 TGAAAACTCGAAAGACCCGTTATGAGGTCGGCTTTTAAAACTGCTGAAGTCTGACAAAAGATGAC
1 TGAAAACTGGAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGCTAAAGTCTGAGAAAAGATGAC
* *
16766 CTGTTCTGAGGCCAACTTTGATAACTGCTGAAAAGTAGAAAAGA-C---CTGAGGTCGGCTTTTA
66 CTGTTCTGAGGCCAACTTTGATAACTGCTGAAAAAT-GGAAAGACCTGTCTGAGGTCGGCTTTTA
* * * *
16827 AAACTGCTAAAGTCTGAGAAAAGATGACCTGTTCTAAGGCCAACTTTGATAACTGCTGAAAATTG
130 AAACTGCTAAAGTCTGAGAAAAGATGAACTGTTCTAAGGCCAACTATGATAACTACTGAAAACTG
* * * *
16892 GAAAAGACCTGTTCCGAGGTCGACTTTTAAAACTGCTAAAGTCTGAGAAAAGATGGCCTGTCCTG
195 GAAAAGACCCGTTCCAAGGTCGACTTTTAAAACTGCTAAAATCTGAGAAAAGATGACCTGTCCTG
* *
16957 AGGCCAACTTTGACAACTGT
260 AGGCCAAATCTGACAACTGT
*
16977 TGAAAACTGGAAAGACCTATTCTGAGGTCGGCTTTTAAAACTGCTAAAGTCTGAGAAAAGATGAC
1 TGAAAACTGGAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGCTAAAGTCTGAGAAAAGATGAC
17042 CTGTTCTGAGGCCAACTTTGATAACTGCTGAAAAATGGAAAGACCTGTTCTGAGGTCGGCTTTTA
66 CTGTTCTGAGGCCAACTTTGATAACTGCTGAAAAATGGAAAGACCTG-TCTGAGGTCGGCTTTTA
* * * *
17107 AAACTGCTAAAGTCTGAGAAAAGATGAATTGTTTTCAGGCCAACTATGATAACTATTGAAAACTG
130 AAACTGCTAAAGTCTGAGAAAAGATGAACTGTTCTAAGGCCAACTATGATAACTACTGAAAACTG
* * * **
17172 GGAAAGACCCGTTCTAAGGTCGGCTTTTAAAACTGCTAAAATCTGAGAAAAGATGACCTGTTTTG
195 GAAAAGACCCGTTCCAAGGTCGACTTTTAAAACTGCTAAAATCTGAGAAAAGATGACCTGTCCTG
*
17237 AGGCCAAATCTGATAACTGT
260 AGGCCAAATCTGACAACTGT
* * * * *
17257 TGAAAACTGGAAGGACCTGTTCTGAGGTCGACTTATAAAACTGCTAAAATCTAAGAAAAGATGAC
1 TGAAAACTGGAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGCTAAAGTCTGAGAAAAGATGAC
* * * * *
17322 CTGTTCTGAGGCCAACTTCGAAAACTGCTGAAGACTGAGAAAGACCTGCTCTGAGGTCGACTTTT
66 CTGTTCTGAGGCCAACTTTGATAACTGCTGAAAAATG-GAAAGACCTG-TCTGAGGTCGGCTTTT
*
17387 AAAACTTCTAAA-TCTGAGAAAAGATGA
129 AAAACTGCTAAAGTCTGAGAAAAGATGA
17414 CCTATTTCAA
Statistics
Matches: 390, Mismatches: 41, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
275 6 0.02
276 95 0.24
280 253 0.65
281 36 0.09
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (279 bp):
TGAAAACTGGAAAGACCTGTTCTGAGGTCGGCTTTTAAAACTGCTAAAGTCTGAGAAAAGATGAC
CTGTTCTGAGGCCAACTTTGATAACTGCTGAAAAATGGAAAGACCTGTCTGAGGTCGGCTTTTAA
AACTGCTAAAGTCTGAGAAAAGATGAACTGTTCTAAGGCCAACTATGATAACTACTGAAAACTGG
AAAAGACCCGTTCCAAGGTCGACTTTTAAAACTGCTAAAATCTGAGAAAAGATGACCTGTCCTGA
GGCCAAATCTGACAACTGT
Found at i:17363 original size:49 final size:49
Alignment explanation
Indices: 17200--17416 Score: 172
Period size: 49 Copynumber: 4.6 Consensus size: 49
17190 GTCGGCTTTT
* *
17200 AAAACTGCTAAAATCTGAGAAAAGATGACCTGTTTTGAGGCCAA-ATCTG
1 AAAACTGCTAAAATCTGAGAAAAGATGACCTGTTCTGAGGCCAACTTC-G
* * * * **
17249 ATAACTGTTGAAAA-CTG-G--AAG--GACCTGTTCTGAGGTCGACTTAT
1 AAAACTGCT-AAAATCTGAGAAAAGATGACCTGTTCTGAGGCCAACTTCG
*
17293 AAAACTGCTAAAATCTAAGAAAAGATGACCTGTTCTGAGGCCAACTTCG
1 AAAACTGCTAAAATCTGAGAAAAGATGACCTGTTCTGAGGCCAACTTCG
* * * * **
17342 AAAACTGCTGAAGA-CTGAG--AA-A-GACCTGCTCTGAGGTCGACTTTT
1 AAAACTGCT-AAAATCTGAGAAAAGATGACCTGTTCTGAGGCCAACTTCG
*
17387 AAAACTTCT-AAATCTGAGAAAAGATGACCT
1 AAAACTGCTAAAATCTGAGAAAAGATGACCT
17417 ATTTCAAGTC
Statistics
Matches: 130, Mismatches: 24, Indels: 29
0.71 0.13 0.16
Matches are distributed among these distances:
43 6 0.05
44 29 0.22
45 28 0.22
46 6 0.05
47 6 0.05
48 6 0.05
49 42 0.32
50 7 0.05
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (49 bp):
AAAACTGCTAAAATCTGAGAAAAGATGACCTGTTCTGAGGCCAACTTCG
Found at i:17520 original size:38 final size:37
Alignment explanation
Indices: 17406--17703 Score: 343
Period size: 38 Copynumber: 7.9 Consensus size: 37
17396 AAATCTGAGA
* *
17406 AAAGATGACCTATTTCAAGTCGACTTTGATAATTGCTG
1 AAAGATGACCTGTTTCAAGTCAACTTTGATAATT-CTG
* ** *
17444 AAAGATGACATGTTTCCAA-T-AGA--AAGATAATTGTTG
1 AAAGATGACCTGTTT-CAAGTCA-ACTTTGATAATT-CTG
*
17480 AAAGATGACCTGTTTCAAGTCAAGTTTGATAATTCTTG
1 AAAGATGACCTGTTTCAAGTCAACTTTGATAATTC-TG
*
17518 AAAGATGACCTGTTTCCAGTCAACTTTGATAATTTCTG
1 AAAGATGACCTGTTTCAAGTCAACTTTGATAA-TTCTG
* *
17556 AAAGATAACCTGTTTCTAGTCAACTTTGATAATGTCTG
1 AAAGATGACCTGTTTCAAGTCAACTTTGATAAT-TCTG
* * *
17594 AAAGATGATCTGTTTCCAGTCAACTTTGATAACGTCTG
1 AAAGATGACCTGTTTCAAGTCAACTTTGATAA-TTCTG
*
17632 AAAGATGACCTGTTTCAAGTCAACTTTGATAATGTCTA
1 AAAGATGACCTGTTTCAAGTCAACTTTGATAAT-TCTG
* *
17670 AAAAATGACCTGTTTCCAGTCAACTTTGATAATT
1 AAAGATGACCTGTTTCAAGTCAACTTTGATAATT
17704 TTTTTGAGTT
Statistics
Matches: 225, Mismatches: 24, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
35 3 0.01
36 26 0.12
37 3 0.01
38 187 0.83
39 6 0.03
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (37 bp):
AAAGATGACCTGTTTCAAGTCAACTTTGATAATTCTG
Found at i:17577 original size:76 final size:76
Alignment explanation
Indices: 17406--17704 Score: 394
Period size: 76 Copynumber: 4.0 Consensus size: 76
17396 AAATCTGAGA
* * * *
17406 AAAGATGACCTATTTCAAGTCGACTTTGATAAT-TGCTGAAAGATGACATGTTTCCAAT-AGA--
1 AAAGATGACCTGTTTCAAGTCAACTTTGATAATGT-CTGAAAGATGACCTGTTTCCAGTCA-ACT
**
17467 AAGATAATTGT-TG
64 TTGATAATT-TCTG
*
17480 AAAGATGACCTGTTTCAAGTCAAGTTTGATAAT-TCTTGAAAGATGACCTGTTTCCAGTCAACTT
1 AAAGATGACCTGTTTCAAGTCAACTTTGATAATGTC-TGAAAGATGACCTGTTTCCAGTCAACTT
17544 TGATAATTTCTG
65 TGATAATTTCTG
* * *
17556 AAAGATAACCTGTTTCTAGTCAACTTTGATAATGTCTGAAAGATGATCTGTTTCCAGTCAACTTT
1 AAAGATGACCTGTTTCAAGTCAACTTTGATAATGTCTGAAAGATGACCTGTTTCCAGTCAACTTT
**
17621 GATAACGTCTG
66 GATAATTTCTG
* *
17632 AAAGATGACCTGTTTCAAGTCAACTTTGATAATGTCTAAAAAATGACCTGTTTCCAGTCAACTTT
1 AAAGATGACCTGTTTCAAGTCAACTTTGATAATGTCTGAAAGATGACCTGTTTCCAGTCAACTTT
17697 GATAATTT
66 GATAATTT
17705 TTTTGAGTTT
Statistics
Matches: 199, Mismatches: 20, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
73 1 0.01
74 52 0.26
75 2 0.01
76 142 0.71
77 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (76 bp):
AAAGATGACCTGTTTCAAGTCAACTTTGATAATGTCTGAAAGATGACCTGTTTCCAGTCAACTTT
GATAATTTCTG
Found at i:17815 original size:27 final size:27
Alignment explanation
Indices: 17785--17862 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
17775 TGGTCAAAAC
* *
17785 TGAATGAGGCCAGTATGTGGCCGATGT
1 TGAAAGAGGCCAGTCTGTGGCCGATGT
* * *
17812 TGAAAGAGACCAATCTGTGGTCGATGT
1 TGAAAGAGGCCAGTCTGTGGCCGATGT
* *
17839 TGAAGGAGGCCAGTCCGTGGCCGA
1 TGAAAGAGGCCAGTCTGTGGCCGA
17863 CATTGACGCT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (27 bp):
TGAAAGAGGCCAGTCTGTGGCCGATGT
Found at i:17965 original size:62 final size:62
Alignment explanation
Indices: 17813--17967 Score: 197
Period size: 62 Copynumber: 2.5 Consensus size: 62
17803 GGCCGATGTT
* * * *
17813 GAAAGAGACCAA-TCTGTGGTCGATGTTGAAGGAGGCCAGTCCGTGGCCGACATTGACGCTTG
1 GAAAGAGACCAATTC-GTGGTAGATATTGAAGGAGGCCAGTCCGTGGCCGACATAGACACTTG
* * * *
17875 GAAAGAGATCAATCCGTGGTTA-ACATTGAAGGAGGCCAGTCCGTGGCCGACATAGATACTTG
1 GAAAGAGACCAATTCGTGG-TAGATATTGAAGGAGGCCAGTCCGTGGCCGACATAGACACTTG
*
17937 GGAAGAGACCAATTCGTGGTAGATATTGAAG
1 GAAAGAGACCAATTCGTGGTAGATATTGAAG
17968 TAAACTCGTC
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
61 2 0.03
62 74 0.95
63 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.32, T:0.21
Consensus pattern (62 bp):
GAAAGAGACCAATTCGTGGTAGATATTGAAGGAGGCCAGTCCGTGGCCGACATAGACACTTG
Found at i:18874 original size:2 final size:2
Alignment explanation
Indices: 18869--18925 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
18859 CTTTATTTCT
*
18869 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
18911 TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC T
18926 TTTGACTGGT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:29295 original size:55 final size:54
Alignment explanation
Indices: 29234--29951 Score: 1062
Period size: 55 Copynumber: 13.1 Consensus size: 54
29224 TCCTATTTTA
** * * *
29234 CTTTTTACACTTCTTTACTTTGAATTAAGCCAATTAATGGTTACCATTTTTTACT
1 CTTTTTA-ACTTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTACT
* * * * *
29289 CCTTTTAACTTAATCACTCTAAATTAAGCCAATTACTGATTACTAATATTTTACT
1 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTAC-CATTTTTTACT
* * * * *
29344 CTTTTAAACTTAATTCCTCTGAATTAAGCCAATTACAGATTACTATATTTTACT
1 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTACT
* *
29398 CCTTTTAACTTAATCACTCTGAATTAAGCCAATTAC-GTATTACCATTTTTTACTTT
1 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTG-ATTACCATTTTTTAC--T
* *
29454 TTTTTTAACTTAAGTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTAACT
1 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTT-ACT
* *
29509 CTTGTTAACTTAATTACTCTGAATTAAGCCAAATACTGATTACCATTTTTTTACT
1 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCA-TTTTTTACT
29564 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTACT
1 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTACT
*
29618 CTTTTTAACTTAATTACTCTGAATTAAGCTAATTACTGATTACCA-TTTTTACT
1 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTACT
* *
29671 TTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTCATTACCATTTTTTTTACT
1 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCA--TTTTTTACT
* *
29727 CTTTTTAACTTAATTACTCTAAATTAAGCCAATTACTGAGTACCATTTTTTACT
1 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTACT
*
29781 CTTTCTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTTACT
1 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCA-TTTTTTACT
29836 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTTACT
1 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCA-TTTTTTACT
29891 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTTACT
1 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCA-TTTTTTACT
*
29946 TTTTTT
1 CTTTTT
29952 TTACCCTCTT
Statistics
Matches: 606, Mismatches: 46, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
53 51 0.08
54 188 0.31
55 263 0.43
56 101 0.17
57 3 0.00
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.46
Consensus pattern (54 bp):
CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTACT
Found at i:29950 original size:109 final size:109
Alignment explanation
Indices: 29234--29951 Score: 1068
Period size: 109 Copynumber: 6.6 Consensus size: 109
29224 TCCTATTTTA
** * * * *
29234 CTTTTTACACTTCTTTACTTTGAATTAAGCCAATTAATGGTTACCA-TTTTTTACTCCTTTTAAC
1 CTTTTTA-ACTTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTTACTCTTTTTAAC
* * * *
29298 TTAATCACTCTAAATTAAGCCAATTACTGATTACTAATATTTTACT
65 TTAATTACTCTGAATTAAGCCAATTACTGATTAC-CATTTTTTACT
* * * * * *
29344 CTTTTAAACTTAATTCCTCTGAATTAAGCCAATTACAGATTACTA-TATTTTACTCCTTTTAACT
1 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTTACTCTTTTTAACT
*
29408 TAATCACTCTGAATTAAGCCAATTAC-GTATTACCATTTTTTACTTT
66 TAATTACTCTGAATTAAGCCAATTACTG-ATTACCATTTTTTAC--T
* * * *
29454 TTTTTTAACTTAAGTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTAACTCTTGTTAACT
1 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTTACTCTTTTTAACT
*
29519 TAATTACTCTGAATTAAGCCAAATACTGATTACCATTTTTTTACT
66 TAATTACTCTGAATTAAGCCAATTACTGATTACCA-TTTTTTACT
29564 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCA-TTTTTTACTCTTTTTAACT
1 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTTACTCTTTTTAACT
*
29628 TAATTACTCTGAATTAAGCTAATTACTGATTACCA-TTTTTACT
66 TAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTACT
* *
29671 TTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTCATTACCATTTTTTTTACTCTTTTTAAC
1 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCA-TTTTTTTACTCTTTTTAAC
* *
29736 TTAATTACTCTAAATTAAGCCAATTACTGAGTACCATTTTTTACT
65 TTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTACT
*
29781 CTTTCTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTTACTCTTTTTAACT
1 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTTACTCTTTTTAACT
29846 TAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTTACT
66 TAATTACTCTGAATTAAGCCAATTACTGATTACCA-TTTTTTACT
*
29891 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTTACTTTTTTT
1 CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTTACTCTTTTT
29952 TTACCCTCTT
Statistics
Matches: 555, Mismatches: 43, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
107 51 0.09
108 9 0.02
109 232 0.42
110 208 0.37
111 46 0.08
112 9 0.02
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.46
Consensus pattern (109 bp):
CTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTTACTCTTTTTAACT
TAATTACTCTGAATTAAGCCAATTACTGATTACCATTTTTTACT
Found at i:49951 original size:33 final size:33
Alignment explanation
Indices: 49872--49951 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
49862 GCAGGCTGCA
* *
49872 GCCCCGTGCTTGGCGTGCGGGCTGGCCTGGTGGT
1 GCCCCGTGC-TGGCGCGCGGGCTAGCCTGGTGGT
*** * *
49906 GCCCCCCACTGGCGCGCGGGTTAGCCTGGTTGT
1 GCCCCGTGCTGGCGCGCGGGCTAGCCTGGTGGT
49939 GCCCCGTGCTGGC
1 GCCCCGTGCTGGC
49952 ACGGTCCGTC
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
33 30 0.83
34 6 0.17
ACGTcount: A:0.03, C:0.35, G:0.41, T:0.21
Consensus pattern (33 bp):
GCCCCGTGCTGGCGCGCGGGCTAGCCTGGTGGT
Found at i:50095 original size:20 final size:21
Alignment explanation
Indices: 50066--50120 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
50056 TACCCTGGTG
50066 TGGCCCGGTCATGT-GCGGCA
1 TGGCCCGGTCATGTCGCGGCA
*
50086 TGGCCTGGTC-TGGTGCGCGGCA
1 TGGCCCGGTCAT-GT-CGCGGCA
*
50108 TGGCCGGGTCATG
1 TGGCCCGGTCATG
50121 GCCTGGCTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 1 0.03
20 11 0.38
22 16 0.55
23 1 0.03
ACGTcount: A:0.07, C:0.27, G:0.44, T:0.22
Consensus pattern (21 bp):
TGGCCCGGTCATGTCGCGGCA
Found at i:57467 original size:31 final size:31
Alignment explanation
Indices: 57429--57490 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
57419 TCCCCGCTTT
57429 GAAAGCGATTCTAGAGGGAGCATCAATCATG
1 GAAAGCGATTCTAGAGGGAGCATCAATCATG
57460 GAAAGCGATTCTAGAGGGAGCATCAATCATG
1 GAAAGCGATTCTAGAGGGAGCATCAATCATG
57491 AACTCTCTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.19
Consensus pattern (31 bp):
GAAAGCGATTCTAGAGGGAGCATCAATCATG
Found at i:67777 original size:30 final size:30
Alignment explanation
Indices: 67741--68066 Score: 376
Period size: 30 Copynumber: 10.8 Consensus size: 30
67731 TTAACTGATG
67741 AAGCAATGATCCCAAACCAGGATTAAAATA
1 AAGCAATGATCCCAAACCAGGATTAAAATA
** *
67771 AAGCAATGATCATAAAACAGGATTAAAATA
1 AAGCAATGATCCCAAACCAGGATTAAAATA
* * *
67801 AAGTAATGATCCTAAACAAGGATTAAAATA
1 AAGCAATGATCCCAAACCAGGATTAAAATA
* *
67831 AAGCAATGATCCTAAACTAGGATTAAAATA
1 AAGCAATGATCCCAAACCAGGATTAAAATA
*
67861 AAGCAATGATCCTC-AACCAGGATTAACTCATA
1 AAGCAATGATCC-CAAACCAGGATTAA--AATA
67893 AAGCAATGATCCTC-AACCAGGATT-AAATA
1 AAGCAATGATCC-CAAACCAGGATTAAAATA
*
67922 AAGCAATGATCCTC-AACCAGGATTAACATA
1 AAGCAATGATCC-CAAACCAGGATTAAAATA
*
67952 AAGCAATGATCCTC-AACCAAGATTAAAATA
1 AAGCAATGATCC-CAAACCAGGATTAAAATA
* *
67982 AAGCAATGATCATC-AACCAGGATTAACTCATA
1 AAGCAATGATC-CCAAACCAGGATTAA--AATA
* *
68014 AAGCAATGATCCTAAATCAGGATTAAAATA
1 AAGCAATGATCCCAAACCAGGATTAAAATA
* *
68044 AAGCAATGATCCTAAACTAGGAT
1 AAGCAATGATCCCAAACCAGGAT
68067 CGAAATTGAC
Statistics
Matches: 263, Mismatches: 25, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
29 27 0.10
30 183 0.70
31 1 0.00
32 52 0.20
ACGTcount: A:0.48, C:0.18, G:0.13, T:0.21
Consensus pattern (30 bp):
AAGCAATGATCCCAAACCAGGATTAAAATA
Found at i:67831 original size:60 final size:60
Alignment explanation
Indices: 67706--68066 Score: 447
Period size: 60 Copynumber: 5.9 Consensus size: 60
67696 AAATTAACTT
* * * * * * *
67706 ATAAAGCAATGATCCTACATCGGGATTAACTGATGAAGCAATGATCCCAAACCAGGATTAAA
1 ATAAAGCAATGATCCTAAAACAGGATTAA--AATAAAGCAATGATCCTAAACCAGGATTAAC
* * * *
67768 ATAAAGCAATGATCATAAAACAGGATTAAAATAAAGTAATGATCCTAAACAAGGATTAAA
1 ATAAAGCAATGATCCTAAAACAGGATTAAAATAAAGCAATGATCCTAAACCAGGATTAAC
*
67828 ATAAAGCAATGATCCT-AAACTAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAACTC
1 ATAAAGCAATGATCCTAAAAC-AGGATTAAAATAAAGCAATGATCCTAAACCAGGATTAA--C
* * *
67890 ATAAAGCAATGATCCTCAACCAGGATT-AAATAAAGCAATGATCCTCAACCAGGATTAAC
1 ATAAAGCAATGATCCTAAAACAGGATTAAAATAAAGCAATGATCCTAAACCAGGATTAAC
* * * * *
67949 ATAAAGCAATGATCCTCAACCAAGATTAAAATAAAGCAATGATCATCAACCAGGATTAACTC
1 ATAAAGCAATGATCCTAAAACAGGATTAAAATAAAGCAATGATCCTAAACCAGGATTAA--C
* *
68011 ATAAAGCAATGATCCTAAATCAGGATTAAAATAAAGCAATGATCCTAAACTAGGAT
1 ATAAAGCAATGATCCTAAAACAGGATTAAAATAAAGCAATGATCCTAAACCAGGAT
68067 CGAAATTGAC
Statistics
Matches: 269, Mismatches: 23, Indels: 14
0.88 0.08 0.05
Matches are distributed among these distances:
59 31 0.12
60 106 0.39
61 31 0.12
62 98 0.36
63 3 0.01
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.22
Consensus pattern (60 bp):
ATAAAGCAATGATCCTAAAACAGGATTAAAATAAAGCAATGATCCTAAACCAGGATTAAC
Found at i:67976 original size:121 final size:122
Alignment explanation
Indices: 67741--68066 Score: 489
Period size: 121 Copynumber: 2.7 Consensus size: 122
67731 TTAACTGATG
* *
67741 AAGCAATGATCC-CAAACCAGGATTAA--AATAAAGCAATGATCATAAAACAGGATTAAAATAAA
1 AAGCAATGATCCTC-AACCAGGATTAACTCATAAAGCAATGATCCTAAAACAGGATTAAAATAAA
* * *
67803 GTAATGATCCTAAACAAGGATTAAAATAAAGCAATGATCCTAAACTAGGATTAAAATA
65 GCAATGATCCTAAACAAGGATTAAAATAAAGCAATGATCCTAAACCAAGATTAAAATA
* *
67861 AAGCAATGATCCTCAACCAGGATTAACTCATAAAGCAATGATCCTCAACCAGGATT-AAATAAAG
1 AAGCAATGATCCTCAACCAGGATTAACTCATAAAGCAATGATCCTAAAACAGGATTAAAATAAAG
* * * *
67925 CAATGATCCTCAACCAGGATTAACATAAAGCAATGATCCTCAACCAAGATTAAAATA
66 CAATGATCCTAAACAAGGATTAAAATAAAGCAATGATCCTAAACCAAGATTAAAATA
* *
67982 AAGCAATGATCATCAACCAGGATTAACTCATAAAGCAATGATCCTAAATCAGGATTAAAATAAAG
1 AAGCAATGATCCTCAACCAGGATTAACTCATAAAGCAATGATCCTAAAACAGGATTAAAATAAAG
*
68047 CAATGATCCTAAACTAGGAT
66 CAATGATCCTAAACAAGGAT
68067 CGAAATTGAC
Statistics
Matches: 186, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
120 24 0.13
121 112 0.60
122 50 0.27
ACGTcount: A:0.48, C:0.18, G:0.13, T:0.21
Consensus pattern (122 bp):
AAGCAATGATCCTCAACCAGGATTAACTCATAAAGCAATGATCCTAAAACAGGATTAAAATAAAG
CAATGATCCTAAACAAGGATTAAAATAAAGCAATGATCCTAAACCAAGATTAAAATA
Found at i:68348 original size:19 final size:20
Alignment explanation
Indices: 68304--68349 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
68294 ATGCAAACTT
*
68304 TGAA-TTTAAACCTTGAACA
1 TGAATTTTAAACCTTAAACA
* *
68323 AGGATTTTAAA-CTTAAACA
1 TGAATTTTAAACCTTAAACA
68342 TGAATTTT
1 TGAATTTT
68350 TGATGAAAAC
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (20 bp):
TGAATTTTAAACCTTAAACA
Found at i:68599 original size:169 final size:169
Alignment explanation
Indices: 68143--68882 Score: 1088
Period size: 169 Copynumber: 4.4 Consensus size: 169
68133 TTTAAATTGA
* * *
68143 AACCTTGAACAAGGATTTTAAACTTAAACATGAATTTTTTATGAAAAACTTGATGAAATGAAATG
1 AACCTTAAACAAGGATTTTAAACTTAAACATGAATTTTTAATGAAAAACTTGATAAAATGAAATG
* * * *
68208 GTACCCGGAGGCTTTACAGATTGCCCGGATGACTTATCAAAATTAATACCCGGAGGATTCTGAAT
66 GTACCCGGAGGCTTTACCGATTGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAAT
** * ****
68273 TTGTGCTTGGAGGACTTACCAATGCAAACTTTGAATTTA
131 TTGTGCCCGGAGGACTTACCAATGCAAACTCTGAAAAGG
* *
68312 AACCTTGAACAAGGATTTTAAACTTAAACATGAATTTTTGATG-AAAACTTGATAAAATGAAATG
1 AACCTTAAACAAGGATTTTAAACTTAAACATGAATTTTTAATGAAAAACTTGATAAAATGAAATG
* * *
68376 ATACCCGGAGGCTTTACCAATTGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTATGAAT
66 GTACCCGGAGGCTTTACCGATTGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAAT
68441 TTGTGCCCGGAGGACTTACCAATGCAAACTCTGAAAAGG
131 TTGTGCCCGGAGGACTTACCAATGCAAACTCTGAAAAGG
* * * * *
68480 AATCTTAAATAAGGATTTTAAACTTAAACATGAATCTTTAATGAAAAACTTAATAAAATGAAGTG
1 AACCTTAAACAAGGATTTTAAACTTAAACATGAATTTTTAATGAAAAACTTGATAAAATGAAATG
* * *
68545 GTACCCGGAGGCTTTACCGATTGCCCGGACGACTTATCAGAATTAAGACCCGGAGGTTTCTGAAC
66 GTACCCGGAGGCTTTACCGATTGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAAT
68610 TTGTGCCCGGAGGACTTACCAATGCAAACTCTGAAAAGG
131 TTGTGCCCGGAGGACTTACCAATGCAAACTCTGAAAAGG
* * *
68649 AACCTTAAACAAGGATTTTAAACTTAAACATGAATATTTAATGCAAAACTTAATAAAATGAAATG
1 AACCTTAAACAAGGATTTTAAACTTAAACATGAATTTTTAATGAAAAACTTGATAAAATGAAATG
* *
68714 GTACCCGAAGGCTTTACCGATTGCCCGGTGGACTTATCAGAATTAATACCCGGAGGTTTCTGAAT
66 GTACCCGGAGGCTTTACCGATTGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAAT
* * * * *
68779 TTGTGCTCGGAAGACTTACAAATGCAAACTTTGAATA-G
131 TTGTGCCCGGAGGACTTACCAATGCAAACTCTGAAAAGG
* * * *
68817 AGACCTTGACCAAGGATTTTAAACTTAAACATGAATTTTTGATGAAAAACTTGATGAAATGAAAT
1 A-ACCTTAAACAAGGATTTTAAACTTAAACATGAATTTTTAATGAAAAACTTGATAAAATGAAAT
68882 G
65 G
68883 ATACTCGCAG
Statistics
Matches: 518, Mismatches: 51, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
168 150 0.29
169 368 0.71
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.28
Consensus pattern (169 bp):
AACCTTAAACAAGGATTTTAAACTTAAACATGAATTTTTAATGAAAAACTTGATAAAATGAAATG
GTACCCGGAGGCTTTACCGATTGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAAT
TTGTGCCCGGAGGACTTACCAATGCAAACTCTGAAAAGG
Found at i:69122 original size:70 final size:70
Alignment explanation
Indices: 69041--69178 Score: 267
Period size: 70 Copynumber: 2.0 Consensus size: 70
69031 CCTAAACTGC
*
69041 CTCGTATGGAAACGAGTTTGACTTATGGAAAAGTCAAAGCATTCGGATGGAACCGATGCACAAAA
1 CTCGTATGGAAAAGAGTTTGACTTATGGAAAAGTCAAAGCATTCGGATGGAACCGATGCACAAAA
69106 TCTGA
66 TCTGA
69111 CTCGTATGGAAAAGAGTTTGACTTATGGAAAAGTCAAAGCATTCGGATGGAACCGATGCACAAAA
1 CTCGTATGGAAAAGAGTTTGACTTATGGAAAAGTCAAAGCATTCGGATGGAACCGATGCACAAAA
69176 TCT
66 TCT
69179 TGAAAATTAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (70 bp):
CTCGTATGGAAAAGAGTTTGACTTATGGAAAAGTCAAAGCATTCGGATGGAACCGATGCACAAAA
TCTGA
Found at i:70452 original size:18 final size:20
Alignment explanation
Indices: 70429--70471 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
70419 CCTAGAGCTA
70429 TTTTCTTTCCTTTT-TCC-T
1 TTTTCTTTCCTTTTCTCCAT
*
70447 TTTTCTTTTCTTTTCTCCAT
1 TTTTCTTTCCTTTTCTCCAT
70467 TTTTC
1 TTTTC
70472 ATTTTTTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.59
19 3 0.14
20 6 0.27
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTCTTTCCTTTTCTCCAT
Found at i:70797 original size:14 final size:13
Alignment explanation
Indices: 70778--70811 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
70768 TCTTTCTCTT
70778 TTTTTTTCGATTGA
1 TTTTTTT-GATTGA
*
70792 TTTTTTTTATTGA
1 TTTTTTTGATTGA
70805 TTTTTTT
1 TTTTTTT
70812 TTATTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.12, C:0.03, G:0.09, T:0.76
Consensus pattern (13 bp):
TTTTTTTGATTGA
Found at i:70798 original size:17 final size:16
Alignment explanation
Indices: 70776--70830 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
70766 ATTCTTTCTC
*
70776 TTTTTTTTTCGATTGA
1 TTTTTTTTTTGATTGA
70792 TTTTTTTTATTGATT--
1 TTTTTTTT-TTGATTGA
70807 TTTTTTTATTT--TTGA
1 TTTTTTT-TTTGATTGA
70822 TTTTTTTTT
1 TTTTTTTTT
70831 ATTATTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
13 2 0.06
14 2 0.06
15 16 0.47
16 9 0.26
17 5 0.15
ACGTcount: A:0.11, C:0.02, G:0.07, T:0.80
Consensus pattern (16 bp):
TTTTTTTTTTGATTGA
Found at i:70811 original size:13 final size:14
Alignment explanation
Indices: 70776--70840 Score: 71
Period size: 17 Copynumber: 4.4 Consensus size: 14
70766 ATTCTTTCTC
70776 TTTTTTTTTCGATTGA
1 TTTTTTTTT--ATTGA
70792 -TTTTTTTTATTGA
1 TTTTTTTTTATTGA
70805 TTTTTTTTTATTTTTGA
1 TTTTTTTTTA---TTGA
70822 TTTTTTTTTATT-A
1 TTTTTTTTTATTGA
70835 TTTTTT
1 TTTTTT
70841 CGAATTTCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
13 12 0.27
14 11 0.24
15 8 0.18
17 14 0.31
ACGTcount: A:0.12, C:0.02, G:0.06, T:0.80
Consensus pattern (14 bp):
TTTTTTTTTATTGA
Found at i:70812 original size:30 final size:30
Alignment explanation
Indices: 70776--70840 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
70766 ATTCTTTCTC
*
70776 TTTTTTTTT-CGATTGA-TTTTTTTTATTGA
1 TTTTTTTTTATGATTGATTTTTTTTTATT-A
**
70805 TTTTTTTTTATTTTTGATTTTTTTTTATTA
1 TTTTTTTTTATGATTGATTTTTTTTTATTA
70835 TTTTTT
1 TTTTTT
70841 CGAATTTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 9 0.29
30 11 0.35
31 11 0.35
ACGTcount: A:0.12, C:0.02, G:0.06, T:0.80
Consensus pattern (30 bp):
TTTTTTTTTATGATTGATTTTTTTTTATTA
Found at i:70831 original size:17 final size:17
Alignment explanation
Indices: 70792--70836 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
70782 TTTCGATTGA
70792 TTTTTT-TTATTGATTT
1 TTTTTTATTATTGATTT
*
70808 TTTTTTATTTTTGATTT
1 TTTTTTATTATTGATTT
70825 TTTTTTATTATT
1 TTTTTTATTATT
70837 TTTTCGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.13, C:0.00, G:0.04, T:0.82
Consensus pattern (17 bp):
TTTTTTATTATTGATTT
Found at i:71245 original size:14 final size:16
Alignment explanation
Indices: 71226--71258 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
71216 TTTATTTTCA
71226 TTTTTTCA-TCATT-T
1 TTTTTTCATTCATTCT
71240 TTTTTTCATTCATTCT
1 TTTTTTCATTCATTCT
71256 TTT
1 TTT
71259 CTTTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 5 0.29
16 4 0.24
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTCATTCATTCT
Found at i:79284 original size:7 final size:7
Alignment explanation
Indices: 79260--79285 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
79250 AACAAAAACA
79260 AAATACG
1 AAATACG
79267 AAATACG
1 AAATACG
79274 AAATACG
1 AAATACG
79281 AAATA
1 AAATA
79286 AAACAAAACT
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:0.62, C:0.12, G:0.12, T:0.15
Consensus pattern (7 bp):
AAATACG
Done.