Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 102 of 208
Found at i:34287434 original size:14 final size:12
Alignment explanation
Indices: 34287394--34287432 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
34287384 TATTCTATAT
*
34287394 AAATAAAAT-AA
1 AAATATAATAAA
34287405 AAATATAATAAA
1 AAATATAATAAA
34287417 AAATATTAATAAA
1 AAATA-TAATAAA
34287430 AAA
1 AAA
34287433 ATTTATCACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 8 0.32
12 7 0.28
13 10 0.40
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATAATAAA
Found at i:34289819 original size:22 final size:22
Alignment explanation
Indices: 34289791--34289839 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
34289781 CCCCGACCCA
34289791 CCACCCATGTGGGTCCCTAGAC
1 CCACCCATGTGGGTCCCTAGAC
*
34289813 CCACCCATGTGGGTCCGTAGAC
1 CCACCCATGTGGGTCCCTAGAC
34289835 CCACC
1 CCACC
34289840 TAATCTCGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.18, C:0.43, G:0.22, T:0.16
Consensus pattern (22 bp):
CCACCCATGTGGGTCCCTAGAC
Found at i:34291020 original size:15 final size:15
Alignment explanation
Indices: 34291002--34291054 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
34290992 AAGTATTTTT
34291002 TTTAATTTTATTTAA
1 TTTAATTTTATTTAA
* *
34291017 TTTAATTATATTCAA
1 TTTAATTTTATTTAA
** *
34291032 AATATTTTTATTTAAA
1 TTTAATTTTATTT-AA
34291048 TTTAATT
1 TTTAATT
34291055 ATAAAGTATA
Statistics
Matches: 27, Mismatches: 10, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
15 21 0.78
16 6 0.22
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTAATTTTATTTAA
Found at i:34291969 original size:28 final size:29
Alignment explanation
Indices: 34291918--34291974 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
34291908 TAATGTTTGG
*
34291918 AATTTTTTTAAAAAAATCATAATT-TTTT
1 AATTTTTTTAAAAAAATCACAATTGTTTT
*
34291946 AATTTTTTTAATAGAAAT-ACAATTGTTTT
1 AATTTTTTTAA-AAAAATCACAATTGTTTT
34291975 TTAAATTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (29 bp):
AATTTTTTTAAAAAAATCACAATTGTTTT
Found at i:34297405 original size:14 final size:14
Alignment explanation
Indices: 34297375--34297440 Score: 59
Period size: 14 Copynumber: 4.8 Consensus size: 14
34297365 CACACATGTA
*
34297375 GTTCACACCT-AGAG
1 GTTCACACATAAG-G
34297389 GTTCACACATAAGG
1 GTTCACACATAAGG
*
34297403 GTTCACTCAAGTAA-G
1 GTTCACAC-A-TAAGG
34297418 G-TCACACAT-AGG
1 GTTCACACATAAGG
34297430 GTTCACACATA
1 GTTCACACATA
34297441 TAGATTTTGC
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
11 1 0.02
12 3 0.07
13 9 0.21
14 22 0.51
15 5 0.12
16 3 0.07
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (14 bp):
GTTCACACATAAGG
Found at i:34297405 original size:41 final size:41
Alignment explanation
Indices: 34297360--34297440 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
34297350 TACATAAGTG
* * *
34297360 GGGTTCACACATGT-AGTTCACACCTAGAGGTTCACACATAA
1 GGGTTCACACAAGTAAGGTCACACATAG-GGTTCACACATAA
*
34297401 GGGTTCACTCAAGTAAGGTCACACATAGGGTTCACACATA
1 GGGTTCACACAAGTAAGGTCACACATAGGGTTCACACATA
34297441 TAGATTTTGC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 24 0.69
42 11 0.31
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (41 bp):
GGGTTCACACAAGTAAGGTCACACATAGGGTTCACACATAA
Found at i:34299095 original size:23 final size:23
Alignment explanation
Indices: 34299067--34299146 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
34299057 ACATGATATA
34299067 TCCTATAGGGTTCGCATAACATT
1 TCCTATAGGGTTCGCATAACATT
* *
34299090 TACTAT-GGGATTCGCATAACAGT
1 TCCTATAGGG-TTCGCATAACATT
* * * *
34299113 TCCTATACGGTTCACATGATATT
1 TCCTATAGGGTTCGCATAACATT
34299136 TCCTATAGGGT
1 TCCTATAGGGT
34299147 AAACATATAC
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
22 3 0.07
23 41 0.89
24 2 0.04
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (23 bp):
TCCTATAGGGTTCGCATAACATT
Found at i:34299468 original size:23 final size:23
Alignment explanation
Indices: 34299415--34299473 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
34299405 ACAATAATAG
34299415 TTCCTATAGGGTTCACATAACAA
1 TTCCTATAGGGTTCACATAACAA
** **
34299438 TTATTATAGGGTTTGCATAACAGA
1 TTCCTATAGGGTTCACATAACA-A
34299462 -TCCTATAGGGTT
1 TTCCTATAGGGTT
34299474 GGTATGATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.36
Consensus pattern (23 bp):
TTCCTATAGGGTTCACATAACAA
Found at i:34301081 original size:32 final size:32
Alignment explanation
Indices: 34301039--34301104 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
34301029 TTAATTTCAC
*
34301039 AAATCGAACCAAAACACGTTATTATATCAAGT
1 AAATCAAACCAAAACACGTTATTATATCAAGT
34301071 AAATCAAACCAAAACACGTTATTATATCAAGT
1 AAATCAAACCAAAACACGTTATTATATCAAGT
34301103 AA
1 AA
34301105 GTTTCGTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.50, C:0.18, G:0.08, T:0.24
Consensus pattern (32 bp):
AAATCAAACCAAAACACGTTATTATATCAAGT
Found at i:34315162 original size:44 final size:45
Alignment explanation
Indices: 34315025--34315164 Score: 110
Period size: 44 Copynumber: 3.2 Consensus size: 45
34315015 GATGGCAAAT
34315025 CTTATCTTTCCAAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
1 CTTATCTTTCCAAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
* ** * * * * *** **
34315070 CTTATC-TCCCTCAGCAGCAGT-GG-AGTA-AGTTGAAGACGGAAAAT
1 CTTATCTTTCCAAAG-A-TAGTGGGAAGCAGA-TTTAAGCCACCAAGC
34315114 CTTATCTTTCC-AAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
1 CTTATCTTTCCAAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
34315158 CTTATCT
1 CTTATCT
34315165 CCTTGAGCAG
Statistics
Matches: 65, Mismatches: 23, Indels: 15
0.63 0.22 0.15
Matches are distributed among these distances:
42 3 0.05
43 4 0.06
44 42 0.65
45 13 0.20
46 3 0.05
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (45 bp):
CTTATCTTTCCAAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
Found at i:34315174 original size:88 final size:88
Alignment explanation
Indices: 34314969--34315248 Score: 488
Period size: 88 Copynumber: 3.2 Consensus size: 88
34314959 CAGATCGGTG
*
34314969 AAGCCACCAAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATGGCAAATCTTATCTTT
1 AAGCCACCAAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATGGAAAATCTTATCTTT
34315034 CCAAAGATAGTGGGAAGCAGATTT
66 CC-AAGATAGTGGGAAGCAGATTT
* * *
34315058 AAGCCACCAAGCCTTATCTCCCTCAGCAGCAGTGGAGTAAGTTGAAGACGGAAAATCTTATCTTT
1 AAGCCACCAAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATGGAAAATCTTATCTTT
34315123 CCAAGATAGTGGGAAGCAGATTT
66 CCAAGATAGTGGGAAGCAGATTT
* *
34315146 AAGCCACCAAGCCTTATCTCCTTGAGCAGTAGTGGAGTAGGTTGAAGATGGAAAATCTTATCTTT
1 AAGCCACCAAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATGGAAAATCTTATCTTT
*
34315211 CCAAGATAGTGGGAAGTAGATTT
66 CCAAGATAGTGGGAAGCAGATTT
34315234 AAGCCACCAAGCCTT
1 AAGCCACCAAGCCTT
34315249 GCCCCCTTAA
Statistics
Matches: 181, Mismatches: 10, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
88 118 0.65
89 63 0.35
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (88 bp):
AAGCCACCAAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATGGAAAATCTTATCTTT
CCAAGATAGTGGGAAGCAGATTT
Found at i:34315273 original size:88 final size:88
Alignment explanation
Indices: 34314969--34315282 Score: 468
Period size: 88 Copynumber: 3.6 Consensus size: 88
34314959 CAGATCGGTG
* *
34314969 AAGCCACCAAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATGGCAAATCTTATCTTT
1 AAGCCACCAAGCCTTATCCCCCTGAGCAGCAGTGGAGTAGGTTGAAGATGGAAAATCTTATCTTT
34315034 CCAAAGATAGTGGGAAGCAGATTT
66 CC-AAGATAGTGGGAAGCAGATTT
* * * *
34315058 AAGCCACCAAGCCTTATCTCCCTCAGCAGCAGTGGAGTAAGTTGAAGACGGAAAATCTTATCTTT
1 AAGCCACCAAGCCTTATCCCCCTGAGCAGCAGTGGAGTAGGTTGAAGATGGAAAATCTTATCTTT
34315123 CCAAGATAGTGGGAAGCAGATTT
66 CCAAGATAGTGGGAAGCAGATTT
* * *
34315146 AAGCCACCAAGCCTTATCTCCTTGAGCAGTAGTGGAGTAGGTTGAAGATGGAAAATCTTATCTTT
1 AAGCCACCAAGCCTTATCCCCCTGAGCAGCAGTGGAGTAGGTTGAAGATGGAAAATCTTATCTTT
*
34315211 CCAAGATAGTGGGAAGTAGATTT
66 CCAAGATAGTGGGAAGCAGATTT
* * * * *
34315234 AAGCCACCAAGCCTT-GCCCCCTTAACCAGCAGCGAAGTAGGTTGAAGAT
1 AAGCCACCAAGCCTTATCCCCC-TGAGCAGCAGTGGAGTAGGTTGAAGAT
34315283 TACAAATCCT
Statistics
Matches: 206, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
87 3 0.01
88 140 0.68
89 63 0.31
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (88 bp):
AAGCCACCAAGCCTTATCCCCCTGAGCAGCAGTGGAGTAGGTTGAAGATGGAAAATCTTATCTTT
CCAAGATAGTGGGAAGCAGATTT
Found at i:34321627 original size:29 final size:29
Alignment explanation
Indices: 34321591--34321659 Score: 111
Period size: 29 Copynumber: 2.3 Consensus size: 29
34321581 AAATTGTTGT
34321591 GAAAATAAATCACGATGATAATATGTGTA
1 GAAAATAAATCACGATGATAATATGTGTA
*
34321620 GAAAATAAATCACGATGATATTATGTGTA
1 GAAAATAAATCACGATGATAATATGTGTA
*
34321649 GTAATATAAAT
1 G-AAAATAAAT
34321660 GCACCAAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
29 29 0.78
30 8 0.22
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.30
Consensus pattern (29 bp):
GAAAATAAATCACGATGATAATATGTGTA
Found at i:34321880 original size:18 final size:19
Alignment explanation
Indices: 34321857--34321892 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
34321847 GGTTTGTAAT
34321857 CACATAAAAG-AATATGAA
1 CACATAAAAGTAATATGAA
*
34321875 CACATAAATGTAATATGA
1 CACATAAAAGTAATATGA
34321893 TAAAAATGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (19 bp):
CACATAAAAGTAATATGAA
Found at i:34322670 original size:19 final size:18
Alignment explanation
Indices: 34322643--34322680 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
34322633 TTTCTCTCTT
*
34322643 TTTTTATATATATATTATA
1 TTTTGATATATAT-TTATA
34322662 TTTTGATATATATTTATA
1 TTTTGATATATATTTATA
34322680 T
1 T
34322681 GTATGCAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTTGATATATATTTATA
Found at i:34323469 original size:45 final size:44
Alignment explanation
Indices: 34323400--34323514 Score: 124
Period size: 44 Copynumber: 2.6 Consensus size: 44
34323390 TTTTAGTCTA
* * * * * *
34323400 CTCCACTGGAACATCAGGGAGATAATATTTGTTATA-TTCAGCCTG
1 CTCCACTGCAACTTTAGGGAGATAAGACTTG-TA-ACTTCAACCTG
* * *
34323445 CTCCACTGCGACTTTAGGGTGATAAGACTTGTAACTTCAACTTG
1 CTCCACTGCAACTTTAGGGAGATAAGACTTGTAACTTCAACCTG
34323489 CTCCACTGCAACTTTAGGGAGATAAG
1 CTCCACTGCAACTTTAGGGAGATAAG
34323515 GTTTGCTATG
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
43 1 0.02
44 33 0.57
45 24 0.41
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.30
Consensus pattern (44 bp):
CTCCACTGCAACTTTAGGGAGATAAGACTTGTAACTTCAACCTG
Found at i:34323543 original size:41 final size:40
Alignment explanation
Indices: 34323486--34323596 Score: 150
Period size: 41 Copynumber: 2.7 Consensus size: 40
34323476 TAACTTCAAC
*
34323486 TTGCTCCACTGCAACTTTAGGGAGATAAGGTTTGCTATGA
1 TTGCTCTACTGCAACTTTAGGGAGATAAGGTTTGCTATGA
* *
34323526 TCTGCTCTACTGCAACTTCAGGGAGATAAGGTTTGCTGTGA
1 T-TGCTCTACTGCAACTTTAGGGAGATAAGGTTTGCTATGA
* * *
34323567 TTCACTTTACTGCAACTTTAGAGAGATAAG
1 TT-GCTCTACTGCAACTTTAGGGAGATAAG
34323597 ATATCTAATT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
40 2 0.03
41 60 0.97
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (40 bp):
TTGCTCTACTGCAACTTTAGGGAGATAAGGTTTGCTATGA
Found at i:34324061 original size:45 final size:45
Alignment explanation
Indices: 34323946--34324191 Score: 282
Period size: 45 Copynumber: 5.5 Consensus size: 45
34323936 TGTTCCATTA
* * * * *
34323946 CAACTTCAGGGAAACAAGATTTGCTATCTTTAGTCTGCTCTACTG
1 CAACTTCAAGGAGATAAGACTTGCTATCTTTAGTCTGCTCCACTG
* * * *
34323991 -TACTTTAGGGAGATAAGACTTGCTATCTTTAGTCCGCTCCACTG
1 CAACTTCAAGGAGATAAGACTTGCTATCTTTAGTCTGCTCCACTG
* * * *
34324035 CAACTTCAGGGAGATTAGAATTGCTATCTTCAGTCTGCTCCACTG
1 CAACTTCAAGGAGATAAGACTTGCTATCTTTAGTCTGCTCCACTG
* * * *
34324080 CAACTTCAAGGAGACAAGACTTGGTATCTTCAGTCTGCTCCACTT
1 CAACTTCAAGGAGATAAGACTTGCTATCTTTAGTCTGCTCCACTG
** *
34324125 CAACTTCAAGGAGAT-AGACTTG-TGGCTTTAATCTGCTCCACTG
1 CAACTTCAAGGAGATAAGACTTGCTATCTTTAGTCTGCTCCACTG
*
34324168 CAACTTCAAGGAGATAAGATTTGC
1 CAACTTCAAGGAGATAAGACTTGC
34324192 AGCCTGTCTT
Statistics
Matches: 172, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
43 31 0.18
44 50 0.29
45 91 0.53
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (45 bp):
CAACTTCAAGGAGATAAGACTTGCTATCTTTAGTCTGCTCCACTG
Found at i:34324115 original size:134 final size:132
Alignment explanation
Indices: 34323946--34324191 Score: 314
Period size: 134 Copynumber: 1.8 Consensus size: 132
34323936 TGTTCCATTA
* * * * * *
34323946 CAACTTCAGGGAAACAAGATTTGCTATCTTTAGTCTGCTCTACTGT-ACTTTAGGGAGATAAGAC
1 CAACTTCAAGGAAACAAGACTTGCTATCTTCAGTCTGCTCCACT-TAACTTCAAGGAGAT-AGAC
* * * *
34324010 TTGCTATCTTTAGTCCGCTCCACTGCAACTTCAGGGAGATTAGAATTGCTATCTTCAGTCTGCTC
64 TTG-TAGCTTTAATCCGCTCCACTGCAACTTCAAGGAGATAAGAATTGCTATCTTCAGTCTGCTC
34324075 CACTG
128 CACTG
* *
34324080 CAACTTCAAGGAGACAAGACTTGGTATCTTCAGTCTGCTCCACTTCAACTTCAAGGAGATAGACT
1 CAACTTCAAGGAAACAAGACTTGCTATCTTCAGTCTGCTCCACTT-AACTTCAAGGAGATAGACT
* * *
34324145 TGTGGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGC
65 TGTAGCTTTAATCCGCTCCACTGCAACTTCAAGGAGATAAGAATTGC
34324192 AGCCTGTCTT
Statistics
Matches: 95, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
133 39 0.41
134 45 0.47
135 11 0.12
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (132 bp):
CAACTTCAAGGAAACAAGACTTGCTATCTTCAGTCTGCTCCACTTAACTTCAAGGAGATAGACTT
GTAGCTTTAATCCGCTCCACTGCAACTTCAAGGAGATAAGAATTGCTATCTTCAGTCTGCTCCAC
TG
Found at i:34326937 original size:16 final size:19
Alignment explanation
Indices: 34326890--34326937 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
34326880 GGTTTGTATC
34326890 ACATAAA-AGAATATGAAT
1 ACATAAATAGAATATGAAT
*
34326908 ACATAAATATAATATG-AT
1 ACATAAATAGAATATGAAT
34326926 A-A-AAATAGAATA
1 ACATAAATAGAATA
34326938 AATGCATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 9 0.33
17 1 0.04
18 10 0.37
19 7 0.26
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.25
Consensus pattern (19 bp):
ACATAAATAGAATATGAAT
Found at i:34331744 original size:19 final size:20
Alignment explanation
Indices: 34331699--34331744 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
34331689 AATATATAAA
* *
34331699 TTATAAAATTTAAAAGCATG
1 TTATAAAATTCAAAAACATG
34331719 -TAT-AAATTCAAAAAC-TG
1 TTATAAAATTCAAAAACATG
34331736 TTATAAAAT
1 TTATAAAAT
34331745 AAAGAGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
17 2 0.09
18 13 0.59
19 7 0.32
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.35
Consensus pattern (20 bp):
TTATAAAATTCAAAAACATG
Found at i:34337264 original size:40 final size:40
Alignment explanation
Indices: 34337175--34337476 Score: 418
Period size: 40 Copynumber: 7.6 Consensus size: 40
34337165 TTGAATGCTG
* * *
34337175 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
** * *
34337214 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
34337254 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
34337293 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
34337333 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
34337373 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
34337413 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
34337454 -CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
34337477 CGAACAAGGA
Statistics
Matches: 242, Mismatches: 14, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
39 53 0.22
40 179 0.74
41 10 0.04
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:34337496 original size:120 final size:120
Alignment explanation
Indices: 34337175--34337511 Score: 359
Period size: 120 Copynumber: 2.8 Consensus size: 120
34337165 TTGAATGCTG
* * * *
34337175 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAA-TTACTAA-ATCCGGGCTAAG-TCCCGAAGGCA
* ** * * *
34337236 TTTGTGCGAGAT-ACTAATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
63 TTCGAACAAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * * *
34337293 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCTGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTAAATCCGGGCTAAGTCCCGAAGGCATTC
** * *
34337358 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
66 GAACAAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
34337413 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
* * *
34337477 CGAACAAG-GAGCTATATCC-GGTTAAATTCCGAAGG
65 CGAACAAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
34337512 TACGTGATTT
Statistics
Matches: 190, Mismatches: 21, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
118 22 0.12
119 61 0.32
120 105 0.55
121 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTAAATCCGGGCTAAGTCCCGAAGGCATTC
GAACAAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:34342409 original size:18 final size:18
Alignment explanation
Indices: 34342388--34342422 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34342378 GATGGAATTC
34342388 CAGAGACAGATACAAATA
1 CAGAGACAGATACAAATA
**
34342406 CAGATTCAGATACAAAT
1 CAGAGACAGATACAAAT
34342423 GCGGACACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.17
Consensus pattern (18 bp):
CAGAGACAGATACAAATA
Found at i:34342448 original size:12 final size:12
Alignment explanation
Indices: 34342414--34342448 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
34342404 TACAGATTCA
34342414 GATACAAATGCG
1 GATACAAATGCG
*
34342426 GACACAAATGCG
1 GATACAAATGCG
*
34342438 GATACAGATGC
1 GATACAAATGC
34342449 AGGCACAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (12 bp):
GATACAAATGCG
Found at i:34344062 original size:15 final size:14
Alignment explanation
Indices: 34344038--34344069 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
34344028 CCACTCTTGG
34344038 TTTCACTAACCCAA
1 TTTCACTAACCCAA
34344052 TTTCTACTAACCCAA
1 TTTC-ACTAACCCAA
34344067 TTT
1 TTT
34344070 TTGGGGTCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (14 bp):
TTTCACTAACCCAA
Found at i:34347037 original size:12 final size:13
Alignment explanation
Indices: 34347015--34347044 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
34347005 ATTGATATTG
34347015 TATGTCATGATTT
1 TATGTCATGATTT
34347028 TATG-CATGATTT
1 TATGTCATGATTT
34347040 TATGT
1 TATGT
34347045 TTTAGCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.23, C:0.07, G:0.17, T:0.53
Consensus pattern (13 bp):
TATGTCATGATTT
Found at i:34348156 original size:25 final size:25
Alignment explanation
Indices: 34348128--34348179 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
34348118 TAGTATATAA
34348128 TGGGACTACTATAGATAGACTGTAC
1 TGGGACTACTATAGATAGACTGTAC
*
34348153 TGGGACTATTATAGATAGACTGTAC
1 TGGGACTACTATAGATAGACTGTAC
34348178 TG
1 TG
34348180 AAAACACTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (25 bp):
TGGGACTACTATAGATAGACTGTAC
Found at i:34354184 original size:12 final size:13
Alignment explanation
Indices: 34354162--34354191 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
34354152 ATTGATACTG
34354162 TATGTCATGATTT
1 TATGTCATGATTT
34354175 TATG-CATGATTT
1 TATGTCATGATTT
34354187 TATGT
1 TATGT
34354192 TTTAGCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.23, C:0.07, G:0.17, T:0.53
Consensus pattern (13 bp):
TATGTCATGATTT
Found at i:34355946 original size:29 final size:29
Alignment explanation
Indices: 34355868--34355952 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
34355858 ATGACAGGCC
* * *
34355868 GTGTGAGCCACACAAACGTGTGGCTGGCT
1 GTGTTAGCCACACAGACGTGTGGTTGGCT
* *
34355897 GTGTTAGCCACACAGATGTGTGGTTGGTT
1 GTGTTAGCCACACAGACGTGTGGTTGGCT
** *
34355926 GTGTTAGCCACATGGGCGTGTGGTTGG
1 GTGTTAGCCACACAGACGTGTGGTTGG
34355953 ACATGTAGGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.16, C:0.18, G:0.38, T:0.28
Consensus pattern (29 bp):
GTGTTAGCCACACAGACGTGTGGTTGGCT
Found at i:34360429 original size:114 final size:113
Alignment explanation
Indices: 34360210--34361179 Score: 1467
Period size: 113 Copynumber: 8.6 Consensus size: 113
34360200 GTTTATTTGT
* * *
34360210 AAGCGCCGTAAAATATCTTAACCAAAACGCAGTGTTTGGTCTTGAGGTA-ATTAAAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
* * *
34360274 GCTTATGCAAAAACGCCGCTAAAGCATAGTATTAGCGGCGCACTATAAA
66 GCTTATG-AAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTACAAA
* * * *
34360323 AAACGCCGCAAAATATCGTAACCAAAACGCAACATTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
* * * * * *
34360388 ACTTATGCACAAACGCCGCTAAAGCACAATATTAGCTGCGCACTATAAA
66 GCTTATG-AAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTACAAA
** *
34360437 AAATGCCACAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
*
34360502 GCTTATGAAAAACGCCGCTAAAGCACAGTATTAGCGGCACATTACAAA
66 GCTTATGAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTACAAA
* * * *
34360550 AAGCACCGCAAAATATCTTAACCAAAACGCAACGTTTGGTCTTGAGATGTATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
*
34360615 GATTATGAAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTACAAA
66 GCTTATG-AAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTACAAA
* * * *
34360664 AAGCACCCCAAAATATCTTACCCAAAACACAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
34360729 GCTTATGAAAAAACGCCGCTAAAGCACAGTATT-GCGGCGCATTACAAA
66 GCTTATG-AAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTACAAA
* * *
34360777 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCATTTGGTTTTGAGGTATATTAGAATTTGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
* *
34360842 GCTTATGAAAAACGCCACTAAAGCACAATATTAGCGGCGCATTACAAA
66 GCTTATGAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTACAAA
*
34360890 AAGCGCCGCAAAATATCTTAACCAAAACGAAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
* **
34360955 GCTTATGAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCTTTGTAAA
66 GCTTATGAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTACAAA
* *
34361003 AAGCACCGCAAAAAATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
** *
34361068 GCTTATGAAAAAACGAAGCTAAAGCACAGTATTAGCGGTGCATTACAAA
66 GCTTATG-AAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTACAAA
* * *
34361117 AAGCGCCGCAAAAAATCTTAACCAAAATGCAGCGTTTGGTCTTGAGGTATATTAAAATTAGTG
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTG
34361180 TTTAGGGTTT
Statistics
Matches: 783, Mismatches: 70, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
112 23 0.03
113 410 0.52
114 350 0.45
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.24
Consensus pattern (113 bp):
AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
GCTTATGAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTACAAA
Found at i:34360483 original size:227 final size:227
Alignment explanation
Indices: 34360210--34361179 Score: 1462
Period size: 227 Copynumber: 4.3 Consensus size: 227
34360200 GTTTATTTGT
* * *
34360210 AAGCGCCGTAAAATATCTTAACCAAAACGCAGTGTTTGGTCTTGAGGTA-ATTAAAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
* * * * *
34360274 GCTTATGCAAAAACGCCGCTAAAGCATAGTATTAGCGGCGCACTATAAAAAACGCCGCAAAATAT
66 GCTTATG-AAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTACAAAAAGCACCGCAAAATAT
* * *
34360339 CGTAACCAAAACGCAACATTTGGTCTTGAGGTATATTAGAATTAGTGGCACTTATGCACAAACGC
130 CTTAACCAAAACGCAACATTTGGTCTTGAGGTATATTAGAATTAGTGGCACTTATGAAAAAACGC
* * *
34360404 CGCTAAAGCACAATATTAGCTGCGCACTATAAA
195 CGCTAAAGCACAATATTAGCGGCGCATTACAAA
** *
34360437 AAATGCCACAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
*
34360502 GCTTATGAAAAACGCCGCTAAAGCACAGTATTAGCGGCACATTACAAAAAGCACCGCAAAATATC
66 GCTTATGAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTACAAAAAGCACCGCAAAATATC
* * *
34360567 TTAACCAAAACGCAACGTTTGGTCTTGAGATGTATTAGAATTAGTGGCGA-TTATGAAAAAACGC
131 TTAACCAAAACGCAACATTTGGTCTTGAGGTATATTAGAATTAGTGGC-ACTTATGAAAAAACGC
*
34360631 CGCTAAAGCACAGTATTAGCGGCGCATTACAAA
195 CGCTAAAGCACAATATTAGCGGCGCATTACAAA
* * * *
34360664 AAGCACCCCAAAATATCTTACCCAAAACACAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
*
34360729 GCTTATGAAAAAACGCCGCTAAAGCACAGTATT-GCGGCGCATTACAAAAAGCGCCGCAAAATAT
66 GCTTATG-AAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTACAAAAAGCACCGCAAAATAT
* * * *
34360793 CTTAACCAAAACGCAGCATTTGGTTTTGAGGTATATTAGAATTTGTGGCGCTTATG-AAAAACGC
130 CTTAACCAAAACGCAACATTTGGTCTTGAGGTATATTAGAATTAGTGGCACTTATGAAAAAACGC
*
34360857 CACTAAAGCACAATATTAGCGGCGCATTACAAA
195 CGCTAAAGCACAATATTAGCGGCGCATTACAAA
*
34360890 AAGCGCCGCAAAATATCTTAACCAAAACGAAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
* ** *
34360955 GCTTATGAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCTTTGTAAAAAGCACCGCAAAAAATC
66 GCTTATGAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTACAAAAAGCACCGCAAAATATC
* * * **
34361020 TTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATGAAAAAACGAA
131 TTAACCAAAACGCAACATTTGGTCTTGAGGTATATTAGAATTAGTGGCACTTATGAAAAAACGCC
* *
34361085 GCTAAAGCACAGTATTAGCGGTGCATTACAAA
196 GCTAAAGCACAATATTAGCGGCGCATTACAAA
* * *
34361117 AAGCGCCGCAAAAAATCTTAACCAAAATGCAGCGTTTGGTCTTGAGGTATATTAAAATTAGTG
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTG
34361180 TTTAGGGTTT
Statistics
Matches: 676, Mismatches: 61, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
225 25 0.04
226 185 0.27
227 419 0.62
228 47 0.07
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.24
Consensus pattern (227 bp):
AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
GCTTATGAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTACAAAAAGCACCGCAAAATATC
TTAACCAAAACGCAACATTTGGTCTTGAGGTATATTAGAATTAGTGGCACTTATGAAAAAACGCC
GCTAAAGCACAATATTAGCGGCGCATTACAAA
Found at i:34361473 original size:22 final size:21
Alignment explanation
Indices: 34361448--34361488 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
34361438 TATAGTTTTA
* *
34361448 GGTTTAGGGTTTGGGAGTTTGG
1 GGTTTAAGGTATGGG-GTTTGG
34361470 GGTTTAAGGTATGGGGTTT
1 GGTTTAAGGTATGGGGTTT
34361489 AGGCCACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.12, C:0.00, G:0.46, T:0.41
Consensus pattern (21 bp):
GGTTTAAGGTATGGGGTTTGG
Found at i:34363023 original size:123 final size:123
Alignment explanation
Indices: 34362804--34363048 Score: 490
Period size: 123 Copynumber: 2.0 Consensus size: 123
34362794 TCAAAATCCT
34362804 TAAACAGCCAGAGGGAAATACTCCAAGAGAGCAGTTCGTCGAGAAGTTTTTCCCCCGATTCATCA
1 TAAACAGCCAGAGGGAAATACTCCAAGAGAGCAGTTCGTCGAGAAGTTTTTCCCCCGATTCATCA
34362869 ATTGGTTGCTTTAGCAGCAAGGAAAAGGTTTATTTTTTGGGTTTCTTGCAAAGTTACC
66 ATTGGTTGCTTTAGCAGCAAGGAAAAGGTTTATTTTTTGGGTTTCTTGCAAAGTTACC
34362927 TAAACAGCCAGAGGGAAATACTCCAAGAGAGCAGTTCGTCGAGAAGTTTTTCCCCCGATTCATCA
1 TAAACAGCCAGAGGGAAATACTCCAAGAGAGCAGTTCGTCGAGAAGTTTTTCCCCCGATTCATCA
34362992 ATTGGTTGCTTTAGCAGCAAGGAAAAGGTTTATTTTTTGGGTTTCTTGCAAAGTTAC
66 ATTGGTTGCTTTAGCAGCAAGGAAAAGGTTTATTTTTTGGGTTTCTTGCAAAGTTAC
34363049 ATAACCCACA
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 122 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (123 bp):
TAAACAGCCAGAGGGAAATACTCCAAGAGAGCAGTTCGTCGAGAAGTTTTTCCCCCGATTCATCA
ATTGGTTGCTTTAGCAGCAAGGAAAAGGTTTATTTTTTGGGTTTCTTGCAAAGTTACC
Found at i:34363700 original size:29 final size:30
Alignment explanation
Indices: 34363656--34363717 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
34363646 AGCATTTTGA
*
34363656 ATGTTAAGCATAGTTTTGACTGTTAAGC-T
1 ATGTTAAGCATAGTTTTGAATGTTAAGCAT
34363685 ATGTTAAGC-TATGTTTTGAATGTTAAGCAT
1 ATGTTAAGCATA-GTTTTGAATGTTAAGCAT
34363715 ATG
1 ATG
34363718 AGTTCCTGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 2 0.07
29 24 0.80
30 4 0.13
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (30 bp):
ATGTTAAGCATAGTTTTGAATGTTAAGCAT
Found at i:34364131 original size:21 final size:21
Alignment explanation
Indices: 34364107--34364179 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 21
34364097 GTTTTGGGAC
*
34364107 TATTTATTTATATTTTCAGCG
1 TATTTATTTATATTTTCAGCA
* *
34364128 TATTTAATATTATTGATATT-A-TA
1 TATTT-AT-TTA-T-ATTTTCAGCA
34364151 TTATTTATTTATATTTTCAGCA
1 -TATTTATTTATATTTTCAGCA
34364173 TATTTAT
1 TATTTAT
34364180 ATAAACATCT
Statistics
Matches: 40, Mismatches: 5, Indels: 14
0.68 0.08 0.24
Matches are distributed among these distances:
20 4 0.10
21 14 0.35
22 6 0.15
23 5 0.12
24 7 0.17
25 4 0.10
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (21 bp):
TATTTATTTATATTTTCAGCA
Found at i:34364737 original size:9 final size:9
Alignment explanation
Indices: 34364723--34365352 Score: 207
Period size: 9 Copynumber: 74.4 Consensus size: 9
34364713 ACTCTCACAT
34364723 CTTACATAA
1 CTTACATAA
*
34364732 CTTACATAG
1 CTTACATAA
*
34364741 CTTA-ATTA
1 CTTACATAA
*
34364749 --TACTTAA
1 CTTACATAA
34364756 CTTACATAA
1 CTTACATAA
*
34364765 CTTACATTA
1 CTTACATAA
*
34364774 --TACACAA
1 CTTACATAA
34364781 CTTACATAA
1 CTTACATAA
*
34364790 CTTTCATTATACA
1 C-TT-A-CATA-A
*
34364803 CATACATAA
1 CTTACATAA
34364812 CTTACATATA
1 CTTACATA-A
* *
34364822 -ATACACAA
1 CTTACATAA
*
34364830 CATACATAA
1 CTTACATAA
34364839 CTTACATAA
1 CTTACATAA
* *
34364848 TTTTCAT-A
1 CTTACATAA
* *
34364856 -GTACATGA
1 CTTACATAA
34364864 CTTACATAA
1 CTTACATAA
*
34364873 --TA-TTGAA
1 CTTACAT-AA
34364880 CTTACATAA
1 CTTACATAA
* *
34364889 TTTTCATAA
1 CTTACATAA
34364898 --TACATAA
1 CTTACATAA
*
34364905 CTTACTTAA
1 CTTACATAA
* *
34364914 TTTTCATAA
1 CTTACATAA
*
34364923 --TAAATAA
1 CTTACATAA
34364930 CTTACATAA
1 CTTACATAA
34364939 CTTACATAA
1 CTTACATAA
* *
34364948 TTTTCATAA
1 CTTACATAA
*
34364957 CCTACATAA
1 CTTACATAA
* *
34364966 CTTATACAA
1 CTTACATAA
*
34364975 --TACACAA
1 CTTACATAA
34364982 CTTACATAA
1 CTTACATAA
* *
34364991 TTTTCATAA
1 CTTACATAA
34365000 --TACATAA
1 CTTACATAA
34365007 CTTACATAA
1 CTTACATAA
*
34365016 --TA-TTGAA
1 CTTACAT-AA
34365023 CTTACATAA
1 CTTACATAA
* * *
34365032 TTTTCGTAA
1 CTTACATAA
34365041 --TACATAA
1 CTTACATAA
34365048 CTTACATAA
1 CTTACATAA
*
34365057 --TA-TTGAA
1 CTTACAT-AA
34365064 CTTACATAA
1 CTTACATAA
* *
34365073 TTTTCA-AA
1 CTTACATAA
*
34365081 -ATACATAA
1 CTTACATAA
34365089 CTTACATAA
1 CTTACATAA
*
34365098 --TA-TTGAA
1 CTTACAT-AA
*
34365105 CGTACATAA
1 CTTACATAA
* *
34365114 TTTTCATAA
1 CTTACATAA
34365123 --TACATAA
1 CTTACATAA
*
34365130 GTTA-ATTAA
1 CTTACA-TAA
* *
34365139 TTTTCATAA
1 CTTACATAA
* *
34365148 --TAAAAAA
1 CTTACATAA
34365155 CTTACATAA
1 CTTACATAA
34365164 CTTACATAA
1 CTTACATAA
* *
34365173 TTTTCATAA
1 CTTACATAA
34365182 CTTACATAA
1 CTTACATAA
* *
34365191 CTTATACAA
1 CTTACATAA
* *
34365200 --TACACAG
1 CTTACATAA
34365207 CTTACATAA
1 CTTACATAA
* *
34365216 TTTTCATAA
1 CTTACATAA
34365225 --TACATAA
1 CTTACATAA
34365232 CTTACATAA
1 CTTACATAA
34365241 -TTGATCATAA
1 CTT-A-CATAA
*
34365251 --TCCA-ACA
1 CTTACATA-A
34365258 CTTACATAA
1 CTTACATAA
*
34365267 -TT-CACAA
1 CTTACATAA
34365274 CTTACATAA
1 CTTACATAA
*
34365283 -TATTCATAA
1 CT-TACATAA
34365292 --TACATAA
1 CTTACATAA
34365299 CTTACATAA
1 CTTACATAA
* *
34365308 TTTTCATAA
1 CTTACATAA
*
34365317 --TAAATAA
1 CTTACATAA
34365324 CTTACATAA
1 CTTACATAA
34365333 --TACATAA
1 CTTACATAA
*
34365340 CTTACATAG
1 CTTACATAA
34365349 CTTA
1 CTTA
34365353 AGTATACTTA
Statistics
Matches: 454, Mismatches: 101, Indels: 132
0.66 0.15 0.19
Matches are distributed among these distances:
6 7 0.02
7 104 0.23
8 17 0.04
9 301 0.66
10 17 0.04
11 2 0.00
12 4 0.01
13 2 0.00
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.36
Consensus pattern (9 bp):
CTTACATAA
Found at i:34364782 original size:25 final size:25
Alignment explanation
Indices: 34364725--34365266 Score: 280
Period size: 25 Copynumber: 21.6 Consensus size: 25
34364715 TCTCACATCT
* *
34364725 TACATAACTTACATAGCTTA-ATTA
1 TACATAACTTACATAACTTACATAA
* *
34364749 TACTTAACTTACATAACTTACATTA
1 TACATAACTTACATAACTTACATAA
* * *
34364774 TACACAACTTACATAACTTTCATTA
1 TACATAACTTACATAACTTACATAA
*
34364799 TAC---ACATACATAACTTACATATAA
1 TACATAACTTACATAACTTAC--ATAA
* *
34364823 TACACAACATACATAACTTACATAA
1 TACATAACTTACATAACTTACATAA
* * *
34364848 TTTTCAT-A-GTACATGACTTACATAA
1 --TACATAACTTACATAACTTACATAA
* * *
34364873 TA-TTGAACTTACATAATTTTCATAA
1 TACAT-AACTTACATAACTTACATAA
* * *
34364898 TACATAACTTACTTAATTTTCATAA
1 TACATAACTTACATAACTTACATAA
*
34364923 TAAATAACTTACATAACTTACATAA
1 TACATAACTTACATAACTTACATAA
* * * *
34364948 TTTTCATAACCTACATAACTTATACAA
1 --TACATAACTTACATAACTTACATAA
* * *
34364975 TACACAACTTACATAATTTTCATAA
1 TACATAACTTACATAACTTACATAA
*
34365000 TACATAACTTACATAA--TA-TTGAA
1 TACATAACTTACATAACTTACAT-AA
* * *
34365023 CTTACATAATTTTCGTAA--TACATAA
1 --TACATAACTTACATAACTTACATAA
*
34365048 CTTACATAA--TA-TTGAACTTACATAA
1 --TACATAACTTACAT-AACTTACATAA
* *
34365073 TTTTCA-AA-ATACATAACTTACATAA
1 --TACATAACTTACATAACTTACATAA
* * * *
34365098 TA-TTGAACGTACATAATTTTCATAA
1 TACAT-AACTTACATAACTTACATAA
* * *
34365123 TACATAAGTTA-ATTAATTTTCATAA
1 TACATAACTTACA-TAACTTACATAA
* *
34365148 TAAAAAACTTACATAACTTACATAA
1 TACATAACTTACATAACTTACATAA
* * *
34365173 TTTTCATAACTTACATAACTTATACAA
1 --TACATAACTTACATAACTTACATAA
* * * *
34365200 TACACAGCTTACATAATTTTCATAA
1 TACATAACTTACATAACTTACATAA
34365225 TACATAACTTACATAA-TTGATCATAA
1 TACATAACTTACATAACTT-A-CATAA
*
34365251 TCCA-ACACTTACATAA
1 TACATA-ACTTACATAA
34365267 TTCACAACTT
Statistics
Matches: 407, Mismatches: 77, Indels: 66
0.74 0.14 0.12
Matches are distributed among these distances:
22 16 0.04
23 8 0.02
24 32 0.08
25 269 0.66
26 24 0.06
27 58 0.14
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.36
Consensus pattern (25 bp):
TACATAACTTACATAACTTACATAA
Found at i:34364882 original size:41 final size:41
Alignment explanation
Indices: 34364837--34364914 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
34364827 CAACATACAT
* *
34364837 AACTTACATAATTTTCATAGTACATGACTTACATAATATTG
1 AACTTACATAATTTTCATAATACATAACTTACATAATATTG
*
34364878 AACTTACATAATTTTCATAATACATAACTTACTTAAT
1 AACTTACATAATTTTCATAATACATAACTTACATAAT
34364915 TTTCATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.41, C:0.15, G:0.04, T:0.40
Consensus pattern (41 bp):
AACTTACATAATTTTCATAATACATAACTTACATAATATTG
Found at i:34364938 original size:41 final size:41
Alignment explanation
Indices: 34364882--34365129 Score: 280
Period size: 41 Copynumber: 6.2 Consensus size: 41
34364872 ATATTGAACT
* * *
34364882 TACATAATTTTCATAATACAT-AACTTACTTAATTTTCATAA
1 TACATAACTTACATAATA-ATGAACTTACATAATTTTCATAA
*
34364923 TAAATAACTTAC------AT-AACTTACATAATTTTCATAA
1 TACATAACTTACATAATAATGAACTTACATAATTTTCATAA
* * *
34364957 CCTACATAACTTATACAATACA-CAACTTACATAATTTTCATAA
1 --TACATAACTTACATAATA-ATGAACTTACATAATTTTCATAA
* *
34365000 TACATAACTTACATAATATTGAACTTACATAATTTTCGTAA
1 TACATAACTTACATAATAATGAACTTACATAATTTTCATAA
* *
34365041 TACATAACTTACATAATATTGAACTTACATAATTTTCAAAA
1 TACATAACTTACATAATAATGAACTTACATAATTTTCATAA
* *
34365082 TACATAACTTACATAATATTGAACGTACATAATTTTCATAA
1 TACATAACTTACATAATAATGAACTTACATAATTTTCATAA
34365123 TACATAA
1 TACATAA
34365130 GTTAATTAAT
Statistics
Matches: 181, Mismatches: 15, Indels: 22
0.83 0.07 0.10
Matches are distributed among these distances:
34 21 0.12
36 10 0.06
41 129 0.71
43 21 0.12
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (41 bp):
TACATAACTTACATAATAATGAACTTACATAATTTTCATAA
Found at i:34365003 original size:16 final size:16
Alignment explanation
Indices: 34364758--34365347 Score: 151
Period size: 16 Copynumber: 36.9 Consensus size: 16
34364748 ATACTTAACT
*
34364758 TACATAACTTACATTA
1 TACATAACTTACATAA
*
34364774 TACACAACTTACATAA
1 TACATAACTTACATAA
* * *
34364790 CTTTCATTA--TACA-CA
1 --TACATAACTTACATAA
34364805 TACATAACTTACATATAA
1 TACATAACTTAC--ATAA
* *
34364823 TACACAACATACATAA
1 TACATAACTTACATAA
* * *
34364839 CTTACATAATTTTCATAG
1 --TACATAACTTACATAA
*
34364857 TACATGACTTACATAA
1 TACATAACTTACATAA
*
34364873 TA-TTGAACTTACATAA
1 TACAT-AACTTACATAA
*
34364889 TTTTCATAA--TACATAA
1 --TACATAACTTACATAA
* * *
34364905 CTTACTTAATTTTCATAA
1 --TACATAACTTACATAA
*
34364923 TAAATAACTTACATAA
1 TACATAACTTACATAA
* *
34364939 CTTACATAATTTTCATAA
1 --TACATAACTTACATAA
* *
34364957 CCTACATAACTTATACAA
1 --TACATAACTTACATAA
*
34364975 TACACAACTTACATAA
1 TACATAACTTACATAA
34364991 T---T---TT-CATAA
1 TACATAACTTACATAA
34365000 TACATAACTTACATAA
1 TACATAACTTACATAA
*
34365016 TA-TTGAACTTACATAA
1 TACAT-AACTTACATAA
*
34365032 T---T---TT-CGTAA
1 TACATAACTTACATAA
34365041 TACATAACTTACATAA
1 TACATAACTTACATAA
*
34365057 TA-TTGAACTTACATAA
1 TACAT-AACTTACATAA
*
34365073 T---T---TT-CAAAA
1 TACATAACTTACATAA
34365082 TACATAACTTACATAA
1 TACATAACTTACATAA
* *
34365098 TA-TTGAACGTACATAA
1 TACAT-AACTTACATAA
*
34365114 TTTTCATAA--TACATAA
1 --TACATAACTTACATAA
* *
34365130 GTTA-ATTAATTTTCATAA
1 --TACA-TAACTTACATAA
* *
34365148 TAAAAAACTTACATAA
1 TACATAACTTACATAA
* *
34365164 CTTACATAATTTTCATAA
1 --TACATAACTTACATAA
* *
34365182 CTTACATAACTTATACAA
1 --TACATAACTTACATAA
* *
34365200 TACACAGCTTACATAA
1 TACATAACTTACATAA
*
34365216 TTTTCATAA--TACATAA
1 --TACATAACTTACATAA
34365232 CTTACATAA-TTGATCATAA
1 --TACATAACTT-A-CATAA
*
34365251 TCCA-ACACTTACATAA
1 TACATA-ACTTACATAA
* *
34365267 TTCACAACTTACATAA
1 TACATAACTTACATAA
34365283 TATTCATAA--TACATAA
1 TA--CATAACTTACATAA
* *
34365299 CTTACATAATTTTCATAA
1 --TACATAACTTACATAA
*
34365317 TAAATAACTTACATAA
1 TACATAACTTACATAA
34365333 TACATAACTTACATA
1 TACATAACTTACATA
34365348 GCTTAAGTAT
Statistics
Matches: 424, Mismatches: 86, Indels: 128
0.66 0.13 0.20
Matches are distributed among these distances:
9 16 0.04
10 6 0.01
12 3 0.01
13 5 0.01
14 2 0.00
15 15 0.04
16 246 0.58
17 9 0.02
18 115 0.27
19 7 0.02
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:34365094 original size:225 final size:225
Alignment explanation
Indices: 34364837--34365241 Score: 729
Period size: 225 Copynumber: 1.8 Consensus size: 225
34364827 CAACATACAT
* * * *
34364837 AACTTACATAATTTTCATAGTACATGACTTACATAATATTGAACTTACATAATTTTCATAATACA
1 AACTTACATAATTTTCAAAATACATAACTTACATAATATTGAACGTACATAATTTTCATAATACA
* *
34364902 TAACTTACTTAATTTTCATAATAAATAACTTACATAACTTACATAATTTTCATAACCTACATAAC
66 TAACTTAATTAATTTTCATAATAAAAAACTTACATAACTTACATAATTTTCATAACCTACATAAC
34364967 TTATACAATACACAACTTACATAATTTTCATAATACATAACTTACATAATATTGAACTTACATAA
131 TTATACAATACACAACTTACATAATTTTCATAATACATAACTTACATAATATTGAACTTACATAA
34365032 TTTTCGTAATACATAACTTACATAATATTG
196 TTTTCGTAATACATAACTTACATAATATTG
34365062 AACTTACATAATTTTCAAAATACATAACTTACATAATATTGAACGTACATAATTTTCATAATACA
1 AACTTACATAATTTTCAAAATACATAACTTACATAATATTGAACGTACATAATTTTCATAATACA
* *
34365127 TAAGTTAATTAATTTTCATAATAAAAAACTTACATAACTTACATAATTTTCATAACTTACATAAC
66 TAACTTAATTAATTTTCATAATAAAAAACTTACATAACTTACATAATTTTCATAACCTACATAAC
*
34365192 TTATACAATACACAGCTTACATAATTTTCATAATACATAACTTACATAAT
131 TTATACAATACACAACTTACATAATTTTCATAATACATAACTTACATAAT
34365242 TGATCATAAT
Statistics
Matches: 171, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
225 171 1.00
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (225 bp):
AACTTACATAATTTTCAAAATACATAACTTACATAATATTGAACGTACATAATTTTCATAATACA
TAACTTAATTAATTTTCATAATAAAAAACTTACATAACTTACATAATTTTCATAACCTACATAAC
TTATACAATACACAACTTACATAATTTTCATAATACATAACTTACATAATATTGAACTTACATAA
TTTTCGTAATACATAACTTACATAATATTG
Found at i:34365190 original size:43 final size:40
Alignment explanation
Indices: 34365143--34365233 Score: 94
Period size: 43 Copynumber: 2.2 Consensus size: 40
34365133 AATTAATTTT
*
34365143 CATAA-TAAAAAACTTACATAACTTACATAATTTTCATAACTTA
1 CATAACTAAAAAA--TACACAACTTACATAATTTTCATAA--TA
* * *
34365186 CATAACTTATACAATACACAGCTTACATAATTTTCATAATA
1 CATAAC-TAAAAAATACACAACTTACATAATTTTCATAATA
34365227 CATAACT
1 CATAACT
34365234 TACATAATTG
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
40 1 0.02
41 8 0.19
43 28 0.67
45 5 0.12
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.34
Consensus pattern (40 bp):
CATAACTAAAAAATACACAACTTACATAATTTTCATAATA
Found at i:34365294 original size:92 final size:93
Alignment explanation
Indices: 34365163--34365333 Score: 249
Period size: 92 Copynumber: 1.8 Consensus size: 93
34365153 AACTTACATA
* * *
34365163 ACTTACATAATTTTCATAACTTACATAACTTATACAATACACAGCTTACATAATTTTCATAATAC
1 ACTTACATAA-TTTCACAACTTACATAACTTATACAATACACAACTTACATAATTTTCATAATAA
34365228 ATAACTTACATAATTGATCATAATCCAAC
65 ATAACTTACATAATTGATCATAATCCAAC
* *
34365257 ACTTACATAA-TTCACAACTTACATAA--TATTCATAATACATAACTTACATAATTTTCATAATA
1 ACTTACATAATTTCACAACTTACATAACTTA-T-ACAATACACAACTTACATAATTTTCATAATA
34365319 AATAACTTACATAAT
64 AATAACTTACATAAT
34365334 ACATAACTTA
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
90 2 0.03
91 1 0.01
92 57 0.81
94 10 0.14
ACGTcount: A:0.44, C:0.19, G:0.01, T:0.36
Consensus pattern (93 bp):
ACTTACATAATTTCACAACTTACATAACTTATACAATACACAACTTACATAATTTTCATAATAAA
TAACTTACATAATTGATCATAATCCAAC
Found at i:34365300 original size:25 final size:25
Alignment explanation
Indices: 34365262--34365334 Score: 110
Period size: 25 Copynumber: 2.9 Consensus size: 25
34365252 CCAACACTTA
* *
34365262 CATAATTCACAACTTACATAATATT
1 CATAATACATAACTTACATAATATT
*
34365287 CATAATACATAACTTACATAATTTT
1 CATAATACATAACTTACATAATATT
*
34365312 CATAATAAATAACTTACATAATA
1 CATAATACATAACTTACATAATA
34365335 CATAACTTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (25 bp):
CATAATACATAACTTACATAATATT
Found at i:34365302 original size:41 final size:41
Alignment explanation
Indices: 34364934--34365347 Score: 285
Period size: 41 Copynumber: 9.9 Consensus size: 41
34364924 AAATAACTTA
* * *
34364934 CATAACTTACATAATTTTCATAACCTACATAACTTATACAATA
1 CATAACTTACATAATTTTCATAA--TACATAACTTACATAATT
*
34364977 CACAACTTACATAATTTTCATAATACATAACTTACATAA-T
1 CATAACTTACATAATTTTCATAATACATAACTTACATAATT
*
34365017 -ATTGAACTTACATAATTTTCGTAATACATAACTTACATAA-T
1 CA-T-AACTTACATAATTTTCATAATACATAACTTACATAATT
*
34365058 -ATTGAACTTACATAATTTTCAAAATACATAACTTACATAA-T
1 CA-T-AACTTACATAATTTTCATAATACATAACTTACATAATT
* *
34365099 -ATTGAACGTACATAATTTTCATAATACATAAGTTA-ATTAATTTT
1 CA-T-AACTTACATAATTTTCATAATACATAACTTACA-TAA--TT
* * * * * *
34365143 CATAA--TAAAAAACTTACATAACTTACATAATTTTCATAACTT
1 CATAACTTACATAATTTTCATAA--TACATAACTTACATAA-TT
* * *** *** * * *
34365185 ACATAACTTATACAATACACAGCTTACATAATTTTCATAATA
1 -CATAACTTACATAATTTTCATAATACATAACTTACATAATT
* *
34365227 CATAACTTACATAATTGATCATAATCCA-ACACTTACATAATT
1 CATAACTTACATAATT-TTCATAATACATA-ACTTACATAATT
* *
34365269 CACAACTTACATAATATTCATAATACATAACTTACATAATTTT
1 CATAACTTACATAATTTTCATAATACATAACTTACATAA--TT
* * *
34365312 CATAA--TAAATAACTTACATAATACATAACTTACATA
1 CATAACTTACATAATTTTCATAATACATAACTTACATA
34365348 GCTTAAGTAT
Statistics
Matches: 305, Mismatches: 48, Indels: 38
0.78 0.12 0.10
Matches are distributed among these distances:
39 1 0.00
40 1 0.00
41 196 0.64
42 32 0.10
43 63 0.21
44 3 0.01
45 9 0.03
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (41 bp):
CATAACTTACATAATTTTCATAATACATAACTTACATAATT
Found at i:34373419 original size:413 final size:413
Alignment explanation
Indices: 34372652--34373481 Score: 1570
Period size: 413 Copynumber: 2.0 Consensus size: 413
34372642 TATGTTGGGA
* * *
34372652 GTTTTGACTACTCCATTGTTCTCTAACCTGTTAGAACAAGTGTTAGAACAACATTTGTGTTACTA
1 GTTTTGACTACTCCATTGTTCTATAACATGTTAGAACAAGTGATAGAACAACATTTGTGTTACTA
**
34372717 TAAAAACTTGTTGATTGGCATGCTTGACAGTATATGGGCCTCGAGTGCATCTTAATAAACCAACA
66 TAAAAACTCATTGATTGGCATGCTTGACAGTATATGGGCCTCGAGTGCATCTTAATAAACCAACA
34372782 AAACATTTTGTACGCAATATTTTAGAGCTATCAACACCATCATACATATCTTGAAGAAGAAGCAT
131 AAACATTTTGTACGCAATATTTTAGAGCTATCAACACCATCATACATATCTTGAAGAAGAAGCAT
* *
34372847 GGAAAGTTTAAATTATTTGGTTTACTAAAGCTTATCCTTATCTTATCGGATAAGGGCACTTTATC
196 AGAAAGTTTAAATTATTTGGTTTACTAAAGCTTATCATTATCTTATCGGATAAGGGCACTTTATC
34372912 AGCCATGAGATACCTGATTATGATGTTGTTTATGATATTATTGTCAAGATAATTATTTAAATAAA
261 AGCCATGAGATACCTGATTATGATGTTGTTTATGATATTATTGTCAAGATAATTATTTAAATAAA
* *
34372977 ATCAACGTTTAAATTAGTGATAAGTTCTTATCTTAATCAACGTTGGAGAATAGTTGTAATAGCTA
326 ATCAACGTTTAAATTAGTGATAAGTTCTTATCTTAATCAACGTTGGAAAATAGCTGTAATAGCTA
34373042 GCTGATCAACTTCCTCATTAGTC
391 GCTGATCAACTTCCTCATTAGTC
34373065 GTTTTGACTACTCCATTGTTCTATAACATGTTAGAACAAGTGATAGAACAACATTTGTGTTACTA
1 GTTTTGACTACTCCATTGTTCTATAACATGTTAGAACAAGTGATAGAACAACATTTGTGTTACTA
*
34373130 TCAAAACTCATTGATTGGCATGCTTGACAGTATATGGGCCTCGAGTGCATCTTAATAAACCAACA
66 TAAAAACTCATTGATTGGCATGCTTGACAGTATATGGGCCTCGAGTGCATCTTAATAAACCAACA
34373195 AAACATTTTGTACGCAATATTTTAGAGCTATCAACACCATCATACATATCTTGAAGAAGAAGCAT
131 AAACATTTTGTACGCAATATTTTAGAGCTATCAACACCATCATACATATCTTGAAGAAGAAGCAT
34373260 AGAAAGTTTAAATTATTTGGTTTACTAAAGCTTATCATTATCTTATCGGATAAGGGCACTTTATC
196 AGAAAGTTTAAATTATTTGGTTTACTAAAGCTTATCATTATCTTATCGGATAAGGGCACTTTATC
34373325 AGCCATGAGATACCTGATTATGATGTTGTTTATGATATTATTGTCAAGATAATTATTTAAATAAA
261 AGCCATGAGATACCTGATTATGATGTTGTTTATGATATTATTGTCAAGATAATTATTTAAATAAA
34373390 ATCAACGTTTAAATTAGTGATAAGTTCTTATCTTAATCAACGTTGGAAAATAGCTGTAATAGCTA
326 ATCAACGTTTAAATTAGTGATAAGTTCTTATCTTAATCAACGTTGGAAAATAGCTGTAATAGCTA
34373455 GCTGATCAACTTCCTCATTAGTC
391 GCTGATCAACTTCCTCATTAGTC
34373478 GTTT
1 GTTT
34373482 GGGGTGTGTG
Statistics
Matches: 407, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
413 407 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (413 bp):
GTTTTGACTACTCCATTGTTCTATAACATGTTAGAACAAGTGATAGAACAACATTTGTGTTACTA
TAAAAACTCATTGATTGGCATGCTTGACAGTATATGGGCCTCGAGTGCATCTTAATAAACCAACA
AAACATTTTGTACGCAATATTTTAGAGCTATCAACACCATCATACATATCTTGAAGAAGAAGCAT
AGAAAGTTTAAATTATTTGGTTTACTAAAGCTTATCATTATCTTATCGGATAAGGGCACTTTATC
AGCCATGAGATACCTGATTATGATGTTGTTTATGATATTATTGTCAAGATAATTATTTAAATAAA
ATCAACGTTTAAATTAGTGATAAGTTCTTATCTTAATCAACGTTGGAAAATAGCTGTAATAGCTA
GCTGATCAACTTCCTCATTAGTC
Found at i:34378243 original size:60 final size:60
Alignment explanation
Indices: 34378169--34378285 Score: 216
Period size: 60 Copynumber: 1.9 Consensus size: 60
34378159 ATACTAAACT
*
34378169 AAACACAACAATTTATAACATAATCTTAAATTACTAATAAATTAATTTTAAAATAATAAC
1 AAACACAACAATTTATAACATAATCTTAAATTACTAACAAATTAATTTTAAAATAATAAC
*
34378229 AAACACAACCATTTATAACATAATCTTAAATTACTAACAAATTAATTTTAAAATAAT
1 AAACACAACAATTTATAACATAATCTTAAATTACTAACAAATTAATTTTAAAATAAT
34378286 TTTAAAAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (60 bp):
AAACACAACAATTTATAACATAATCTTAAATTACTAACAAATTAATTTTAAAATAATAAC
Found at i:34384743 original size:18 final size:18
Alignment explanation
Indices: 34384720--34384779 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
34384710 CTCCCCCTTC
34384720 TTCCTCACCTACATCTTT
1 TTCCTCACCTACATCTTT
*
34384738 TTCCTCGA-CTAC-CCTTT
1 TTCCTC-ACCTACATCTTT
*
34384755 CTTCCTCACCTACATCTTC
1 -TTCCTCACCTACATCTTT
34384774 TTCCTC
1 TTCCTC
34384780 TGTCGCATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
17 5 0.14
18 26 0.74
19 4 0.11
ACGTcount: A:0.13, C:0.43, G:0.02, T:0.42
Consensus pattern (18 bp):
TTCCTCACCTACATCTTT
Found at i:34384793 original size:36 final size:36
Alignment explanation
Indices: 34384716--34384799 Score: 102
Period size: 36 Copynumber: 2.3 Consensus size: 36
34384706 TTCGCTCCCC
* *
34384716 CTTCTTCCTCACCTACATCTTTTTCCTCGACTACCCT
1 CTTCTTCCTCACCTACATCTTCTTCCTCGA-TACCAT
34384753 -TTCTTCCTCACCTACATCTTCTTCCTCTG-T-CGCAT
1 CTTCTTCCTCACCTACATCTTCTTCCTC-GATAC-CAT
34384788 CTTCTTCCTCAC
1 CTTCTTCCTCAC
34384800 ATATGACTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
34 1 0.02
35 3 0.07
36 37 0.88
37 1 0.02
ACGTcount: A:0.12, C:0.43, G:0.04, T:0.42
Consensus pattern (36 bp):
CTTCTTCCTCACCTACATCTTCTTCCTCGATACCAT
Found at i:34402214 original size:21 final size:22
Alignment explanation
Indices: 34402181--34402223 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
34402171 ATGAATACGG
* *
34402181 GGTATTAGTGTTAC-ATTTAGT
1 GGTATCAGAGTTACGATTTAGT
34402202 GGTATCAGAGTTACGATTTAGT
1 GGTATCAGAGTTACGATTTAGT
34402224 CAGTTCTCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.42
Consensus pattern (22 bp):
GGTATCAGAGTTACGATTTAGT
Found at i:34406188 original size:24 final size:23
Alignment explanation
Indices: 34406134--34406211 Score: 63
Period size: 22 Copynumber: 3.4 Consensus size: 23
34406124 GAATAAACAA
*
34406134 GAAATGGTATTTGGTTTAGGTAC
1 GAAATGGTATTTGGATTAGGTAC
**
34406157 GATTTGGTATTTCGGAATT-GGTAC
1 GAAATGGTATTT-GG-ATTAGGTAC
*
34406181 GAAATGGTA--TGGTATTTGGTAC
1 GAAATGGTATTTGG-ATTAGGTAC
*
34406203 GAATTGGTA
1 GAAATGGTA
34406212 ATGGTTCAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
21 5 0.11
22 14 0.31
23 10 0.22
24 14 0.31
25 2 0.04
ACGTcount: A:0.26, C:0.05, G:0.31, T:0.38
Consensus pattern (23 bp):
GAAATGGTATTTGGATTAGGTAC
Found at i:34406202 original size:22 final size:23
Alignment explanation
Indices: 34406174--34406216 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
34406164 TATTTCGGAA
34406174 TTGGTACGAAATGGT-ATGGTAT
1 TTGGTACGAAATGGTAATGGTAT
*
34406196 TTGGTACGAATTGGTAATGGT
1 TTGGTACGAAATGGTAATGGT
34406217 TCAAAAAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.26, C:0.05, G:0.33, T:0.37
Consensus pattern (23 bp):
TTGGTACGAAATGGTAATGGTAT
Found at i:34406987 original size:20 final size:20
Alignment explanation
Indices: 34406962--34407002 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
34406952 GCTCACCAAT
34406962 TTGATGCATGTATCTCCAGG
1 TTGATGCATGTATCTCCAGG
34406982 TTGATGCATGTATCTCCAGG
1 TTGATGCATGTATCTCCAGG
34407002 T
1 T
34407003 GCAATGTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGATGCATGTATCTCCAGG
Found at i:34407070 original size:31 final size:32
Alignment explanation
Indices: 34407025--34407091 Score: 77
Period size: 31 Copynumber: 2.1 Consensus size: 32
34407015 ACATGCATGC
*
34407025 ACCTTGCTAAAATGAATCTCCA-A-ATTCGGCTA
1 ACCTTGCTAAAATG-ATC-CCACACATTCGGCCA
*
34407057 ACCTTG-TTAAATGATCCCACACATTCGGCCA
1 ACCTTGCTAAAATGATCCCACACATTCGGCCA
34407088 ACCT
1 ACCT
34407092 ATATAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 3 0.10
30 4 0.13
31 18 0.58
32 6 0.19
ACGTcount: A:0.31, C:0.30, G:0.12, T:0.27
Consensus pattern (32 bp):
ACCTTGCTAAAATGATCCCACACATTCGGCCA
Found at i:34407423 original size:30 final size:30
Alignment explanation
Indices: 34407365--34407423 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
34407355 TTGAAAATGT
* *
34407365 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
34407395 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
34407424 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:34411012 original size:25 final size:22
Alignment explanation
Indices: 34410959--34411002 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
34410949 CATATTAGAG
*
34410959 TGTAGTTTAACCACCAATGGTT
1 TGTAGATTAACCACCAATGGTT
*
34410981 TGTAGATTAACTACCAATGGTT
1 TGTAGATTAACCACCAATGGTT
34411003 GTGGATAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (22 bp):
TGTAGATTAACCACCAATGGTT
Found at i:34418607 original size:19 final size:19
Alignment explanation
Indices: 34418583--34418626 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
34418573 TATTTATTTT
*
34418583 TTTAATTAGAATCGAAAAG
1 TTTAATTAGAATAGAAAAG
34418602 TTTAATTAGAATAGAAAAG
1 TTTAATTAGAATAGAAAAG
*
34418621 TATAAT
1 TTTAAT
34418627 AAAAGTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.50, C:0.02, G:0.14, T:0.34
Consensus pattern (19 bp):
TTTAATTAGAATAGAAAAG
Found at i:34419581 original size:27 final size:26
Alignment explanation
Indices: 34419551--34419667 Score: 153
Period size: 26 Copynumber: 4.4 Consensus size: 26
34419541 AAAATGATCG
*
34419551 TAGGGTAAAATGACTGAAATACCCCCA
1 TAGGGTAAAAT-ACCGAAATACCCCCA
* * *
34419578 TAGGGAAAAATAACCGAAATACCCTCG
1 TAGGGTAAAAT-ACCGAAATACCCCCA
* *
34419605 TAGGGTAGAATACCGAAATACCCTCA
1 TAGGGTAAAATACCGAAATACCCCCA
*
34419631 TAGGGTAGAATACCGAAATACCCCCA
1 TAGGGTAAAATACCGAAATACCCCCA
34419657 TAGGGTAAAAT
1 TAGGGTAAAAT
34419668 GATCATAATA
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
26 49 0.61
27 31 0.39
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (26 bp):
TAGGGTAAAATACCGAAATACCCCCA
Found at i:34419715 original size:21 final size:21
Alignment explanation
Indices: 34419686--34419729 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
34419676 TACCCCTGTG
*
34419686 TGGGTTGTTCGTGATATAAAT
1 TGGGATGTTCGTGATATAAAT
34419707 TGGGATGTTCGTGATATAAAT
1 TGGGATGTTCGTGATATAAAT
34419728 TG
1 TG
34419730 AATTGTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.05, G:0.30, T:0.41
Consensus pattern (21 bp):
TGGGATGTTCGTGATATAAAT
Found at i:34422552 original size:25 final size:26
Alignment explanation
Indices: 34422502--34422552 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
34422492 TTTAAAACAC
*
34422502 AAAAATAAATACCAAAATGGGTTTAT
1 AAAAATAAATACCAAAATGGGATTAT
34422528 AAAAATAAATACCAAAAT-GGATTAT
1 AAAAATAAATACCAAAATGGGATTAT
34422553 TTGCTTGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.57, C:0.08, G:0.10, T:0.25
Consensus pattern (26 bp):
AAAAATAAATACCAAAATGGGATTAT
Found at i:34428934 original size:18 final size:20
Alignment explanation
Indices: 34428895--34428934 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
34428885 TAAAATATTG
*
34428895 TATTTAATTTTTTTTCAATA
1 TATTTAATTTATTTTCAATA
34428915 TATTTAA-TTATTTT-AATA
1 TATTTAATTTATTTTCAATA
34428933 TA
1 TA
34428935 AGCTTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 6 0.32
20 7 0.37
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTAATTTATTTTCAATA
Found at i:34430066 original size:26 final size:26
Alignment explanation
Indices: 34430037--34430117 Score: 81
Period size: 26 Copynumber: 3.1 Consensus size: 26
34430027 TATTTTTTAG
*
34430037 TCAATTCAATTGGTCCATATCGATTC
1 TCAATTCAATTGATCCATATCGATTC
*** * * *
34430063 TCAATTCAACCAATCTATATCGACTA
1 TCAATTCAATTGATCCATATCGATTC
* *
34430089 TCAATCCAATTGATCCATATCGGTTC
1 TCAATTCAATTGATCCATATCGATTC
34430115 TCA
1 TCA
34430118 GCCCAACTAA
Statistics
Matches: 40, Mismatches: 15, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.35
Consensus pattern (26 bp):
TCAATTCAATTGATCCATATCGATTC
Found at i:34432577 original size:24 final size:25
Alignment explanation
Indices: 34432545--34432649 Score: 77
Period size: 25 Copynumber: 4.2 Consensus size: 25
34432535 ATTCATGTAT
* *
34432545 GCTCATACAAGATGTA-AACGGGAA
1 GCTCATACAAGATGAATAACGGAAA
* *
34432569 GCTCCTACAAGTTGAATAACGGAAA
1 GCTCATACAAGATGAATAACGGAAA
* * * * *
34432594 GCTCATGCGAGCTAAATAACGGGAA
1 GCTCATACAAGATGAATAACGGAAA
* * * * *
34432619 GCTCATGCGAGCTAAATAACGGGAA
1 GCTCATACAAGATGAATAACGGAAA
34432644 GCTCAT
1 GCTCAT
34432650 GTGAGTTAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
24 13 0.19
25 57 0.81
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18
Consensus pattern (25 bp):
GCTCATACAAGATGAATAACGGAAA
Found at i:34432611 original size:25 final size:25
Alignment explanation
Indices: 34432583--34432694 Score: 170
Period size: 25 Copynumber: 4.5 Consensus size: 25
34432573 CTACAAGTTG
*
34432583 AATAACGGAAAGCTCATGCGAGCTA
1 AATAACGGGAAGCTCATGCGAGCTA
34432608 AATAACGGGAAGCTCATGCGAGCTA
1 AATAACGGGAAGCTCATGCGAGCTA
* *
34432633 AATAACGGGAAGCTCATGTGAGTTA
1 AATAACGGGAAGCTCATGCGAGCTA
* *
34432658 AATAACAGGAAGCTCATGCGAGCTT
1 AATAACGGGAAGCTCATGCGAGCTA
*
34432683 TATAACGGGAAG
1 AATAACGGGAAG
34432695 ATATGCAAGC
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 78 1.00
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.19
Consensus pattern (25 bp):
AATAACGGGAAGCTCATGCGAGCTA
Found at i:34432619 original size:50 final size:50
Alignment explanation
Indices: 34432561--34432674 Score: 147
Period size: 50 Copynumber: 2.3 Consensus size: 50
34432551 ACAAGATGTA
* * *
34432561 AACGGGAAGCTCCTACAAGTTGAATAACGGAAAGCTCATGCGAGCTAAAT
1 AACGGGAAGCTCATACAAGCTAAATAACGGAAAGCTCATGCGAGCTAAAT
* * * * *
34432611 AACGGGAAGCTCATGCGAGCTAAATAACGGGAAGCTCATGTGAGTTAAAT
1 AACGGGAAGCTCATACAAGCTAAATAACGGAAAGCTCATGCGAGCTAAAT
*
34432661 AACAGGAAGCTCAT
1 AACGGGAAGCTCAT
34432675 GCGAGCTTTA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.18
Consensus pattern (50 bp):
AACGGGAAGCTCATACAAGCTAAATAACGGAAAGCTCATGCGAGCTAAAT
Found at i:34432705 original size:24 final size:25
Alignment explanation
Indices: 34432659--34432705 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
34432649 TGTGAGTTAA
* *
34432659 ATAACAGGAAGCTCATGCGAGCTTT
1 ATAACAGGAAGATCATGCAAGCTTT
*
34432684 ATAACGGGAAGAT-ATGCAAGCT
1 ATAACAGGAAGATCATGCAAGCT
34432706 GTGGTGTGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (25 bp):
ATAACAGGAAGATCATGCAAGCTTT
Found at i:34433869 original size:15 final size:15
Alignment explanation
Indices: 34433849--34433885 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
34433839 ATCGTTCTTT
34433849 TATTTTTCATTTATA
1 TATTTTTCATTTATA
* *
34433864 TATTTTTCATTTTTT
1 TATTTTTCATTTATA
34433879 TATTTTT
1 TATTTTT
34433886 TCTCTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (15 bp):
TATTTTTCATTTATA
Found at i:34434523 original size:19 final size:19
Alignment explanation
Indices: 34434495--34434553 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
34434485 TTTTTTATAT
*
34434495 TATTAATATTGTTTATTTA
1 TATTATTATTGTTTATTTA
34434514 TATTATTATTGTATTA-TTA
1 TATTATTATTGT-TTATTTA
*
34434533 TTAGTTTTTATT-TTTATTTA
1 -TA-TTATTATTGTTTATTTA
34434553 T
1 T
34434554 TATATTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
19 18 0.53
20 9 0.26
21 7 0.21
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
TATTATTATTGTTTATTTA
Found at i:34434543 original size:33 final size:34
Alignment explanation
Indices: 34434492--34434571 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 34
34434482 CTATTTTTTA
*
34434492 TATTATTAATATTGTTTATTTATA-TTATTAT-T
1 TATTATTATTATTGTTTATTTATATTTATTATAT
*
34434524 GTATTATTATTAGTT-TTTATTTTTATTTATTATAT
1 -TATTATTATTA-TTGTTTATTTATATTTATTATAT
34434559 TATATATTATTAT
1 TAT-TATTATTAT
34434572 ACCTATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
33 19 0.46
34 13 0.32
35 9 0.22
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (34 bp):
TATTATTATTATTGTTTATTTATATTTATTATAT
Found at i:34434566 original size:22 final size:21
Alignment explanation
Indices: 34434483--34434571 Score: 76
Period size: 22 Copynumber: 4.1 Consensus size: 21
34434473 TTTGTTATTC
* *
34434483 TATTTTTTATATTATTAATAT
1 TATTTATTATATTATTATTAT
*
34434504 TGTTTATTTATATTATTATTGTAT
1 TATTTA-TTATATTATTA-T-TAT
*
34434528 TA-TTATTAGT-TT-TTATTTT
1 TATTTATTA-TATTATTATTAT
34434547 TATTTATTATATTATATATTAT
1 TATTTATTATATTAT-TATTAT
34434569 TAT
1 TAT
34434572 ACCTATATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
19 5 0.09
20 9 0.17
21 8 0.15
22 24 0.44
23 4 0.07
24 4 0.07
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.67
Consensus pattern (21 bp):
TATTTATTATATTATTATTAT
Found at i:34440739 original size:10 final size:10
Alignment explanation
Indices: 34440724--34440759 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
34440714 TTAAAATATT
34440724 TATTTTTTAA
1 TATTTTTTAA
34440734 TATTTTATT-A
1 TATTTT-TTAA
34440744 TATTTTTTAA
1 TATTTTTTAA
34440754 TATTTT
1 TATTTT
34440760 AATTCTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 2 0.08
10 20 0.83
11 2 0.08
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TATTTTTTAA
Found at i:34440740 original size:15 final size:16
Alignment explanation
Indices: 34440709--34440742 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
34440699 TGTCATATGA
34440709 ATTTTTTAAAATATTT
1 ATTTTTTAAAATATTT
*
34440725 ATTTTTTAATAT-TTT
1 ATTTTTTAAAATATTT
34440740 ATT
1 ATT
34440743 ATATTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTTTAAAATATTT
Found at i:34440749 original size:20 final size:19
Alignment explanation
Indices: 34440720--34440760 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
34440710 TTTTTTAAAA
34440720 TATTTATTTTTTAATATTT
1 TATTTATTTTTTAATATTT
34440739 TATTATATTTTTTAATATTT
1 TATT-TATTTTTTAATATTT
34440759 TA
1 TA
34440761 ATTCTACTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTATTTTTTAATATTT
Found at i:34443293 original size:71 final size:68
Alignment explanation
Indices: 34443203--34443358 Score: 183
Period size: 71 Copynumber: 2.3 Consensus size: 68
34443193 ACTTAAATCA
* *
34443203 TAGAAAG-AAA-CTTTTGAAAAATCAAAGAACG-TTAGAAAAAGAAGTTTTTGAGAAACCAAAGA
1 TAGAAAGAAAAGCTTTTGAAAAACCAAAGAACGTTTA-AAAAAGAAGCTTTTGAGAAA-C--AGA
34443265 AGAGCAT
62 AGAGCAT
* * * *
34443272 TAGAAAGAAAAGCTTTTGAAAAACCAGAGAGCGTTTAAAAGAGAAGCTTTTGAGAAACTGAAGAG
1 TAGAAAGAAAAGCTTTTGAAAAACCAAAGAACGTTTAAAAAAGAAGCTTTTGAGAAACAGAAGAG
34443337 CAT
66 CAT
* *
34443340 TTGAAAGACAAGCTTTTGA
1 TAGAAAGAAAAGCTTTTGA
34443359 GAGAAGTAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
68 26 0.34
69 7 0.09
70 4 0.05
71 36 0.47
72 3 0.04
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.22
Consensus pattern (68 bp):
TAGAAAGAAAAGCTTTTGAAAAACCAAAGAACGTTTAAAAAAGAAGCTTTTGAGAAACAGAAGAG
CAT
Found at i:34443359 original size:34 final size:33
Alignment explanation
Indices: 34443263--34443360 Score: 115
Period size: 34 Copynumber: 2.9 Consensus size: 33
34443253 AGAAACCAAA
* *
34443263 GAAGAGCATTAGAAAGAAAAGCTTTTGAAAAAC
1 GAAGAGCATTTGAAAGAAAAGCTTTTGAGAAAC
* * * *
34443296 CAGAGAGCGTTTAAAAGAGAAGCTTTTGAGAAAC
1 GA-AGAGCATTTGAAAGAAAAGCTTTTGAGAAAC
*
34443330 TGAAGAGCATTTGAAAGACAAGCTTTTGAGA
1 -GAAGAGCATTTGAAAGAAAAGCTTTTGAGA
34443361 GAAGTAAAAC
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
33 1 0.02
34 51 0.96
35 1 0.02
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.21
Consensus pattern (33 bp):
GAAGAGCATTTGAAAGAAAAGCTTTTGAGAAAC
Found at i:34445044 original size:23 final size:22
Alignment explanation
Indices: 34445018--34445071 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
34445008 TGTATACGCG
34445018 TACATAATAAAAATATATACTAA
1 TACATAATAAAAATA-ATACTAA
* *
34445041 TACATAATAATAATAATAGTAA
1 TACATAATAAAAATAATACTAA
34445063 TAC-TAATAA
1 TACATAATAA
34445072 TACTAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 6 0.21
22 9 0.31
23 14 0.48
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.31
Consensus pattern (22 bp):
TACATAATAAAAATAATACTAA
Found at i:34445052 original size:3 final size:3
Alignment explanation
Indices: 34445021--34445086 Score: 60
Period size: 3 Copynumber: 21.3 Consensus size: 3
34445011 ATACGCGTAC
* * * *
34445021 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA ATA GTA ATA CTA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
34445068 ATA ATA CTA ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA A
34445087 CAAGGATATT
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:34445573 original size:11 final size:12
Alignment explanation
Indices: 34445553--34445590 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
34445543 AGAAAAAAAA
34445553 GAAGAGAGAGAGG
1 GAAGAGAGA-AGG
34445566 GAAGAGAGAAGG
1 GAAGAGAGAAGG
34445578 G-AGAGAGAAGG
1 GAAGAGAGAAGG
34445589 GA
1 GA
34445591 GGGGGGAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.46
12 4 0.17
13 9 0.38
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:34448376 original size:14 final size:14
Alignment explanation
Indices: 34448357--34448396 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
34448347 TTGATTGCCA
34448357 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
34448371 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
34448385 GGAAAATGTTTT
1 GTAAAATGTTTT
34448397 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:34448409 original size:34 final size:35
Alignment explanation
Indices: 34448365--34448432 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 35
34448355 CAGTAAAATG
* *
34448365 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAAGGATTTACTGGAAAATATTTTAC
* *
34448399 TTTTCTGTAAAGGGATTTACTGGAAAATATTTTA
1 TTTTCCGTAAAAGGATTTACTGGAAAATATTTTA
34448433 TGGTGTTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 15 0.52
35 14 0.48
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (35 bp):
TTTTCCGTAAAAGGATTTACTGGAAAATATTTTAC
Found at i:34448533 original size:20 final size:20
Alignment explanation
Indices: 34448508--34448560 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 20
34448498 TGAAAAAGTT
34448508 ATTTTTACATATATT-AATAA
1 ATTTTTACATATATTAAAT-A
* *
34448528 ATTTTT--ATATTTTAAATT
1 ATTTTTACATATATTAAATA
34448546 ATTTTTACATATATT
1 ATTTTTACATATATT
34448561 GCAATGATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 12 0.44
19 3 0.11
20 12 0.44
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTTTACATATATTAAATA
Found at i:34450986 original size:14 final size:14
Alignment explanation
Indices: 34450967--34451006 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
34450957 TTGATTGCCA
34450967 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
34450981 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
34450995 GGAAAATGTTTT
1 GTAAAATGTTTT
34451007 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:34451015 original size:20 final size:20
Alignment explanation
Indices: 34450990--34451029 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
34450980 CGTAAAATGA
*
34450990 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
34451010 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
34451030 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:34451019 original size:34 final size:35
Alignment explanation
Indices: 34450975--34451041 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
34450965 CAGTAAAATG
*
34450975 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
34451009 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
34451042 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:34451045 original size:14 final size:15
Alignment explanation
Indices: 34450969--34451045 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
34450959 GATTGCCAGT
* *
34450969 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
34450983 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
34450997 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
34451017 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
34451032 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
34451046 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:34451801 original size:11 final size:11
Alignment explanation
Indices: 34451785--34451809 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
34451775 GTCTACAGGT
34451785 ATTGAATCTTC
1 ATTGAATCTTC
34451796 ATTGAATCTTC
1 ATTGAATCTTC
34451807 ATT
1 ATT
34451810 ACCATCATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (11 bp):
ATTGAATCTTC
Found at i:34452427 original size:35 final size:36
Alignment explanation
Indices: 34452381--34452449 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
34452371 TGTCAATCAT
34452381 TTCAATATCCAACAACCTTAAAACATAAT-AATAAA
1 TTCAATATCCAACAACCTTAAAACATAATCAATAAA
**
34452416 TTCAATATCCAACAAGGTTAAAACATAATCAATA
1 TTCAATATCCAACAACCTTAAAACATAATCAATA
34452450 TCTAACAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 27 0.87
36 4 0.13
ACGTcount: A:0.52, C:0.19, G:0.03, T:0.26
Consensus pattern (36 bp):
TTCAATATCCAACAACCTTAAAACATAATCAATAAA
Found at i:34452447 original size:27 final size:28
Alignment explanation
Indices: 34452417--34452485 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
34452407 AATAATAAAT
*
34452417 TCAATATCCAACAAGGTT-AAAACATA-A
1 TCAATATCCAACAA-ATTCAAAACATATA
* *
34452444 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAACAAATTCAAAACATATA
*
34452472 TCAAAATCCAACAA
1 TCAATATCCAACAA
34452486 TCTAAAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 2 0.06
27 20 0.57
28 13 0.37
ACGTcount: A:0.52, C:0.20, G:0.04, T:0.23
Consensus pattern (28 bp):
TCAATATCCAACAAATTCAAAACATATA
Found at i:34454928 original size:28 final size:28
Alignment explanation
Indices: 34454884--34454940 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
34454874 TCTCTAGCAT
* *
34454884 CAAATACTAACAGATCATTAAGTGCTAA
1 CAAATACTAACAAATCAGTAAGTGCTAA
34454912 CAAATACTAACAAATCAGTAAGTGCTAA
1 CAAATACTAACAAATCAGTAAGTGCTAA
34454940 C
1 C
34454941 TAGAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.23
Consensus pattern (28 bp):
CAAATACTAACAAATCAGTAAGTGCTAA
Found at i:34457381 original size:5 final size:5
Alignment explanation
Indices: 34457344--34457404 Score: 81
Period size: 5 Copynumber: 12.2 Consensus size: 5
34457334 TTTTTATGTT
*
34457344 TTATA TATATA TTATT TTAT- TATATA TTA-A TTATA TTATA TTATA TTATA
1 TTATA T-TATA TTATA TTATA T-TATA TTATA TTATA TTATA TTATA TTATA
34457394 TTATA TTATA T
1 TTATA TTATA T
34457405 AAACTAAATA
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
4 5 0.10
5 40 0.78
6 6 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:34457632 original size:22 final size:22
Alignment explanation
Indices: 34457593--34457640 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
34457583 AAATAAAAGA
*
34457593 AAAAGAAACAAAGGAAGA-ACAG
1 AAAAGAAACAAAGAAAGAGAC-G
*
34457615 AAAAGAAACAGAGAAAGAGACG
1 AAAAGAAACAAAGAAAGAGACG
34457637 AAAA
1 AAAA
34457641 CAGGGGAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.69, C:0.08, G:0.23, T:0.00
Consensus pattern (22 bp):
AAAAGAAACAAAGAAAGAGACG
Found at i:34457670 original size:30 final size:30
Alignment explanation
Indices: 34457617--34457675 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
34457607 AAGAACAGAA
* * * *
34457617 AAGAAACAGAGAAAGAGACGAAAACAGGGG
1 AAGAAAAAGAGAAAGAAAAGAAAAAAGGGG
*
34457647 AAGAAAAAGGGAAAGAAAAGAAAAAAGGG
1 AAGAAAAAGAGAAAGAAAAGAAAAAAGGG
34457676 AAAATTCAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.63, C:0.05, G:0.32, T:0.00
Consensus pattern (30 bp):
AAGAAAAAGAGAAAGAAAAGAAAAAAGGGG
Found at i:34458023 original size:22 final size:24
Alignment explanation
Indices: 34457998--34458041 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
34457988 TATAGTAAGA
*
34457998 AATTAAG-TGGAAAAG-AAGTATG
1 AATTAAGTTAGAAAAGTAAGTATG
34458020 AATTAAGTTAGAAAAGTAAGTA
1 AATTAAGTTAGAAAAGTAAGTA
34458042 AGCTTAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 7 0.37
24 5 0.26
ACGTcount: A:0.52, C:0.00, G:0.23, T:0.25
Consensus pattern (24 bp):
AATTAAGTTAGAAAAGTAAGTATG
Found at i:34467044 original size:23 final size:23
Alignment explanation
Indices: 34467014--34467089 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
34467004 ATAAGTGACA
*
34467014 CACTGATATGTAACCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
34467037 CACTGATATGTGGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
34467060 CGCTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
34467083 CACTGAT
1 CACTGAT
34467090 CAATAACACT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:34467333 original size:18 final size:17
Alignment explanation
Indices: 34467307--34467345 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
34467297 ATTTTCCTTC
34467307 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
34467324 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
34467342 CACA
1 CACA
34467346 AGTTATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:34467422 original size:22 final size:22
Alignment explanation
Indices: 34467397--34467445 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
34467387 ACAATTTATA
*
34467397 TTATATTATATTTAGAGGTATT
1 TTATATTATATTTACAGGTATT
34467419 TTATATTATATTTACAGGTATT
1 TTATATTATATTTACAGGTATT
34467441 TTATA
1 TTATA
34467446 CCATAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (22 bp):
TTATATTATATTTACAGGTATT
Found at i:34469593 original size:23 final size:23
Alignment explanation
Indices: 34469563--34469638 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
34469553 ATAAGTGACA
*
34469563 CACTGATATGTAACCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
34469586 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
34469609 CATTGAAATGTAGCCGAAGCTGC
1 CACTGATATGTAGCCGAAGCTAC
34469632 CACTGAT
1 CACTGAT
34469639 CAATAACACT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:34471516 original size:23 final size:25
Alignment explanation
Indices: 34471485--34471533 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
34471475 ATAATGGGTG
34471485 AATTCATCCGAC-AAAAATTTAAAA
1 AATTCATCCGACAAAAAATTTAAAA
*
34471509 AATT-ATCCTACAAAAAATTTAAAA
1 AATTCATCCGACAAAAAATTTAAAA
34471533 A
1 A
34471534 TGACCCATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (25 bp):
AATTCATCCGACAAAAAATTTAAAA
Found at i:34483370 original size:3 final size:3
Alignment explanation
Indices: 34483362--34483386 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
34483352 TTAAAACTTG
34483362 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
34483387 TGTAGGTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:34488104 original size:6 final size:6
Alignment explanation
Indices: 34488093--34488119 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
34488083 GGCTTTAACT
34488093 AAAACG AAAACG AAAACG AAAACG AAA
1 AAAACG AAAACG AAAACG AAAACG AAA
34488120 TCTCATAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.15, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAACG
Found at i:34491950 original size:24 final size:25
Alignment explanation
Indices: 34491914--34491970 Score: 80
Period size: 26 Copynumber: 2.3 Consensus size: 25
34491904 ATAAAAAATA
* *
34491914 ACCAAAATGTTAT-TTTTTTTATTT
1 ACCAAAATATTATAATTTTTTATTT
34491938 ACCAAAATATTATAAATTTTTTATTT
1 ACCAAAATATTAT-AATTTTTTATTT
34491964 ACCAAAA
1 ACCAAAA
34491971 CATACTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 12 0.41
26 17 0.59
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (25 bp):
ACCAAAATATTATAATTTTTTATTT
Found at i:34492003 original size:15 final size:16
Alignment explanation
Indices: 34491979--34492008 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
34491969 AACATACTAA
34491979 AAAAACAAAAACCTGC
1 AAAAACAAAAACCTGC
34491995 AAAAA-AAAAACCTG
1 AAAAACAAAAACCTG
34492009 ACAACAGCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.20, G:0.07, T:0.07
Consensus pattern (16 bp):
AAAAACAAAAACCTGC
Found at i:34492064 original size:27 final size:27
Alignment explanation
Indices: 34492043--34492099 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
34492033 CATTGGCGGC
34492043 ACCAAAGGTGCCAAAGAGATTGGCCCG
1 ACCAAAGGTGCCAAAGAGATTGGCCCG
*
34492070 ACCAAAGGTGCCAAAGAGATTGGCCTG
1 ACCAAAGGTGCCAAAGAGATTGGCCCG
34492097 ACC
1 ACC
34492100 GGACTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.33, C:0.26, G:0.28, T:0.12
Consensus pattern (27 bp):
ACCAAAGGTGCCAAAGAGATTGGCCCG
Found at i:34492546 original size:19 final size:19
Alignment explanation
Indices: 34492522--34492584 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
34492512 AAGCAATAGT
34492522 TTATTAAAGTAAAATAGAG
1 TTATTAAAGTAAAATAGAG
*** ** * *
34492541 TTATTACTTTTTAATAAAC
1 TTATTAAAGTAAAATAGAG
34492560 TTATTAAAGTAAAATAGAG
1 TTATTAAAGTAAAATAGAG
34492579 TTATTA
1 TTATTA
34492585 CTTAATTAGA
Statistics
Matches: 30, Mismatches: 14, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (19 bp):
TTATTAAAGTAAAATAGAG
Found at i:34493233 original size:27 final size:27
Alignment explanation
Indices: 34493194--34493269 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
34493184 TAGTATTGGC
*
34493194 GCCTATCTCAGAGGCGCCAATGGTGGT
1 GCCTATCTGAGAGGCGCCAATGGTGGT
* * * *
34493221 GCCTATCTGAGAGGTGTCATTAGTGGT
1 GCCTATCTGAGAGGCGCCAATGGTGGT
*
34493248 GCC-ATGTTGAGAGGCGCCAATG
1 GCCTAT-CTGAGAGGCGCCAATG
34493270 ATATTATTTT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 2 0.05
27 36 0.95
ACGTcount: A:0.20, C:0.21, G:0.34, T:0.25
Consensus pattern (27 bp):
GCCTATCTGAGAGGCGCCAATGGTGGT
Found at i:34493356 original size:15 final size:16
Alignment explanation
Indices: 34493336--34493372 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
34493326 ACAAAATCAA
34493336 ATAAAA-TTACATAAT
1 ATAAAAGTTACATAAT
*
34493351 ATAAAAGTTACATTAT
1 ATAAAAGTTACATAAT
34493367 ATAAAA
1 ATAAAA
34493373 ATTAAATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
ATAAAAGTTACATAAT
Found at i:34493646 original size:27 final size:27
Alignment explanation
Indices: 34493610--34494002 Score: 603
Period size: 27 Copynumber: 15.0 Consensus size: 27
34493600 ACAATATTCA
34493610 TACAAAATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
*
34493637 TACAAAATTACAATATTCATATAAAAT
1 TACAAAATTACAATATTCATACAAAAT
34493664 TACAAAATTACAATATTCATAC--AA-
1 TACAAAATTACAATATTCATACAAAAT
*
34493688 -ACAATATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
*
34493714 TACAAAATTACAATATTCATATAAAAT
1 TACAAAATTACAATATTCATACAAAAT
34493741 TACAAAATTACAATATTCATAC--AA-
1 TACAAAATTACAATATTCATACAAAAT
*
34493765 -ACAATATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
*
34493791 TACAAAATTACAATATTCATATAAAAT
1 TACAAAATTACAATATTCATACAAAAT
*
34493818 TACAATATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
*
34493845 TATAAAATTACAATATTCATAC--AA-
1 TACAAAATTACAATATTCATACAAAAT
*
34493869 -ACAATATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
*
34493895 TACAAAATTACAATATTCATATAAAAT
1 TACAAAATTACAATATTCATACAAAAT
*
34493922 TACAATATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
*
34493949 TATAAAATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
34493976 TACAAAATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
34494003 ACTAATCCAA
Statistics
Matches: 332, Mismatches: 22, Indels: 24
0.88 0.06 0.06
Matches are distributed among these distances:
23 59 0.18
25 12 0.04
27 261 0.79
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (27 bp):
TACAAAATTACAATATTCATACAAAAT
Found at i:34493712 original size:77 final size:77
Alignment explanation
Indices: 34493596--34494000 Score: 612
Period size: 77 Copynumber: 5.3 Consensus size: 77
34493586 ATTATAAAAT
34493596 AATTACAATATTCATAC--A-AA-ATTACAATATTCATACAAAATTACAAAATTACAATATTCAT
1 AATTACAATATTCATACAAACAATATTACAATATTCATACAAAATTACAAAATTACAATATTCAT
34493657 ATAAAATTACAA
66 ATAAAATTACAA
34493669 AATTACAATATTCATACAAACAATATTACAATATTCATACAAAATTACAAAATTACAATATTCAT
1 AATTACAATATTCATACAAACAATATTACAATATTCATACAAAATTACAAAATTACAATATTCAT
34493734 ATAAAATTACAA
66 ATAAAATTACAA
34493746 AATTACAATATTCATACAAACAATATTACAATATTCATACAAAATTACAAAATTACAATATTCAT
1 AATTACAATATTCATACAAACAATATTACAATATTCATACAAAATTACAAAATTACAATATTCAT
34493811 ATAAAATTACAA
66 ATAAAATTACAA
* *
34493823 TATTACAATATTCATACAAA-ATTATAAAATTACAATATTCATAC--AA--ACAATATTACAATA
1 AATTACAATATTCATACAAACA--AT---ATTACAATATTCATACAAAATTACAAAATTACAATA
*
34493883 TTCATACAAAATTACAA
61 TTCATATAAAATTACAA
* *
34493900 AATTACAATATTCATATAAAATTACAATATTACAATATTCATACAAAATTATAAAATTACAATAT
1 AATTACAATATTC--ATACAA--ACAATATTACAATATTCATACAAAATTACAAAATTACAATAT
*
34493965 TCATACAAAATTACAA
62 TCATATAAAATTACAA
34493981 AATTACAATATTCATACAAA
1 AATTACAATATTCATACAAA
34494001 ATACTAATCC
Statistics
Matches: 306, Mismatches: 8, Indels: 32
0.88 0.02 0.09
Matches are distributed among these distances:
73 17 0.06
75 1 0.00
76 3 0.01
77 207 0.68
78 2 0.01
79 14 0.05
80 2 0.01
81 59 0.19
82 1 0.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (77 bp):
AATTACAATATTCATACAAACAATATTACAATATTCATACAAAATTACAAAATTACAATATTCAT
ATAAAATTACAA
Found at i:34494049 original size:104 final size:106
Alignment explanation
Indices: 34493610--34494084 Score: 566
Period size: 104 Copynumber: 4.5 Consensus size: 106
34493600 ACAATATTCA
* * *
34493610 TACAAAATTACAATATTCATACAAAATTACAAAATTACAATATTCATATAAAATTACAAAATTAC
1 TACAATATTACAATATT-ATACAAAATTATAAAATTACAATATTCATACAAAA-TACAAAATTAC
*
34493675 AATATTCATAC--AA--ACAATATTACAATATTCATACAAAAT
64 AATATTCATACAAAATTACAAAATTACAATATTCATACAAAAT
* * * *
34493714 TACAAAATTACAATATTCATATAAAATTACAAAATTACAATATTCATAC--AA-ACAATATTACA
1 TACAATATTACAATATT-ATACAAAATTATAAAATTACAATATTCATACAAAATACAAAATTACA
*
34493776 ATATTCATACAAAATTACAAAATTACAATATTCATATAAAAT
65 ATATTCATACAAAATTACAAAATTACAATATTCATACAAAAT
*
34493818 TACAATATTACAATATTCATACAAAATTATAAAATTACAATATTCATAC--AA-ACAATATTACA
1 TACAATATTACAATATT-ATACAAAATTATAAAATTACAATATTCATACAAAATACAAAATTACA
*
34493880 ATATTCATACAAAATTACAAAATTACAATATTCATATAAAAT
65 ATATTCATACAAAATTACAAAATTACAATATTCATACAAAAT
34493922 TACAATATTACAATATTCATACAAAATTATAAAATTACAATATTCATACAAAATTACAAAATTAC
1 TACAATATTACAATATT-ATACAAAATTATAAAATTACAATATTCATACAAAA-TACAAAATTAC
* * * **
34493987 AATATTCATACAAAA-TAC-TAATCCAAAACTATAAATACAAAAT
64 AATATTCATACAAAATTACAAAAT-TACAA-TATTCATACAAAAT
* * * *
34494030 TA-ATTA-TAAAATAAT-TACAATATTCATACAAAATTACAATATTCATACAAAATAC
1 TACAATATTACAATATTATACAAAATT-AT--AAAATTACAATATTCATACAAAATAC
34494085 TAATCAAAAA
Statistics
Matches: 339, Mismatches: 19, Indels: 24
0.89 0.05 0.06
Matches are distributed among these distances:
100 20 0.06
102 4 0.01
104 229 0.68
105 2 0.01
106 15 0.04
107 32 0.09
108 37 0.11
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (106 bp):
TACAATATTACAATATTATACAAAATTATAAAATTACAATATTCATACAAAATACAAAATTACAA
TATTCATACAAAATTACAAAATTACAATATTCATACAAAAT
Found at i:34494077 original size:80 final size:80
Alignment explanation
Indices: 34493976--34494168 Score: 341
Period size: 80 Copynumber: 2.4 Consensus size: 80
34493966 CATACAAAAT
*
34493976 TACAAAATTACAATATTCATACAAAATACTAATCCAAAACTATAAATACAAAATTAATTATAAAA
1 TACAAAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAA
34494041 TAATTACAATATTCA
66 TAATTACAATATTCA
*
34494056 TACAAAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATATAAAATTAATTATAAAA
1 TACAAAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAA
34494121 TAATTACAATATTCA
66 TAATTACAATATTCA
* *
34494136 TACAAAATTATAATATTCATATAAAATTACTAA
1 TACAAAATTACAATATTCATACAAAA-TACTAA
34494169 ATTACAATAT
Statistics
Matches: 108, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
80 102 0.94
81 6 0.06
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (80 bp):
TACAAAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAA
TAATTACAATATTCA
Found at i:34494189 original size:80 final size:77
Alignment explanation
Indices: 34493614--34494191 Score: 400
Period size: 77 Copynumber: 7.3 Consensus size: 77
34493604 TATTCATACA
** * * *
34493614 AAATTACAATATTCATACAAAATTACAAAATTACAATATTCATATAAAATTACAAAATTACAATA
1 AAATTACAATATTCATACAAAATTA-ATTA-TAAAATAAT--TACAAAATTACAAAATTACAATA
34493679 TTCATAC--AA--AC-
62 TTCATACAAAATTACT
** * * *
34493690 AATATTACAATATTCATACAAAATTACAAAATTACAATATTCATATAAAATTACAAAATTACAAT
1 AA-ATTACAATATTCATACAAAATTA-ATTA-TAAAATAAT--TACAAAATTACAAAATTACAAT
34493755 ATTCATAC--AA--AC-
61 ATTCATACAAAATTACT
** * * * *
34493767 AATATTACAATATTCATACAAAATTACAAAATTACAATATTCATATAAAATTACAATATTACAAT
1 AA-ATTACAATATTCATACAAAATTA-ATTA-TAAAATAAT--TACAAAATTACAAAATTACAAT
34493832 ATTCATACAAAATTA-T
61 ATTCATACAAAATTACT
* * * *
34493848 AAAATTACAATATTCATACAAACAAT-ATTACAATATTCA-TACAAAATTACAAAATTACAATAT
1 -AAATTACAATATTCATACAAA-ATTAATTATAA-AATAATTACAAAATTACAAAATTACAATAT
*
34493911 TCATATAAAATTAC-
63 TCATACAAAATTACT
** * *
34493925 AATATTACAATATTCATACAAAATTATAAAATTACAATATTCATACAAAATTACAAAATTACAAT
1 AA-ATTACAATATTCATACAAAATTA-ATTA-TAAAATAAT--TACAAAATTACAAAATTACAAT
34493990 ATTCATACAAAA-TACT
61 ATTCATACAAAATTACT
* * ** *
34494006 -AATCCAAAACTATAAATACAAAATTAATTATAAAATAATTACAATATTCATACAAAATTACAAT
1 AAAT-TACAA-TATTCATACAAAATTAATTATAAAATAATTACAA-AAT--TACAAAATTACAAT
34494070 ATTCATACAAAA-TACT
61 ATTCATACAAAATTACT
* * ** * * *
34494086 -AATCAAAAACTATAAATATAAAATTAATTATAAAATAATTACAATATTCATACAAAATTATAAT
1 AAAT-TACAA-TATTCATACAAAATTAATTATAAAATAATTACAA-AAT--TACAAAATTACAAT
*
34494150 ATTCATATAAAATTACT
61 ATTCATACAAAATTACT
34494167 AAATTACAATATTCATACAAAATTA
1 AAATTACAATATTCATACAAAATTA
34494192 CAATATTAAT
Statistics
Matches: 438, Mismatches: 39, Indels: 46
0.84 0.07 0.09
Matches are distributed among these distances:
76 6 0.01
77 204 0.47
78 6 0.01
79 13 0.03
80 128 0.29
81 74 0.17
82 7 0.02
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (77 bp):
AAATTACAATATTCATACAAAATTAATTATAAAATAATTACAAAATTACAAAATTACAATATTCA
TACAAAATTACT
Found at i:34494199 original size:27 final size:27
Alignment explanation
Indices: 34494136--34494199 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
34494126 ACAATATTCA
* *
34494136 TACAAAATTATAATATTCATATAAAAT
1 TACAAAATTACAATATTCATACAAAAT
*
34494163 TACTAAATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
*
34494190 TACAATATTA
1 TACAAAATTA
34494200 ATTGTATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (27 bp):
TACAAAATTACAATATTCATACAAAAT
Found at i:34495625 original size:46 final size:45
Alignment explanation
Indices: 34495558--34495837 Score: 285
Period size: 46 Copynumber: 6.6 Consensus size: 45
34495548 TTTGAGTACT
* *
34495558 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
34495604 TCTGATTAAGTGAAAAAGTGATAA---GTA-C-TA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
34495640 CCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
34495676 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
34495722 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* *
34495768 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* * *
34495813 TCTAATC-AG-GGACAAGTGATAAGTG
1 TCTGATCAAGTGAAAAAGTGATAAGTG
34495838 ATCATACGTA
Statistics
Matches: 207, Mismatches: 16, Indels: 25
0.83 0.06 0.10
Matches are distributed among these distances:
36 60 0.29
38 1 0.00
39 1 0.00
40 3 0.01
41 1 0.00
42 3 0.01
43 16 0.08
44 3 0.01
45 19 0.09
46 100 0.48
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:34495702 original size:36 final size:36
Alignment explanation
Indices: 34495594--34495702 Score: 173
Period size: 36 Copynumber: 3.0 Consensus size: 36
34495584 GGTAGCTTTA
* *
34495594 GCTACACTTATCTGATTAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
34495630 ACTATACTTACCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
34495666 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
34495702 G
1 G
34495703 TTAGCCTTAG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (36 bp):
GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:34497284 original size:27 final size:27
Alignment explanation
Indices: 34497246--34497303 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
34497236 CATTTTAGTC
* * * *
34497246 TGGTCAGGCCAATCTCTTTGGCACTTT
1 TGGTCAGACCAATCACTTTGACACCTT
34497273 TGGTCAGACCAATCACTTTGACACCTT
1 TGGTCAGACCAATCACTTTGACACCTT
34497300 TGGT
1 TGGT
34497304 GCCGCCAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (27 bp):
TGGTCAGACCAATCACTTTGACACCTT
Found at i:34497311 original size:27 final size:26
Alignment explanation
Indices: 34497246--34497312 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
34497236 CATTTTAGTC
* * *
34497246 TGGTCAGGCCAATCTCTTTGGCACTTT
1 TGGTCA-GCCAATCACTTTGACACCTT
34497273 TGGTCAGACCAATCACTTTGACACCTT
1 TGGTCAG-CCAATCACTTTGACACCTT
*
34497300 TGGTGCCGCCAAT
1 TGGT-CAGCCAAT
34497313 GTGATTGGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
26 1 0.03
27 31 0.91
28 2 0.06
ACGTcount: A:0.19, C:0.28, G:0.21, T:0.31
Consensus pattern (26 bp):
TGGTCAGCCAATCACTTTGACACCTT
Found at i:34497427 original size:27 final size:27
Alignment explanation
Indices: 34497373--34497436 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
34497363 TTTTTTTGGT
***
34497373 ATATTTTGGTAAATAAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAAGGATA
34497400 ATATTTTGGTAAATAAAAAAAAGGATA
1 ATATTTTGGTAAATAAAAAAAAGGATA
*
34497427 ACATTTTGGT
1 ATATTTTGGT
34497437 TATTTTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAAGGATA
Found at i:34498970 original size:20 final size:20
Alignment explanation
Indices: 34498918--34498960 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
34498908 AAATTCTATT
34498918 TTTTTTAATTTTATAACATA
1 TTTTTTAATTTTATAACATA
34498938 TTTTTTAATTTTATAA-ATA
1 TTTTTTAATTTTATAACATA
34498957 TTTT
1 TTTT
34498961 ATGTATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTTAATTTTATAACATA
Found at i:34500120 original size:103 final size:105
Alignment explanation
Indices: 34499914--34500121 Score: 285
Period size: 103 Copynumber: 2.0 Consensus size: 105
34499904 TGAATAGGTG
* * *
34499914 AAATACTTGGGAAGAAAATTTGGAAAAGCCAGATTAAATAGGCAAAATAAAATTTCCTAAAAGGT
1 AAATACTTGGGAAGAAAATTTAGAAAAGCCAGACTAAATAGGCAAAATAAAATGTCCTAAAAGGT
** *
34499979 AAATTTGGTGAAACAATCTTGAATAGGTGAAATATAATGC
66 AAATTTGACGAAACAATCTTGAAGAGGTGAAATATAATGC
* * * * *
34500019 AAATACTT-GGAAGCAAATTTAGAAAAGTCAGACTAAATAGGCAAAATAAGATGT-CTTAGAGGT
1 AAATACTTGGGAAGAAAATTTAGAAAAGCCAGACTAAATAGGCAAAATAAAATGTCCTAAAAGGT
* *
34500082 AAATTTGACGAAGCAGTCTTGAAGAGGTGAAATATAATGC
66 AAATTTGACGAAACAATCTTGAAGAGGTGAAATATAATGC
34500122 CTTGGAGGTA
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
103 42 0.47
104 40 0.44
105 8 0.09
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.25
Consensus pattern (105 bp):
AAATACTTGGGAAGAAAATTTAGAAAAGCCAGACTAAATAGGCAAAATAAAATGTCCTAAAAGGT
AAATTTGACGAAACAATCTTGAAGAGGTGAAATATAATGC
Done.