Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 261 of 373
Found at i:88615675 original size:19 final size:19
Alignment explanation
Indices: 88615651--88615701 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
88615641 AAAAGCTATG
* *
88615651 TGTTATACGGATGAATTAT
1 TGTTATACGGATGAAGTAC
* *
88615670 TGTTATAGGGTTGAAGTAC
1 TGTTATACGGATGAAGTAC
88615689 TGTTTATACGGAT
1 TG-TTATACGGAT
88615702 CAGTTACTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.27, C:0.06, G:0.25, T:0.41
Consensus pattern (19 bp):
TGTTATACGGATGAAGTAC
Found at i:88626998 original size:93 final size:93
Alignment explanation
Indices: 88626887--88627058 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
88626877 GCCCATAAGT
* * * *
88626887 GAACTCGGACTCAACTCAACTAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAATTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
88626952 CGAGCCCGGATGCCTAGTTACATCTCAC
66 CGAGCCCGGATGCCTAGTTACATCTCAC
* *
88626980 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
**
88627045 CGAGTTCGGATGCC
66 CGAGCCCGGATGCC
88627059 CAAATATCCC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCCCGGATGCCTAGTTACATCTCAC
Found at i:88627054 original size:46 final size:46
Alignment explanation
Indices: 88626879--88627054 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
88626869 TGTAACCCGC
* * * *
88626879 CCATAAGTGAACTCGGACTCAACTCAACTAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
* * * *
88626925 CCATAAGTGAACTCGGACTCAATTCAACGAGCCCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-ATTTGCAT
* * *
88626975 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
*
88627018 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
88627055 TGCCCAAATA
Statistics
Matches: 106, Mismatches: 17, Indels: 14
0.77 0.12 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 62 0.58
47 26 0.25
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
Found at i:88630650 original size:37 final size:37
Alignment explanation
Indices: 88630600--88630678 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
88630590 TTATTACGAA
* * *
88630600 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
88630637 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
88630674 GTCTT
1 GTCTT
88630679 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:88630884 original size:47 final size:47
Alignment explanation
Indices: 88630797--88631144 Score: 570
Period size: 47 Copynumber: 7.4 Consensus size: 47
88630787 CCCTTCGGGA
* * ** * * *
88630797 CTTATCACATTTATACACTTTCACATCCATCATGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
88630844 CCTGTCACATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
88630891 GTTACCACATATATACACTTTCACATTCATCACATCGTCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
88630938 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
88630985 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
88631032 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
88631079 CTTATCACATATATACACTTTCACATTCATAACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
88631126 CTTATCACATATATACACT
1 CTTATCACATATATACACT
88631145 GTCTTGGCTG
Statistics
Matches: 281, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 281 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:88634349 original size:40 final size:40
Alignment explanation
Indices: 88634305--88634686 Score: 330
Period size: 40 Copynumber: 9.6 Consensus size: 40
88634295 CCAGCATGAT
* * * * *
88634305 TGCTCTTCGGGACCTAGCCAGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** * *
88634345 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
88634385 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
88634425 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
88634465 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * * * * *
88634505 TGCTCTTCGGGACTTAGCCCTGTTATAGTAACTCGCACAAA
1 TGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCACGAA
* * *** * * *
88634546 TGC-CTTCGGGACTTAACCCGAATTTTGTAACTCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGA-TACATCACTAGCACGAA
* * * *
88634586 TGC-CTTCGGG-CTTAGCCCGGAATTA-GTAACTCGCACAAA
1 TGCTCTTCGGGACTTAGCCCGG-A-TACATCACTAGCACGAA
* **
88634625 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC-AA
1 TGCTCTTCGGGA-CTTAGCCCGGATA-CATCAC-TAGCACGAA
*
88634665 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
88634687 CATCATTCGA
Statistics
Matches: 292, Mismatches: 41, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
38 4 0.01
39 29 0.10
40 237 0.81
41 22 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:88634670 original size:79 final size:80
Alignment explanation
Indices: 88634509--88634686 Score: 211
Period size: 79 Copynumber: 2.2 Consensus size: 80
88634499 CATGAATGCT
* * * *
88634509 CTTCGGGACTTAGCCCTG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAATTTTG
1 CTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAATATGG
* *
88634573 TAACTCGCACCAATGC
65 TAACTAGCACCAAAGC
** *
88634589 CTTCGGG-CTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGG
1 CTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGAATATGG
*
88634652 TCACTTAGCA-CAAAGC
65 TAAC-TAGCACCAAAGC
88634668 CTTCGGGACTTAGCCCGGA
1 CTTCGGGACTTAGCCCGGA
88634687 CATCATTCGA
Statistics
Matches: 84, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
78 3 0.04
79 58 0.69
80 23 0.27
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAATATGGT
AACTAGCACCAAAGC
Found at i:88636592 original size:37 final size:37
Alignment explanation
Indices: 88636542--88636620 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
88636532 TTATTACGAA
* * *
88636542 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
* *
88636579 GTCTTACCCGGACAAAATCCCCGCACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
88636616 GTCTT
1 GTCTT
88636621 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:88636817 original size:47 final size:47
Alignment explanation
Indices: 88636739--88637133 Score: 673
Period size: 47 Copynumber: 8.4 Consensus size: 47
88636729 CCCTTCGGGA
* * * * * *
88636739 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
88636786 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
88636833 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
88636880 CTTATCACATATATACACTTTCACATTCAGCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
88636927 CTTATCACATATATACACTTTCACATTCATCACATCGGCCAATAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
88636974 CTTATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
88637021 CTTATCACATATATACACTTTCACGTTGATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
88637068 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
88637115 CTTATCACATATATACACT
1 CTTATCACATATATACACT
88637134 GTCTTGGCTG
Statistics
Matches: 328, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 328 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:88640337 original size:40 final size:40
Alignment explanation
Indices: 88640293--88640548 Score: 318
Period size: 40 Copynumber: 6.4 Consensus size: 40
88640283 CCAGCATGAT
* * * *
88640293 TGCTCTTCGGGACCTAGCCGGGATATAAT-ACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATA-CATCACTAGCACGAA
** * *
88640333 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
88640373 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
88640413 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
88640453 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * * * * *
88640493 TGCTCTTCGGGAATTAGCCCGGTTATAGTAACTCGCACAAA
1 TGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCACGAA
88640534 TGC-CTTCGGGACTTA
1 TGCTCTTCGGGACTTA
88640549 ACTCGAATTT
Statistics
Matches: 188, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
39 2 0.01
40 174 0.93
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:88640564 original size:40 final size:39
Alignment explanation
Indices: 88640518--88640621 Score: 138
Period size: 39 Copynumber: 2.6 Consensus size: 39
88640508 AGCCCGGTTA
*
88640518 TAGTAACTCGCACAAATGCCTTCGGGACTTAACTC-GAATT
1 TAGTAACTCGCACAAATGCCTTCGGG-CTTAACCCGGAA-T
* * * *
88640558 TTGTAACTCGCACCAATGCCTTCGAGCTTAGCCCGGAAT
1 TAGTAACTCGCACAAATGCCTTCGGGCTTAACCCGGAAT
88640597 TAGTAACTCGCACAAATGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGG
88640622 ATCTTAGTCC
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
39 29 0.53
40 26 0.47
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (39 bp):
TAGTAACTCGCACAAATGCCTTCGGGCTTAACCCGGAAT
Found at i:88640581 original size:120 final size:119
Alignment explanation
Indices: 88640346--88640672 Score: 272
Period size: 120 Copynumber: 2.7 Consensus size: 119
88640336 TCTTCGGGGT
* * * **
88640346 TTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATG
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATAACTAGCACA
* * * *
88640411 AATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
66 AATGCTCTTCGGGACTTAACCCGAATACATAACTAGCACCAATGCTCTTC-GAAC
* * * *
88640466 TTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGAA-TTAGCCCGGTTATAGTAACTCGCA
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTC-GGAACTTAGCCCGGATACA-TAACTAGCA
* *** * *
88640530 CAAATGC-CTTCGGGACTTAACTCGAATTTTGTAACTCGCACCAATGC-CTTCGAGC
64 CAAATGCTCTTCGGGACTTAACCCGAA-TACATAACTAGCACCAATGCTCTTCGAAC
* * * * * * ** *
88640585 TTAGCCCGGAATTA-GTAACTCGCACAAATGC-CTTCGGATCTTAGTCCGGATATGGTCACTTAG
1 TTAGCCCGG-A-TACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATA-CATAAC-TAG
*
88640648 CACAAA-GC-CTTCGGGACTTAGCCCG
62 CACAAATGCTCTTCGGGACTTAACCCG
88640673 GACATCATTC
Statistics
Matches: 166, Mismatches: 33, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
118 3 0.02
119 46 0.28
120 85 0.51
121 32 0.19
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (119 bp):
TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATAACTAGCACA
AATGCTCTTCGGGACTTAACCCGAATACATAACTAGCACCAATGCTCTTCGAAC
Found at i:88640628 original size:40 final size:40
Alignment explanation
Indices: 88640411--88640674 Score: 179
Period size: 40 Copynumber: 6.6 Consensus size: 40
88640401 CACTAGCATG
* * * *
88640411 AATGCTCTTCGGGACTTAGCCCGG-A-TACATCACTAGCACG
1 AATGC-CTTCGGGACTTAGCCCGGAATTA-GTAACTCGCACA
* * * * **
88640451 AATGCTCTTCGGAACTTAGCCCGG-A-TACATCACTAGCATG
1 AATGC-CTTCGGGACTTAGCCCGGAATTA-GTAACTCGCACA
* *
88640491 AATGCTCTTCGGGAATTAGCCCGG-TTATAGTAACTCGCACA
1 AATGC-CTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACA
* * * *
88640532 AATGCCTTCGGGACTTAACTC-GAATTTTGTAACTCGCACC
1 AATGCCTTCGGGACTTAGCCCGGAA-TTAGTAACTCGCACA
*
88640572 AATGCCTTCGAG-CTTAGCCCGGAATTAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACA
* * * *
88640611 AATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCACA
88640652 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
88640675 CATCATTCGA
Statistics
Matches: 186, Mismatches: 27, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
38 1 0.01
39 31 0.17
40 128 0.69
41 24 0.13
42 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACA
Found at i:88640658 original size:79 final size:80
Alignment explanation
Indices: 88640518--88640674 Score: 187
Period size: 79 Copynumber: 2.0 Consensus size: 80
88640508 AGCCCGGTTA
* * * *
88640518 TAGTAACTCGCACAAATGCCTTCGGGACTTAACTCGAATTTTGTAACTCGCACCAATGCCTTCGA
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACTCGAATATGGTAACTAGCACCAAAGCCTTCGA
88640583 G-CTTAGCCCGGAAT
66 GACTTAGCCCGGAAT
* * *
88640597 TAGTAACTCGCACAAATGCCTTC-GGATCTT-AGTCCGGATATGGTCACTTAGCA-CAAAGCCTT
1 TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACT-CGAATATGGTAAC-TAGCACCAAAGCCTT
*
88640659 CGGGACTTAGCCCGGA
63 CGAGACTTAGCCCGGA
88640675 CATCATTCGA
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
78 5 0.08
79 46 0.70
80 15 0.23
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (80 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACTCGAATATGGTAACTAGCACCAAAGCCTTCGA
GACTTAGCCCGGAAT
Found at i:88642580 original size:37 final size:37
Alignment explanation
Indices: 88642530--88642608 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
88642520 TTATTACGAA
* * *
88642530 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
* *
88642567 GTCTTACCCGGACAAAATCCCCGCACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
88642604 GTCTT
1 GTCTT
88642609 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:88642805 original size:47 final size:47
Alignment explanation
Indices: 88642727--88643121 Score: 673
Period size: 47 Copynumber: 8.4 Consensus size: 47
88642717 CCCTTCGGGA
* * * * * *
88642727 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
88642774 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
88642821 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
88642868 CTTATCACATATATACACTTTCACATTCAGCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
88642915 CTTATCACATATATACACTTTCACATTCATCACATCGGCCAATAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
88642962 CTTATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
88643009 CTTATCACATATATACACTTTCACGTTGATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
88643056 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
88643103 CTTATCACATATATACACT
1 CTTATCACATATATACACT
88643122 GTCTTGGCTG
Statistics
Matches: 328, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 328 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:88651365 original size:13 final size:13
Alignment explanation
Indices: 88651347--88651371 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88651337 TGTAAGGCAC
88651347 GGCCGTGCGACAG
1 GGCCGTGCGACAG
88651360 GGCCGTGCGACA
1 GGCCGTGCGACA
88651372 CACACGCCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.44, T:0.08
Consensus pattern (13 bp):
GGCCGTGCGACAG
Found at i:88653275 original size:18 final size:17
Alignment explanation
Indices: 88653248--88653282 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
88653238 AATCCTCCTA
*
88653248 TTTTATTTTTATTTTTC
1 TTTTATTTTTAGTTTTC
88653265 TTTTGATTTTTAGTTTTC
1 TTTT-ATTTTTAGTTTTC
88653283 AATTTTCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.77
Consensus pattern (17 bp):
TTTTATTTTTAGTTTTC
Found at i:88656217 original size:13 final size:13
Alignment explanation
Indices: 88656201--88656233 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
88656191 TTTGATTAAA
*
88656201 TTAGTTAATTAGT
1 TTAGATAATTAGT
88656214 TTAGATAATTAGT
1 TTAGATAATTAGT
88656227 TTA-ATAA
1 TTAGATAA
88656234 ACAAATCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:88657518 original size:42 final size:42
Alignment explanation
Indices: 88657455--88657539 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
88657445 ACTAGGAAAA
*
88657455 TTATGTGATCTGAACTCATGAGCTGTGGTCTGAGTTCATGAT
1 TTATGTGATCTGAACTAATGAGCTGTGGTCTGAGTTCATGAT
* * * *
88657497 TTATGTGATTTGAACTAATGAGTTGTGGTTTGAGTTTATGAT
1 TTATGTGATCTGAACTAATGAGCTGTGGTCTGAGTTCATGAT
88657539 T
1 T
88657540 ATGAGTCACA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.22, C:0.08, G:0.26, T:0.44
Consensus pattern (42 bp):
TTATGTGATCTGAACTAATGAGCTGTGGTCTGAGTTCATGAT
Found at i:88668925 original size:25 final size:25
Alignment explanation
Indices: 88668897--88668947 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
88668887 TGAATGAAGG
88668897 TTTCATAAAAAATGGAAAAGAACTA
1 TTTCATAAAAAATGGAAAAGAACTA
*
88668922 TTTCATAAAAAATGGCAAAGAACTA
1 TTTCATAAAAAATGGAAAAGAACTA
88668947 T
1 T
88668948 CATTAGAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (25 bp):
TTTCATAAAAAATGGAAAAGAACTA
Found at i:88685727 original size:15 final size:13
Alignment explanation
Indices: 88685698--88685724 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
88685688 GCTCCGCAGG
88685698 GACACGCCCGTGT
1 GACACGCCCGTGT
88685711 GACACGCCCGTGT
1 GACACGCCCGTGT
88685724 G
1 G
88685725 TGATTGCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:88694880 original size:17 final size:18
Alignment explanation
Indices: 88694858--88694891 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
88694848 TCAATTGGGC
88694858 CGTGT-GGACCACACGGG
1 CGTGTGGGACCACACGGG
*
88694875 CGTGTGGGCCCACACGG
1 CGTGTGGGACCACACGG
88694892 TTGAACCACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.15, C:0.32, G:0.41, T:0.12
Consensus pattern (18 bp):
CGTGTGGGACCACACGGG
Found at i:88694986 original size:17 final size:17
Alignment explanation
Indices: 88694964--88695019 Score: 85
Period size: 17 Copynumber: 3.2 Consensus size: 17
88694954 TTTGGGCCGT
88694964 GTGGGCCACACGGGCGC
1 GTGGGCCACACGGGCGC
88694981 GTGGGCCACACGGGCGC
1 GTGGGCCACACGGGCGC
*
88694998 GTGGGCCTACATGGGCAGC
1 GTGGGCC-ACACGGGC-GC
88695017 GTG
1 GTG
88695020 TGAGGCCATT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
17 24 0.67
18 7 0.19
19 5 0.14
ACGTcount: A:0.12, C:0.30, G:0.46, T:0.11
Consensus pattern (17 bp):
GTGGGCCACACGGGCGC
Found at i:88704132 original size:39 final size:40
Alignment explanation
Indices: 88704058--88704138 Score: 110
Period size: 39 Copynumber: 2.0 Consensus size: 40
88704048 CACAGAAAAG
* * *
88704058 TCAATCTAGAAAAATAAAGGAAGAACTACATGAAGTTAAT
1 TCAATCGAGAAAAATAAAGAAAGAACTACAGGAAGTTAAT
**
88704098 TCAATCGAGAAAAATAAA-AAAGAACTGTAGGAAGTTAAT
1 TCAATCGAGAAAAATAAAGAAAGAACTACAGGAAGTTAAT
88704137 TC
1 TC
88704139 CACATTCCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 19 0.53
40 17 0.47
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.22
Consensus pattern (40 bp):
TCAATCGAGAAAAATAAAGAAAGAACTACAGGAAGTTAAT
Found at i:88706365 original size:27 final size:27
Alignment explanation
Indices: 88706301--88706396 Score: 81
Period size: 27 Copynumber: 3.6 Consensus size: 27
88706291 TTATAGTGAT
** *
88706301 AATCATGAAAGAAAAGCCTTTGTGGCAA
1 AATCATGAAAGAAAATTCTTTGTGG-AG
* *
88706329 AAT-ATAAAAGAAAATTCTTTGTGGTG
1 AATCATGAAAGAAAATTCTTTGTGGAG
*
88706355 AATCATGAAAG-AAATAT-TTTGTGGCG
1 AATCATGAAAGAAAAT-TCTTTGTGGAG
* *
88706381 AAACATGAAAAAAAAT
1 AATCATGAAAGAAAAT
88706397 CGTTGTAACG
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
26 24 0.43
27 29 0.52
28 3 0.05
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.26
Consensus pattern (27 bp):
AATCATGAAAGAAAATTCTTTGTGGAG
Found at i:88706402 original size:26 final size:26
Alignment explanation
Indices: 88706304--88706430 Score: 78
Period size: 26 Copynumber: 4.8 Consensus size: 26
88706294 TAGTGATAAT
** *
88706304 CATGAAAGAAAAGCCTTTGTGGCAAAA
1 CATGAAA-AAAAATCTTTGTGGCGAAA
* * *
88706331 TAT-AAAAGAAAATTCTTTGTGGTGAAT
1 CATGAAAA-AAAA-TCTTTGTGGCGAAA
*
88706358 CATGAAAGAAATAT-TTTGTGGCGAAA
1 CATGAAA-AAAAATCTTTGTGGCGAAA
* **
88706384 CATGAAAAAAAATCGTTGTAACGAAA
1 CATGAAAAAAAATCTTTGTGGCGAAA
* **
88706410 TATGAAAGAAAAGCCTTTGTG
1 CATGAAA-AAAAATCTTTGTG
88706431 ATGAATTATG
Statistics
Matches: 75, Mismatches: 19, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
25 6 0.08
26 38 0.51
27 24 0.32
28 6 0.08
29 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.26
Consensus pattern (26 bp):
CATGAAAAAAAATCTTTGTGGCGAAA
Found at i:88706429 original size:27 final size:27
Alignment explanation
Indices: 88706399--88706456 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
88706389 AAAAAAATCG
88706399 TTGTAACGAAATATGAAAGAAAAGCCT
1 TTGTAACGAAATATGAAAGAAAAGCCT
* * * * * *
88706426 TTGTGATGAATTATGAAGGGATAGCCT
1 TTGTAACGAAATATGAAAGAAAAGCCT
88706453 TTGT
1 TTGT
88706457 GGCAAACCCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.31
Consensus pattern (27 bp):
TTGTAACGAAATATGAAAGAAAAGCCT
Found at i:88706429 original size:53 final size:54
Alignment explanation
Indices: 88706301--88706430 Score: 135
Period size: 53 Copynumber: 2.4 Consensus size: 54
88706291 TTATAGTGAT
* * ***
88706301 AATCATGAAAGAAAAGCCTTTGTGGCAAAATATAAAAGAAAATTCTTTGTGGTG
1 AATCATGAAAGAAAAGCCTTTGTGGCAAAACATAAAAGAAAATTCGTTGTAACG
* *
88706355 AATCATGAAAGAAATA--TTTTGTGGCGAAACATGAAAA-AAAA-TCGTTGTAACG
1 AATCATGAAAGAAA-AGCCTTTGTGGCAAAACAT-AAAAGAAAATTCGTTGTAACG
88706407 AAAT-ATGAAAGAAAAGCCTTTGTG
1 -AATCATGAAAGAAAAGCCTTTGTG
88706431 ATGAATTATG
Statistics
Matches: 63, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
51 1 0.02
52 17 0.27
53 26 0.41
54 18 0.29
55 1 0.02
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.26
Consensus pattern (54 bp):
AATCATGAAAGAAAAGCCTTTGTGGCAAAACATAAAAGAAAATTCGTTGTAACG
Found at i:88706475 original size:27 final size:27
Alignment explanation
Indices: 88706445--88706502 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
88706435 ATTATGAAGG
88706445 GATAGCCTTTGTGGCAAACCCTACAAT
1 GATAGCCTTTGTGGCAAACCCTACAAT
* *
88706472 GATAGCTTTTGTGGCAAATCCTACAAT
1 GATAGCCTTTGTGGCAAACCCTACAAT
88706499 GATA
1 GATA
88706503 ACTTTTATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (27 bp):
GATAGCCTTTGTGGCAAACCCTACAAT
Found at i:88706507 original size:27 final size:27
Alignment explanation
Indices: 88706452--88706508 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
88706442 AGGGATAGCC
*
88706452 TTTGTGGCAAACCCTACAATGATAGCT
1 TTTGTGGCAAACCCTACAATGATAACT
*
88706479 TTTGTGGCAAATCCTACAATGATAACT
1 TTTGTGGCAAACCCTACAATGATAACT
88706506 TTT
1 TTT
88706509 ATGGTGATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (27 bp):
TTTGTGGCAAACCCTACAATGATAACT
Found at i:88709903 original size:101 final size:100
Alignment explanation
Indices: 88709771--88710007 Score: 312
Period size: 101 Copynumber: 2.4 Consensus size: 100
88709761 TAAGACAGTT
* * * *
88709771 TTAGGTCACGTGTGTAGTACCAAGTGCAGGCTACTACGTGCTACAGATTGTTAGGTCGCATGTGT
1 TTAGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGCTACAGATGGTTAGGTCACATGTGT
* *
88709836 AGTACTAAGTGCAGGCTACTATGCGTACCCGATAG
66 AGTACTAAGTGCAGGCTACTACGCGTACCAGATAG
* * * * * *
88709871 CTTCGATCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTTTCCGATGGTTAGGTCACGTGTG
1 -TTAGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGCTACAGATGGTTAGGTCACATGTG
* *
88709936 TAGTACTAAGTGCAGGCTACTACGTGTACCAGATTG
65 TAGTACTAAGTGCAGGCTACTACGCGTACCAGATAG
* * *
88709972 TTAGGTCACATGTGTAGTACTAAGTGTAGGCTACTA
1 TTAGATCACGTGTGTAGTACTAAGTGCAGGCTACTA
88710008 TGCGTACCAG
Statistics
Matches: 118, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
100 32 0.27
101 86 0.73
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (100 bp):
TTAGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGCTACAGATGGTTAGGTCACATGTGT
AGTACTAAGTGCAGGCTACTACGCGTACCAGATAG
Found at i:88710005 original size:151 final size:153
Alignment explanation
Indices: 88709729--88710025 Score: 456
Period size: 151 Copynumber: 2.0 Consensus size: 153
88709719 TGAGAACACA
* * *
88709729 TGTGTAGTACTATGTGCAAGCTACTTTGTGTTTAAGACAGTTTTAGGTCACGTGTGTAGTACCAA
1 TGTGTAGTACTAAGTGCAAGCTACTATGTGTTTAAGACAGTGTTAGGTCACGTGTGTAGTACCAA
*
88709794 GTGCAGGCTACTACGTGCTACAGATTGTTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATG
66 GTGCAGGCTACTACGTGCTACAGATTGTTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTATG
* *
88709859 CGTACCCGATAGCTTCGATCACG
131 CGTACCAGAGAGCTTCGATCACG
* ** * *
88709882 TGTGTAGTACTAAGTGCAGGCTACTATGTGTTTCCGA-TG-GTTAGGTCACGTGTGTAGTACTAA
1 TGTGTAGTACTAAGTGCAAGCTACTATGTGTTTAAGACAGTGTTAGGTCACGTGTGTAGTACCAA
*
88709945 GTGCAGGCTACTACGTG-TACCAGATTGTTAGGTCACATGTGTAGTACTAAGTGTAGGCTACTAT
66 GTGCAGGCTACTACGTGCTA-CAGATTGTTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTAT
88710009 GCGTACCAGAGAGCTTC
130 GCGTACCAGAGAGCTTC
88710026 AGTTACAAGG
Statistics
Matches: 131, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
150 2 0.02
151 96 0.73
152 1 0.01
153 32 0.24
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (153 bp):
TGTGTAGTACTAAGTGCAAGCTACTATGTGTTTAAGACAGTGTTAGGTCACGTGTGTAGTACCAA
GTGCAGGCTACTACGTGCTACAGATTGTTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTATG
CGTACCAGAGAGCTTCGATCACG
Found at i:88710015 original size:50 final size:50
Alignment explanation
Indices: 88709771--88710018 Score: 313
Period size: 50 Copynumber: 4.9 Consensus size: 50
88709761 TAAGACAGTT
*
88709771 TTAGGTCACGTGTGTAGTACCAAGTGCAGGCTACTACGTGC-TA-CAGATTG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTA--TGCGTACCAGATTG
* * * *
88709821 TTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATTG
* * * * *
88709871 CTTCGATCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTTTCC-GATGG
1 -TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCG-TACCAGATTG
* *
88709922 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATTG
* *
88709972 TTAGGTCACATGTGTAGTACTAAGTGTAGGCTACTATGCGTACCAGA
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
88710019 GAGCTTCAGT
Statistics
Matches: 172, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
48 3 0.02
49 5 0.03
50 122 0.71
51 39 0.23
52 3 0.02
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (50 bp):
TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATTG
Found at i:88713177 original size:45 final size:47
Alignment explanation
Indices: 88713108--88713196 Score: 121
Period size: 45 Copynumber: 1.9 Consensus size: 47
88713098 TCAAAATATA
*
88713108 TTTTACATCGATTTTTTAATGACATTATAGGTATGTCAT-ATCTCAT
1 TTTTACATCAATTTTTTAATGACATTATAGGTATGTCATGATCTCAT
* *
88713154 TTTTACAT-AATTTTTT-ATGGACATTATGGGTGTGTCATGATCT
1 TTTTACATCAATTTTTTAAT-GACATTATAGGTATGTCATGATCT
88713197 TTTTATATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 2 0.05
45 24 0.63
46 12 0.32
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (47 bp):
TTTTACATCAATTTTTTAATGACATTATAGGTATGTCATGATCTCAT
Found at i:88717308 original size:19 final size:17
Alignment explanation
Indices: 88717284--88717341 Score: 52
Period size: 19 Copynumber: 3.4 Consensus size: 17
88717274 TCCAAAATCA
88717284 AAATTTAAGCAAAAACATT
1 AAATTTAA-CAAAAA-ATT
88717303 AAATTT---AAAAAA-T
1 AAATTTAACAAAAAATT
88717316 AAATTTAAACAAAAATATT
1 AAATTT-AACAAAAA-ATT
88717335 AAATTTA
1 AAATTTA
88717342 TTTAAAACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
13 7 0.21
14 1 0.03
15 5 0.15
17 5 0.15
18 2 0.06
19 13 0.39
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (17 bp):
AAATTTAACAAAAAATT
Found at i:88750911 original size:22 final size:23
Alignment explanation
Indices: 88750885--88750934 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
88750875 AGGTGATTTG
* * *
88750885 TGAAT-GTGAAATTGGTATGTTT
1 TGAATAGTAAAATTGGGATGTTA
88750907 TGAATAGGTAAAATTGGGATGTTA
1 TGAATA-GTAAAATTGGGATGTTA
88750931 TGAA
1 TGAA
88750935 CATTATAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 5 0.22
24 18 0.78
ACGTcount: A:0.34, C:0.00, G:0.28, T:0.38
Consensus pattern (23 bp):
TGAATAGTAAAATTGGGATGTTA
Found at i:88751270 original size:12 final size:12
Alignment explanation
Indices: 88751253--88751278 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
88751243 GTTTTGGCAT
88751253 GGCCTAGCACAC
1 GGCCTAGCACAC
88751265 GGCCTAGCACAC
1 GGCCTAGCACAC
88751277 GG
1 GG
88751279 GCATGTGAGG
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:0.23, C:0.38, G:0.31, T:0.08
Consensus pattern (12 bp):
GGCCTAGCACAC
Found at i:88752511 original size:20 final size:19
Alignment explanation
Indices: 88752481--88752521 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
88752471 AAAGTAGTGG
88752481 AAATTTATTTTCTTAGAAT
1 AAATTTATTTTCTTAGAAT
* *
88752500 AAATTCTATTTTTTTGGAAT
1 AAATT-TATTTTCTTAGAAT
88752520 AA
1 AA
88752522 TAATTTCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (19 bp):
AAATTTATTTTCTTAGAAT
Found at i:88753565 original size:24 final size:24
Alignment explanation
Indices: 88753538--88753602 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
88753528 CAGTCACAGT
*
88753538 ATTGCACAGAAGTGCCACATTTT-G
1 ATTGCACAGAAGTGCCAC-TTTTCA
*
88753562 ATTGCACTGAAGTGCCACTTTTCA
1 ATTGCACAGAAGTGCCACTTTTCA
* *
88753586 AGTGCACCGAAGTGCCA
1 ATTGCACAGAAGTGCCA
88753603 TATTCATTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 4 0.11
24 32 0.89
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.26
Consensus pattern (24 bp):
ATTGCACAGAAGTGCCACTTTTCA
Found at i:88754165 original size:5 final size:5
Alignment explanation
Indices: 88754155--88754186 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
88754145 CTAGATAAAC
88754155 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA AT
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA AT
88754187 ATCTGATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTAA
Found at i:88760024 original size:19 final size:19
Alignment explanation
Indices: 88759988--88760026 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
88759978 TAGTCATCAT
* *
88759988 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
88760007 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
88760026 A
1 A
88760027 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:88760537 original size:28 final size:28
Alignment explanation
Indices: 88760497--88760578 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
88760487 GTCACCAGAT
* * *
88760497 ACAGATATTTTGTGGCAGTGCTACCAAA
1 ACAGATAATTTGTGGCAGGGCCACCAAA
* *
88760525 ACAGATAATTTGTGGCAGGGCCGCCAGA
1 ACAGATAATTTGTGGCAGGGCCACCAAA
**
88760553 ACAGATAATTTGTGGCATAGCCACCA
1 ACAGATAATTTGTGGCAGGGCCACCA
88760579 GGACGCTTCC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (28 bp):
ACAGATAATTTGTGGCAGGGCCACCAAA
Found at i:88765002 original size:40 final size:40
Alignment explanation
Indices: 88764951--88765155 Score: 270
Period size: 40 Copynumber: 5.1 Consensus size: 40
88764941 AGATGATAAT
*
88764951 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATA
* *
88764990 TTCCGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATA
*
88765031 TCCGAGCTAAGTCCCGAAGGCATTTGTG-TGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGTTACTATA
* * **
88765071 TCCGGGCTAAGTCCCGAAGACATTTGTGCGAACTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATA
* * **
88765111 TCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGGCTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATA
88765151 TCCGG
1 TCCGG
88765156 TTAAAGCCCG
Statistics
Matches: 145, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
40 144 0.99
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATA
Found at i:88774019 original size:19 final size:19
Alignment explanation
Indices: 88773983--88774021 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
88773973 TTTTCATCAT
* *
88773983 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
88774002 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
88774021 A
1 A
88774022 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:88774531 original size:28 final size:28
Alignment explanation
Indices: 88774482--88774572 Score: 103
Period size: 28 Copynumber: 3.2 Consensus size: 28
88774472 GTGACAGAGT
*
88774482 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCAGTGC
* * *
88774511 CACCAGAGCAGATAATTTGTGCCAGGGC
1 CACCAGAACAGATAATTTGTGGCAGTGC
* *
88774539 CACCAGAATAGATAACTTGTGGCA-TAGC
1 CACCAGAACAGATAATTTGTGGCAGT-GC
88774567 CACCAG
1 CACCAG
88774573 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
28 45 0.87
29 7 0.13
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCAGTGC
Found at i:88774725 original size:28 final size:28
Alignment explanation
Indices: 88774678--88774742 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
88774668 AAATTAACCC
*
88774678 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
*
88774706 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
88774734 TAGGGGTAT
1 TAGGGGTAT
88774743 TCTAGTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCATACA
Found at i:88777966 original size:33 final size:33
Alignment explanation
Indices: 88777919--88778001 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
88777909 CATGGTAGTG
* ** *
88777919 TTTATATGTAAGACCATATTTGGGCTATGGCA-T
1 TTTA-ATGAAAGACCATAACTGGGCTATGGCACC
*
88777952 TTTAATGAAAAGACCATAACTGGGTTATGGCACC
1 TTTAATG-AAAGACCATAACTGGGCTATGGCACC
*
88777986 TTTAATGTAAGACCAT
1 TTTAATGAAAGACCAT
88778002 GGTTGGACCA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
32 3 0.07
33 32 0.76
34 7 0.17
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (33 bp):
TTTAATGAAAGACCATAACTGGGCTATGGCACC
Found at i:88778068 original size:98 final size:99
Alignment explanation
Indices: 88777892--88778101 Score: 271
Period size: 98 Copynumber: 2.1 Consensus size: 99
88777882 AATTGAAAGA
* ** * ** *
88777892 TAAGACTATGGTTGGACCATGGTAGTGTTTATATGTAAGACCATATTTGGGCTATGGCATTTTAA
1 TAAGACCATGGTTGGACCATGACAGTATTTATATGT-A-ACCATAGCTGGGCTATGGCATTCTAA
* *
88777957 TGAAAAGACCATAACTGGGTTATGGCACCT-TTAATG
64 TGAAAAGACCATAACTGGGTTATGACA-CTATAAATG
*
88777993 TAAGACCATGGTTGGACCATGACAGTATTTATATGT-ACCATAGCTGGGCTATGGCATTCTGATG
1 TAAGACCATGGTTGGACCATGACAGTATTTATATGTAACCATAGCTGGGCTATGGCATTCTAATG
* *
88778057 ATAAGACCATAATTGGGTTATGACACTATAAATG
66 AAAAGACCATAACTGGGTTATGACACTATAAATG
88778091 TAAGACCATGG
1 TAAGACCATGG
88778102 CAAGGCCATG
Statistics
Matches: 96, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
97 2 0.02
98 62 0.65
101 32 0.33
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.31
Consensus pattern (99 bp):
TAAGACCATGGTTGGACCATGACAGTATTTATATGTAACCATAGCTGGGCTATGGCATTCTAATG
AAAAGACCATAACTGGGTTATGACACTATAAATG
Found at i:88778399 original size:16 final size:17
Alignment explanation
Indices: 88778380--88778412 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
88778370 ATGATAATAC
*
88778380 ATGAAAT-ATTGATATA
1 ATGAAATGAGTGATATA
88778396 ATGAAATGAGTGATATA
1 ATGAAATGAGTGATATA
88778413 TGTTTATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.33
Consensus pattern (17 bp):
ATGAAATGAGTGATATA
Found at i:88781000 original size:43 final size:43
Alignment explanation
Indices: 88780895--88781058 Score: 224
Period size: 43 Copynumber: 3.8 Consensus size: 43
88780885 ATCAAATATA
* * * **
88780895 GATGCCATTGTCCCAGACAGGGTCTTACACGAAATCAT-A-TAC
1 GATGCCAATGTCCCAGACATGGTCTTACACGTAATC-TCAGTTT
* *
88780937 GATGCCAATGTCCCATACATGGTCTTACATGTAATCTCAGTTT
1 GATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCAGTTT
*
88780980 GATGCCAATGTCCAAGACATGGTCTTACACGTAATCTCAGTTT
1 GATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCAGTTT
*
88781023 GATGCCAATGTCCCAGACATGGTCTTACACGAAATC
1 GATGCCAATGTCCCAGACATGGTCTTACACGTAATC
88781059 AAATCTCGGA
Statistics
Matches: 108, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
41 1 0.01
42 32 0.30
43 75 0.69
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (43 bp):
GATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCAGTTT
Found at i:88781051 original size:86 final size:85
Alignment explanation
Indices: 88780895--88781051 Score: 226
Period size: 85 Copynumber: 1.8 Consensus size: 85
88780885 ATCAAATATA
* * *
88780895 GATGCCATTGTCCCAGACAGGGTCTTACACGAAATCATATACGATGCCAATGTCCCATACATGGT
1 GATGCCAATGTCCAAGACAGGGTCTTACACGAAATCATATACGATGCCAATGTCCCAGACATGGT
88780960 CTTACATGTAATCTCAGTTT
66 CTTACATGTAATCTCAGTTT
* * **
88780980 GATGCCAATGTCCAAGACATGGTCTTACACGTAATC-TCAGTTTGATGCCAATGTCCCAGACATG
1 GATGCCAATGTCCAAGACAGGGTCTTACACGAAATCAT-A-TACGATGCCAATGTCCCAGACATG
88781044 GTCTTACA
64 GTCTTACA
88781052 CGAAATCAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
84 1 0.02
85 33 0.52
86 29 0.46
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (85 bp):
GATGCCAATGTCCAAGACAGGGTCTTACACGAAATCATATACGATGCCAATGTCCCAGACATGGT
CTTACATGTAATCTCAGTTT
Found at i:88787096 original size:16 final size:17
Alignment explanation
Indices: 88787077--88787114 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
88787067 GAATTTGACA
*
88787077 TTTGGCAAACTCT-AGG
1 TTTGGCAAACCCTAAGG
88787093 TTTGGCAAACCCTAAGG
1 TTTGGCAAACCCTAAGG
88787110 TTTGG
1 TTTGG
88787115 TGGGCTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (17 bp):
TTTGGCAAACCCTAAGG
Found at i:88787444 original size:29 final size:29
Alignment explanation
Indices: 88787402--88787465 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
88787392 CATGTTTGTA
88787402 CATTTTGTTTATGTTTCTTTTTTTCCTTT
1 CATTTTGTTTATGTTTCTTTTTTTCCTTT
88787431 CATTTTGTTTATGTTTCTTTTTTTCCTTT
1 CATTTTGTTTATGTTTCTTTTTTTCCTTT
88787460 CATTTT
1 CATTTT
88787466 CACTGAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.08, C:0.14, G:0.06, T:0.72
Consensus pattern (29 bp):
CATTTTGTTTATGTTTCTTTTTTTCCTTT
Found at i:88791462 original size:44 final size:42
Alignment explanation
Indices: 88791325--88791475 Score: 137
Period size: 43 Copynumber: 3.5 Consensus size: 42
88791315 AATGTGAACA
* * * *
88791325 TCCCAGACGTGGTCTTGCATGTAATCAAATATCAATGCC-ACTG
1 TCCCAGACGTGGTCTTACACGAAATCAAGTA-CAATGCCAAC-G
* *
88791368 TTCCAGATAG-GGTCTTACACGAAATCAAGTACAATGCCAACG
1 TCCCAGA-CGTGGTCTTACACGAAATCAAGTACAATGCCAACG
* *
88791410 TCCCAGACGTGGTCTTACACGTAAATCATAAGT-CGATGCCAACT
1 TCCCAGACGTGGTCTTACACG-AAATC--AAGTACAATGCCAACG
* *
88791454 TCCTAGACGTGGCCTTACACGA
1 TCCCAGACGTGGTCTTACACGA
88791476 TAACACATAT
Statistics
Matches: 90, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
41 1 0.01
42 25 0.28
43 31 0.34
44 29 0.32
45 4 0.04
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (42 bp):
TCCCAGACGTGGTCTTACACGAAATCAAGTACAATGCCAACG
Found at i:88800677 original size:46 final size:45
Alignment explanation
Indices: 88800627--88800801 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 45
88800617 TGGTTGAGCA
88800627 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
88800673 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
88800720 TCC-AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
88800765 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
88800802 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 16
0.80 0.09 0.12
Matches are distributed among these distances:
42 1 0.01
43 3 0.03
44 1 0.01
45 6 0.06
46 86 0.79
47 7 0.06
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:88800790 original size:92 final size:93
Alignment explanation
Indices: 88800624--88800793 Score: 297
Period size: 92 Copynumber: 1.8 Consensus size: 93
88800614 GGATGGTTGA
* *
88800624 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
88800689 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
88800717 GCATCC-AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
88800781 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
88800794 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 67 0.92
93 6 0.08
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:88804798 original size:43 final size:42
Alignment explanation
Indices: 88804673--88804799 Score: 116
Period size: 43 Copynumber: 3.0 Consensus size: 42
88804663 TGAAAAGCTT
* * *
88804673 GTACAATGCCAAC-ACTCCAGACGTGGTCTTACATGAAATCAA
1 GTACAATGCCAACGTC-CCAGACATGGTCTTACAAGAAATCAA
* * * *
88804715 ATATCGATGCC-ACTGTCTCAGACAGGGTCTTACACA-AAATCAA
1 GTA-CAATGCCAAC-GTCCCAGACATGGTCTTACA-AGAAATCAA
*
88804758 GTACAATGCCAACGTCCCAGACATGGTCTTATAAGTAAATCA
1 GTACAATGCCAACGTCCCAGACATGGTCTTACAAG-AAATCA
88804800 TAAGTCGGTA
Statistics
Matches: 66, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
41 1 0.02
42 27 0.41
43 37 0.56
44 1 0.02
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (42 bp):
GTACAATGCCAACGTCCCAGACATGGTCTTACAAGAAATCAA
Found at i:88806916 original size:21 final size:21
Alignment explanation
Indices: 88806891--88806932 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
88806881 AAAAAGAGAA
88806891 TAATTAGCCAAAATTGCAATT
1 TAATTAGCCAAAATTGCAATT
* *
88806912 TAATTAGCCGAAATTGTAATT
1 TAATTAGCCAAAATTGCAATT
88806933 GAGGTAAGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (21 bp):
TAATTAGCCAAAATTGCAATT
Found at i:88807379 original size:46 final size:44
Alignment explanation
Indices: 88807304--88807432 Score: 143
Period size: 46 Copynumber: 2.8 Consensus size: 44
88807294 AGGTTATTTG
* * **
88807304 TGTGCCAATGTAAGACATGTCTGGGACATGCATTGGCCT-CGAGA
1 TGTGCCAGTGTAAAACATGTCTGGGACATGCATCAG-CTACGAGA
*
88807348 TGTAAGCCAGTGTAAAACATGTCTAGGACATGCATCAGCTACGAGA
1 TGT--GCCAGTGTAAAACATGTCTGGGACATGCATCAGCTACGAGA
* *
88807394 TGTGTCAGTGTAAGACCATGTCTGGGACATGGCATCAGC
1 TGTGCCAGTGTAA-AACATGTCTGGGACAT-GCATCAGC
88807433 ATGGATATAT
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
44 12 0.17
45 16 0.22
46 44 0.61
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (44 bp):
TGTGCCAGTGTAAAACATGTCTGGGACATGCATCAGCTACGAGA
Found at i:88807521 original size:49 final size:50
Alignment explanation
Indices: 88807397--88807580 Score: 144
Period size: 50 Copynumber: 3.8 Consensus size: 50
88807387 TACGAGATGT
*
88807397 GTCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATGGATATATGAGA
1 GTCAGTGTAAGACCATGTCTGGGACATAGCATCAGCATGGATATATGAGA
* * * * * * * * *
88807447 G-CTAGTGCAATACCATGTCCGGGACATAGCGTCGGCCTTGAT-TTTGATA
1 GTC-AGTGTAAGACCATGTCTGGGACATAGCATCAGCATGGATATATGAGA
* * * * **
88807496 GTCAGTGTAAGACCATGTCTAGGACATGGCATC-GAATTGATGGAT--GA
1 GTCAGTGTAAGACCATGTCTGGGACATAGCATCAGCATGGATATATGAGA
* * * *
88807543 GCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCAT
1 GTCAGTGTAAGACCATGTCTGGGACATAGCATCAGCAT
88807581 TATACCCTAT
Statistics
Matches: 105, Mismatches: 25, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
47 31 0.30
48 9 0.09
49 32 0.30
50 33 0.31
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (50 bp):
GTCAGTGTAAGACCATGTCTGGGACATAGCATCAGCATGGATATATGAGA
Found at i:88810923 original size:7 final size:7
Alignment explanation
Indices: 88810911--88810935 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
88810901 GATAAAAAAA
88810911 ATCAAAT
1 ATCAAAT
88810918 ATCAAAT
1 ATCAAAT
88810925 ATCAAAT
1 ATCAAAT
88810932 ATCA
1 ATCA
88810936 TCTCAATTTA
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:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
ATCAAAT
Found at i:88817585 original size:21 final size:21
Alignment explanation
Indices: 88817536--88817585 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
88817526 AAATTTTTCT
*
88817536 AAGTTTTCCCAAAACTTTCCA
1 AAGTTTTTCCAAAACTTTCCA
88817557 AAGTTTTTCCAAAACTTTCCA
1 AAGTTTTTCCAAAACTTTCCA
88817578 AAGTTTTT
1 AAGTTTTT
88817586 GGTTTAGTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (21 bp):
AAGTTTTTCCAAAACTTTCCA
Found at i:88819225 original size:18 final size:17
Alignment explanation
Indices: 88819182--88819226 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
88819172 AATGTTTTTC
88819182 TATAAAAACAAAGGTTT
1 TATAAAAACAAAGGTTT
*
88819199 TATACAAACAAAGGTTTT
1 TATAAAAACAAAGG-TTT
*
88819217 TCTAAAAACA
1 TATAAAAACA
88819227 CGACTGTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (17 bp):
TATAAAAACAAAGGTTT
Found at i:88824807 original size:19 final size:19
Alignment explanation
Indices: 88824767--88824808 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
88824757 TTATTCTCTT
*
88824767 TCTTTTTTTGAATTTTTGC
1 TCTTTTTTTGAAGTTTTGC
*
88824786 TCTTTATTTTGACGTTTT-C
1 TCTTT-TTTTGAAGTTTTGC
88824805 TCTT
1 TCTT
88824809 CCTCTCCCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.10, C:0.14, G:0.10, T:0.67
Consensus pattern (19 bp):
TCTTTTTTTGAAGTTTTGC
Found at i:88826389 original size:18 final size:18
Alignment explanation
Indices: 88826348--88826390 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
88826338 TGTTTTTCTT
*
88826348 TAAAAACAACGGTTTTAC
1 TAAAAACAAAGGTTTTAC
* *
88826366 T-CAAACAAAGGTTTTTC
1 TAAAAACAAAGGTTTTAC
88826383 TAAAAACA
1 TAAAAACA
88826391 CAACTGTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (18 bp):
TAAAAACAAAGGTTTTAC
Found at i:88826551 original size:16 final size:16
Alignment explanation
Indices: 88826521--88826550 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
88826511 TGATTAGACG
88826521 AGAAAACTCCATTTTC
1 AGAAAACTCCATTTTC
88826537 AGAAAACT-CATTTT
1 AGAAAACTCCATTTT
88826551 TTGTGACATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (16 bp):
AGAAAACTCCATTTTC
Found at i:88832371 original size:33 final size:35
Alignment explanation
Indices: 88832276--88832372 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
88832266 TTAATATTTT
*
88832276 AATATATGAAATATAAATTTTAAATATTT--TTAAGC
1 AATATAT-AAAT-TATATTTTAAATATTTAATTAAGC
* *
88832311 AATAAATATTAATTAT-TTATAAA-ATTTAATT-AG-
1 AAT--ATATAAATTATATTTTAAATATTTAATTAAGC
88832344 AATATATAAATTATATTTTAAATATTTAA
1 AATATATAAATTATATTTTAAATATTTAA
88832373 ATATAACCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 10 0.20
32 6 0.12
33 13 0.25
34 8 0.16
35 7 0.14
36 3 0.06
37 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (35 bp):
AATATATAAATTATATTTTAAATATTTAATTAAGC
Found at i:88832786 original size:14 final size:13
Alignment explanation
Indices: 88832767--88832804 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
88832757 ATTTAATGTT
88832767 TAATTATATTAGGA
1 TAATTAT-TTAGGA
*
88832781 TAATTATTAAGGA
1 TAATTATTTAGGA
88832794 TAATTATTTAG
1 TAATTATTTAG
88832805 ATTTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (13 bp):
TAATTATTTAGGA
Found at i:88832833 original size:10 final size:10
Alignment explanation
Indices: 88832818--88832869 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
88832808 TAAATTTAGG
88832818 ATTTATTTTT
1 ATTTATTTTT
*
88832828 ATTTATCTTT
1 ATTTATTTTT
* *
88832838 AATTATCTTT
1 ATTTATTTTT
*
88832848 ATTTATTTGT
1 ATTTATTTTT
88832858 ATTTATCTTTT
1 ATTTAT-TTTT
88832869 A
1 A
88832870 GAATTTAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
10 31 0.89
11 4 0.11
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.69
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:88838455 original size:16 final size:16
Alignment explanation
Indices: 88838424--88838483 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
88838414 GCAACCTAAT
* *
88838424 TTTTTATTTCTCTTTA
1 TTTTTATTTTTATTTA
88838440 TTTTTATTTTTATTTA
1 TTTTTATTTTTATTTA
*
88838456 TTATTT-TATTTTAATTA
1 TT-TTTAT-TTTTATTTA
88838473 TTTATTATTTT
1 TTT-TTATTTT
88838484 ATCTTAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 18 0.49
17 18 0.49
18 1 0.03
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTATTTTTATTTA
Found at i:88838462 original size:18 final size:19
Alignment explanation
Indices: 88838441--88838512 Score: 67
Period size: 21 Copynumber: 3.6 Consensus size: 19
88838431 TTCTCTTTAT
88838441 TTTTATTT-TTATTTATTA
1 TTTTATTTATTATTTATTA
88838459 TTTTATTTTAATTATTTATTA
1 TTTTA-TTT-ATTATTTATTA
88838480 TTTTATCTTAATTATGTTACTTA
1 TTTTAT-TT-ATTAT-TTA-TTA
*
88838503 -ATTATTTATT
1 TTTTATTTATT
88838513 TTATTTTGGT
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
18 5 0.11
19 3 0.06
20 4 0.09
21 25 0.53
22 7 0.15
23 3 0.06
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.69
Consensus pattern (19 bp):
TTTTATTTATTATTTATTA
Found at i:88838474 original size:14 final size:12
Alignment explanation
Indices: 88838436--88838513 Score: 58
Period size: 12 Copynumber: 6.6 Consensus size: 12
88838426 TTTATTTCTC
88838436 TTTATTT-TTATT
1 TTTATTTATTA-T
88838448 TTTATTTATTAT
1 TTTATTTATTAT
88838460 TTTA-TT-TTA-
1 TTTATTTATTAT
*
88838469 ATTATTTATTAT
1 TTTATTTATTAT
88838481 TTTATCTTAATTAT
1 TTTAT-TT-ATTAT
* *
88838495 GTTACTTAATTA-
1 TTTA-TTTATTAT
88838507 TTTATTT
1 TTTATTT
88838514 TATTTTGGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
9 3 0.06
10 5 0.09
11 7 0.13
12 19 0.36
13 9 0.17
14 9 0.17
15 1 0.02
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.71
Consensus pattern (12 bp):
TTTATTTATTAT
Found at i:88838475 original size:21 final size:21
Alignment explanation
Indices: 88838449--88838494 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
88838439 ATTTTTATTT
*
88838449 TTATTTATTATTTTATTTTAA
1 TTATTTATTATTTTATCTTAA
88838470 TTATTTATTATTTTATCTTAA
1 TTATTTATTATTTTATCTTAA
88838491 TTAT
1 TTAT
88838495 GTTACTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (21 bp):
TTATTTATTATTTTATCTTAA
Found at i:88838481 original size:34 final size:34
Alignment explanation
Indices: 88838437--88838512 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
88838427 TTATTTCTCT
* *
88838437 TTATTT-TTATTTTTAT-TT-ATTATTTTATTTTAA
1 TTATTTATTA-TTTTATCTTAATTATGTTA-CTTAA
88838470 TTATTTATTATTTTATCTTAATTATGTTACTTAA
1 TTATTTATTATTTTATCTTAATTATGTTACTTAA
88838504 TTATTTATT
1 TTATTTATT
88838513 TTATTTTGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
33 12 0.32
34 18 0.47
35 8 0.21
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.70
Consensus pattern (34 bp):
TTATTTATTATTTTATCTTAATTATGTTACTTAA
Found at i:88841994 original size:14 final size:13
Alignment explanation
Indices: 88841975--88842012 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
88841965 ATTTAATGTT
88841975 TAATTATATTAGGA
1 TAATTAT-TTAGGA
*
88841989 TAATTATTAAGGA
1 TAATTATTTAGGA
88842002 TAATTATTTAG
1 TAATTATTTAG
88842013 ATTTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (13 bp):
TAATTATTTAGGA
Found at i:88844345 original size:23 final size:24
Alignment explanation
Indices: 88844319--88844365 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
88844309 ATTTAAAAAA
*
88844319 TTTAAAAAAATTA-TAAAATTATT
1 TTTAAAAAAAGTATTAAAATTATT
*
88844342 TTTAAAAGAAGTATTAAAATTATT
1 TTTAAAAAAAGTATTAAAATTATT
88844366 GAAAAAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
TTTAAAAAAAGTATTAAAATTATT
Found at i:88852610 original size:21 final size:22
Alignment explanation
Indices: 88852584--88852630 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
88852574 TTTTGCATTC
*
88852584 TTTTTCTCAT-TATTCTTTTCT
1 TTTTTCACATCTATTCTTTTCT
88852605 TTTTTCACATCTATTCTTTTCT
1 TTTTTCACATCTATTCTTTTCT
88852627 TTTT
1 TTTT
88852631 CTCTTAATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTTCACATCTATTCTTTTCT
Found at i:88852631 original size:21 final size:20
Alignment explanation
Indices: 88852581--88852631 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
88852571 TATTTTTGCA
*
88852581 TTCTTTTTCTCATTATTCTT
1 TTCTTTTTCACATTATTCTT
88852601 TTCTTTTTTCACATCTATTCTT
1 TTC-TTTTTCACAT-TATTCTT
88852623 TTCTTTTTC
1 TTCTTTTTC
88852632 TCTTAATTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 3 0.11
21 15 0.54
22 10 0.36
ACGTcount: A:0.10, C:0.22, G:0.00, T:0.69
Consensus pattern (20 bp):
TTCTTTTTCACATTATTCTT
Found at i:88854798 original size:12 final size:12
Alignment explanation
Indices: 88854776--88854800 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
88854766 AAATATAAAT
88854776 ATTCATATAATC
1 ATTCATATAATC
88854788 ATTCATATAATC
1 ATTCATATAATC
88854800 A
1 A
88854801 CAATTTTAAT
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:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTCATATAATC
Found at i:88867359 original size:21 final size:19
Alignment explanation
Indices: 88867330--88867368 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
88867320 ACAAAACATA
88867330 CCATAACAAACCATTACCAAG
1 CCATAACAAA-C-TTACCAAG
*
88867351 CCATTACAAACTTACCAA
1 CCATAACAAACTTACCAA
88867369 AAGAACCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 1 0.06
21 9 0.53
ACGTcount: A:0.46, C:0.33, G:0.03, T:0.18
Consensus pattern (19 bp):
CCATAACAAACTTACCAAG
Found at i:88874897 original size:21 final size:19
Alignment explanation
Indices: 88874868--88874906 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
88874858 ACAAAACATA
88874868 CCATAACAAACCATTACCAAG
1 CCATAACAAA-C-TTACCAAG
*
88874889 CCATTACAAACTTACCAA
1 CCATAACAAACTTACCAA
88874907 AAGAACTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 1 0.06
21 9 0.53
ACGTcount: A:0.46, C:0.33, G:0.03, T:0.18
Consensus pattern (19 bp):
CCATAACAAACTTACCAAG
Found at i:88884177 original size:42 final size:43
Alignment explanation
Indices: 88884077--88884177 Score: 100
Period size: 43 Copynumber: 2.4 Consensus size: 43
88884067 AGTTCATACA
* * * *
88884077 ATGCCAAC-GTCCCAGACATGGTCTTTCATGTAATCAAACATCG
1 ATGCC-ACTGTCCCAGACAGGGTCTTACACGAAATCAAACATCG
* * *
88884120 ATGCCACTATCCCAGACAGGGTCTTACACGAAATCATATA-CG
1 ATGCCACTGTCCCAGACAGGGTCTTACACGAAATCAAACATCG
88884162 ATGCCGA-TGTCCCAGA
1 ATGCC-ACTGTCCCAGA
88884178 ATGTCCCAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
42 17 0.35
43 31 0.65
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.23
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACAGGGTCTTACACGAAATCAAACATCG
Found at i:88887527 original size:83 final size:83
Alignment explanation
Indices: 88887388--88887554 Score: 334
Period size: 83 Copynumber: 2.0 Consensus size: 83
88887378 ATCGAACTAA
88887388 TCCAAAACTTTTGCTTTGCCTTGATCTAGGTCCGTGCGTGGTCTATCTTGATCTAAATAGACAAT
1 TCCAAAACTTTTGCTTTGCCTTGATCTAGGTCCGTGCGTGGTCTATCTTGATCTAAATAGACAAT
88887453 TTTAATCCATTGAATACT
66 TTTAATCCATTGAATACT
88887471 TCCAAAACTTTTGCTTTGCCTTGATCTAGGTCCGTGCGTGGTCTATCTTGATCTAAATAGACAAT
1 TCCAAAACTTTTGCTTTGCCTTGATCTAGGTCCGTGCGTGGTCTATCTTGATCTAAATAGACAAT
88887536 TTTAATCCATTGAATACT
66 TTTAATCCATTGAATACT
88887554 T
1 T
88887555 ATAGTATTCA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (83 bp):
TCCAAAACTTTTGCTTTGCCTTGATCTAGGTCCGTGCGTGGTCTATCTTGATCTAAATAGACAAT
TTTAATCCATTGAATACT
Found at i:88893023 original size:55 final size:52
Alignment explanation
Indices: 88892882--88893089 Score: 190
Period size: 55 Copynumber: 3.8 Consensus size: 52
88892872 ATCCTTTTGA
* * *
88892882 AACTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATG
1 AACTTA-CAATGCCATGTCTTGACATGGTCTTACATAGTATCCTTGCCTTATG
* * *
88892935 AACTCACTAATGCCATGCCTTGGCATGGTCTTACATAAG-A-CCTTTGCCTTATAG
1 AACTTAC-AATGCCATGTCTTGACATGGTCTTACAT-AGTATCC-TTGCCTTAT-G
*
88892989 TAACTTATCAATGCCATGTCTTGACATGGTCTTACATGGTATCGC-TGCCTTA-G
1 -AACTTA-CAATGCCATGTCTTGACATGGTCTTACATAGTATC-CTTGCCTTATG
* * *
88893042 AAACCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -AA-CTTA-CAA-TGCCATGTCTTGACATGGTCTTACATAGTATCCTT
88893090 AAACCCTAAT
Statistics
Matches: 129, Mismatches: 14, Indels: 22
0.78 0.08 0.13
Matches are distributed among these distances:
52 3 0.02
53 42 0.33
54 11 0.09
55 70 0.54
56 2 0.02
57 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (52 bp):
AACTTACAATGCCATGTCTTGACATGGTCTTACATAGTATCCTTGCCTTATG
Found at i:88893026 original size:108 final size:110
Alignment explanation
Indices: 88892882--88893080 Score: 307
Period size: 108 Copynumber: 1.8 Consensus size: 110
88892872 ATCCTTTTGA
* *
88892882 AACTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATC-CTTGCCTTATG-AA-CTCACTA
1 AACTTACCAATGCCATGTCTCGACATGGTCTTACATGGTATCGC-TGCCTTA-GAAACCTCACCA
88892944 A-TGCCATGCCTTGGCATGGTCTTACATAAGACCTTTGCCTTATAGT
64 ATTGCCATGCCTTGGCATGGTCTTACATAAGACCTTTGCCTTATAGT
* * *
88892990 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGGTATCGCTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTCGACATGGTCTTACATGGTATCGCTGCCTTAGAAACCTCACCAAT
88893055 TGCCATGCCTTGGCATGGTCTTACAT
66 TGCCATGCCTTGGCATGGTCTTACAT
88893081 GGTATCCTTA
Statistics
Matches: 82, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
107 1 0.01
108 48 0.59
109 7 0.09
110 26 0.32
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTCGACATGGTCTTACATGGTATCGCTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATAAGACCTTTGCCTTATAGT
Found at i:88898507 original size:44 final size:44
Alignment explanation
Indices: 88898444--88898534 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
88898434 AACTCTATTT
* *
88898444 TTAGTTTCTCACTTAAACTCTGATTAATTTAGGTTATTTTAATA
1 TTAGTTTCTCACTTAAACTCTGATTAATGTAGGTTATGTTAATA
* *
88898488 TTAGTTTC-CTACTTAAACTCTTATTAGTGTAGGTTATGTTAATA
1 TTAGTTTCTC-ACTTAAACTCTGATTAATGTAGGTTATGTTAATA
88898532 TTA
1 TTA
88898535 TTTGACCTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 1 0.02
44 41 0.98
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (44 bp):
TTAGTTTCTCACTTAAACTCTGATTAATGTAGGTTATGTTAATA
Found at i:88898658 original size:21 final size:21
Alignment explanation
Indices: 88898634--88898687 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
88898624 TTTTAAAGAA
88898634 TTTTGTATTTATGTTTTGAGG
1 TTTTGTATTTATGTTTTGAGG
* *
88898655 TTTTTTATTTTATGTTTTGGGG
1 TTTTGTA-TTTATGTTTTGAGG
*
88898677 TTTAGT-TTTAT
1 TTTTGTATTTAT
88898688 CTCCATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 5 0.18
21 6 0.21
22 17 0.61
ACGTcount: A:0.13, C:0.00, G:0.20, T:0.67
Consensus pattern (21 bp):
TTTTGTATTTATGTTTTGAGG
Found at i:88903242 original size:3 final size:3
Alignment explanation
Indices: 88903234--88903289 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
88903224 ATGGCTTTAG
88903234 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
88903282 ATT ATT AT
1 ATT ATT AT
88903290 ATGCATAGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:88907426 original size:43 final size:44
Alignment explanation
Indices: 88907365--88907523 Score: 148
Period size: 43 Copynumber: 3.7 Consensus size: 44
88907355 CAACGCCATA
* * * *
88907365 TCCTAGATATGGTCTTACATGTTATCACATATA-GATGCCACTG
1 TCCTAAATAGGGTCTTACATGTAATCACATATACGATGCCAATG
* * *
88907408 TCCTAAATAGGGTCTTACACGAAATCATATA-ACGATGCCAATG
1 TCCTAAATAGGGTCTTACATGTAATCACATATACGATGCCAATG
* *
88907451 TCC-AGACAT-GGTTCTTACATGTAATCACA-ATACAATGCCAATG
1 TCCTA-A-ATAGGGTCTTACATGTAATCACATATACGATGCCAATG
* * * *
88907494 TCCCAGACATGGTCTTACATGTAATCACAT
1 TCCTAAATAGGGTCTTACATGTAATCACAT
88907524 CTCAGTAATC
Statistics
Matches: 93, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
42 4 0.04
43 86 0.92
44 3 0.03
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (44 bp):
TCCTAAATAGGGTCTTACATGTAATCACATATACGATGCCAATG
Found at i:88923913 original size:25 final size:25
Alignment explanation
Indices: 88923845--88923918 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 25
88923835 CTAATTTTCA
*
88923845 CAAAATTTTACTGGGGATAAAATGGT
1 CAAAATTTTACTGGGG-TAAAATAGT
* *
88923871 CACAATTTT-TTGGGGGGTAAAATAGT
1 CAAAATTTTACT--GGGGTAAAATAGT
*
88923897 CAAAATTTTACTAGGGTAAAAT
1 CAAAATTTTACTGGGGTAAAAT
88923919 TGGGATGAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
25 10 0.26
26 24 0.62
27 5 0.13
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (25 bp):
CAAAATTTTACTGGGGTAAAATAGT
Found at i:88931664 original size:365 final size:364
Alignment explanation
Indices: 88930815--88931903 Score: 2009
Period size: 365 Copynumber: 3.0 Consensus size: 364
88930805 GCTCGGATGC
* * * * *
88930815 CACATATATCACAAACCCGAACCACTCAACAAGTTCAGACTTCTTAATTCCTAGTGACATGTCAC
1 CACATATATCACGAACCCGGACCACTCAACGAGTTCGGAATTCTTAATTCCTAGTGACATGTCAC
*
88930880 TTGTATTCTAAACTATTCCTAAGGTTCAAATGGGGTTTTTCTCACATGCACATTGCACCTCTATT
66 TTGTATTCTAAACTATTCCTAAGGTTCAAATGGGGTTTTTCTCACTTGCACATTGCACCTCTATT
*
88930945 GCACTTGCTCGTGACGTAGTGGATAGCGACCATAATATAATTCATGCTTACAGTAGTACCATTAG
131 GCACTTGCTCGTGACGTAGTGGATAGCGACCATAATATCATTCATGCTTACAGTAGTACCATTAG
88931010 ACATAGCATACATAATAAGCAATAAAATAATTATCACATAATGTTAACACAACATAACATACCAC
196 ACATAGCATACATAATAAGCAATAAAATAATTATCACATAATGTTAACACAACATAACATACCAC
88931075 ATTGTCACATTATTCACACATGTACTTACCTCAGT-AAAAAATGATGGTAATCGAGCCTAATCGT
261 ATTGTCACATTATTCACACATGTACTTACCTCAGTAAAAAAATGATGGTAATCGAGCCTAATCGT
88931139 CGTATACTTTATTCTTCCCTCGATCAAGACCCGGTTATT
326 CGTATACTTTATTCTTCCCTCGATCAAGACCCGGTTATT
88931178 CACATATATCACGAACCCGGACCACTCAACGAGTTCGGAATTCTTAATTCCTAGTGACATGTCAC
1 CACATATATCACGAACCCGGACCACTCAACGAGTTCGGAATTCTTAATTCCTAGTGACATGTCAC
*
88931243 TTGTATTCTAAAATATTCCTAAGGTTCAAATGGGGTTTTTCTCACTTGCACATTGCACCTCTATT
66 TTGTATTCTAAACTATTCCTAAGGTTCAAATGGGGTTTTTCTCACTTGCACATTGCACCTCTATT
*
88931308 GCACTTGCTCGTGACGTAGTGGATAGCAACCATAATATCATTCATGCTTACAGTAGTACCATTAG
131 GCACTTGCTCGTGACGTAGTGGATAGCGACCATAATATCATTCATGCTTACAGTAGTACCATTAG
* *
88931373 ACATAACATACATAATAAGCAATAAAATAGTTATCACATAATGTTAACACAACATAACATACCAC
196 ACATAGCATACATAATAAGCAATAAAATAATTATCACATAATGTTAACACAACATAACATACCAC
88931438 ATTGTCACATTATTCACACATGTACTTACCTCAGTAAAAAAAATGATGGTAATCGAGCCTAATCG
261 ATTGTCACATTATTCACACATGTACTTACCTCAGT-AAAAAAATGATGGTAATCGAGCCTAATCG
88931503 TCGTATACTTTATTCTTCCCTCGATCAAGACCCGGTTATT
325 TCGTATACTTTATTCTTCCCTCGATCAAGACCCGGTTATT
88931543 CACATATATCACGAACCCGGACCACTCAACGAGTTCGGAATTCTTAATTCCTAGTGACATGTCAC
1 CACATATATCACGAACCCGGACCACTCAACGAGTTCGGAATTCTTAATTCCTAGTGACATGTCAC
* *
88931608 TTGTATTCTAAACTATTCCTGATGTTCAAATGGGGTTTTTCTCACTTGCACATTGCACCTCTATT
66 TTGTATTCTAAACTATTCCTAAGGTTCAAATGGGGTTTTTCTCACTTGCACATTGCACCTCTATT
*
88931673 GCATTTGCTCGTGACGTAGTGGATAGCGACCATAATATCATTCATGCTTACAGTAGTACCATTAG
131 GCACTTGCTCGTGACGTAGTGGATAGCGACCATAATATCATTCATGCTTACAGTAGTACCATTAG
*
88931738 ACATAGCATACATAATAAGCAATAAAATAATTATCACATAATGTTAACACAACCTAACATACCAC
196 ACATAGCATACATAATAAGCAATAAAATAATTATCACATAATGTTAACACAACATAACATACCAC
* *
88931803 ATTGTCACATTATTCACACATGTACTTACCTCGGTACAAAAATGATGGTAATCGAGCCTAATCGT
261 ATTGTCACATTATTCACACATGTACTTACCTCAGTAAAAAAATGATGGTAATCGAGCCTAATCGT
88931868 CGTATACTTTATTCTTCCCTCGATCAAGACCCGGTT
326 CGTATACTTTATTCTTCCCTCGATCAAGACCCGGTT
88931904 CATATTTTTC
Statistics
Matches: 703, Mismatches: 21, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
363 284 0.40
364 65 0.09
365 354 0.50
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (364 bp):
CACATATATCACGAACCCGGACCACTCAACGAGTTCGGAATTCTTAATTCCTAGTGACATGTCAC
TTGTATTCTAAACTATTCCTAAGGTTCAAATGGGGTTTTTCTCACTTGCACATTGCACCTCTATT
GCACTTGCTCGTGACGTAGTGGATAGCGACCATAATATCATTCATGCTTACAGTAGTACCATTAG
ACATAGCATACATAATAAGCAATAAAATAATTATCACATAATGTTAACACAACATAACATACCAC
ATTGTCACATTATTCACACATGTACTTACCTCAGTAAAAAAATGATGGTAATCGAGCCTAATCGT
CGTATACTTTATTCTTCCCTCGATCAAGACCCGGTTATT
Found at i:88933415 original size:49 final size:49
Alignment explanation
Indices: 88933300--88933415 Score: 124
Period size: 49 Copynumber: 2.4 Consensus size: 49
88933290 ACTCCAGCTC
** *** *
88933300 ATGGTGGTTATACATTCATGGGTTGAAGTATAAATAAGGCTCCTAATTG
1 ATGGTGGTTATACGGTCATGGGTTGAAGTATAAATAAGAAGCCTAATTA
* * * * *
88933349 ATGGTTGTTATATGGTCATGGGTTGGAGTATAAGTCAGAAGCCTAATTA
1 ATGGTGGTTATACGGTCATGGGTTGAAGTATAAATAAGAAGCCTAATTA
*
88933398 ATGGTGGTTATGCGGTCA
1 ATGGTGGTTATACGGTCA
88933416 CGAGTTCAAG
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.34
Consensus pattern (49 bp):
ATGGTGGTTATACGGTCATGGGTTGAAGTATAAATAAGAAGCCTAATTA
Found at i:88934936 original size:13 final size:13
Alignment explanation
Indices: 88934918--88934947 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
88934908 TAAATATCAC
88934918 ACAAAAAAATTTA
1 ACAAAAAAATTTA
*
88934931 ACAAAAAAATTTT
1 ACAAAAAAATTTA
88934944 ACAA
1 ACAA
88934948 TAATATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (13 bp):
ACAAAAAAATTTA
Found at i:88939608 original size:108 final size:108
Alignment explanation
Indices: 88939416--88939616 Score: 359
Period size: 108 Copynumber: 1.9 Consensus size: 108
88939406 GTTTTTTAAA
88939416 AATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCTAACAAAATTGTATTAAAATTT
1 AATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCTAACAAAATTGTATTAAAATTT
* *
88939481 TTGTTAATTACTTTGAT-AAATGTTTTGATTAGTTTAACAAAAC
66 TTGTTAATTACTCTAATAAAAT-TTTTGATTAGTTTAACAAAAC
*
88939524 AATGATATGTTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAAAATTGTATTAAAATTT
1 AATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCTAACAAAATTGTATTAAAATTT
88939589 TTGTTAATTACTCTAATAAAATTTTTGA
66 TTGTTAATTACTCTAATAAAATTTTTGA
88939617 CGTGTTTTTT
Statistics
Matches: 89, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
108 85 0.96
109 4 0.04
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (108 bp):
AATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCTAACAAAATTGTATTAAAATTT
TTGTTAATTACTCTAATAAAATTTTTGATTAGTTTAACAAAAC
Found at i:88940649 original size:38 final size:38
Alignment explanation
Indices: 88940606--88940725 Score: 104
Period size: 36 Copynumber: 3.2 Consensus size: 38
88940596 TATTAAAATA
* *
88940606 TAAAAATATTTAAAAGTTGCAAAATTATTTAAATTTTG
1 TAAAAATATTTAAAAATTGAAAAATTATTTAAATTTTG
* * **
88940644 T-AAAA-ATTTAAAAATTGTGAAAATCA-TTAAAAATT-
1 TAAAAATATTTAAAAATTG-AAAAATTATTTAAATTTTG
* * *
88940679 TAAAAATGATTTAAAATTATAAAAAAATATTTAAATTTTG
1 TAAAAAT-ATTTAAAAAT-TGAAAAATTATTTAAATTTTG
88940719 TAAAAAT
1 TAAAAAT
88940726 CATAAGAAAT
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
35 1 0.02
36 22 0.35
37 10 0.16
38 15 0.24
39 8 0.13
40 7 0.11
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (38 bp):
TAAAAATATTTAAAAATTGAAAAATTATTTAAATTTTG
Found at i:88940684 original size:18 final size:19
Alignment explanation
Indices: 88940651--88940703 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
88940641 TTGTAAAAAT
* *
88940651 TTAAAAATTGTGAAAATCA
1 TTAAAAATTATAAAAATCA
*
88940670 TTAAAAATT-TAAAAATGA
1 TTAAAAATTATAAAAATCA
*
88940688 TTTAAAATTATAAAAA
1 TTAAAAATTATAAAAA
88940704 AATATTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (19 bp):
TTAAAAATTATAAAAATCA
Found at i:88940701 original size:27 final size:26
Alignment explanation
Indices: 88940626--88940703 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 26
88940616 TAAAAGTTGC
* * *
88940626 AAAATTATTTAAATTTTGTAAAAATTT
1 AAAAATATTTAAA-ATTATAAAAATTT
* *
88940653 AAAAAT-TGTGAAAATCATTAAAAATTT
1 AAAAATAT-TTAAAATTA-TAAAAATTT
88940680 AAAAATGATTTAAAATTATAAAAA
1 AAAAAT-ATTTAAAATTATAAAAA
88940704 AATATTTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
26 2 0.05
27 30 0.75
28 7 0.17
29 1 0.03
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.37
Consensus pattern (26 bp):
AAAAATATTTAAAATTATAAAAATTT
Found at i:88940724 original size:19 final size:19
Alignment explanation
Indices: 88940606--88940725 Score: 95
Period size: 19 Copynumber: 6.4 Consensus size: 19
88940596 TATTAAAATA
*
88940606 TAAAAATATTTAAAAGTTG
1 TAAAAATATTTAAAATTTG
* * *
88940625 CAAAATTATTTAAATTTTG
1 TAAAAATATTTAAAATTTG
*
88940644 T-AAAA-ATTTAAAAATTG
1 TAAAAATATTTAAAATTTG
* *
88940661 TGAAAATCA-TTAAAAATT-
1 TAAAAAT-ATTTAAAATTTG
*
88940679 TAAAAATGATTTAAAATTATA
1 TAAAAAT-ATTTAAAATT-TG
* *
88940700 AAAAAATATTTAAATTTTG
1 TAAAAATATTTAAAATTTG
88940719 TAAAAAT
1 TAAAAAT
88940726 CATAAGAAAT
Statistics
Matches: 80, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
17 11 0.14
18 14 0.17
19 38 0.47
20 11 0.14
21 6 0.08
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (19 bp):
TAAAAATATTTAAAATTTG
Found at i:88941014 original size:16 final size:17
Alignment explanation
Indices: 88940993--88941026 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
88940983 TTAGTTTGGG
*
88940993 TTATGG-TTAAGGTTTT
1 TTATGGTTTAAAGTTTT
88941009 TTATGGTTTAAAGTTTT
1 TTATGGTTTAAAGTTTT
88941026 T
1 T
88941027 AAGGTAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (17 bp):
TTATGGTTTAAAGTTTT
Found at i:88942127 original size:27 final size:27
Alignment explanation
Indices: 88942089--88942157 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
88942079 CAGATTTCAA
*
88942089 CCAAACATACCAGAATAAATAATCCTC
1 CCAAACACACCAGAATAAATAATCCTC
88942116 CCAAACACACCAGAATAAATAATCCTC
1 CCAAACACACCAGAATAAATAATCCTC
*
88942143 CCAAACACACTAGAA
1 CCAAACACACCAGAA
88942158 AGGCATTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.49, C:0.32, G:0.04, T:0.14
Consensus pattern (27 bp):
CCAAACACACCAGAATAAATAATCCTC
Found at i:88943355 original size:18 final size:18
Alignment explanation
Indices: 88943312--88943358 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
88943302 CTTGTCTTGA
* *
88943312 TTTAATTTAATTTATTTG
1 TTTAATATAATTTATATG
*
88943330 TTTTATATAATTTAATAT-
1 TTTAATATAATTT-ATATG
88943348 TTTAATATAAT
1 TTTAATATAAT
88943359 AAAAATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTAATATAATTTATATG
Found at i:88949675 original size:27 final size:27
Alignment explanation
Indices: 88949632--88949700 Score: 111
Period size: 27 Copynumber: 2.6 Consensus size: 27
88949622 CTGATTTCAA
*
88949632 CCAAACACACCAAAATAAATAATCCTC
1 CCAAACACACCAGAATAAATAATCCTC
*
88949659 CCAAACACACTAGAATAAATAATCCTC
1 CCAAACACACCAGAATAAATAATCCTC
*
88949686 CTAAACACACCAGAA
1 CCAAACACACCAGAA
88949701 AGGTATTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.51, C:0.32, G:0.03, T:0.14
Consensus pattern (27 bp):
CCAAACACACCAGAATAAATAATCCTC
Found at i:88953317 original size:27 final size:27
Alignment explanation
Indices: 88953287--88953464 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
88953277 ATATTGAGTC
* * *
88953287 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAAAT
*
88953314 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
*
88953341 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAA-T
* * *
88953369 CGCACACTTAGTGCCACATGATCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
* **
88953396 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAAAT
* *
88953423 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
88953450 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
88953465 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
26 1 0.01
27 106 0.81
28 24 0.18
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:88953426 original size:82 final size:81
Alignment explanation
Indices: 88953287--88953463 Score: 239
Period size: 82 Copynumber: 2.2 Consensus size: 81
88953277 ATATTGAGTC
* * * *
88953287 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAG
1 CGCACACTTAGTGCCACATAATCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAG
*
88953352 TGCTACATAGTCAAACT
66 TGCAACATAGTCAAA-T
* * * **
88953369 CGCACACTTAGTGCCACATGATCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTA
1 CGCACACTTAGTGCCACATAATCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTA
88953433 GTGCAACATAGTCAAAT
65 GTGCAACATAGTCAAAT
88953450 CGCACACTTAGTGC
1 CGCACACTTAGTGC
88953464 TGTACAATTT
Statistics
Matches: 84, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
81 16 0.19
82 68 0.81
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (81 bp):
CGCACACTTAGTGCCACATAATCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAG
TGCAACATAGTCAAAT
Found at i:88954810 original size:18 final size:18
Alignment explanation
Indices: 88954766--88954810 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
88954756 ATGAAGCCTT
*
88954766 TTTTCTTTTCTTTTTTTTA
1 TTTTC-TTTCTTTTTATTA
* *
88954785 TTTGCTTTCTTTTTATTC
1 TTTTCTTTCTTTTTATTA
88954803 TTTTCTTT
1 TTTTCTTT
88954811 TATTCATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTCTTTCTTTTTATTA
Found at i:88961350 original size:27 final size:27
Alignment explanation
Indices: 88961320--88961497 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
88961310 ATATTGAGTC
* *
88961320 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
88961347 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
88961374 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
88961402 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
88961429 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
88961456 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
88961483 TGCACACTTAGTGCT
1 CGCACACTTAGTGCT
88961498 GTACAATTTA
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:88961459 original size:82 final size:81
Alignment explanation
Indices: 88961341--88961496 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
88961331 TGCTATATAA
* *
88961341 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
88961406 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
88961423 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATTGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
88961487 CACTTAGTGC
65 CACTTAGTGC
88961497 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 51 0.77
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:88965558 original size:26 final size:26
Alignment explanation
Indices: 88965529--88965636 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
88965519 TGGTAAAAAT
*
88965529 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
** *
88965555 TGATAATGAATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
88965581 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
88965607 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
88965633 TGAT
1 TGAT
88965637 GGGCATTTCA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:88967275 original size:27 final size:27
Alignment explanation
Indices: 88967245--88967320 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
88967235 GGTGGCAATG
*
88967245 CCACAAATATCAGATCTGGTGGCTCTA
1 CCACAAATATCTGATCTGGTGGCTCTA
* * *
88967272 CCACATATATCTGTTCTGGTGGCTCTG
1 CCACAAATATCTGATCTGGTGGCTCTA
* *
88967299 CCACGATTATCTGTATCTGGTG
1 CCACAAATATCTG-ATCTGGTG
88967321 AGTCTGTCAC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 33 0.82
28 7 0.17
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (27 bp):
CCACAAATATCTGATCTGGTGGCTCTA
Found at i:88967334 original size:27 final size:26
Alignment explanation
Indices: 88967259--88967344 Score: 111
Period size: 27 Copynumber: 3.2 Consensus size: 26
88967249 AAATATCAGA
*
88967259 TCTGGTGGCTCTACCACATATATCTGT
1 TCTGGTGGCTCTGCCACAT-TATCTGT
88967286 TCTGGTGGCTCTGCCACGATTATCTGT
1 TCTGGTGGCTCTGCCAC-ATTATCTGT
*
88967313 ATCTGGTGAG-TCTGTCACATTATCTGT
1 -TCTGGTG-GCTCTGCCACATTATCTGT
88967340 TCTGG
1 TCTGG
88967345 CAGCCATGCT
Statistics
Matches: 54, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
26 5 0.09
27 32 0.59
28 16 0.30
29 1 0.02
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (26 bp):
TCTGGTGGCTCTGCCACATTATCTGT
Found at i:88984055 original size:24 final size:24
Alignment explanation
Indices: 88984019--88984128 Score: 79
Period size: 24 Copynumber: 4.6 Consensus size: 24
88984009 AAAAGATGTT
*
88984019 ATAAAAGCAATTTTAAGTGAAT-AAC
1 ATAAAA-CAATTTAAAGT-AATCAAC
*
88984044 ATAAAACAATTTAAAATAATCAAC
1 ATAAAACAATTTAAAGTAATCAAC
88984068 ATACAAAACAATTTAAAGT-A--AA-
1 AT--AAAACAATTTAAAGTAATCAAC
* * *
88984090 ATAAAGCGATTTAAAATAAAT-AAC
1 ATAAAACAATTTAAAGT-AATCAAC
*
88984114 ATATAACAATTTAAA
1 ATAAAACAATTTAAA
88984129 AGAACATATA
Statistics
Matches: 69, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
20 12 0.17
22 3 0.04
23 7 0.10
24 26 0.38
25 7 0.10
26 14 0.20
ACGTcount: A:0.59, C:0.09, G:0.05, T:0.26
Consensus pattern (24 bp):
ATAAAACAATTTAAAGTAATCAAC
Found at i:88984140 original size:46 final size:45
Alignment explanation
Indices: 88984052--88984181 Score: 108
Period size: 45 Copynumber: 2.8 Consensus size: 45
88984042 ACATAAAACA
88984052 ATTTAAAAT-AATCAACATACAAAACAATTTAAAGTAAAAT-AAAGCG
1 ATTTAAAATAAAT-AACATA-AAAACAATTTAAAGTAAAATAAAAG-G
*
88984098 ATTTAAAATAAATAACAT-ATAACAATTTAAAAG-AACATATAAAAGG
1 ATTTAAAATAAATAACATAAAAACAATTT-AAAGTAA-A-ATAAAAGG
* * * *
88984144 -TCTAAAATAAATAATATAGAAAAAAATAGTAAAGTAAA
1 ATTTAAAATAAATAACATA-AAAACAAT-TTAAAGTAAA
88984182 TAATATACAT
Statistics
Matches: 69, Mismatches: 6, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
44 11 0.16
45 20 0.29
46 17 0.25
47 18 0.26
48 3 0.04
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.25
Consensus pattern (45 bp):
ATTTAAAATAAATAACATAAAAACAATTTAAAGTAAAATAAAAGG
Found at i:88984233 original size:19 final size:18
Alignment explanation
Indices: 88984173--88984243 Score: 74
Period size: 19 Copynumber: 4.0 Consensus size: 18
88984163 AAAAAAATAG
* *
88984173 TAAAGTAAATAATATACA
1 TAAAATAAATAATATATA
*
88984191 TAAAATAAA-AATAT-TT
1 TAAAATAAATAATATATA
*
88984207 TAATATAAATAATATATA
1 TAAAATAAATAATATATA
*
88984225 TAAAAATAAATAATGTATA
1 T-AAAATAAATAATATATA
88984244 AAGAGTTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
16 8 0.19
17 10 0.23
18 10 0.23
19 15 0.35
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (18 bp):
TAAAATAAATAATATATA
Found at i:88986407 original size:29 final size:29
Alignment explanation
Indices: 88986349--88986434 Score: 95
Period size: 29 Copynumber: 2.9 Consensus size: 29
88986339 GTTATTGTAC
* *
88986349 TATTTGTAAA-TTTAAATTTTAGTCTATT
1 TATTTTTAAATTTTAAAATTTAGTCTATT
* *
88986377 TATTTTT-ATTTTTAAAAATTTAGTCTCTT
1 TATTTTTAAATTTT-AAAATTTAGTCTATT
88986406 TATTTTTCAAATTTTAAAATTTAGATCTA
1 TATTTTT-AAATTTTAAAATTTAG-TCTA
88986435 ACTGTTAACA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
27 1 0.02
28 9 0.19
29 20 0.43
30 9 0.19
31 8 0.17
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.57
Consensus pattern (29 bp):
TATTTTTAAATTTTAAAATTTAGTCTATT
Found at i:88995556 original size:26 final size:26
Alignment explanation
Indices: 88995525--88995632 Score: 207
Period size: 26 Copynumber: 4.2 Consensus size: 26
88995515 ATGAATGCCC
*
88995525 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
88995551 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
88995577 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
88995603 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
88995629 ATCA
1 ATCA
88995633 ATTTGTACCA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.36, C:0.26, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:89001372 original size:26 final size:26
Alignment explanation
Indices: 89001336--89001443 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
89001326 TGAAATGCCA
*
89001336 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
89001362 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
89001388 ATCATGAAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
89001414 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
89001440 ATCA
1 ATCA
89001444 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:89004480 original size:17 final size:17
Alignment explanation
Indices: 89004458--89004493 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
89004448 ATTTACATTT
*
89004458 AAATTATTAACATCTTG
1 AAATTATTAACATATTG
89004475 AAATTATTAACATATTG
1 AAATTATTAACATATTG
89004492 AA
1 AA
89004494 TTTTAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (17 bp):
AAATTATTAACATATTG
Found at i:89006045 original size:11 final size:11
Alignment explanation
Indices: 89006031--89006086 Score: 76
Period size: 11 Copynumber: 4.9 Consensus size: 11
89006021 AGATAAATAT
89006031 TATTTTATTAA
1 TATTTTATTAA
*
89006042 TATTTTAATAATA
1 TATTTT-ATTA-A
89006055 TATTTTATTAA
1 TATTTTATTAA
*
89006066 TATTTTAATAA
1 TATTTTATTAA
89006077 TATTTTATTA
1 TATTTTATTA
89006087 GTATATAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
11 26 0.67
12 6 0.15
13 7 0.18
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:89006058 original size:24 final size:24
Alignment explanation
Indices: 89006026--89006086 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
89006016 TAATTAGATA
89006026 AATATTATTTTATTAATATTTTAAT
1 AATA-TATTTTATTAATATTTTAAT
89006051 AATATATTTTATTAATATTTTAAT
1 AATATATTTTATTAATATTTTAAT
89006075 -A-ATATTTTATTA
1 AATATATTTTATTA
89006087 GTATATAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
22 11 0.31
23 1 0.03
24 20 0.56
25 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
AATATATTTTATTAATATTTTAAT
Done.