Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 102 of 206
Found at i:30005155 original size:40 final size:39
Alignment explanation
Indices: 30005111--30005204 Score: 134
Period size: 40 Copynumber: 2.4 Consensus size: 39
30005101 CATGCGGTTT
30005111 AGCTCACTTGAGCTCAAGTCAGCTTATTCGAGCTCAAGTC
1 AGCTCA-TTGAGCTCAAGTCAGCTTATTCGAGCTCAAGTC
* * * *
30005151 AGCTCATTTATGCTCAATTCAGCTTATTCGAGCTCAATTT
1 AGCTCATTGA-GCTCAAGTCAGCTTATTCGAGCTCAAGTC
30005191 AGCTCATTGAGCTC
1 AGCTCATTGAGCTC
30005205 GTTCTTAGCT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
39 7 0.15
40 41 0.85
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (39 bp):
AGCTCATTGAGCTCAAGTCAGCTTATTCGAGCTCAAGTC
Found at i:30005188 original size:20 final size:19
Alignment explanation
Indices: 30005111--30005204 Score: 98
Period size: 20 Copynumber: 4.7 Consensus size: 19
30005101 CATGCGGTTT
30005111 AGCTCACTTGAGCTCAAGTC
1 AGCTCA-TTGAGCTCAAGTC
*
30005131 AGCTTATTCGAGCTCAAGTC
1 AGCTCATT-GAGCTCAAGTC
* *
30005151 AGCTCATTTATGCTCAATTC
1 AGCTCATTGA-GCTCAAGTC
* * *
30005171 AGCTTATTCGAGCTCAATTT
1 AGCTCATT-GAGCTCAAGTC
30005191 AGCTCATTGAGCTC
1 AGCTCATTGAGCTC
30005205 GTTCTTAGCT
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
19 9 0.14
20 53 0.84
21 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (19 bp):
AGCTCATTGAGCTCAAGTC
Found at i:30005194 original size:10 final size:10
Alignment explanation
Indices: 30005111--30005196 Score: 52
Period size: 10 Copynumber: 8.6 Consensus size: 10
30005101 CATGCGGTTT
* *
30005111 AGCTCACTTG
1 AGCTCAATTC
*
30005121 AGCTCAAGTC
1 AGCTCAATTC
*
30005131 AGCT-TATTC
1 AGCTCAATTC
*
30005140 GAGCTCAAGTC
1 -AGCTCAATTC
*
30005151 AGCTC-ATTT
1 AGCTCAATTC
30005160 ATGCTCAATTC
1 A-GCTCAATTC
*
30005171 AGCT-TATTC
1 AGCTCAATTC
*
30005180 GAGCTCAATTT
1 -AGCTCAATTC
30005191 AGCTCA
1 AGCTCA
30005197 TTGAGCTCGT
Statistics
Matches: 57, Mismatches: 13, Indels: 12
0.70 0.16 0.15
Matches are distributed among these distances:
9 10 0.18
10 37 0.65
11 10 0.18
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:30005321 original size:22 final size:24
Alignment explanation
Indices: 30005296--30005339 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
30005286 ACTTGTCAGA
30005296 TTATTACATGT-T-TTTTAATTGT
1 TTATTACATGTATGTTTTAATTGT
30005318 TTATTACATGTATGTTTTAATT
1 TTATTACATGTATGTTTTAATT
30005340 ATGTTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.55
23 1 0.05
24 8 0.40
ACGTcount: A:0.25, C:0.05, G:0.09, T:0.61
Consensus pattern (24 bp):
TTATTACATGTATGTTTTAATTGT
Found at i:30006733 original size:15 final size:16
Alignment explanation
Indices: 30006715--30006753 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
30006705 AAAAATTTCG
30006715 AAAAAAAAAGT-GAGC
1 AAAAAAAAAGTCGAGC
30006730 -AAAAAAAA-TCGAGC
1 AAAAAAAAAGTCGAGC
30006744 AAAAAAAAAG
1 AAAAAAAAAG
30006754 AATTGAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 12 0.57
15 8 0.38
ACGTcount: A:0.72, C:0.08, G:0.15, T:0.05
Consensus pattern (16 bp):
AAAAAAAAAGTCGAGC
Found at i:30007869 original size:17 final size:18
Alignment explanation
Indices: 30007833--30007874 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
30007823 AAAAAATTGA
*
30007833 AAATGAGATTGAAGAAAG
1 AAATGAGAGTGAAGAAAG
*
30007851 AAATGAGAGTGCA-AAAG
1 AAATGAGAGTGAAGAAAG
30007868 AAATGAG
1 AAATGAG
30007875 TGATATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.55, C:0.02, G:0.29, T:0.14
Consensus pattern (18 bp):
AAATGAGAGTGAAGAAAG
Found at i:30009642 original size:20 final size:20
Alignment explanation
Indices: 30009610--30009703 Score: 129
Period size: 20 Copynumber: 4.8 Consensus size: 20
30009600 CATGCGGTTT
*
30009610 AGCTCACTT-GAGCTCAAGTT
1 AGCTCA-TTCGAGCTCAAGTC
*
30009630 AACTCATTCGAGCTCAAGTC
1 AGCTCATTCGAGCTCAAGTC
30009650 AGCTCATTCGAGCTCAAGTC
1 AGCTCATTCGAGCTCAAGTC
* *
30009670 AGCTCATTCGAGCTCAATTT
1 AGCTCATTCGAGCTCAAGTC
30009690 AGCTCATT-GAGCTC
1 AGCTCATTCGAGCTC
30009704 GTTATTAGCT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.12
20 60 0.88
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.29
Consensus pattern (20 bp):
AGCTCATTCGAGCTCAAGTC
Found at i:30009645 original size:10 final size:10
Alignment explanation
Indices: 30009632--30009703 Score: 62
Period size: 10 Copynumber: 7.3 Consensus size: 10
30009622 CTCAAGTTAA
30009632 CTCATTCGAG
1 CTCATTCGAG
*
30009642 CTCAAGTC-AG
1 CTC-ATTCGAG
30009652 CTCATTCGAG
1 CTCATTCGAG
*
30009662 CTCAAGTC-AG
1 CTC-ATTCGAG
30009672 CTCATTCGAG
1 CTCATTCGAG
*
30009682 CTCAATT-TAG
1 CTC-ATTCGAG
30009692 CTCATT-GAG
1 CTCATTCGAG
30009701 CTC
1 CTC
30009704 GTTATTAGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
9 14 0.27
10 28 0.55
11 9 0.18
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (10 bp):
CTCATTCGAG
Found at i:30009714 original size:40 final size:39
Alignment explanation
Indices: 30009607--30009714 Score: 98
Period size: 40 Copynumber: 2.7 Consensus size: 39
30009597 TCTCATGCGG
30009607 TTTAGCTCACTTGAGCTCAAGTTA-A-CTCATTCGAGCTCAA
1 TTTAGCTCA-TTGAGCTC--GTTATAGCTCATTCGAGCTCAA
* * *
30009647 GTCAGCTCATTCGAGCTCAAG-T-CAGCTCATTCGAGCTCAA
1 TTTAGCTCATT-GAGCTC--GTTATAGCTCATTCGAGCTCAA
30009687 TTTAGCTCATTGAGCTCGTTATTAGCTC
1 TTTAGCTCATTGAGCTCGTTA-TAGCTC
30009715 TTTAGTTCAT
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
37 1 0.02
38 1 0.02
39 10 0.18
40 45 0.79
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (39 bp):
TTTAGCTCATTGAGCTCGTTATAGCTCATTCGAGCTCAA
Found at i:30022352 original size:27 final size:30
Alignment explanation
Indices: 30022316--30022396 Score: 114
Period size: 27 Copynumber: 2.7 Consensus size: 30
30022306 GAATATAAAG
30022316 GGGGTTGCTAAGTGCTGATTCCC-C-CA-A
1 GGGGTTGCTAAGTGCTGATTCCCACTCATA
*
30022343 GGGGTTGCTAAGTGCTGATTCCCGACTCATT
1 GGGGTTGCTAAGTGCTGATTCCC-ACTCATA
30022374 GGTGGTTGCTAAGTGCTGATTCC
1 GG-GGTTGCTAAGTGCTGATTCC
30022397 ACCGTATCTT
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
27 23 0.48
29 1 0.02
30 2 0.04
31 2 0.04
32 20 0.42
ACGTcount: A:0.16, C:0.22, G:0.31, T:0.31
Consensus pattern (30 bp):
GGGGTTGCTAAGTGCTGATTCCCACTCATA
Found at i:30029447 original size:28 final size:28
Alignment explanation
Indices: 30029410--30029518 Score: 146
Period size: 28 Copynumber: 3.9 Consensus size: 28
30029400 AATAGTACAA
*
30029410 TGTGGGCCTTAGCCCAATATAGTAATAG
1 TGTGGGCCTTAGCCCAATACAGTAATAG
*** * *
30029438 TACCGGCCTTAGCCTAATACAATAATAG
1 TGTGGGCCTTAGCCCAATACAGTAATAG
* *
30029466 TGTGGGCCTTAGCCCAATAAAGTAACAG
1 TGTGGGCCTTAGCCCAATACAGTAATAG
30029494 TGTGGGCCTTAGCCCAATACAGTAA
1 TGTGGGCCTTAGCCCAATACAGTAA
30029519 CCAATACAGT
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 67 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (28 bp):
TGTGGGCCTTAGCCCAATACAGTAATAG
Found at i:30029903 original size:27 final size:27
Alignment explanation
Indices: 30029873--30030192 Score: 320
Period size: 27 Copynumber: 11.9 Consensus size: 27
30029863 GGTATAACAA
30029873 TCATTTTACCCTATGGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTTGG
* * * * *
30029900 TCATTCTACCTTATAGAGGTATTTTAG
1 TCATTTTACCCTATGGGGGTATTTTGG
* * * *
30029927 CCATTTTACACTACGAGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTTGG
*
30029954 TCATTTTACCCTATAGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTTGG
30029981 TCATTTTACCCTATGGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTTGG
* * ** * *
30030008 TCATTTTATCTTATAAGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTTGG
* * * * *
30030035 TTAGTTTACCCTGTGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTTGG
* * *
30030062 TTATTTTACCCTATGGGGGGATTCTGG
1 TCATTTTACCCTATGGGGGTATTTTGG
* * *
30030089 TCATTTTACACTATGAGAGTATTGTT-G
1 TCATTTTACCCTATGGGGGTATT-TTGG
* *
30030116 TCATTTTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTTGG
* *
30030143 TTATTTTACCATAT-GGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTTGG
* *
30030169 TCATTTTACCTTATGAGGGTATTT
1 TCATTTTACCCTATGGGGGTATTT
30030193 CAGTCAATTA
Statistics
Matches: 233, Mismatches: 57, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
26 23 0.10
27 209 0.90
28 1 0.00
ACGTcount: A:0.20, C:0.14, G:0.22, T:0.44
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTTGG
Found at i:30029982 original size:81 final size:80
Alignment explanation
Indices: 30029873--30030192 Score: 356
Period size: 81 Copynumber: 4.0 Consensus size: 80
30029863 GGTATAACAA
* * * * * * * *
30029873 TCATTTTACCCTATGGGGGTATTTTGGTCATTCTACCTTATAGAGGTATTTTAGCCATTTTACAC
1 TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTGGTCATTTTAC-C
*
30029938 TACGAGGGTATTTTGG
65 TATGAGGGTATTTTGG
* * * *
30029954 TCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTTGGTCATTTTATCT
1 TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTGGTCATTTTA-CC
* * *
30030019 TATAAGGGTATTTCGA
65 TATGAGGGTATTTTGG
* * * * * *
30030035 TTAGTTTACCCTGTGGGGGTATTTCGATTATTTTACCCTATGGGGGGATTCTGGTCATTTTACAC
1 TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTGGTCATTTTAC-C
*
30030100 TATGAGAGTATTGTT-G
65 TATGAGGGTATT-TTGG
* *
30030116 TCATTTTACCCTATGGGGGTATTTCGATTATTTTACCATAT-GGGGTATTTTGGTCATTTTACCT
1 TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTGGTCATTTTACC-
30030180 TATGAGGGTATTT
65 TATGAGGGTATTT
30030193 CAGTCAATTA
Statistics
Matches: 202, Mismatches: 33, Indels: 10
0.82 0.13 0.04
Matches are distributed among these distances:
79 2 0.01
80 31 0.15
81 167 0.83
82 2 0.01
ACGTcount: A:0.20, C:0.14, G:0.22, T:0.44
Consensus pattern (80 bp):
TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCT
ATGAGGGTATTTTGG
Found at i:30030229 original size:25 final size:25
Alignment explanation
Indices: 30030201--30030260 Score: 84
Period size: 25 Copynumber: 2.3 Consensus size: 25
30030191 TTCAGTCAAT
*
30030201 TATTTTGGTCATTTTACCCTATGGG
1 TATTTCGGTCATTTTACCCTATGGG
*
30030226 TATTTCGTTCATTTTACCCTATGGGGG
1 TATTTCGGTCATTTTACCCTAT--GGG
30030253 TATTTCGG
1 TATTTCGG
30030261 GGTCTCGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 20 0.67
27 10 0.33
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.47
Consensus pattern (25 bp):
TATTTCGGTCATTTTACCCTATGGG
Found at i:30035657 original size:20 final size:20
Alignment explanation
Indices: 30035624--30035668 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
30035614 TAAATTCACA
30035624 TAATTAAAACAAGACAC-AAT
1 TAATTAAAACAAGAC-CTAAT
**
30035644 TAATTAAATTAAGACCTAAT
1 TAATTAAAACAAGACCTAAT
30035664 TAATT
1 TAATT
30035669 CGGTTAGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.31
Consensus pattern (20 bp):
TAATTAAAACAAGACCTAAT
Found at i:30037597 original size:27 final size:25
Alignment explanation
Indices: 30037559--30037615 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
30037549 TTTCACATCC
* *
30037559 TTTTCCAATCTCAATTTCTTTTTTCT
1 TTTTCCAATCTCAATCTC-ATTTTCT
*
30037585 TTTTCTCAATCTCACTCTCATTTTCT
1 TTTTC-CAATCTCAATCTCATTTTCT
30037611 TTTTC
1 TTTTC
30037616 GATTTCTTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.14, C:0.26, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTTCCAATCTCAATCTCATTTTCT
Found at i:30038633 original size:20 final size:22
Alignment explanation
Indices: 30038610--30038657 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 22
30038600 TTCGTACTCT
*
30038610 TTTTTTTTCTC-AATTT-TTTC
1 TTTTTTTTCCCTAATTTCTTTC
30038630 TTTTTTTTCCCTAATTTCCTTTC
1 TTTTTTTTCCCTAATTT-CTTTC
30038653 TTTTT
1 TTTTT
30038658 CAATTACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 10 0.42
21 5 0.21
23 9 0.38
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTTTTTCCCTAATTTCTTTC
Found at i:30046543 original size:20 final size:20
Alignment explanation
Indices: 30046520--30046563 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
30046510 AGCTCCAACC
*
30046520 AGCTCATTTGAGCTCAATTT
1 AGCTCATTCGAGCTCAATTT
30046540 AGCTCATTCGAGCTCAATTT
1 AGCTCATTCGAGCTCAATTT
30046560 AGCT
1 AGCT
30046564 TTCCATCAGC
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:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (20 bp):
AGCTCATTCGAGCTCAATTT
Found at i:30053388 original size:16 final size:16
Alignment explanation
Indices: 30053369--30053400 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30053359 TTCGCATGCC
*
30053369 TTTTACATCACTTCAA
1 TTTTAAATCACTTCAA
30053385 TTTTAAATCACTTCAA
1 TTTTAAATCACTTCAA
30053401 ATAGATTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.22, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTTAAATCACTTCAA
Found at i:30063325 original size:16 final size:16
Alignment explanation
Indices: 30063306--30063337 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30063296 TTCGCATGCC
*
30063306 TTTTACATCACTTCAA
1 TTTTAAATCACTTCAA
30063322 TTTTAAATCACTTCAA
1 TTTTAAATCACTTCAA
30063338 ATAGATTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.22, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTTAAATCACTTCAA
Found at i:30068670 original size:9 final size:10
Alignment explanation
Indices: 30068649--30068684 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
30068639 ATTTCACGAT
*
30068649 TTTTTTTAAA
1 TTTTTTTGAA
*
30068659 TTTTTTTGAT
1 TTTTTTTGAA
30068669 TTTTTTTGAA
1 TTTTTTTGAA
30068679 TTTTTT
1 TTTTTT
30068685 ACAATACCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:30068671 original size:20 final size:20
Alignment explanation
Indices: 30068646--30068684 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
30068636 TGGATTTCAC
30068646 GATTTTTTTTAAATTTTTTT
1 GATTTTTTTTAAATTTTTTT
*
30068666 GATTTTTTTTGAATTTTTT
1 GATTTTTTTTAAATTTTTT
30068685 ACAATACCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (20 bp):
GATTTTTTTTAAATTTTTTT
Found at i:30072182 original size:39 final size:39
Alignment explanation
Indices: 30072128--30072205 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
30072118 CATAGGAATT
30072128 TATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAG
1 TATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAG
*
30072167 TATTCATGAAGTCTAAAAATTAAAACTAAGTATTTAAAG
1 TATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAG
30072206 AATTAAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.33
Consensus pattern (39 bp):
TATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAG
Found at i:30076608 original size:20 final size:20
Alignment explanation
Indices: 30076578--30076624 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
30076568 AAGCTAAAAG
* *
30076578 TAAGCTAAATTGAGCTCGAA
1 TAAGCTGAATTGAGCTCAAA
*
30076598 TGAGCTGAATTGAGCTCAAA
1 TAAGCTGAATTGAGCTCAAA
30076618 TAAGCTG
1 TAAGCTG
30076625 GTTGGATCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (20 bp):
TAAGCTGAATTGAGCTCAAA
Found at i:30079772 original size:19 final size:20
Alignment explanation
Indices: 30079748--30079798 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
30079738 AAAGGAAGAC
30079748 AGAAAAAGA-AATAAAAAAA
1 AGAAAAAGAGAATAAAAAAA
* *
30079767 AGAAAAAGAGAATGAAAAAG
1 AGAAAAAGAGAATAAAAAAA
30079787 AGCAAAAAGAGA
1 AG-AAAAAGAGA
30079799 TTGAGAGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 9 0.32
20 10 0.36
21 9 0.32
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.04
Consensus pattern (20 bp):
AGAAAAAGAGAATAAAAAAA
Found at i:30081581 original size:33 final size:34
Alignment explanation
Indices: 30081544--30081615 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 34
30081534 GAGTTAGTTT
**
30081544 ATTAAATTTAGTTCTGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCACCTCAAATAAGTGTTAGTA
* *
30081577 ATTAATTTTAGTTCACCTTAAATAAGTGTTAGTA
1 ATTAAATTTAGTTCACCTCAAATAAGTGTTAGTA
30081611 ATTAA
1 ATTAA
30081616 TTTGTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 28 0.82
34 6 0.18
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (34 bp):
ATTAAATTTAGTTCACCTCAAATAAGTGTTAGTA
Found at i:30083714 original size:11 final size:11
Alignment explanation
Indices: 30083698--30083723 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
30083688 ATTCTAGACA
30083698 TCTTATTTTTT
1 TCTTATTTTTT
30083709 TCTTATTTTTT
1 TCTTATTTTTT
30083720 TCTT
1 TCTT
30083724 TTGGAATACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.81
Consensus pattern (11 bp):
TCTTATTTTTT
Found at i:30088851 original size:39 final size:39
Alignment explanation
Indices: 30088797--30088872 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
30088787 TAGGAATTTG
*
30088797 TTCATAAAGTCTAAAAATTAAAACAAAGTATTTAAAGTA
1 TTCATAAAGTCTAAAAAATAAAACAAAGTATTTAAAGTA
*
30088836 TTCATAAAGTCTAAAAAATAAAACTAAGTATTTAAAG
1 TTCATAAAGTCTAAAAAATAAAACAAAGTATTTAAAG
30088873 AATTAAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.30
Consensus pattern (39 bp):
TTCATAAAGTCTAAAAAATAAAACAAAGTATTTAAAGTA
Found at i:30092420 original size:10 final size:10
Alignment explanation
Indices: 30092405--30092433 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
30092395 ATAAAATAAT
30092405 TTCAAAAAAA
1 TTCAAAAAAA
30092415 TTCAAAAAAA
1 TTCAAAAAAA
30092425 TT-AAAAAAA
1 TTCAAAAAAA
30092434 GGAGATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.37
10 12 0.63
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (10 bp):
TTCAAAAAAA
Found at i:30094575 original size:20 final size:20
Alignment explanation
Indices: 30094547--30094586 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
30094537 TAAAAAACTA
30094547 AATTCAGCTCG-AATGAGCTG
1 AATTCAGCT-GAAATGAGCTG
*
30094567 AATTGAGCTGAAATGAGCTG
1 AATTCAGCTGAAATGAGCTG
30094587 GTTGGAGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.25
Consensus pattern (20 bp):
AATTCAGCTGAAATGAGCTG
Found at i:30094594 original size:20 final size:20
Alignment explanation
Indices: 30094558--30094605 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
30094548 ATTCAGCTCG
*
30094558 AATGAGCTGAATTGAGCTGA
1 AATGAGCTGAATTGAGCTAA
*
30094578 AATGAGCTG-GTTGGAGCTAA
1 AATGAGCTGAATT-GAGCTAA
*
30094598 AACGAGCT
1 AATGAGCT
30094606 AGGAGAGCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.33, C:0.12, G:0.31, T:0.23
Consensus pattern (20 bp):
AATGAGCTGAATTGAGCTAA
Found at i:30098255 original size:9 final size:9
Alignment explanation
Indices: 30098241--30098266 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
30098231 ATTCATTACT
30098241 TTTTAGTTA
1 TTTTAGTTA
30098250 TTTTAGTTA
1 TTTTAGTTA
30098259 TTTTAGTT
1 TTTTAGTT
30098267 TGTGTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.69
Consensus pattern (9 bp):
TTTTAGTTA
Found at i:30099361 original size:9 final size:9
Alignment explanation
Indices: 30099347--30099377 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
30099337 GTTAAACGAA
30099347 TCGAGTTAT
1 TCGAGTTAT
*
30099356 TCGAGTTAA
1 TCGAGTTAT
30099365 TCGAGTTAT
1 TCGAGTTAT
30099374 TCGA
1 TCGA
30099378 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:30099448 original size:9 final size:9
Alignment explanation
Indices: 30099431--30099476 Score: 83
Period size: 9 Copynumber: 5.1 Consensus size: 9
30099421 TGAGTTTTCG
30099431 AATTCGAAT
1 AATTCGAAT
*
30099440 AACTCGAAT
1 AATTCGAAT
30099449 AATTCGAAT
1 AATTCGAAT
30099458 AATTCGAAT
1 AATTCGAAT
30099467 AATTCGAAT
1 AATTCGAAT
30099476 A
1 A
30099477 TCAAAACCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:30113460 original size:17 final size:17
Alignment explanation
Indices: 30113438--30113470 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
30113428 AAATGAGGGG
30113438 ATCTTTTAAGAACTAAA
1 ATCTTTTAAGAACTAAA
30113455 ATCTTTTAAGAACTAA
1 ATCTTTTAAGAACTAA
30113471 GTCACGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
ATCTTTTAAGAACTAAA
Found at i:30138169 original size:30 final size:30
Alignment explanation
Indices: 30138120--30138176 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
30138110 TGAATTAAAG
*
30138120 CATGAATGTGTTTAAGGAGCTGAATGGAGC
1 CATGAATGTATTTAAGGAGCTGAATGGAGC
* *
30138150 CATGCATGTATTTAGGGAGCTGAATGG
1 CATGAATGTATTTAAGGAGCTGAATGG
30138177 GGAAGCTAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.28, C:0.11, G:0.33, T:0.28
Consensus pattern (30 bp):
CATGAATGTATTTAAGGAGCTGAATGGAGC
Found at i:30139572 original size:16 final size:15
Alignment explanation
Indices: 30139551--30139585 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
30139541 ATTTTGGGGA
30139551 TTTTTTTTAAAATTT
1 TTTTTTTTAAAATTT
*
30139566 CTTTTTTTTCAAATTT
1 -TTTTTTTTAAAATTT
30139582 TTTT
1 TTTT
30139586 CTAAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTTTTAAAATTT
Found at i:30139584 original size:11 final size:12
Alignment explanation
Indices: 30139568--30139601 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
30139558 TAAAATTTCT
30139568 TTTTTTTC-AAA
1 TTTTTTTCTAAA
30139579 TTTTTTTCTAAA
1 TTTTTTTCTAAA
30139591 TTTTTTT-TAAA
1 TTTTTTTCTAAA
30139602 CATTACTCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTTTCTAAA
Found at i:30149027 original size:20 final size:18
Alignment explanation
Indices: 30149004--30149048 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
30148994 TCAATCTTTT
30149004 TTTTTCTCTTTTTCATTCTC
1 TTTTTCT-TTTTTCATT-TC
*
30149024 TTTTTCTTTTTTGATTTC
1 TTTTTCTTTTTTCATTTC
30149042 TTTTTCT
1 TTTTTCT
30149049 GTCTTTCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 9 0.38
19 8 0.33
20 7 0.29
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTTCTTTTTTCATTTC
Found at i:30149031 original size:18 final size:17
Alignment explanation
Indices: 30149005--30149048 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
30148995 CAATCTTTTT
30149005 TTTTCTCTTTTTCATTCTC
1 TTTT-TCTTTTTCATT-TC
*
30149024 TTTTTCTTTTTTGATTTC
1 TTTTTC-TTTTTCATTTC
30149042 TTTTTCT
1 TTTTTCT
30149049 GTCTTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 1 0.04
18 10 0.43
19 12 0.52
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTTCTTTTTCATTTC
Found at i:30149059 original size:18 final size:17
Alignment explanation
Indices: 30148998--30149059 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 17
30148988 TCACTCTCAA
*
30148998 TCTTTTTTTTTCTCTTTT
1 TCTTTCTTTTTCT-TTTT
30149016 TCATTCTCTTTTTCTTTTT
1 TC-TT-TCTTTTTCTTTTT
* *
30149035 TGATTTCTTTTTCTGTCTT
1 T-CTTTCTTTTTCT-TTTT
30149054 TCTTTC
1 TCTTTC
30149060 ATTACAAGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
18 15 0.42
19 13 0.36
20 8 0.22
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.74
Consensus pattern (17 bp):
TCTTTCTTTTTCTTTTT
Found at i:30184297 original size:19 final size:20
Alignment explanation
Indices: 30184260--30184297 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
30184250 AAATTCAAAA
**
30184260 AAATAGAAAATTACGAAATC
1 AAATAGAAAATTAAAAAATC
30184280 AAATA-AAAATTAAAAAAT
1 AAATAGAAAATTAAAAAAT
30184298 ATTCAGCGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (20 bp):
AAATAGAAAATTAAAAAATC
Found at i:30185162 original size:18 final size:19
Alignment explanation
Indices: 30185141--30185177 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
30185131 AAAGGAAGAC
30185141 AGAAAAAGA-AATCAAAAA
1 AGAAAAAGAGAATCAAAAA
*
30185159 AGAAAAAGAGAATGAAAAA
1 AGAAAAAGAGAATCAAAAA
30185178 GAGCAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (19 bp):
AGAAAAAGAGAATCAAAAA
Found at i:30186974 original size:33 final size:34
Alignment explanation
Indices: 30186937--30187008 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 34
30186927 GAGTTAGTTT
* *
30186937 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCAACTCAAATAAGTGGTAGTA
* *
30186970 ATTAATTTTAGTTCAACTTAAATAAGTGGTAGTA
1 ATTAAATTTAGTTCAACTCAAATAAGTGGTAGTA
30187004 ATTAA
1 ATTAA
30187009 TTTGTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 28 0.82
34 6 0.18
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (34 bp):
ATTAAATTTAGTTCAACTCAAATAAGTGGTAGTA
Found at i:30189130 original size:18 final size:20
Alignment explanation
Indices: 30189086--30189135 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
30189076 TCACTCTCAA
30189086 TCTCTTTTTTCTATTTTTCAT
1 TCTC-TTTTTCTATTTTTCAT
*
30189107 TCTCTTTTTCT-TTTTTGAT
1 TCTCTTTTTCTATTTTTCAT
30189126 T-TCTTTTTCT
1 TCTCTTTTTCT
30189136 GTCTTTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
19 8 0.29
20 7 0.25
21 4 0.14
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.74
Consensus pattern (20 bp):
TCTCTTTTTCTATTTTTCAT
Found at i:30195355 original size:16 final size:17
Alignment explanation
Indices: 30195323--30195355 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
30195313 CCATGTCCTC
30195323 CAACTCAACATAATGTTG
1 CAACTCAACA-AATGTTG
30195341 CAACTCAAC-AATGTT
1 CAACTCAACAAATGTT
30195356 AGAAATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.27
Consensus pattern (17 bp):
CAACTCAACAAATGTTG
Found at i:30196757 original size:28 final size:27
Alignment explanation
Indices: 30196725--30196782 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
30196715 TCGGCTGGAC
* *
30196725 TTAGACATCATTAA-AGCTTGTAATAAGA
1 TTAGACA-CATTAATAACATGTAATAA-A
30196753 TTAGACACATTAATAACATGTAATAAA
1 TTAGACACATTAATAACATGTAATAAA
30196780 TTA
1 TTA
30196783 AAATACATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 10 0.37
28 17 0.63
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (27 bp):
TTAGACACATTAATAACATGTAATAAA
Found at i:30211278 original size:71 final size:71
Alignment explanation
Indices: 30211189--30211329 Score: 264
Period size: 71 Copynumber: 2.0 Consensus size: 71
30211179 GCTAGCCTAT
*
30211189 AGATAGGCCTTTGCATTGTACAGAATTCATTCAATTCATTATTATTCAACTTCTCTTTTGTGTTT
1 AGATAGGCCTTTGCATTGTAAAGAATTCATTCAATTCATTATTATTCAACTTCTCTTTTGTGTTT
30211254 ATAAAG
66 ATAAAG
*
30211260 AGATGGGCCTTTGCATTGTAAAGAATTCATTCAATTCATTATTATTCAACTTCTCTTTTGTGTTT
1 AGATAGGCCTTTGCATTGTAAAGAATTCATTCAATTCATTATTATTCAACTTCTCTTTTGTGTTT
30211325 ATAAA
66 ATAAA
30211330 TTCTCTTTAA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (71 bp):
AGATAGGCCTTTGCATTGTAAAGAATTCATTCAATTCATTATTATTCAACTTCTCTTTTGTGTTT
ATAAAG
Found at i:30212606 original size:19 final size:19
Alignment explanation
Indices: 30212582--30212621 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
30212572 AGGCATCGAA
30212582 ATGTCACATTCGTTACTGG
1 ATGTCACATTCGTTACTGG
*
30212601 ATGTCACATTCGTTGCTGG
1 ATGTCACATTCGTTACTGG
30212620 AT
1 AT
30212622 CAACTACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (19 bp):
ATGTCACATTCGTTACTGG
Found at i:30213600 original size:14 final size:15
Alignment explanation
Indices: 30213581--30213610 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
30213571 TAAATCCAAT
30213581 AGCCATAATT-ATCC
1 AGCCATAATTCATCC
30213595 AGCCATAATTCATCC
1 AGCCATAATTCATCC
30213610 A
1 A
30213611 CACATCTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.37, C:0.30, G:0.07, T:0.27
Consensus pattern (15 bp):
AGCCATAATTCATCC
Found at i:30222735 original size:23 final size:22
Alignment explanation
Indices: 30222692--30222749 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
30222682 AAAGGGTATC
* *
30222692 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
30222713 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
30222736 TACATATCATATCT
1 TACAAATCATATCT
30222750 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:30222743 original size:17 final size:17
Alignment explanation
Indices: 30222721--30222773 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 17
30222711 ATTACAAAAT
30222721 CATATCTTCTAAGATTA
1 CATATCTTCTAAGATTA
*
30222738 CATATCATATCTAAGATTG
1 CATATC-T-TCTAAGATTA
* *
30222757 CATATCCTCGAAGATTA
1 CATATCTTCTAAGATTA
30222774 TGTTTCCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 14 0.47
18 1 0.03
19 15 0.50
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (17 bp):
CATATCTTCTAAGATTA
Found at i:30222752 original size:19 final size:20
Alignment explanation
Indices: 30222705--30222762 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 20
30222695 AAATTAAATC
*
30222705 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-ATATCATA--T
30222728 TCTAAGATTACATATCATA-
1 TCTAAGATTACATATCATAT
*
30222747 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
30222763 CTCGAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.45
22 7 0.21
23 11 0.33
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (20 bp):
TCTAAGATTACATATCATAT
Found at i:30223257 original size:44 final size:44
Alignment explanation
Indices: 30223156--30224089 Score: 443
Period size: 44 Copynumber: 21.6 Consensus size: 44
30223146 CTTTCTCGAG
* * * * *
30223156 TCTGCTCCACTGCAACTTTAGGGAGATAAGA-C--TCGATATGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
* * *
30223197 TCTCCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
* * * * * *
30223241 TCCGCTCCACTGCAACTTCAGGGAGACAGGATTTGT-TTATTTAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGT-TTTAA
* * *** * *
30223285 TATGCCCCACTGCAACTTCAGGGAGATAAGAT-TCGACATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCT-GTGGT-TTTAA
* * *
30223330 TCTGC-CTCATTGCAACTTCA-GGAGGATAAGA-CT-TGATTACTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGATCTGTGGTT--TTAA
* * * ***
30223374 TCTGCTCCATTGCAACTTCAGGGAGATAAGA-C--TAGATGCGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
* * **
30223415 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
** * * * *
30223458 TCAACTCCACTGCAACTTCAGGAAGATAGGAT-TATCGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGT-GGTTTTAA
* * ** * * *
30223502 CCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCCTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGT-TTTAA
* ***
30223547 TCTGC-CTCACTGCAACTTCA-GGAGGATAAGA-CT-T-GATGCGA
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGATCTGTGGTTTTAA
* * ***
30223588 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
** * * * *
30223631 TCCACTCCACTGCAACTTCAGGAAGATAGGAT-TATCGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGT-GGTTTTAA
* * *** *
30223675 CCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGT-TTTAA
* *
30223720 TCTGC-CTCACTGCAACTTCA-GGAGGATAAGA-CT-TGCTTGCTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGATCTGTGGTT--TTAA
* * * ***
30223764 TCTGCTCCATTGCAACTTCAGGGAGATAAGA-C--TAGATACGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
* * *
30223805 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTGT-GATTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
* * *
30223847 TCTGCTCCACTGCAACTTCAGAGAGATAGGAT-TGTCGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGT-GGTTTTAA
* * * *** * *
30223891 TTTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGT-TTTAA
* * *
30223936 TCTGC-CTCACTGCAACTTCA-GAAGGATAAGA-CT-TGCTTACTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGATCTGTGGTT--TTAA
* * * * **
30223980 TCTGCTCCACTGCAACTTTAGGGAGATAAG-GC--TAGATGCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
* * ****
30224021 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCCAAAGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
30224064 TCTGCTCCACTGCAACTTCAGGGAGA
1 TCTGCTCCACTGCAACTTCAGGGAGA
30224090 CAAGGCTTGG
Statistics
Matches: 674, Mismatches: 163, Indels: 109
0.71 0.17 0.12
Matches are distributed among these distances:
40 81 0.12
41 58 0.09
42 17 0.03
43 65 0.10
44 328 0.49
45 125 0.19
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
Found at i:30223334 original size:174 final size:176
Alignment explanation
Indices: 30223065--30223404 Score: 444
Period size: 174 Copynumber: 1.9 Consensus size: 176
30223055 TCCATCACTC
*
30223065 TAATCCACTCCACTACAACTTAGGGAGACAGGATTTGTTTATTTAGTATGCCCCACTGCAATTTC
1 TAATCCACTCCACTACAACTTAGGGAGACAGGATTTGTTTATTTAGTATGCCCCACTGCAACTTC
* * * *
30223130 AGGGGGATAAGGGTTGCTTTCTCGAGTCTG-CTCCACTGCAACTTTAGG-GAGATAAGACTCGA-
66 AGGGAGATAAGGATTGCTCTCTCGAGTCTGCCT-CACTGCAACTTCAGGAG-GATAAGACTCGAT
*
30223192 TA-TGA-TCTCCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTT
129 TACTGAGTCTCCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTT
* *
30223238 TAATCCGCTCCACTGCAACTTCAGGGAGACAGGATTTGTTTATTTAGTATGCCCCACTGCAACTT
1 TAATCCACTCCACTACAACTT-AGGGAGACAGGATTTGTTTATTTAGTATGCCCCACTGCAACTT
* *
30223303 CAGGGAGATAA-GATTCGACATCT-TC-AGTCTGCCTCATTGCAACTTCAGGAGGATAAGACTTG
65 CAGGGAGATAAGGATT-G-C-TCTCTCGAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTCG
* * * *
30223365 ATTACTTAGTCTGCTCCATTGCAACTTCAGGGAGATAAGA
127 ATTACTGAGTCTCCTCCACTGCAACTTCAGAGAGATAAGA
30223405 CTAGATGCGA
Statistics
Matches: 144, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
173 22 0.15
174 83 0.58
175 8 0.06
176 4 0.03
177 27 0.19
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (176 bp):
TAATCCACTCCACTACAACTTAGGGAGACAGGATTTGTTTATTTAGTATGCCCCACTGCAACTTC
AGGGAGATAAGGATTGCTCTCTCGAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTCGATTA
CTGAGTCTCCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTT
Found at i:30223382 original size:133 final size:129
Alignment explanation
Indices: 30223162--30223789 Score: 310
Period size: 133 Copynumber: 4.8 Consensus size: 129
30223152 CGAGTCTGCT
* *
30223162 CCACTGCAACTTTAGGGAGATAAGACTCGATATGATCTCCTCTACTGCAACTTCAGAGAGATAAG
1 CCACTGCAACTTCAGGGAGATAAGACTCGATATCATCTCCTCTACTGCAACTTCAGAGAGATAAG
*
30223227 ATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGACAGGATTTGTTTATTTAGTATGCC
66 ATCTGTGATTTTAATCCGCTCCACTGCAACTTCAGGGAGACAGGATTTGTTTATTTAGTATGCC
* * *
30223291 CCACTGCAACTTCAGGGAGATAAGATTCGACATCTTCAGTCTGCCTC-ATTGCAACTTCAG-GAG
1 CCACTGCAACTTCAGGGAGATAAGACTCG--AT-ATCA-TCT-CCTCTACTGCAACTTCAGAGA-
* * * * * * * **
30223354 GATAAGA-CT-TGATTACTTAGTCTGCTCCATTGCAACTTCAGGGAGATAAGACTAG---A-TGC
60 GATAAGATCTGTGATT--TTAATCCGCTCCACTGCAACTTCAGGGAGACAGGATTTGTTTATTTA
*
30223413 GATCTG-C
123 G-TATGCC
* * * * * * * ** *
30223420 TCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCAACTCCACTGCAACTTCAG-GAAGA
1 CCACTGCAACTTCAGGGAGATAAGA-CT--CGATATCATCTCCTCTACTGCAACTTCAGAG-AGA
* * ** * * * *
30223484 TAGGAT-TATCGGCTTTAA-CCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TCATCCTCA
62 TAAGATCTGT-GATTTTAATCC-GCTCCACTGCAACTTCAGGGAGACAGGATTTGTTTAT--TTA
*
30223546 GTCTGCC
123 GTATGCC
* * * *
30223553 TCACTGCAACTTCA-GGAGGATAAGACTTGAT-GCGATCTGCTCT-CTGCAACTTCAGAGAGATA
1 CCACTGCAACTTCAGGGA-GATAAGACTCGATATC-ATCTCCTCTACTGCAACTTCAGAGAGATA
*** * * * * ** ***
30223615 AGATCCAAGGTTTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCG--GCTTTAACCT
64 AGATCTGTGATTTTAATCCGCTCCACTGCAACTTCAGGGAGACAGGATT-T-GTTTATTTAGTAT
*
30223678 GCT
127 GCC
* * *
30223681 CCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAATCTGCCTC-ACTGCAACTTCAG-GAG
1 CCACTGCAACTTCAGGGAGATAAGA-CT-CGAT-ATC-ATCT-CCTCTACTGCAACTTCAGAGA-
* * * *
30223744 GATAAGA-CT-TGCTTGCTTAGTCTGCTCCATTGCAACTTCAGGGAGA
60 GATAAGATCTGTGATT--TTAATCCGCTCCACTGCAACTTCAGGGAGA
30223790 TAAGACTAGA
Statistics
Matches: 385, Mismatches: 73, Indels: 78
0.72 0.14 0.15
Matches are distributed among these distances:
127 4 0.01
128 80 0.21
129 115 0.30
130 25 0.06
131 10 0.03
132 23 0.06
133 124 0.32
134 4 0.01
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (129 bp):
CCACTGCAACTTCAGGGAGATAAGACTCGATATCATCTCCTCTACTGCAACTTCAGAGAGATAAG
ATCTGTGATTTTAATCCGCTCCACTGCAACTTCAGGGAGACAGGATTTGTTTATTTAGTATGCC
Found at i:30223447 original size:217 final size:214
Alignment explanation
Indices: 30223156--30224089 Score: 884
Period size: 217 Copynumber: 4.3 Consensus size: 214
30223146 CTTTCTCGAG
* * * * * * * *
30223156 TCTGCTCCACTGCAACTTTAGGGAGATAAGA-CTCGATATGATCTCCTCTACTGCAACTTCAGAG
1 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTAGATTTAATCTGCTCCACTGCAACTTCAGAG
* * * * **
30223220 AGATAAGATCTGT-GGTTTTAATCCGCTCCACTGCAACTTCAGGGAGACAGGATTTGTTTAT-TT
65 AGATAAGAT-TATCGGCTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTTG-CCATCTT
* *
30223283 -AGTATGCCCCACTGCAACTTCAGGGAGATAAGATTCGACATCTTCAGTCTGCCTCATTGCAACT
128 CAATCTGCCCCACTGCAACTTCAGGGAGATAAGATT-G-CATCTTCAGTCTGCCTCATTGCAACT
*
30223347 TCAGGAGGATAAGACTTGATTACTTA
191 TCAGGAGGATAAGACTTGA-TAC-GA
* *** *
30223373 GTCTGCTC-CATTGCAACTTCAGGGAGATAAGA-CTAGATGCGATCTGCT-CTCTGCAACTTCAG
1 -TCTGCTCTC--TGCAACTTCAGAGAGATAAGATCTAGATTTAATCTGCTCCACTGCAACTTCAG
* * ** * * *
30223435 AGAGATAAGATCTA-AGGTTTTAATCAACTCCACTGCAACTTCAGGAAGATAGGATTATCGGC-T
63 AGAGATAAGAT-TATCGGCTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATT-T-GCCAT
* * * *
30223498 -TT-AACCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCCTCAGTCTGCCTCACTGCA
125 CTTCAATCTGCCCCACTGCAACTTCAGGGAGATAAGA-TTG-CATCTTCAGTCTGCCTCATTGCA
*
30223561 ACTTCAGGAGGATAAGACTTGATGCGA
188 ACTTCAGGAGGATAAGACTTGATACGA
* * **
30223588 TCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCACTCCACTGCAACTTCAG-
1 TCTGCTCTCTGCAACTTCAGAGAGATAAGAT-CTA-GATTTAATCTGCTCCACTGCAACTTCAGA
*
30223652 GAAGATAGGATTATCGGCTTTAA-CCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCT
64 G-AGATAAGATTATCGGCTTTAATCC-GCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCT
* *
30223716 TCAATCTGCCTCACTGCAACTTCA-GGAGGATAAGACTTGCTTGCTT-AGTCTG-CTCCATTGCA
127 TCAATCTGCCCCACTGCAACTTCAGGGA-GATAAGA-TTGCAT-CTTCAGTCTGCCT-CATTGCA
*
30223778 ACTTCAGG-GAGATAAGACTAGATACGA
188 ACTTCAGGAG-GATAAGACTTGATACGA
*
30223805 TCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTAATCTGCTCCACTGCAACTTCAGAG
1 TCTGCTCTCTGCAACTTCAGAGAGATAAGATCT-AGATTTAATCTGCTCCACTGCAACTTCAGAG
* * ** *
30223870 AGATAGGATTGTCGGCTTTAATTTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCA
65 AGATAAGATTATCGGCTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCA
* * * * *
30223935 GTCTGCCTCACTGCAACTTCA-GAAGGATAAGACTTGCTTACTT-AGTCTG-CTCCACTGCAACT
130 ATCTGCCCCACTGCAACTTCAGGGA-GATAAGA-TTGCAT-CTTCAGTCTGCCT-CATTGCAACT
* * * * *
30223997 TTAGG-GAGATAAGGCTAGATGCAA
191 TCAGGAG-GATAAGACTTGATACGA
* * *
30224021 TCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAAGTTTTAATCTGCTCCACTGCAACTTCAGG
1 TCTGCTCTCTGCAACTTCAGAGAGATAAGAT-C-TAGATTTAATCTGCTCCACTGCAACTTCAGA
30224086 GAGA
64 GAGA
30224090 CAAGGCTTGG
Statistics
Matches: 620, Mismatches: 70, Indels: 53
0.83 0.09 0.07
Matches are distributed among these distances:
213 20 0.03
214 7 0.01
215 6 0.01
216 214 0.35
217 300 0.48
218 72 0.12
219 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (214 bp):
TCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAGATTTAATCTGCTCCACTGCAACTTCAGAGA
GATAAGATTATCGGCTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAA
TCTGCCCCACTGCAACTTCAGGGAGATAAGATTGCATCTTCAGTCTGCCTCATTGCAACTTCAGG
AGGATAAGACTTGATACGA
Found at i:30223753 original size:173 final size:173
Alignment explanation
Indices: 30223384--30223794 Score: 673
Period size: 173 Copynumber: 2.4 Consensus size: 173
30223374 TCTGCTCCAT
* *
30223384 TGCAACTTCAGG-GAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
1 TGCAACTTCAGGAG-GATAAGACTTGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCC
30223448 AAGGTTTTAATCAACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAACCTGCTCCACT
65 AAGGTTTTAATCAACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAACCTGCTCCACT
* *
30223513 GCAACTTCAGGGAGATAAGATTTGTCATCCTCAGTCTGCCTCAC
130 GCAACTTCAGGGAGATAAGATTTGCCATCCTCAATCTGCCTCAC
30223557 TGCAACTTCAGGAGGATAAGACTTGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCA
1 TGCAACTTCAGGAGGATAAGACTTGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCA
*
30223622 AGGTTTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAACCTGCTCCACTG
66 AGGTTTTAATCAACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAACCTGCTCCACTG
*
30223687 CAACTTCAGGGAGATAAGATTTGCCATCTTCAATCTGCCTCAC
131 CAACTTCAGGGAGATAAGATTTGCCATCCTCAATCTGCCTCAC
* * *
30223730 TGCAACTTCAGGAGGATAAGACTTGCTTGCTTAGTCTGCTC-CATTGCAACTTCAGGGAGATAAG
1 TGCAACTTCAGGAGGATAAGACTTG-ATGC-GA-TCTGCTCTC--TGCAACTTCAGAGAGATAAG
30223794 A
61 A
30223795 CTAGATACGA
Statistics
Matches: 223, Mismatches: 9, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
173 190 0.85
174 4 0.02
175 2 0.01
176 7 0.03
177 20 0.09
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (173 bp):
TGCAACTTCAGGAGGATAAGACTTGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCA
AGGTTTTAATCAACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAACCTGCTCCACTG
CAACTTCAGGGAGATAAGATTTGCCATCCTCAATCTGCCTCAC
Found at i:30223819 original size:173 final size:172
Alignment explanation
Indices: 30223384--30223879 Score: 612
Period size: 173 Copynumber: 2.9 Consensus size: 172
30223374 TCTGCTCCAT
* *
30223384 TGCAACTTCAGG-GAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
1 TGCAACTTCAGGAG-GATAAGACTTGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGA-CC
* ** *
30223448 AAGGTTTTAATCAACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAACCTGCTCCACT
64 AAGGATACAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAACCTGCTCCACT
* *
30223513 GCAACTTCAGGGAGATAAGATTTGTCATCCTCAGTCTGCCTCAC
129 GCAACTTCAGGGAGATAAGATTTGCCATCCTCAATCTGCCTCAC
30223557 TGCAACTTCAGGAGGATAAGACTTGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCA
1 TGCAACTTCAGGAGGATAAGACTTGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGA-CCA
* **
30223622 AGGTTTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAACCTGCTCCACTG
65 AGGATACAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAACCTGCTCCACTG
*
30223687 CAACTTCAGGGAGATAAGATTTGCCATCTTCAATCTGCCTCAC
130 CAACTTCAGGGAGATAAGATTTGCCATCCTCAATCTGCCTCAC
* * *
30223730 TGCAACTTCAGGAGGATAAGACTTGCTTGCTTAGTCTGCTC-CATTGCAACTTCAGGGAGATAAG
1 TGCAACTTCAGGAGGATAAGACTTG-ATGC-GA-TCTGCTCTC--TGCAACTTCAGAGAGATAAG
* * ** * * * * *
30223794 A-CTA-GATACGATCTGCT-CTCTGCAACTTCA-GAGAGATAAGA-TCT-GTGATTTAATCTGCT
61 ACCAAGGATACAATCCACTCCACTGCAACTTCAGGA-AGATAGGATTATCG-GCTTTAACCTGCT
* *
30223853 CCACTGCAACTTCAGAGAGATAGGATT
124 CCACTGCAACTTCAGGGAGATAAGATT
30223880 GTCGGCTTTA
Statistics
Matches: 292, Mismatches: 23, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
171 1 0.00
172 40 0.14
173 209 0.72
174 11 0.04
175 4 0.01
176 7 0.02
177 20 0.07
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.28
Consensus pattern (172 bp):
TGCAACTTCAGGAGGATAAGACTTGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGACCAA
GGATACAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAACCTGCTCCACTGC
AACTTCAGGGAGATAAGATTTGCCATCCTCAATCTGCCTCAC
Found at i:30224182 original size:216 final size:214
Alignment explanation
Indices: 30223509--30224089 Score: 796
Period size: 216 Copynumber: 2.7 Consensus size: 214
30223499 TAACCTGCTC
* * * * *
30223509 CACTGCAACTTCAGGGA-GATAAGATTTGTCATCCTCAGTCTGC-CTCACTGCAACTTCA-GGAG
1 CACTGCAACTTCAGAGAGGATAAGACTTG-CTTACTTAGTCTGCTC-CACTGCAACTTCAGGGA-
* * **
30223571 GATAAGACTTGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCAC
63 GATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAAGTTTTAATCTGC
* * *
30223636 TCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAACCTGCTCCACTGCAACTTCAGGGAGA
128 TCCACTGCAACTTCAGGGAGATAGGATTGTCGGCTTTAATCTGCTCCACT-CAACTT--GGGAGA
30223701 TAAGATTTGCCATCTTCAATCTGCCT
190 TAAGATTTGCCATCTTC-ATCTGCCT
* *
30223727 CACTGCAACTTCAG-GAGGATAAGACTTGCTTGCTTAGTCTGCTCCATTGCAACTTCAGGGAGAT
1 CACTGCAACTTCAGAGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGAT
* *** *
30223791 AAGACTAGATACGATCTGCTCTCTGCAACTTCAGAGAGATAAGAT-CTGTGATTTAATCTGCTCC
66 AAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAAGTTTTAATCTGCTCC
* * *
30223855 ACTGCAACTTCAGAGAGATAGGATTGTCGGCTTTAATTTGCTCCACTGCAACCTCAGGGAGATAA
131 ACTGCAACTTCAGGGAGATAGGATTGTCGGCTTTAATCTGCTCCACT-CAA-CT-TGGGAGATAA
30223920 GATTTGCCATCTTCAGTCTGCCT
193 GATTTGCCATCTTCA-TCTGCCT
*
30223943 CACTGCAACTTCAGA-AGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTTAGGGAGAT
1 CACTGCAACTTCAGAGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGAT
* *
30224007 AAGGCTAGATGCAATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAAGTTTTAATCTGCTCC
66 AAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAAGTTTTAATCTGCTCC
30224072 ACTGCAACTTCAGGGAGA
131 ACTGCAACTTCAGGGAGA
30224090 CAAGGCTTGG
Statistics
Matches: 325, Mismatches: 30, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
215 1 0.00
216 191 0.59
217 105 0.32
218 28 0.09
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (214 bp):
CACTGCAACTTCAGAGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGAT
AAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAAGTTTTAATCTGCTCC
ACTGCAACTTCAGGGAGATAGGATTGTCGGCTTTAATCTGCTCCACTCAACTTGGGAGATAAGAT
TTGCCATCTTCATCTGCCT
Found at i:30224183 original size:132 final size:131
Alignment explanation
Indices: 30224081--30224466 Score: 592
Period size: 132 Copynumber: 2.9 Consensus size: 131
30224071 CACTGCAACT
* *
30224081 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATATGATTTACCG
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTATCG
* * *
30224146 TCTTCGACCTGCTCCACTACTGCTTAGAGAGATAAGATCTACAATCTTCAACCTACTCTGCTGCT
66 TCTTCGATCTACTCCACTACTGCTTAGAGAGATAAGATCTACAATCTTCAACCTACTCCGCTGC-
*
30224211 GC
130 AC
* *
30224213 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGTCG
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTATCG
* * * * *
30224278 TCTTCAATCTTCTCCACTACTACTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCT
66 TCTTCGATCTACTCCACTACTGCTTAGAGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCA
30224343 C
131 C
* *
30224344 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTTTTG
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTATCG
* * * *
30224409 TCCTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTACGATCCTCAACCTACTC
66 TCTTCGATCTACTCCACTACTGCTTAGAGAGATAAGATCTACAATCTTCAACCTACTC
30224467 TGCTATTGCT
Statistics
Matches: 234, Mismatches: 20, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
131 115 0.49
132 119 0.51
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (131 bp):
TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTATCG
TCTTCGATCTACTCCACTACTGCTTAGAGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCA
C
Found at i:30231259 original size:19 final size:21
Alignment explanation
Indices: 30231221--30231259 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
30231211 CCTTTTTTAA
*
30231221 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
30231242 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
30231260 AGAAAACAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:30231492 original size:19 final size:19
Alignment explanation
Indices: 30231468--30231541 Score: 103
Period size: 19 Copynumber: 3.8 Consensus size: 19
30231458 AACCATATCT
30231468 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
*
30231487 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
30231508 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
30231527 TCTAAGATTGCATAT
1 TCTAAGATTACATAT
30231542 GCTCGAAGAT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 32 0.64
21 18 0.36
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:30231505 original size:21 final size:21
Alignment explanation
Indices: 30231479--30231541 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
30231469 CTAAGATTAC
30231479 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
30231500 ATATCATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
30231519 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
30231540 AT
1 AT
30231542 GCTCGAAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
19 19 0.47
21 21 0.52
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:30241767 original size:13 final size:13
Alignment explanation
Indices: 30241749--30241786 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
30241739 GTAGATTTGT
30241749 AAAAAAATTGT-C
1 AAAAAAATTGTAC
*
30241761 AAAAAAATCGTAC
1 AAAAAAATTGTAC
30241774 AAAAAAAGTTGTA
1 AAAAAAA-TTGTA
30241787 TTTATTTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 10 0.45
13 8 0.36
14 4 0.18
ACGTcount: A:0.61, C:0.08, G:0.11, T:0.21
Consensus pattern (13 bp):
AAAAAAATTGTAC
Found at i:30245202 original size:27 final size:28
Alignment explanation
Indices: 30245167--30245220 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
30245157 TGTGTTTTAA
* *
30245167 TTTATTACATGTTATTAATG-TGTCTAAT
1 TTTATTACAAGCT-TTAATGATGTCTAAT
30245195 TTTA-TACAAGCTTTAATGATGTCTAA
1 TTTATTACAAGCTTTAATGATGTCTAA
30245221 GTCCAGCCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 6 0.26
27 13 0.57
28 4 0.17
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.48
Consensus pattern (28 bp):
TTTATTACAAGCTTTAATGATGTCTAAT
Found at i:30255536 original size:33 final size:34
Alignment explanation
Indices: 30255485--30255559 Score: 107
Period size: 33 Copynumber: 2.2 Consensus size: 34
30255475 AGATTTAAAC
* *
30255485 AAATTAATTACTAACACTTTTTTAAGGTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
30255519 AAATTAATT-CTAACACTTATTTGAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
30255552 AATTTAAT
1 AAATTAAT
30255560 AAACTAACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 28 0.76
34 9 0.24
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTAAGCTGAACTA
Found at i:30258921 original size:52 final size:52
Alignment explanation
Indices: 30258838--30258938 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
30258828 TAAGAAAACG
* *
30258838 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
*
30258890 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTTAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
30258939 TATGTGCATG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.28
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:30262441 original size:22 final size:21
Alignment explanation
Indices: 30262409--30262450 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
30262399 TTGGTATTTC
30262409 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
30262430 GGAATTTGGTACGAATTGGTA
1 GGAA-TTGGTACGAAATGGTA
30262451 ATGGTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.31, C:0.05, G:0.33, T:0.31
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:30263664 original size:30 final size:30
Alignment explanation
Indices: 30263606--30263664 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
30263596 TTGAAAAGGT
* *
30263606 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
30263636 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
30263665 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:30276359 original size:13 final size:14
Alignment explanation
Indices: 30276343--30276381 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 14
30276333 AAAAAAAATC
30276343 AAAATTC-AAAAAA
1 AAAATTCGAAAAAA
30276356 AAAATTCG---AAA
1 AAAATTCGAAAAAA
30276367 AAAATTCGAAAAAA
1 AAAATTCGAAAAAA
30276381 A
1 A
30276382 GAAGTGAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
11 11 0.50
13 7 0.32
14 4 0.18
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (14 bp):
AAAATTCGAAAAAA
Found at i:30276367 original size:11 final size:11
Alignment explanation
Indices: 30276353--30276381 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
30276343 AAAATTCAAA
30276353 AAAAAAATTCG
1 AAAAAAATTCG
30276364 AAAAAAATTCG
1 AAAAAAATTCG
30276375 AAAAAAA
1 AAAAAAA
30276382 GAAGTGAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (11 bp):
AAAAAAATTCG
Found at i:30277553 original size:12 final size:12
Alignment explanation
Indices: 30277536--30277575 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
30277526 AGTGAAAAGC
30277536 AAAAAGAGATTG
1 AAAAAGAGATTG
*
30277548 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
30277560 AAAGAGAGCTTG
1 AAAAAGAGATTG
30277572 AAAA
1 AAAA
30277576 GAAATCGAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.60, C:0.03, G:0.23, T:0.15
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:30284972 original size:10 final size:10
Alignment explanation
Indices: 30284957--30284998 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
30284947 TTTGCAAGTT
30284957 TTGAGCTAAA
1 TTGAGCTAAA
* *
30284967 TTGAGCTGAT
1 TTGAGCTAAA
*
30284977 TTGAGCT-CA
1 TTGAGCTAAA
30284986 TTGAGCTAAA
1 TTGAGCTAAA
30284996 TTG
1 TTG
30284999 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:30285576 original size:14 final size:14
Alignment explanation
Indices: 30285557--30285609 Score: 76
Period size: 13 Copynumber: 4.0 Consensus size: 14
30285547 AACTAGCTCT
30285557 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
30285571 TTTTTTTTTCA-AA
1 TTTTTTTTTCACAA
*
30285584 TTTTTTTTT-TCAA
1 TTTTTTTTTCACAA
30285597 -TTTTTTTTCACAA
1 TTTTTTTTTCACAA
30285610 CTTGATATCC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 8 0.23
13 16 0.46
14 11 0.31
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTTTTTTCACAA
Found at i:30285665 original size:13 final size:13
Alignment explanation
Indices: 30285647--30285694 Score: 69
Period size: 13 Copynumber: 3.6 Consensus size: 13
30285637 TGGAAACTAG
30285647 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
*
30285660 TTTTTTTTTTGAAA
1 TTTTTTTTTCG-AA
*
30285674 TTTTTTTTTCGAG
1 TTTTTTTTTCGAA
30285687 TTTTTTTT
1 TTTTTTTT
30285695 CGAGAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
13 19 0.61
14 12 0.39
ACGTcount: A:0.12, C:0.04, G:0.08, T:0.75
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:30285666 original size:14 final size:14
Alignment explanation
Indices: 30285647--30285694 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
30285637 TGGAAACTAG
30285647 TTTTTTTTTCGAAT
1 TTTTTTTTTCGAAT
*
30285661 TTTTTTTTT-GAAA
1 TTTTTTTTTCGAAT
*
30285674 TTTTTTTTTCGAGT
1 TTTTTTTTTCGAAT
30285688 TTTTTTT
1 TTTTTTT
30285695 CGAGAAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 12 0.40
14 18 0.60
ACGTcount: A:0.12, C:0.04, G:0.08, T:0.75
Consensus pattern (14 bp):
TTTTTTTTTCGAAT
Found at i:30290594 original size:16 final size:16
Alignment explanation
Indices: 30290573--30290615 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
30290563 TAGCTTCTTC
30290573 TTTTTTTTTCACAAAA
1 TTTTTTTTTCACAAAA
30290589 TTTTTTTTTCACAAAA
1 TTTTTTTTTCACAAAA
30290605 TTTTTTTTTCA
1 TTTTTTTTTCA
30290616 ACTTGATATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTTTTTTCACAAAA
Found at i:30290671 original size:12 final size:12
Alignment explanation
Indices: 30290654--30290688 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
30290644 TGGAAACCAA
30290654 TTTTTTTTGAAT
1 TTTTTTTTGAAT
*
30290666 TTTTTTTCGAAT
1 TTTTTTTTGAAT
30290678 TTTTTTTTGAA
1 TTTTTTTTGAA
30290689 GAAACTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.17, C:0.03, G:0.09, T:0.71
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:30291724 original size:21 final size:23
Alignment explanation
Indices: 30291679--30291725 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
30291669 TCACCTGCAA
* *
30291679 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
30291702 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
30291723 TAA
1 TAA
30291726 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:30301929 original size:21 final size:21
Alignment explanation
Indices: 30301903--30301965 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
30301893 TTGGTATTTG
30301903 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
30301924 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
30301945 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
30301966 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:30307691 original size:17 final size:17
Alignment explanation
Indices: 30307669--30307708 Score: 73
Period size: 16 Copynumber: 2.4 Consensus size: 17
30307659 CCGTATACAA
30307669 TTTTTTTCTTTC-AATT
1 TTTTTTTCTTTCGAATT
30307685 TTTTTTTCTTTCGAATT
1 TTTTTTTCTTTCGAATT
30307702 TTTTTTT
1 TTTTTTT
30307709 GTTTTTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTTTTTCTTTCGAATT
Found at i:30307723 original size:27 final size:27
Alignment explanation
Indices: 30307683--30307735 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
30307673 TTTCTTTCAA
* *
30307683 TTTTTTTTTCTTTCGAATTTTTTTTTG
1 TTTTTTTTTCTTTCAAAATTTTTTTTG
30307710 TTTTTGTTTT-TTTCAAAATTTTTTTT
1 TTTTT-TTTTCTTTCAAAATTTTTTTT
30307736 CAAACTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.77
Consensus pattern (27 bp):
TTTTTTTTTCTTTCAAAATTTTTTTTG
Found at i:30307732 original size:13 final size:13
Alignment explanation
Indices: 30307716--30307748 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
30307706 TTTGTTTTTG
30307716 TTTTTTTCAAAAT
1 TTTTTTTCAAAAT
*
30307729 TTTTTTTCAAACT
1 TTTTTTTCAAAAT
30307742 TTTTTTT
1 TTTTTTT
30307749 ACGTACCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTTTCAAAAT
Found at i:30308073 original size:21 final size:21
Alignment explanation
Indices: 30308047--30308103 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
30308037 TTGGTATTTG
30308047 GGAATTGGTACGAAATGATAT
1 GGAATTGGTACGAAATGATAT
* *
30308068 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGATAT
*
30308089 GGTATTTGGTACGAA
1 GG-AATTGGTACGAA
30308104 TTGGTAATGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 21 0.68
22 10 0.32
ACGTcount: A:0.33, C:0.04, G:0.32, T:0.32
Consensus pattern (21 bp):
GGAATTGGTACGAAATGATAT
Found at i:30309300 original size:30 final size:30
Alignment explanation
Indices: 30309242--30309300 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
30309232 TTGAAAAGGT
* *
30309242 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
30309272 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
30309301 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:30314197 original size:20 final size:20
Alignment explanation
Indices: 30314159--30314209 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
30314149 AGCTAATAAC
* *
30314159 GAGCTC-AATGTGCTGACTT
1 GAGCTCGAATGAGCTAACTT
30314178 GAGCTCGAATGAGCTAACTT
1 GAGCTCGAATGAGCTAACTT
30314198 GAGCTCGAATGA
1 GAGCTCGAATGA
30314210 ACCAAAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (20 bp):
GAGCTCGAATGAGCTAACTT
Found at i:30329166 original size:11 final size:10
Alignment explanation
Indices: 30329138--30329165 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
30329128 GAGAGAGAAA
30329138 GAAAAAAATT
1 GAAAAAAATT
30329148 GAAAAAAATT
1 GAAAAAAATT
30329158 GAAAAAAA
1 GAAAAAAA
30329166 AGAGAAGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (10 bp):
GAAAAAAATT
Found at i:30331526 original size:22 final size:21
Alignment explanation
Indices: 30331494--30331535 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
30331484 TTGGTATTTA
30331494 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
30331515 GGAATTTGGTACGAATTGGTA
1 GGAA-TTGGTACGAAATGGTA
30331536 ATGGTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.31, C:0.05, G:0.33, T:0.31
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:30336889 original size:18 final size:18
Alignment explanation
Indices: 30336868--30336931 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
30336858 GACCTCACTC
30336868 TCTTTTTTGATTTCTTTT
1 TCTTTTTTGATTTCTTTT
** *
30336886 TCTTTTTCAATCTCTTTT
1 TCTTTTTTGATTTCTTTT
30336904 TCTTTTCTTTTGATTTCTTTT
1 TC--TT-TTTTGATTTCTTTT
30336925 TCTTTTT
1 TCTTTTT
30336932 CAATCTCTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 20 0.54
19 2 0.05
20 2 0.05
21 13 0.35
ACGTcount: A:0.06, C:0.16, G:0.03, T:0.75
Consensus pattern (18 bp):
TCTTTTTTGATTTCTTTT
Found at i:30352200 original size:27 final size:29
Alignment explanation
Indices: 30352170--30352223 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
30352160 AAAAGACTTT
30352170 TCACTT-TTT-TTTACTTGATTTTTTTGC
1 TCACTTCTTTATTTACTTGATTTTTTTGC
**
30352197 TCACTTCTTTATTTTTTTGATTTTTTT
1 TCACTTCTTTATTTACTTGATTTTTTT
30352224 TACTTCGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 6 0.26
28 3 0.13
29 14 0.61
ACGTcount: A:0.11, C:0.13, G:0.06, T:0.70
Consensus pattern (29 bp):
TCACTTCTTTATTTACTTGATTTTTTTGC
Found at i:30355166 original size:20 final size:21
Alignment explanation
Indices: 30355141--30355181 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
30355131 CCGTCCATTG
30355141 CATGTACCTAA-AATTAAATA
1 CATGTACCTAATAATTAAATA
*
30355161 CATGTAGCTAATTAATTAAAT
1 CATGTACCTAA-TAATTAAAT
30355182 GAGAACACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.34
Consensus pattern (21 bp):
CATGTACCTAATAATTAAATA
Found at i:30370800 original size:37 final size:37
Alignment explanation
Indices: 30370759--30370837 Score: 158
Period size: 37 Copynumber: 2.1 Consensus size: 37
30370749 TAGGGTTTAG
30370759 TATGATTCTACTTAAGGTGGATTCCTAAGGTTCATTA
1 TATGATTCTACTTAAGGTGGATTCCTAAGGTTCATTA
30370796 TATGATTCTACTTAAGGTGGATTCCTAAGGTTCATTA
1 TATGATTCTACTTAAGGTGGATTCCTAAGGTTCATTA
30370833 TATGA
1 TATGA
30370838 GGTTTGGCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.41
Consensus pattern (37 bp):
TATGATTCTACTTAAGGTGGATTCCTAAGGTTCATTA
Found at i:30373233 original size:15 final size:15
Alignment explanation
Indices: 30373215--30373251 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
30373205 AATCTTTGAT
30373215 TTTCTTTGCTGTTTA
1 TTTCTTTGCTGTTTA
30373230 TTTCTTTGCTGTTTA
1 TTTCTTTGCTGTTTA
30373245 TTTCTTT
1 TTTCTTT
30373252 CCTTGTATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.05, C:0.14, G:0.11, T:0.70
Consensus pattern (15 bp):
TTTCTTTGCTGTTTA
Found at i:30374968 original size:19 final size:18
Alignment explanation
Indices: 30374928--30374968 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
30374918 TTGAGCTTGG
*
30374928 ATTTCACCATATTAAGCC
1 ATTTCACCATATTAAGCA
*
30374946 ATTTCACCATTATTGAGCA
1 ATTTCACCA-TATTAAGCA
30374965 ATTT
1 ATTT
30374969 TTTGTCATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (18 bp):
ATTTCACCATATTAAGCA
Found at i:30376799 original size:26 final size:28
Alignment explanation
Indices: 30376766--30376826 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
30376756 AAAAATAACT
30376766 AAAATATTAT-AA-CTTTTTTATTTATC
1 AAAATATTATAAATCTTTTTTATTTATC
*
30376792 AAAATATTATAAATTTTTTTTATTTATC
1 AAAATATTATAAATCTTTTTTATTTATC
30376820 AAAATAT
1 AAAATAT
30376827 ACCAAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 10 0.31
27 2 0.06
28 20 0.62
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (28 bp):
AAAATATTATAAATCTTTTTTATTTATC
Found at i:30377077 original size:11 final size:11
Alignment explanation
Indices: 30377061--30377157 Score: 57
Period size: 11 Copynumber: 9.4 Consensus size: 11
30377051 ATTTTTTTAA
30377061 TTTTAAAATAC
1 TTTTAAAATAC
30377072 TTTTAAAATAC
1 TTTTAAAATAC
*
30377083 TTTTTTTAAAT--
1 --TTTTAAAATAC
*
30377094 TTTT-TAA-A-
1 TTTTAAAATAC
**
30377102 TTTTAAAATTT
1 TTTTAAAATAC
30377113 TTTTAAAATAC
1 TTTTAAAATAC
* *
30377124 TTTT---TTAT
1 TTTTAAAATAC
*
30377132 TTTTAAAATAT
1 TTTTAAAATAC
30377143 TTTTAAAATAC
1 TTTTAAAATAC
30377154 TTTT
1 TTTT
30377158 TTTTAATTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 18
0.71 0.11 0.19
Matches are distributed among these distances:
8 12 0.18
9 6 0.09
11 41 0.61
13 8 0.12
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:30377105 original size:41 final size:41
Alignment explanation
Indices: 30377051--30377129 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
30377041 ATTATTTTTT
*
30377051 ATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTAA
1 ATTTTTTAAATTTTAAAATACTTTTAAAATACTTTTTTTAA
**
30377092 ATTTTTTAAATTTTAAAATTTTTTTAAAATACTTTTTT
1 ATTTTTTAAATTTTAAAATACTTTTAAAATACTTTTTT
30377130 ATTTTTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (41 bp):
ATTTTTTAAATTTTAAAATACTTTTAAAATACTTTTTTTAA
Found at i:30377147 original size:41 final size:40
Alignment explanation
Indices: 30377045--30377157 Score: 124
Period size: 41 Copynumber: 2.8 Consensus size: 40
30377035 ATTTTTATTA
**
30377045 TTTTTT-ATTTTTTTAATTTTAAAATACTTTTAAAATACT
1 TTTTTTAATTTTTAAAATTTTAAAATACTTTTAAAATACT
* **
30377084 TTTTTTAAATTTTTTAAATTTTAAAATTTTTTTAAAATAC-
1 TTTTTT-AATTTTTAAAATTTTAAAATACTTTTAAAATACT
30377124 TTTTTT-ATTTTTAAAATATTTTTAAAATACTTTT
1 TTTTTTAATTTTT-AAA-A-TTTTAAAATACTTTT
30377158 TTTTAATTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
38 6 0.10
39 8 0.13
40 7 0.11
41 42 0.67
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (40 bp):
TTTTTTAATTTTTAAAATTTTAAAATACTTTTAAAATACT
Found at i:30377159 original size:30 final size:30
Alignment explanation
Indices: 30377072--30377159 Score: 108
Period size: 30 Copynumber: 2.9 Consensus size: 30
30377062 TTTAAAATAC
* *
30377072 TTTTAAAATACTTTTTTTAAAT--TTTTTAAA
1 TTTTAAAATA--TTTTTAAAATACTTTTTTAA
* *
30377102 TTTTAAAATTTTTTTAAAATACTTTTTTAT
1 TTTTAAAATATTTTTAAAATACTTTTTTAA
30377132 TTTTAAAATATTTTTAAAATACTTTTTT
1 TTTTAAAATATTTTTAAAATACTTTTTT
30377160 TTAATTTTTG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
28 9 0.18
30 42 0.82
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTTAAAATATTTTTAAAATACTTTTTTAA
Found at i:30377525 original size:18 final size:18
Alignment explanation
Indices: 30377504--30377538 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30377494 GTAATAACTC
*
30377504 TATTTTAATTTAATAAAT
1 TATTCTAATTTAATAAAT
*
30377522 TATTCTCATTTAATAAA
1 TATTCTAATTTAATAAA
30377539 CTCTAATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTCTAATTTAATAAAT
Found at i:30377549 original size:15 final size:15
Alignment explanation
Indices: 30377529--30377558 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
30377519 AATTATTCTC
30377529 ATTTAATAAACTCTA
1 ATTTAATAAACTCTA
30377544 ATTTAATAAACTCTA
1 ATTTAATAAACTCTA
30377559 TTTTGGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTAATAAACTCTA
Found at i:30377592 original size:23 final size:23
Alignment explanation
Indices: 30377566--30377637 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
30377556 CTATTTTGGT
30377566 AATTTGATGAGAATAGTTTATTA
1 AATTTGATGAGAATAGTTTATTA
*
30377589 AA-TT-A--A-AATAGAGTTATTAA
1 AATTTGATGAGAATAG-TTTATT-A
30377609 GTAATTTGATGAGAATAGTTTATTA
1 --AATTTGATGAGAATAGTTTATTA
30377634 AATT
1 AATT
30377638 AAAATAGAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 18
0.66 0.03 0.31
Matches are distributed among these distances:
18 5 0.13
19 6 0.16
20 1 0.03
21 1 0.03
22 4 0.11
23 8 0.21
24 1 0.03
25 1 0.03
26 6 0.16
27 5 0.13
ACGTcount: A:0.43, C:0.00, G:0.15, T:0.42
Consensus pattern (23 bp):
AATTTGATGAGAATAGTTTATTA
Found at i:30377659 original size:45 final size:45
Alignment explanation
Indices: 30377564--30377652 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
30377554 CTCTATTTTG
30377564 GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTAA
1 GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTAA
30377609 GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTA
1 GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTA
30377653 CTTAATTAGN
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (45 bp):
GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTAA
Found at i:30378374 original size:27 final size:28
Alignment explanation
Indices: 30378340--30378404 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
30378330 TGTTTTTGGT
*
30378340 ATATTTTGGTAAAT-AAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
*
30378367 ATATTTTGATAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
30378395 ATATTTTGGT
1 ATATTTTGGT
30378405 TATTTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 13 0.38
28 21 0.62
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:30378789 original size:19 final size:17
Alignment explanation
Indices: 30378705--30378802 Score: 56
Period size: 19 Copynumber: 5.4 Consensus size: 17
30378695 CCTGACACCC
*
30378705 TTATTTTATTTTTTATTT
1 TTATTTT-TTTTTAATTT
*
30378723 TTACTTTTTTATTAACTTT
1 TTA-TTTTTTTTTAA-TTT
* *
30378742 TGTCTTTTTCTTTAAATTT
1 T-TATTTTT-TTTTAATTT
*
30378761 TTTTTATTTTTTTAAGTTT
1 TTATT-TTTTTTTAA-TTT
30378780 TATATTTTTTTCTT-A-TT
1 T-TATTTTTTT-TTAATTT
30378797 TTATTT
1 TTATTT
30378803 ATTTATTGTT
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
16 5 0.08
17 3 0.05
18 16 0.25
19 30 0.47
20 10 0.16
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (17 bp):
TTATTTTTTTTTAATTT
Found at i:30378843 original size:23 final size:22
Alignment explanation
Indices: 30378817--30378889 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 22
30378807 ATTGTTATTA
30378817 ATTTTGAAAAATTTGAAATATAT
1 ATTTTGAAAAATTT-AAATATAT
**
30378840 A-TTTGAAATGTTTTATAATATAT
1 ATTTTGAAA-AATTTA-AATATAT
*
30378863 ATTTTTTAAAAATTTAAATAT-T
1 A-TTTTGAAAAATTTAAATATAT
30378885 ATTTT
1 ATTTT
30378890 TAAATTATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
21 4 0.10
22 10 0.24
23 17 0.41
24 4 0.10
25 6 0.15
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
ATTTTGAAAAATTTAAATATAT
Found at i:30378915 original size:32 final size:34
Alignment explanation
Indices: 30378861--30378931 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 34
30378851 TTTATAATAT
30378861 ATATTTTTTAAAAATTTAAATATTAT-TTTTAAA
1 ATATTTTTTAAAAATTTAAATATTATGTTTTAAA
* * *
30378894 TTATTTTTT-AAATTTTGAATATTATGTTTTAAA
1 ATATTTTTTAAAAATTTAAATATTATGTTTTAAA
30378927 ATATT
1 ATATT
30378932 AATTATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (34 bp):
ATATTTTTTAAAAATTTAAATATTATGTTTTAAA
Found at i:30378918 original size:21 final size:20
Alignment explanation
Indices: 30378885--30378926 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
30378875 TTTAAATATT
* *
30378885 ATTTTTAAATTATTTTTTAA
1 ATTTTGAAATTATGTTTTAA
30378905 ATTTTGAATATTATGTTTTAA
1 ATTTTGAA-ATTATGTTTTAA
30378926 A
1 A
30378927 ATATTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
ATTTTGAAATTATGTTTTAA
Found at i:30379017 original size:10 final size:10
Alignment explanation
Indices: 30379002--30379074 Score: 51
Period size: 10 Copynumber: 6.8 Consensus size: 10
30378992 TTATTATTAG
30379002 TTTTTAAATA
1 TTTTTAAATA
30379012 TTTTT-AATA
1 TTTTTAAATA
*
30379021 TTATTT-AATT
1 TT-TTTAAATA
30379031 TGTTTTATAATA
1 T-TTTTA-AATA
*
30379043 TTTTAAATTATGA
1 TTTTTAA--AT-A
30379056 TTTTTAAATTA
1 TTTTTAAA-TA
30379067 TTTTTAAA
1 TTTTTAAA
30379075 GATATTCGGC
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
9 6 0.12
10 16 0.31
11 15 0.29
12 7 0.14
13 7 0.14
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:30379044 original size:22 final size:23
Alignment explanation
Indices: 30379011--30379069 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
30379001 GTTTTTAAAT
30379011 ATTTTTAATATTATTTAATT-TG
1 ATTTTTAATATTATTTAATTATG
*
30379033 -TTTTATAATATT-TTAAATTATG
1 ATTTT-TAATATTATTTAATTATG
30379055 ATTTTTAA-ATTATTT
1 ATTTTTAATATTATTT
30379070 TTAAAGATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
21 13 0.42
22 14 0.45
23 4 0.13
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (23 bp):
ATTTTTAATATTATTTAATTATG
Found at i:30379307 original size:21 final size:21
Alignment explanation
Indices: 30379283--30379346 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 21
30379273 TTTTAAATTC
30379283 TATTTGAAATTTAAAAAATAA
1 TATTTGAAATTTAAAAAATAA
*
30379304 TATTT--TATTTAAAAAAGTGAA
1 TATTTGAAATTTAAAAAA-T-AA
*
30379325 -ATTTGAATTAATTAAAAAATAA
1 TATTTGAA--ATTTAAAAAATAA
30379347 AAAATATTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 11
0.71 0.06 0.23
Matches are distributed among these distances:
19 10 0.29
20 5 0.15
21 7 0.21
22 2 0.06
23 1 0.03
24 9 0.26
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (21 bp):
TATTTGAAATTTAAAAAATAA
Found at i:30379365 original size:15 final size:17
Alignment explanation
Indices: 30379345--30379403 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
30379335 ATTAAAAAAT
30379345 AAAAAATA-TT-TGTTA
1 AAAAAATATTTATGTTA
* *
30379360 AAAAAAGATTTATTTTA
1 AAAAAATATTTATGTTA
30379377 AAAAAATAAATTTAT-TTA
1 AAAAAAT--ATTTATGTTA
*
30379395 AAAATATAT
1 AAAAAATAT
30379404 ATATTAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
15 7 0.19
16 4 0.11
17 10 0.28
18 9 0.25
19 6 0.17
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AAAAAATATTTATGTTA
Found at i:30379657 original size:9 final size:9
Alignment explanation
Indices: 30379643--30379675 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
30379633 CAAATTTTTA
30379643 AAAATAAAT
1 AAAATAAAT
30379652 AAAATAAAT
1 AAAATAAAT
30379661 AAACA-AAAT
1 AAA-ATAAAT
30379670 AAAATA
1 AAAATA
30379676 TGAAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.05
9 20 0.91
10 1 0.05
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (9 bp):
AAAATAAAT
Found at i:30379724 original size:20 final size:19
Alignment explanation
Indices: 30379694--30379745 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
30379684 ATGAAACTTA
*
30379694 AAAAAAGAAAAAATTTAA-
1 AAAAAAGAAAAAAGTTAAT
30379712 AGAAAAAGAAAAAAGTTAAT
1 A-AAAAAGAAAAAAGTTAAT
30379732 AAAAAAGTAAAAAA
1 AAAAAAG-AAAAAA
30379746 AAAAGTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 1 0.03
19 22 0.73
20 7 0.23
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (19 bp):
AAAAAAGAAAAAAGTTAAT
Found at i:30379735 original size:12 final size:12
Alignment explanation
Indices: 30379710--30379755 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
30379700 GAAAAAATTT
*
30379710 AAAGAAAAAGAAA
1 AAAGTAAAA-AAA
* *
30379723 AAAGTTAATAAA
1 AAAGTAAAAAAA
30379735 AAAGTAAAAAAA
1 AAAGTAAAAAAA
30379747 AAAGTAAAA
1 AAAGTAAAA
30379756 GAAGGGTGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 22 0.79
13 6 0.21
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (12 bp):
AAAGTAAAAAAA
Found at i:30380671 original size:7 final size:7
Alignment explanation
Indices: 30380659--30380683 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30380649 TGTTAGAGTT
30380659 TAAAGTA
1 TAAAGTA
30380666 TAAAGTA
1 TAAAGTA
30380673 TAAAGTA
1 TAAAGTA
30380680 TAAA
1 TAAA
30380684 TATTAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (7 bp):
TAAAGTA
Found at i:30388540 original size:21 final size:19
Alignment explanation
Indices: 30388510--30388549 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
30388500 AAAAAATAAA
*
30388510 AAATAATTTTTTATATTTTT
1 AAATAATTTTATA-ATTTTT
30388530 AAATAAATTTTATAATTTTT
1 AAAT-AATTTTATAATTTTT
30388550 TGAATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AAATAATTTTATAATTTTT
Found at i:30389442 original size:13 final size:13
Alignment explanation
Indices: 30389426--30389491 Score: 71
Period size: 13 Copynumber: 5.1 Consensus size: 13
30389416 TTTAAACCAA
*
30389426 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
*
30389439 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
*
30389452 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
*
30389465 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
*
30389478 ATTTTTCAAAAGC
1 ACTTTTCAAAAGC
30389491 A
1 A
30389492 TTACTAAACT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
12 4 0.09
13 35 0.81
14 4 0.09
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:30391065 original size:25 final size:25
Alignment explanation
Indices: 30391008--30391103 Score: 84
Period size: 25 Copynumber: 3.8 Consensus size: 25
30390998 CCGAGCTGTA
* * * *
30391008 AACGGAAAGCTCCTCCGAGCTGAAT
1 AACGGGAAGCTCATGCGAGCTAAAT
** * * *
30391033 AATAGGAAGTTCATGTGATCTAAAT
1 AACGGGAAGCTCATGCGAGCTAAAT
**
30391058 AACGGGAAGCTCATGCGAGCTGTAT
1 AACGGGAAGCTCATGCGAGCTAAAT
*
30391083 AACGGGAAGCTCATACGAGCT
1 AACGGGAAGCTCATGCGAGCT
30391104 GTGGCGTATC
Statistics
Matches: 54, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 54 1.00
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (25 bp):
AACGGGAAGCTCATGCGAGCTAAAT
Done.