Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 117 of 193
Found at i:37178548 original size:39 final size:39
Alignment explanation
Indices: 37178502--37178711 Score: 226
Period size: 39 Copynumber: 5.4 Consensus size: 39
37178492 TAATAACCTG
* * * *
37178502 GTAGTGTTTACAGTGTCACTACCACTTCAATATAATATT
1 GTAGTGTTTACAGTGTCACTGCCAATTCAGTATAACATT
* * *
37178541 GTGGTGTTTTCAGTGTCA-TCGCCAATTCAGTATAACATC
1 GTAGTGTTTACAGTGTCACT-GCCAATTCAGTATAACATT
* *
37178580 GTAGTGTTTACAGTGTCACTGCTATTTTC-GTATAACATT
1 GTAGTGTTTACAGTGTCACTGCCA-ATTCAGTATAACATT
* *
37178619 GTAGTGTTTACAGTGTAACTGCCGATTCAGTATAACATT
1 GTAGTGTTTACAGTGTCACTGCCAATTCAGTATAACATT
** * ** *
37178658 ACAGTGTTTATAGTGTCACTGCCAATTCAGTAATATTATC
1 GTAGTGTTTACAGTGTCACTGCCAATTCAGT-ATAACATT
37178698 GTAGTGTTTACAGT
1 GTAGTGTTTACAGT
37178712 CACTACCAGT
Statistics
Matches: 139, Mismatches: 27, Indels: 9
0.79 0.15 0.05
Matches are distributed among these distances:
38 4 0.03
39 115 0.83
40 20 0.14
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.39
Consensus pattern (39 bp):
GTAGTGTTTACAGTGTCACTGCCAATTCAGTATAACATT
Found at i:37180740 original size:62 final size:62
Alignment explanation
Indices: 37180643--37180842 Score: 346
Period size: 62 Copynumber: 3.2 Consensus size: 62
37180633 CAGGATTTCC
37180643 GACATCGGACCTTTAATCCGTAATAGGATTCATTTCTCATGTAATACTCACGATATCACAAA
1 GACATCGGACCTTTAATCCGTAATAGGATTCATTTCTCATGTAATACTCACGATATCACAAA
* *
37180705 GACATCAGACCTTTAATCCGTAATAGGATCCATTTCTCATGTAATACTCACGATATCACAAA
1 GACATCGGACCTTTAATCCGTAATAGGATTCATTTCTCATGTAATACTCACGATATCACAAA
* * * *
37180767 TACATCGGATCTTTAATCTGTAATAGGATTGATTTCTCATGTAATACTCACGATATCACAAA
1 GACATCGGACCTTTAATCCGTAATAGGATTCATTTCTCATGTAATACTCACGATATCACAAA
37180829 GACATCGGACCTTT
1 GACATCGGACCTTT
37180843 TCATTTTCCA
Statistics
Matches: 128, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 128 1.00
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.32
Consensus pattern (62 bp):
GACATCGGACCTTTAATCCGTAATAGGATTCATTTCTCATGTAATACTCACGATATCACAAA
Found at i:37185918 original size:59 final size:59
Alignment explanation
Indices: 37185820--37186250 Score: 420
Period size: 59 Copynumber: 7.3 Consensus size: 59
37185810 TGACTTTTGA
* * * *
37185820 GGGTAAAACTGG-AA-TTCTGGTGAAA-CCAGGGTTAAAAATGGAATTTTAGAAAG-TTCG
1 GGGTAAAA-TGGTAATTTTTGGTGAAATCGA-GGTTAAAAATGGAATTTTGGAAAGTTTAG
* * *
37185877 AGGGTAAAATAGTAATTTTTAGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTAG
1 -GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAG
* ** *
37185937 GGGT-AAATTGTAATTTTTGGTGAAATTAAGGGTTAAAAATGAAATTTTGGAAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGA-GGTTAAAAATGGAATTTTGGAAAGTTTAG
* *
37185996 GGGTAAAATGGTAATTTTTGCT-AAAACTGAGGTTAAAAATGGAATTTTGGAAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGTGAAATC-GAGGTTAAAAATGGAATTTTGGAAAGTTTAG
* * * *
37186055 GGGT-AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTAGAAAGTTTAA
1 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAG
* * * *
37186113 GGGTAAAATGGTAATTTTT--TGAAGTTTTGGGGTTAAAAATGGAATTTTGAAAAGTTT-G
1 GGGTAAAATGGTAATTTTTGGTGAA--ATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAG
* * * * * * *
37186171 GTGGTAAAATGGTAA-TTTT-G-GAAGTTTTGGGGTCAAAAAATAGAATTTTGGAATGTTTGG
1 G-GGTAAAATGGTAATTTTTGGTGAA--ATCGAGGT-TAAAAATGGAATTTTGGAAAGTTTAG
37186231 GGGTAAAATGGTAATTTTTG
1 GGGTAAAATGGTAATTTTTG
37186251 AACAGTTCAG
Statistics
Matches: 321, Mismatches: 35, Indels: 31
0.83 0.09 0.08
Matches are distributed among these distances:
57 6 0.02
58 96 0.30
59 192 0.60
60 27 0.08
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAG
Found at i:37186246 original size:29 final size:28
Alignment explanation
Indices: 37185913--37186257 Score: 182
Period size: 29 Copynumber: 11.8 Consensus size: 28
37185903 ATCGAGGTCA
*
37185913 AAAATGGAATTTTGGAAAGTTTAGGGGT
1 AAAATGGAATTTTGGAAAGTTTGGGGGT
* * ** *
37185941 AAATTGTAATTTTTGGTGAAA-TTAAGGGTT
1 AAAATGGAA-TTTT-G-GAAAGTTTGGGGGT
* *
37185971 AAAAATGAAATTTTGGAAAGTTTAGGGGT
1 -AAAATGGAATTTTGGAAAGTTTGGGGGT
* ** * *
37186000 AAAATGGTAATTTTTGCTAAA-ACTGAGGTT
1 AAAATGG-AA-TTTTG-GAAAGTTTGGGGGT
*
37186030 AAAAATGGAATTTTGGAAAGTTTAGGGGT
1 -AAAATGGAATTTTGGAAAGTTTGGGGGT
* *
37186059 -AAATGGTAATTTTTGGTGAAA--TCGGGGTT
1 AAAATGG-AA-TTTT-G-GAAAGTTTGGGGGT
* * **
37186088 AAAAATGGGATTTTAGAAAGTTTAAGGGT
1 -AAAATGGAATTTTGGAAAGTTTGGGGGT
* *
37186117 AAAATGGTAATTTTTTG-AAGTTTTGGGGTT
1 AAAATGG-AA-TTTTGGAAAG-TTTGGGGGT
* *
37186147 AAAAATGGAATTTTGAAAAGTTTGGTGGT
1 -AAAATGGAATTTTGGAAAGTTTGGGGGT
*
37186176 AAAATGGTAATTTTGG-AAGTTTTGGGGT
1 AAAATGG-AATTTTGGAAAGTTTGGGGGT
* *
37186204 CAAAAAATAGAATTTTGGAATGTTTGGGGGT
1 ---AAAATGGAATTTTGGAAAGTTTGGGGGT
*
37186235 AAAATGGTAATTTTTGAACAGTT
1 AAAATGG-AATTTTGGAA-AGTT
37186258 CAGGGACCTA
Statistics
Matches: 239, Mismatches: 48, Indels: 58
0.69 0.14 0.17
Matches are distributed among these distances:
27 10 0.04
28 52 0.22
29 71 0.30
30 52 0.22
31 54 0.23
ACGTcount: A:0.35, C:0.01, G:0.27, T:0.36
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTTGGGGGT
Found at i:37188086 original size:6 final size:6
Alignment explanation
Indices: 37188069--37188128 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
37188059 TTGGACATCT
* * **
37188069 AATTTA ATTTTA AATTTA AATTTA TAA--TA AATTTA AATTT- TATGCA
1 AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTTA AATTTA
37188115 AATTTA AATTTA AA
1 AATTTA AATTTA AA
37188129 ATAAATCTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
4 2 0.05
5 4 0.10
6 34 0.81
7 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:37188101 original size:17 final size:17
Alignment explanation
Indices: 37188079--37188134 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
37188069 AATTTAATTT
37188079 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
37188096 TAAATTTAAATTT-T-A
1 TAAATTTAAATTTATAA
*
37188111 TGCAAATTTAAATTTAAAA
1 T--AAATTTAAATTTATAA
37188130 TAAAT
1 TAAAT
37188135 CTAACTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
15 2 0.06
16 1 0.03
17 29 0.85
19 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:37188152 original size:34 final size:35
Alignment explanation
Indices: 37188079--37188154 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 35
37188069 AATTTAATTT
* * * * **
37188079 TAAATTTAAATTTATAATAAATTTAAATTTTATGC
1 TAAATTTAAATTTAAAATAAATCTAAACTTAAAAC
37188114 -AAATTTAAATTTAAAATAAATCT-AACTTAAAAC
1 TAAATTTAAATTTAAAATAAATCTAAACTTAAAAC
37188147 TAAATTTA
1 TAAATTTA
37188155 TATCTCATTG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
33 6 0.18
34 28 0.82
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (35 bp):
TAAATTTAAATTTAAAATAAATCTAAACTTAAAAC
Found at i:37188844 original size:200 final size:200
Alignment explanation
Indices: 37188494--37189135 Score: 919
Period size: 200 Copynumber: 3.2 Consensus size: 200
37188484 CCTGGCCCTC
* * * * * * *
37188494 TCTCTGTGTCTCATCAAGAGGATGACCGTAATC-ATCTGTTTTAATTCGCTTCTCTGGATCTTCT
1 TCTCTGTATCTCATCAGGAAGATGACCG-CATCGCT-TGTTTTGATTCGCTTCTCTGGATCTCCT
* * * *
37188558 CAGGAAGACGAATTTGGTCCACTTCTCTATGTCTCATTAGGAAGCTAACCTTTTTATTGCTTCGA
64 CAGGAAGACGAATCTAGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTCGA
** * * * *
37188623 CCTGCTTCTCAGTACCTCATCAGGAAGCTGGGTTCGAAGGTTTGTTCGCATTGAGCGTTGAGTTG
129 CCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGTATTGAGCGCTGAGTTG
37188688 GTTTTCT
194 GTTTTCT
** *
37188695 TCTCTGTATCTCATCAGGAAGATGACCGTGTCGCTTGTTTTGATTCGCTTCTCTAGATCTCCTCA
1 TCTCTGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTTGATTCGCTTCTCTGGATCTCCTCA
* *
37188760 GGAAGACGAATCTAGTCCACTTCTCTGTGTCTCATCAGGAAGCTGACCTTTTTATTGCCTCGACC
66 GGAAGACGAATCTAGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTCGACC
* *
37188825 TGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGTGTTGAGCGCTGGGTTGGT
131 TGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGTATTGAGCGCTGAGTTGGT
37188890 TTTCT
196 TTTCT
* *
37188895 TCTCTGTATCTCATTAGGAAGATGACCGCCAT-GCTTGTTTTGATTCGCTTTTCTGGATCTCCTC
1 TCTCTGTATCTCATCAGGAAGATGACCG-CATCGCTTGTTTTGATTCGCTTCTCTGGATCTCCTC
*
37188959 AGGAAGACGAATCTAGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTCAAC
65 AGGAAGACGAATCTAGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTCGAC
* * * * *
37189024 CTACTTCTCAGTGTCTCATCAGGAACCTGGGTTCGAAGATTTACCCGTGTTTTGAGCGCTGAGTT
130 CTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTC--GTATTGAGCGCTGAGTT
*
37189089 GGTGTTCT
193 GGTTTTCT
*
37189097 TCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTT
1 TCTCTGTATCTCATCAGGAAGATGACCGCATCGCTTGTT
37189136 GAACTACTCC
Statistics
Matches: 396, Mismatches: 40, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
200 311 0.79
201 29 0.07
202 56 0.14
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.36
Consensus pattern (200 bp):
TCTCTGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTTGATTCGCTTCTCTGGATCTCCTCA
GGAAGACGAATCTAGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTCGACC
TGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGTATTGAGCGCTGAGTTGGT
TTTCT
Found at i:37201281 original size:29 final size:29
Alignment explanation
Indices: 37201249--37201352 Score: 115
Period size: 29 Copynumber: 3.6 Consensus size: 29
37201239 CTTTTAAGGG
*
37201249 TAAAAATGGAATTTTGGTGAAACCGAGGT
1 TAAAAATGGAATTTTGGTGAAATCGAGGT
*
37201278 TAAAAATGGAATTTT-G-GAAAGTTCGAGGG
1 TAAAAATGGAATTTTGGTGAAA--TCGAGGT
*
37201307 T-AAAATGGTAATTTTTGGTGAAATCGGGGT
1 TAAAAATGG-AA-TTTTGGTGAAATCGAGGT
*
37201337 CAAAAATGGAATTTTG
1 TAAAAATGGAATTTTG
37201353 AAAAGTTTAG
Statistics
Matches: 63, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
27 4 0.06
28 8 0.13
29 28 0.44
30 11 0.17
31 8 0.13
32 4 0.06
ACGTcount: A:0.37, C:0.05, G:0.28, T:0.31
Consensus pattern (29 bp):
TAAAAATGGAATTTTGGTGAAATCGAGGT
Found at i:37201307 original size:58 final size:57
Alignment explanation
Indices: 37201245--37201608 Score: 243
Period size: 58 Copynumber: 6.3 Consensus size: 57
37201235 TTTACTTTTA
* *
37201245 AGGGTAAAAATGG-AATTTTGGTGAAACCGAGGTTAAAAATGGAATTTTGGAAAGTTCG
1 AGGGT-AAAATGGTAATTTTGGTGAAACCGAGGTCAAAAATGGAATTTTGAAAAGTT-G
* * *
37201303 AGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGAAAAGTTT
1 AGGGTAAAATGGTAA-TTTTGGTGAAACCGAGGTCAAAAATGGAATTTTGAAAAGTTG
**** ** *
37201361 AGGGGTAAAATGGTAATTTT-G-GAAGTTTTAAGGTCAAAAATAAAATTTTGGAAAGTTTG
1 A-GGGTAAAATGGTAATTTTGGTGAA--ACCGAGGTCAAAAATGGAATTTTGAAAAG-TTG
* * ** * *
37201420 GGGGTAAAATGGTAATTTTTGGTAAAATTG-GG--GAAAATGGAATTTTGGAAAGTTTG
1 AGGGTAAAATGGTAA-TTTTGGTGAAACCGAGGTCAAAAATGGAATTTTGAAAAG-TTG
* * * **
37201476 GGGGT-AAATGGTAATTTTTGGTGAAATC-AGGGTTAAAAATAGG-ATTTCAAAAAGTTTG
1 AGGGTAAAATGGTAA-TTTTGGTGAAACCGA-GGTCAAAAAT-GGAATTTTGAAAAG-TTG
* **
37201534 -GGGTAAAATGGTAATTTTTG-GAAGTTTCG-GGTC-AAAATGGAATTTT-AGAAAGTTTG
1 AGGGTAAAATGGTAATTTTGGTGAA--ACCGAGGTCAAAAATGGAATTTTGA-AAAG-TTG
37201590 AGGGTAAAATGGTAATTTT
1 AGGGTAAAATGGTAATTTT
37201609 CGAACAGTCC
Statistics
Matches: 255, Mismatches: 30, Indels: 43
0.78 0.09 0.13
Matches are distributed among these distances:
55 24 0.09
56 51 0.20
57 38 0.15
58 78 0.31
59 61 0.24
60 1 0.00
61 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (57 bp):
AGGGTAAAATGGTAATTTTGGTGAAACCGAGGTCAAAAATGGAATTTTGAAAAGTTG
Found at i:37201386 original size:28 final size:27
Alignment explanation
Indices: 37201280--37201608 Score: 165
Period size: 28 Copynumber: 11.5 Consensus size: 27
37201270 ACCGAGGTTA
*
37201280 AAAATGG-AATTTTGGAAAGTTCGAGGGT
1 AAAATGGTAATTTTGG-AAGTTTG-GGGT
* *
37201308 AAAATGGTAATTTTTGGTGAA-ATCGGGGT
1 AAAATGGTAA-TTTT-G-GAAGTTTGGGGT
*
37201337 CAAAAATGG-AATTTTGAAAAGTTTAGGGGT
1 --AAAATGGTAATTTTG-GAAGTTT-GGGGT
**
37201367 AAAATGGTAATTTTGGAAGTTTTAAGGT
1 AAAATGGTAATTTTGGAAG-TTTGGGGT
**
37201395 CAAAAAT-AAAATTTTGGAAAGTTTGGGGGT
1 --AAAATGGTAATTTTGG-AAGTTT-GGGGT
**
37201425 AAAATGGTAATTTTTGGTAAAATTGGGG-
1 AAAATGGTAA-TTTTGG-AAGTTTGGGGT
37201453 AAAATGG-AATTTTGGAAAGTTTGGGGGT
1 AAAATGGTAATTTTGG-AAGTTT-GGGGT
* ** *
37201481 -AAATGGTAATTTTTGGTGAAATCAGGGTT
1 AAAATGGTAA-TTTT-G-GAAGTTTGGGGT
***
37201510 AAAAATAGG--ATTTCAAAAAGTTTGGGGT
1 -AAAAT-GGTAATTT-TGGAAGTTTGGGGT
*
37201538 AAAATGGTAATTTTTGGAAGTTTCGGGT
1 AAAATGGTAA-TTTTGGAAGTTTGGGGT
*
37201566 CAAAATGG-AATTTTAGAAAGTTTGAGGGT
1 -AAAATGGTAATTTT-GGAAGTTTG-GGGT
37201595 AAAATGGTAATTTT
1 AAAATGGTAATTTT
37201609 CGAACAGTCC
Statistics
Matches: 231, Mismatches: 37, Indels: 65
0.69 0.11 0.20
Matches are distributed among these distances:
26 12 0.05
27 21 0.09
28 71 0.31
29 69 0.30
30 40 0.17
31 15 0.06
32 3 0.01
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (27 bp):
AAAATGGTAATTTTGGAAGTTTGGGGT
Found at i:37203426 original size:6 final size:6
Alignment explanation
Indices: 37203409--37203468 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
37203399 TTGGACATCT
* * **
37203409 AATTTA ATTTTA AATTTA AATTTA TAA--TA AATTTA AATTT- TATGCA
1 AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTTA AATTTA
37203455 AATTTA AATTTA AA
1 AATTTA AATTTA AA
37203469 ATAAATCTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
4 2 0.05
5 4 0.10
6 34 0.81
7 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:37203441 original size:17 final size:17
Alignment explanation
Indices: 37203419--37203474 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
37203409 AATTTAATTT
37203419 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
37203436 TAAATTTAAATTT-T-A
1 TAAATTTAAATTTATAA
*
37203451 TGCAAATTTAAATTTAAAA
1 T--AAATTTAAATTTATAA
37203470 TAAAT
1 TAAAT
37203475 CTAACTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
15 2 0.06
16 1 0.03
17 29 0.85
19 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:37203492 original size:34 final size:35
Alignment explanation
Indices: 37203419--37203493 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 35
37203409 AATTTAATTT
* * * * **
37203419 TAAATTTAAATTTATAATAAATTTAAATTTTATGC
1 TAAATTTAAATTTAAAATAAATCTAAACTTAAAAC
37203454 -AAATTTAAATTTAAAATAAATCT-AACTTAAAAC
1 TAAATTTAAATTTAAAATAAATCTAAACTTAAAAC
37203487 TAAATTT
1 TAAATTT
37203494 TTATCTCATT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
33 6 0.18
34 27 0.82
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (35 bp):
TAAATTTAAATTTAAAATAAATCTAAACTTAAAAC
Found at i:37205552 original size:22 final size:21
Alignment explanation
Indices: 37205518--37205562 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
37205508 TAAACTGAGT
37205518 AAAAATTTATAAAATTTATAA
1 AAAAATTTATAAAATTTATAA
* *
37205539 AAAAATATTTTAAAATTTTTAA
1 AAAAAT-TTATAAAATTTATAA
37205561 AA
1 AA
37205563 TTAATTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAATTTATAAAATTTATAA
Found at i:37207547 original size:15 final size:16
Alignment explanation
Indices: 37207517--37207555 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
37207507 TAGTAAAAAT
37207517 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
37207534 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
37207549 ATAATTT
1 ATAATTT
37207556 TAAAATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:37207572 original size:24 final size:24
Alignment explanation
Indices: 37207519--37207572 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
37207509 GTAAAAATAT
* *
37207519 AATTTTATTATTTTAATAATTTAT
1 AATTTTATAATTTTAATAATTTAA
*
37207543 ATTTTTATAATTTTAA-AATATTAA
1 AATTTTATAATTTTAATAAT-TTAA
37207567 AATTTT
1 AATTTT
37207573 TAAGGGGTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
AATTTTATAATTTTAATAATTTAA
Found at i:37212712 original size:20 final size:21
Alignment explanation
Indices: 37212687--37212737 Score: 59
Period size: 25 Copynumber: 2.3 Consensus size: 21
37212677 CTAAACCTTA
37212687 AATTAA-CCAAATAACATTTC
1 AATTAACCCAAATAACATTTC
37212707 AATTAATCAACCCAAATAACATTTC
1 AA-T--T-AACCCAAATAACATTTC
37212732 AATTAA
1 AATTAA
37212738 TCAACCACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
20 2 0.08
21 3 0.12
22 1 0.04
23 1 0.04
24 3 0.12
25 16 0.62
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (21 bp):
AATTAACCCAAATAACATTTC
Found at i:37212721 original size:25 final size:25
Alignment explanation
Indices: 37212693--37212743 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
37212683 CTTAAATTAA
37212693 CCAAATAACATTTCAATTAATCAAC
1 CCAAATAACATTTCAATTAATCAAC
37212718 CCAAATAACATTTCAATTAATCAAC
1 CCAAATAACATTTCAATTAATCAAC
37212743 C
1 C
37212744 ACAAGTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.27
Consensus pattern (25 bp):
CCAAATAACATTTCAATTAATCAAC
Found at i:37219554 original size:27 final size:27
Alignment explanation
Indices: 37219516--37219569 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
37219506 AATCTCAAAC
* * *
37219516 TTCAACATGAAGCGAACAACAGTGAGA
1 TTCAACACGAAGCCAACAACAGCGAGA
37219543 TTCAACACGAAGCCAACAACAGCGAGA
1 TTCAACACGAAGCCAACAACAGCGAGA
37219570 AAGTTGCTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.11
Consensus pattern (27 bp):
TTCAACACGAAGCCAACAACAGCGAGA
Found at i:37224422 original size:15 final size:14
Alignment explanation
Indices: 37224367--37224422 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 14
37224357 TTTAACTTTT
37224367 AAAAAATTATTAAA-
1 AAAAAATT-TTAAAG
37224381 ATAAAAATTTT-AAG
1 A-AAAAATTTTAAAG
37224395 AAATAAATGTTTAAAG
1 AAA-AAAT-TTTAAAG
37224411 AATAAAATTTTA
1 AA-AAAATTTTA
37224423 TTATTTATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
13 4 0.11
14 8 0.22
15 14 0.39
16 9 0.25
17 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (14 bp):
AAAAAATTTTAAAG
Found at i:37229558 original size:17 final size:17
Alignment explanation
Indices: 37229536--37229572 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
37229526 AGGTGGAGAA
* *
37229536 CTTATTCGTTGAGAGTT
1 CTTATTCGTAGAGAATT
37229553 CTTATTCGTAGAGAATT
1 CTTATTCGTAGAGAATT
37229570 CTT
1 CTT
37229573 GTCAAGGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.46
Consensus pattern (17 bp):
CTTATTCGTAGAGAATT
Found at i:37230528 original size:7 final size:7
Alignment explanation
Indices: 37230518--37230542 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
37230508 TTTTGCTTTT
37230518 GTGGCAA
1 GTGGCAA
37230525 GTGGCAA
1 GTGGCAA
37230532 GTGGCAA
1 GTGGCAA
37230539 GTGG
1 GTGG
37230543 TTTTGGTTTT
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:0.24, C:0.12, G:0.48, T:0.16
Consensus pattern (7 bp):
GTGGCAA
Found at i:37232866 original size:17 final size:17
Alignment explanation
Indices: 37232844--37232877 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
37232834 CATGCTTGTC
37232844 AAACCCTTAATCTACTT
1 AAACCCTTAATCTACTT
37232861 AAACCCTTAATCTACTT
1 AAACCCTTAATCTACTT
37232878 GTTGAGTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (17 bp):
AAACCCTTAATCTACTT
Found at i:37233153 original size:17 final size:17
Alignment explanation
Indices: 37233118--37233159 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
37233108 GGAAAAAGTA
*
37233118 GTTACAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
*
37233136 GTTAAAGAAGATGGAAG
1 GTTAAAGAAGATGAAAG
37233153 GTTAAAG
1 GTTAAAG
37233160 GTCAAAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.29, T:0.21
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:37234731 original size:21 final size:20
Alignment explanation
Indices: 37234686--37234745 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 20
37234676 TATAATATTG
*
37234686 AATTTACTATATATT-TCATTC
1 AATTTTCTATATATTAT--TTC
37234707 AATTTTCTATATATTATTTC
1 AATTTTCTATATATTATTTC
*
37234727 TAATTGTT-TCTATATTATT
1 -AATT-TTCTATATATTATT
37234746 GTGTCTCAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 3 0.09
21 28 0.82
22 3 0.09
ACGTcount: A:0.30, C:0.10, G:0.02, T:0.58
Consensus pattern (20 bp):
AATTTTCTATATATTATTTC
Found at i:37240262 original size:5 final size:5
Alignment explanation
Indices: 37240247--37240278 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
37240237 AGTAGTGTAC
*
37240247 ATACA ACACA ATACA ATACA ATACA ATACA AT
1 ATACA ATACA ATACA ATACA ATACA ATACA AT
37240279 GGCCCCAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.59, C:0.22, G:0.00, T:0.19
Consensus pattern (5 bp):
ATACA
Found at i:37246262 original size:20 final size:20
Alignment explanation
Indices: 37246233--37246283 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
37246223 AAAGTTCAAG
*
37246233 GTTTAAGGTTCATGA-TTTGA
1 GTTTAGGGTT-ATGAGTTTGA
*
37246253 GTTTAGGGTTTTGAGTTTGA
1 GTTTAGGGTTATGAGTTTGA
37246273 GATTTAGGGTT
1 G-TTTAGGGTT
37246284 TAGGTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 3 0.11
20 15 0.56
21 9 0.33
ACGTcount: A:0.20, C:0.02, G:0.31, T:0.47
Consensus pattern (20 bp):
GTTTAGGGTTATGAGTTTGA
Found at i:37246292 original size:28 final size:28
Alignment explanation
Indices: 37246253--37246329 Score: 120
Period size: 28 Copynumber: 2.8 Consensus size: 28
37246243 CATGATTTGA
* *
37246253 GTTTAGGGTTTTGAGTTTGAGATTTAGG
1 GTTTAGGTTTTTAAGTTTGAGATTTAGG
37246281 GTTTAGGTTTTTAAGTTTGAGATTTAGG
1 GTTTAGGTTTTTAAGTTTGAGATTTAGG
37246309 GTTTAGG-TTTTAAGGTTTGAG
1 GTTTAGGTTTTTAA-GTTTGAG
37246330 GTTTGAATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
27 6 0.13
28 40 0.87
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.48
Consensus pattern (28 bp):
GTTTAGGTTTTTAAGTTTGAGATTTAGG
Found at i:37246331 original size:7 final size:7
Alignment explanation
Indices: 37246295--37246404 Score: 65
Period size: 7 Copynumber: 16.6 Consensus size: 7
37246285 AGGTTTTTAA
37246295 GTTTGAG
1 GTTTGAG
*
37246302 ATTT-AGG
1 GTTTGA-G
37246309 GTTT-AG
1 GTTTGAG
*
37246315 GTTTTAAG
1 G-TTTGAG
37246323 GTTTGAG
1 GTTTGAG
37246330 GTTTGA-
1 GTTTGAG
* *
37246336 ATTTGTG
1 GTTTGAG
*
37246343 ATTTGAG
1 GTTTGAG
*
37246350 GTTTAAG
1 GTTTGAG
*
37246357 GCTT-AG
1 GTTTGAG
37246363 GTTT-AG
1 GTTTGAG
* *
37246369 ATTTAAG
1 GTTTGAG
37246376 GTTTGA-
1 GTTTGAG
37246382 GTTTGA-
1 GTTTGAG
37246388 GTTTGAG
1 GTTTGAG
37246395 GTTT-AG
1 GTTTGAG
37246401 GTTT
1 GTTT
37246405 AAGATTTAGG
Statistics
Matches: 84, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
6 35 0.42
7 46 0.55
8 3 0.04
ACGTcount: A:0.20, C:0.01, G:0.32, T:0.47
Consensus pattern (7 bp):
GTTTGAG
Found at i:37246375 original size:19 final size:18
Alignment explanation
Indices: 37246351--37246412 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 18
37246341 TGATTTGAGG
37246351 TTTAAGGCTTAGGTTTAGA
1 TTTAAGG-TTAGGTTTAGA
*
37246370 TTTAAGGTTTGAGTTT-GA
1 TTTAAGGTTAG-GTTTAGA
*
37246388 GTTTGAGGTTTAGGTTTAAGA
1 -TTTAAGG-TTAGGTTT-AGA
37246409 TTTA
1 TTTA
37246413 GGATTTAAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
18 5 0.15
19 21 0.62
20 6 0.18
21 2 0.06
ACGTcount: A:0.24, C:0.02, G:0.27, T:0.47
Consensus pattern (18 bp):
TTTAAGGTTAGGTTTAGA
Found at i:37246421 original size:14 final size:13
Alignment explanation
Indices: 37246342--37246426 Score: 59
Period size: 13 Copynumber: 6.5 Consensus size: 13
37246332 TTGAATTTGT
37246342 GATTTGAGGTTTAA
1 GATTT-AGGTTTAA
**
37246356 GGCTTAGGTTT-A
1 GATTTAGGTTTAA
*
37246368 GATTTAAGGTTTGA
1 GATTT-AGGTTTAA
*
37246382 G-TTT-GAGTTTGA
1 GATTTAG-GTTTAA
*
37246394 GGTTTAGGTTTAA
1 GATTTAGGTTTAA
37246407 GATTTAGGATTTAA
1 GATTTAGG-TTTAA
*
37246421 GGTTTA
1 GATTTA
37246427 AGGTAAAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
11 1 0.02
12 11 0.19
13 30 0.52
14 16 0.28
ACGTcount: A:0.25, C:0.01, G:0.29, T:0.45
Consensus pattern (13 bp):
GATTTAGGTTTAA
Found at i:37246429 original size:7 final size:7
Alignment explanation
Indices: 37246348--37246430 Score: 61
Period size: 7 Copynumber: 12.6 Consensus size: 7
37246338 TTGTGATTTG
37246348 AGGTTTA
1 AGGTTTA
*
37246355 AGGCTT-
1 AGGTTTA
37246361 AGGTTT-
1 AGGTTTA
*
37246367 AGATTTA
1 AGGTTTA
*
37246374 AGGTTTG
1 AGGTTTA
*
37246381 A-GTTTG
1 AGGTTTA
*
37246387 A-GTTTG
1 AGGTTTA
37246393 AGGTTT-
1 AGGTTTA
37246399 AGGTTTA
1 AGGTTTA
*
37246406 AGATTT-
1 AGGTTTA
37246412 AGGATTTA
1 AGG-TTTA
37246420 AGGTTTA
1 AGGTTTA
37246427 AGGT
1 AGGT
37246431 AAAAATTTAC
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
6 30 0.47
7 31 0.48
8 3 0.05
ACGTcount: A:0.25, C:0.01, G:0.30, T:0.43
Consensus pattern (7 bp):
AGGTTTA
Found at i:37247670 original size:46 final size:47
Alignment explanation
Indices: 37247603--37247723 Score: 138
Period size: 47 Copynumber: 2.6 Consensus size: 47
37247593 AAGTTGAACA
* * *
37247603 GTTTATCTACACCATTTTAGCAACTTCTATAT-T-CACCGTTTAAGTG
1 GTTTATCCACACCGTATTAGCAACTT-TATATCTGCACCGTTTAAGTG
* * * *
37247649 GTTTATCCACACCGTATTAGCAAGTTTTTATCTGCACTGTTTGAGTG
1 GTTTATCCACACCGTATTAGCAACTTTATATCTGCACCGTTTAAGTG
* *
37247696 GTTTAACCACACCGTATTAGCAATTTTA
1 GTTTATCCACACCGTATTAGCAACTTTA
37247724 ATTTGCAAAC
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
45 4 0.06
46 23 0.37
47 36 0.57
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (47 bp):
GTTTATCCACACCGTATTAGCAACTTTATATCTGCACCGTTTAAGTG
Found at i:37248400 original size:12 final size:12
Alignment explanation
Indices: 37248345--37248460 Score: 59
Period size: 12 Copynumber: 10.0 Consensus size: 12
37248335 AACATCCAAA
*
37248345 CAACCAAAATAG
1 CAACAAAAATAG
37248357 CAACTAAAACAGTAG
1 CAAC-AAAA-A-TAG
37248372 CAA-AAATAATAG
1 CAACAAA-AATAG
37248384 --A-AAAAATAG
1 CAACAAAAATAG
*
37248393 CAACAAAAATAA
1 CAACAAAAATAG
* *
37248405 CAATAAAAACAG
1 CAACAAAAATAG
*
37248417 C-ACCAAAATAG
1 CAACAAAAATAG
* *
37248428 -TA-AAAAATAA
1 CAACAAAAATAG
* *
37248438 C-ACCAAAACAG
1 CAACAAAAATAG
37248449 CAACAAAAATAG
1 CAACAAAAATAG
37248461 TAAAAAAGCA
Statistics
Matches: 78, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
9 5 0.06
10 11 0.14
11 15 0.19
12 32 0.41
13 7 0.09
14 2 0.03
15 6 0.08
ACGTcount: A:0.65, C:0.17, G:0.08, T:0.10
Consensus pattern (12 bp):
CAACAAAAATAG
Found at i:37248412 original size:24 final size:24
Alignment explanation
Indices: 37248362--37248424 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
37248352 AATAGCAACT
* * *
37248362 AAAACAGTAGCAAAAATAATAGAA
1 AAAACAGCAACAAAAATAACAGAA
*
37248386 AAAATAGCAACAAAAATAACA-ATA
1 AAAACAGCAACAAAAATAACAGA-A
*
37248410 AAAACAGCACCAAAA
1 AAAACAGCAACAAAA
37248425 TAGTAAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 1 0.03
24 31 0.97
ACGTcount: A:0.68, C:0.14, G:0.08, T:0.10
Consensus pattern (24 bp):
AAAACAGCAACAAAAATAACAGAA
Found at i:37248436 original size:33 final size:33
Alignment explanation
Indices: 37248397--37248467 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
37248387 AAATAGCAAC
* *
37248397 AAAAATAACAATAAAAACAGC-ACCAAAATAGTA
1 AAAAATAAC-ACAAAAACAGCAACAAAAATAGTA
*
37248430 AAAAATAACACCAAAACAGCAACAAAAATAGTA
1 AAAAATAACACAAAAACAGCAACAAAAATAGTA
37248463 AAAAA
1 AAAAA
37248468 GCATCAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 9 0.26
33 25 0.74
ACGTcount: A:0.69, C:0.15, G:0.06, T:0.10
Consensus pattern (33 bp):
AAAAATAACACAAAAACAGCAACAAAAATAGTA
Found at i:37248467 original size:22 final size:22
Alignment explanation
Indices: 37248442--37248543 Score: 95
Period size: 23 Copynumber: 4.7 Consensus size: 22
37248432 AAATAACACC
37248442 AAAACAGCAACAAAAATAGT-A
1 AAAACAGCAACAAAAATAGTAA
*
37248463 AAAA-AGCATC-AAAATAGTAA
1 AAAACAGCAACAAAAATAGTAA
*
37248483 AAAACA-CAACACCAAAATAGCAA
1 AAAACAGCAACA--AAAATAGTAA
* * *
37248506 AAAATAGCAACCAAAACAGTAAA
1 AAAACAGCAACAAAAATAGT-AA
*
37248529 AAAACAGCACCAAAA
1 AAAACAGCAACAAAA
37248544 CAACAATATA
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
19 8 0.12
20 13 0.20
21 5 0.08
22 6 0.09
23 28 0.44
24 4 0.06
ACGTcount: A:0.66, C:0.19, G:0.08, T:0.08
Consensus pattern (22 bp):
AAAACAGCAACAAAAATAGTAA
Found at i:37248512 original size:52 final size:53
Alignment explanation
Indices: 37248408--37248509 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 53
37248398 AAAATAACAA
*
37248408 TAAAAACAGCACCAAAATAGTAAAAAATAACACCAAAACAGCAACAAAAATAG
1 TAAAAACAGCACCAAAATAGTAAAAAACAACACCAAAACAGCAACAAAAATAG
* *
37248461 TAAAAA-AGCATCAAAATAGTAAAAAACACAACACCAAAATAGCAA-AAAA
1 TAAAAACAGCACCAAAATAGT-AAAAA-ACAACACCAAAACAGCAACAAAA
37248510 TAGCAACCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
52 13 0.30
53 15 0.34
54 16 0.36
ACGTcount: A:0.66, C:0.18, G:0.07, T:0.10
Consensus pattern (53 bp):
TAAAAACAGCACCAAAATAGTAAAAAACAACACCAAAACAGCAACAAAAATAG
Found at i:37248544 original size:22 final size:22
Alignment explanation
Indices: 37248462--37248545 Score: 82
Period size: 22 Copynumber: 3.8 Consensus size: 22
37248452 CAAAAATAGT
* *
37248462 AAAAA-AGCATCAAAATAGTAA
1 AAAAACAGCACCAAAACAGTAA
* * *
37248483 AAAACACAACACCAAAATAG-CA
1 AAAA-ACAGCACCAAAACAGTAA
*
37248505 AAAAATAGCAACCAAAACAGTAA
1 AAAAACAGC-ACCAAAACAGTAA
37248528 AAAAACAGCACCAAAACA
1 AAAAACAGCACCAAAACA
37248546 ACAATATAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
21 7 0.14
22 24 0.47
23 20 0.39
ACGTcount: A:0.65, C:0.20, G:0.07, T:0.07
Consensus pattern (22 bp):
AAAAACAGCACCAAAACAGTAA
Found at i:37250267 original size:29 final size:30
Alignment explanation
Indices: 37250230--37250288 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
37250220 TATGGTTTAA
*
37250230 TGTGTAATTGTATACAT-AAACTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
* *
37250259 TGTGCAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
37250289 GATCCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.49
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAACTTTGATTT
Found at i:37250297 original size:30 final size:29
Alignment explanation
Indices: 37250235--37250303 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
37250225 TTTAATGTGT
* *
37250235 AATTGTATACATAAACTTTGATTTTGTGC
1 AATTTTATACATAAACTTTGATTTTGTCC
*
37250264 AATTTTATACATGAAATTTTGA-TTTGATCC
1 AATTTTATACAT-AAACTTTGATTTTG-TCC
37250294 AATTCTTATA
1 AATT-TTATA
37250304 AATTATTAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 15 0.44
30 14 0.41
31 5 0.15
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (29 bp):
AATTTTATACATAAACTTTGATTTTGTCC
Found at i:37250510 original size:29 final size:30
Alignment explanation
Indices: 37250431--37250541 Score: 118
Period size: 31 Copynumber: 3.7 Consensus size: 30
37250421 GATTAAATCT
* ** *
37250431 AAATTAAAGTTTCAAGTATACGTTTGAACC
1 AAATTAAAGTTTCATGTATACAATTGCACC
*
37250461 ACAATTAAAGTTTCATGTATATAATTGCACC
1 A-AATTAAAGTTTCATGTATACAATTGCACC
*
37250492 AAATTAAAG-TTCATGTATACAATTGCACATT
1 AAATTAAAGTTTCATGTATACAATTGCAC--C
*
37250523 AAATCAAAG-TTCATGTATA
1 AAATTAAAGTTTCATGTATA
37250542 ATTTTGAAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
29 18 0.26
30 9 0.13
31 43 0.61
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (30 bp):
AAATTAAAGTTTCATGTATACAATTGCACC
Found at i:37256145 original size:14 final size:14
Alignment explanation
Indices: 37256122--37256174 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
37256112 TTTATACTTA
37256122 AAACCTTAAACTAT
1 AAACCTTAAACTAT
*
37256136 AAACCATAAAC-ATT
1 AAACCTTAAACTA-T
*
37256150 AAACCTTAAACTTT
1 AAACCTTAAACTAT
*
37256164 AAAACTTAAAC
1 AAACCTTAAAC
37256175 CCTAAACCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 1 0.03
14 32 0.97
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (14 bp):
AAACCTTAAACTAT
Found at i:37256159 original size:21 final size:21
Alignment explanation
Indices: 37256122--37256182 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
37256112 TTTATACTTA
*
37256122 AAACCTTAAA-CTATAAACCAT
1 AAACATTAAACCT-TAAACCAT
**
37256143 AAACATTAAACCTTAAACTTT
1 AAACATTAAACCTTAAACCAT
*
37256164 AAA-ACTTAAACCCTAAACC
1 AAACA-TTAAACCTTAAACC
37256183 CCTAAAATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 1 0.03
21 30 0.91
22 2 0.06
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (21 bp):
AAACATTAAACCTTAAACCAT
Found at i:37257154 original size:43 final size:43
Alignment explanation
Indices: 37257091--37257190 Score: 166
Period size: 43 Copynumber: 2.3 Consensus size: 43
37257081 AATTGCACAA
*
37257091 TTAATAACATGTCACAATATTAACA-AGGGTCAATTAATATAAT
1 TTAATAACATGTCACAATATTAACATA-GGTCAAGTAATATAAT
*
37257134 TTAATAACATGTCACGATATTAACATAGGTCAAGTAATATAAT
1 TTAATAACATGTCACAATATTAACATAGGTCAAGTAATATAAT
37257177 TTAATAACATGTCA
1 TTAATAACATGTCA
37257191 AGGAATAACA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
43 53 0.98
44 1 0.02
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (43 bp):
TTAATAACATGTCACAATATTAACATAGGTCAAGTAATATAAT
Found at i:37258584 original size:5 final size:5
Alignment explanation
Indices: 37258574--37258601 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
37258564 CTTACTAACA
37258574 AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAA
37258602 AGCAACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:37259040 original size:47 final size:48
Alignment explanation
Indices: 37258958--37259048 Score: 125
Period size: 47 Copynumber: 1.9 Consensus size: 48
37258948 ATTAAAAACA
*
37258958 AATTACATAAAAATTAAACAAAACAAAACAAAACAAATCATTTATAAT
1 AATTACATAAAAATTAAACAAAACAAAACAAAACAAAACATTTATAAT
*
37259006 AATTAC-TAAAAATTAAA-TAAA-AAAACAAACAACAAAACATTTA
1 AATTACATAAAAATTAAACAAAACAAAAC-AA-AACAAAACATTTA
37259049 CCTTTCTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
45 5 0.13
46 5 0.13
47 23 0.59
48 6 0.15
ACGTcount: A:0.66, C:0.12, G:0.00, T:0.22
Consensus pattern (48 bp):
AATTACATAAAAATTAAACAAAACAAAACAAAACAAAACATTTATAAT
Found at i:37263368 original size:29 final size:29
Alignment explanation
Indices: 37263326--37263384 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
37263316 GATTGAAATC
*
37263326 TACTACTGGAAATAAGCATGTTTACTTTG
1 TACTACTGGAAATAAGCACGTTTACTTTG
37263355 TACTACTGGAAATAAGCACGTTTACTTTG
1 TACTACTGGAAATAAGCACGTTTACTTTG
37263384 T
1 T
37263385 GCTAGAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (29 bp):
TACTACTGGAAATAAGCACGTTTACTTTG
Found at i:37269753 original size:18 final size:18
Alignment explanation
Indices: 37269732--37269779 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
37269722 CGCAGTCTGT
*
37269732 TGTGGCTGCATCCGATTA
1 TGTGGCTGCATCCAATTA
* * *
37269750 TGTGGTTACATCTAATTA
1 TGTGGCTGCATCCAATTA
*
37269768 TGTGACTGCATC
1 TGTGGCTGCATC
37269780 TGGGTATATG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (18 bp):
TGTGGCTGCATCCAATTA
Found at i:37271026 original size:137 final size:137
Alignment explanation
Indices: 37270788--37271054 Score: 444
Period size: 137 Copynumber: 1.9 Consensus size: 137
37270778 GAAATTCCCA
* * *
37270788 GCTTGTGTTGTTGGTCTAACAACCCCTGGTTGTAAATCATCGAGCACAGGAACAATAAAATCTCT
1 GCTTGTATTATTGGTCTAACAACCCCTAGTTGTAAATCATCGAGCACAGGAACAATAAAATCTCT
* *
37270853 AATTGTCCTGTTTTGAATTTGCTCCTCTTGTGGCGGCAGTTTATTATTGATGTCTTGTGGCTGTA
66 AATTGTCCTGTTTTGAATTTGCTCCTCTTGTGGCGGCAGTCTATTATTGACGTCTTGTGGCTGTA
37270918 ATTCACG
131 ATTCACG
* *
37270925 GCTTGTATTATTGGTCTAACAACCCTTAGTTGTAGATCATCGAGCACAGGAACAATAAAATCTCT
1 GCTTGTATTATTGGTCTAACAACCCCTAGTTGTAAATCATCGAGCACAGGAACAATAAAATCTCT
* * *
37270990 AATTGTCCTGTTTTGAATTTGCTCTTCTTGTGGCGGCAGTCTATTGTTGACGTGTTGTGGCTGTA
66 AATTGTCCTGTTTTGAATTTGCTCCTCTTGTGGCGGCAGTCTATTATTGACGTCTTGTGGCTGTA
37271055 CTAGAGGAAC
Statistics
Matches: 120, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
137 120 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (137 bp):
GCTTGTATTATTGGTCTAACAACCCCTAGTTGTAAATCATCGAGCACAGGAACAATAAAATCTCT
AATTGTCCTGTTTTGAATTTGCTCCTCTTGTGGCGGCAGTCTATTATTGACGTCTTGTGGCTGTA
ATTCACG
Found at i:37280440 original size:52 final size:52
Alignment explanation
Indices: 37280379--37280701 Score: 407
Period size: 52 Copynumber: 6.2 Consensus size: 52
37280369 AAACATTCAA
*
37280379 ATCATGAGTATATGAATCCTTTACGAATTATGAGGTCCGATGACTATGTGTC
1 ATCATGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTC
* * * * * * *
37280431 ATCGTGAGTATATGAATCCTTTATGAATTATGAGTTTCGATTACTATGTATC
1 ATCATGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTC
* * * * *
37280483 ATCATGAGTATATAAATCCTTTACGGATTATGAGATCCGATAAGTATATGTC
1 ATCATGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTC
37280535 ATCATGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGA-TAATGTGTC
1 ATCATGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACT-ATGTGTC
*
37280587 ATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTC
1 ATCATGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTC
* * * * * * * *
37280639 ATCGTAAGCATATGGATCCTTTTTCGGGTT-TAAGGTCCGATGACTTTGTGTC
1 ATCATGAGTATATGAATCC-TTTACGGATTATGAGGTCCGATGACTATGTGTC
*
37280691 ATTATGAGTAT
1 ATCATGAGTAT
37280702 TAAATGGGAA
Statistics
Matches: 236, Mismatches: 32, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
51 1 0.00
52 226 0.96
53 9 0.04
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (52 bp):
ATCATGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTC
Found at i:37285762 original size:52 final size:52
Alignment explanation
Indices: 37285670--37286107 Score: 595
Period size: 52 Copynumber: 8.5 Consensus size: 52
37285660 AGGGAAAAGT
* * *
37285670 TCCGATGAATATGTGTCATCGTGAGTGTATGAATCATTTACGGATTATGAGG
1 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGG
* * * *
37285722 TTCGATGACTATGTGTTATCGTGAGTATATAAATCCTTTACGAATTATGAGG
1 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGG
* * ** *
37285774 TTCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTATTGATTATAAGG
1 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGG
*
37285826 TCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATGAGG
1 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGG
* * *
37285878 TCCGATGACTATGTGTCATCATGAGTATATGAATCTTTTACGGATTATGAGA
1 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGG
37285930 TCCGATGACTATGTGTCATCGTGAG----T--ATCCTTTACGGATTATGAGG
1 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGG
*
37285976 TCCGATGACTATGTGTCATCGTTG-GTATATGAATCCTTTACAGATTATGAGG
1 TCCGATGACTATGTGTCATCG-TGAGTATATGAATCCTTTACGGATTATGAGG
* * * *
37286028 TCCGATGACTATGTGTCATCGTGAGCATATGGATCCTTTTTCGGATT-TAAGG
1 TCCGATGACTATGTGTCATCGTGAGTATATGAATCC-TTTACGGATTATGAGG
* *
37286080 TCCAATGACTTTGTGTCATCGTGAGTAT
1 TCCGATGACTATGTGTCATCGTGAGTAT
37286108 TAAATGCAAA
Statistics
Matches: 343, Mismatches: 34, Indels: 18
0.87 0.09 0.05
Matches are distributed among these distances:
46 40 0.12
47 2 0.01
48 1 0.00
50 1 0.00
51 2 0.01
52 289 0.84
53 8 0.02
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (52 bp):
TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGG
Found at i:37286034 original size:150 final size:150
Alignment explanation
Indices: 37285670--37286107 Score: 592
Period size: 150 Copynumber: 2.9 Consensus size: 150
37285660 AGGGAAAAGT
* * * *
37285670 TCCGATGAATATGTGTCATCGTGAGTGTATGAATCATTTACGGATTATGAGGTTCGATGACTATG
1 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATG
* * * * *
37285735 TGTTATCGTGAGTATATAAATCCTTTACGAATTATGAGGTTCAATGACTATGTGTCATCGTGAGT
66 TGTCATCGTGAGTATATGAATCTTTTACGGATTATGAGGTCCAATGACTATGTGTCATCGTGAG-
**
37285800 ATATGAATCCTTTATTGATTATAAGG
130 ---T--ATCCTTTACGGATTATAAGG
*
37285826 TCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATG
1 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATG
* * *
37285891 TGTCATCATGAGTATATGAATCTTTTACGGATTATGAGATCCGATGACTATGTGTCATCGTGAGT
66 TGTCATCGTGAGTATATGAATCTTTTACGGATTATGAGGTCCAATGACTATGTGTCATCGTGAGT
*
37285956 ATCCTTTACGGATTATGAGG
131 ATCCTTTACGGATTATAAGG
*
37285976 TCCGATGACTATGTGTCATCGTTG-GTATATGAATCCTTTACAGATTATGAGGTCCGATGACTAT
1 TCCGATGACTATGTGTCATCG-TGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTAT
* * * * *
37286040 GTGTCATCGTGAGCATATGGATCCTTTTTCGGATT-TAAGGTCCAATGACTTTGTGTCATCGTGA
65 GTGTCATCGTGAGTATATGAAT-CTTTTACGGATTATGAGGTCCAATGACTATGTGTCATCGTGA
37286104 GTAT
129 GTAT
37286108 TAAATGCAAA
Statistics
Matches: 254, Mismatches: 26, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
150 124 0.49
151 13 0.05
152 1 0.00
156 116 0.46
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (150 bp):
TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATG
TGTCATCGTGAGTATATGAATCTTTTACGGATTATGAGGTCCAATGACTATGTGTCATCGTGAGT
ATCCTTTACGGATTATAAGG
Found at i:37287549 original size:14 final size:14
Alignment explanation
Indices: 37287530--37287556 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
37287520 ATGTTGTTTA
37287530 ATAGATGAACAGTG
1 ATAGATGAACAGTG
37287544 ATAGATGAACAGT
1 ATAGATGAACAGT
37287557 AGGATACCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.26, T:0.22
Consensus pattern (14 bp):
ATAGATGAACAGTG
Found at i:37288170 original size:14 final size:15
Alignment explanation
Indices: 37288151--37288184 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
37288141 TAATTATTAT
37288151 TTTTAATTAAAT-AA
1 TTTTAATTAAATGAA
*
37288165 TTTTAATTAATTGAA
1 TTTTAATTAAATGAA
37288180 TTTTA
1 TTTTA
37288185 TAAATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
TTTTAATTAAATGAA
Found at i:37305371 original size:17 final size:18
Alignment explanation
Indices: 37305335--37305372 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
37305325 TATCAACGAC
* *
37305335 ATTGAATTTTTTTACAAA
1 ATTGAAATTCTTTACAAA
37305353 ATTGAAATTCTTT-CAAA
1 ATTGAAATTCTTTACAAA
37305370 ATT
1 ATT
37305373 ATTGAATCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.47
Consensus pattern (18 bp):
ATTGAAATTCTTTACAAA
Found at i:37305672 original size:20 final size:20
Alignment explanation
Indices: 37305606--37305679 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
37305596 ACTATTTATT
*
37305606 TTACAAAATTACCT-AATTTC
1 TTACAAAATTA-TTAAATTTC
* **
37305626 TTA-AAAATAATTGGA-TTC
1 TTACAAAATTATTAAATTTC
*
37305644 GTTATAAAATTATTAAATTTC
1 -TTACAAAATTATTAAATTTC
37305665 TTACAAAATTATTAA
1 TTACAAAATTATTAA
37305680 GTTTTGTTGG
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
18 4 0.09
19 10 0.23
20 26 0.60
21 3 0.07
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (20 bp):
TTACAAAATTATTAAATTTC
Found at i:37306606 original size:20 final size:20
Alignment explanation
Indices: 37306580--37306633 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
37306570 TATTATAGAA
*
37306580 TTACTAAATTTCTTATAAGAT
1 TTACTAAATTTCTTACAA-AT
*
37306601 TT-CTAAATTTATTACAAAT
1 TTACTAAATTTCTTACAAAT
37306620 TTACTAAATTTCTT
1 TTACTAAATTTCTT
37306634 TTAATATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 23 0.79
21 2 0.07
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (20 bp):
TTACTAAATTTCTTACAAAT
Found at i:37315556 original size:19 final size:19
Alignment explanation
Indices: 37315532--37315569 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
37315522 AACGGTTAGG
37315532 GTTTCCAAAGATTGAATTT
1 GTTTCCAAAGATTGAATTT
37315551 GTTTCCAAAGATTGAATTT
1 GTTTCCAAAGATTGAATTT
37315570 TGCTATAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (19 bp):
GTTTCCAAAGATTGAATTT
Found at i:37315997 original size:17 final size:17
Alignment explanation
Indices: 37315977--37316010 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
37315967 TTAATTTATT
37315977 ATTAAATTAAATTATAA
1 ATTAAATTAAATTATAA
* *
37315994 ATTACATTATATTATAA
1 ATTAAATTAAATTATAA
37316011 TATAATTGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTAAATTAAATTATAA
Found at i:37316286 original size:20 final size:20
Alignment explanation
Indices: 37316261--37316298 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
37316251 TATATTTGAA
37316261 ATGTTA-CATTTTAGTTACTT
1 ATGTTATCATTTT-GTTACTT
37316281 ATGTTATCATTTTGTTAC
1 ATGTTATCATTTTGTTAC
37316299 GAAGTAGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.55
Consensus pattern (20 bp):
ATGTTATCATTTTGTTACTT
Found at i:37320659 original size:19 final size:20
Alignment explanation
Indices: 37320635--37320672 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
37320625 GACTTCAGTC
37320635 TGCAGACCAAAG-AATCATG
1 TGCAGACCAAAGTAATCATG
37320654 TGCAGACCAAAGTAATCAT
1 TGCAGACCAAAGTAATCAT
37320673 ATTCTACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
TGCAGACCAAAGTAATCATG
Found at i:37325912 original size:24 final size:24
Alignment explanation
Indices: 37325880--37325951 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
37325870 TTGACTCAAG
*
37325880 CAAATAAACAGAGTTTAATTGAAA
1 CAAACAAACAGAGTTTAATTGAAA
* *
37325904 CAACCAAACATAGTTTAATTGAAA
1 CAAACAAACAGAGTTTAATTGAAA
* *
37325928 CAAATAAACAGAGTTTAACTGAAA
1 CAAACAAACAGAGTTTAATTGAAA
37325952 GATTATTTCT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.53, C:0.12, G:0.11, T:0.24
Consensus pattern (24 bp):
CAAACAAACAGAGTTTAATTGAAA
Found at i:37333534 original size:52 final size:52
Alignment explanation
Indices: 37333453--37333692 Score: 317
Period size: 52 Copynumber: 4.6 Consensus size: 52
37333443 TAAATGAAAA
* *
37333453 AAGGTCCGATGACTAAGTGTCATCATGAGTACATGATTCCTTCATGGATTAT
1 AAGGTCCGATGACTAAGTGTCATCGTGAGTACATGAATCCTTCATGGATTAT
* * *
37333505 AAGGTCCGATGACTAAGTGTCATCGTGAGTGCATAAATCCTTCGTGGATTAT
1 AAGGTCCGATGACTAAGTGTCATCGTGAGTACATGAATCCTTCATGGATTAT
* *
37333557 AAGGTCCGATGACTAAGTGTCACCGTGAGTACATGAATCCTTCACGGATTAT
1 AAGGTCCGATGACTAAGTGTCATCGTGAGTACATGAATCCTTCATGGATTAT
* **
37333609 AAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATTTCCTTACA--GAACA-
1 AAGGTCCGATGACTAAGTGTCATCGTGAGTACATGAA--TCCTT-CATGGATTAT
37333661 AGAGGTCCGATGACTATA-TGTCATCGTGAGTA
1 A-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
37333693 TTAAACGTAA
Statistics
Matches: 169, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
52 130 0.77
53 31 0.18
54 6 0.04
55 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (52 bp):
AAGGTCCGATGACTAAGTGTCATCGTGAGTACATGAATCCTTCATGGATTAT
Found at i:37336861 original size:30 final size:30
Alignment explanation
Indices: 37336825--37336886 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
37336815 TCTCTCAAGT
*
37336825 ATGGTTCGATTTAAGGCAATGGAGGAGTGA
1 ATGGTTCGATTAAAGGCAATGGAGGAGTGA
*
37336855 ATGGTTCGATTAAAGGCGATGGAGGAGTGA
1 ATGGTTCGATTAAAGGCAATGGAGGAGTGA
37336885 AT
1 AT
37336887 AGATTGCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.31, C:0.06, G:0.37, T:0.26
Consensus pattern (30 bp):
ATGGTTCGATTAAAGGCAATGGAGGAGTGA
Found at i:37346726 original size:60 final size:60
Alignment explanation
Indices: 37346612--37346729 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 60
37346602 TTTCAATTCG
* * * *
37346612 CATTTGATACTCACGATGACACAGAGTCATCGAACCTTTAATCTGTAATGGGATTCATTT
1 CATTTAATACTCACGATGACACAGAATCATCGAACCTTTAATCCGTAATAGGATTCATTT
* * *
37346672 CATTTAATACTCATGATGACACATAATCATCGGACCTCTTAATCCGTAA-AGGATTCAT
1 CATTTAATACTCACGATGACACAGAATCATCGAACCT-TTAATCCGTAATAGGATTCAT
37346730 ATACTCACGA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 40 0.80
61 10 0.20
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (60 bp):
CATTTAATACTCACGATGACACAGAATCATCGAACCTTTAATCCGTAATAGGATTCATTT
Found at i:37346751 original size:52 final size:52
Alignment explanation
Indices: 37346678--37346813 Score: 211
Period size: 52 Copynumber: 2.6 Consensus size: 52
37346668 ATTTCATTTA
* *
37346678 ATACTCATGATGACACATAATCATCGGACCTCT-TAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAATCATCGGACCT-TATAATCCGTAAAAGATTCAT
**
37346730 ATACTCACGATGACACATAATCATCGGACCTTATAATTTGTAAAAGATTCAT
1 ATACTCACGATGACACATAATCATCGGACCTTATAATCCGTAAAAGATTCAT
*
37346782 ATACTCACGATGACACATAGTCATCGGACCTT
1 ATACTCACGATGACACATAATCATCGGACCTT
37346814 TTTCATTTAC
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
51 1 0.01
52 77 0.99
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (52 bp):
ATACTCACGATGACACATAATCATCGGACCTTATAATCCGTAAAAGATTCAT
Found at i:37348320 original size:29 final size:28
Alignment explanation
Indices: 37348253--37348564 Score: 273
Period size: 29 Copynumber: 10.4 Consensus size: 28
37348243 AAATTTATGG
* * *
37348253 AAAGGTTATATTCGAAATGGATGTCAAATGA
1 AAAGGTTATATCCG-AATGGATATC--TTGA
*
37348284 AAAAGTTATATCCGAATGGATATTCTTGA
1 AAAGGTTATATCCGAATGGATA-TCTTGA
*
37348313 AAAGGTTATATCCGAAATGGATATCAAATGA
1 AAAGGTTATATCCG-AATGGATATC--TTGA
*
37348344 AAAGGTTATATCCGAATGGATATTATTGA
1 AAAGGTTATATCCGAATGGATA-TCTTGA
* *
37348373 AAATGTTATATCCGAAATGGATATCAATTGT
1 AAAGGTTATATCCG-AATGGATATC--TTGA
** * *
37348404 AAAGGTTATATTCAAAATGGATATCAAATGT
1 AAAGGTTATA-TCCGAATGGATATC--TTGA
** *
37348435 AAAGGTTATATTTGAATGGATATTCGTGA
1 AAAGGTTATATCCGAATGGATA-TCTTGA
37348464 AAAGGTTATATCCGAATGGATATTCTTGA
1 AAAGGTTATATCCGAATGGATA-TCTTGA
* * *
37348493 AAAGGTTATATCCGAAATGAATATCAAATGT
1 AAAGGTTATATCCG-AATGGATATC--TTGA
*
37348524 GAAGGTTATATCCGAATGGATACTCTTGA
1 AAAGGTTATATCCGAATGGATA-TCTTGA
37348553 AAAGGTTATATC
1 AAAGGTTATATC
37348565 TGAAAAGGAT
Statistics
Matches: 236, Mismatches: 31, Indels: 30
0.79 0.10 0.10
Matches are distributed among these distances:
29 92 0.39
30 54 0.23
31 88 0.37
32 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (28 bp):
AAAGGTTATATCCGAATGGATATCTTGA
Found at i:37348346 original size:60 final size:60
Alignment explanation
Indices: 37348253--37348574 Score: 400
Period size: 60 Copynumber: 5.4 Consensus size: 60
37348243 AAATTTATGG
* * *
37348253 AAAGGTTATATTCGAAATGGATGTCAAATGAAAAAGTTATATCCGAATGGATATTCTTGA
1 AAAGGTTATATCCGAAATGGATATCAAATGAAAAGGTTATATCCGAATGGATATTCTTGA
*
37348313 AAAGGTTATATCCGAAATGGATATCAAATGAAAAGGTTATATCCGAATGGATATTATTGA
1 AAAGGTTATATCCGAAATGGATATCAAATGAAAAGGTTATATCCGAATGGATATTCTTGA
* * * ** * *
37348373 AAATGTTATATCCGAAATGGATATCAATTGTAAAGGTTATATTCAAAATGGATA-TCAAATGT
1 AAAGGTTATATCCGAAATGGATATCAAATGAAAAGGTTATA-TCCGAATGGATATTC--TTGA
** *
37348435 AAAGGTTATATTTG-AATGGATATTC--GTGAAAAGGTTATATCCGAATGGATATTCTTGA
1 AAAGGTTATATCCGAAATGGATA-TCAAATGAAAAGGTTATATCCGAATGGATATTCTTGA
* ** *
37348493 AAAGGTTATATCCGAAATGAATATCAAATGTGAAGGTTATATCCGAATGGATACTCTTGA
1 AAAGGTTATATCCGAAATGGATATCAAATGAAAAGGTTATATCCGAATGGATATTCTTGA
* *
37348553 AAAGGTTATATCTGAAAAGGAT
1 AAAGGTTATATCCGAAATGGAT
37348575 TAACATACGA
Statistics
Matches: 223, Mismatches: 31, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
58 16 0.07
59 17 0.08
60 157 0.70
61 18 0.08
62 15 0.07
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (60 bp):
AAAGGTTATATCCGAAATGGATATCAAATGAAAAGGTTATATCCGAATGGATATTCTTGA
Found at i:37353364 original size:27 final size:29
Alignment explanation
Indices: 37353334--37353395 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 29
37353324 AAATAAAATA
* *
37353334 AAAAACTT-AAA-AACATATTTGTTAATT
1 AAAAACTTAAAATAACAAATTTATTAATT
37353361 AAAAACTTGAAAATAACAAATTTATTAATT
1 AAAAACTT-AAAATAACAAATTTATTAATT
37353391 AAAAA
1 AAAAA
37353396 AATAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 8 0.27
29 3 0.10
30 19 0.63
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.32
Consensus pattern (29 bp):
AAAAACTTAAAATAACAAATTTATTAATT
Found at i:37358875 original size:68 final size:68
Alignment explanation
Indices: 37358720--37358875 Score: 231
Period size: 68 Copynumber: 2.3 Consensus size: 68
37358710 ATATGTGCTA
* * * * *
37358720 CTTTGGACAGCATAAATCAACAAATAAAACAGGGCATTAAACAGCAATAACACCATTAATATGTC
1 CTTTGGACAACATAAATCAGCAAACAAAACAGAGCATGAAACAGCAATAACACCATTAATATGTC
37358785 TGG
66 TGG
** * *
37358788 CTTTGGACAACATAAATCAGCAAACAAAACAGAGCATGAAACAGTTATAGCACCATTAATATGTG
1 CTTTGGACAACATAAATCAGCAAACAAAACAGAGCATGAAACAGCAATAACACCATTAATATGTC
37358853 TGG
66 TGG
37358856 CTTTGGACAACATAAATCAG
1 CTTTGGACAACATAAATCAG
37358876 TAACAATGCA
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 79 1.00
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (68 bp):
CTTTGGACAACATAAATCAGCAAACAAAACAGAGCATGAAACAGCAATAACACCATTAATATGTC
TGG
Found at i:37361091 original size:21 final size:20
Alignment explanation
Indices: 37361057--37361096 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
37361047 AATTTTAGGA
*
37361057 AAATTTTTATTTTAAAAAAT
1 AAATTTTTAATTTAAAAAAT
37361077 AAATATTTTAATTTATAAAA
1 AAAT-TTTTAATTTA-AAAA
37361097 CTTTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 9 0.53
22 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTTTTAATTTAAAAAAT
Found at i:37365237 original size:3 final size:3
Alignment explanation
Indices: 37365229--37365270 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
37365219 GGATCAGTAC
37365229 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
37365271 GAAACCAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:37365584 original size:36 final size:35
Alignment explanation
Indices: 37365537--37365607 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
37365527 TTGCCACCTT
37365537 CCATTCCTGATATTAAGAGAGCAAAAGGAAGAGGAA
1 CCATTCCTGATATTAAGAGAGCAAAAGGAAG-GGAA
*
37365573 CCATTCTTGATATTAAGAGAGCAAAAGGAAGGGAA
1 CCATTCCTGATATTAAGAGAGCAAAAGGAAGGGAA
37365608 AAACGAGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 4 0.12
36 30 0.88
ACGTcount: A:0.44, C:0.13, G:0.25, T:0.18
Consensus pattern (35 bp):
CCATTCCTGATATTAAGAGAGCAAAAGGAAGGGAA
Found at i:37368080 original size:16 final size:16
Alignment explanation
Indices: 37368059--37368089 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
37368049 ATATGAAAAA
37368059 TCTCATAAAAGGAAAT
1 TCTCATAAAAGGAAAT
37368075 TCTCATAAAAGGAAA
1 TCTCATAAAAGGAAA
37368090 AAATCTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.23
Consensus pattern (16 bp):
TCTCATAAAAGGAAAT
Found at i:37369803 original size:24 final size:22
Alignment explanation
Indices: 37369751--37369806 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
37369741 TAAATATTAA
*
37369751 ATTGATTTAATTAATTTAATTT
1 ATTGATTTAATTAAATTAATTT
*
37369773 AGCTTGATTTAATTCAAATTGATTT
1 A--TTGATTTAATT-AAATTAATTT
37369798 CATTGATTT
1 -ATTGATTT
37369807 TTAATGGATC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 1 0.04
24 18 0.64
25 8 0.29
26 1 0.04
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.54
Consensus pattern (22 bp):
ATTGATTTAATTAAATTAATTT
Found at i:37376468 original size:37 final size:37
Alignment explanation
Indices: 37376399--37376531 Score: 151
Period size: 37 Copynumber: 3.6 Consensus size: 37
37376389 CTACACAAAG
* * * * *
37376399 GCCTGCTAGGCATATAGCCCGAGTACACCGACACGAA
1 GCCTACTAGGCACATAGCTCGAATACATCGACACGAA
* * *
37376436 GTCTAATAGGCACATAGCTCGAATACATCGACATGAA
1 GCCTACTAGGCACATAGCTCGAATACATCGACACGAA
* * *
37376473 GCCTACTAGGCACATAGC-CTAAATACATCGGCACTAA
1 GCCTACTAGGCACATAGCTC-GAATACATCGACACGAA
37376510 GCCTACTAGGCACATAGCTCGA
1 GCCTACTAGGCACATAGCTCGA
37376532 TTTACTTAAA
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
36 1 0.01
37 77 0.97
38 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (37 bp):
GCCTACTAGGCACATAGCTCGAATACATCGACACGAA
Found at i:37379858 original size:68 final size:68
Alignment explanation
Indices: 37379748--37379902 Score: 204
Period size: 68 Copynumber: 2.3 Consensus size: 68
37379738 ATATGTGCTA
* * * * *
37379748 CTTTGGACAGCATAAATAAGCAAATACAACAGGGCATTAAACAACAATAACACCATTAATATGTC
1 CTTTGGACAACATAAATCAGCAAACACAACAGAGCATGAAACAACAATAACACCATTAATATGTC
37379813 TGG
66 TGG
*** *
37379816 CTTTGGACAACATAAATCAGCAAACA-AAGCAGAGCATGAAACAGTTATAGCACCATTAATATGT
1 CTTTGGACAACATAAATCAGCAAACACAA-CAGAGCATGAAACAACAATAACACCATTAATATGT
*
37379880 GTGG
65 CTGG
37379884 CTTTGGACAACATAAATCA
1 CTTTGGACAACATAAATCA
37379903 TTAACAATGC
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
67 2 0.03
68 74 0.97
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.23
Consensus pattern (68 bp):
CTTTGGACAACATAAATCAGCAAACACAACAGAGCATGAAACAACAATAACACCATTAATATGTC
TGG
Found at i:37383458 original size:20 final size:17
Alignment explanation
Indices: 37383416--37383449 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
37383406 ATTGTGTCTC
*
37383416 ATTTTTTTTATATATTA
1 ATTTTTTTAATATATTA
37383433 ATTTTTTTAATATATTA
1 ATTTTTTTAATATATTA
37383450 CTATATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTTTTAATATATTA
Found at i:37388690 original size:38 final size:37
Alignment explanation
Indices: 37388647--37388730 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 37
37388637 ATTTCTAGAA
37388647 TGCATCCA-AGACCGTCT-CTGCATAAATATTCTTCAAAT
1 TGCATCCAGA-ACCGT-TGCTGCATAAATATTCTTC-AAT
* *
37388685 TGCATCCAGAACTGTTGCTGCATAAGTATTCTTCAAT
1 TGCATCCAGAACCGTTGCTGCATAAATATTCTTCAAT
*
37388722 TGCACCCAG
1 TGCATCCAG
37388731 GAATGTCACT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
37 12 0.29
38 28 0.68
39 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (37 bp):
TGCATCCAGAACCGTTGCTGCATAAATATTCTTCAAT
Found at i:37388743 original size:37 final size:38
Alignment explanation
Indices: 37388664--37388744 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 38
37388654 AAGACCGTCT
* **
37388664 CTGCATAAATATTCTTCAAATTGCATCCAGAACTGTTG
1 CTGCATAAATATTCTTCAAATTGCACCCAGAACTGTCA
*
37388702 CTGCATAAGTATTCTTC-AATTGCACCCAGGAA-TGTCA
1 CTGCATAAATATTCTTCAAATTGCACCCA-GAACTGTCA
37388739 CTGCAT
1 CTGCAT
37388745 GAACATGTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 19 0.50
38 19 0.50
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (38 bp):
CTGCATAAATATTCTTCAAATTGCACCCAGAACTGTCA
Found at i:37388763 original size:26 final size:26
Alignment explanation
Indices: 37388727--37388784 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
37388717 TCAATTGCAC
*
37388727 CCAGGAATGTCACTGCATGAACATGT
1 CCAGAAATGTCACTGCATGAACATGT
*
37388753 CCAGAAATGTCGCTGCATGAACATGT
1 CCAGAAATGTCACTGCATGAACATGT
*
37388779 CTAGAA
1 CCAGAA
37388785 TTGTGCCCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (26 bp):
CCAGAAATGTCACTGCATGAACATGT
Found at i:37396333 original size:46 final size:46
Alignment explanation
Indices: 37396281--37396374 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
37396271 TTTTTATCTG
*
37396281 ACATATAATAGAAAATAGAGGTGATGTCGCTTACCTGACGGCCTCC
1 ACATATAATAGAAAATAGAGGTGATGTCGCTTACCTGACAGCCTCC
* *
37396327 ACATATAATAGAAAATAGGGGTGATGTCGCTTACCTGATAGCCTCC
1 ACATATAATAGAAAATAGAGGTGATGTCGCTTACCTGACAGCCTCC
37396373 AC
1 AC
37396375 TACCTCAAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (46 bp):
ACATATAATAGAAAATAGAGGTGATGTCGCTTACCTGACAGCCTCC
Found at i:37396674 original size:22 final size:22
Alignment explanation
Indices: 37396644--37396686 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
37396634 TATCCAAACA
*
37396644 ATAATAACAAAATAGCAACAAT
1 ATAACAACAAAATAGCAACAAT
*
37396666 ATAACAACAAAATAGTAACAA
1 ATAACAACAAAATAGCAACAA
37396687 AACAATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.65, C:0.14, G:0.05, T:0.16
Consensus pattern (22 bp):
ATAACAACAAAATAGCAACAAT
Found at i:37396693 original size:14 final size:14
Alignment explanation
Indices: 37396659--37396696 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
37396649 AACAAAATAG
37396659 CAACAATATAACAA
1 CAACAATATAACAA
37396673 CAA-AATAGTAACAA
1 CAACAATA-TAACAA
37396687 -AACAATATAA
1 CAACAATATAA
37396697 AAAAGGCAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.66, C:0.16, G:0.03, T:0.16
Consensus pattern (14 bp):
CAACAATATAACAA
Found at i:37401194 original size:12 final size:12
Alignment explanation
Indices: 37401179--37401203 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37401169 ATTAAAGAAT
37401179 TAATAGCATTCA
1 TAATAGCATTCA
37401191 TAATAGCATTCA
1 TAATAGCATTCA
37401203 T
1 T
37401204 CATGATAATA
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATAGCATTCA
Found at i:37403324 original size:19 final size:19
Alignment explanation
Indices: 37403286--37403324 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
37403276 ATGTCCTCAT
*
37403286 TGTTAAAAACAATAGAGAA
1 TGTTAAAAACAAAAGAGAA
*
37403305 TGTTAAAAACAAAAGTGAA
1 TGTTAAAAACAAAAGAGAA
37403324 T
1 T
37403325 AAATACTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.15, T:0.23
Consensus pattern (19 bp):
TGTTAAAAACAAAAGAGAA
Found at i:37404026 original size:21 final size:21
Alignment explanation
Indices: 37404002--37404049 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
37403992 CTTAGGATCC
*
37404002 TCTTCTGGATCTTTTTCTTCT
1 TCTTCTGGATCTTCTTCTTCT
* *
37404023 TCTTCAGGGTCTTCTTCTTCT
1 TCTTCTGGATCTTCTTCTTCT
37404044 TCTTCT
1 TCTTCT
37404050 TCTTCAGCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.04, C:0.27, G:0.10, T:0.58
Consensus pattern (21 bp):
TCTTCTGGATCTTCTTCTTCT
Found at i:37404965 original size:16 final size:17
Alignment explanation
Indices: 37404946--37404991 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
37404936 AACTATTTAA
*
37404946 AATAAATTAAA-AAGTT
1 AATAAATTAAAGAAATT
37404962 AATAAATTAAAGAAATT
1 AATAAATTAAAGAAATT
37404979 AA-AAATTAGAAGA
1 AATAAATTA-AAGA
37404992 TAAATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (17 bp):
AATAAATTAAAGAAATT
Found at i:37406347 original size:12 final size:12
Alignment explanation
Indices: 37406330--37406354 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37406320 TGTTATCATG
37406330 ATGAATGCTATT
1 ATGAATGCTATT
37406342 ATGAATGCTATT
1 ATGAATGCTATT
37406354 A
1 A
37406355 ATTCTTTAAT
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:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:37409807 original size:24 final size:24
Alignment explanation
Indices: 37409774--37409828 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
37409764 GTTAAGAGTA
37409774 AAAATTGTCAGTGCAAAAGTAATAT
1 AAAA-TGTCAGTGCAAAAGTAATAT
**
37409799 AAAATGTCAGTGCAACTGTAATAT
1 AAAATGTCAGTGCAAAAGTAATAT
37409823 AAAATG
1 AAAATG
37409829 AATTGATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.27
Consensus pattern (24 bp):
AAAATGTCAGTGCAAAAGTAATAT
Found at i:37411400 original size:13 final size:12
Alignment explanation
Indices: 37411370--37411403 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
37411360 TATATATATA
37411370 TTTTTCTTTCTT
1 TTTTTCTTTCTT
*
37411382 TATTTCTTTCCTT
1 TTTTTCTTT-CTT
37411395 TTTTTCTTT
1 TTTTTCTTT
37411404 TATACGACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:37412085 original size:3 final size:3
Alignment explanation
Indices: 37412077--37412151 Score: 61
Period size: 3 Copynumber: 25.7 Consensus size: 3
37412067 TGAGGCAATA
*
37412077 TCT TCT TCT TTT TCT TCCT TCT TCT TCT TCT TCT T-T TCTT TCT TC-
1 TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT TC-T TCT TCT
* *
37412122 TCT T-T T-T TCT TGT TCT T-T TCCT TTT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT T-CT TCT TCT TC
37412152 CTCTGCCTCA
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
2 10 0.17
3 41 0.69
4 8 0.14
ACGTcount: A:0.00, C:0.28, G:0.01, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:37412149 original size:30 final size:30
Alignment explanation
Indices: 37412077--37412153 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 30
37412067 TGAGGCAATA
37412077 TCTTCTTCTTTTTCTTCCTTCTTCTTCTTCT
1 TCTT-TTCTTTTTCTTCCTTCTTCTTCTTCT
*
37412108 TCTTTTC--TTTCTTCTCTT-TT-TTCTTGT
1 TCTTTTCTTTTTCTTC-CTTCTTCTTCTTCT
37412135 TCTTTTCCTTTTTCTTCCT
1 TCTTTT-CTTTTTCTTCCT
37412154 CTGCCTCAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
27 12 0.29
28 10 0.24
29 5 0.12
30 10 0.24
31 4 0.10
ACGTcount: A:0.00, C:0.29, G:0.01, T:0.70
Consensus pattern (30 bp):
TCTTTTCTTTTTCTTCCTTCTTCTTCTTCT
Found at i:37419947 original size:24 final size:24
Alignment explanation
Indices: 37419914--37419968 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
37419904 GTTAAGAGTA
37419914 AAAATTGTCAGTGCAAAAGTAATAT
1 AAAA-TGTCAGTGCAAAAGTAATAT
**
37419939 AAAATGTCAGTGCAACTGTAATAT
1 AAAATGTCAGTGCAAAAGTAATAT
37419963 AAAATG
1 AAAATG
37419969 AATTGATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.27
Consensus pattern (24 bp):
AAAATGTCAGTGCAAAAGTAATAT
Found at i:37425669 original size:3 final size:3
Alignment explanation
Indices: 37425651--37425777 Score: 86
Period size: 3 Copynumber: 42.7 Consensus size: 3
37425641 AGCAACATAG
*
37425651 ATA ATA A-A A-A AAA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
37425695 ATA ATA ATA AT- ATA ACTA CGATG ATA GTA GTA ATA ACA TTA ATCA A-A
1 ATA ATA ATA ATA ATA A-TA --ATA ATA ATA ATA ATA ATA ATA AT-A ATA
* * *
37425742 GATG ATA ATA ATA AAA ATA ATA ATA ACA ATA ATA AT
1 -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
37425778 TATTATAATC
Statistics
Matches: 99, Mismatches: 15, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
2 11 0.11
3 82 0.83
4 4 0.04
5 1 0.01
6 1 0.01
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:37425689 original size:11 final size:11
Alignment explanation
Indices: 37425663--37425709 Score: 85
Period size: 11 Copynumber: 4.2 Consensus size: 11
37425653 AATAAAAAAA
37425663 AATAATAATAAT
1 AATAATAAT-AT
37425675 AATAATAATAT
1 AATAATAATAT
37425686 AATAATAATAT
1 AATAATAATAT
37425697 AATAATAATAT
1 AATAATAATAT
37425708 AA
1 AA
37425710 CTACGATGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 26 0.74
12 9 0.26
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AATAATAATAT
Found at i:37425689 original size:14 final size:14
Alignment explanation
Indices: 37425667--37425706 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
37425657 AAAAAAAATA
37425667 ATAATAATAATAAT
1 ATAATAATAATAAT
37425681 A-ATATAATAATAAT
1 ATA-ATAATAATAAT
37425695 ATAATAATAATA
1 ATAATAATAATA
37425707 TAACTACGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.04
14 22 0.92
15 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:37425765 original size:28 final size:28
Alignment explanation
Indices: 37425664--37425765 Score: 84
Period size: 28 Copynumber: 3.7 Consensus size: 28
37425654 ATAAAAAAAA
* *
37425664 ATAATAATAATAATAATAAT-ATA-ATA
1 ATAATAATAATAATAATAATCAAAGATG
* * *
37425690 ATAAT-ATAATAATAATATAACTACGATG
1 ATAATAATAATAATAATA-ATCAAAGATG
* * * *
37425718 ATAGTAGTAATAACATTAATCAAAGATG
1 ATAATAATAATAATAATAATCAAAGATG
*
37425746 ATAATAATAAAAATAATAAT
1 ATAATAATAATAATAATAAT
37425766 AACAATAATA
Statistics
Matches: 55, Mismatches: 17, Indels: 6
0.71 0.22 0.08
Matches are distributed among these distances:
25 12 0.22
26 6 0.11
28 28 0.51
29 9 0.16
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (28 bp):
ATAATAATAATAATAATAATCAAAGATG
Found at i:37433226 original size:15 final size:15
Alignment explanation
Indices: 37433208--37433248 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
37433198 AACTTCCTCT
*
37433208 TTTTCTTCTTCTTTC
1 TTTTCTTCTTCTTTA
37433223 TTTTCTTCTTCTTTA
1 TTTTCTTCTTCTTTA
*
37433238 TTCTCTTCTTC
1 TTTTCTTCTTC
37433249 CTCGATACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTCTTCTTCTTTA
Found at i:37433233 original size:18 final size:18
Alignment explanation
Indices: 37433204--37433248 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
37433194 CAAAAACTTC
*
37433204 CTCTTTTTCTTCTTCT-TT
1 CTCTTCTTCTTCTT-TATT
*
37433222 CTTTTCTTCTTCTTTATT
1 CTCTTCTTCTTCTTTATT
37433240 CTCTTCTTC
1 CTCTTCTTC
37433249 CTCGATACCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (18 bp):
CTCTTCTTCTTCTTTATT
Found at i:37439410 original size:18 final size:18
Alignment explanation
Indices: 37439389--37439430 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
37439379 ACCGCATACA
* *
37439389 AGCATGTGATTGCATCTG
1 AGCATGTGACTACATCTG
37439407 AGCATGTGACTACATCTG
1 AGCATGTGACTACATCTG
*
37439425 ATCATG
1 AGCATG
37439431 ATGTGCTTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (18 bp):
AGCATGTGACTACATCTG
Found at i:37454006 original size:98 final size:99
Alignment explanation
Indices: 37453756--37454011 Score: 220
Period size: 101 Copynumber: 2.6 Consensus size: 99
37453746 CCAATCCACT
* * * * * * *
37453756 GCAACTTCAAGGACATAGGATTTGATGTTGTAGCTTCATATTGCTCCACTACAACTTCAAGGAGA
1 GCAACTTCAAGGATATAGGATTT-AGGTTGTAGCTTTATCTTGCTTCACTGCAACTTCAAAGAGA
* *
37453821 TAAAAATTTGCTTTCATGACTTTAATCTGACTCACA
65 TAAAAATTTGCTGTCAT-ACTTCAATCTGACTCACA
* * * * * *
37453857 GAAACTTTAGGGGTATAGGATTT-GGTTTTGTAGCTTCT-TCCTAC-TCTACTGCAACTTCAAAG
1 GCAACTTCAAGGATATAGGATTTAGG--TTGTAGCTT-TATCTTGCTTC-ACTGCAACTTCAAAG
* *
37453919 AGATAAGAATTTGCTCGT-AT-CTTCAATCTGA-TC-CTT
62 AGATAAAAATTTGCT-GTCATACTTCAATCTGACTCAC-A
*
37453955 TCAACTTCAAGGATATAGGATTTAGGCTTGTAGCTTTATCTTGCTTCACTGCAACTT
1 GCAACTTCAAGGATATAGGATTTAGG-TTGTAGCTTTATCTTGCTTCACTGCAACTT
37454012 TAGGGAGATA
Statistics
Matches: 121, Mismatches: 25, Indels: 21
0.72 0.15 0.13
Matches are distributed among these distances:
97 2 0.02
98 43 0.36
99 15 0.12
100 1 0.01
101 59 0.49
102 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (99 bp):
GCAACTTCAAGGATATAGGATTTAGGTTGTAGCTTTATCTTGCTTCACTGCAACTTCAAAGAGAT
AAAAATTTGCTGTCATACTTCAATCTGACTCACA
Found at i:37455203 original size:18 final size:19
Alignment explanation
Indices: 37455180--37455222 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
37455170 TCTTATTTTC
*
37455180 TTTTTTCTTTCTTTC-CTT
1 TTTTTTCCTTCTTTCTCTT
*
37455198 TTTTTTCCTTGTTTCTCTT
1 TTTTTTCCTTCTTTCTCTT
37455217 TTTTTT
1 TTTTTT
37455223 GCGTTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTTTCCTTCTTTCTCTT
Found at i:37455922 original size:64 final size:64
Alignment explanation
Indices: 37455807--37455927 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 64
37455797 AGATACATAT
**
37455807 TTTCAAGATGCCCTTTGCGGGTTTTCATCTTGACTTTTTTTCTTTTCTTTCTTCTTTCCTTGGG
1 TTTCAAGATGCCCTTTGCGGGTTTTCATCTTGACCCTTTTTCTTTTCTTTCTTCTTTCCTTGGG
** *
37455871 TTTCAAGATGCCCTTTGCGATTTTTTTTATCTTGACCCTTTTTC-TTT-TTTCTTCTTT
1 TTTCAAGATGCCCTTTGCG--GGTTTTCATCTTGACCCTTTTTCTTTTCTTTCTTCTTT
37455928 TTTTACCTCC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
64 29 0.58
65 3 0.06
66 18 0.36
ACGTcount: A:0.09, C:0.21, G:0.12, T:0.57
Consensus pattern (64 bp):
TTTCAAGATGCCCTTTGCGGGTTTTCATCTTGACCCTTTTTCTTTTCTTTCTTCTTTCCTTGGG
Found at i:37456415 original size:16 final size:16
Alignment explanation
Indices: 37456394--37456434 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
37456384 AAAAGGGGAT
37456394 TCAAAGAATAATTGAA
1 TCAAAGAATAATTGAA
37456410 TCAAAGAATAATTGAA
1 TCAAAGAATAATTGAA
*
37456426 TTAAAGAAT
1 TCAAAGAAT
37456435 GGTTAATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.27
Consensus pattern (16 bp):
TCAAAGAATAATTGAA
Found at i:37459365 original size:26 final size:25
Alignment explanation
Indices: 37459322--37459391 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 25
37459312 AAAACAAAAT
*
37459322 AAAAGAATTAATTTAAAAAGGATA-A
1 AAAAGATTTAA-TTAAAAAGGATACA
37459347 AAAATGATTTAATTAAAAA-GATACA
1 AAAA-GATTTAATTAAAAAGGATACA
37459372 AAAAGATTTAAATATAAAAA
1 AAAAGATTT-AAT-TAAAAA
37459392 AGAATAGAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
24 9 0.22
25 19 0.47
26 12 0.30
ACGTcount: A:0.64, C:0.01, G:0.09, T:0.26
Consensus pattern (25 bp):
AAAAGATTTAATTAAAAAGGATACA
Found at i:37459558 original size:29 final size:27
Alignment explanation
Indices: 37459506--37459562 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 27
37459496 TATGATTGTA
37459506 TTTAAAAAAAAACAAAAAAGGTTAAAT
1 TTTAAAAAAAAACAAAAAAGGTTAAAT
37459533 TTTAAAAAAAAA-AAAATTAAGAGTTAAAT
1 TTTAAAAAAAAACAAAA--AAG-GTTAAAT
37459562 T
1 T
37459563 AAAATAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 4 0.15
27 12 0.44
28 3 0.11
29 8 0.30
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (27 bp):
TTTAAAAAAAAACAAAAAAGGTTAAAT
Found at i:37459566 original size:24 final size:24
Alignment explanation
Indices: 37459539--37459593 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
37459529 AAATTTTAAA
* *
37459539 AAAAAAAAAATTAAGAGTTAAATT
1 AAAAAAAAAATAAAGAGTTAAAGT
* **
37459563 AAAATAAAAATAAAGTTTTAAAGT
1 AAAAAAAAAATAAAGAGTTAAAGT
37459587 AAAAAAA
1 AAAAAAA
37459594 TAAAAAGGAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (24 bp):
AAAAAAAAAATAAAGAGTTAAAGT
Found at i:37459571 original size:29 final size:26
Alignment explanation
Indices: 37459505--37459572 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
37459495 ATATGATTGT
*
37459505 ATTTAAAAAAAAACAAAAAAGGTTAA
1 ATTTAAAAAAAAAAAAAAAAGGTTAA
*
37459531 ATTTTAAAAAAAAAAAAATTAAGAGTTAA
1 A-TTTAAAAAAAAAAAAA-AAAG-GTTAA
*
37459560 A-TTAAAATAAAAA
1 ATTTAAAAAAAAAA
37459573 TAAAGTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 1 0.03
27 26 0.72
28 3 0.08
29 6 0.17
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.24
Consensus pattern (26 bp):
ATTTAAAAAAAAAAAAAAAAGGTTAA
Found at i:37473240 original size:35 final size:36
Alignment explanation
Indices: 37473194--37473261 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
37473184 TTACCACCTT
*
37473194 CCATTCCTGATATT-CGAGAGCAAAAGGAAGGGGAA
1 CCATTCCTGATATTAAGAGAGCAAAAGGAAGGGGAA
*
37473229 CCATTCTTGATATTAAGAGAGCAAAAGGAAGGG
1 CCATTCCTGATATTAAGAGAGCAAAAGGAAGGG
37473262 AAAAACGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 13 0.43
36 17 0.57
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.19
Consensus pattern (36 bp):
CCATTCCTGATATTAAGAGAGCAAAAGGAAGGGGAA
Found at i:37475162 original size:79 final size:77
Alignment explanation
Indices: 37475076--37475219 Score: 180
Period size: 79 Copynumber: 1.8 Consensus size: 77
37475066 CTGTTTCGGG
* * *
37475076 ATTTATTCCTACAGTTAAACAAAATTTAATCGATTTTTTTTGTTTCCAAATAGAAATTAATTAAA
1 ATTTATTCCTACAGTTAAACAAAATTTAATCGA--GTTTCTGTTTCCAAATAGAAATAAATTAAA
37475141 CATTCTATTTCAAT
64 CATTCTATTTCAAT
* * * * * * *
37475155 ATTTATTCTTGCCGTTCAACAGAATTTAATCGAGTTTCTGTTTTCAAATAGAAATAAATTGAACA
1 ATTTATTCCTACAGTTAAACAAAATTTAATCGAGTTTCTGTTTCCAAATAGAAATAAATTAAACA
37475220 ATTTTGTTTC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
77 27 0.49
79 28 0.51
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (77 bp):
ATTTATTCCTACAGTTAAACAAAATTTAATCGAGTTTCTGTTTCCAAATAGAAATAAATTAAACA
TTCTATTTCAAT
Found at i:37477799 original size:39 final size:40
Alignment explanation
Indices: 37477745--37477843 Score: 155
Period size: 39 Copynumber: 2.5 Consensus size: 40
37477735 TATGCACTCA
37477745 ATGGACACCTTTTGAAGAGTCACAAC-CCTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACTCCTTTCATATTGG
* * *
37477784 ATGGATACCTTTTGAAAAGTCACAACTCTTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACTCCTTTCATATTGG
37477824 ATGGACACCTTTTGGAAGAG
1 ATGGACACCTTTT-GAAGAG
37477844 ACTTGTCCCA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
39 24 0.45
40 24 0.45
41 5 0.09
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (40 bp):
ATGGACACCTTTTGAAGAGTCACAACTCCTTTCATATTGG
Found at i:37477828 original size:40 final size:39
Alignment explanation
Indices: 37477745--37477837 Score: 150
Period size: 40 Copynumber: 2.4 Consensus size: 39
37477735 TATGCACTCA
*
37477745 ATGGACACCTTTTGAAGAGTCACAACCCTTTCATATTGG
1 ATGGACACCTTTTGAAAAGTCACAACCCTTTCATATTGG
* *
37477784 ATGGATACCTTTTGAAAAGTCACAACTCTTTTCATATTGG
1 ATGGACACCTTTTGAAAAGTCACAAC-CCTTTCATATTGG
37477824 ATGGACACCTTTTG
1 ATGGACACCTTTTG
37477838 GAAGAGACTT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 24 0.49
40 25 0.51
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (39 bp):
ATGGACACCTTTTGAAAAGTCACAACCCTTTCATATTGG
Found at i:37482712 original size:39 final size:40
Alignment explanation
Indices: 37482658--37482756 Score: 155
Period size: 39 Copynumber: 2.5 Consensus size: 40
37482648 TATGCACTCA
37482658 ATGGACACCTTTTGAAGAGTCACAACCC-TTTCATATTAG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCATATTAG
* * *
37482697 ATGGATACCTTTTGAAAAGTCACAACCCTTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCATATTAG
37482737 ATGGACACCTTTTGGAAGAG
1 ATGGACACCTTTT-GAAGAG
37482757 ACTTGTCCCA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
39 26 0.49
40 22 0.42
41 5 0.09
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Consensus pattern (40 bp):
ATGGACACCTTTTGAAGAGTCACAACCCTTTTCATATTAG
Found at i:37485450 original size:74 final size:74
Alignment explanation
Indices: 37485346--37485603 Score: 302
Period size: 74 Copynumber: 3.5 Consensus size: 74
37485336 ATAGGCCGAG
* * *
37485346 TACACC-AGCACGAACCCTACTAGGCACATAGCCCGAATACACCGACACGAAGCCTAATAGGCAC
1 TACACCGA-CACGAAGCCTGCTAGGCACATAGCCCGAATACACCGACACGAAGCCTGATAGGCAC
*
37485410 ATAGCCCAAA
65 ATAACCCAAA
* * * * * * *
37485420 TACACCGACACGAAGCTTGCTAGGCACATAGTCTGAATACACTGGCACGAAGACTGCTAGGCACA
1 TACACCGACACGAAGCCTGCTAGGCACATAGCCCGAATACACCGACACGAAGCCTGATAGGCACA
37485485 TAACCCAAA
66 TAACCCAAA
* * * * * * *
37485494 TACACCGGCACGAAACCTGCTAGGCACATAGCCCAAATATACCGATACAAAGCCTGATAGGCATA
1 TACACCGACACGAAGCCTGCTAGGCACATAGCCCGAATACACCGACACGAAGCCTGATAGGCACA
*
37485559 TAACCCGAA
66 TAACCCAAA
* * *
37485568 TACACCGACACAAAGCCTGCTAGGCATATTGCCCGA
1 TACACCGACACGAAGCCTGCTAGGCACATAGCCCGA
37485604 TTTACTTAAA
Statistics
Matches: 151, Mismatches: 32, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
74 150 0.99
75 1 0.01
ACGTcount: A:0.36, C:0.31, G:0.18, T:0.14
Consensus pattern (74 bp):
TACACCGACACGAAGCCTGCTAGGCACATAGCCCGAATACACCGACACGAAGCCTGATAGGCACA
TAACCCAAA
Found at i:37485594 original size:37 final size:37
Alignment explanation
Indices: 37485316--37485603 Score: 265
Period size: 37 Copynumber: 7.8 Consensus size: 37
37485306 TAATCACTGG
* * * *
37485316 CACAAAGGCCTCCTAGGCATATAGGCCGAGTACACC-A
1 CACAAA-GCCTGCTAGGCACATAGCCCGAATACACCGA
* * *
37485353 GCACGAACCCTACTAGGCACATAGCCCGAATACACCGA
1 -CACAAAGCCTGCTAGGCACATAGCCCGAATACACCGA
* ** *
37485391 CACGAAGCCTAATAGGCACATAGCCCAAATACACCGA
1 CACAAAGCCTGCTAGGCACATAGCCCGAATACACCGA
* * * * * *
37485428 CACGAAGCTTGCTAGGCACATAGTCTGAATACACTGG
1 CACAAAGCCTGCTAGGCACATAGCCCGAATACACCGA
* * * * *
37485465 CACGAAGACTGCTAGGCACATAACCCAAATACACCGG
1 CACAAAGCCTGCTAGGCACATAGCCCGAATACACCGA
* *
37485502 CACGAAA-CCTGCTAGGCACATAGCCCAAATATACCGA
1 CAC-AAAGCCTGCTAGGCACATAGCCCGAATACACCGA
* * * *
37485539 TACAAAGCCTGATAGGCATATAACCCGAATACACCGA
1 CACAAAGCCTGCTAGGCACATAGCCCGAATACACCGA
* *
37485576 CACAAAGCCTGCTAGGCATATTGCCCGA
1 CACAAAGCCTGCTAGGCACATAGCCCGA
37485604 TTTACTTAAA
Statistics
Matches: 208, Mismatches: 39, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
36 3 0.01
37 197 0.95
38 8 0.04
ACGTcount: A:0.35, C:0.31, G:0.19, T:0.14
Consensus pattern (37 bp):
CACAAAGCCTGCTAGGCACATAGCCCGAATACACCGA
Found at i:37490721 original size:16 final size:16
Alignment explanation
Indices: 37490668--37490721 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
37490658 TGAATAAGGT
**
37490668 TGTAATGGAATAGGAC
1 TGTAATGGAATAAAAC
*
37490684 TGTAATGGAATAAAGC
1 TGTAATGGAATAAAAC
*
37490700 TATAATGGAATAAAAC
1 TGTAATGGAATAAAAC
37490716 TGTAAT
1 TGTAAT
37490722 CATATTCAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (16 bp):
TGTAATGGAATAAAAC
Found at i:37498394 original size:36 final size:36
Alignment explanation
Indices: 37498347--37498445 Score: 162
Period size: 36 Copynumber: 2.8 Consensus size: 36
37498337 TGGTAATAGG
37498347 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
*
37498383 CATGACCTTTGGGTCAACAGAGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
* * *
37498419 CATGGCCTTTGGGTTAACAAGGAGTAA
1 CATGACCTTTGGGTCAACAGGGAGTAA
37498446 GCATGACCTT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.23
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
Done.