Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 83 of 131
Found at i:27858939 original size:29 final size:29
Alignment explanation
Indices: 27858913--27858983 Score: 115
Period size: 29 Copynumber: 2.4 Consensus size: 29
27858903 TCAAGTTATA
27858913 TTTTAGTCACTTATGTTTGAAATGTTACG
1 TTTTAGTCACTTATGTTTGAAATGTTACG
* * *
27858942 TTTTAATTACTTATGTTTGAAATTTTACG
1 TTTTAGTCACTTATGTTTGAAATGTTACG
27858971 TTTTAGTCACTTA
1 TTTTAGTCACTTA
27858984 CGTTATCGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.25, C:0.10, G:0.13, T:0.52
Consensus pattern (29 bp):
TTTTAGTCACTTATGTTTGAAATGTTACG
Found at i:27862421 original size:54 final size:54
Alignment explanation
Indices: 27862311--27862423 Score: 138
Period size: 54 Copynumber: 2.1 Consensus size: 54
27862301 GTTGTAGTCC
* * * **
27862311 GTGTGCCAGATCGTGTAACTCTCTAACTTGTGACACACGGTCGTGTCACAGGCT
1 GTGTGCCAGATCGTGTAACACGCTAACTTATGACACACGGTCGTGTCACAAACT
* * *
27862365 GTGTGCTAGGTCGTGTAACACGCTAACTTAAT-ACACACGGTCGTGTCTCAAACT
1 GTGTGCCAGATCGTGTAACACGCTAACTT-ATGACACACGGTCGTGTCACAAACT
27862419 GTGTG
1 GTGTG
27862424 TGGCACACGA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
54 49 0.98
55 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (54 bp):
GTGTGCCAGATCGTGTAACACGCTAACTTATGACACACGGTCGTGTCACAAACT
Found at i:27877362 original size:17 final size:17
Alignment explanation
Indices: 27877342--27877374 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
27877332 TAGAATTTGG
27877342 TTGAGAAAA-TAATTTAA
1 TTGA-AAAATTAATTTAA
27877359 TTGAAAAATTAATTTA
1 TTGAAAAATTAATTTA
27877375 GTTACTTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (17 bp):
TTGAAAAATTAATTTAA
Found at i:27877534 original size:30 final size:29
Alignment explanation
Indices: 27877500--27877557 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
27877490 TTGAATTTTG
* *
27877500 AAATATCAAGAGTAGAGGAACTAAATTCTT
1 AAATAT-AAAAGTACAGGAACTAAATTCTT
**
27877530 AAATATAAAAGTACATTAACTAAATTCT
1 AAATATAAAAGTACAGGAACTAAATTCT
27877558 AAAGACTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.29
Consensus pattern (29 bp):
AAATATAAAAGTACAGGAACTAAATTCTT
Found at i:27886028 original size:10 final size:10
Alignment explanation
Indices: 27885997--27886050 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
27885987 AGCTAATAAC
27885997 GAGCTC-AAT
1 GAGCTCGAAT
*
27886006 GAG-TTGAATT
1 GAGCTCGAA-T
27886016 GAGCTCGAAT
1 GAGCTCGAAT
*
27886026 GAGCT-GACTT
1 GAGCTCGA-AT
27886036 GAGCTCGAAT
1 GAGCTCGAAT
27886046 GAGCT
1 GAGCT
27886051 GAACCACATG
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
8 1 0.03
9 7 0.19
10 22 0.61
11 6 0.17
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (10 bp):
GAGCTCGAAT
Found at i:27886028 original size:20 final size:20
Alignment explanation
Indices: 27885997--27886053 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
27885987 AGCTAATAAC
*
27885997 GAGCTC-AATGAGTTGAATT
1 GAGCTCGAATGAGCTGAATT
*
27886016 GAGCTCGAATGAGCTGACTT
1 GAGCTCGAATGAGCTGAATT
27886036 GAGCTCGAATGAGCTGAA
1 GAGCTCGAATGAGCTGAA
27886054 CCACATGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 6 0.18
20 28 0.82
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (20 bp):
GAGCTCGAATGAGCTGAATT
Found at i:27890388 original size:41 final size:41
Alignment explanation
Indices: 27890354--27890459 Score: 194
Period size: 41 Copynumber: 2.6 Consensus size: 41
27890344 ACCGGCAATT
27890354 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
*
27890395 AGCCTGCTAGATGTAAAGTCTGAAACATTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
*
27890436 AGCCTGCTAAACGTAAAGTCTGAA
1 AGCCTGCTAGACGTAAAGTCTGAA
27890460 TTATCTCATT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.23
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
Found at i:27895568 original size:84 final size:84
Alignment explanation
Indices: 27895386--27895868 Score: 370
Period size: 84 Copynumber: 5.7 Consensus size: 84
27895376 TTATATCATT
* * * * * * *
27895386 AAATCAAAATAAAATTTTGTTAAACGACGAGAATAAATCCCGAAATAGA-ATTATTTGA-TTACG
1 AAATC-AAATAAAATCTTATTAAACGACGGGAATAAATCCCGAAACAGATTTTATTTAATTTA-A
* * *
27895449 TCTTTG-TTAGGAAACAAAACA
64 T-TCTGATTTGGAAACAAAATA
* * * * *
27895470 ATATCGAATAAAATCTTATTAAACGGCGGGAATAAATCCCAAAATAGATTTTATTTAATTTAATT
1 AAATCAAATAAAATCTTATTAAACGACGGGAATAAATCCCGAAACAGATTTTATTTAATTTAATT
27895535 C-GAATTTGGAAACAAAATA
66 CTG-ATTTGGAAACAAAATA
* * * *
27895554 AAATAAAATAAAATCTTGTTAAATGACGGGAATAAATCCCGAAACAAATTTTATTTAATTTAATT
1 AAATCAAATAAAATCTTATTAAACGACGGGAATAAATCCCGAAACAGATTTTATTTAATTTAATT
27895619 CTGATTTGGAAACAAAATA
66 CTGATTTGGAAACAAAATA
* * * *
27895638 AAATCAAAGAAAATCTTATTAAACGACGAGAAAAAATCCTGAAACAGATTTTATTTAATTTTAAT
1 AAATCAAATAAAATCTTATTAAACGACGGGAATAAATCCCGAAACAGATTTTATTTAA-TTTAA-
* *
27895703 TTTTCGTTTTTGGAAACAAAATCA
64 TTCT-G-ATTTGGAAACAAAAT-A
* ** ** * * * *
27895727 AAGTGTAAT-AAATC-CGTTGAACAACGGGAATAAATCCCGAAACATATTTTAATTTAGCTTTAA
1 AAATCAAATAAAATCTTATTAAACGACGGGAATAAATCCCGAAACAGATTTT-ATTTA-ATTTAA
* * *
27895790 TACTCAGCTTTGGAAATAAAATCGA
64 T--TCTGATTTGGAAACAAAAT--A
* ** * * * * *
27895815 AATTGGAATAAAATC--GTTGAACGACGGGTATCAATCCCGAAACGGATTTTATTT
1 AAATCAAATAAAATCTTATTAAACGACGGGAATAAATCCCGAAACAGATTTTATTT
27895869 TACTCGTTTT
Statistics
Matches: 326, Mismatches: 57, Indels: 29
0.79 0.14 0.07
Matches are distributed among these distances:
82 1 0.00
83 38 0.12
84 148 0.45
85 9 0.03
86 3 0.01
87 47 0.14
88 68 0.21
89 12 0.04
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (84 bp):
AAATCAAATAAAATCTTATTAAACGACGGGAATAAATCCCGAAACAGATTTTATTTAATTTAATT
CTGATTTGGAAACAAAATA
Found at i:27895689 original size:168 final size:171
Alignment explanation
Indices: 27895386--27895782 Score: 425
Period size: 168 Copynumber: 2.3 Consensus size: 171
27895376 TTATATCATT
* * * * *
27895386 AAATCAAAATAAAATTTTGTTAAACGACGAGAATAAATCCCGAAATAGAA--TTATTTGATTACG
1 AAAT-AAAATAAAATCTTGTTAAACGACGGGAATAAATCCCGAAACA-AATTTTATTTAATTACA
* * * * * * *
27895449 TCTTTGTTAGGAAACAAAACAATATCGAATAAAATCTTATTAAACGGCGGGAATAAATCCCAAAA
64 TCTCTGTTAGGAAACAAAACAAAATCAAAGAAAATCTTATTAAACGACGAGAAAAAATCCCAAAA
*
27895514 TAGATTTTATTTAA-TTTAA-TTCGAATTTGGAAACAAAAT-A
129 CAGATTTTATTTAATTTTAATTTCGAATTTGGAAACAAAATCA
*
27895554 AAATAAAATAAAATCTTGTTAAATGACGGGAATAAATCCCGAAACAAATTTTATTTAATTTA-AT
1 AAATAAAATAAAATCTTGTTAAACGACGGGAATAAATCCCGAAACAAATTTTATTTAA-TTACAT
* * **
27895618 -TCTGATTTGGAAACAAAATAAAATCAAAGAAAATCTTATTAAACGACGAGAAAAAATCCTGAAA
65 CTCTG-TTAGGAAACAAAACAAAATCAAAGAAAATCTTATTAAACGACGAGAAAAAATCCCAAAA
**
27895682 CAGATTTTATTTAATTTTAATTTTTCGTTTTTGGAAACAAAATCA
129 CAGATTTTATTTAATTTTAA--TTTCGAATTTGGAAACAAAATCA
* ** * * * *
27895727 AAGTGTAAT-AAATC-CGTTGAACAACGGGAATAAATCCCGAAACATATTTTAATTTA
1 AAATAAAATAAAATCTTGTTAAACGACGGGAATAAATCCCGAAACAAATTTT-ATTTA
27895783 GCTTTAATAC
Statistics
Matches: 191, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
166 2 0.01
167 41 0.21
168 74 0.39
169 8 0.04
171 31 0.16
172 28 0.15
173 7 0.04
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (171 bp):
AAATAAAATAAAATCTTGTTAAACGACGGGAATAAATCCCGAAACAAATTTTATTTAATTACATC
TCTGTTAGGAAACAAAACAAAATCAAAGAAAATCTTATTAAACGACGAGAAAAAATCCCAAAACA
GATTTTATTTAATTTTAATTTCGAATTTGGAAACAAAATCA
Found at i:27896026 original size:79 final size:78
Alignment explanation
Indices: 27895798--27896014 Score: 326
Period size: 79 Copynumber: 2.7 Consensus size: 78
27895788 AATACTCAGC
* * * *
27895798 TTTGGAAATAAAATCGAAATTGGAATAAAATCGTTGAACGACGGGTATCAATCCCGAAACGGATT
1 TTTGGAAATAAAA-CAAAATTTGAATAAAATCGTTGAACGGCGGGAATCAATCCCGAAACGGATT
27895863 TTATTTTACTCGTT
65 TTATTTTACTCGTT
* *
27895877 TTTGGAAATAAAATAAAATTTGAAATAAAATCGTTGAACAGCGGGAATCAATCCCGAAACGGATT
1 TTTGGAAATAAAACAAAATTTG-AATAAAATCGTTGAACGGCGGGAATCAATCCCGAAACGGATT
27895942 TTATTTTACTCGTT
65 TTATTTTACTCGTT
* * *
27895956 TTTGGAAATAAAACAAAATTTAGAATAAAATCATTGAATGGCGGGAATCAATCTCGAAA
1 TTTGGAAATAAAACAAAATTT-GAATAAAATCGTTGAACGGCGGGAATCAATCCCGAAA
27896015 TGAATCTTAT
Statistics
Matches: 125, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
78 6 0.05
79 118 0.94
80 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (78 bp):
TTTGGAAATAAAACAAAATTTGAATAAAATCGTTGAACGGCGGGAATCAATCCCGAAACGGATTT
TATTTTACTCGTT
Found at i:27896111 original size:89 final size:88
Alignment explanation
Indices: 27895956--27896163 Score: 262
Period size: 89 Copynumber: 2.4 Consensus size: 88
27895946 TTTACTCGTT
* ** * *
27895956 TTTGGAAATAAAA-CAAAAT-TTAGAATAAAATCATTGAATGGCGGGAATCAATCTCGAAATGAA
1 TTTGGAAATAAAATCAAAATAATAGAATAAAATCATTGAACAGCGGGAATAAATCTCGAAAAGAA
27896019 TCTTATTTACCTTTAATTTCTCA
66 TCTTATTTACCTTTAATTTCTCA
*
27896042 TTTGGAAATAAAATCAAAATAATAGAATAAAATCTATT-ATACAGTGGGAATAAATCTCGAAAAG
1 TTTGGAAATAAAATCAAAATAATAGAATAAAATC-ATTGA-ACAGCGGGAATAAATCTCGAAAAG
* * *
27896106 GATCTTATTTACTTTTAATTTCTCG
64 AATCTTATTTACCTTTAATTTCTCA
* * *
27896131 TTTGAAAAT-AAATAAAAATAATGGAATAAAATC
1 TTTGGAAATAAAATCAAAATAATAGAATAAAATC
27896164 CGTTGAACGG
Statistics
Matches: 106, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
86 13 0.12
87 6 0.06
88 35 0.33
89 52 0.49
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (88 bp):
TTTGGAAATAAAATCAAAATAATAGAATAAAATCATTGAACAGCGGGAATAAATCTCGAAAAGAA
TCTTATTTACCTTTAATTTCTCA
Found at i:27896274 original size:40 final size:40
Alignment explanation
Indices: 27896230--27896344 Score: 144
Period size: 40 Copynumber: 2.9 Consensus size: 40
27896220 GTTTGGATAA
* * *
27896230 AAAACGCCGCTAAAAATCAAGCATTACCGGGGCTTTTAAG
1 AAAACGCCACTAAAAATCGAGCATTACCGGCGCTTTTAAG
* * * *
27896270 AAAACGCCACTAAAGATCGAGTATTAGCGGCGCTTTTAGG
1 AAAACGCCACTAAAAATCGAGCATTACCGGCGCTTTTAAG
*
27896310 AAAACGCCACTAAAAAT-GAGCATTAGCGGCG-TTTT
1 AAAACGCCACTAAAAATCGAGCATTACCGGCGCTTTT
27896345 CCAAAAACCG
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
38 4 0.06
39 13 0.20
40 49 0.74
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.22
Consensus pattern (40 bp):
AAAACGCCACTAAAAATCGAGCATTACCGGCGCTTTTAAG
Found at i:27896459 original size:41 final size:41
Alignment explanation
Indices: 27896397--27896623 Score: 328
Period size: 41 Copynumber: 5.5 Consensus size: 41
27896387 TTTTGAGTTT
* *
27896397 TCGGGTCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATTC
1 TCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
* * * *
27896438 TCGGGTCTTTAGCGGCTTTTTTTAAGAAGCGCTGCTAATTC
1 TCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
*
27896479 TCGGGTCTTTAGCGGCGTTTCTGAAGAAGCGCCGCTAATGC
1 TCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
** * * *
27896520 TCTAGTCTTTAGTGGCGATTCTGAAGAAGCGCCGCTAATGC
1 TCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
* *
27896561 TCGGGTCTTTAGCAGCGTTTTTGAAGAAGCGCCACTAATGC
1 TCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
27896602 TCGGGTCTTTAGCGGCGTTTTT
1 TCGGGTCTTTAGCGGCGTTTTT
27896624 AAAAAGGCGC
Statistics
Matches: 166, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 166 1.00
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.33
Consensus pattern (41 bp):
TCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
Found at i:27896973 original size:9 final size:9
Alignment explanation
Indices: 27896962--27897037 Score: 98
Period size: 9 Copynumber: 8.4 Consensus size: 9
27896952 TTTGGTTAAA
*
27896962 AATTAACCA
1 AATTAACCG
27896971 AATTAACCG
1 AATTAACCG
*
27896980 AATTACCCG
1 AATTAACCG
* *
27896989 AATTACCCA
1 AATTAACCG
27896998 AATTAACCG
1 AATTAACCG
*
27897007 AATTACCCG
1 AATTAACCG
27897016 AATTAACCG
1 AATTAACCG
*
27897025 AATTAACCA
1 AATTAACCG
27897034 AATT
1 AATT
27897038 GAATCACTAC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 59 1.00
ACGTcount: A:0.45, C:0.25, G:0.07, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:27897000 original size:27 final size:27
Alignment explanation
Indices: 27896962--27897037 Score: 125
Period size: 27 Copynumber: 2.8 Consensus size: 27
27896952 TTTGGTTAAA
27896962 AATTAACCAAATTAACCGAATTACCCG
1 AATTAACCAAATTAACCGAATTACCCG
*
27896989 AATTACCCAAATTAACCGAATTACCCG
1 AATTAACCAAATTAACCGAATTACCCG
* *
27897016 AATTAACCGAATTAACCAAATT
1 AATTAACCAAATTAACCGAATT
27897038 GAATCACTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.45, C:0.25, G:0.07, T:0.24
Consensus pattern (27 bp):
AATTAACCAAATTAACCGAATTACCCG
Found at i:27897184 original size:18 final size:18
Alignment explanation
Indices: 27897144--27897187 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
27897134 TAATTTTATG
**
27897144 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
27897162 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
27897180 CTTGGGTT
1 ATTGGGTT
27897188 TAGATTAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:27900091 original size:47 final size:47
Alignment explanation
Indices: 27900022--27900121 Score: 200
Period size: 47 Copynumber: 2.1 Consensus size: 47
27900012 GATGATTCTC
27900022 TTTATTATTTAAAAAGAAAACATACTCTGATCTGGTAGGCTAATAAG
1 TTTATTATTTAAAAAGAAAACATACTCTGATCTGGTAGGCTAATAAG
27900069 TTTATTATTTAAAAAGAAAACATACTCTGATCTGGTAGGCTAATAAG
1 TTTATTATTTAAAAAGAAAACATACTCTGATCTGGTAGGCTAATAAG
27900116 TTTATT
1 TTTATT
27900122 CCTCCATAGC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (47 bp):
TTTATTATTTAAAAAGAAAACATACTCTGATCTGGTAGGCTAATAAG
Found at i:27900771 original size:178 final size:178
Alignment explanation
Indices: 27900472--27900804 Score: 639
Period size: 178 Copynumber: 1.9 Consensus size: 178
27900462 ATTCATGAAA
* *
27900472 TTATCATTTTGGAAAAATGGAAGAATGGGCATGGTGAAGTGTGTTTCATTATTGCTTTTAGGAAG
1 TTATCATATTGGAAAAATGGAAGAATGGGCATAGTGAAGTGTGTTTCATTATTGCTTTTAGGAAG
27900537 ACATCTAAATTCTATCTTCTTTCTTGTCATTCAATAGTATTCATAATGCTCATCCGAATTGAATG
66 ACATCTAAATTCTATCTTCTTTCTTGTCATTCAATAGTATTCATAATGCTCATCCGAATTGAATG
27900602 CAGCAGATACAACAGTTTCTCAAAGTATGTGGAGTTAGGGGCTTTTTT
131 CAGCAGATACAACAGTTTCTCAAAGTATGTGGAGTTAGGGGCTTTTTT
27900650 TTATCATATTGGAAAAATGGAAGAATGGGCATAGTGAAGTGTGTTTCATTATTGCTTTTAGGAAG
1 TTATCATATTGGAAAAATGGAAGAATGGGCATAGTGAAGTGTGTTTCATTATTGCTTTTAGGAAG
27900715 ACATCTAAATTCTATCTTCTTTCTTGTCATTCAATAGTATTCATAATGCTCATCCGAATTGAATG
66 ACATCTAAATTCTATCTTCTTTCTTGTCATTCAATAGTATTCATAATGCTCATCCGAATTGAATG
*
27900780 CAGCAGATACAACTGTTTCTCAAAG
131 CAGCAGATACAACAGTTTCTCAAAG
27900805 GTTTTCCTCA
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
178 152 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (178 bp):
TTATCATATTGGAAAAATGGAAGAATGGGCATAGTGAAGTGTGTTTCATTATTGCTTTTAGGAAG
ACATCTAAATTCTATCTTCTTTCTTGTCATTCAATAGTATTCATAATGCTCATCCGAATTGAATG
CAGCAGATACAACAGTTTCTCAAAGTATGTGGAGTTAGGGGCTTTTTT
Found at i:27910001 original size:13 final size:14
Alignment explanation
Indices: 27909970--27909996 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27909960 ATTGATATCT
27909970 CAAAACAAAAATTA
1 CAAAACAAAAATTA
27909984 CAAAACAAAAATT
1 CAAAACAAAAATT
27909997 GAAAATGAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (14 bp):
CAAAACAAAAATTA
Found at i:27910001 original size:49 final size:49
Alignment explanation
Indices: 27909946--27910043 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
27909936 TTTGTCAATT
* *
27909946 TTGAAAATGATCAAATTGATATCTCAAAACAAAAATTACAAAACAAAAA
1 TTGAAAATGAGCAAATTGATATCTCAAAACAAAAATTACAAAAAAAAAA
27909995 TTGAAAATGAGCAAATTGATATCTCAAAACAAAAATTACAAAAAAAAAA
1 TTGAAAATGAGCAAATTGATATCTCAAAACAAAAATTACAAAAAAAAAA
27910044 AAATTAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.60, C:0.11, G:0.07, T:0.21
Consensus pattern (49 bp):
TTGAAAATGAGCAAATTGATATCTCAAAACAAAAATTACAAAAAAAAAA
Found at i:27910076 original size:18 final size:18
Alignment explanation
Indices: 27910042--27910097 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
27910032 ACAAAAAAAA
* *
27910042 AAAAATTAAAATAATTTTT
1 AAAATTTAAAAT-ATTTAT
*
27910061 TAAATTTAAAATATTTAT
1 AAAATTTAAAATATTTAT
27910079 AAAATTTCAAAA-ATTTAT
1 AAAATTT-AAAATATTTAT
27910097 A
1 A
27910098 TATGTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 18 0.56
19 14 0.44
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAATTTAAAATATTTAT
Found at i:27910115 original size:22 final size:24
Alignment explanation
Indices: 27910087--27910138 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
27910077 ATAAAATTTC
27910087 AAAAATTTA-TAT-ATGTTTTTTA
1 AAAAATTTATTATAATGTTTTTTA
*
27910109 AAAAA-TTATTATAATTTTTTTTA
1 AAAAATTTATTATAATGTTTTTTA
27910132 AAAAATT
1 AAAAATT
27910139 CTAAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 3 0.12
22 8 0.31
23 14 0.54
24 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
AAAAATTTATTATAATGTTTTTTA
Found at i:27910128 original size:23 final size:24
Alignment explanation
Indices: 27910093--27910138 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
27910083 TTTCAAAAAT
27910093 TTATATATGTTTTTTAAAAAATTA
1 TTATATATGTTTTTTAAAAAATTA
*
27910117 TTATA-ATTTTTTTTAAAAAATT
1 TTATATATGTTTTTTAAAAAATT
27910139 CTAAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TTATATATGTTTTTTAAAAAATTA
Found at i:27917109 original size:51 final size:51
Alignment explanation
Indices: 27917050--27917147 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
27917040 TTCATGTCTA
* * *
27917050 AGTCCACTTGAAACTTTATTTTATATAGTCTCCAAAGAAAGTGAGTGGGCC
1 AGTCCACTTGAAACTTCAATTTATATAGTCTCCAAAGAAAATGAGTGGGCC
* *
27917101 AGTCCACTTGAAACTTCAATTTATCTAGTCTCCGAAGAAAATGAGTG
1 AGTCCACTTGAAACTTCAATTTATATAGTCTCCAAAGAAAATGAGTG
27917148 CATTCAAAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (51 bp):
AGTCCACTTGAAACTTCAATTTATATAGTCTCCAAAGAAAATGAGTGGGCC
Found at i:27918895 original size:15 final size:14
Alignment explanation
Indices: 27918852--27918897 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
27918842 TATTTAAAAA
*
27918852 TTTATAACTTAATT
1 TTTATAATTTAATT
27918866 TTTATAATTCT-ATT
1 TTTATAATT-TAATT
27918880 TTTATAAATTTAATT
1 TTTAT-AATTTAATT
27918895 TTT
1 TTT
27918898 TTTACTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTATAATTTAATT
Found at i:27919996 original size:30 final size:31
Alignment explanation
Indices: 27919960--27920017 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
27919950 GGTATACAAA
*
27919960 TTTTTTAGGC-CCTTAAAAATTAAAAAAACT
1 TTTTTTAGACTCCTTAAAAATTAAAAAAACT
* *
27919990 TTTTTTATACTCCTTAAAAATTAGAAAA
1 TTTTTTAGACTCCTTAAAAATTAAAAAA
27920018 TAATATTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 8 0.33
31 16 0.67
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (31 bp):
TTTTTTAGACTCCTTAAAAATTAAAAAAACT
Found at i:27923061 original size:16 final size:16
Alignment explanation
Indices: 27922992--27923061 Score: 59
Period size: 16 Copynumber: 4.4 Consensus size: 16
27922982 AGTACACGTT
* *
27922992 TGTAATGAAATAAAGC
1 TGTAATGGAATAGAGC
* *
27923008 TGTAATTGAATAGAGT
1 TGTAATGGAATAGAGC
* **
27923024 TGTAATTGAATAGCTC
1 TGTAATGGAATAGAGC
*
27923040 TCTAATGGAATAGAGC
1 TGTAATGGAATAGAGC
*
27923056 TATAAT
1 TGTAAT
27923062 CAGTAATTCA
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGC
Found at i:27923327 original size:21 final size:21
Alignment explanation
Indices: 27923303--27923351 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
27923293 AATTATTATT
27923303 ATATATAAT-TTA-ACAATAATA
1 ATATATAATATTAGA-AA-AATA
27923324 ATATATAATATTAGAAAAATA
1 ATATATAATATTAGAAAAATA
27923345 ATATATA
1 ATATATA
27923352 GCCATAATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 20 0.77
22 5 0.19
23 1 0.04
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATATAATATTAGAAAAATA
Found at i:27929654 original size:11 final size:11
Alignment explanation
Indices: 27929638--27929662 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
27929628 GGGCCTGTAG
27929638 AATAGACTTGT
1 AATAGACTTGT
27929649 AATAGACTTGT
1 AATAGACTTGT
27929660 AAT
1 AAT
27929663 GGCATAGCTA
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):
AATAGACTTGT
Found at i:27932656 original size:9 final size:9
Alignment explanation
Indices: 27932642--27932675 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
27932632 TATTTAAAAA
27932642 ATATATAAT
1 ATATATAAT
27932651 ATATATAAT
1 ATATATAAT
*
27932660 ATATATAAA
1 ATATATAAT
27932669 ATATATA
1 ATATATA
27932676 TATTTGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
ATATATAAT
Found at i:27932656 original size:11 final size:11
Alignment explanation
Indices: 27932626--27932678 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
27932616 ACCCATATTA
*
27932626 AATATATATTT
1 AATATATATAT
* *
27932637 AAAAAATATAT
1 AATATATATAT
27932648 -A-ATATATAT
1 AATATATATAT
*
27932657 AATATATATAA
1 AATATATATAT
27932668 AATATATATAT
1 AATATATATAT
27932679 TTGATTAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 7 0.21
10 2 0.06
11 25 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AATATATATAT
Found at i:27932696 original size:27 final size:28
Alignment explanation
Indices: 27932636--27932713 Score: 81
Period size: 27 Copynumber: 2.8 Consensus size: 28
27932626 AATATATATT
* *
27932636 TAAAAAATATATA-ATATATATAATATA
1 TAAAAAATATATATATTTATATAATAAA
*
27932663 TATAAAATATATATATTTGAT-TAA-AAA
1 TAAAAAATATATATATTT-ATATAATAAA
*
27932690 TAAAAAAAATATATATTTAATATA
1 TAAAAAATATATATATTT-ATATA
27932714 TAATTCGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
27 32 0.76
28 8 0.19
29 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (28 bp):
TAAAAAATATATATATTTATATAATAAA
Found at i:27936920 original size:54 final size:54
Alignment explanation
Indices: 27936861--27936968 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
27936851 TTAATTGAAA
* *
27936861 AAGAAAATATGGTCGACATATAAAATTTTCTTACCAAATCTATTCTTTACCCAT
1 AAGAAAATATGGTCGAAATATAAAAGTTTCTTACCAAATCTATTCTTTACCCAT
27936915 AAGAAAATATGGTCGAAATATAAAAGTTTCTTACCAAATCTATTCTTTACCCAT
1 AAGAAAATATGGTCGAAATATAAAAGTTTCTTACCAAATCTATTCTTTACCCAT
27936969 GCTTGTACAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (54 bp):
AAGAAAATATGGTCGAAATATAAAAGTTTCTTACCAAATCTATTCTTTACCCAT
Found at i:27938641 original size:19 final size:20
Alignment explanation
Indices: 27938619--27938658 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
27938609 TTCTATCCAT
27938619 AAAATAT-TAAACCATAATC
1 AAAATATCTAAACCATAATC
27938638 AAAATATGCCTAAACCATAAT
1 AAAATAT--CTAAACCATAAT
27938659 TCACTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
22 11 0.61
ACGTcount: A:0.55, C:0.17, G:0.03, T:0.25
Consensus pattern (20 bp):
AAAATATCTAAACCATAATC
Found at i:27943207 original size:15 final size:15
Alignment explanation
Indices: 27943186--27943224 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
27943176 TGGTAAGTCT
*
27943186 CCTCCTCCTAGTGTT
1 CCTCCTCCTAGTGTG
* *
27943201 TCTCCTCTTAGTGTG
1 CCTCCTCCTAGTGTG
27943216 CCTCCTCCT
1 CCTCCTCCT
27943225 GTGGAGCTAC
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.05, C:0.41, G:0.13, T:0.41
Consensus pattern (15 bp):
CCTCCTCCTAGTGTG
Found at i:27944676 original size:68 final size:69
Alignment explanation
Indices: 27944465--27944734 Score: 285
Period size: 69 Copynumber: 3.9 Consensus size: 69
27944455 TAATCAGTTG
* * * * * *
27944465 GGAGCTTTGCTCTTGCTAACTAG-ATTGGAGGTTGCGACTCTTCGCCTGCGAGCCTTAGTATGAC
1 GGAGCTTTACTCTCGCTAACT-GTATTTGAGGCTGCGACTCTTCGCCTACGAGCCTTAATATGAC
27944529 AGCTA
65 AGCTA
* * * * * * ***
27944534 GGAGTTTTGCTCTCGCTAACTGTGTTAGAGGCTGCGGCTCTTCGCTTGTAAGCCTTAATATGACA
1 GGAGCTTTACTCTCGCTAACTGTATTTGAGGCTGCGACTCTTCGCCTACGAGCCTTAATATGACA
27944599 GCTA
66 GCTA
* * *
27944603 AGAGCTTTACTCTCGTTAACTGTATTTGAGGCTGC-ACTCTTCGCCTACGAGCCTTAATATGATA
1 GGAGCTTTACTCTCGCTAACTGTATTTGAGGCTGCGACTCTTCGCCTACGAGCCTTAATATGACA
*
27944667 GCTG
66 GCTA
* * * * * *
27944671 GGAGCTTTACTCTCGCTAACTATA-CTGGGGCTGTGGCTCTTCGCCTACTAGCCTTAATATGACA
1 GGAGCTTTACTCTCGCTAACTGTATTTGAGGCTGCGACTCTTCGCCTACGAGCCTTAATATGACA
27944735 TGAATGTTGT
Statistics
Matches: 167, Mismatches: 32, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
67 7 0.04
68 74 0.44
69 86 0.51
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (69 bp):
GGAGCTTTACTCTCGCTAACTGTATTTGAGGCTGCGACTCTTCGCCTACGAGCCTTAATATGACA
GCTA
Found at i:27952677 original size:41 final size:40
Alignment explanation
Indices: 27952620--27952755 Score: 145
Period size: 37 Copynumber: 3.5 Consensus size: 40
27952610 CGACTTCAAG
27952620 TCGATGAGACACTGGGTGTCAATTTATTACTTCAGATTTAT
1 TCGATGAGACACTGGGTGTCAATTTATTACTTC-GATTTAT
* * *
27952661 TCGATGAGACACTGGGTGCCAA---CTTACTTCGGTTTA-
1 TCGATGAGACACTGGGTGTCAATTTATTACTTCGATTTAT
* * *
27952697 ACTGATGAGACACTGGGTGTCAATTTACTACTTCGAATTAT
1 TC-GATGAGACACTGGGTGTCAATTTATTACTTCGATTTAT
* * *
27952738 CCGATGTGGCACTGGGTG
1 TCGATGAGACACTGGGTG
27952756 CCAAACTGGG
Statistics
Matches: 78, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
36 1 0.01
37 24 0.31
38 7 0.09
40 24 0.31
41 22 0.28
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGTCAATTTATTACTTCGATTTAT
Found at i:27952751 original size:40 final size:39
Alignment explanation
Indices: 27952621--27952755 Score: 148
Period size: 40 Copynumber: 3.4 Consensus size: 39
27952611 GACTTCAAGT
*
27952621 CGATGAGACACTGGGTGTCAATTTATTACTTCAGATTTATT
1 CGATGAGACACTGGGTGTCAATTTA-TACTTC-GATTTATC
* * * *
27952662 CGATGAGACACTGGGTGCCAA-CT-TACTTCGGTTTAAC
1 CGATGAGACACTGGGTGTCAATTTATACTTCGATTTATC
* *
27952699 TGATGAGACACTGGGTGTCAATTTACTACTTCGAATTATC
1 CGATGAGACACTGGGTGTCAATTTA-TACTTCGATTTATC
* *
27952739 CGATGTGGCACTGGGTG
1 CGATGAGACACTGGGTG
27952756 CCAAACTGGG
Statistics
Matches: 77, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
37 24 0.31
38 7 0.09
40 26 0.34
41 20 0.26
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAATTTATACTTCGATTTATC
Found at i:27953530 original size:83 final size:83
Alignment explanation
Indices: 27953391--27953640 Score: 500
Period size: 83 Copynumber: 3.0 Consensus size: 83
27953381 TCAATACTTT
27953391 TGAATGTTTTGATTTTGGTTATAATGACATTAAAACATCAAAAGTATAACTTTCATGCCAAAACA
1 TGAATGTTTTGATTTTGGTTATAATGACATTAAAACATCAAAAGTATAACTTTCATGCCAAAACA
27953456 ATTAATCTTACTTACCAA
66 ATTAATCTTACTTACCAA
27953474 TGAATGTTTTGATTTTGGTTATAATGACATTAAAACATCAAAAGTATAACTTTCATGCCAAAACA
1 TGAATGTTTTGATTTTGGTTATAATGACATTAAAACATCAAAAGTATAACTTTCATGCCAAAACA
27953539 ATTAATCTTACTTACCAA
66 ATTAATCTTACTTACCAA
27953557 TGAATGTTTTGATTTTGGTTATAATGACATTAAAACATCAAAAGTATAACTTTCATGCCAAAACA
1 TGAATGTTTTGATTTTGGTTATAATGACATTAAAACATCAAAAGTATAACTTTCATGCCAAAACA
27953622 ATTAATCTTACTTACCAA
66 ATTAATCTTACTTACCAA
27953640 T
1 T
27953641 TTAAGCATGC
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 167 1.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (83 bp):
TGAATGTTTTGATTTTGGTTATAATGACATTAAAACATCAAAAGTATAACTTTCATGCCAAAACA
ATTAATCTTACTTACCAA
Found at i:27959440 original size:15 final size:15
Alignment explanation
Indices: 27959416--27959451 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
27959406 ATTTTTAGTA
*
27959416 AAAAACCCTAAATCC
1 AAAAATCCTAAATCC
*
27959431 AAAAATCCTAAATCT
1 AAAAATCCTAAATCC
27959446 AAAAAT
1 AAAAAT
27959452 ATTAAAACCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.58, C:0.22, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAAATCCTAAATCC
Found at i:27960531 original size:18 final size:20
Alignment explanation
Indices: 27960496--27960532 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
27960486 GTAAATCATA
*
27960496 AAAAAATTATAAAGAATATT
1 AAAAAATGATAAAGAATATT
27960516 AAAAAATGA-AAA-AATAT
1 AAAAAATGATAAAGAATAT
27960533 ATATGAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 3 0.19
20 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24
Consensus pattern (20 bp):
AAAAAATGATAAAGAATATT
Found at i:27960677 original size:44 final size:44
Alignment explanation
Indices: 27960629--27960717 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
27960619 AAAAAATAAA
27960629 ATATTTTTAAAACTCTACTAGCAATGTACCAAATAATTTTCCTT
1 ATATTTTTAAAACTCTACTAGCAATGTACCAAATAATTTTCCTT
27960673 ATATTTTTAAAACTCTACTAGCAATGTACCAAATAATTTTCCTT
1 ATATTTTTAAAACTCTACTAGCAATGTACCAAATAATTTTCCTT
27960717 A
1 A
27960718 CAAAAAATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.40
Consensus pattern (44 bp):
ATATTTTTAAAACTCTACTAGCAATGTACCAAATAATTTTCCTT
Found at i:27961180 original size:29 final size:29
Alignment explanation
Indices: 27961117--27961179 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
27961107 CATGTACTTT
*
27961117 TATTTTTAATAAATTTTAATATATTTGGA
1 TATTTTTAATAAATTTTAATATATTTAGA
*
27961146 TATTTTTAATAAATTTT-ATA-ATTTATA
1 TATTTTTAATAAATTTTAATATATTTAGA
27961173 TATTTTT
1 TATTTTT
27961180 TCATGTATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 12 0.38
28 3 0.09
29 17 0.53
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (29 bp):
TATTTTTAATAAATTTTAATATATTTAGA
Found at i:27961249 original size:19 final size:19
Alignment explanation
Indices: 27961116--27961284 Score: 74
Period size: 19 Copynumber: 9.2 Consensus size: 19
27961106 ACATGTACTT
*
27961116 TTATTTTTAATAAATTTTAA
1 TTATTTTT-ATAATTTTTAA
**
27961136 TATATTTGGAT-ATTTTTAA
1 T-TATTTTTATAATTTTTAA
* * *
27961155 TAAATTTTATAATTTAT-A
1 TTATTTTTATAATTTTTAA
* * *
27961173 -TATTTTT-TCATGTATAA
1 TTATTTTTATAATTTTTAA
*
27961190 -TATTTTTCTATATTGTTATAA
1 TTATTTTTATA-ATT-TT-TAA
*
27961211 TT-TTTTT-TCATTTTT-A
1 TTATTTTTATAATTTTTAA
27961227 -TATTTTTATAATTTTTAA
1 TTATTTTTATAATTTTTAA
* *
27961245 TTATTTCTATGATTTTGTAA
1 TTATTTTTATAATTTT-TAA
*
27961265 --ATTTTTATGA-TTTTAA
1 TTATTTTTATAATTTTTAA
27961281 TTAT
1 TTAT
27961285 AAAATATTAG
Statistics
Matches: 114, Mismatches: 20, Indels: 32
0.69 0.12 0.19
Matches are distributed among these distances:
15 1 0.01
16 15 0.13
17 24 0.21
18 21 0.18
19 31 0.27
20 8 0.07
21 13 0.11
22 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (19 bp):
TTATTTTTATAATTTTTAA
Found at i:27961250 original size:27 final size:27
Alignment explanation
Indices: 27961117--27961271 Score: 95
Period size: 27 Copynumber: 5.6 Consensus size: 27
27961107 CATGTACTTT
* **
27961117 TATTTTTAATAAATTTTAATATATTTGGA
1 TATTTTT-ATAATTTTTAAT-TATTTTTA
* * *
27961146 TATTTTTAATAAATTTT-ATAATTTATA
1 TATTTTT-ATAATTTTTAATTATTTTTA
* * *
27961173 TATTTTT-TCATGTATAA-TATTTTTCTA
1 TATTTTTATAATTTTTAATTA-TTTT-TA
* *
27961200 TATTGTTATAATTTTT-TTTCATTTTTA
1 TATTTTTATAATTTTTAATT-ATTTTTA
*
27961227 TATTTTTATAATTTTTAATTATTTCTA
1 TATTTTTATAATTTTTAATTATTTTTA
27961254 TGATTTTGTA-AATTTTTA
1 T-ATTTT-TATAATTTTTA
27961272 TGATTTTAAT
Statistics
Matches: 100, Mismatches: 17, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
25 5 0.05
26 4 0.04
27 44 0.44
28 27 0.27
29 20 0.20
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.63
Consensus pattern (27 bp):
TATTTTTATAATTTTTAATTATTTTTA
Found at i:27961277 original size:9 final size:9
Alignment explanation
Indices: 27961147--27961278 Score: 58
Period size: 9 Copynumber: 14.6 Consensus size: 9
27961137 ATATTTGGAT
27961147 ATTTTTAATA
1 ATTTTT-ATA
*
27961157 AATTTTATA
1 ATTTTTATA
*
27961166 ATTTATAT-
1 ATTTTTATA
*
27961174 ATTTTT-TC
1 ATTTTTATA
* *
27961182 ATGTATA-A
1 ATTTTTATA
*
27961190 TATTTTTCTA
1 -ATTTTTATA
*
27961200 TATTGTTATA
1 -ATTTTTATA
* *
27961210 ATTTTTTTTC
1 A-TTTTTATA
27961220 ATTTTTAT-
1 ATTTTTATA
27961228 ATTTTTATA
1 ATTTTTATA
*
27961237 ATTTTTAATT
1 ATTTTT-ATA
* *
27961247 ATTTCTATG
1 ATTTTTATA
27961256 ATTTTGTA-A
1 ATTTT-TATA
*
27961265 ATTTTTATG
1 ATTTTTATA
27961274 ATTTT
1 ATTTT
27961279 AATTATAAAA
Statistics
Matches: 91, Mismatches: 22, Indels: 19
0.69 0.17 0.14
Matches are distributed among these distances:
7 1 0.01
8 19 0.21
9 42 0.46
10 29 0.32
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (9 bp):
ATTTTTATA
Found at i:27961843 original size:19 final size:18
Alignment explanation
Indices: 27961779--27961879 Score: 62
Period size: 19 Copynumber: 5.4 Consensus size: 18
27961769 ATAACAAGTT
* *
27961779 TATAAAATTATAAAACTCA
1 TATAAAAATATAAAAAT-A
*
27961798 TAGAAAAATCATAAAAATGA
1 TATAAAAAT-ATAAAAAT-A
*
27961818 -ATGAAAATATAAAAATA
1 TATAAAAATATAAAAATA
* **
27961835 TTATAAAAATTTTGAAATA
1 -TATAAAAATATAAAAATA
*
27961854 TATAAAAACATAGAAAA-A
1 TATAAAAATATA-AAAATA
27961872 TTATAAAA
1 -TATAAAA
27961880 TATTATTAAA
Statistics
Matches: 63, Mismatches: 14, Indels: 10
0.72 0.16 0.11
Matches are distributed among these distances:
17 1 0.02
18 18 0.29
19 36 0.57
20 8 0.13
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (18 bp):
TATAAAAATATAAAAATA
Found at i:27961870 original size:28 final size:29
Alignment explanation
Indices: 27961818--27961891 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
27961808 ATAAAAATGA
* *
27961818 ATGAAA-ATATAAAAATATTATAAAAATT
1 ATGAAATATATAAAAACATTAGAAAAATT
*
27961846 TTGAAATATATAAAAACA-TAGAAAAATT
1 ATGAAATATATAAAAACATTAGAAAAATT
*
27961874 ATAAAATATTATTAAAAA
1 ATGAAATA-TA-TAAAAA
27961892 TGGTTGAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
28 20 0.53
29 12 0.32
30 6 0.16
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (29 bp):
ATGAAATATATAAAAACATTAGAAAAATT
Found at i:27961890 original size:20 final size:19
Alignment explanation
Indices: 27961867--27961952 Score: 66
Period size: 20 Copynumber: 4.4 Consensus size: 19
27961857 AAAAACATAG
27961867 AAAAATTATAAAATATTATT
1 AAAAATTATAAAATATTA-T
** **
27961887 AAAAATGGTTGAATATTAT
1 AAAAATTATAAAATATTAT
* **
27961906 AAATATTATTAGTATATTAT
1 AAAAATTA-TAAAATATTAT
27961926 GAAAAA-TATGAAAATATTAT
1 -AAAAATTAT-AAAATATTAT
27961946 AAAAATT
1 AAAAATT
27961953 TAGAAATGAT
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
19 12 0.24
20 34 0.68
21 4 0.08
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (19 bp):
AAAAATTATAAAATATTAT
Found at i:27962813 original size:46 final size:46
Alignment explanation
Indices: 27962760--27962852 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
27962750 TCAAAATGCC
*
27962760 AATTTGGTATTGATATTAAAGAAGGTATCGATAAAGGTGTACTTCT
1 AATTTGGTATCGATATTAAAGAAGGTATCGATAAAGGTGTACTTCT
27962806 AATTTGGTATCGATATTAAAGAAGGTATCGATAAAGGTGTACTTCT
1 AATTTGGTATCGATATTAAAGAAGGTATCGATAAAGGTGTACTTCT
27962852 A
1 A
27962853 TCGATACTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (46 bp):
AATTTGGTATCGATATTAAAGAAGGTATCGATAAAGGTGTACTTCT
Found at i:27967972 original size:33 final size:32
Alignment explanation
Indices: 27967935--27967999 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
27967925 TCATTTGGGC
*
27967935 TAGATTTAAGCTTTAACCCCTCATTCTTCTTGG
1 TAGATTCAAGCTTTAACCCCTCATTCTT-TTGG
* *
27967968 TAGATTCAAGCTTTAACCCGTTATTCTTTTGG
1 TAGATTCAAGCTTTAACCCCTCATTCTTTTGG
27968000 AATATTCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 4 0.14
33 25 0.86
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.43
Consensus pattern (32 bp):
TAGATTCAAGCTTTAACCCCTCATTCTTTTGG
Found at i:27968091 original size:174 final size:174
Alignment explanation
Indices: 27967784--27968102 Score: 476
Period size: 174 Copynumber: 1.8 Consensus size: 174
27967774 TATGAGATCC
* * *
27967784 TTCTCCTTAGTAGATTCAAGCTTTAACCCCTCATTCTTTTGGAATCTTCTTCCTCTATTGGACTT
1 TTCTCCTTAGTAGATTCAAGCTTTAACCCCTCATTCTTTTGGAATATTCTTACTCTATTGAACTT
* * * ***
27967849 TAGGAATCTCTTCAATCTCCTAGTAAACATGCTTATCTCTTTGTCTTCATCCACCTCATCACTTG
66 CAGGAATCTATTCAATCTCCTAGCAAACATGAACATCTCTTTGTCTTCATCCACCTCATCACTTG
27967914 ATTCACTATCTTCATTTGGGCTAGATTTAAGCTTTAACCCCTCA
131 ATTCACTATCTTCATTTGGGCTAGATTTAAGCTTTAACCCCTCA
* * * *
27967958 TTCTTCTTGGTAGATTCAAGCTTTAACCCGTTATTCTTTTGGAATATTCTTACTCTATTGAACTT
1 TTCTCCTTAGTAGATTCAAGCTTTAACCCCTCATTCTTTTGGAATATTCTTACTCTATTGAACTT
* * * * *
27968023 CATGAATCTATTGAATCTCCTAGCAAACATGAACATCTCTTTTTCTTCATCCACCTCTTCAGTTG
66 CAGGAATCTATTCAATCTCCTAGCAAACATGAACATCTCTTTGTCTTCATCCACCTCATCACTTG
27968088 ATTCACTATCTTCAT
131 ATTCACTATCTTCAT
27968103 GTGGTGGATT
Statistics
Matches: 127, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
174 127 1.00
ACGTcount: A:0.23, C:0.25, G:0.10, T:0.42
Consensus pattern (174 bp):
TTCTCCTTAGTAGATTCAAGCTTTAACCCCTCATTCTTTTGGAATATTCTTACTCTATTGAACTT
CAGGAATCTATTCAATCTCCTAGCAAACATGAACATCTCTTTGTCTTCATCCACCTCATCACTTG
ATTCACTATCTTCATTTGGGCTAGATTTAAGCTTTAACCCCTCA
Found at i:27974522 original size:10 final size:10
Alignment explanation
Indices: 27974509--27974566 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
27974499 AACAAAAATA
27974509 ATAAAAAGTT
1 ATAAAAAGTT
27974519 ATAAAAA-TT
1 ATAAAAAGTT
**
27974528 ATTAAAATTTT
1 A-TAAAAAGTT
*
27974539 ATTAAATAGTT
1 A-TAAAAAGTT
*
27974550 ATAAAAAATT
1 ATAAAAAGTT
27974560 ATAAAAA
1 ATAAAAA
27974567 TATTAAAGAG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
9 3 0.08
10 26 0.65
11 11 0.28
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (10 bp):
ATAAAAAGTT
Found at i:27974566 original size:11 final size:10
Alignment explanation
Indices: 27974502--27974571 Score: 52
Period size: 10 Copynumber: 6.8 Consensus size: 10
27974492 TTAGTTTAAC
*
27974502 AAAAATAATA
1 AAAAATTATA
*
27974512 AAAAGTTAT-
1 AAAAATTATA
27974521 AAAAATTATTA
1 AAAAATTA-TA
**
27974532 AAATTTTATTA
1 AAAAATTA-TA
* *
27974543 AATAGTTATA
1 AAAAATTATA
27974553 AAAAATTATA
1 AAAAATTATA
27974563 AAAATATTA
1 AAAA-ATTA
27974572 AAGAGTATAG
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
9 7 0.15
10 22 0.47
11 18 0.38
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (10 bp):
AAAAATTATA
Found at i:27976975 original size:30 final size:29
Alignment explanation
Indices: 27976917--27976984 Score: 57
Period size: 29 Copynumber: 2.3 Consensus size: 29
27976907 ACGTTGTAAT
* ** * *
27976917 TTTTTAAAATTATGAAAATATTATAAAAT
1 TTTTTAAAATTATGAAAAAAACAAAAAAA
27976946 TTTTATAAAATTAT-AAAAAAACAAAAAAA
1 TTTT-TAAAATTATGAAAAAAACAAAAAAA
27976975 TATTATTAAA
1 T-TT-TTAAA
27976985 TATGATAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
29 15 0.48
30 15 0.48
31 1 0.03
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (29 bp):
TTTTTAAAATTATGAAAAAAACAAAAAAA
Found at i:27979015 original size:26 final size:26
Alignment explanation
Indices: 27978986--27979089 Score: 109
Period size: 26 Copynumber: 4.0 Consensus size: 26
27978976 GCCTAGCGAG
*
27978986 CTTGAGTTTAAGTGGGTCAAAGGACC
1 CTTGAGTTTAAGTTGGTCAAAGGACC
* * **
27979012 CTTGAGTTTAAGTAGGTTAGGGGACC
1 CTTGAGTTTAAGTTGGTCAAAGGACC
* * **
27979038 CCTGAGTTTGAGTTGGTCGGAGGACC
1 CTTGAGTTTAAGTTGGTCAAAGGACC
* *
27979064 CTTGAGTTTGAGTTGGTCGAAGGACC
1 CTTGAGTTTAAGTTGGTCAAAGGACC
27979090 ATGAGCATAT
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 66 1.00
ACGTcount: A:0.21, C:0.15, G:0.35, T:0.29
Consensus pattern (26 bp):
CTTGAGTTTAAGTTGGTCAAAGGACC
Found at i:27979726 original size:13 final size:13
Alignment explanation
Indices: 27979708--27979732 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27979698 TAATTTAATA
27979708 TTATTTTGTGTGT
1 TTATTTTGTGTGT
27979721 TTATTTTGTGTG
1 TTATTTTGTGTG
27979733 CATTTGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:27985437 original size:23 final size:22
Alignment explanation
Indices: 27985405--27985447 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
27985395 ATTGGAATTT
*
27985405 TAAAATTTATAAAATATAAAAAA
1 TAAAAATTATAAAAT-TAAAAAA
*
27985428 TAAAAATTATCAAATTAAAA
1 TAAAAATTATAAAATTAAAA
27985448 TACATGAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAAATTATAAAATTAAAAAA
Found at i:27992554 original size:12 final size:12
Alignment explanation
Indices: 27992531--27992564 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
27992521 TAGAATAAAC
27992531 CAATAT-GACAT
1 CAATATAGACAT
27992542 CAATATAGACAT
1 CAATATAGACAT
27992554 CAATATAGACA
1 CAATATAGACA
27992565 ACTACAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.50, C:0.18, G:0.09, T:0.24
Consensus pattern (12 bp):
CAATATAGACAT
Found at i:27997680 original size:25 final size:25
Alignment explanation
Indices: 27997652--27997729 Score: 93
Period size: 25 Copynumber: 3.1 Consensus size: 25
27997642 AGAGAAGAGT
* * *
27997652 AAAACAAAACATAGTAGAACATAAC
1 AAAACATAACAAAGTAGAACAGAAC
* *
27997677 AAAACATAACAGAGTAGAGCAGAAC
1 AAAACATAACAAAGTAGAACAGAAC
* *
27997702 ATAACATAACAAAATAGAACAGAAC
1 AAAACATAACAAAGTAGAACAGAAC
27997727 AAA
1 AAA
27997730 GTAGAGCATA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.63, C:0.15, G:0.12, T:0.10
Consensus pattern (25 bp):
AAAACATAACAAAGTAGAACAGAAC
Found at i:27997740 original size:35 final size:35
Alignment explanation
Indices: 27997669--27997740 Score: 81
Period size: 35 Copynumber: 2.1 Consensus size: 35
27997659 AACATAGTAG
* ** *
27997669 AACATAACAAAACATAACAGAGTAGAGCAGAACAT
1 AACATAACAAAACAGAACAGAACAAAGCAGAACAT
* * *
27997704 AACATAACAAAATAGAACAGAACAAAGTAGAGCAT
1 AACATAACAAAACAGAACAGAACAAAGCAGAACAT
27997739 AA
1 AA
27997741 TAGAATAAAG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.60, C:0.15, G:0.14, T:0.11
Consensus pattern (35 bp):
AACATAACAAAACAGAACAGAACAAAGCAGAACAT
Found at i:27997745 original size:20 final size:20
Alignment explanation
Indices: 27997722--27997774 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
27997712 AAAATAGAAC
*
27997722 AGAACAAAGTAGAGCATAAT
1 AGAACAAAGCAGAGCATAAT
* *
27997742 AGAATAAAGCAGAGCATAAC
1 AGAACAAAGCAGAGCATAAT
* *
27997762 ATAACATAGCAGA
1 AGAACAAAGCAGA
27997775 ACAGAACAGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.55, C:0.13, G:0.19, T:0.13
Consensus pattern (20 bp):
AGAACAAAGCAGAGCATAAT
Found at i:27997777 original size:15 final size:15
Alignment explanation
Indices: 27997751--27997799 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
27997741 TAGAATAAAG
*
27997751 CAGAGCATAACATAA
1 CAGAGCAAAACATAA
* * *
27997766 CATAGCAGAACAGAA
1 CAGAGCAAAACATAA
*
27997781 CAGAGAAAAACATAA
1 CAGAGCAAAACATAA
27997796 CAGA
1 CAGA
27997800 ACAGAATAGA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.57, C:0.18, G:0.16, T:0.08
Consensus pattern (15 bp):
CAGAGCAAAACATAA
Found at i:27997782 original size:20 final size:20
Alignment explanation
Indices: 27997674--27997782 Score: 58
Period size: 20 Copynumber: 5.5 Consensus size: 20
27997664 AGTAGAACAT
* * *
27997674 AACAAAACATAACAGAGTAG
1 AACAGAACATAACAAAGCAG
* *
27997694 AGCAGAACATAACATAA-CAA
1 AACAGAACATAACA-AAGCAG
* * *
27997714 AATAGAACAGAACAAAGTAG
1 AACAGAACATAACAAAGCAG
* * * * *
27997734 AGCATAATAGAATAAAGCAG
1 AACAGAACATAACAAAGCAG
* * *
27997754 AGCATAACATAACATAGCAG
1 AACAGAACATAACAAAGCAG
27997774 AACAGAACA
1 AACAGAACA
27997783 GAGAAAAACA
Statistics
Matches: 65, Mismatches: 22, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
19 2 0.03
20 62 0.95
21 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.16, T:0.11
Consensus pattern (20 bp):
AACAGAACATAACAAAGCAG
Found at i:27997817 original size:25 final size:25
Alignment explanation
Indices: 27997764--27997859 Score: 84
Period size: 25 Copynumber: 3.8 Consensus size: 25
27997754 AGCATAACAT
*
27997764 AACATAGCAGAACAGAACAGAGAAA
1 AACATAACAGAACAGAACAGAGAAA
* ***
27997789 AACATAACAGAACAGAATAGAGTGG
1 AACATAACAGAACAGAACAGAGAAA
* * * *
27997814 AACATAACAAAATAGAACAAAGCAA
1 AACATAACAGAACAGAACAGAGAAA
* * *
27997839 AGCAAAACAGAACATAACAGA
1 AACATAACAGAACAGAACAGA
27997860 ATAGAGTAGA
Statistics
Matches: 53, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.60, C:0.16, G:0.17, T:0.07
Consensus pattern (25 bp):
AACATAACAGAACAGAACAGAGAAA
Found at i:27997889 original size:20 final size:20
Alignment explanation
Indices: 27997847--27997889 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
27997837 AAAGCAAAAC
* * * *
27997847 AGAACATAACAGAATAGAGT
1 AGAACATAAAAAAACAGAAT
27997867 AGAACATAAAAAAACAGAAT
1 AGAACATAAAAAAACAGAAT
27997887 AGA
1 AGA
27997890 GCAGAGCAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.63, C:0.09, G:0.16, T:0.12
Consensus pattern (20 bp):
AGAACATAAAAAAACAGAAT
Found at i:27997906 original size:55 final size:55
Alignment explanation
Indices: 27997674--27997915 Score: 180
Period size: 55 Copynumber: 4.3 Consensus size: 55
27997664 AGTAGAACAT
* * * * * * *
27997674 AACAAAACATAACAGAGTAGAGCAGAACATAACATAACAAAATAGAACAGAACAA
1 AACAGAACATAACAGAATAGAGCAGAACATAAAAAAACAGAACAGAACAGAGCAA
** * * * * *
27997729 AGTAGAGCATAATAGAATAAAGCAGAGCATAACATAACATAGCAGAACAGAACAGAGAAA
1 AACAGAACATAACAGAATAGAGCAGAACATAA-A-AA-A-A-CAGAACAGAACAGAGCAA
* * ** * * *
27997789 AACATAACAGAACAGAATAGAGTGGAACATAACAAAATAGAACA-AAGCAAAGCAA
1 AACAGAACATAACAGAATAGAGCAGAACATAAAAAAACAGAACAGAA-CAGAGCAA
* * * *
27997844 AACAGAACATAACAGAATAGAGTAGAACATAAAAAAACAGAATAGAGCAGAGCAG
1 AACAGAACATAACAGAATAGAGCAGAACATAAAAAAACAGAACAGAACAGAGCAA
* *
27997899 AATAGAACAAAACAGAA
1 AACAGAACATAACAGAA
27997916 GAAAAAAAAC
Statistics
Matches: 141, Mismatches: 39, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
54 2 0.01
55 95 0.67
56 2 0.01
57 2 0.01
58 3 0.02
59 1 0.01
60 36 0.26
ACGTcount: A:0.60, C:0.14, G:0.17, T:0.10
Consensus pattern (55 bp):
AACAGAACATAACAGAATAGAGCAGAACATAAAAAAACAGAACAGAACAGAGCAA
Found at i:27997907 original size:25 final size:25
Alignment explanation
Indices: 27997839--27997900 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
27997829 AACAAAGCAA
* * *
27997839 AGCAAAACAGAACATAACAGAATAG
1 AGCAGAACAGAAAAAAACAGAATAG
* *
27997864 AGTAGAACATAAAAAAACAGAATAG
1 AGCAGAACAGAAAAAAACAGAATAG
*
27997889 AGCAGAGCAGAA
1 AGCAGAACAGAA
27997901 TAGAACAAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.60, C:0.13, G:0.19, T:0.08
Consensus pattern (25 bp):
AGCAGAACAGAAAAAAACAGAATAG
Found at i:27997914 original size:15 final size:15
Alignment explanation
Indices: 27997877--27997964 Score: 70
Period size: 15 Copynumber: 5.9 Consensus size: 15
27997867 AGAACATAAA
*
27997877 AAAACAGAATAGAGC
1 AAAACAGAATAGAAC
* *
27997892 AGAGCAGAATAGAAC
1 AAAACAGAATAGAAC
* *
27997907 AAAACAGAAGA-AAA
1 AAAACAGAATAGAAC
* * *
27997921 AAAACAAAACAGAAT
1 AAAACAGAATAGAAC
* *
27997936 AAAATAGAATAGAGC
1 AAAACAGAATAGAAC
*
27997951 AAAACATAATAGAA
1 AAAACAGAATAGAA
27997965 TAGAACTGAA
Statistics
Matches: 54, Mismatches: 18, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
14 11 0.20
15 43 0.80
ACGTcount: A:0.66, C:0.10, G:0.16, T:0.08
Consensus pattern (15 bp):
AAAACAGAATAGAAC
Found at i:28000717 original size:21 final size:21
Alignment explanation
Indices: 28000693--28000733 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28000683 AAAAAATTGG
*
28000693 ATAAAAACTTAAAAATAAAAA
1 ATAAAAAATTAAAAATAAAAA
*
28000714 ATAAAAAATTAAAAGTAAAA
1 ATAAAAAATTAAAAATAAAA
28000734 CCTACTCACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
ATAAAAAATTAAAAATAAAAA
Found at i:28002917 original size:32 final size:32
Alignment explanation
Indices: 28002875--28002936 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
28002865 GAATGATACA
* *
28002875 AACTTAAAATAATTTAAATTAAAAAT-AACTTG
1 AACTCAAAATAATGT-AATTAAAAATCAACTTG
*
28002907 AACTCAAAATAATGTGATTAAAAATCAACT
1 AACTCAAAATAATGTAATTAAAAATCAACT
28002937 CAATTAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 9 0.35
32 17 0.65
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.31
Consensus pattern (32 bp):
AACTCAAAATAATGTAATTAAAAATCAACTTG
Found at i:28011361 original size:16 final size:16
Alignment explanation
Indices: 28011337--28011370 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28011327 AGTAGGAAAT
*
28011337 TATGGTATAAAATTTA
1 TATGGTATAAAACTTA
*
28011353 TATGTTATAAAACTTA
1 TATGGTATAAAACTTA
28011369 TA
1 TA
28011371 ATTTAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (16 bp):
TATGGTATAAAACTTA
Found at i:28017484 original size:23 final size:23
Alignment explanation
Indices: 28017454--28017503 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
28017444 AAGGAAAAGT
*
28017454 CCATGGCACCATATTGTGTAAGC
1 CCATGGCACCATATTGTGTAAGA
**
28017477 CCATGGCAGGATATTGTGTAAGA
1 CCATGGCACCATATTGTGTAAGA
28017500 CCAT
1 CCAT
28017504 AGCTAGTGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (23 bp):
CCATGGCACCATATTGTGTAAGA
Found at i:28017744 original size:27 final size:27
Alignment explanation
Indices: 28017694--28017794 Score: 98
Period size: 27 Copynumber: 3.7 Consensus size: 27
28017684 ACACGCTAGA
* *
28017694 AAATAGAAGCCTTTGTGATC-ATCTATG
1 AAATGGAAGCCTTTGTG-GCAATCTATG
* *
28017721 TAATGGAAGCCTTTTTGGCAATCTATG
1 AAATGGAAGCCTTTGTGGCAATCTATG
**
28017748 AAATGGAAGCCTTTGTGGTGATCTATGG
1 AAATGGAAGCCTTTGTGGCAATCTAT-G
*
28017776 AAA-GGAATGCCTTCGTGGC
1 AAATGGAA-GCCTTTGTGGC
28017795 GTATTTTAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
26 1 0.02
27 47 0.77
28 13 0.21
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.32
Consensus pattern (27 bp):
AAATGGAAGCCTTTGTGGCAATCTATG
Found at i:28017958 original size:27 final size:27
Alignment explanation
Indices: 28017928--28017979 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
28017918 AGATTGGTAG
*
28017928 ATATGGC-ATACTATAAAGGAATAGTAC
1 ATATGGCGA-ACTATAAAGAAATAGTAC
*
28017955 ATATGGCGAACTCTAAAGAAATAGT
1 ATATGGCGAACTATAAAGAAATAGT
28017980 TCCGTAGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (27 bp):
ATATGGCGAACTATAAAGAAATAGTAC
Found at i:28023921 original size:24 final size:24
Alignment explanation
Indices: 28023889--28023937 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
28023879 GTTTGCAGAT
28023889 ACCTGTTGTCAGTTAACTTAAAAC
1 ACCTGTTGTCAGTTAACTTAAAAC
28023913 ACCTGTTGTCAGTTAACTTAAAAC
1 ACCTGTTGTCAGTTAACTTAAAAC
28023937 A
1 A
28023938 ACAAAGCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (24 bp):
ACCTGTTGTCAGTTAACTTAAAAC
Found at i:28028342 original size:17 final size:18
Alignment explanation
Indices: 28028320--28028354 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28028310 GATCCAACAT
*
28028320 TTGGTTT-ATATGTATTG
1 TTGGTTTAACATGTATTG
28028337 TTGGTTTAACATGTATTG
1 TTGGTTTAACATGTATTG
28028355 GTAACCTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.54
Consensus pattern (18 bp):
TTGGTTTAACATGTATTG
Found at i:28028755 original size:18 final size:18
Alignment explanation
Indices: 28028732--28028769 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
28028722 AATGTTAAGG
28028732 TAAGTTAAGTAAATTTCA
1 TAAGTTAAGTAAATTTCA
28028750 TAAGTTAAGTAAATTTCA
1 TAAGTTAAGTAAATTTCA
28028768 TA
1 TA
28028770 TGGACTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (18 bp):
TAAGTTAAGTAAATTTCA
Found at i:28038384 original size:17 final size:17
Alignment explanation
Indices: 28038362--28038403 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
28038352 GCCATATTGG
*
28038362 GTGGGCTACAC-AGTCAT
1 GTGGGCCACACGAG-CAT
28038379 GTGGGCCCACACGAGCAT
1 GTGGG-CCACACGAGCAT
28038397 GTGGGCC
1 GTGGGCC
28038404 CATAACTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 13 0.59
19 2 0.09
ACGTcount: A:0.19, C:0.29, G:0.36, T:0.17
Consensus pattern (17 bp):
GTGGGCCACACGAGCAT
Found at i:28039551 original size:16 final size:17
Alignment explanation
Indices: 28039518--28039559 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
28039508 TAAATATTAT
*
28039518 TTTTTTAATTAATTTAA
1 TTTTTTAATTAATATAA
*
28039535 TTTTTTCATTAA-ATAA
1 TTTTTTAATTAATATAA
28039551 TTTTCTTAA
1 TTTT-TTAA
28039560 CCCAATTCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTTAATTAATATAA
Found at i:28045259 original size:61 final size:62
Alignment explanation
Indices: 28045188--28045312 Score: 180
Period size: 61 Copynumber: 2.0 Consensus size: 62
28045178 TCTTATATCT
* * * * *
28045188 AAAAATTCAACAAATTTAGCCCTCAATATTTAC-AAAATTTGCCATCTAGTTCTAATTCTAA
1 AAAAAATCAACAAATTTAGCCCTAAATATTTACAAAAATTTGCAATCTAATTCTAATACTAA
* *
28045249 AAAAAATCAACAAATTTAGCCCTAAATATTTACAAAAATTTTCAATTTAATTCTAATACTAA
1 AAAAAATCAACAAATTTAGCCCTAAATATTTACAAAAATTTGCAATCTAATTCTAATACTAA
28045311 AA
1 AA
28045313 GTTAAAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
61 31 0.55
62 25 0.45
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (62 bp):
AAAAAATCAACAAATTTAGCCCTAAATATTTACAAAAATTTGCAATCTAATTCTAATACTAA
Found at i:28051880 original size:3 final size:3
Alignment explanation
Indices: 28051872--28051941 Score: 133
Period size: 3 Copynumber: 23.7 Consensus size: 3
28051862 CTTGTTTCCA
28051872 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28051919 ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT AT
28051942 GAGTTGAACT
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 64 0.97
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:28052428 original size:46 final size:46
Alignment explanation
Indices: 28052376--28052468 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
28052366 AATATACTTG
*
28052376 TTAAAGTAACTGCTCGGTTGTTGAAGTCGTTTTACTTTTCTACCTC
1 TTAAAGTAACTGCTCGGTTGTCGAAGTCGTTTTACTTTTCTACCTC
*
28052422 TTAAAGTAACTGTTCGGTTGTCGAAGTCGTTTTACTTTTCTACCTC
1 TTAAAGTAACTGCTCGGTTGTCGAAGTCGTTTTACTTTTCTACCTC
28052468 T
1 T
28052469 GGATTATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.44
Consensus pattern (46 bp):
TTAAAGTAACTGCTCGGTTGTCGAAGTCGTTTTACTTTTCTACCTC
Found at i:28058130 original size:31 final size:31
Alignment explanation
Indices: 28058092--28058159 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
28058082 GAAAATAAGT
28058092 TGGAAGGAAGGAGTACCTTGATATTTAGAGA
1 TGGAAGGAAGGAGTACCTTGATATTTAGAGA
28058123 TGGAAGGAAGGAGTACCTTGATATTTAGAGA
1 TGGAAGGAAGGAGTACCTTGATATTTAGAGA
28058154 T-GAAGG
1 TGGAAGG
28058160 CAATAGGGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 5 0.14
31 32 0.86
ACGTcount: A:0.35, C:0.06, G:0.34, T:0.25
Consensus pattern (31 bp):
TGGAAGGAAGGAGTACCTTGATATTTAGAGA
Found at i:28061844 original size:29 final size:29
Alignment explanation
Indices: 28061802--28061865 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
28061792 CTGTTCGACT
* * *
28061802 TGCATCACTTCTTTACCCTTGAAGTCTGA
1 TGCATCACTCCTTTACCCTTAAAGTCCGA
28061831 TGCATCACTCCTTTACCCTTAAAGTCCGA
1 TGCATCACTCCTTTACCCTTAAAGTCCGA
*
28061860 TACATC
1 TGCATC
28061866 GCCCACCTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.31, G:0.11, T:0.34
Consensus pattern (29 bp):
TGCATCACTCCTTTACCCTTAAAGTCCGA
Found at i:28063948 original size:35 final size:33
Alignment explanation
Indices: 28063887--28063957 Score: 83
Period size: 35 Copynumber: 2.1 Consensus size: 33
28063877 AAATCATGGG
28063887 ATTTACAAGATACGTCATATCAAATCTAATCTAAT
1 ATTTACAAGATACGTCATATCAAATCT--TCTAAT
*
28063922 ATTTACAAGATATGATTC-TATC-AATCTTCTAAT
1 ATTTACAAGATACG--TCATATCAAATCTTCTAAT
28063955 ATT
1 ATT
28063958 AGTTACCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
33 9 0.27
35 18 0.55
36 4 0.12
37 2 0.06
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.39
Consensus pattern (33 bp):
ATTTACAAGATACGTCATATCAAATCTTCTAAT
Found at i:28067643 original size:20 final size:20
Alignment explanation
Indices: 28067596--28067643 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
28067586 AGTTTATGCT
*
28067596 AAGTAAATGAAATGGAAAGC
1 AAGTAAATGAAATGGAAAGA
* * * *
28067616 AAGAAAATGGAATGGTAATA
1 AAGTAAATGAAATGGAAAGA
28067636 AAGTAAAT
1 AAGTAAAT
28067644 AGAGTGGTTC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.56, C:0.02, G:0.23, T:0.19
Consensus pattern (20 bp):
AAGTAAATGAAATGGAAAGA
Found at i:28082821 original size:133 final size:134
Alignment explanation
Indices: 28082610--28082876 Score: 518
Period size: 133 Copynumber: 2.0 Consensus size: 134
28082600 TACTATTATT
*
28082610 TTTATTGTGTTTAAAAGTTTATAGTTTAATTTTATTTTATAATTATTAATTTTATTTTTCTTTTA
1 TTTATTGTGTTTAAAAGTTTATAGTTTAATTTTATTTTATAATTATTAATTTTATTTATCTTTTA
28082675 AGATATTGTAGTTATGAAGTCGAAAACAACTGATTTATTTATTTTTAATTAAAAAAAGTCCAAGA
66 AGATATTGTAGTTATGAAGTCGAAAACAACTGATTTATTTATTTTTAATTAAAAAAAGTCCAAGA
28082740 CAAC
131 CAAC
28082744 TTTATTGTG-TTAAAAGTTTATAGTTTAATTTTATTTTATAATTATTAATTTTATTTATCTTTTA
1 TTTATTGTGTTTAAAAGTTTATAGTTTAATTTTATTTTATAATTATTAATTTTATTTATCTTTTA
28082808 AGATATTGTAGTTATGAAGTCGAAAACAACTGATTTATTTATTTTTAATTAAAAAAAGTCCAAGA
66 AGATATTGTAGTTATGAAGTCGAAAACAACTGATTTATTTATTTTTAATTAAAAAAAGTCCAAGA
28082873 CAAC
131 CAAC
28082877 ACAATCACTA
Statistics
Matches: 132, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
133 123 0.93
134 9 0.07
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.48
Consensus pattern (134 bp):
TTTATTGTGTTTAAAAGTTTATAGTTTAATTTTATTTTATAATTATTAATTTTATTTATCTTTTA
AGATATTGTAGTTATGAAGTCGAAAACAACTGATTTATTTATTTTTAATTAAAAAAAGTCCAAGA
CAAC
Found at i:28083791 original size:49 final size:49
Alignment explanation
Indices: 28083738--28083834 Score: 133
Period size: 49 Copynumber: 2.0 Consensus size: 49
28083728 TGAAAATTCA
*
28083738 TAAAAAATCTAATATTTTATAAAAAATTATA-AAATTAATAAAACATATT
1 TAAAAAATCTAAAATTTTATAAAAAATTATAGAAATTAA-AAAACATATT
* * * *
28083787 TAAAACATTTAAAATTTTATAAAAATTTATAGAAATTAAAAAATATAT
1 TAAAAAATCTAAAATTTTATAAAAAATTATAGAAATTAAAAAACATAT
28083835 AAAAATTATG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
49 35 0.83
50 7 0.17
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (49 bp):
TAAAAAATCTAAAATTTTATAAAAAATTATAGAAATTAAAAAACATATT
Found at i:28083828 original size:18 final size:18
Alignment explanation
Indices: 28083807--28083842 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28083797 AAAATTTTAT
* *
28083807 AAAAATTTATAGAAATTA
1 AAAAATATATAAAAATTA
28083825 AAAAATATATAAAAATTA
1 AAAAATATATAAAAATTA
28083843 TGAAAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAAATATATAAAAATTA
Found at i:28083848 original size:9 final size:10
Alignment explanation
Indices: 28083755--28083849 Score: 53
Period size: 10 Copynumber: 10.0 Consensus size: 10
28083745 TCTAATATTT
28083755 TATA-AAAAA
1 TATATAAAAA
*
28083764 T-TATAAAAT
1 TATATAAAAA
28083773 TA-ATAAAACA
1 TATATAAAA-A
*
28083783 TATTTAAAACA
1 TATATAAAA-A
*
28083794 T-T-TAAAAT
1 TATATAAAAA
*
28083802 TTTATAAAAA
1 TATATAAAAA
* *
28083812 TTTATAGAAA
1 TATATAAAAA
28083822 T-TA-AAAAA
1 TATATAAAAA
28083830 TATATAAAAA
1 TATATAAAAA
28083840 T-TATGAAAAA
1 TATAT-AAAAA
28083850 ATAGAAATTA
Statistics
Matches: 70, Mismatches: 7, Indels: 17
0.74 0.07 0.18
Matches are distributed among these distances:
8 8 0.11
9 25 0.36
10 29 0.41
11 8 0.11
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (10 bp):
TATATAAAAA
Found at i:28083868 original size:18 final size:17
Alignment explanation
Indices: 28083815--28083868 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
28083805 ATAAAAATTT
28083815 ATAGAAATTA-AAAAATA
1 ATAGAAATTATAAAAA-A
* *
28083832 TATAAAAATTATGAAAAA
1 -ATAGAAATTATAAAAAA
28083850 ATAGAAATTATTAAAAAA
1 ATAGAAATTA-TAAAAAA
28083868 A
1 A
28083869 CTCATTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 9 0.30
18 17 0.57
19 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (17 bp):
ATAGAAATTATAAAAAA
Found at i:28084849 original size:21 final size:22
Alignment explanation
Indices: 28084807--28084850 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
28084797 CCAAAACCCC
*
28084807 AAACAGTCCCAAAATATCCAAA
1 AAACAGTCCCAAAATATACAAA
*
28084829 AAACAGT-CCAAAATTTACAAA
1 AAACAGTCCCAAAATATACAAA
28084850 A
1 A
28084851 CACGTTAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.57, C:0.23, G:0.05, T:0.16
Consensus pattern (22 bp):
AAACAGTCCCAAAATATACAAA
Found at i:28087366 original size:23 final size:22
Alignment explanation
Indices: 28087323--28087366 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
28087313 TTCTAAGTCG
28087323 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
28087346 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
28087367 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:28089830 original size:4 final size:4
Alignment explanation
Indices: 28089790--28089814 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
28089780 CAAAATAAAT
28089790 ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA A
28089815 ATCAACTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:28090659 original size:10 final size:10
Alignment explanation
Indices: 28090644--28090832 Score: 65
Period size: 10 Copynumber: 18.9 Consensus size: 10
28090634 TGCTTAAAAA
28090644 TTATAATTTT
1 TTATAATTTT
**
28090654 TTATAATTCA
1 TTATAATTTT
* * *
28090664 TTAGAACTTA
1 TTATAATTTT
*
28090674 TTATGAATCTT
1 TTAT-AATTTT
*
28090685 TTATAACTTT
1 TTATAATTTT
*
28090695 TGATAAATTTTTT
1 TTAT-AA--TTTT
28090708 TTGATAA-TTT
1 TT-ATAATTTT
*
28090718 TTATAAGTTT
1 TTATAATTTT
* *
28090728 ATAGAATGTTT
1 TTATAAT-TTT
28090739 TTAT-ATTTT
1 TTATAATTTT
* *
28090748 TAAT-A-TGT
1 TTATAATTTT
*
28090756 TT-T-ATCTT
1 TTATAATTTT
28090764 TTATAATTACTT
1 TTATAATT--TT
*
28090776 TTATAATTTA
1 TTATAATTTT
28090786 TTAGT-A-TTT
1 TTA-TAATTTT
28090795 TTATAA-TTT
1 TTATAATTTT
*
28090804 TTATAA-TAT
1 TTATAATTTT
*
28090813 TTATAAGTTT
1 TTATAATTTT
28090823 TTATGAATTT
1 TTAT-AATTT
28090833 CTTCAAGTTT
Statistics
Matches: 133, Mismatches: 30, Indels: 31
0.69 0.15 0.16
Matches are distributed among these distances:
7 2 0.02
8 7 0.05
9 35 0.26
10 52 0.39
11 19 0.14
12 10 0.08
13 6 0.05
14 2 0.02
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (10 bp):
TTATAATTTT
Found at i:28090723 original size:9 final size:9
Alignment explanation
Indices: 28090705--28090941 Score: 76
Period size: 9 Copynumber: 24.8 Consensus size: 9
28090695 TGATAAATTT
28090705 TTTTTGATAA
1 TTTTT-ATAA
28090715 TTTTTATAA
1 TTTTTATAA
* *
28090724 GTTTATAGAA
1 -TTTTTATAA
28090734 TGTTTT-TATA
1 T-TTTTATA-A
28090744 TTTTTA-ATA
1 TTTTTATA-A
28090753 TGTTTTAT--
1 T-TTTTATAA
*
28090761 CTTTTATAA
1 TTTTTATAA
28090770 TTACTTTTATAA
1 -T--TTTTATAA
28090782 TTTATTAGT-A
1 TTT-TTA-TAA
28090792 TTTTTATAA
1 TTTTTATAA
28090801 TTTTTATAA
1 TTTTTATAA
*
28090810 TATTTATAA
1 TTTTTATAA
28090819 GTTTTTATGAA
1 -TTTTTAT-AA
*
28090830 TTTCTT-CAA
1 TTT-TTATAA
* *
28090839 GTTTTATGATT
1 TTTTTAT-A-A
* *
28090850 TTTTTGTAG
1 TTTTTATAA
*
28090859 CTTTTATAA
1 TTTTTATAA
*
28090868 GTTTCTATAAA
1 -TTTTTAT-AA
* *
28090879 TATTTCATAT
1 T-TTTTATAA
28090889 TTTTTAATAA
1 TTTTT-ATAA
28090899 -TTTTA-AA
1 TTTTTATAA
**
28090906 TTTGCAATAA
1 TTT-TTATAA
*
28090916 TCTTTTATGA
1 T-TTTTATAA
28090926 TTTTTATAA
1 TTTTTATAA
28090935 TTTTTAT
1 TTTTTAT
28090942 GAGAAAAATA
Statistics
Matches: 168, Mismatches: 31, Indels: 57
0.66 0.12 0.22
Matches are distributed among these distances:
7 8 0.05
8 6 0.04
9 69 0.41
10 58 0.35
11 19 0.11
12 8 0.05
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:28090785 original size:19 final size:19
Alignment explanation
Indices: 28090763--28090803 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
28090753 TGTTTTATCT
*
28090763 TTTATAATTACTTTTATAA
1 TTTATAAGTACTTTTATAA
* *
28090782 TTTATTAGTATTTTTATAA
1 TTTATAAGTACTTTTATAA
28090801 TTT
1 TTT
28090804 TTATAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTATAAGTACTTTTATAA
Found at i:28090832 original size:18 final size:18
Alignment explanation
Indices: 28090775--28090826 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
28090765 TATAATTACT
*
28090775 TTTATAATTTATTAGT-ATT
1 TTTATAATTT-TTA-TAATA
28090794 TTTATAATTTTTATAATA
1 TTTATAATTTTTATAATA
28090812 TTTATAAGTTTTTAT
1 TTTATAA-TTTTTAT
28090827 GAATTTCTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 1 0.03
18 12 0.40
19 17 0.57
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (18 bp):
TTTATAATTTTTATAATA
Found at i:28092049 original size:20 final size:20
Alignment explanation
Indices: 28092026--28092068 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
28092016 CATTTTTTTA
28092026 TTTTATTCTTTCT-TTTCCTC
1 TTTTATT-TTTCTATTTCCTC
*
28092046 TTTTCTTTTTCTATTTCCTC
1 TTTTATTTTTCTATTTCCTC
28092066 TTT
1 TTT
28092069 CAATTGAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTATTTTTCTATTTCCTC
Found at i:28093079 original size:2 final size:2
Alignment explanation
Indices: 28093074--28093108 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
28093064 TATATATATA
28093074 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
28093109 ATGAATTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:28093736 original size:15 final size:15
Alignment explanation
Indices: 28093716--28093746 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28093706 AAAACAACAT
28093716 AACTCTTAACCTTTC
1 AACTCTTAACCTTTC
*
28093731 AACTCTTGACCTTTC
1 AACTCTTAACCTTTC
28093746 A
1 A
28093747 CTTACATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.32, G:0.03, T:0.39
Consensus pattern (15 bp):
AACTCTTAACCTTTC
Found at i:28097785 original size:15 final size:15
Alignment explanation
Indices: 28097765--28097795 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28097755 AAAATAACAT
28097765 AACTCTTAACCTTTC
1 AACTCTTAACCTTTC
*
28097780 AACTCTTGACCTTTC
1 AACTCTTAACCTTTC
28097795 A
1 A
28097796 CTTACATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.32, G:0.03, T:0.39
Consensus pattern (15 bp):
AACTCTTAACCTTTC
Found at i:28100798 original size:16 final size:16
Alignment explanation
Indices: 28100773--28100815 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
28100763 TAATTTTTTA
* *
28100773 TTAAATATATAAACAT
1 TTAAAAATATAAAAAT
*
28100789 TTAAACATATAAAAAT
1 TTAAAAATATAAAAAT
*
28100805 ATAAAAATATA
1 TTAAAAATATA
28100816 TATGTATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (16 bp):
TTAAAAATATAAAAAT
Found at i:28107877 original size:28 final size:28
Alignment explanation
Indices: 28107847--28107902 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
28107837 TGTAAAGCAA
*
28107847 GGGATAAAATTGTAAAATCTAAA-AAATAG
1 GGGA-AAAATTATAAAATC-AAAGAAATAG
28107876 GGGAAAAATTATAAAATCAAAGAAATA
1 GGGAAAAATTATAAAATCAAAGAAATA
28107903 AAGAACAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 3 0.12
28 18 0.72
29 4 0.16
ACGTcount: A:0.59, C:0.04, G:0.16, T:0.21
Consensus pattern (28 bp):
GGGAAAAATTATAAAATCAAAGAAATAG
Found at i:28112079 original size:20 final size:21
Alignment explanation
Indices: 28112056--28112095 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28112046 TTTGTACTTA
*
28112056 TCTAATGTC-TTTTTCTTTCT
1 TCTAATGTCATTTATCTTTCT
*
28112076 TCTAATTTCATTTATCTTTC
1 TCTAATGTCATTTATCTTTC
28112096 CAAGTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.15, C:0.20, G:0.03, T:0.62
Consensus pattern (21 bp):
TCTAATGTCATTTATCTTTCT
Found at i:28114832 original size:29 final size:29
Alignment explanation
Indices: 28114799--28114866 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
28114789 ATCGACAAAT
** *
28114799 GAAAAGGGATAGTTTCGGCTATCGAATAC
1 GAAAAGGGATACCTTCAGCTATCGAATAC
* *
28114828 GAAAAGGGATACCTTCAGCTATCGATTAT
1 GAAAAGGGATACCTTCAGCTATCGAATAC
28114857 GAAAAGGGAT
1 GAAAAGGGAT
28114867 GATGACAACC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (29 bp):
GAAAAGGGATACCTTCAGCTATCGAATAC
Found at i:28114887 original size:29 final size:29
Alignment explanation
Indices: 28114855--28114924 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
28114845 GCTATCGATT
28114855 ATGAAAAGGGATGATGACAACCATCAACA
1 ATGAAAAGGGATGATGACAACCATCAACA
* * *
28114884 ATGAAAAGGGATGGTGACGACCATCGACA
1 ATGAAAAGGGATGATGACAACCATCAACA
28114913 ATGAAAAGGGAT
1 ATGAAAAGGGAT
28114925 AGCTTTGGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.44, C:0.14, G:0.27, T:0.14
Consensus pattern (29 bp):
ATGAAAAGGGATGATGACAACCATCAACA
Found at i:28114949 original size:30 final size:30
Alignment explanation
Indices: 28114913--28115074 Score: 146
Period size: 30 Copynumber: 5.4 Consensus size: 30
28114903 ACCATCGACA
*
28114913 ATGAAAAGGGATAGCTTTGGCTATCAAATT
1 ATGAAAAGGGATAGCTTCGGCTATCAAATT
* * * * * *
28114943 ATGAAAAGGGAT-GGTGACGACCATCGAACT
1 ATGAAAAGGGATAGCT-TCGGCTATCAAATT
* **
28114973 ATGAAAAGGGATAACTTCAACTATCAAATT
1 ATGAAAAGGGATAGCTTCGGCTATCAAATT
* * **
28115003 ATGAAAAGGGATAGCTTCGGCTGTCGAACA
1 ATGAAAAGGGATAGCTTCGGCTATCAAATT
* * *
28115033 ATGAAAAGGGATAACTTCGGTTATCAAATC
1 ATGAAAAGGGATAGCTTCGGCTATCAAATT
*
28115063 ACGAAAAGGGAT
1 ATGAAAAGGGAT
28115075 GTGTCAACCA
Statistics
Matches: 102, Mismatches: 28, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
29 2 0.02
30 99 0.97
31 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.23
Consensus pattern (30 bp):
ATGAAAAGGGATAGCTTCGGCTATCAAATT
Found at i:28115006 original size:60 final size:60
Alignment explanation
Indices: 28114884--28115075 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
28114874 ACCATCAACA
* *
28114884 ATGAAAAGGGATGGTGACGACCATCG-ACAATGAAAAGGGATAGCTTTGGCTATCAAATT
1 ATGAAAAGGGATGGTGACGACCATCGAACAATGAAAAGGGATAACTTCGGCTATCAAATT
* **
28114943 ATGAAAAGGGATGGTGACGACCATCGAACTATGAAAAGGGATAACTTCAACTATCAAATT
1 ATGAAAAGGGATGGTGACGACCATCGAACAATGAAAAGGGATAACTTCGGCTATCAAATT
* * * ** * *
28115003 ATGAAAAGGGATAGCT-TCGGCTGTCGAACAATGAAAAGGGATAACTTCGGTTATCAAATC
1 ATGAAAAGGGAT-GGTGACGACCATCGAACAATGAAAAGGGATAACTTCGGCTATCAAATT
*
28115063 ACGAAAAGGGATG
1 ATGAAAAGGGATG
28115076 TGTCAACCAT
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
59 27 0.23
60 86 0.75
61 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.21
Consensus pattern (60 bp):
ATGAAAAGGGATGGTGACGACCATCGAACAATGAAAAGGGATAACTTCGGCTATCAAATT
Found at i:28122530 original size:29 final size:29
Alignment explanation
Indices: 28122497--28122564 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
28122487 ATCGACAAAT
*
28122497 GAAAAGGGATAGTTTCAG-CTATCGAATAC
1 GAAAAGGGATAG-CTCAGACTATCGAATAC
* * *
28122526 GAAAAGGGATAGCTCCGACTATCGATTAT
1 GAAAAGGGATAGCTCAGACTATCGAATAC
28122555 GAAAAGGGAT
1 GAAAAGGGAT
28122565 GGTGATGACC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.22
Consensus pattern (29 bp):
GAAAAGGGATAGCTCAGACTATCGAATAC
Found at i:28122646 original size:30 final size:30
Alignment explanation
Indices: 28122610--28122861 Score: 179
Period size: 30 Copynumber: 8.4 Consensus size: 30
28122600 GGCCATCGAC
* *
28122610 TATGAAAAGGGATAGCTTCGGCTATCCAAT
1 TATGAAAAGGGATAGCTTCGACTATCGAAT
* * *
28122640 TATGAAAAGGGAT-GGTGACGACCATCGAAT
1 TATGAAAAGGGATAGCT-TCGACTATCGAAT
* * * * * *
28122670 AATGAAAAGGGCT-GGTGACGACCATCGAAC
1 TATGAAAAGGGATAGCT-TCGACTATCGAAT
*
28122700 TATGAAAAGGGATAGCTTCGACTATCAAAT
1 TATGAAAAGGGATAGCTTCGACTATCGAAT
* * * * *
28122730 TATGAAAAGGGAT-GGTGACGACCATTGAAC
1 TATGAAAAGGGATAGCT-TCGACTATCGAAT
* **
28122760 TATGAAAAGGGATAGCTTCGGCTATTAAAT
1 TATGAAAAGGGATAGCTTCGACTATCGAAT
* * * * *
28122790 TATGAAAAGGGATGGCTTTGGCTGTCGAAC
1 TATGAAAAGGGATAGCTTCGACTATCGAAT
* * **
28122820 TATGAAAAGGGATAACTTTGGTTATCGAAT
1 TATGAAAAGGGATAGCTTCGACTATCGAAT
*
28122850 TA-AAAAAGGGAT
1 TATGAAAAGGGAT
28122862 GGATCAACGA
Statistics
Matches: 179, Mismatches: 39, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
29 13 0.07
30 162 0.91
31 4 0.02
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.24
Consensus pattern (30 bp):
TATGAAAAGGGATAGCTTCGACTATCGAAT
Found at i:28122732 original size:90 final size:89
Alignment explanation
Indices: 28122517--28122772 Score: 358
Period size: 90 Copynumber: 2.9 Consensus size: 89
28122507 AGTTTCAGCT
* * * *
28122517 ATCGAA-TACGAAAAGGGATAGCTCCGACTATCGATTATGAAAAGGGATGGTGATGACCATC-AA
1 ATCGAACTATGAAAAGGGATAGCTTCGACTATCAATTATGAAAAGGGATGGTGACGACCATCGAA
* * *
28122580 CAATGAAAAAGGATGGTAACGGCC
66 TAATGAAAAGGGATGGTAACGACC
*
28122604 ATCG-ACTATGAAAAGGGATAGCTTCGGCTATCCAATTATGAAAAGGGATGGTGACGACCATCGA
1 ATCGAACTATGAAAAGGGATAGCTTCGACTAT-CAATTATGAAAAGGGATGGTGACGACCATCGA
* *
28122668 ATAATGAAAAGGGCTGGTGACGACC
65 ATAATGAAAAGGGATGGTAACGACC
*
28122693 ATCGAACTATGAAAAGGGATAGCTTCGACTATCAAATTATGAAAAGGGATGGTGACGACCATTGA
1 ATCGAACTATGAAAAGGGATAGCTTCGACTATC-AATTATGAAAAGGGATGGTGACGACCATCGA
28122758 ACT-ATGAAAAGGGAT
65 A-TAATGAAAAGGGAT
28122773 AGCTTCGGCT
Statistics
Matches: 150, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
86 1 0.01
87 26 0.17
88 28 0.19
89 26 0.17
90 68 0.45
91 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.20
Consensus pattern (89 bp):
ATCGAACTATGAAAAGGGATAGCTTCGACTATCAATTATGAAAAGGGATGGTGACGACCATCGAA
TAATGAAAAGGGATGGTAACGACC
Found at i:28122824 original size:90 final size:90
Alignment explanation
Indices: 28122526--28122832 Score: 327
Period size: 90 Copynumber: 3.4 Consensus size: 90
28122516 TATCGAATAC
* * * * *
28122526 GAAAAGGGATAGCTCCGACTATC-GATTATGAAAAGGGATGGTGATGACCATC-AACAATGAAAA
1 GAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATGGTGACGACCATCGAATAATGAAAA
* * * * *
28122589 AGGATGGTAACGGCCATC-GACTAT
66 GGGATGCTGACGACCATCAAACTAT
*
28122613 GAAAAGGGATAGCTTCGGCTATCCAATTATGAAAAGGGATGGTGACGACCATCGAATAATGAAAA
1 GAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATGGTGACGACCATCGAATAATGAAAA
* * *
28122678 GGGCTGGTGACGACCATCGAACTAT
66 GGGATGCTGACGACCATCAAACTAT
* *
28122703 GAAAAGGGATAGCTTCGACTATCAAATTATGAAAAGGGATGGTGACGACCATTGAACT-ATGAAA
1 GAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATGGTGACGACCATCGAA-TAATGAAA
* * * * *
28122767 AGGGATAGCT-TCGGCTATTAAATTAT
65 AGGGAT-GCTGACGACCATCAAACTAT
* * * * *
28122793 GAAAAGGGATGGCTTTGGCTGTCGAACTATGAAAAGGGAT
1 GAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGAT
28122833 AACTTTGGTT
Statistics
Matches: 188, Mismatches: 27, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
87 21 0.11
88 27 0.14
89 24 0.13
90 113 0.60
91 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.22
Consensus pattern (90 bp):
GAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATGGTGACGACCATCGAATAATGAAAA
GGGATGCTGACGACCATCAAACTAT
Found at i:28122833 original size:60 final size:60
Alignment explanation
Indices: 28122517--28122804 Score: 257
Period size: 60 Copynumber: 4.9 Consensus size: 60
28122507 AGTTTCAGCT
* * * *
28122517 ATCGAA-TACGAAAAGGGATAGCTCCGACTATC-GATTATGAAAAGGGATGGTGATGACC
1 ATCGAACTATGAAAAGGGATAGCTTCGACTATCAAATTATGAAAAGGGATGGTGACGACC
* * * * * * * * * * * *
28122575 ATC-AACAATGAAAAAGGAT-GGTAACGGCCATC-GACTATGAAAAGGGATAGCT-TCGGCT
1 ATCGAACTATGAAAAGGGATAGCT-TCGACTATCAAATTATGAAAAGGGAT-GGTGACGACC
* * * * * * * *
28122633 ATCCAATTATGAAAAGGGAT-GGTGACGACCATCGAATAATGAAAAGGGCTGGTGACGACC
1 ATCGAACTATGAAAAGGGATAGCT-TCGACTATCAAATTATGAAAAGGGATGGTGACGACC
28122693 ATCGAACTATGAAAAGGGATAGCTTCGACTATCAAATTATGAAAAGGGATGGTGACGACC
1 ATCGAACTATGAAAAGGGATAGCTTCGACTATCAAATTATGAAAAGGGATGGTGACGACC
* * *
28122753 ATTGAACTATGAAAAGGGATAGCTTCGGCTATTAAATTATGAAAAGGGATGG
1 ATCGAACTATGAAAAGGGATAGCTTCGACTATCAAATTATGAAAAGGGATGG
28122805 CTTTGGCTGT
Statistics
Matches: 186, Mismatches: 37, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
57 4 0.02
58 39 0.21
59 28 0.15
60 113 0.61
61 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.21
Consensus pattern (60 bp):
ATCGAACTATGAAAAGGGATAGCTTCGACTATCAAATTATGAAAAGGGATGGTGACGACC
Found at i:28122851 original size:60 final size:60
Alignment explanation
Indices: 28122517--28122863 Score: 253
Period size: 60 Copynumber: 5.9 Consensus size: 60
28122507 AGTTTCAGCT
* * * * *
28122517 ATCGAA-TACGAAAAGGGATAGCTCCGACTATC-GATTATGAAAAGGGATGGTGATGACC
1 ATCGAACTATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATGGTGACGACC
* * * * * * * * * * *
28122575 ATC-AACAATGAAAAAGGAT-GGTAACGGCCATC-GACTATGAAAAGGGATAGCT-TCGGCT
1 ATCGAACTATGAAAAGGGATAGCT-TCGGCTATCAAATTATGAAAAGGGAT-GGTGACGACC
* * * * * * * * *
28122633 ATCCAATTATGAAAAGGGAT-GGTGACGACCATCGAATAATGAAAAGGGCTGGTGACGACC
1 ATCGAACTATGAAAAGGGATAGCT-TCGGCTATCAAATTATGAAAAGGGATGGTGACGACC
*
28122693 ATCGAACTATGAAAAGGGATAGCTTCGACTATCAAATTATGAAAAGGGATGGTGACGACC
1 ATCGAACTATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATGGTGACGACC
* * ** * *
28122753 ATTGAACTATGAAAAGGGATAGCTTCGGCTATTAAATTATGAAAAGGGATGGCT-TTGGCT
1 ATCGAACTATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATGG-TGACGACC
* * * * * *
28122813 GTCGAACTATGAAAAGGGATAACTTTGGTTATCGAATTA-AAAAAGGGATGG
1 ATCGAACTATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATGG
28122864 ATCAACGATC
Statistics
Matches: 232, Mismatches: 49, Indels: 15
0.78 0.17 0.05
Matches are distributed among these distances:
57 4 0.02
58 39 0.17
59 39 0.17
60 147 0.63
61 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.22
Consensus pattern (60 bp):
ATCGAACTATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATGGTGACGACC
Found at i:28124958 original size:29 final size:29
Alignment explanation
Indices: 28124909--28124975 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
28124899 TTGAAAAATG
* * *
28124909 AAAAGGGATAGTTTTGGCTATCGAATACA
1 AAAAGGGATAGCTTCGACTATCGAATACA
* **
28124938 AAAAGGGATAGCTTCGACTATCGATTATG
1 AAAAGGGATAGCTTCGACTATCGAATACA
28124967 AAAAGGGAT
1 AAAAGGGAT
28124976 GGTGACGACA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.25
Consensus pattern (29 bp):
AAAAGGGATAGCTTCGACTATCGAATACA
Found at i:28124984 original size:29 final size:29
Alignment explanation
Indices: 28124952--28125214 Score: 116
Period size: 30 Copynumber: 8.8 Consensus size: 29
28124942 GGGATAGCTT
*
28124952 CGACTATCGATTATGAAAAGGGATGGTGA
1 CGACCATCGATTATGAAAAGGGATGGTGA
* * ** * *
28124981 CGACAATCAACAATGAAAAGGGATAGTGG
1 CGACCATCGATTATGAAAAGGGATGGTGA
* * *
28125010 CGACCATCGACTATGAAAAGGGATAGCT-T
1 CGACCATCGATTATGAAAAGGGAT-GGTGA
* * * * *
28125039 CGGCTATCAAATTATTAAAATGGATGGTGA
1 CGACCATC-GATTATGAAAAGGGATGGTGA
* *
28125069 CGACCATCGAATAATGAAAAGGGATAGTGA
1 CGACCATCG-ATTATGAAAAGGGATGGTGA
** * * * *
28125099 CGGTCATTGAAATATGAAAAGGGATCGCT-T
1 CGACCATCG-ATTATGAAAAGGGAT-GGTGA
* * * * *
28125129 CGGCTATCAAATTATGAAAAAAGGATGGGGA
1 CGACCATC-GATTATG-AAAAGGGATGGTGA
* ** * *
28125160 TGACCATCGAACAATGGAGAGGGATGGTGA
1 CGACCATCG-ATTATGAAAAGGGATGGTGA
* *
28125190 CGACCATCAAATTATGAAAAAGGAT
1 CGACCATC-GATTATGAAAAGGGAT
28125215 AGCTTCAGCT
Statistics
Matches: 163, Mismatches: 61, Indels: 19
0.67 0.25 0.08
Matches are distributed among these distances:
29 52 0.32
30 93 0.57
31 18 0.11
ACGTcount: A:0.39, C:0.13, G:0.27, T:0.21
Consensus pattern (29 bp):
CGACCATCGATTATGAAAAGGGATGGTGA
Found at i:28125048 original size:58 final size:57
Alignment explanation
Indices: 28124906--28125095 Score: 152
Period size: 58 Copynumber: 3.2 Consensus size: 57
28124896 TCATTGAAAA
* * * * * * *
28124906 ATGAAAAGGGATAGTTTTGGCTATCGAATACAAAAAGGGATAGCT-TCGACTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCAAATA-TAAAAGGGATAG-TGACGACCATCGAAT
* * * * * *
28124964 ATGAAAAGGGAT-GGTGACGACAATCAACA-ATGAAAAGGGATAGTGGCGACCATCGACT
1 ATGAAAAGGGATAGCT-TCGGCTATCAA-ATAT-AAAAGGGATAGTGACGACCATCGAAT
* *
28125022 ATGAAAAGGGATAGCTTCGGCTATCAAATTATTAAAATGGATGGTGACGACCATCGAAT
1 ATGAAAAGGGATAGCTTCGGCTATCAAA-TA-TAAAAGGGATAGTGACGACCATCGAAT
28125081 AATGAAAAGGGATAG
1 -ATGAAAAGGGATAG
28125096 TGACGGTCAT
Statistics
Matches: 105, Mismatches: 18, Indels: 16
0.76 0.13 0.12
Matches are distributed among these distances:
57 4 0.04
58 60 0.57
59 26 0.25
60 15 0.14
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.22
Consensus pattern (57 bp):
ATGAAAAGGGATAGCTTCGGCTATCAAATATAAAAGGGATAGTGACGACCATCGAAT
Found at i:28125206 original size:91 final size:90
Alignment explanation
Indices: 28124938--28125239 Score: 351
Period size: 91 Copynumber: 3.4 Consensus size: 90
28124928 ATCGAATACA
* * * *
28124938 AAAAGGGATAGCTTCGACTATC-GATTATG-AAAAGGGATGGTGACGACAATC-AACAATGAAAA
1 AAAAGGGATAGCTTCGGCTATCAAATTATGAAAAAAGGATGGTGACGACCATCGAACAATGAAAA
* * *
28125000 GGGATAGTGGCGACCATCGACTATG
66 GGGATAGTGACGACCATCAAATATG
* * *
28125025 AAAAGGGATAGCTTCGGCTATCAAATTAT-TAAAATGGATGGTGACGACCATCGAATAATGAAAA
1 AAAAGGGATAGCTTCGGCTATCAAATTATGAAAAAAGGATGGTGACGACCATCGAACAATGAAAA
** *
28125089 GGGATAGTGACGGTCATTGAAATATG
66 GGGATAGTGACGACCA-TCAAATATG
* * * * *
28125115 AAAAGGGATCGCTTCGGCTATCAAATTATGAAAAAAGGATGGGGATGACCATCGAACAATGGAGA
1 AAAAGGGATAGCTTCGGCTATCAAATTATGAAAAAAGGATGGTGACGACCATCGAACAATGAAAA
*
28125180 GGGATGGTGACGACCATCAAATTATG
66 GGGATAGTGACGACCATCAAA-TATG
* * * *
28125206 AAAAAGGATAGCTTCAGCTATCGAACTATGAAAA
1 AAAAGGGATAGCTTCGGCTATCAAATTATGAAAA
28125240 GGGTAACTTC
Statistics
Matches: 181, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
87 21 0.12
88 25 0.14
89 23 0.13
90 38 0.21
91 74 0.41
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.21
Consensus pattern (90 bp):
AAAAGGGATAGCTTCGGCTATCAAATTATGAAAAAAGGATGGTGACGACCATCGAACAATGAAAA
GGGATAGTGACGACCATCAAATATG
Done.