Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 154 of 204
Found at i:46308786 original size:127 final size:126
Alignment explanation
Indices: 46308483--46308790 Score: 420
Period size: 127 Copynumber: 2.4 Consensus size: 126
46308473 AAATTAGTGG
* * * ** **
46308483 CGTTTTTTATAAAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTGTGATGAAAGCGCCGCT
1 CGTTTTTTAT-TAAGCGCCGCTAAAGAACATAACCTTTAGCGGCGTTT-TTTTCTAAGCGCCGCT
*
46308548 AAAGAACATGATCTTTAGCGGCGTTTCTATTTAAGCGCCGCTAAAGAACATGATCTTTAGCGA
64 AAAGAACATGATCTTAAGCGGCGTTTCTATTTAAGCGCCGCTAAAGAACATGATCTTTAGCGA
* * *
46308611 CGTCTTTTT-TTAAGCGCCGCTAAAGAACATAATCTTTAGCGGCATTTTTTTCTAAGTGCCGCTA
1 CGT-TTTTTATTAAGCGCCGCTAAAGAACATAACCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTA
* * *
46308675 AAGAACATGATCTTAAGCGGCGTCTTTTTTTTAAGCGCCGCTAAAGAACATGATCTTTAGCGG
65 AAGAACATGATCTTAAGCGGCGT-TTCTATTTAAGCGCCGCTAAAGAACATGATCTTTAGCGA
* * *
46308738 TGTTTTTTATTAAGCGCCGCTAAAGAACATGACCTTTAGTGGCGTTTTTTTCT
1 CGTTTTTTATTAAGCGCCGCTAAAGAACATAACCTTTAGCGGCGTTTTTTTCT
46308791 GTAAATGCTG
Statistics
Matches: 158, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
126 39 0.25
127 110 0.70
128 4 0.03
129 5 0.03
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.34
Consensus pattern (126 bp):
CGTTTTTTATTAAGCGCCGCTAAAGAACATAACCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAA
AGAACATGATCTTAAGCGGCGTTTCTATTTAAGCGCCGCTAAAGAACATGATCTTTAGCGA
Found at i:46310567 original size:45 final size:44
Alignment explanation
Indices: 46310466--46310625 Score: 167
Period size: 45 Copynumber: 3.6 Consensus size: 44
46310456 TGAGAAATAT
* * * ** ***
46310466 CATAGTTGAAAGATATTATGGCATTAAACCGGAGTGAATAAGAC
1 CATAGTTGAAAGATACTATGGCACTAATCCAAAACAAATAAGAC
* * * *
46310510 TATAGTTGAAAGATACGATGGCACTAATCCGAAAATATATAAGAC
1 CATAGTTGAAAGATACTATGGCACTAATCC-AAAACAAATAAGAC
* * *
46310555 CATGGTTGAAAGATACTATGGCATTAAATCCAATACAAATAAGAC
1 CATAGTTGAAAGATACTATGGCACT-AATCCAAAACAAATAAGAC
46310600 CATAGTTGAAAGATACTATGGCACTA
1 CATAGTTGAAAGATACTATGGCACTA
46310626 GTTCAGGAAT
Statistics
Matches: 95, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
44 26 0.27
45 64 0.67
46 5 0.05
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (44 bp):
CATAGTTGAAAGATACTATGGCACTAATCCAAAACAAATAAGAC
Found at i:46310642 original size:45 final size:44
Alignment explanation
Indices: 46310466--46310646 Score: 150
Period size: 45 Copynumber: 4.0 Consensus size: 44
46310456 TGAGAAATAT
* * * * * *
46310466 CATAGTTGAAAGATATTATGGCATTAAACCGGAGTGAATAAGAC
1 CATAGTTGAAAGATACTATGGCACTAATCAGGAATAAATAAGAC
* * * * *
46310510 TATAGTTGAAAGATACGATGGCACTAATCCGAAAATATATAAGAC
1 CATAGTTGAAAGATACTATGGCACTAATCAG-GAATAAATAAGAC
* * *
46310555 CATGGTTGAAAGATACTATGGCATTAAATCCA--ATACAAATAAGAC
1 CATAGTTGAAAGATACTATGGCACT-AAT-CAGGA-ATAAATAAGAC
* **
46310600 CATAGTTGAAAGATACTATGGCACTAGTTCAGGAATGTATAAGAC
1 CATAGTTGAAAGATACTATGGCACTA-ATCAGGAATAAATAAGAC
46310645 CA
1 CA
46310647 GGGTTAGAAG
Statistics
Matches: 108, Mismatches: 22, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
44 30 0.28
45 73 0.68
46 4 0.04
47 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (44 bp):
CATAGTTGAAAGATACTATGGCACTAATCAGGAATAAATAAGAC
Found at i:46310666 original size:90 final size:90
Alignment explanation
Indices: 46310502--46310667 Score: 219
Period size: 90 Copynumber: 1.8 Consensus size: 90
46310492 AACCGGAGTG
* * *
46310502 AATAAGACTATAGTTGAAAGATACGATGGCACTAATCCGAAAATATATAAGACCATGGTTGAAAG
1 AATAAGACCATAGTTGAAAGATACGATGGCACTAATCAGAAAATATATAAGACCAGGGTTGAAAG
* *
46310567 ATACTATGGCATTAAATCCAATACA
66 AAACCATGGCATTAAATCCAATACA
* * * *
46310592 AATAAGACCATAGTTGAAAGATACTATGGCACTAGTTCAG-GAATGTATAAGACCAGGGTT-AGA
1 AATAAGACCATAGTTGAAAGATACGATGGCACTA-ATCAGAAAATATATAAGACCAGGGTTGA-A
46310655 AGAAACCATGGCA
64 AGAAACCATGGCA
46310668 CCCTTTGGAA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
89 1 0.02
90 61 0.94
91 3 0.05
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (90 bp):
AATAAGACCATAGTTGAAAGATACGATGGCACTAATCAGAAAATATATAAGACCAGGGTTGAAAG
AAACCATGGCATTAAATCCAATACA
Found at i:46311122 original size:10 final size:10
Alignment explanation
Indices: 46311107--46311131 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
46311097 GTGACCCCTG
46311107 TTTCAAAAAT
1 TTTCAAAAAT
46311117 TTTCAAAAAT
1 TTTCAAAAAT
46311127 TTTCA
1 TTTCA
46311132 TGTTTTCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTCAAAAAT
Found at i:46312677 original size:40 final size:40
Alignment explanation
Indices: 46312628--46312767 Score: 190
Period size: 40 Copynumber: 3.5 Consensus size: 40
46312618 TATACGATCT
* * * **
46312628 GGGGTACGTATGTGAAATCAGGGGTGCCGAAGTACAAGCA
1 GGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAATA
* *
46312668 GGGGCACGTATCTGCAATCAGGGGTACTGAAGTACAAATA
1 GGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAATA
* * *
46312708 GGGGCACGTATGTGCAATTAGGGTTACCAAAGTACAAATA
1 GGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAATA
46312748 GGGGCACGTATGTGCAATCA
1 GGGGCACGTATGTGCAATCA
46312768 TTCAATAATT
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.31, C:0.16, G:0.32, T:0.20
Consensus pattern (40 bp):
GGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAATA
Found at i:46312711 original size:60 final size:60
Alignment explanation
Indices: 46312561--46312711 Score: 139
Period size: 60 Copynumber: 2.5 Consensus size: 60
46312551 GGTACTGAAG
* * * * *
46312561 TACAAT-AGGGGCACGTAAGT-ACAATCAAGGATACCGAAGTACAAACAGGGGCACGTGTA
1 TACAATCAGGGGTACGTAAGTCA-AATCAGGGGTGCCGAAGTACAAACAGGGGCACGTATA
* * * * * *
46312620 TACGATCTGGGGTACGTATGTGAAATCAGGGGTGCCGAAGTACAAGCAGGGGCACGTATC
1 TACAATCAGGGGTACGTAAGTCAAATCAGGGGTGCCGAAGTACAAACAGGGGCACGTATA
*
46312680 TGCAATCAGGGGTAC-TGAAGTACAAAT-AGGGG
1 TACAATCAGGGGTACGT-AAGT-CAAATCAGGGG
46312712 CACGTATGTG
Statistics
Matches: 73, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
59 6 0.08
60 62 0.85
61 5 0.07
ACGTcount: A:0.33, C:0.17, G:0.32, T:0.18
Consensus pattern (60 bp):
TACAATCAGGGGTACGTAAGTCAAATCAGGGGTGCCGAAGTACAAACAGGGGCACGTATA
Found at i:46322283 original size:63 final size:63
Alignment explanation
Indices: 46322157--46322300 Score: 161
Period size: 63 Copynumber: 2.3 Consensus size: 63
46322147 TCACAACCCC
* * * *
46322157 TTACACGACTTGGACACACGCCCATGTCCCTGGCCCGTGTGACCTTGAATTCAAAACTGTGAG
1 TTACACGGCCTGGACACACGCCCATGTCCCTAGCCCGTGTGACCTTGAATTCAAAACTATGAG
* * * *
46322220 TTATACGGCCTGGACACACGCCTATGTCCCTAGCCCTTGTG-TCTCT-AATTCGAAAA-TAATGA
1 TTACACGGCCTGGACACACGCCCATGTCCCTAGCCCGTGTGACCT-TGAATTC-AAAACT-ATGA
46322282 G
63 G
46322283 TTACACGGCCT-GACACAC
1 TTACACGGCCTGGACACAC
46322301 TGTCGTGTGG
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
62 15 0.22
63 54 0.78
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (63 bp):
TTACACGGCCTGGACACACGCCCATGTCCCTAGCCCGTGTGACCTTGAATTCAAAACTATGAG
Found at i:46323134 original size:20 final size:21
Alignment explanation
Indices: 46323095--46323134 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
46323085 CGATCTCATA
46323095 CACATAAACAAAGTACTTAAC
1 CACATAAACAAAGTACTTAAC
*
46323116 CACATATACAAAG-ACTTAA
1 CACATAAACAAAGTACTTAA
46323135 TTATTGACCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.53, C:0.23, G:0.05, T:0.20
Consensus pattern (21 bp):
CACATAAACAAAGTACTTAAC
Found at i:46325840 original size:15 final size:14
Alignment explanation
Indices: 46325820--46325866 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
46325810 GTCATCAATC
46325820 TTTCTTGTCTCTTTT
1 TTTCTT-TCTCTTTT
*
46325835 TTTCTTCCTCTTTT
1 TTTCTTTCTCTTTT
46325849 TTGT-TTTCT-TTTT
1 TT-TCTTTCTCTTTT
46325862 TTTCT
1 TTTCT
46325867 GTTTTTGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 1 0.04
13 7 0.25
14 13 0.46
15 7 0.25
ACGTcount: A:0.00, C:0.19, G:0.04, T:0.77
Consensus pattern (14 bp):
TTTCTTTCTCTTTT
Found at i:46334253 original size:20 final size:20
Alignment explanation
Indices: 46334228--46334271 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
46334218 ACCTGAACCC
*
46334228 AAAAGATTTAAACTCGAATT
1 AAAAGATTTAAACTCAAATT
46334248 AAAAGATTTAAACTCAAATT
1 AAAAGATTTAAACTCAAATT
46334268 AAAA
1 AAAA
46334272 TCCCAAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.57, C:0.09, G:0.07, T:0.27
Consensus pattern (20 bp):
AAAAGATTTAAACTCAAATT
Found at i:46337025 original size:16 final size:16
Alignment explanation
Indices: 46337004--46337035 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
46336994 CAGGTTTAAA
46337004 AGAGTTTTGGAAGTAT
1 AGAGTTTTGGAAGTAT
46337020 AGAGTTTTGGAAGTAT
1 AGAGTTTTGGAAGTAT
46337036 GTATTGACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (16 bp):
AGAGTTTTGGAAGTAT
Found at i:46340103 original size:74 final size:75
Alignment explanation
Indices: 46339920--46340129 Score: 332
Period size: 74 Copynumber: 2.8 Consensus size: 75
46339910 TATCCGTTAT
* * *
46339920 CGGTGGATTCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGTAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
*
46339985 ATTTAAGAAA
66 ATCTAAGAAA
* *
46339995 CGGTGGGATCAGCACTTAGGAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
* *
46340060 A-CTCAGATA
66 ATCTAAGAAA
*
46340069 CGGTGGAACCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTT
46340130 GGGGGAATCA
Statistics
Matches: 124, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
74 63 0.51
75 61 0.49
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.20
Consensus pattern (75 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
ATCTAAGAAA
Found at i:46340193 original size:104 final size:102
Alignment explanation
Indices: 46340030--46340262 Score: 369
Period size: 104 Copynumber: 2.3 Consensus size: 102
46340020 CCAATGATTC
*
46340030 GGGGAATCAGCACTTAGCAA-CCCCTTTCACACTCAGATACGGTGGAACCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTTCACACTAAGATACGGTGGAACCAGCACTTAGCAACCA
46340094 CCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
66 CCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
* ** **
46340131 GGGGAATCAGCACTTAGCAACCCCCTTTTACTTTTAAAGATACGGTGGAGTCAGCACTTAGCAAC
1 GGGGAATCAGCACTTAGCAACCCCCTTTCAC-ACT-AAGATACGGTGGAACCAGCACTTAGCAAC
*
46340196 CACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTG
64 CACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
*
46340235 AGGGAATCAGCACTTAGCAACCCCCTTT
1 GGGGAATCAGCACTTAGCAACCCCCTTT
46340263 ATATTCAATA
Statistics
Matches: 121, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
101 20 0.17
102 9 0.07
103 1 0.01
104 91 0.75
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCCTTTCACACTAAGATACGGTGGAACCAGCACTTAGCAACCA
CCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
Found at i:46347087 original size:33 final size:33
Alignment explanation
Indices: 46347032--46347238 Score: 128
Period size: 33 Copynumber: 5.7 Consensus size: 33
46347022 TTATCCGTTA
*
46347032 TCGGTGGATTCAGCACTTAGCAACCACCCATGAG
1 TCGG-GGAATCAGCACTTAGCAACCACCCATGAG
* * *
46347066 TCGGGGAATCAACACTTAGCAACCCCTTTCACATTTAAG
1 TCGGGGAATCAGCACTTAGCAACCAC---C-CA--TGAG
* * * *
46347105 ATACGGTGGGATCAGCGCTTAGCAACCACCAATGAT
1 -T-CGG-GGAATCAGCACTTAGCAACCACCCATGAG
* *
46347141 TCGGGGAATCAGCACTTAGCAACCCCTTTCACACTTAG
1 TCGGGGAATCAGCACTTAGCAACCAC---C-CA-TGAG
*
46347179 ATACGGTGGAATCAGCACTTAGCAACCACCAATGA-
1 -T-CGG-GGAATCAGCACTTAGCAACCACCCATGAG
*
46347214 TCTGGGGAATCAGCACGTAGCAACC
1 TC-GGGGAATCAGCACTTAGCAACC
46347239 CCTTAGGGGG
Statistics
Matches: 134, Mismatches: 21, Indels: 37
0.70 0.11 0.19
Matches are distributed among these distances:
33 58 0.43
34 10 0.07
35 1 0.01
36 6 0.04
37 4 0.03
38 4 0.03
39 5 0.04
40 4 0.03
41 24 0.18
42 18 0.13
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (33 bp):
TCGGGGAATCAGCACTTAGCAACCACCCATGAG
Found at i:46347157 original size:75 final size:73
Alignment explanation
Indices: 46347033--46347242 Score: 314
Period size: 74 Copynumber: 2.8 Consensus size: 73
46347023 TATCCGTTAT
* *
46347033 CGGT-GGATTCAGCACTTAGCAACCACCCATGAGTCGGGGAATCAACACTTAGCAACCCCTTTCA
1 CGGTGGGA-TCAGCACTTAGCAACCACCAATGA-TCGGGGAATCAGCACTTAGCAACCCCTTTCA
*
46347097 CATTTAAGATA
64 CACTT-AGATA
*
46347108 CGGTGGGATCAGCGCTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGGATCAGCACTTAGCAACCACCAATGA-TCGGGGAATCAGCACTTAGCAACCCCTTTCAC
46347173 ACTTAGATA
65 ACTTAGATA
* *
46347182 CGGTGGAATCAGCACTTAGCAACCACCAATGATCTGGGGAATCAGCACGTAGCAACCCCTT
1 CGGTGGGATCAGCACTTAGCAACCACCAATGATC-GGGGAATCAGCACTTAGCAACCCCTT
46347243 AGGGGGATTT
Statistics
Matches: 125, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
73 2 0.02
74 60 0.48
75 60 0.48
76 3 0.02
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.21
Consensus pattern (73 bp):
CGGTGGGATCAGCACTTAGCAACCACCAATGATCGGGGAATCAGCACTTAGCAACCCCTTTCACA
CTTAGATA
Found at i:46347210 original size:74 final size:74
Alignment explanation
Indices: 46347033--46347242 Score: 323
Period size: 75 Copynumber: 2.8 Consensus size: 74
46347023 TATCCGTTAT
* * *
46347033 CGGTGGATTCAGCACTTAGCAACCACCCATGAGTCGGGGAATCAACACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGA-TCGGGGAATCAGCACTTAGCAACCCCTTTCAC
*
46347098 ATTTAAGATA
65 ACTTAAGATA
* *
46347108 CGGTGGGATCAGCGCTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGA-TCGGGGAATCAGCACTTAGCAACCCCTTTCAC
46347173 ACTT-AGATA
65 ACTTAAGATA
*
46347182 CGGTGGAATCAGCACTTAGCAACCACCAATGATCTGGGGAATCAGCACGTAGCAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATC-GGGGAATCAGCACTTAGCAACCCCTT
46347243 AGGGGGATTT
Statistics
Matches: 124, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
73 2 0.02
74 60 0.48
75 62 0.50
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.21
Consensus pattern (74 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGATCGGGGAATCAGCACTTAGCAACCCCTTTCACA
CTTAAGATA
Found at i:46347303 original size:105 final size:102
Alignment explanation
Indices: 46347143--46347376 Score: 346
Period size: 105 Copynumber: 2.3 Consensus size: 102
46347133 CCAATGATTC
46347143 GGGGAATCAGCACTTAGCAA-CCCCTTTCACACTTAGATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTTCACACTTAGATACGGTGGAATCAGCACTTAGCAACCA
*
46347207 CCAATGA-TCTGGGGAATCAGCACGTAGCAACCCCTTAG
66 CCAATGATTC-GGGGAATCAACACGTAGCAACCCCTT-G
* * * * *
46347245 GGGGATTTAGCACTTAGCAACCCCCTTTTACATTTAAAGATACGGTGGAGTCAGCACTTAGCAAC
1 GGGGAATCAGCACTTAGCAACCCCCTTTCACACTT--AGATACGGTGGAATCAGCACTTAGCAAC
* *
46347310 CACCAGTGATTCGGGGAATCAACACTTAGCAACCCCTTG
64 CACCAATGATTCGGGGAATCAACACGTAGCAACCCCTTG
46347349 GGGGAATCAGCACTTAGCAACCCCCTTT
1 GGGGAATCAGCACTTAGCAACCCCCTTT
46347377 ATATTCAATA
Statistics
Matches: 118, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
102 18 0.15
103 12 0.10
104 27 0.23
105 59 0.50
106 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCCTTTCACACTTAGATACGGTGGAATCAGCACTTAGCAACCA
CCAATGATTCGGGGAATCAACACGTAGCAACCCCTTG
Found at i:46349268 original size:23 final size:23
Alignment explanation
Indices: 46349224--46349268 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
46349214 CTTTTCAATA
*
46349224 TATAAAAATAATAAAATATTAAG
1 TATAAAAATAATAAAAGATTAAG
* * *
46349247 TATATAAATAATATAAGGTTAA
1 TATAAAAATAATAAAAGATTAA
46349269 TAGATCAAGC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (23 bp):
TATAAAAATAATAAAAGATTAAG
Found at i:46349346 original size:14 final size:15
Alignment explanation
Indices: 46349319--46349347 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
46349309 TAGTCATTAT
46349319 ACTTAAATATTTTTA
1 ACTTAAATATTTTTA
46349334 ACTTAAA-ATTTTTA
1 ACTTAAATATTTTTA
46349348 GTCCAGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (15 bp):
ACTTAAATATTTTTA
Found at i:46355232 original size:11 final size:11
Alignment explanation
Indices: 46355211--46355254 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
46355201 ATCTTAATAG
46355211 AATTGAATTAAA
1 AATT-AATTAAA
46355223 AATTAATTAAA
1 AATTAATTAAA
*
46355234 TAA-TAATAAAA
1 -AATTAATTAAA
46355245 AATTAATTAA
1 AATTAATTAA
46355255 CTTGAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
10 2 0.07
11 20 0.71
12 6 0.21
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (11 bp):
AATTAATTAAA
Found at i:46355327 original size:24 final size:26
Alignment explanation
Indices: 46355299--46355351 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 26
46355289 ATTCAACTGA
46355299 ATTTTATTATTTTTAAT-ATTT-TTT
1 ATTTTATTATTTTTAATAATTTATTT
46355323 A--TT-TTATTTTTAATAATTTATTT
1 ATTTTATTATTTTTAATAATTTATTT
46355346 ATTTTA
1 ATTTTA
46355352 AATTAGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
21 11 0.46
22 6 0.25
23 4 0.17
24 1 0.04
25 2 0.08
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (26 bp):
ATTTTATTATTTTTAATAATTTATTT
Found at i:46355331 original size:21 final size:23
Alignment explanation
Indices: 46355305--46355351 Score: 80
Period size: 21 Copynumber: 2.1 Consensus size: 23
46355295 CTGAATTTTA
46355305 TTATTTTTAAT-ATTT-TTTATT
1 TTATTTTTAATAATTTATTTATT
46355326 TTATTTTTAATAATTTATTTATT
1 TTATTTTTAATAATTTATTTATT
46355349 TTA
1 TTA
46355352 AATTAGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 11 0.46
22 4 0.17
23 9 0.38
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (23 bp):
TTATTTTTAATAATTTATTTATT
Found at i:46356876 original size:8 final size:8
Alignment explanation
Indices: 46356863--46356892 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
46356853 TGACTTGGGG
46356863 AGAAGAGA
1 AGAAGAGA
46356871 AGAAGAGA
1 AGAAGAGA
*
46356879 GGAAGAGA
1 AGAAGAGA
46356887 AGAAGA
1 AGAAGA
46356893 AATAAATTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (8 bp):
AGAAGAGA
Found at i:46358348 original size:11 final size:11
Alignment explanation
Indices: 46358334--46358358 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
46358324 TAATATATTG
46358334 TTAAACAATAT
1 TTAAACAATAT
46358345 TTAAACAATAT
1 TTAAACAATAT
46358356 TTA
1 TTA
46358359 GAATAGATGA
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (11 bp):
TTAAACAATAT
Found at i:46384975 original size:43 final size:43
Alignment explanation
Indices: 46384928--46385027 Score: 132
Period size: 43 Copynumber: 2.3 Consensus size: 43
46384918 TAGGACCATG
*
46384928 TCTGGGACGTTGGCATCGA-CTTGTGTTTTCATGTAAGACCACA
1 TCTGGGACGTTGGCATCGATC-TGTGTTTACATGTAAGACCACA
**
46384971 TCTGGGACAG-TGGCATCGATCTGTGTTTACATGTAAGACCATG
1 TCTGGGAC-GTTGGCATCGATCTGTGTTTACATGTAAGACCACA
*
46385014 TTTGGGACGTTGGC
1 TCTGGGACGTTGGC
46385028 GTTGTACGAG
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
42 1 0.02
43 47 0.94
44 2 0.04
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.32
Consensus pattern (43 bp):
TCTGGGACGTTGGCATCGATCTGTGTTTACATGTAAGACCACA
Found at i:46390994 original size:22 final size:22
Alignment explanation
Indices: 46390969--46391017 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
46390959 TTTTTTTTCG
* *
46390969 AGACAAATAAGCTTTTGTCTCA
1 AGACAAACAAGCTTTTGTCTAA
**
46390991 AGACATGCAAGCTTTTGTCTAA
1 AGACAAACAAGCTTTTGTCTAA
46391013 AGACA
1 AGACA
46391018 GTAGCCCCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (22 bp):
AGACAAACAAGCTTTTGTCTAA
Found at i:46391675 original size:16 final size:18
Alignment explanation
Indices: 46391656--46391693 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
46391646 AGTTTTATTG
46391656 TTTAT-ATGTT-TATAAT
1 TTTATAATGTTATATAAT
*
46391672 TTTATAATTTTATATAAT
1 TTTATAATGTTATATAAT
46391690 TTTA
1 TTTA
46391694 ATTTAGAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 4 0.21
18 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTATAATGTTATATAAT
Found at i:46392013 original size:15 final size:17
Alignment explanation
Indices: 46391982--46392013 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
46391972 AAATTTTTTA
46391982 ATTTATAAATGATTATT
1 ATTTATAAATGATTATT
46391999 ATTT-TAAAT-ATTATT
1 ATTTATAAATGATTATT
46392014 TACATTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
ATTTATAAATGATTATT
Found at i:46394464 original size:22 final size:22
Alignment explanation
Indices: 46394438--46394479 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
46394428 GGTTGCTGCC
46394438 ATTATTTTTATTC-AATTTTGCT
1 ATTATTTTT-TTCTAATTTTGCT
46394460 ATTATTTTTTTCTAATTTTG
1 ATTATTTTTTTCTAATTTTG
46394480 GGGTTAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (22 bp):
ATTATTTTTTTCTAATTTTGCT
Found at i:46403906 original size:36 final size:36
Alignment explanation
Indices: 46403859--46403932 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
46403849 AAACGAAATG
46403859 TATAATTATTTCAGAAAACTTCCTACCCAACTCTAC
1 TATAATTATTTCAGAAAACTTCCTACCCAACTCTAC
46403895 TATAATTATTTCAGAAAACTTCCTACCCAACTCTAC
1 TATAATTATTTCAGAAAACTTCCTACCCAACTCTAC
46403931 TA
1 TA
46403933 CACAACAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (36 bp):
TATAATTATTTCAGAAAACTTCCTACCCAACTCTAC
Found at i:46407487 original size:3 final size:3
Alignment explanation
Indices: 46407479--46407508 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
46407469 TTTTATATTG
46407479 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
46407509 TTATGTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:46408587 original size:22 final size:22
Alignment explanation
Indices: 46408535--46408588 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 22
46408525 AGCAATTTAA
46408535 TTTTTTTTCCTTTTATGTTCTT
1 TTTTTTTTCCTTTTATGTTCTT
**** * *
46408557 TAGACTTTCCTTTTTTTTTCTT
1 TTTTTTTTCCTTTTATGTTCTT
46408579 TTTTTTTTCC
1 TTTTTTTTCC
46408589 ATTCTCTTTT
Statistics
Matches: 22, Mismatches: 10, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.74
Consensus pattern (22 bp):
TTTTTTTTCCTTTTATGTTCTT
Found at i:46409130 original size:22 final size:22
Alignment explanation
Indices: 46409104--46409149 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
46409094 AATGGAAAAT
*
46409104 AAAGAAAAAAAAAGGAAAGTTA
1 AAAGAAAAAAAAAGAAAAGTTA
* * *
46409126 AAAGAACATAAAAGAAAATTTA
1 AAAGAAAAAAAAAGAAAAGTTA
46409148 AA
1 AA
46409150 TTACTCAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.72, C:0.02, G:0.13, T:0.13
Consensus pattern (22 bp):
AAAGAAAAAAAAAGAAAAGTTA
Found at i:46412374 original size:24 final size:24
Alignment explanation
Indices: 46412326--46412372 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
46412316 ACTTGTCATA
*
46412326 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
46412350 GAGAGAGTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
46412373 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.40, T:0.23
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:46413643 original size:27 final size:27
Alignment explanation
Indices: 46413457--46413632 Score: 255
Period size: 27 Copynumber: 6.5 Consensus size: 27
46413447 ATAGATACTT
*
46413457 ATAGGGTAAAATGACGGAAATACCCCC
1 ATAGGGTAAAATGACTGAAATACCCCC
*
46413484 ATAGGGTAAAATGACTAAAATACCCCC
1 ATAGGGTAAAATGACTGAAATACCCCC
** ** *
46413511 ATAGATTAAAGGGA-TCGAAATACCCTC
1 ATAGGGTAAAATGACT-GAAATACCCCC
*
46413538 ATAGGGTAAAATGATTGAAATACCCCC
1 ATAGGGTAAAATGACTGAAATACCCCC
*
46413565 ATAGGGTAAAATGACTGAAATACCCCT
1 ATAGGGTAAAATGACTGAAATACCCCC
46413592 ATAGGGTAAAATGACTGAAATACCCCC
1 ATAGGGTAAAATGACTGAAATACCCCC
46413619 ATAGGGTAAAATGA
1 ATAGGGTAAAATGA
46413633 TTGTTATACC
Statistics
Matches: 131, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
26 1 0.01
27 129 0.98
28 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (27 bp):
ATAGGGTAAAATGACTGAAATACCCCC
Found at i:46413656 original size:54 final size:53
Alignment explanation
Indices: 46413457--46413658 Score: 235
Period size: 54 Copynumber: 3.7 Consensus size: 53
46413447 ATAGATACTT
** * *
46413457 ATAGGGTAAAATGACGGAAATACCCCCATAGGGTAAAATGACTAAAATACCCCC
1 ATAGGGTAAAATGATTGAAATA-CCCTATAGGGTAAAATGACTGAAATACCCCC
** ** * *
46413511 ATAGATTAAAGGGATCGAAATACCCTCATAGGGTAAAATGATTGAAATACCCCC
1 ATAGGGTAAAATGATTGAAATACCCT-ATAGGGTAAAATGACTGAAATACCCCC
*
46413565 ATAGGGTAAAATGACTGAAATACCCCTATAGGGTAAAATGACTGAAATACCCCC
1 ATAGGGTAAAATGATTGAAATA-CCCTATAGGGTAAAATGACTGAAATACCCCC
**
46413619 ATAGGGTAAAATGATTGTTATACCCT-TAGGAGATAAAATG
1 ATAGGGTAAAATGATTGAAATACCCTATAGG-G-TAAAATG
46413659 GCTGTTATGG
Statistics
Matches: 125, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
52 4 0.03
53 8 0.06
54 109 0.87
55 4 0.03
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (53 bp):
ATAGGGTAAAATGATTGAAATACCCTATAGGGTAAAATGACTGAAATACCCCC
Found at i:46413896 original size:26 final size:26
Alignment explanation
Indices: 46413867--46413943 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 26
46413857 TGTGCCACAT
46413867 ATACTATTACTAGCAGCTTTGCTGCG
1 ATACTATTACTAGCAGCTTTGCTGCG
* * *
46413893 ATACTGA-TATTGGCAGCTCTGCTGCG
1 ATACT-ATTACTAGCAGCTTTGCTGCG
* * *
46413919 TTGCTATTACTTGCAGCTTTGCTGC
1 ATACTATTACTAGCAGCTTTGCTGC
46413944 AATATTGGTG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
25 1 0.02
26 39 0.95
27 1 0.02
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.36
Consensus pattern (26 bp):
ATACTATTACTAGCAGCTTTGCTGCG
Found at i:46422196 original size:19 final size:19
Alignment explanation
Indices: 46422172--46422209 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
46422162 ACCTAACGAG
*
46422172 ATGATTGATGTATTTTTTT
1 ATGATTAATGTATTTTTTT
46422191 ATGATTAATGTATTTTTTT
1 ATGATTAATGTATTTTTTT
46422210 TCTAAATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.63
Consensus pattern (19 bp):
ATGATTAATGTATTTTTTT
Found at i:46427817 original size:28 final size:29
Alignment explanation
Indices: 46427758--46427825 Score: 95
Period size: 30 Copynumber: 2.4 Consensus size: 29
46427748 CAGTTGAACA
46427758 TAAATTTTAAAAATAAAAAATAGAGTAAT
1 TAAATTTTAAAAATAAAAAATAGAGTAAT
* *
46427787 TAAATTTCTATAAATAAAAAATATA-T-AT
1 TAAATTT-TAAAAATAAAAAATAGAGTAAT
46427815 TAAATTTTAAA
1 TAAATTTTAAA
46427826 TTTACTAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 3 0.09
28 9 0.26
29 8 0.23
30 15 0.43
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (29 bp):
TAAATTTTAAAAATAAAAAATAGAGTAAT
Found at i:46428108 original size:12 final size:12
Alignment explanation
Indices: 46428091--46428115 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46428081 AAATTTTATT
46428091 AAATTTAATTTA
1 AAATTTAATTTA
46428103 AAATTTAATTTA
1 AAATTTAATTTA
46428115 A
1 A
46428116 TTTTTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATTTAATTTA
Found at i:46428640 original size:29 final size:29
Alignment explanation
Indices: 46428607--46428662 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
46428597 CTCAAAGGAA
46428607 TTTTAGAATATTTTCAAATGTGTCATTAT
1 TTTTAGAATATTTTCAAATGTGTCATTAT
* * *
46428636 TTTTAGATTTTTTTTAAATGTGTCATT
1 TTTTAGAATATTTTCAAATGTGTCATT
46428663 TTACTCATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (29 bp):
TTTTAGAATATTTTCAAATGTGTCATTAT
Found at i:46431648 original size:25 final size:25
Alignment explanation
Indices: 46431601--46431649 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
46431591 GTTCACTTTT
*
46431601 TTACAAAAATAATATAAACAATTAA
1 TTACAAAAATAATATAAAAAATTAA
*
46431626 TTACAAAAATAGGTA-AAAAAATTA
1 TTACAAAAATA-ATATAAAAAATTA
46431650 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (25 bp):
TTACAAAAATAATATAAAAAATTAA
Found at i:46431965 original size:17 final size:18
Alignment explanation
Indices: 46431924--46431966 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
46431914 GGCTCCATAA
*
46431924 TTTCCCTTTCTTTTCTTT
1 TTTCTCTTTCTTTTCTTT
*
46431942 CTT-TCTTTCTTTT-TTT
1 TTTCTCTTTCTTTTCTTT
46431958 TTTCTCTTT
1 TTTCTCTTT
46431967 TCATGTTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 5 0.24
17 14 0.67
18 2 0.10
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTCTCTTTCTTTTCTTT
Found at i:46433488 original size:2 final size:2
Alignment explanation
Indices: 46433481--46433510 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
46433471 GTCTTTGAAC
*
46433481 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46433511 AATTAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:46435875 original size:24 final size:24
Alignment explanation
Indices: 46435848--46435899 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
46435838 TTTCTAGGAG
* **
46435848 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
46435872 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
46435896 ATTT
1 ATTT
46435900 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:46440300 original size:24 final size:24
Alignment explanation
Indices: 46440238--46440289 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
46440228 TTTCTAGAAG
* **
46440238 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGTATTTATTAACATAATAT
46440262 ATTTAGTATTTATTAACATAATAT
1 ATTTAGTATTTATTAACATAATAT
46440286 ATTT
1 ATTT
46440290 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGTATTTATTAACATAATAT
Found at i:46440934 original size:31 final size:31
Alignment explanation
Indices: 46440898--46440957 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
46440888 ATTCATTTAA
46440898 TGGCTTTTCAAATATATGAAAATTTTGAAAT
1 TGGCTTTTCAAATATATGAAAATTTTGAAAT
46440929 TGGCTTTTCAAATATATGAAAATTTTGAA
1 TGGCTTTTCAAATATATGAAAATTTTGAA
46440958 TATATTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (31 bp):
TGGCTTTTCAAATATATGAAAATTTTGAAAT
Found at i:46454968 original size:19 final size:20
Alignment explanation
Indices: 46454944--46454981 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
46454934 CCCTATTTTT
46454944 AATTTTTTT-TATTTTTTCC
1 AATTTTTTTGTATTTTTTCC
*
46454963 AATTTTTTTGTGTTTTTTC
1 AATTTTTTTGTATTTTTTC
46454982 AAAATGATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.13, C:0.08, G:0.05, T:0.74
Consensus pattern (20 bp):
AATTTTTTTGTATTTTTTCC
Found at i:46469263 original size:14 final size:15
Alignment explanation
Indices: 46469239--46469267 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
46469229 TTTTTCTATT
46469239 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
46469254 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
46469268 AGTTTCGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:46470486 original size:43 final size:43
Alignment explanation
Indices: 46470424--46470548 Score: 130
Period size: 43 Copynumber: 2.9 Consensus size: 43
46470414 GATTTTCGAG
*
46470424 GTGTGTTATCGTGTAAGACCACGTCTGGGACGTTGGCATCGACT-T
1 GTGT-TTA-CGTGTAAGACCACGTCTGGGACGTTGGCATCGA-TAC
*
46470469 GTGTTTACGTGTGAGACC-CTGTCTGGGACAG-TGGCATCGATAC
1 GTGTTTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATAC
* ** *
46470512 GTGATTACAAGTAAGACCACGTCTGGGATGTTGGCAT
1 GTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCAT
46470549 TGTAAGAGTT
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
42 3 0.04
43 56 0.82
44 5 0.07
45 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (43 bp):
GTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCATCGATAC
Found at i:46471418 original size:23 final size:23
Alignment explanation
Indices: 46471391--46471561 Score: 96
Period size: 23 Copynumber: 7.3 Consensus size: 23
46471381 ATGAGTTGAA
*
46471391 CCAATTTGTTACAAATATGTTGT
1 CCAATTTGTTACAAATATGCTGT
* * * **
46471414 CCAATTTTGATGCTTAA-ATGCTAC
1 CCAA-TTTGTTAC-AAATATGCTGT
*
46471438 CCAATTTGTTACATATATGCTGT
1 CCAATTTGTTACAAATATGCTGT
* * * *
46471461 CCAATTTTGATGCTTAA-ATGCTGC
1 CCAA-TTTGTTAC-AAATATGCTGT
*
46471485 CCAATTTGTTACATATATGCTGT
1 CCAATTTGTTACAAATATGCTGT
* ** *
46471508 CCAATTTTGATGATTAA-ATGCTGC
1 CCAA-TTTG-TTACAAATATGCTGT
* *
46471532 CCAATTTGTTACATATATGATGT
1 CCAATTTGTTACAAATATGCTGT
*
46471555 CTAATTT
1 CCAATTT
46471562 TGATGCTTAA
Statistics
Matches: 105, Mismatches: 34, Indels: 18
0.67 0.22 0.11
Matches are distributed among these distances:
22 5 0.05
23 50 0.48
24 44 0.42
25 6 0.06
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (23 bp):
CCAATTTGTTACAAATATGCTGT
Found at i:46471528 original size:24 final size:24
Alignment explanation
Indices: 46471414--46471585 Score: 113
Period size: 24 Copynumber: 7.3 Consensus size: 24
46471404 AATATGTTGT
* *
46471414 CCAATTTTGATGCTTAAATGCTAC
1 CCAATTTTGATGATTAAATGCTGC
* * * *
46471438 CCAA-TTTG-TTACATATATGCTGT
1 CCAATTTTGATGA-TTAAATGCTGC
*
46471461 CCAATTTTGATGCTTAAATGCTGC
1 CCAATTTTGATGATTAAATGCTGC
* * * *
46471485 CCAA-TTTG-TTACATATATGCTGT
1 CCAATTTTGATGA-TTAAATGCTGC
46471508 CCAATTTTGATGATTAAATGCTGC
1 CCAATTTTGATGATTAAATGCTGC
* * * * *
46471532 CCAA-TTTG-TTACATATATGATGT
1 CCAATTTTGATGA-TTAAATGCTGC
* *
46471555 CTAATTTTGATGCTTAAATGCTGC
1 CCAATTTTGATGATTAAATGCTGC
46471579 CCAATTT
1 CCAATTT
46471586 GTTGCATATA
Statistics
Matches: 106, Mismatches: 33, Indels: 18
0.68 0.21 0.11
Matches are distributed among these distances:
22 4 0.04
23 45 0.42
24 53 0.50
25 4 0.04
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (24 bp):
CCAATTTTGATGATTAAATGCTGC
Found at i:46471621 original size:47 final size:47
Alignment explanation
Indices: 46471391--46471610 Score: 359
Period size: 47 Copynumber: 4.7 Consensus size: 47
46471381 ATGAGTTGAA
* * *
46471391 CCAATTTGTTACAAATATGTTGTCCAATTTTGATGCTTAAATGCTAC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
46471438 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
*
46471485 CCAATTTGTTACATATATGCTGTCCAATTTTGATGATTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
* *
46471532 CCAATTTGTTACATATATGATGTCTAATTTTGATGCTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
* * *
46471579 CCAATTTGTTGCATATATGCTATCCAGTTTTG
1 CCAATTTGTTACATATATGCTGTCCAATTTTG
46471611 GTGTAAAAAT
Statistics
Matches: 161, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 161 1.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (47 bp):
CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
Found at i:46471642 original size:94 final size:94
Alignment explanation
Indices: 46471391--46471644 Score: 303
Period size: 94 Copynumber: 2.7 Consensus size: 94
46471381 ATGAGTTGAA
* * * * * * **
46471391 CCAATTTGTTACAAATATGTTGTCCAATTTTGATGCTTAAATGCTACCCAATTTGTTACATATAT
1 CCAATTTGTTACATATATGCTATCCAATTTTGATGATAAAATGCTGCCCAAACTGTTACATATAT
*
46471456 GCTGTCCAATTTTGATGCTTAAATGCTGC
66 GATGTCCAATTTTGATGCTTAAATGCTGC
* * **
46471485 CCAATTTGTTACATATATGCTGTCCAATTTTGATGATTAAATGCTGCCCAATTTGTTACATATAT
1 CCAATTTGTTACATATATGCTATCCAATTTTGATGATAAAATGCTGCCCAAACTGTTACATATAT
*
46471550 GATGTCTAATTTTGATGCTTAAATGCTGC
66 GATGTCCAATTTTGATGCTTAAATGCTGC
* * * * * **
46471579 CCAATTTGTTGCATATATGCTATCCAGTTTTGGTG-TAAAAATGTTGCTCAAACTGTTGTATATA
1 CCAATTTGTTACATATATGCTATCCAATTTTGATGAT-AAAATGCTGCCCAAACTGTTACATATA
46471643 TG
65 TG
46471645 CTGCCCAAAT
Statistics
Matches: 142, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
93 1 0.01
94 141 0.99
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (94 bp):
CCAATTTGTTACATATATGCTATCCAATTTTGATGATAAAATGCTGCCCAAACTGTTACATATAT
GATGTCCAATTTTGATGCTTAAATGCTGC
Found at i:46471645 original size:141 final size:141
Alignment explanation
Indices: 46471391--46471652 Score: 364
Period size: 141 Copynumber: 1.9 Consensus size: 141
46471381 ATGAGTTGAA
*
46471391 CCAATTTGTTACAAATATGTTGTCCAATTTTGATGCTTAAATGCTACCCAATTTGTTACATATAT
1 CCAATTTGTTACAAATATGATGTCCAATTTTGATGCTTAAATGCTACCCAATTTGTTACATATAT
* * ** *
46471456 GCTGTCCAATTTTGATGCTTAAATGCTGCCCAATTTGTTACATATATGCTGTCCAATTTTGATGA
66 GCTATCCAATTTTGATGCTAAAATGCTGCCCAAACTGTTACATATATGCTGCCCAATTTTGATGA
46471521 TTAAATGCTGC
131 TTAAATGCTGC
* * * *
46471532 CCAATTTGTTACATATATGATGTCTAATTTTGATGCTTAAATGCTGCCCAATTTGTTGCATATAT
1 CCAATTTGTTACAAATATGATGTCCAATTTTGATGCTTAAATGCTACCCAATTTGTTACATATAT
* * * * **
46471597 GCTATCCAGTTTTGGTG-TAAAAATGTTGCTCAAACTGTTGTATATATGCTGCCCAA
66 GCTATCCAATTTTGATGCT-AAAATGCTGCCCAAACTGTTACATATATGCTGCCCAA
46471653 ATTGATGTAT
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
140 1 0.01
141 103 0.99
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.40
Consensus pattern (141 bp):
CCAATTTGTTACAAATATGATGTCCAATTTTGATGCTTAAATGCTACCCAATTTGTTACATATAT
GCTATCCAATTTTGATGCTAAAATGCTGCCCAAACTGTTACATATATGCTGCCCAATTTTGATGA
TTAAATGCTGC
Found at i:46471653 original size:23 final size:23
Alignment explanation
Indices: 46471627--46471676 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
46471617 AAATGTTGCT
*
46471627 CAAACTGTTGTATATATGCTGCC
1 CAAACTGATGTATATATGCTGCC
* * *
46471650 CAAATTGATGTATTTATGCTGTC
1 CAAACTGATGTATATATGCTGCC
46471673 CAAA
1 CAAA
46471677 TTTTGGTGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (23 bp):
CAAACTGATGTATATATGCTGCC
Found at i:46471677 original size:23 final size:23
Alignment explanation
Indices: 46471635--46471678 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
46471625 CTCAAACTGT
46471635 TGTATATATGCTGCCCAAATTGA
1 TGTATATATGCTGCCCAAATTGA
* *
46471658 TGTATTTATGCTGTCCAAATT
1 TGTATATATGCTGCCCAAATT
46471679 TTGGTGTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (23 bp):
TGTATATATGCTGCCCAAATTGA
Found at i:46471717 original size:71 final size:73
Alignment explanation
Indices: 46471569--46471748 Score: 192
Period size: 71 Copynumber: 2.5 Consensus size: 73
46471559 TTTTGATGCT
* * * * *
46471569 TAAATGCTGCCCAATTTGTTGCATATATGCTATCC-AGTTTTGGTGTAAAAATGTTGCTCAAACT
1 TAAATGCTGCCCAAATTGATGTATATATGCTGTCCAAATTTTGGTGTAAAAATGTTGCTCAAACT
46471633 GTTGTATA
66 GTTGTATA
* * *
46471641 T--ATGCTGCCCAAATTGATGTATTTATGCTGTCCAAATTTTGGTGTGAAAATGTTG-TCTAA-T
1 TAAATGCTGCCCAAATTGATGTATATATGCTGTCCAAATTTTGGTGTAAAAATGTTGCTCAAACT
46471702 -TTGGTATA
66 GTT-GTATA
** * * *
46471710 TAAATGCTGTTCAAATTTATGTATAAAAGCTGTCCAAAT
1 TAAATGCTGCCCAAATTGATGTATATATGCTGTCCAAAT
46471749 ATGGTAGATT
Statistics
Matches: 90, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
68 2 0.02
69 7 0.08
70 31 0.34
71 49 0.54
72 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.39
Consensus pattern (73 bp):
TAAATGCTGCCCAAATTGATGTATATATGCTGTCCAAATTTTGGTGTAAAAATGTTGCTCAAACT
GTTGTATA
Found at i:46478085 original size:25 final size:25
Alignment explanation
Indices: 46478057--46478110 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
46478047 TTTGTGATCA
46478057 TTTTTGAACCAA-TATTCTTTCAGTC
1 TTTTTGAA-CAATTATTCTTTCAGTC
* *
46478082 TTTTTGAATAATTATTCTTTCATTC
1 TTTTTGAACAATTATTCTTTCAGTC
46478107 TTTT
1 TTTT
46478111 GGATTTCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.22, C:0.15, G:0.06, T:0.57
Consensus pattern (25 bp):
TTTTTGAACAATTATTCTTTCAGTC
Found at i:46479247 original size:13 final size:13
Alignment explanation
Indices: 46479231--46479323 Score: 57
Period size: 13 Copynumber: 7.3 Consensus size: 13
46479221 AATCACAATC
*
46479231 AAAATCAAAAAAG
1 AAAATAAAAAAAG
* **
46479244 AAAAGAAAAATTG
1 AAAATAAAAAAAG
*
46479257 AAATTAAAAAAAG
1 AAAATAAAAAAAG
* *
46479270 -TAATAAAAAAAT
1 AAAATAAAAAAAG
* *
46479282 AAAATCAAAAAAT
1 AAAATAAAAAAAG
* *
46479295 AAAA-AAAAGAAC
1 AAAATAAAAAAAG
46479307 AAAA-AAAAGAAAG
1 AAAATAAAA-AAAG
46479320 AAAA
1 AAAA
46479324 AGAAGAAGAA
Statistics
Matches: 60, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
12 22 0.37
13 38 0.63
ACGTcount: A:0.78, C:0.03, G:0.08, T:0.11
Consensus pattern (13 bp):
AAAATAAAAAAAG
Found at i:46479252 original size:12 final size:11
Alignment explanation
Indices: 46479237--46479336 Score: 58
Period size: 12 Copynumber: 8.3 Consensus size: 11
46479227 AATCAAAATC
46479237 AAAAAAGAAAA
1 AAAAAAGAAAA
*
46479248 GAAAAATTGAAATTA
1 -AAAAA-AGAAA--A
*
46479263 AAAAAAGTAATA
1 AAAAAAG-AAAA
*
46479275 AAAAAATAAAA
1 AAAAAAGAAAA
* *
46479286 TCAAAAA-ATAA
1 -AAAAAAGAAAA
46479297 AAAAAAGAACAA
1 AAAAAAGAA-AA
46479309 AAAAAAGAAAGA
1 AAAAAAGAAA-A
46479321 AAAAGAAGAAGAA
1 AAAA-AAGAA-AA
46479334 AAA
1 AAA
46479337 GTCAAAATCA
Statistics
Matches: 69, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
10 5 0.07
11 8 0.12
12 33 0.48
13 14 0.20
14 8 0.12
15 1 0.01
ACGTcount: A:0.79, C:0.02, G:0.10, T:0.09
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:46479298 original size:19 final size:19
Alignment explanation
Indices: 46479271--46479312 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
46479261 TAAAAAAAGT
*
46479271 AATAAAAAAATAAAATCAAAA
1 AATAAAAAAA-AGAA-CAAAA
46479292 AATAAAAAAAAGAACAAAA
1 AATAAAAAAAAGAACAAAA
46479311 AA
1 AA
46479313 AAGAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 3 0.15
21 10 0.50
ACGTcount: A:0.83, C:0.05, G:0.02, T:0.10
Consensus pattern (19 bp):
AATAAAAAAAAGAACAAAA
Found at i:46479310 original size:25 final size:25
Alignment explanation
Indices: 46479230--46479310 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
46479220 AAATCACAAT
*
46479230 CAAAATCAAAAAAG-AAAAGAAAAATT
1 CAAAATCAAAAAAGTAAAA-AAAAA-A
* * * *
46479256 GAAATTAAAAAAAGTAATAAAAAAA
1 CAAAATCAAAAAAGTAAAAAAAAAA
*
46479281 TAAAATCAAAAAA-TAAAAAAAAGAA
1 CAAAATCAAAAAAGTAAAAAAAA-AA
46479306 CAAAA
1 CAAAA
46479311 AAAAGAAAGA
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
24 8 0.19
25 16 0.37
26 16 0.37
27 3 0.07
ACGTcount: A:0.77, C:0.05, G:0.06, T:0.12
Consensus pattern (25 bp):
CAAAATCAAAAAAGTAAAAAAAAAA
Found at i:46479313 original size:22 final size:22
Alignment explanation
Indices: 46479295--46479337 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
46479285 ATCAAAAAAT
46479295 AAAAAAAAGAACAAAAAAAAGA
1 AAAAAAAAGAACAAAAAAAAGA
* * *
46479317 AAGAAAAAGAAGAAGAAAAAG
1 AAAAAAAAGAACAAAAAAAAG
46479338 TCAAAATCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.00
Consensus pattern (22 bp):
AAAAAAAAGAACAAAAAAAAGA
Found at i:46481918 original size:216 final size:217
Alignment explanation
Indices: 46481539--46482047 Score: 763
Period size: 216 Copynumber: 2.3 Consensus size: 217
46481529 TCAATGAAAT
* * *
46481539 TACAAATCTTATCTCCCTAAGTC-GTAGTGGAGCAGATCGAAGATGGCAGATCTTATCTCCCTAA
1 TACAGATCTTATCTCCCTAAG-CAGTAGTGGAGCAGATCGAAGATGACAAATCTTATCTCCCTAA
* *
46481603 GCAGTAGTGGAGCAGATTAAAGCCAGTAATCATATCTCTCTGAAGTTGCAGTGGAGTGGATTAAA
65 GCAGTAGTGGAACAGATTAAAGCCAGTAATCATATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA
* *
46481668 ATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGG
130 ATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATAAGGTCTTATCACCCTGAGG
46481733 TTACAGCGGAGCAGACCGAAGAA
195 TTACAGCGGAGCAGACCGAAGAA
* * *
46481756 -GCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATCACAAATCTTATCTCCCTAAG
1 TACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAAATCTTATCTCCCTAAG
* *
46481820 CAGTAGTGGAACAGATTGAAA-CCAGTAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAA
66 CAGTAGTGGAACAGATT-AAAGCCAGTAATCATATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA
** *
46481884 ATAAAAGATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATCGCATAAGGTCTTATCACTCTGAGG
130 ATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATAAGGTCTTATCACCCTGAGG
**
46481949 TTGTAGCGGAGCAGACCGAAGAA
195 TTACAGCGGAGCAGACCGAAGAA
* * ** *
46481972 TTACAGATATTATCTCCCTAAGCAGTAGTGGAGCTGATCGAAGATGACAAGCCTTATCTCCCTGA
1 -TACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAAATCTTATCTCCCTAA
*
46482037 GCAGCAGTGGA
65 GCAGTAGTGGA
46482048 GTAGGTTGAA
Statistics
Matches: 262, Mismatches: 26, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
215 1 0.00
216 193 0.74
217 3 0.01
218 65 0.25
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (217 bp):
TACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAAATCTTATCTCCCTAAG
CAGTAGTGGAACAGATTAAAGCCAGTAATCATATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAA
TAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATAAGGTCTTATCACCCTGAGGT
TACAGCGGAGCAGACCGAAGAA
Found at i:46482059 original size:44 final size:44
Alignment explanation
Indices: 46481981--46482406 Score: 290
Period size: 44 Copynumber: 9.8 Consensus size: 44
46481971 ATTACAGATA
* * * * *
46481981 TTATCTCCCTAAGCAGTAGTGGAGCT-GATCGAAGATGACA-AGCC
1 TTATCTCCCTGAGCAGCAGTGGAG-TAGGTTGAAGATCACAGA-CC
***
46482025 TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGACC
1 TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATCACAGACC
* * ***
46482069 TTATCTCCTTGAGCAGCAGTGGAGTAGGTTGGAGATTGTAGACC
1 TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATCACAGACC
* * * * * *
46482113 TTATCTCCCTTAGTAGCTGTGGAGTAGGTTGAAAATTACAGATC
1 TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATCACAGACC
* * * * * * * *
46482157 TTATCTCCCTAAGTAGTAGTGAAGCAGATCGAAG-TCCCCAG-CC
1 TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAT-CACAGACC
* * * **
46482200 TTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATT
1 TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATCACAGACC
* * ** * * *
46482244 TTATCTCCCTAAGCAGTAGTGGACCAGATCGAAG-TCTCCAG-CC
1 TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATC-ACAGACC
* * * *
46482287 TTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
1 TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATCACAGACC
* * * * * *
46482331 TGATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACCACAG-CC
1 TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATCACAGACC
* * * *
46482374 TTGTCTCCATGAGTAGCAGTAGAGTAGGTTGAA
1 TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAA
46482407 AATAACAAAT
Statistics
Matches: 290, Mismatches: 84, Indels: 17
0.74 0.21 0.04
Matches are distributed among these distances:
43 86 0.30
44 203 0.70
45 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (44 bp):
TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATCACAGACC
Found at i:46482233 original size:87 final size:87
Alignment explanation
Indices: 46481970--46482421 Score: 528
Period size: 87 Copynumber: 5.2 Consensus size: 87
46481960 CAGACCGAAG
* * ** * *
46481970 AATTACAGATATTATCTCCCTAAGCAGTAGTGGAGCTGATCGAAGATGACAAGCCTTATCTCCCT
1 AATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG-TCCCCAGCCTTGTCTCCCT
46482035 GAGCAGCAGTGGAGTAGGTTGAA
65 GAGCAGCAGTGGAGTAGGTTGAA
* ** * * * * * * * * *** *
46482058 GATTGTAGACCTTATCTCCTTGAGCAGCAGTGGAGTAGGTTGGAGAT-TGTAGACCTTATCTCCC
1 AATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG-TCCCCAG-CCTTGTCTCCC
* * *
46482122 TTAGTAGCTGTGGAGTAGGTTGAA
64 TGAGCAGCAGTGGAGTAGGTTGAA
* *
46482146 AATTACAGATCTTATCTCCCTAAGTAGTAGTGAAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTG
1 AATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTG
46482211 AGCAGCAGTGGAGTAGGTTGAA
66 AGCAGCAGTGGAGTAGGTTGAA
* * *
46482233 AATTACAGATTTTATCTCCCTAAGCAGTAGTGGACCAGATCGAAGTCTCCAGCCTTGTCTCCCTG
1 AATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTG
46482298 AGCAGCAGTGGAGTAGGTTGAA
66 AGCAGCAGTGGAGTAGGTTGAA
* * * * *
46482320 AATTACAGATCTGATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACCACAGCCTTGTCTCCATG
1 AATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTG
* *
46482385 AGTAGCAGTAGAGTAGGTTGAA
66 AGCAGCAGTGGAGTAGGTTGAA
* *
46482407 AATAACAAATCTTAT
1 AATTACAGATCTTAT
46482422 ATTCCTGTAT
Statistics
Matches: 305, Mismatches: 57, Indels: 5
0.83 0.16 0.01
Matches are distributed among these distances:
87 205 0.67
88 100 0.33
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.27
Consensus pattern (87 bp):
AATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTG
AGCAGCAGTGGAGTAGGTTGAA
Found at i:46482302 original size:43 final size:43
Alignment explanation
Indices: 46482160--46482381 Score: 137
Period size: 43 Copynumber: 5.1 Consensus size: 43
46482150 ACAGATCTTA
* * * *
46482160 TCTCCCTAAGTAGTAGTGAAGCAGATCGAAGTCCCCAGCCTTG
1 TCTCCCTAAGCAGCAGTGGAGCAGATCGAAGTCTCCAGCCTTG
* * * * * * ** *
46482203 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAT-TACAGATTTTA
1 TCTCCCTAAGCAGCAGTGGAGCAGATCG-AAGTCTCCAG-CCTTG
* *
46482247 TCTCCCTAAGCAGTAGTGGACCAGATCGAAGTCTCCAGCCTTG
1 TCTCCCTAAGCAGCAGTGGAGCAGATCGAAGTCTCCAGCCTTG
* * * * * * *
46482290 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAT-TACAG-ATCTG
1 TCTCCCTAAGCAGCAGTGGAGCAGATCG-AAGTCTCCAGCCT-TG
* * *
46482333 ATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGAC-CACAGCCTTG
1 -TCTCCCTAAGCAGCAGTGGAGCAGATCGAAGTCTC-CAGCCTTG
46482377 TCTCC
1 TCTCC
46482382 ATGAGTAGCA
Statistics
Matches: 129, Mismatches: 41, Indels: 18
0.69 0.22 0.10
Matches are distributed among these distances:
42 1 0.01
43 64 0.50
44 63 0.49
45 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (43 bp):
TCTCCCTAAGCAGCAGTGGAGCAGATCGAAGTCTCCAGCCTTG
Found at i:46482632 original size:50 final size:51
Alignment explanation
Indices: 46482578--46482721 Score: 170
Period size: 50 Copynumber: 2.9 Consensus size: 51
46482568 GTAGAGGAAC
* *
46482578 AGATTGAAGCTACAACAGTGAATTTTGCTTCCCCGACATTGCAATT-AATA
1 AGATTGAAGCTACAACAGTGAATCTTGTTTCCCCGACATTGCAATTAAATA
* * *
46482628 AGATTGAAGCTACAAC-GACGAATCTTGTTTCCCCAACATTGCAGTTAAATA
1 AGATTGAAGCTACAACAG-TGAATCTTGTTTCCCCGACATTGCAATTAAATA
* * *
46482679 A-ATTTAAGCTACAA-AGGTGAATCTTGTTTCCCTGGCATTGCAA
1 AGATTGAAGCTACAACA-GTGAATCTTGTTTCCCCGACATTGCAA
46482722 CGGAGTAGAT
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
49 1 0.01
50 72 0.91
51 6 0.08
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (51 bp):
AGATTGAAGCTACAACAGTGAATCTTGTTTCCCCGACATTGCAATTAAATA
Found at i:46484489 original size:3 final size:3
Alignment explanation
Indices: 46484474--46484525 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
46484464 ATTGTGTTGG
* * *
46484474 TAT TAT CAT TAT TAT TAT TAC TACT T-T TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
*
46484519 TAC TAT T
1 TAT TAT T
46484526 GTTGCTATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.92
4 1 0.03
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:46487807 original size:68 final size:67
Alignment explanation
Indices: 46487708--46488012 Score: 295
Period size: 68 Copynumber: 4.6 Consensus size: 67
46487698 GGAGTTTGTT
* *
46487708 AGGACATTAAACATGGGTTCATAATGTGTAAGACCGTAGCTC-GACTATGGCAACATATGGAGTC
1 AGGACATTAAACAT-GGTTCATAATGTGTAAGATCGTAGCTCAG-CTATGGCAACATATGGAATC
* *
46487772 TACT
64 TGCC
* * * *
46487776 AGGACATTAAACATAGGTTCATAATATGTAAGATTGTAGCTCAGCGATGACAACATATGGAA--T
1 AGGACATTAAACAT-GGTTCATAATGTGTAAGATCGTAGCTCAGCTATGGCAACATATGGAATCT
46487839 -CC
65 GCC
* *
46487841 --G--ATTAAACATGGCTTCATAATGTGTAAGGTCGTAGCTTAGCTATGGCAACATATGGAATCT
1 AGGACATTAAACATGG-TTCATAATGTGTAAGATCGTAGCTCAGCTATGGCAACATATGGAATCT
46487902 GCC
65 GCC
* ** * * *
46487905 AAGTTATTAAGCATGAGTTCATAATGTGTAAGA-CTGTAGCTCAGCTATGGCAACATATAGAGTC
1 AGGACATTAAACATG-GTTCATAATGTGTAAGATC-GTAGCTCAGCTATGGCAACATATGGAATC
46487969 TGCC
64 TGCC
* * * * *
46487973 AGGACATTAAATATGGGATCATATTGTGTAATATCATAGC
1 AGGACATTAAACAT-GGTTCATAATGTGTAAGATCGTAGC
46488013 ACGACTATGG
Statistics
Matches: 196, Mismatches: 28, Indels: 26
0.78 0.11 0.10
Matches are distributed among these distances:
60 2 0.01
61 48 0.24
63 2 0.01
64 2 0.01
65 1 0.01
66 2 0.01
67 1 0.01
68 134 0.68
69 4 0.02
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.29
Consensus pattern (67 bp):
AGGACATTAAACATGGTTCATAATGTGTAAGATCGTAGCTCAGCTATGGCAACATATGGAATCTG
CC
Found at i:46487876 original size:61 final size:61
Alignment explanation
Indices: 46487781--46487900 Score: 170
Period size: 61 Copynumber: 2.0 Consensus size: 61
46487771 CTACTAGGAC
*
46487781 ATTAAACATAGGTTCATAATATGTAAGATTGTAGCTCAGCGATGACAACATATGGAATCCG
1 ATTAAACATAGGTTCATAATATGTAAGATCGTAGCTCAGCGATGACAACATATGGAATCCG
* * * * *
46487842 ATTAAACAT-GGCTTCATAATGTGTAAGGTCGTAGCTTAGCTATGGCAACATATGGAATC
1 ATTAAACATAGG-TTCATAATATGTAAGATCGTAGCTCAGCGATGACAACATATGGAATC
46487901 TGCCAAGTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 2 0.04
61 50 0.96
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (61 bp):
ATTAAACATAGGTTCATAATATGTAAGATCGTAGCTCAGCGATGACAACATATGGAATCCG
Found at i:46487943 original size:129 final size:129
Alignment explanation
Indices: 46487713--46487962 Score: 333
Period size: 129 Copynumber: 1.9 Consensus size: 129
46487703 TTGTTAGGAC
* * * * *
46487713 ATTAAACATGGGTTCATAATGTGTAAGACCGTAGCTCGACTATGGCAACATATGGAGTCTACTAG
1 ATTAAACATGGCTTCATAATGTGTAAGACCGTAGCTAGACTATGGCAACATATGGAATCTACCAA
*
46487778 GACATTAAACATAGGTTCATAATATGTAAGATTGTAGCTCAGCGATGACAACATATGGAATCCG
66 GACATTAAACATAGGTTCATAATATGTAAGACTGTAGCTCAGCGATGACAACATATGGAATCCG
** *
46487842 ATTAAACATGGCTTCATAATGTGTAAGGTCGTAGCTTAG-CTATGGCAACATATGGAATCTGCCA
1 ATTAAACATGGCTTCATAATGTGTAAGACCGTAGC-TAGACTATGGCAACATATGGAATCTACCA
** * * * *
46487906 AGTTATTAAGCAT-GAGTTCATAATGTGTAAGACTGTAGCTCAGCTATGGCAACATAT
65 AGACATTAAACATAG-GTTCATAATATGTAAGACTGTAGCTCAGCGATGACAACATAT
46487963 AGAGTCTGCC
Statistics
Matches: 104, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
128 1 0.01
129 101 0.97
130 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.29
Consensus pattern (129 bp):
ATTAAACATGGCTTCATAATGTGTAAGACCGTAGCTAGACTATGGCAACATATGGAATCTACCAA
GACATTAAACATAGGTTCATAATATGTAAGACTGTAGCTCAGCGATGACAACATATGGAATCCG
Found at i:46492516 original size:26 final size:25
Alignment explanation
Indices: 46492372--46492539 Score: 138
Period size: 26 Copynumber: 6.5 Consensus size: 25
46492362 GGGATGTACT
* * *
46492372 TTATTTAGCAGGCCTTAAGTCGATGT
1 TTATTTAGCAGGCTTTGAG-CGATGA
* *
46492398 TTGTTTAGCAGGCTTTGAGCCGATGT
1 TTATTTAGCAGGCTTTGAG-CGATGA
* * *
46492424 TTATTTAACAGCCTTTGAGCAAGTGA
1 TTATTTAGCAGGCTTTGAGCGA-TGA
* ** *
46492450 TTATTTAGCAGGCCTTGAGCTGGCGC
1 TTATTTAGCAGGCTTTGAGC-GATGA
*
46492476 TTATCTAGCAGGCTTTGAGTCGATGA
1 TTATTTAGCAGGCTTTGAG-CGATGA
* * *
46492502 TTATTTAGCAAGCTTTGAGCCAGTAA
1 TTATTTAGCAGGCTTTGAGCGA-TGA
46492528 TTATTTAGCAGG
1 TTATTTAGCAGG
46492540 TACTATGTAC
Statistics
Matches: 112, Mismatches: 26, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
25 4 0.04
26 107 0.96
27 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (25 bp):
TTATTTAGCAGGCTTTGAGCGATGA
Found at i:46492537 original size:52 final size:50
Alignment explanation
Indices: 46492371--46492539 Score: 153
Period size: 52 Copynumber: 3.3 Consensus size: 50
46492361 CGGGATGTAC
* * * *
46492371 TTTATTTAGCAGGCCTTAAGTCGATGTTTGTTTAGCAGGCTTTGAGCCGATG
1 TTTATTTAGCAGGCTTTGAGTCGATGATTATTTAGCAGGCTTTGAGCC-A-G
* * * *
46492423 TTTATTTAACAGCCTTTGAG-CAAGTGATTATTTAGCAGGCCTTGAGCTGGC-G
1 TTTATTTAGCAGGCTTTGAGTCGA-TGATTATTTAGCAGGCTTTGAGC---CAG
* * *
46492475 CTTATCTAGCAGGCTTTGAGTCGATGATTATTTAGCAAGCTTTGAGCCAG
1 TTTATTTAGCAGGCTTTGAGTCGATGATTATTTAGCAGGCTTTGAGCCAG
46492525 TAATTATTTAGCAGG
1 T--TTATTTAGCAGG
46492540 TACTATGTAC
Statistics
Matches: 92, Mismatches: 17, Indels: 16
0.74 0.14 0.13
Matches are distributed among these distances:
49 1 0.01
50 1 0.01
51 2 0.02
52 85 0.92
53 2 0.02
55 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (50 bp):
TTTATTTAGCAGGCTTTGAGTCGATGATTATTTAGCAGGCTTTGAGCCAG
Found at i:46498820 original size:8 final size:9
Alignment explanation
Indices: 46498802--46498918 Score: 62
Period size: 9 Copynumber: 12.7 Consensus size: 9
46498792 ATTGTTTTAG
46498802 AAAATTTTT
1 AAAATTTTT
46498811 AAAA-TTTT
1 AAAATTTTT
*
46498819 AAATTTCTTT
1 AAAATT-TTT
*
46498829 ATATATTTTTT
1 A-A-AATTTTT
*
46498840 AGAATTTTT
1 AAAATTTTT
** *
46498849 AAAAAATAT
1 AAAATTTTT
46498858 -AAA-TTTT
1 AAAATTTTT
*
46498865 AAAATTGTT
1 AAAATTTTT
46498874 ATAAATATTTT
1 A-AAAT-TTTT
46498885 -AAATTTTT
1 AAAATTTTT
46498893 AAAATTATTT
1 AAAATT-TTT
**
46498903 TGAATTTTT
1 AAAATTTTT
46498912 GAAAATT
1 -AAAATT
46498919 ATTTTGAATT
Statistics
Matches: 82, Mismatches: 15, Indels: 21
0.69 0.13 0.18
Matches are distributed among these distances:
7 2 0.02
8 17 0.21
9 32 0.39
10 19 0.23
11 8 0.10
12 4 0.05
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (9 bp):
AAAATTTTT
Found at i:46498846 original size:10 final size:9
Alignment explanation
Indices: 46498806--46498932 Score: 53
Period size: 9 Copynumber: 13.6 Consensus size: 9
46498796 TTTTAGAAAA
46498806 TTTTTAAA-
1 TTTTTAAAT
*
46498814 ATTTTAAAT
1 TTTTTAAAT
46498823 TTCTTTATATAT
1 TT-TTTA-A-AT
46498835 TTTTTAGAA-
1 TTTTTA-AAT
*
46498844 TTTTTAAAA
1 TTTTTAAAT
** *
46498853 AATATAAA-
1 TTTTTAAAT
*
46498861 TTTTAAAAT
1 TTTTTAAAT
*
46498870 TGTTATAAAT
1 T-TTTTAAAT
*
46498880 ATTTTAAAT
1 TTTTTAAAT
*
46498889 TTTTAAAAT
1 TTTTTAAAT
*
46498898 TATTTTGAAT
1 T-TTTTAAAT
*
46498908 TTTTGAAAAT
1 TTTT-TAAAT
*
46498918 TATTTTGAAT
1 T-TTTTAAAT
46498928 TTTTT
1 TTTTT
46498933 TTTATAATTT
Statistics
Matches: 87, Mismatches: 22, Indels: 19
0.68 0.17 0.15
Matches are distributed among these distances:
8 13 0.15
9 35 0.40
10 26 0.30
11 9 0.10
12 4 0.05
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.57
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:46498901 original size:19 final size:19
Alignment explanation
Indices: 46498860--46498931 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
46498850 AAAAATATAA
*
46498860 ATTTTAAAATTGTTATAAA-T
1 ATTTT-AAATTTTTA-AAATT
46498880 ATTTTAAATTTTTAAAATT
1 ATTTTAAATTTTTAAAATT
*
46498899 ATTTTGAATTTTTGAAAATT
1 ATTTTAAATTTTT-AAAATT
*
46498919 ATTTTGAATTTTT
1 ATTTTAAATTTTT
46498932 TTTTATAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
18 3 0.06
19 21 0.44
20 24 0.50
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (19 bp):
ATTTTAAATTTTTAAAATT
Found at i:46498916 original size:20 final size:19
Alignment explanation
Indices: 46498879--46498931 Score: 88
Period size: 20 Copynumber: 2.7 Consensus size: 19
46498869 TTGTTATAAA
*
46498879 TATTTTAAATTTTTAAAAT
1 TATTTTGAATTTTTAAAAT
46498898 TATTTTGAATTTTTGAAAAT
1 TATTTTGAATTTTT-AAAAT
46498918 TATTTTGAATTTTT
1 TATTTTGAATTTTT
46498932 TTTTATAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 13 0.41
20 19 0.59
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (19 bp):
TATTTTGAATTTTTAAAAT
Found at i:46506849 original size:51 final size:51
Alignment explanation
Indices: 46506789--46507226 Score: 420
Period size: 51 Copynumber: 8.6 Consensus size: 51
46506779 TATCGAAGAA
** * * *
46506789 CACATGTGTAGTACTGCGTGAAGGCTACTACGTGAATCGATATA-TTATGGT
1 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGAACCGATAAACTT-TGGT
* * * * *
46506840 CACATGTGTAGTACTAAGTAAAGGCTACAATGTGTACCGAGAAGCTTTGGT
1 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGAACCGATAAACTTTGGT
* ** * * *
46506891 CACGTGTGTAGTACTGCGTGAAGGCTACTAAGTGAATCGATAAA-TGATGGT
1 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGAACCGATAAACT-TTGGT
* * * *
46506942 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
1 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGAACCGATAAACTTTGGT
* * * * *
46506993 CACGTGTGTAGTAC-AGTGTGAAGGCTACTACGTGAATCGATAAA-TGATGGT
1 CACATGTGTAGTACTA-AGTGAAGGCTACTATGTGAACCGATAAACT-TTGGT
* * * *
46507044 CACATGTGTAGTACTAAGTGAAGGCTACGATGTGTACCGAGAAGCTTTGGT
1 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGAACCGATAAACTTTGGT
** ** * * *
46507095 CATGTGTGTAGTACTGTGTGAAGGCTACTAAGTGAATCGATAAA-TGATGGT
1 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGAACCGATAAACT-TTGGT
* *
46507146 CACATGTGTAGTACTAAGTGAAGGTTACTATGTGTACCGA-AAAGCTTTGGT
1 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGAACCGATAAA-CTTTGGT
* *
46507197 CACGTGTGTAGTACTATGTGAAGGCTACTA
1 CACATGTGTAGTACTAAGTGAAGGCTACTA
46507227 CGTGTATAGA
Statistics
Matches: 305, Mismatches: 72, Indels: 20
0.77 0.18 0.05
Matches are distributed among these distances:
50 7 0.02
51 292 0.96
52 6 0.02
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (51 bp):
CACATGTGTAGTACTAAGTGAAGGCTACTATGTGAACCGATAAACTTTGGT
Found at i:46507269 original size:102 final size:102
Alignment explanation
Indices: 46506793--46507230 Score: 750
Period size: 102 Copynumber: 4.3 Consensus size: 102
46506783 GAAGAACACA
* * *
46506793 TGTGTAGTACTGCGTGAAGGCTACTACGTGAATCGATATATTATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAG
*
46506858 TAAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACG
66 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACG
* *
46506895 TGTGTAGTACTGCGTGAAGGCTACTAAGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAG
46506960 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACG
66 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACG
*
46506997 TGTGTAGTACAGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAG
* *
46507062 TGAAGGCTACGATGTGTACCGAGAAGCTTTGGTCATG
66 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACG
*
46507099 TGTGTAGTACTGTGTGAAGGCTACTAAGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAG
* * *
46507164 TGAAGGTTACTATGTGTACCGAAAAGCTTTGGTCACG
66 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACG
*
46507201 TGTGTAGTACTATGTGAAGGCTACTACGTG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTG
46507231 TATAGAATGA
Statistics
Matches: 319, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 319 1.00
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (102 bp):
TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAG
TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACG
Found at i:46512266 original size:39 final size:39
Alignment explanation
Indices: 46512129--46512263 Score: 216
Period size: 39 Copynumber: 3.5 Consensus size: 39
46512119 ATTCTCTTTT
* *
46512129 AAGCATATATCACATTACACATATAATCGCATAACATTC
1 AAGCATATATCACAATACACATATAATCACATAACATTC
*
46512168 AAGCATATATCACAATACACATATAACCACATAACATTC
1 AAGCATATATCACAATACACATATAATCACATAACATTC
* * *
46512207 AAGCATATATCACAACACTCATCTAATCACATAACATTC
1 AAGCATATATCACAATACACATATAATCACATAACATTC
46512246 AAGCATATATCACAATAC
1 AAGCATATATCACAATAC
46512264 TCAAAAACAT
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 88 1.00
ACGTcount: A:0.46, C:0.25, G:0.04, T:0.25
Consensus pattern (39 bp):
AAGCATATATCACAATACACATATAATCACATAACATTC
Found at i:46517077 original size:45 final size:45
Alignment explanation
Indices: 46517013--46517171 Score: 165
Period size: 45 Copynumber: 3.4 Consensus size: 45
46517003 ACACCAGTAA
*
46517013 CAGTAATCAGTAACGGTAACAGTGTTTGACACACAAAGTGCCGAAT
1 CAGTAA-CAGTAACAGTAACAGTGTTTGACACACAAAGTGCCGAAT
* * **
46517059 CGGTAACGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTATCGAAT
1 C----A--GTAACAGTAACAGTAACAGTGTTTGACACACAAAGTGCCGAAT
* ** *
46517110 CAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAAT
1 CAGTAACAGTAACAGTAACAGTGTTTGACACACAAAGTGCCGAAT
*
46517155 CTGTAACAGTAACAGTA
1 CAGTAACAGTAACAGTA
46517172 GTCGGCACAT
Statistics
Matches: 97, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
45 55 0.57
46 1 0.01
47 1 0.01
50 1 0.01
51 35 0.36
52 4 0.04
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (45 bp):
CAGTAACAGTAACAGTAACAGTGTTTGACACACAAAGTGCCGAAT
Found at i:46517086 original size:51 final size:50
Alignment explanation
Indices: 46517009--46517171 Score: 194
Period size: 51 Copynumber: 3.3 Consensus size: 50
46516999 AAACACACCA
* * *
46517009 GTAACAGTAATCAGTAACGGTAACAGTGTTTGACACACAAAGTGCCGAATC
1 GTAACAGTAA-CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
*
46517060 GGTAACGGTAACAGTAACAGTAACAGTATTCGACACACAAAGT-----ATC
1 -GTAACAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
* *
46517106 G-AATCAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAATC
1 GTAA-CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
46517156 TGTAACAGTAACAGTA
1 -GTAACAGTAACAGTA
46517172 GTCGGCACAT
Statistics
Matches: 97, Mismatches: 6, Indels: 17
0.81 0.05 0.14
Matches are distributed among these distances:
44 2 0.02
45 37 0.38
46 3 0.03
50 3 0.03
51 41 0.42
52 11 0.11
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (50 bp):
GTAACAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
Found at i:46517459 original size:39 final size:40
Alignment explanation
Indices: 46517375--46517460 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 40
46517365 TTTATTACTT
* * * *
46517375 CAGTAATTTCATAATTCAATGCATTATACATAACAATATT
1 CAGTATTTTCATAATTCAATGCAGTATACAAAACAATATC
*
46517415 CAGTATTTTCATAATTCACT-CAGTACT-CAAAACAATATC
1 CAGTATTTTCATAATTCAATGCAGTA-TACAAAACAATATC
46517454 CAGTATT
1 CAGTATT
46517461 CCCTAATTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
39 21 0.52
40 19 0.47
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.36
Consensus pattern (40 bp):
CAGTATTTTCATAATTCAATGCAGTATACAAAACAATATC
Found at i:46518411 original size:13 final size:13
Alignment explanation
Indices: 46518393--46518433 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
46518383 CTCAAACTTC
46518393 TCTTTTCTTTCTT
1 TCTTTTCTTTCTT
46518406 TCTTTTCTTTCTT
1 TCTTTTCTTTCTT
* *
46518419 TC-CTTCTTTCCT
1 TCTTTTCTTTCTT
46518431 TCT
1 TCT
46518434 CTGTTTCGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TCTTTTCTTTCTT
Found at i:46518645 original size:8 final size:8
Alignment explanation
Indices: 46518634--46518696 Score: 74
Period size: 8 Copynumber: 7.8 Consensus size: 8
46518624 ATTTATTTAA
46518634 AATATAAT
1 AATATAAT
46518642 AATATAAT
1 AATATAAT
46518650 AATATAAT
1 AATATAAT
46518658 AATATAAT
1 AATATAAT
* *
46518666 -ATAATTTAC
1 AAT-A-TAAT
46518675 AATATAAT
1 AATATAAT
*
46518683 AAAATAAT
1 AATATAAT
46518691 AATATA
1 AATATA
46518697 CTTCAAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
7 2 0.04
8 39 0.85
9 3 0.07
10 2 0.04
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (8 bp):
AATATAAT
Found at i:46519629 original size:48 final size:48
Alignment explanation
Indices: 46519572--46519669 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
46519562 TATTCACTTG
* * *
46519572 TGACGTTCAAATTATGGTATTCCTTAATCCTAAGTGGATGGCAGGCTA
1 TGACGTTCAAATTATGGTATACCTTAATCCTAAGTAGATGACAGGCTA
46519620 TGACGTTCAAATTATGGTATACCTTAATCCTAAGTAGATGACAGGCTA
1 TGACGTTCAAATTATGGTATACCTTAATCCTAAGTAGATGACAGGCTA
46519668 TG
1 TG
46519670 TATGCATGAC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (48 bp):
TGACGTTCAAATTATGGTATACCTTAATCCTAAGTAGATGACAGGCTA
Found at i:46521884 original size:12 final size:11
Alignment explanation
Indices: 46521856--46521899 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
46521846 AGATAAATGT
*
46521856 TATTTAATTAA
1 TATTTTATTAA
46521867 TATTTTATTAA
1 TATTTTATTAA
* *
46521878 TATTTTTAGTAT
1 TA-TTTTATTAA
46521890 TATTTTATTA
1 TATTTTATTA
46521900 TTAAATGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:46525440 original size:29 final size:31
Alignment explanation
Indices: 46525375--46525440 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
46525365 AAATGATCAT
* * *
46525375 TAAACTATTGACTTCATTCTATTTTGTTCAC
1 TAAACTATTAACTTCATTCGATTTAGTTCAC
* *
46525406 TCAACTATTAATTTC-TTCGATTTAG-TCAC
1 TAAACTATTAACTTCATTCGATTTAGTTCAC
46525435 TAAACT
1 TAAACT
46525441 TTTCAAAATC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
29 9 0.31
30 8 0.28
31 12 0.41
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.45
Consensus pattern (31 bp):
TAAACTATTAACTTCATTCGATTTAGTTCAC
Found at i:46526026 original size:12 final size:12
Alignment explanation
Indices: 46526009--46526034 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
46525999 CACCACTTAT
46526009 AATAATTGTTGA
1 AATAATTGTTGA
46526021 AATAATTGTTGA
1 AATAATTGTTGA
46526033 AA
1 AA
46526035 AACATGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (12 bp):
AATAATTGTTGA
Found at i:46527354 original size:6 final size:6
Alignment explanation
Indices: 46527343--46527373 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
46527333 ATTACCAACA
*
46527343 ATAATT ATAATT ATAATT ATAATC ATAATT A
1 ATAATT ATAATT ATAATT ATAATT ATAATT A
46527374 ATATACTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (6 bp):
ATAATT
Found at i:46534286 original size:27 final size:26
Alignment explanation
Indices: 46534256--46534322 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 26
46534246 AGATCACCAC
46534256 AAAGGCTTCTATTTCATAGATT-TCTAT
1 AAAGGCTTCTATTTC-TAGATTGTC-AT
46534283 AAAGGCTT-TCATTTTCTAGATTGTCAT
1 AAAGGCTTCT-A-TTTCTAGATTGTCAT
*
46534310 AAAGGTTTC-ATTT
1 AAAGGCTTCTATTT
46534323 TCTGGCGTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
25 3 0.09
26 2 0.06
27 24 0.69
28 6 0.17
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.45
Consensus pattern (26 bp):
AAAGGCTTCTATTTCTAGATTGTCAT
Found at i:46534325 original size:26 final size:27
Alignment explanation
Indices: 46534267--46534325 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
46534257 AAGGCTTCTA
46534267 TTTCATAGATTTCTATAAAGGCTTTCAT
1 TTTC-TAGATTTCTATAAAGGCTTTCAT
46534295 TTTCTAGATTGTC-ATAAAGG-TTTCAT
1 TTTCTAGATT-TCTATAAAGGCTTTCAT
46534321 TTTCT
1 TTTCT
46534326 GGCGTATTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 11 0.37
27 13 0.43
28 6 0.20
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (27 bp):
TTTCTAGATTTCTATAAAGGCTTTCAT
Found at i:46539828 original size:39 final size:39
Alignment explanation
Indices: 46539758--46539930 Score: 159
Period size: 45 Copynumber: 4.2 Consensus size: 39
46539748 ATTTGCCGGC
* * *
46539758 TTACTGATTAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTGATTCGGCACTTTATGTGTCGAATACTGTTACTG
46539796 TTACTGATTCGGCACTTTATGTGTCGAATACTGTTACTG
1 TTACTGATTCGGCACTTTATGTGTCGAATACTGTTACTG
* *
46539835 TTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTAC---T---GATTCGGCACTTTATGTGTCGAATACTGTTACTG
* * *
46539880 TTACTGTTATCGATTCGGCACTTTGTGTATCGAATACTGTTACCG
1 TTAC-----T-GATTCGGCACTTTATGTGTCGAATACTGTTACTG
46539925 TTACTG
1 TTACTG
46539931 TTACAGATTT
Statistics
Matches: 116, Mismatches: 10, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
38 14 0.12
39 26 0.22
40 1 0.01
42 1 0.01
45 72 0.62
47 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (39 bp):
TTACTGATTCGGCACTTTATGTGTCGAATACTGTTACTG
Found at i:46539853 original size:45 final size:45
Alignment explanation
Indices: 46539785--46539984 Score: 283
Period size: 45 Copynumber: 4.4 Consensus size: 45
46539775 ATGTGCCGAC
* *
46539785 TACTGTTACTGTTACTGATTCGGCACTTTATGTGTCGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
*
46539830 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
* *
46539875 TACTGTTACTGTTATCGATTCGGCACTTTGTGTATCGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
* * ** *
46539920 TACCGTTACTGTTACAGATTTAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
* * *
46539965 TACTGCTACCGTTACTGATT
1 TACTGTTACTGTTACCGATT
46539985 ACTGTATACT
Statistics
Matches: 138, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 138 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (45 bp):
TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
Found at i:46542113 original size:32 final size:32
Alignment explanation
Indices: 46542045--46542114 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
46542035 TTAATTAATT
* *
46542045 AATTAAAACTTATTTAATTAGTCCTCAATCAT
1 AATTAAAACTTATTTAATTAATCCTCAATCAC
* * *
46542077 AATTAAATCTTATTTAATTAATCCTTAATTAC
1 AATTAAAACTTATTTAATTAATCCTCAATCAC
46542109 AATTAA
1 AATTAA
46542115 CCAAACTTAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.43, C:0.13, G:0.01, T:0.43
Consensus pattern (32 bp):
AATTAAAACTTATTTAATTAATCCTCAATCAC
Found at i:46544143 original size:45 final size:44
Alignment explanation
Indices: 46544071--46544288 Score: 152
Period size: 45 Copynumber: 4.8 Consensus size: 44
46544061 TTGTTCATGA
* * *
46544071 TGCCATAGGT-TCTTTCAGCCATAGTCTTATCTATTTTTAACA-AG
1 TGCCATA-GTATCTTTCAACTATGGTCTTAT-TATTTTTAACATAG
* * ****
46544115 ATGTCATAGTATCTTTTAACTATGGTCTTATTCATTTTCGGTATAG
1 -TGCCATAGTATCTTTCAACTATGGTCTTATT-ATTTTTAACATAG
* ***
46544161 TGCCATAGTGTCTTTCAACTATGGTCTTATTTATTTTTGGTATAG
1 TGCCATAGTATCTTTCAACTATGGTCTTA-TTATTTTTAACATAG
* * *****
46544206 TGCCATAGTGTCTTTCAAATATGGTCTTATTTATTTCCGGTATAG
1 TGCCATAGTATCTTTCAACTATGGTCTTA-TTATTTTTAACATAG
* * *
46544251 TGCCATAATGTCTTTCAACTATGGTCTTAATCATTTTT
1 TGCCATAGTATCTTTCAACTATGGTCTT-ATTATTTTT
46544289 GAAGCCAATT
Statistics
Matches: 147, Mismatches: 21, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
44 3 0.02
45 139 0.95
46 5 0.03
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.46
Consensus pattern (44 bp):
TGCCATAGTATCTTTCAACTATGGTCTTATTATTTTTAACATAG
Found at i:46544229 original size:90 final size:90
Alignment explanation
Indices: 46544119--46544289 Score: 270
Period size: 90 Copynumber: 1.9 Consensus size: 90
46544109 AACAAGATGT
* * * *
46544119 CATAGTATCTTTTAACTATGGTCTTATTCATTTTCGGTATAGTGCCATAGTGTCTTTCAACTATG
1 CATAGTATCTTTCAAATATGGTCTTATTCATTTCCGGTATAGTGCCATAATGTCTTTCAACTATG
* *
46544184 GTCTTATTTATTTTTGGTATAGTGC
66 GTCTTAATCATTTTTGGTATAGTGC
* *
46544209 CATAGTGTCTTTCAAATATGGTCTTATTTATTTCCGGTATAGTGCCATAATGTCTTTCAACTATG
1 CATAGTATCTTTCAAATATGGTCTTATTCATTTCCGGTATAGTGCCATAATGTCTTTCAACTATG
46544274 GTCTTAATCATTTTTG
66 GTCTTAATCATTTTTG
46544290 AAGCCAATTA
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 73 1.00
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.47
Consensus pattern (90 bp):
CATAGTATCTTTCAAATATGGTCTTATTCATTTCCGGTATAGTGCCATAATGTCTTTCAACTATG
GTCTTAATCATTTTTGGTATAGTGC
Found at i:46548954 original size:18 final size:17
Alignment explanation
Indices: 46548933--46548968 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
46548923 AAGATTGTGA
46548933 TTGAAATGAATGATTGTT
1 TTGAAATGAATGA-TGTT
*
46548951 TTGATATGAATGATGTT
1 TTGAAATGAATGATGTT
46548968 T
1 T
46548969 ATATTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (17 bp):
TTGAAATGAATGATGTT
Found at i:46557818 original size:15 final size:15
Alignment explanation
Indices: 46557798--46557832 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
46557788 ATAATCTGAG
46557798 TGTCTCTTTAGTTCT
1 TGTCTCTTTAGTTCT
46557813 TGTCTCTTTAGTTCT
1 TGTCTCTTTAGTTCT
46557828 TGTCT
1 TGTCT
46557833 TGTTAAAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.06, C:0.20, G:0.14, T:0.60
Consensus pattern (15 bp):
TGTCTCTTTAGTTCT
Found at i:46560049 original size:29 final size:29
Alignment explanation
Indices: 46559994--46560049 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
46559984 ACCATATATT
*
46559994 ACGTTTGTAGGTTTAGTATGCAGTGTATA
1 ACGTTTGTAGGTTTAGTATACAGTGTATA
*
46560023 ACGTTTGTAGGTATT-GTATACATTGTA
1 ACGTTTGTAGGT-TTAGTATACAGTGTA
46560050 CGTTATACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (29 bp):
ACGTTTGTAGGTTTAGTATACAGTGTATA
Found at i:46560797 original size:29 final size:30
Alignment explanation
Indices: 46560764--46560835 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 30
46560754 AAATCAAAAT
* *
46560764 TTCATGTATAAAATTGCACA-AAATTAAAG
1 TTCATGTATAAAATTACACATAAACTAAAG
* *
46560793 TTCATGTATAAAATTATACATTAAACTAATG
1 TTCATGTATAAAATTACACA-TAAACTAAAG
46560824 TTCATGTATAAA
1 TTCATGTATAAA
46560836 TTTGAAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 18 0.49
31 19 0.51
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (30 bp):
TTCATGTATAAAATTACACATAAACTAAAG
Found at i:46564646 original size:3 final size:3
Alignment explanation
Indices: 46564640--46564727 Score: 149
Period size: 3 Copynumber: 29.3 Consensus size: 3
46564630 GAATAATAAT
* * *
46564640 AAG AAG AAG AAG AAG AAG AAT AAG AAT AAG AAT AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
46564688 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
46564728 CTTGTTTTTC
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:46567919 original size:80 final size:80
Alignment explanation
Indices: 46567835--46568053 Score: 233
Period size: 80 Copynumber: 2.7 Consensus size: 80
46567825 ATCGATATTT
* *
46567835 AGCCTACTAAGCACTAAGCTTGATAGATTCACTGGCACAAAGCCTACTAGGCATAAAGCCCAATA
1 AGCCTACTAAGCACTAAGCTTGATAAATTCACTAGCACAAAGCCTACTAGGCATAAAGCCCAATA
* * **
46567900 AGTTCACCGGTACAA
66 ACTACACCGACACAA
** * * * * *
46567915 AGCCTGTTAATCATTAAGCTTGATAAATTCACTAGCACAAAGTCTGA-TAGGCACAAAGCCCGAT
1 AGCCTACTAAGCACTAAGCTTGATAAATTCACTAGCACAAAGCCT-ACTAGGCATAAAGCCCAAT
46567979 AACTACACCGACACAA
65 AACTACACCGACACAA
* * * * *** *
46567995 AACCTACTAGGCACTAAGCTTTATAAATTCACCAGCATGGAGCCTGCTAGGCATAAAGC
1 AGCCTACTAAGCACTAAGCTTGATAAATTCACTAGCACAAAGCCTACTAGGCATAAAGC
46568054 TTGCTAAGCA
Statistics
Matches: 110, Mismatches: 27, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
80 109 0.99
81 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.21
Consensus pattern (80 bp):
AGCCTACTAAGCACTAAGCTTGATAAATTCACTAGCACAAAGCCTACTAGGCATAAAGCCCAATA
ACTACACCGACACAA
Found at i:46582522 original size:2 final size:2
Alignment explanation
Indices: 46582505--46582544 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
46582495 TGACCTAGTA
* *
46582505 AT AT AT AC AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46582545 GATTGTGGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:46583565 original size:21 final size:21
Alignment explanation
Indices: 46583541--46583581 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
46583531 ATTTTCTAAC
46583541 TTAATCTTA-ATTATTAATTAG
1 TTAATC-TAGATTATTAATTAG
*
46583562 TTAATCTAGATTGTTAATTA
1 TTAATCTAGATTATTAATTA
46583582 AATTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (21 bp):
TTAATCTAGATTATTAATTAG
Found at i:46584318 original size:23 final size:23
Alignment explanation
Indices: 46584292--46584337 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
46584282 AAGAATATTA
*
46584292 TAAA-TTATAAAAATTAAATAAAT
1 TAAATTTATAAAAAATAAA-AAAT
46584315 TAAATTTATAAAAAATAAAAAAT
1 TAAATTTATAAAAAATAAAAAAT
46584338 AAAGTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
TAAATTTATAAAAAATAAAAAAT
Found at i:46584802 original size:24 final size:23
Alignment explanation
Indices: 46584760--46584821 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
46584750 TTTATTTTTA
**
46584760 TTTTTATTTTA-AATATATATTCTC
1 TTTTTATTTTATTTTATATA-T-TC
46584784 TTTTTATTTTCATTTTATATATTC
1 TTTTTATTTT-ATTTTATATATTC
*
46584808 ATTTTATTTTATTT
1 TTTTTATTTTATTT
46584822 AAATTTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 4 0.12
24 21 0.64
25 2 0.06
26 6 0.18
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTTTATTTTATTTTATATATTC
Found at i:46584810 original size:13 final size:13
Alignment explanation
Indices: 46584773--46584814 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
46584763 TTATTTTAAA
46584773 TATATATTC-TCTT
1 TATATATTCAT-TT
* *
46584786 TTTATTTTCATTT
1 TATATATTCATTT
46584799 TATATATTCATTT
1 TATATATTCATTT
46584812 TAT
1 TAT
46584815 TTTATTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 23 0.96
14 1 0.04
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.67
Consensus pattern (13 bp):
TATATATTCATTT
Found at i:46584835 original size:30 final size:29
Alignment explanation
Indices: 46584772--46584875 Score: 92
Period size: 29 Copynumber: 3.7 Consensus size: 29
46584762 TTTATTTTAA
* **
46584772 ATATATATTC-TCT-TTTTATTTTCATTT
1 ATATATATTCTTTTATTTTATTTAAATTT
46584799 -TATATATTCATTTTATTTTATTTAAATTT
1 ATATATATTC-TTTTATTTTATTTAAATTT
**
46584828 ATATATATTCTTTT-TTAAAGTTTATAATTT
1 ATATATATTCTTTTATTTTA-TTTA-AATTT
*
46584858 ATATAT-TTCTTATATTTT
1 ATATATATTCTTTTATTTT
46584876 TTGACAAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
26 9 0.15
28 5 0.08
29 26 0.42
30 22 0.35
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (29 bp):
ATATATATTCTTTTATTTTATTTAAATTT
Found at i:46585368 original size:59 final size:57
Alignment explanation
Indices: 46585255--46585384 Score: 172
Period size: 59 Copynumber: 2.2 Consensus size: 57
46585245 TACACTAATC
* * *
46585255 GTCACCTAACTATTAGTATTTTTTTTTTGTGACTCAATTATGAAAAGTTACAAAATG
1 GTCACCTAACTATTAGTATTTTTTTTTGGTCACTCAACTATGAAAAGTTACAAAATG
* *
46585312 GTCACTTAACTATTAGTAAATTTATTTTTTGGTCACTCAACTATG-AAAGTTACAAAATT
1 GTCACCTAACTATTAGT--ATTT-TTTTTTGGTCACTCAACTATGAAAAGTTACAAAATG
*
46585371 GTCACCCAACTATT
1 GTCACCTAACTATT
46585385 CAATTTTATC
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
57 16 0.25
59 29 0.46
60 18 0.29
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (57 bp):
GTCACCTAACTATTAGTATTTTTTTTTGGTCACTCAACTATGAAAAGTTACAAAATG
Found at i:46585399 original size:59 final size:58
Alignment explanation
Indices: 46585255--46585405 Score: 146
Period size: 59 Copynumber: 2.6 Consensus size: 58
46585245 TACACTAATC
* ** * * *
46585255 GTCACCTAACTATTA-GTATTTTTTTTTTGTGACTCAATTATGAAAAGTTACAAAATG
1 GTCACCCAACTATTACAAATTTATTTTTTGTCACTCAACTATGAAAAGTTACAAAATG
** * *
46585312 GTCACTTAACTATTAGTAAATTTATTTTTTGGTCACTCAACTATG-AAAGTTACAAAATT
1 GTCACCCAACTATTA-CAAATTTATTTTTT-GTCACTCAACTATGAAAAGTTACAAAATG
*
46585371 GTCACCCAACTATT-CAATTTTATCTTTTTTGTCAC
1 GTCACCCAACTATTACAAATTTA--TTTTTTGTCAC
46585406 AAGAGGGGGT
Statistics
Matches: 78, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
57 20 0.26
58 5 0.06
59 41 0.53
60 12 0.15
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (58 bp):
GTCACCCAACTATTACAAATTTATTTTTTGTCACTCAACTATGAAAAGTTACAAAATG
Found at i:46588841 original size:25 final size:24
Alignment explanation
Indices: 46588804--46588876 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 24
46588794 CTCTCTCTCT
46588804 TGAGCCATATAACGAGAAGCTCATG
1 TGAGCCAT-TAACGAGAAGCTCATG
46588829 TGAGCCATGTAACG-GAAAGCTCATG
1 TGAGCCAT-TAACGAG-AAGCTCATG
*
46588854 AGAGCCATTAAC-AGGAAGCTCAT
1 TGAGCCATTAACGA-GAAGCTCAT
46588877 AAGAGGTATA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
24 13 0.30
25 30 0.70
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.19
Consensus pattern (24 bp):
TGAGCCATTAACGAGAAGCTCATG
Found at i:46588872 original size:24 final size:24
Alignment explanation
Indices: 46588805--46588998 Score: 124
Period size: 24 Copynumber: 7.8 Consensus size: 24
46588795 TCTCTCTCTT
* *
46588805 GAGCCATATAACGAGAAGCTCATGT
1 GAGCCAT-TAACGGGAAGCTCATGA
*
46588830 GAGCCATGTAACGGAAAGCTCATGA
1 GAGCCAT-TAACGGGAAGCTCATGA
* *
46588855 GAGCCATTAACAGGAAGCTCATAA
1 GAGCCATTAACGGGAAGCTCATGA
** *** * * *
46588879 GAGGTA-TAATCAAAAAGTTCAAGC
1 GAGCCATTAA-CGGGAAGCTCATGA
*
46588903 GAGCCATTATCGGGAAGCTGCA-GA
1 GAGCCATTAACGGGAAGCT-CATGA
*
46588927 GAGCCATTATCGGGAAGCTCCA-GA
1 GAGCCATTAACGGGAAGCT-CATGA
*
46588951 GAGCCATTAATTGGGAAGCTCATGAAA
1 GAGCCATTAA-CGGGAAGCTCATG--A
* *
46588978 GAGTCTTTAATCGGGAAGCTC
1 GAGCCATTAA-CGGGAAGCTC
46588999 CGAAAAGCCA
Statistics
Matches: 133, Mismatches: 29, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
23 3 0.02
24 70 0.53
25 41 0.31
27 19 0.14
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.20
Consensus pattern (24 bp):
GAGCCATTAACGGGAAGCTCATGA
Found at i:46589005 original size:27 final size:26
Alignment explanation
Indices: 46588903--46589009 Score: 107
Period size: 24 Copynumber: 4.3 Consensus size: 26
46588893 AAGTTCAAGC
* *
46588903 GAGCCATT-ATCGGGAAGCTGC-AGA
1 GAGCCATTAATCGGGAAGCTCCGAAA
*
46588927 GAGCCATT-ATCGGGAAGCTCC-AGA
1 GAGCCATTAATCGGGAAGCTCCGAAA
* *
46588951 GAGCCATTAATTGGGAAGCTCATGAAA
1 GAGCCATTAATCGGGAAGCTC-CGAAA
* *
46588978 GAGTCTTTAATCGGGAAGCTCCGAAA
1 GAGCCATTAATCGGGAAGCTCCGAAA
46589004 -AGCCAT
1 GAGCCAT
46589010 ATATCAGGAC
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
24 31 0.44
25 15 0.21
26 4 0.06
27 20 0.29
ACGTcount: A:0.32, C:0.21, G:0.28, T:0.20
Consensus pattern (26 bp):
GAGCCATTAATCGGGAAGCTCCGAAA
Found at i:46612113 original size:8 final size:8
Alignment explanation
Indices: 46612102--46612146 Score: 60
Period size: 7 Copynumber: 6.0 Consensus size: 8
46612092 ATTTTTGGTC
46612102 TTAGGGTT
1 TTAGGGTT
46612110 TTAGGG-T
1 TTAGGGTT
*
46612117 TTAAGG-T
1 TTAGGGTT
46612124 TTAGGGTT
1 TTAGGGTT
46612132 TT-GGGTT
1 TTAGGGTT
46612139 TTAGGGTT
1 TTAGGGTT
46612147 AGTGAAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 19 0.58
8 14 0.42
ACGTcount: A:0.13, C:0.00, G:0.38, T:0.49
Consensus pattern (8 bp):
TTAGGGTT
Found at i:46612128 original size:22 final size:21
Alignment explanation
Indices: 46612102--46612148 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
46612092 ATTTTTGGTC
*
46612102 TTAGGGTTTTAGGGTTTAAGGT
1 TTAGGGTTTT-GGGTTTAAGGG
*
46612124 TTAGGGTTTTGGGTTTTAGGG
1 TTAGGGTTTTGGGTTTAAGGG
46612145 TTAG
1 TTAG
46612149 TGAAAGAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.47
Consensus pattern (21 bp):
TTAGGGTTTTGGGTTTAAGGG
Found at i:46616492 original size:27 final size:26
Alignment explanation
Indices: 46616462--46616563 Score: 80
Period size: 27 Copynumber: 3.8 Consensus size: 26
46616452 CTATTCAGAA
46616462 TTTGCCACAAAGGCATTCCTTTTAGAG
1 TTTGCCACAAAGGCATT-CTTTTAGAG
* ** *
46616489 TTTGCCACTAATGTTATTCTTTTAGGG
1 TTTGCCAC-AAAGGCATTCTTTTAGAG
* * * *
46616516 TTCT-CAACTAAGGTTATTCTTCTAGAG
1 TT-TGCCACAAAGG-CATTCTTTTAGAG
46616543 TTTGCCACAAAGGCTATTCTT
1 TTTGCCACAAAGGC-ATTCTT
46616564 AGTTGTCGTG
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
26 3 0.05
27 47 0.82
28 7 0.12
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.40
Consensus pattern (26 bp):
TTTGCCACAAAGGCATTCTTTTAGAG
Done.