Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 131 of 199
Found at i:39583311 original size:216 final size:211
Alignment explanation
Indices: 39582894--39583350 Score: 646
Period size: 216 Copynumber: 2.1 Consensus size: 211
39582884 GTTTTAATCT
* * * *
39582894 GCTCCACTGCAACTTCAGGGAGATAAGATTAGATGCAATCTGCTCTCTGCAATTTCAGAGAGATA
1 GCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCAACCTGCTCTCTACAATTTCAGAGAAATA
** * * *
39582959 AGATCTGTGATTTCAATCCGCTCTACTGCAACTTCAGGGAGATAGGATTACCGGCTTTAATATGC
66 AGATCTAAGATTTCAATCCACTCCACTGCAACTTCAGCGAGATAGGATTACCGGCTTTAATATGC
* * *
39583024 TCCACTTCAGGGAGATAATATTTGTCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGA
131 TCCACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGAATAAGA
39583089 CTTGCTTACTTAGTCC
196 CTTGCTTACTTAGTCC
**
39583105 GCTCCACTGCAACTTCAGGGAGATAAGACTAGATGTGACCTGCTCTCTACAATTTCAGAGAAATA
1 GCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCAACCTGCTCTCTACAATTTCAGAGAAATA
* * ** *
39583170 AGATCTAAGGTTTTAATCCAC-CCACTGCAACTTCAGCGAGATAGGATTGTCGGCTTTAATCTGC
66 AGATCTAAGATTTCAATCCACTCCACTGCAACTTCAGCGAGATAGGATTACCGGCTTTAATATGC
* *
39583234 TCCACTACAACTTCAGGGAGATAAGATTTGCCCTCTTCAGTCTGCCTCGCTGCAACTTCAGGAGA
131 T---C--C-ACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGA
* *
39583299 ATAAGACTTGCTTATTTAGTCT
190 ATAAGACTTGCTTACTTAGTCC
39583321 GCTCCACTGCAACTTCAGGGAGATAAGACT
1 GCTCCACTGCAACTTCAGGGAGATAAGACT
39583351 CGATCTGTTA
Statistics
Matches: 217, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
210 39 0.18
211 75 0.35
213 1 0.00
215 1 0.00
216 101 0.47
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (211 bp):
GCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCAACCTGCTCTCTACAATTTCAGAGAAATA
AGATCTAAGATTTCAATCCACTCCACTGCAACTTCAGCGAGATAGGATTACCGGCTTTAATATGC
TCCACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGAATAAGA
CTTGCTTACTTAGTCC
Found at i:39583322 original size:44 final size:45
Alignment explanation
Indices: 39583191--39583350 Score: 152
Period size: 44 Copynumber: 3.6 Consensus size: 45
39583181 TTTAATCCAC
* * * *
39583191 CCACTGCAACTTCAGCGAGATAGGA-TTGTCGGCT-TT-AATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGACTTG-C-CCTATTCAGTCTGCT
* * *
39583235 CCACTACAACTTCAGGGAGATAAGATTTGCCCTCTTCAGTCTGC-
1 CCACTGCAACTTCAGGGAGATAAGACTTGCCCTATTCAGTCTGCT
* * *
39583279 CTCGCTGCAACTTCA-GGAGAATAAGACTTG-CTTATTTAGTCTGCT
1 C-CACTGCAACTTCAGGGAG-ATAAGACTTGCCCTATTCAGTCTGCT
39583324 CCACTGCAACTTCAGGGAGATAAGACT
1 CCACTGCAACTTCAGGGAGATAAGACT
39583351 CGATCTGTTA
Statistics
Matches: 97, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
43 2 0.02
44 61 0.63
45 34 0.35
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (45 bp):
CCACTGCAACTTCAGGGAGATAAGACTTGCCCTATTCAGTCTGCT
Found at i:39597198 original size:25 final size:25
Alignment explanation
Indices: 39597147--39597200 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
39597137 TTAATTTAAA
* *
39597147 TATTTTAAAATAAATTTTTTATTTT
1 TATTTTAAAATAAATTTTTGATGTT
*
39597172 TATTTTAAAATAAATTTTTGGTGTT
1 TATTTTAAAATAAATTTTTGATGTT
39597197 TATT
1 TATT
39597201 AAAAAAAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (25 bp):
TATTTTAAAATAAATTTTTGATGTT
Found at i:39597206 original size:25 final size:25
Alignment explanation
Indices: 39597153--39597206 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
39597143 TAAATATTTT
* * **
39597153 AAAATAAATTTTTTATTTTTATTTT
1 AAAATAAATTTTTGATGTTTATTAA
*
39597178 AAAATAAATTTTTGGTGTTTATTAA
1 AAAATAAATTTTTGATGTTTATTAA
39597203 AAAA
1 AAAA
39597207 AGGGCCGGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.52
Consensus pattern (25 bp):
AAAATAAATTTTTGATGTTTATTAA
Found at i:39597897 original size:48 final size:48
Alignment explanation
Indices: 39597826--39597919 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 48
39597816 AAAAACAATG
* * *
39597826 TTGTTAGAGAGATAACTATGAATCCTAAATATCATTCAGCACATGATA
1 TTGTTACAGAGATAACTATGAATCCTAAACATCATTAAGCACATGATA
*
39597874 TTGTTACAGAGATAACTATGAATCCTGAACATCATTAAGCACATGA
1 TTGTTACAGAGATAACTATGAATCCTAAACATCATTAAGCACATGA
39597920 CTAATACCCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (48 bp):
TTGTTACAGAGATAACTATGAATCCTAAACATCATTAAGCACATGATA
Found at i:39599965 original size:26 final size:25
Alignment explanation
Indices: 39599930--39599986 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
39599920 TAAGTTTTTT
39599930 AATTTCT-ATTTA--TTTTT-T-AG
1 AATTTCTAATTTATTTTTTTATAAG
39599950 AATTTTCTAATTTATTTTTTTATAAG
1 AA-TTTCTAATTTATTTTTTTATAAG
39599976 AATTTCTAATT
1 AATTTCTAATT
39599987 AGTTTCTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
20 2 0.06
21 5 0.16
22 5 0.16
24 5 0.16
25 10 0.32
26 4 0.13
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (25 bp):
AATTTCTAATTTATTTTTTTATAAG
Found at i:39599986 original size:25 final size:21
Alignment explanation
Indices: 39599930--39599969 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
39599920 TAAGTTTTTT
39599930 AATTTCT-ATTTATTTTTTAG
1 AATTTCTAATTTATTTTTTAG
39599950 AATTTTCTAATTTATTTTTT
1 AA-TTTCTAATTTATTTTTT
39599970 TATAAGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 5 0.28
22 11 0.61
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (21 bp):
AATTTCTAATTTATTTTTTAG
Found at i:39600503 original size:25 final size:25
Alignment explanation
Indices: 39600475--39600544 Score: 61
Period size: 24 Copynumber: 2.8 Consensus size: 25
39600465 ATAAAATTAA
39600475 AATTTCTAAATTTAGATAAATTTTT
1 AATTTCTAAATTTAGATAAATTTTT
** * * *
39600500 AATTAATAATTTTATAT-ATTTTTT
1 AATTTCTAAATTTAGATAAATTTTT
* *
39600524 ACTTTCTTAATTTAGAGTAAA
1 AATTTCTAAATTTAGA-TAAA
39600545 ATTATTATAA
Statistics
Matches: 31, Mismatches: 12, Indels: 3
0.67 0.26 0.07
Matches are distributed among these distances:
24 16 0.52
25 14 0.45
26 1 0.03
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (25 bp):
AATTTCTAAATTTAGATAAATTTTT
Found at i:39604630 original size:19 final size:20
Alignment explanation
Indices: 39604593--39604632 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
39604583 AATTTCAATT
39604593 TTTTAAAAAAAAACCTTCAAA
1 TTTTAAAAAAAAA-CTTCAAA
*
39604614 TTTTATAAAAAAA-TTCAAA
1 TTTTAAAAAAAAACTTCAAA
39604633 AAAAAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
21 12 0.67
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (20 bp):
TTTTAAAAAAAAACTTCAAA
Found at i:39606024 original size:30 final size:30
Alignment explanation
Indices: 39605990--39606047 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
39605980 CTGAGCATTT
*
39605990 CCACACGGGCTTGGCACACGCCTGTGTGAG
1 CCACACGGGCTTGACACACGCCTGTGTGAG
39606020 CCACACGGGCTTGACACACGCCTGTGTG
1 CCACACGGGCTTGACACACGCCTGTGTG
39606048 CCAGCCGGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.17, C:0.34, G:0.31, T:0.17
Consensus pattern (30 bp):
CCACACGGGCTTGACACACGCCTGTGTGAG
Found at i:39612409 original size:46 final size:46
Alignment explanation
Indices: 39612358--39612452 Score: 163
Period size: 46 Copynumber: 2.1 Consensus size: 46
39612348 ACAAAGATAG
*
39612358 AAACCAAAAAATTATCTCCTAAATTTTAGCATCTAATCTCCTAATT
1 AAACCAAAAAATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
* *
39612404 AAACCAAAACATTATTTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAAAATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
39612450 AAA
1 AAA
39612453 AGAAAAGAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.42, C:0.22, G:0.02, T:0.34
Consensus pattern (46 bp):
AAACCAAAAAATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
Found at i:39615763 original size:16 final size:17
Alignment explanation
Indices: 39615738--39615773 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
39615728 TTCGGAAAAC
39615738 TTTAAAATTTTTATA-A
1 TTTAAAATTTTTATATA
*
39615754 TTTAACATTTTTATATA
1 TTTAAAATTTTTATATA
39615771 TTT
1 TTT
39615774 TTATACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTAAAATTTTTATATA
Found at i:39621604 original size:76 final size:76
Alignment explanation
Indices: 39621524--39621674 Score: 293
Period size: 76 Copynumber: 2.0 Consensus size: 76
39621514 AAGATTACTT
39621524 ATTTGAATTTAATTACAAACAATCAAATCTTAAAAATAAAAAATGATTATAATATACAAGTAATT
1 ATTTGAATTTAATTACAAACAATCAAATCTTAAAAATAAAAAATGATTATAATATACAAGTAATT
39621589 ACAAACAATTA
66 ACAAACAATTA
*
39621600 ATTTGCATTTAATTACAAACAATCAAATCTTAAAAATAAAAAATGATTATAATATACAAGTAATT
1 ATTTGAATTTAATTACAAACAATCAAATCTTAAAAATAAAAAATGATTATAATATACAAGTAATT
39621665 ACAAACAATT
66 ACAAACAATT
39621675 CTGGCAAACC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.32
Consensus pattern (76 bp):
ATTTGAATTTAATTACAAACAATCAAATCTTAAAAATAAAAAATGATTATAATATACAAGTAATT
ACAAACAATTA
Found at i:39622974 original size:8 final size:8
Alignment explanation
Indices: 39622963--39622996 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
39622953 AGTGAAGCAC
39622963 CGTGGAGT
1 CGTGGAGT
39622971 CGTGGAGT
1 CGTGGAGT
39622979 CGTGGA--
1 CGTGGAGT
39622985 CGTGGAGT
1 CGTGGAGT
39622993 CGTG
1 CGTG
39622997 AATTGGTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.25
8 18 0.75
ACGTcount: A:0.12, C:0.15, G:0.50, T:0.24
Consensus pattern (8 bp):
CGTGGAGT
Found at i:39622991 original size:22 final size:22
Alignment explanation
Indices: 39622963--39623014 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
39622953 AGTGAAGCAC
*
39622963 CGTGGAGTCGTGGAGTCGTGGA
1 CGTGGAGTCGTGAAGTCGTGGA
* *
39622985 CGTGGAGTCGTGAATTGGTGGA
1 CGTGGAGTCGTGAAGTCGTGGA
*
39623007 GGTGGAGT
1 CGTGGAGT
39623015 TGGATCCGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.15, C:0.10, G:0.50, T:0.25
Consensus pattern (22 bp):
CGTGGAGTCGTGAAGTCGTGGA
Found at i:39629640 original size:68 final size:71
Alignment explanation
Indices: 39629550--39629687 Score: 212
Period size: 68 Copynumber: 2.0 Consensus size: 71
39629540 TTTAATATAT
39629550 TTAATATTAAATTTAATTTAATACTTATCTTAATAG-T-AT-TT-TATTAATTTAATATTAAAGT
1 TTAATATTAAATTTAATTTAATACTTATCTT-ATAGATAATATTCTATTAATTTAATATTAAAGT
39629611 GATTATC
65 GATTATC
* *
39629618 TTAATATTAAATTTAATTTAATATTTATCTTATAGATAAATATTCTATTAATTTACTATTAAAGT
1 TTAATATTAAATTTAATTTAATACTTATCTTATAGAT-AATATTCTATTAATTTAATATTAAAGT
39629683 GATTA
65 GATTA
39629688 AATTTAATCA
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
67 4 0.06
68 31 0.49
70 2 0.03
71 2 0.03
72 24 0.38
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (71 bp):
TTAATATTAAATTTAATTTAATACTTATCTTATAGATAATATTCTATTAATTTAATATTAAAGTG
ATTATC
Found at i:39631952 original size:15 final size:15
Alignment explanation
Indices: 39631932--39631962 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39631922 CACTAAAAAT
*
39631932 CGAGCATTAGCGGCG
1 CGAGCATCAGCGGCG
39631947 CGAGCATCAGCGGCG
1 CGAGCATCAGCGGCG
39631962 C
1 C
39631963 ATTCCCGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.32, G:0.39, T:0.10
Consensus pattern (15 bp):
CGAGCATCAGCGGCG
Found at i:39632200 original size:82 final size:82
Alignment explanation
Indices: 39632086--39632290 Score: 304
Period size: 82 Copynumber: 2.5 Consensus size: 82
39632076 TTCAACAAAA
*
39632086 CGCCGCTAATTCTCCGGCAC-TTAGCGGCGTTTTTATCTAAGCATCGCTAATGCTCGAATCTTTA
1 CGCCGCTAATTCTCTGGC-CTTTAGCGGCGTTTTTATCTAAGCATCGCTAATGCTCGAATCTTTA
*
39632150 GCGACGTTTTTATCTAAG
65 GCGACATTTTTATCTAAG
* * *
39632168 CGCCGCTAATTCTCTGGCCTTTTGCGGCGTTTTTATCTAAGCGTCGCTAATGCTCGGATCTTTAG
1 CGCCGCTAATTCTCTGGCCTTTAGCGGCGTTTTTATCTAAGCATCGCTAATGCTCGAATCTTTAG
* *
39632233 CGGCATTTTTATCTGAG
66 CGACATTTTTATCTAAG
* * *
39632250 CGCCACTAATTCTCTAGCCTTTAGCGGCGTTTGTATCTAAG
1 CGCCGCTAATTCTCTGGCCTTTAGCGGCGTTTTTATCTAAG
39632291 TGCCGCTAAT
Statistics
Matches: 111, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
81 1 0.01
82 110 0.99
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (82 bp):
CGCCGCTAATTCTCTGGCCTTTAGCGGCGTTTTTATCTAAGCATCGCTAATGCTCGAATCTTTAG
CGACATTTTTATCTAAG
Found at i:39632312 original size:41 final size:41
Alignment explanation
Indices: 39632062--39632341 Score: 244
Period size: 41 Copynumber: 6.8 Consensus size: 41
39632052 ATTTTTTGAG
* * * * * * * *
39632062 CCTTTAGCGGCGCTTTCAACAAAACGCCGCTAATTCTCCGG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGA
**
39632103 CAC-TTAGCGGCGTTTTTATCTAAGCATCGCTAATGCTC-GAA
1 C-CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTG-A
* * * *
39632144 TCTTTAGCGACGTTTTTATCTAAGCGCCGCTAATTCTCTGG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGA
* * *
39632185 CCTTTTGCGGCGTTTTTATCTAAGCGTCGCTAATGCTCGGA
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGA
* * * * *
39632226 TCTTTAGCGGCATTTTTATCTGAGCGCCACTAATTCTCT-A
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGA
* * *
39632266 GCCTTTAGCGGCGTTTGTATCTAAGTGCCGCTAATGCAT-TTA
1 -CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGC-TCTGA
** *
39632308 CCTTTAGCGGCGTTTTTGCCGAAGCGCCGCTAAT
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAAT
39632342 AGTAACAAAA
Statistics
Matches: 190, Mismatches: 42, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
40 3 0.02
41 183 0.96
42 4 0.02
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (41 bp):
CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGA
Found at i:39632334 original size:82 final size:82
Alignment explanation
Indices: 39632062--39632341 Score: 269
Period size: 82 Copynumber: 3.4 Consensus size: 82
39632052 ATTTTTTGAG
* * * * * ** *
39632062 CCTTTAGCGGCGCTTTCAACAAAACGCCGCTAATTCTCCGGCAC-TTAGCGGCGTTTTTATCTAA
1 CCTTTAGCGGCGTTTTTACCGAAGCGCCGCTAATTCTCTAGC-CTTTAGCGGCGTTTGTATCTAA
** *
39632126 GCATCGCTAATGCTCGAA
65 GCGCCGCTAATGCTCGGA
* * * * * * *
39632144 TCTTTAGCGACGTTTTTATCTAAGCGCCGCTAATTCTCTGGCCTTTTGCGGCGTTTTTATCTAAG
1 CCTTTAGCGGCGTTTTTACCGAAGCGCCGCTAATTCTCTAGCCTTTAGCGGCGTTTGTATCTAAG
*
39632209 CGTCGCTAATGCTCGGA
66 CGCCGCTAATGCTCGGA
* * * *
39632226 TCTTTAGCGGCATTTTTATCTG-AGCGCCACTAATTCTCTAGCCTTTAGCGGCGTTTGTATCTAA
1 CCTTTAGCGGCGTTTTTA-CCGAAGCGCCGCTAATTCTCTAGCCTTTAGCGGCGTTTGTATCTAA
* **
39632290 GTGCCGCTAATGCAT-TTA
65 GCGCCGCTAATGC-TCGGA
*
39632308 CCTTTAGCGGCGTTTTTGCCGAAGCGCCGCTAAT
1 CCTTTAGCGGCGTTTTTACCGAAGCGCCGCTAAT
39632342 AGTAACAAAA
Statistics
Matches: 165, Mismatches: 29, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
81 3 0.02
82 161 0.98
83 1 0.01
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (82 bp):
CCTTTAGCGGCGTTTTTACCGAAGCGCCGCTAATTCTCTAGCCTTTAGCGGCGTTTGTATCTAAG
CGCCGCTAATGCTCGGA
Found at i:39637673 original size:21 final size:21
Alignment explanation
Indices: 39637644--39637696 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
39637634 ACATCTTTGA
* *
39637644 TATATATATTTATATACAGTTT
1 TATATATATTTAT-TAAAATTT
39637666 TA-ATATATTTATTAAAATTT
1 TATATATATTTATTAAAATTT
39637686 TATATATATTT
1 TATATATATTT
39637697 GAAAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 8 0.29
21 18 0.64
22 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TATATATATTTATTAAAATTT
Found at i:39637786 original size:12 final size:12
Alignment explanation
Indices: 39637769--39637890 Score: 51
Period size: 12 Copynumber: 10.1 Consensus size: 12
39637759 TACACAACAC
39637769 ATAACTTACATA
1 ATAACTTACATA
39637781 ATAACTTACAT-
1 ATAACTTACATA
* *
39637792 A-AGC-TATAT-
1 ATAACTTACATA
*
39637801 ATAAACTTATAT-
1 AT-AACTTACATA
39637813 ATAACTTACATA
1 ATAACTTACATA
*
39637825 CATAACTTAAATCA
1 -ATAACTTACAT-A
* *
39637839 A-AATTTATAT-
1 ATAACTTACATA
*
39637849 ATAAACTTACACAACA
1 AT-AACTT--AC-ATA
*
39637865 CATAACTTACACA
1 -ATAACTTACATA
39637878 ATAACTTACATA
1 ATAACTTACATA
39637890 A
1 A
39637891 CTTATATATA
Statistics
Matches: 86, Mismatches: 11, Indels: 26
0.70 0.09 0.21
Matches are distributed among these distances:
9 5 0.06
10 3 0.03
11 11 0.13
12 41 0.48
13 14 0.16
14 4 0.05
15 1 0.01
16 5 0.06
17 2 0.02
ACGTcount: A:0.50, C:0.17, G:0.01, T:0.32
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:39637791 original size:21 final size:21
Alignment explanation
Indices: 39637767--39637833 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 21
39637757 CTTACACAAC
39637767 ACATAACTTACATAATAACTT
1 ACATAACTTACATAATAACTT
*
39637788 ACATAAGC-TATAT-ATAAACTTAT
1 ACATAA-CTTACATAAT-AAC-T-T
*
39637811 ATATAACTTACATACATAACTT
1 ACATAACTTACATA-ATAACTT
39637833 A
1 A
39637834 AATCAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 13
0.69 0.06 0.25
Matches are distributed among these distances:
20 2 0.06
21 13 0.36
22 5 0.14
23 11 0.31
24 3 0.08
25 2 0.06
ACGTcount: A:0.48, C:0.16, G:0.01, T:0.34
Consensus pattern (21 bp):
ACATAACTTACATAATAACTT
Found at i:39637892 original size:9 final size:9
Alignment explanation
Indices: 39637852--39638422 Score: 248
Period size: 9 Copynumber: 64.7 Consensus size: 9
39637842 TTTATATATA
*
39637852 AACTTACAC
1 AACTTACAT
39637861 AAC--ACAT
1 AACTTACAT
39637868 AACTTACACAAT
1 AACTT--AC-AT
39637880 AACTTACAT
1 AACTTACAT
*
39637889 AACTTATATAT
1 AAC-T-TACAT
*
39637900 AAACATATATAT
1 -AAC-T-TACAT
*
39637912 AACTTTCAT
1 AACTTACAT
39637921 AACTTAC-T
1 AACTTACAT
*
39637929 TA--TA-AT
1 AACTTACAT
39637935 AACTTACAT
1 AACTTACAT
39637944 AAC--ACAT
1 AACTTACAT
* *
39637951 AGCCTACAT
1 AACTTACAT
*
39637960 GACTTACAT
1 AACTTACAT
*
39637969 AA--TACAC
1 AACTTACAT
*
39637976 AACTTAAAT
1 AACTTACAT
* *
39637985 AATTTAAAT
1 AACTTACAT
39637994 AACTTACAT
1 AACTTACAT
39638003 AA--TACAT
1 AACTTACAT
39638010 AACTTAC--
1 AACTTACAT
39638017 -A-TT-CAT
1 AACTTACAT
39638023 AACTTACAT
1 AACTTACAT
*
39638032 AAACTTATATGTT
1 -AACTTACA---T
*
39638045 ACCTTACAT
1 AACTTACAT
39638054 AA--TACAT
1 AACTTACAT
*
39638061 TACTTACATATT
1 AACTTAC--A-T
39638073 AACTTACAT
1 AACTTACAT
* *
39638082 AAGTTATCTAC
1 AACTTA-C-AT
*
39638093 AAGCTTATATTT
1 AA-CTTACA--T
*
39638105 AAACTTGCAT
1 -AACTTACAT
39638115 AACTTACAT
1 AACTTACAT
*
39638124 AA-TAACAT
1 AACTTACAT
39638132 AACAACTTACAT
1 ---AACTTACAT
39638144 AA--TACAT
1 AACTTACAT
* *
39638151 AGCATACA-
1 AACTTACAT
39638159 AGACTTACAT
1 A-ACTTACAT
*
39638169 AA--TACAA
1 AACTTACAT
39638176 AACTTACAT
1 AACTTACAT
*
39638185 AACTTAAAT
1 AACTTACAT
* *
39638194 ATCTTACAC
1 AACTTACAT
39638203 AACTTACAT
1 AACTTACAT
*
39638212 AACCTACAT
1 AACTTACAT
39638221 AA--TACAT
1 AACTTACAT
39638228 AACTTACAT
1 AACTTACAT
39638237 AACTTACAT
1 AACTTACAT
39638246 AACTTACAT
1 AACTTACAT
*
39638255 AATACATA-AT
1 -A-ACTTACAT
39638265 AACTTAC--
1 AACTTACAT
39638272 AACTTACAT
1 AACTTACAT
*
39638281 AACATACATT
1 AACTTACA-T
**
39638291 AA-TTTGAT
1 AACTTACAT
39638299 AACTTACAT
1 AACTTACAT
*
39638308 AAGTTACAT
1 AACTTACAT
39638317 AA--TACAT
1 AACTTACAT
39638324 AACTTAC--
1 AACTTACAT
*
39638331 AACTTACAC
1 AACTTACAT
*
39638340 AACATACAT
1 AACTTACAT
* **
39638349 TACTTTGAT
1 AACTTACAT
39638358 AACTTACAT
1 AACTTACAT
*
39638367 AAGTTACAT
1 AACTTACAT
*
39638376 AA--TACAC
1 AACTTACAT
39638383 AACTTACAT
1 AACTTACAT
* *
39638392 AGCTTACTT
1 AACTTACAT
39638401 AA--TACAT
1 AACTTACAT
39638408 AACTTACAT
1 AACTTACAT
39638417 AACTTA
1 AACTTA
39638423 TACACGTACA
Statistics
Matches: 425, Mismatches: 72, Indels: 130
0.68 0.11 0.21
Matches are distributed among these distances:
4 1 0.00
5 2 0.00
6 5 0.01
7 84 0.20
8 19 0.04
9 228 0.54
10 22 0.05
11 19 0.04
12 42 0.10
13 3 0.01
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.33
Consensus pattern (9 bp):
AACTTACAT
Found at i:39637930 original size:97 final size:97
Alignment explanation
Indices: 39637713--39637921 Score: 316
Period size: 97 Copynumber: 2.2 Consensus size: 97
39637703 TTTATCAATC
* * *
39637713 ATATCATAATTTACATACATAACATATAT--AAATTCATATATAAACTTACACAACACATAACTT
1 ATAT-ATAACTTACATACATAACTTAAATCAAAATTCATATATAAACTTACACAACACATAACTT
* *
39637776 ACATAATAACTTACATAAGCTATATATAAACTT
65 ACACAATAACTTACATAAGCTATATATAAACAT
*
39637809 ATATATAACTTACATACATAACTTAAATCAAAATTTATATATAAACTTACACAACACATAACTTA
1 ATATATAACTTACATACATAACTTAAATCAAAATTCATATATAAACTTACACAACACATAACTTA
39637874 CACAATAACTTACATAA-CTTATATATAAACAT
66 CACAATAACTTACATAAGC-TATATATAAACAT
*
39637906 ATATATAACTTTCATA
1 ATATATAACTTACATA
39637922 ACTTACTTAT
Statistics
Matches: 103, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
95 21 0.20
96 5 0.05
97 77 0.75
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.33
Consensus pattern (97 bp):
ATATATAACTTACATACATAACTTAAATCAAAATTCATATATAAACTTACACAACACATAACTTA
CACAATAACTTACATAAGCTATATATAAACAT
Found at i:39638183 original size:25 final size:25
Alignment explanation
Indices: 39638135--39638422 Score: 187
Period size: 25 Copynumber: 11.2 Consensus size: 25
39638125 ATAACATAAC
* *
39638135 AACTTACATAATACATAGCATACA-
1 AACTTACATAATACATAACTTACAT
*
39638159 AGACTTACATAATACAAAACTTACAT
1 A-ACTTACATAATACATAACTTACAT
* * *
39638185 AACTTAAATATCTTACACAACTTACAT
1 AACTTACATA--ATACATAACTTACAT
*
39638212 AACCTACATAATACATAACTTACAT
1 AACTTACATAATACATAACTTACAT
*
39638237 AACTTACATAACTTACATAATACATA-AT
1 AACTTACATAA--TACAT-A-ACTTACAT
* *
39638265 AACTTACA-ACTTACATAACATACATT
1 AACTTACATA-ATACATAACTTACA-T
** *
39638291 AA-TTTGATAACTTACATAAGTTACAT
1 AACTTACATAA--TACATAACTTACAT
*
39638317 AA--TACATAACTTAC--AACTTACAC
1 AACTTACATAA--TACATAACTTACAT
* * **
39638340 AACATACATTACTTTGATAACTTACAT
1 AACTTACA-TA-ATACATAACTTACAT
* *
39638367 AAGTTACATAATACACAACTTACAT
1 AACTTACATAATACATAACTTACAT
* *
39638392 AGCTTACTTAATACATAACTTACAT
1 AACTTACATAATACATAACTTACAT
39638417 AACTTA
1 AACTTA
39638423 TACACGTACA
Statistics
Matches: 207, Mismatches: 37, Indels: 39
0.73 0.13 0.14
Matches are distributed among these distances:
23 9 0.04
24 6 0.03
25 108 0.52
26 17 0.08
27 52 0.25
28 11 0.05
29 4 0.02
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.31
Consensus pattern (25 bp):
AACTTACATAATACATAACTTACAT
Found at i:39638201 original size:18 final size:18
Alignment explanation
Indices: 39637852--39638422 Score: 248
Period size: 16 Copynumber: 32.3 Consensus size: 18
39637842 TTTATATATA
*
39637852 AACTTACACAAC--ACAT
1 AACTTACATAACTTACAT
39637868 AACTTACACAATAACTTACAT
1 AACTT--AC-ATAACTTACAT
* *
39637889 AACTTATATATAAACATATATAT
1 AAC-T-TACAT-AAC-T-TACAT
*
39637912 AACTTTCATAACTTAC-T
1 AACTTACATAACTTACAT
*
39637929 TA--TA-ATAACTTACAT
1 AACTTACATAACTTACAT
* *
39637944 AAC--ACATAGCCTACAT
1 AACTTACATAACTTACAT
* *
39637960 GACTTACATAA--TACAC
1 AACTTACATAACTTACAT
* * *
39637976 AACTTAAATAATTTAAAT
1 AACTTACATAACTTACAT
39637994 AACTTACATAA--TACAT
1 AACTTACATAACTTACAT
39638010 AACTTAC---A-TT-CAT
1 AACTTACATAACTTACAT
*
39638023 AACTTACATAAACTTATATGTT
1 AACTTACAT-AACTTACA---T
*
39638045 ACCTTACATAA--TACAT
1 AACTTACATAACTTACAT
*
39638061 TACTTACATATTAACTTACAT
1 AACTTAC--A-TAACTTACAT
* * *
39638082 AAGTTATCTACAAGCTTATATTT
1 AACTTA-C-ATAA-CTTACA--T
*
39638105 AAACTTGCATAACTTACAT
1 -AACTTACATAACTTACAT
*
39638124 AA-TAACATAACAACTTACAT
1 AACTTACAT---AACTTACAT
* *
39638144 AA--TACATAGCATACA-
1 AACTTACATAACTTACAT
*
39638159 AGACTTACATAA--TACAA
1 A-ACTTACATAACTTACAT
*
39638176 AACTTACATAACTTAAAT
1 AACTTACATAACTTACAT
* *
39638194 ATCTTACACAACTTACAT
1 AACTTACATAACTTACAT
*
39638212 AACCTACATAA--TACAT
1 AACTTACATAACTTACAT
39638228 AACTTACATAACTTACAT
1 AACTTACATAACTTACAT
*
39638246 AACTTACATAATACATA-AT
1 AACTTACAT-A-ACTTACAT
39638265 AACTTAC--AACTTACAT
1 AACTTACATAACTTACAT
* **
39638281 AACATACATTAA-TTTGAT
1 AACTTACA-TAACTTACAT
*
39638299 AACTTACATAAGTTACAT
1 AACTTACATAACTTACAT
39638317 AA--TACATAACTTAC--
1 AACTTACATAACTTACAT
* *
39638331 AACTTACACAACATACAT
1 AACTTACATAACTTACAT
* **
39638349 TACTTTGATAACTTACAT
1 AACTTACATAACTTACAT
* *
39638367 AAGTTACATAA--TACAC
1 AACTTACATAACTTACAT
* *
39638383 AACTTACATAGCTTACTT
1 AACTTACATAACTTACAT
39638401 AA--TACATAACTTACAT
1 AACTTACATAACTTACAT
39638417 AACTTA
1 AACTTA
39638423 TACACGTACA
Statistics
Matches: 417, Mismatches: 75, Indels: 124
0.68 0.12 0.20
Matches are distributed among these distances:
13 11 0.03
14 12 0.03
15 9 0.02
16 139 0.33
17 11 0.03
18 117 0.28
19 29 0.07
20 22 0.05
21 37 0.09
22 16 0.04
23 10 0.02
24 4 0.01
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.33
Consensus pattern (18 bp):
AACTTACATAACTTACAT
Found at i:39638227 original size:43 final size:41
Alignment explanation
Indices: 39638161--39638265 Score: 138
Period size: 43 Copynumber: 2.5 Consensus size: 41
39638151 AGCATACAAG
* *
39638161 ACTTACATAATACAAAACTTACATAACTTAAATATCTTACACA
1 ACTTACATAATACATAA--TACATAACTTAAATAACTTACACA
* *
39638204 ACTTACATAACCTACATAATACATAACTTACATAACTTACATA
1 ACTTACATAA--TACATAATACATAACTTAAATAACTTACACA
39638247 ACTTACATAATACATAATA
1 ACTTACATAATACATAATA
39638266 ACTTACAACT
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
41 9 0.16
43 41 0.73
45 6 0.11
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (41 bp):
ACTTACATAATACATAATACATAACTTAAATAACTTACACA
Found at i:39638257 original size:34 final size:35
Alignment explanation
Indices: 39637878--39638422 Score: 192
Period size: 34 Copynumber: 16.2 Consensus size: 35
39637868 AACTTACACA
* * *
39637878 ATAACTTACATAACTTATAT-A-TAAACAT-A-TAT
1 ATAACTTACATAACTTACATAACT-TACATAATTAC
* *
39637910 ATAACTTTCATAACTTAC-TTA--TA-ATAACTTAC
1 ATAACTTACATAACTTACATAACTTACATAA-TTAC
* * *
39637942 ATAAC--ACATAGCCTACATGACTTACATAA-TAC
1 ATAACTTACATAACTTACATAACTTACATAATTAC
* * * *
39637974 ACAACTTAAATAATTTAAATAACTTACATAA-TAC
1 ATAACTTACATAACTTACATAACTTACATAATTAC
*
39638008 ATAACTTAC---A-TT-CATAACTTACATAAACTTAT
1 ATAACTTACATAACTTACATAACTTACAT-AA-TTAC
* *
39638040 ATGTTACCTTACATAA--TACATTACTTACAT-A-T--
1 A---TAACTTACATAACTTACATAACTTACATAATTAC
* * *
39638072 -TAACTTACATAAGTTATCTACAAGCTT--AT-ATT-T
1 ATAACTTACATAACTTA-C-ATAA-CTTACATAATTAC
* *
39638105 A-AACTTGCATAACTTACATAA-TAACATAACAACTTAC
1 ATAACTTACATAACTTACATAACTTACAT---AA-TTAC
* *
39638142 ATAA--TACATAGCATACA-AGACTTACATAA-TAC
1 ATAACTTACATAACTTACATA-ACTTACATAATTAC
* * * *
39638174 AAAACTTACATAACTTAAATATCTTACACAACTTAC
1 ATAACTTACATAACTTACATAACTTACATAA-TTAC
*
39638210 ATAACCTACATAA--TACATAACTTACATAACTTAC
1 ATAACTTACATAACTTACATAACTTACATAA-TTAC
* *
39638244 ATAACTTACATAATACATA-ATAACTTACA-ACTTAC
1 ATAACTTACAT-A-ACTTACATAACTTACATAATTAC
* **
39638279 ATAACATACATTAA-TTTGATAACTTACATAAGTTAC
1 ATAACTTACA-TAACTTACATAACTTACATAA-TTAC
* *
39638315 ATAA--TACATAACTTAC--AACTTACACAACATAC
1 ATAACTTACATAACTTACATAACTTACATAA-TTAC
* ** *
39638347 ATTACTTTGATAACTTACATAAGTTACATAA-TAC
1 ATAACTTACATAACTTACATAACTTACATAATTAC
* * *
39638381 ACAACTTACATAGCTTACTTAA--TACATAACTTAC
1 ATAACTTACATAACTTACATAACTTACATAA-TTAC
39638415 ATAACTTA
1 ATAACTTA
39638423 TACACGTACA
Statistics
Matches: 387, Mismatches: 67, Indels: 116
0.68 0.12 0.20
Matches are distributed among these distances:
28 11 0.03
29 14 0.04
30 16 0.04
31 13 0.03
32 67 0.17
33 22 0.06
34 137 0.35
35 26 0.07
36 48 0.12
37 17 0.04
38 16 0.04
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.33
Consensus pattern (35 bp):
ATAACTTACATAACTTACATAACTTACATAATTAC
Found at i:39638356 original size:59 final size:59
Alignment explanation
Indices: 39638235--39638390 Score: 249
Period size: 59 Copynumber: 2.6 Consensus size: 59
39638225 CATAACTTAC
* *
39638235 ATAACTTACATAACTTACATAATACATAATAACTTACAACTTACATAACATACATTAATTTG
1 ATAACTTACATAAGTTACATAATAC---ATAACTTACAACTTACACAACATACATTAATTTG
*
39638297 ATAACTTACATAAGTTACATAATACATAACTTACAACTTACACAACATACATTACTTTG
1 ATAACTTACATAAGTTACATAATACATAACTTACAACTTACACAACATACATTAATTTG
*
39638356 ATAACTTACATAAGTTACATAATACACAACTTACA
1 ATAACTTACATAAGTTACATAATACATAACTTACA
39638391 TAGCTTACTT
Statistics
Matches: 90, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
59 66 0.73
62 24 0.27
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (59 bp):
ATAACTTACATAAGTTACATAATACATAACTTACAACTTACACAACATACATTAATTTG
Found at i:39638406 original size:59 final size:59
Alignment explanation
Indices: 39638164--39638422 Score: 244
Period size: 59 Copynumber: 4.3 Consensus size: 59
39638154 ATACAAGACT
* * * * *
39638164 TACATAA--TACAAAACTTACATAACTTAAATATCTTACACAACTTACATAACCTACAT-A-A
1 TACATAACTTACATAACTTACATAAGTTACATA--ATACACAACTTAC--AACTTACATAACA
* *
39638223 TACATAACTTACATAACTTACATAACTTACATAATACATAATAACTTACAACTTACATAACA
1 TACATAACTTACATAACTTACATAAGTTACATAATAC---ACAACTTACAACTTACATAACA
** * *
39638285 TACATTAA-TTTGATAACTTACATAAGTTACATAATACATAACTTACAACTTACACAACA
1 TACA-TAACTTACATAACTTACATAAGTTACATAATACACAACTTACAACTTACATAACA
* ** *
39638344 TACATTACTTTGATAACTTACATAAGTTACATAATACACAACTTACATAGCTTAC-TTA-A
1 TACATAACTTACATAACTTACATAAGTTACATAATACACAACTTACA-A-CTTACATAACA
39638403 TACATAACTTACATAACTTA
1 TACATAACTTACATAACTTA
39638423 TACACGTACA
Statistics
Matches: 173, Mismatches: 16, Indels: 22
0.82 0.08 0.10
Matches are distributed among these distances:
58 2 0.01
59 91 0.53
60 10 0.06
61 28 0.16
62 39 0.23
63 3 0.02
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (59 bp):
TACATAACTTACATAACTTACATAAGTTACATAATACACAACTTACAACTTACATAACA
Found at i:39644103 original size:21 final size:21
Alignment explanation
Indices: 39644077--39644125 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
39644067 CTGCAGCTTA
* *
39644077 AAGCAGAGGCGGCATCGAGAG
1 AAGCAGAGGCGGCAGCAAGAG
* *
39644098 AAGCAGAGGCTGCAGCAAGGG
1 AAGCAGAGGCGGCAGCAAGAG
39644119 AAGCAGA
1 AAGCAGA
39644126 CCAGCGTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.18, G:0.41, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCAAGAG
Found at i:39644253 original size:19 final size:19
Alignment explanation
Indices: 39644229--39644267 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
39644219 GTAAATATTT
*
39644229 TTATCATTTTGACTTTTAA
1 TTATCATTTTAACTTTTAA
39644248 TTATCATTTTAACTTTTAA
1 TTATCATTTTAACTTTTAA
39644267 T
1 T
39644268 ATTTTTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.59
Consensus pattern (19 bp):
TTATCATTTTAACTTTTAA
Found at i:39644509 original size:43 final size:43
Alignment explanation
Indices: 39644443--39644794 Score: 328
Period size: 43 Copynumber: 8.2 Consensus size: 43
39644433 TCTGCCAAAA
* * *
39644443 TTAGTGGCGTTTGTAAAAAAAGCGCCGCTAAAGACCATGA-CTT
1 TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGATCATGATC-T
39644486 TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGATCATGATCT
1 TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGATCATGATCT
** *
39644529 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGGTCT
1 TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGATCATGATCT
* ** ** * *
39644572 TTAGCGGCGGTTGTGGGAAAAGCGCTACTAAAGGTCATGGTCT
1 TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGATCATGATCT
** *
39644615 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGA-CATTATCT
1 TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAA-GATCATGATCT
** * * *
39644658 TTAGCGGCGCTTT-CCACACAAA-CGGCGCTAAA-AGTCATGGTCT
1 TTAGCGGCG-TTTGTGA-AAAAAGCGCCGCTAAAGA-TCATGATCT
* *
39644701 TTAGCGGC-TCTTG-GAGAAAAGCGCCGCTAAAGGA-CATGACCT
1 TTAGCGGCGT-TTGTGAAAAAAGCGCCGCTAAA-GATCATGATCT
* *
39644743 TTAGTGGCATTTGT-AGAAAAAGCGCCGCTAAAGGA-CATGATCT
1 TTAGCGGCGTTTGTGA-AAAAAGCGCCGCTAAA-GATCATGATCT
39644786 TTAGCGGCG
1 TTAGCGGCG
39644795 CTTTTTTCTT
Statistics
Matches: 260, Mismatches: 35, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
41 5 0.02
42 29 0.11
43 217 0.83
44 9 0.03
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.24
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGATCATGATCT
Found at i:39644696 original size:129 final size:127
Alignment explanation
Indices: 39644460--39644798 Score: 398
Period size: 129 Copynumber: 2.6 Consensus size: 127
39644450 CGTTTGTAAA
* * *
39644460 AAAAGCGCCGCTAAA-GACCATGACTTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAA-GATCA
1 AAAAGCGCCACTAAAGGA-CATGACCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGA-CA
* ** * * *
39644523 TGATCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGGTTGTGG
64 TGATCTTTAGCGGCGCTT-TGCCAAAAACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTG-GA
39644588 G
127 G
* * ** * *
39644589 AAAAGCGCTACTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGACATT
1 AAAAGCGCCACTAAAGGACATGACCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGACATG
* *
39644654 ATCTTTAGCGGCGCTTT-CCACACAAACGGCGCTAAA-AGTCATGGTCTTTAGCGGCTCTTGGAG
66 ATCTTTAGCGGCGCTTTGCCA-A-AAACGCCGCTAAAGA-TCATGGTCTTTAGCGGCGCTTGGAG
* * * *
39644717 AAAAGCGCCGCTAAAGGACATGACCTTTAGTGGCATTTGTAGAAAAAGCGCCGCTAAAGGACATG
1 AAAAGCGCCACTAAAGGACATGACCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGACATG
39644782 ATCTTTAGCGGCGCTTT
66 ATCTTTAGCGGCGCTTT
39644799 TTTCTTAAAA
Statistics
Matches: 178, Mismatches: 27, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
127 1 0.01
128 77 0.43
129 97 0.54
130 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (127 bp):
AAAAGCGCCACTAAAGGACATGACCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGACATG
ATCTTTAGCGGCGCTTTGCCAAAAACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTGGAG
Found at i:39652733 original size:15 final size:14
Alignment explanation
Indices: 39652683--39652732 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 14
39652673 GTAAAAGTAG
*
39652683 AGAAAATAAATAAAA
1 AGAAAAGAAA-AAAA
39652698 AGAAAAGAAAAAGAA
1 AGAAAAGAAAAA-AA
*
39652713 GGAAAAGAAAAAAA
1 AGAAAAGAAAAAAA
39652727 AGAAAA
1 AGAAAA
39652733 AAATAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 9 0.29
15 22 0.71
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (14 bp):
AGAAAAGAAAAAAA
Found at i:39656965 original size:4 final size:4
Alignment explanation
Indices: 39656948--39656986 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
39656938 GCATGACTAA
* *
39656948 CATT CATT -AGT CATT CATT CACT CATT CATT CATT CATT
1 CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT
39656987 GTATGTACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
3 2 0.07
4 28 0.93
ACGTcount: A:0.26, C:0.26, G:0.03, T:0.46
Consensus pattern (4 bp):
CATT
Found at i:39665720 original size:77 final size:75
Alignment explanation
Indices: 39665304--39666064 Score: 701
Period size: 76 Copynumber: 10.1 Consensus size: 75
39665294 ATCATTTCCT
* * * * *
39665304 ATTTCATTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTAAGCATCGGGTCACACGCTAAG
1 ATTTCATTTTTCGAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
*
39665369 GT-GTTTTCA
66 GTATTTTTCA
** * ** * * * *
39665378 ATTT-ATATTTTTTAAAATCAACTCATAATCTGAGAACTGAGTTGAGCCTTGGGTTGCATGCCGA
1 ATTTCAT-TTTTCGAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGA
* *
39665442 GATATTTTTCT
65 GGTATTTTTCA
* * * *
39665453 ATTTCTATTTTTTGAAAATCAACTCATAATCCGAGAGATGAGTTGAGCCTCGGGTCGCATGCCGA
1 ATTTC-ATTTTTCGAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGA
*
39665518 GATATTTTTCA
65 GGTATTTTTCA
* * * *
39665529 ATTT-TTGTTTTTGAAAGATCAACTCATAGTCCGAAAGGTGAGTTGAGCCTCGGGTCGCACGCTG
1 ATTTCAT-TTTTCGAAA-ATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTG
*
39665593 AGGT-GTTTTCA
64 AGGTATTTTTCA
** * * * ** *
39665604 ATTTTTGTTTTTTTTCAAAAATCAACTCATAATCTGAGAGGTGAGTTGAACCTCAAGTCACACGC
1 A---TT-TCATTTTTCGAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGC
39665669 TGAGGTATATTTTCA
62 TGAGGTAT-TTTTCA
* * *
39665684 ATTTCAGTTTTTCGAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTAGGGTCGCATGCCGA
1 ATTTCA-TTTTTCGAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGA
*
39665749 GGTATTTTTTCT
65 GGTA-TTTTTCA
* * * *
39665761 ATTTCTATTTTTTGAAAATCAACTCATAATCTGAGATGTGAGTTGAGCCTCGGGTCGCATG-TCG
1 ATTTC-ATTTTTCGAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCT-G
39665825 AGGTATTTTTCA
64 AGGTATTTTTCA
* *
39665837 ATTTCTATTTTTC-AAAGATCGACTCATAGTCCGAGAGGTGAGTTGAGCCTCGGGTCGCACG-TC
1 ATTTC-ATTTTTCGAAA-ATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCT-
*
39665900 GAGCTATTTTT-A
63 GAGGTATTTTTCA
* * *
39665912 ATTTTTC-TTTTTC-AAATATCAACTCATAGTCCAAGAGGTGAGTTGAGCCTCAGGTCGCACG-T
1 A--TTTCATTTTTCGAAA-ATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCT
*
39665974 GGAGATA-TTTT-A
63 -GAGGTATTTTTCA
* * * *
39665986 TATTT--TTTTTC-AAAGATCAACCCATAATCCGAGAGATGAGTTGAGCCTCGGGTTGCACGCCG
1 -ATTTCATTTTTCGAAA-ATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTG
* *
39666048 AGG-AATTTTAA
64 AGGTATTTTTCA
39666059 ATTTCA
1 ATTTCA
39666065 ATCTTTTATT
Statistics
Matches: 580, Mismatches: 81, Indels: 52
0.81 0.11 0.07
Matches are distributed among these distances:
71 1 0.00
72 58 0.10
73 6 0.01
74 56 0.10
75 87 0.15
76 180 0.31
77 127 0.22
78 48 0.08
79 8 0.01
80 9 0.02
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (75 bp):
ATTTCATTTTTCGAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
GTATTTTTCA
Found at i:39665864 original size:308 final size:301
Alignment explanation
Indices: 39665305--39666056 Score: 984
Period size: 308 Copynumber: 2.5 Consensus size: 301
39665295 TCATTTCCTA
* * *
39665305 TTTCATTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTT-AAGCATCGGGTCACACGCTAAG
1 TTTC-TTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAA-CCTCAGGTCACACGCTGAG
* * * *
39665369 G-TGTTTTCAATTTATATTTTTTAAAATCAACTCATAATCTGAGA-ACTGAGTTGAGCCTTGGGT
64 GATATTTTCAA-TT-TATTTTTCAAAATCAACTCATAATCCGAGAGA-TGAGTTGAGCCTAGGGT
*
39665432 TGCATGCCGAGATA-TTTTTCTATTTCTATTTTTTGAAAATCAACTCATAATCCGAGAGATGAGT
126 TGCATGCCGAGGTATTTTTTCTATTTCTATTTTTTGAAAATCAACTCATAATCCGAGAGATGAGT
* * *
39665496 TGAGCCTCGGGTCGCATGCCGAGATATTTTTCAATTTTTGTTTTTGAAAGATCAACTCATAGTCC
191 TGAGCCTCGGGTCGCATGCCGAGATATTTTTCAATTTCTATTTTTCAAAGATCAACTCATAGTCC
* *
39665561 GAAAGGTGAGTTGAGCCTCGGGTCGCACG-CTGAGGTGTTTTCAATTTT
256 GAAAGGTGAGTTGAGCCTCGGGTCGCACGTC-GAGCTATTTTCAA--TT
* * *
39665609 TGTTTTTTTTCAAAAATCAACTCATAATCTGAGAGGTGAGTTGAACCTCAAGTCACACGCTGAGG
1 T-TTCTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAACCTCAGGTCACACGCTGAGG
*
39665674 TATATTTTCAATTTCAGTTTTTCGAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTAGGGT
65 -ATATTTTCAATTT-A-TTTTTC-AAAATCAACTCATAATCCGAGAGATGAGTTGAGCCTAGGGT
* *
39665739 CGCATGCCGAGGTATTTTTTCTATTTCTATTTTTTGAAAATCAACTCATAATCTGAGATG-TGAG
126 TGCATGCCGAGGTATTTTTTCTATTTCTATTTTTTGAAAATCAACTCATAATCCGAGA-GATGAG
* * *
39665803 TTGAGCCTCGGGTCGCATGTCGAGGTATTTTTCAATTTCTATTTTTCAAAGATCGACTCATAGTC
190 TTGAGCCTCGGGTCGCATGCCGAGATATTTTTCAATTTCTATTTTTCAAAGATCAACTCATAGTC
* *
39665868 CGAGAGGTGAGTTGAGCCTCGGGTCGCACGTCGAGCTATTTTTAATT
255 CGAAAGGTGAGTTGAGCCTCGGGTCGCACGTCGAGCTATTTTCAATT
* * * * *
39665915 TTTCTTTTTCAAATATCAACTCATAGTCCAAGAGGTGAGTTGAGCCTCAGGTCGCACG-TG-GAG
1 TTTCTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAACCTCAGGTCACACGCTGAG-G
* *
39665978 ATATTTT-ATATTT-TTTTTCAAAGATCAACCCATAATCCGAGAGATGAGTTGAGCCTCGGGTTG
65 ATATTTTCA-ATTTATTTTTCAAA-ATCAACTCATAATCCGAGAGATGAGTTGAGCCTAGGGTTG
* *
39666041 CACGCCGAGGAATTTT
128 CATGCCGAGGTATTTT
39666057 AAATTTCAAT
Statistics
Matches: 396, Mismatches: 38, Indels: 32
0.85 0.08 0.07
Matches are distributed among these distances:
299 3 0.01
300 56 0.14
302 1 0.00
303 12 0.03
304 57 0.14
305 56 0.14
306 16 0.04
307 49 0.12
308 144 0.36
309 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (301 bp):
TTTCTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAACCTCAGGTCACACGCTGAGGA
TATTTTCAATTTATTTTTCAAAATCAACTCATAATCCGAGAGATGAGTTGAGCCTAGGGTTGCAT
GCCGAGGTATTTTTTCTATTTCTATTTTTTGAAAATCAACTCATAATCCGAGAGATGAGTTGAGC
CTCGGGTCGCATGCCGAGATATTTTTCAATTTCTATTTTTCAAAGATCAACTCATAGTCCGAAAG
GTGAGTTGAGCCTCGGGTCGCACGTCGAGCTATTTTCAATT
Found at i:39666600 original size:29 final size:29
Alignment explanation
Indices: 39666546--39666676 Score: 122
Period size: 29 Copynumber: 4.5 Consensus size: 29
39666536 ACAAAAACTA
39666546 AAAATTTACATTTTTAA-CCCTCAACTTTTT
1 AAAATTTACA-TTTTAACCCCT-AACTTTTT
39666576 AAAATTTACATTTTAACCCCTAACTTTTT
1 AAAATTTACATTTTAACCCCTAACTTTTT
** ** * *
39666605 ACTATTTACATTTTGTCCCTTAACTTTCCT
1 AAAATTTACATTTTAACCCCTAACTTT-TT
* * *
39666635 AAAA-TTAAATTTTGACCCCTAATTTTTT
1 AAAATTTACATTTTAACCCCTAACTTTTT
**
39666663 ACTATTTACATTTT
1 AAAATTTACATTTT
39666677 GATCCCCCAA
Statistics
Matches: 82, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
28 3 0.04
29 62 0.76
30 17 0.21
ACGTcount: A:0.31, C:0.20, G:0.02, T:0.48
Consensus pattern (29 bp):
AAAATTTACATTTTAACCCCTAACTTTTT
Found at i:39666655 original size:58 final size:58
Alignment explanation
Indices: 39666549--39666688 Score: 176
Period size: 58 Copynumber: 2.4 Consensus size: 58
39666539 AAAACTAAAA
* *
39666549 ATTTACATTTT-TAACCCTCAACTTTTTAAAATTTACATTTTAACCCCTAACTTTTTACT
1 ATTTACATTTTGT--CCCTCAACTTTCTAAAATTTAAATTTTAACCCCTAACTTTTTACT
* * *
39666608 ATTTACATTTTGTCCCTTAACTTTCCTAAAA-TTAAATTTTGACCCCTAATTTTTTACT
1 ATTTACATTTTGTCCCTCAACTTT-CTAAAATTTAAATTTTAACCCCTAACTTTTTACT
*
39666666 ATTTACATTTTGATCCCCCAACT
1 ATTTACATTTTG-TCCCTCAACT
39666689 GCTACCTGAA
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
58 46 0.65
59 24 0.34
60 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.02, T:0.46
Consensus pattern (58 bp):
ATTTACATTTTGTCCCTCAACTTTCTAAAATTTAAATTTTAACCCCTAACTTTTTACT
Found at i:39666986 original size:19 final size:19
Alignment explanation
Indices: 39666964--39667004 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
39666954 AATAAACAAA
*
39666964 AGGAGAAGAAAGAAAGAGG
1 AGGAAAAGAAAGAAAGAGG
39666983 AGGAAAAGAAAGAAAGAGG
1 AGGAAAAGAAAGAAAGAGG
39667002 AGG
1 AGG
39667005 GAGAGGGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (19 bp):
AGGAAAAGAAAGAAAGAGG
Found at i:39667116 original size:5 final size:5
Alignment explanation
Indices: 39667096--39667160 Score: 64
Period size: 5 Copynumber: 13.2 Consensus size: 5
39667086 TTAAAAGTAG
* *
39667096 AGAAA AGAAA TA-AAA AGAAA AGAAAA AGAAA GGACA AGAAA A-AAA AG-AA
1 AGAAA AGAAA -AGAAA AGAAA AG-AAA AGAAA AGAAA AGAAA AGAAA AGAAA
*
39667145 AGAAA AGAAA GGAAA A
1 AGAAA AGAAA AGAAA A
39667161 ATAATAATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
4 9 0.18
5 34 0.69
6 6 0.12
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.02
Consensus pattern (5 bp):
AGAAA
Found at i:39667150 original size:28 final size:31
Alignment explanation
Indices: 39667100--39667157 Score: 95
Period size: 28 Copynumber: 2.0 Consensus size: 31
39667090 AAGTAGAGAA
39667100 AAGAAATAAAAAGAAAAGAAAAAGAAAGGAC
1 AAGAAATAAAAAGAAAAGAAAAAGAAAGGAC
39667131 AAGAAA-AAAAAG-AAAG-AAAAGAAAGGA
1 AAGAAATAAAAAGAAAAGAAAAAGAAAGGA
39667158 AAAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 11 0.41
29 4 0.15
30 6 0.22
31 6 0.22
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.02
Consensus pattern (31 bp):
AAGAAATAAAAAGAAAAGAAAAAGAAAGGAC
Found at i:39672800 original size:43 final size:43
Alignment explanation
Indices: 39672708--39672802 Score: 138
Period size: 43 Copynumber: 2.2 Consensus size: 43
39672698 GTTTATGTGG
39672708 AAAAACGCCGCTATAGAACATGACCTTTAGCAGCGCTTTTTCC
1 AAAAACGCCGCTATAGAACATGACCTTTAGCAGCGCTTTTTCC
* * * *
39672751 ACAAACGCCGCTGTAGGACATGACCTTTAGCGGCGC-TTTTCC
1 AAAAACGCCGCTATAGAACATGACCTTTAGCAGCGCTTTTTCC
39672793 TAAAAACGCC
1 -AAAAACGCC
39672803 ACTAAAGGTC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 6 0.13
43 40 0.87
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.23
Consensus pattern (43 bp):
AAAAACGCCGCTATAGAACATGACCTTTAGCAGCGCTTTTTCC
Found at i:39673247 original size:66 final size:65
Alignment explanation
Indices: 39673164--39673301 Score: 181
Period size: 66 Copynumber: 2.1 Consensus size: 65
39673154 TCATATTTTG
* *
39673164 AAGTTGCAGCTGGAGTTCGTCATATTTTCTGCTT-GCCTCTACTTCCCT-TATTGCTGTCTCCAC
1 AAGTTGCAGCTGGAGTTCGTCATATTTTCT--TTAGCCTCTACTTCCCTCGA-TGCTGCCTCCAC
39673227 TTT
63 TTT
* * *
39673230 AAGTTGTAGCTGGAGTTCTTCATATTTTCTTTGAGCCTCTACTTCTCTCGATGCTGCCTCCACTT
1 AAGTTGCAGCTGGAGTTCGTCATATTTTCTTT-AGCCTCTACTTCCCTCGATGCTGCCTCCACTT
39673295 T
65 T
39673296 AAGTTG
1 AAGTTG
39673302 AGCAATTTGC
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
64 2 0.03
66 61 0.95
67 1 0.02
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.42
Consensus pattern (65 bp):
AAGTTGCAGCTGGAGTTCGTCATATTTTCTTTAGCCTCTACTTCCCTCGATGCTGCCTCCACTTT
Found at i:39678677 original size:7 final size:7
Alignment explanation
Indices: 39678665--39678696 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
39678655 AGATAGTACA
*
39678665 TATCAAT
1 TATCAAG
39678672 TATCAAG
1 TATCAAG
39678679 TATCAAG
1 TATCAAG
39678686 TATCAAG
1 TATCAAG
39678693 TATC
1 TATC
39678697 TAATGGGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (7 bp):
TATCAAG
Found at i:39678759 original size:9 final size:9
Alignment explanation
Indices: 39678745--39678884 Score: 141
Period size: 9 Copynumber: 16.0 Consensus size: 9
39678735 CAAGTATAAT
39678745 TAAGTTATG
1 TAAGTTATG
39678754 TAAGTTATG
1 TAAGTTATG
* * *
39678763 ATATGATATA
1 -TAAGTTATG
*
39678773 T-ATTTATG
1 TAAGTTATG
39678781 TAAGTTATG
1 TAAGTTATG
39678790 TAAGTTATG
1 TAAGTTATG
*
39678799 -ATA-TGATG
1 TA-AGTTATG
*
39678807 TATATTTATG
1 TA-AGTTATG
39678817 -AA-TTATG
1 TAAGTTATG
39678824 TAAGTTATG
1 TAAGTTATG
39678833 TAAGTTATG
1 TAAGTTATG
*
39678842 TAGGTTATG
1 TAAGTTATG
39678851 TAAGTTATG
1 TAAGTTATG
39678860 T-A-TTATG
1 TAAGTTATG
39678867 TAAGTTATG
1 TAAGTTATG
39678876 TAAGTTATG
1 TAAGTTATG
39678885 ATCCAAAGTT
Statistics
Matches: 110, Mismatches: 12, Indels: 18
0.79 0.09 0.13
Matches are distributed among these distances:
7 11 0.10
8 14 0.13
9 75 0.68
10 10 0.09
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:39678787 original size:36 final size:36
Alignment explanation
Indices: 39678745--39678861 Score: 159
Period size: 36 Copynumber: 3.3 Consensus size: 36
39678735 CAAGTATAAT
39678745 TAAGTTATGTAAGTTATGATATGATATATATTTATG
1 TAAGTTATGTAAGTTATGATATGATATATATTTATG
*
39678781 TAAGTTATGTAAGTTATGATATGATGTATATTTATG
1 TAAGTTATGTAAGTTATGATATGATATATATTTATG
* * * *
39678817 -AA-TTATGTAAGTTATG-TAAGTTATGTAGGTTATG
1 TAAGTTATGTAAGTTATGATATGATATATA-TTTATG
39678851 TAAGTTATGTA
1 TAAGTTATGTA
39678862 TTATGTAAGT
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
33 7 0.10
34 19 0.26
35 4 0.06
36 42 0.58
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (36 bp):
TAAGTTATGTAAGTTATGATATGATATATATTTATG
Found at i:39678827 original size:43 final size:43
Alignment explanation
Indices: 39678776--39678886 Score: 163
Period size: 43 Copynumber: 2.6 Consensus size: 43
39678766 TGATATATAT
*
39678776 TTATGTAAGTTATGTAAGTTATGATA-TGATGTATATTTATGAA
1 TTATGTAAGTTATGTAAGTTATGATAGTGATGTA-AGTTATGAA
* *
39678819 TTATGTAAGTTATGTAAGTTATG-TAGGTTATGTAAGTTATGTA
1 TTATGTAAGTTATGTAAGTTATGATA-GTGATGTAAGTTATGAA
39678862 TTATGTAAGTTATGTAAGTTATGAT
1 TTATGTAAGTTATGTAAGTTATGAT
39678887 CCAAAGTTTT
Statistics
Matches: 62, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
42 2 0.03
43 53 0.85
44 7 0.11
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (43 bp):
TTATGTAAGTTATGTAAGTTATGATAGTGATGTAAGTTATGAA
Found at i:39678944 original size:35 final size:35
Alignment explanation
Indices: 39678905--39678971 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
39678895 TTTTTTTATT
*
39678905 CTTTAAATGTTTATGTAAGTTATGATAATCATAAA
1 CTTTAAATGTTTATGTAAGATATGATAATCATAAA
*
39678940 CTTTAAATGTTTATGTAAGATATGATTATCAT
1 CTTTAAATGTTTATGTAAGATATGATAATCAT
39678972 CTTTAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (35 bp):
CTTTAAATGTTTATGTAAGATATGATAATCATAAA
Found at i:39678990 original size:13 final size:13
Alignment explanation
Indices: 39678972--39678998 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39678962 TGATTATCAT
39678972 CTTTAAATTTTAA
1 CTTTAAATTTTAA
39678985 CTTTAAATTTTAA
1 CTTTAAATTTTAA
39678998 C
1 C
39678999 CCTTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (13 bp):
CTTTAAATTTTAA
Found at i:39680074 original size:21 final size:22
Alignment explanation
Indices: 39680049--39680094 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
39680039 TTTGCAAATA
*
39680049 AAATAT-GAGAATGAAGGCTTT
1 AAATATAGACAATGAAGGCTTT
39680070 AAATATAGGACAATGAAGGCTTT
1 AAATATA-GACAATGAAGGCTTT
39680093 AA
1 AA
39680095 CAGTTTGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.27
23 16 0.73
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.26
Consensus pattern (22 bp):
AAATATAGACAATGAAGGCTTT
Found at i:39680152 original size:12 final size:12
Alignment explanation
Indices: 39680135--39680165 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
39680125 CAATAGCATG
39680135 CTCCATTCTCAA
1 CTCCATTCTCAA
*
39680147 CTCCATTCTCAC
1 CTCCATTCTCAA
39680159 CTCCATT
1 CTCCATT
39680166 TATAACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.45, G:0.00, T:0.35
Consensus pattern (12 bp):
CTCCATTCTCAA
Found at i:39688693 original size:41 final size:41
Alignment explanation
Indices: 39688633--39688751 Score: 150
Period size: 41 Copynumber: 2.9 Consensus size: 41
39688623 TTTAAGGCGT
* *
39688633 TAAACGCCACTACTGCTTGACCTTTTACGGTGTTTTTCTCA
1 TAAACGCCGCTACTGCTTGACCTTTTACGGCGTTTTTCTCA
* * * *
39688674 TAAACGCTGCTACTACTTGATCTTTTGCGGCGTTTTTCTCA
1 TAAACGCCGCTACTGCTTGACCTTTTACGGCGTTTTTCTCA
* * *
39688715 TAAATGCCGCTACTGCTTGACCTATT-GGGCGTTTTTC
1 TAAACGCCGCTACTGCTTGACCTTTTACGGCGTTTTTC
39688752 CATTAGCGCC
Statistics
Matches: 66, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
40 10 0.15
41 56 0.85
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (41 bp):
TAAACGCCGCTACTGCTTGACCTTTTACGGCGTTTTTCTCA
Found at i:39691968 original size:17 final size:18
Alignment explanation
Indices: 39691934--39691969 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
39691924 TTATTTTTCA
*
39691934 TTATTAAATTATAAAAAT
1 TTATTAAAATATAAAAAT
39691952 TTATTAAAATA-AAAAAT
1 TTATTAAAATATAAAAAT
39691969 T
1 T
39691970 GATGTTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTATTAAAATATAAAAAT
Found at i:39695998 original size:29 final size:29
Alignment explanation
Indices: 39695961--39696016 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
39695951 TAATAATATA
39695961 ATATATTTTAAATATAAAATT-ATATTTTC
1 ATATATTTTAAAT-TAAAATTGATATTTTC
* **
39695990 ATATTTTTTTCATTAAAATTGATATTT
1 ATATATTTTAAATTAAAATTGATATTT
39696017 GATTGACTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (29 bp):
ATATATTTTAAATTAAAATTGATATTTTC
Found at i:39701677 original size:22 final size:23
Alignment explanation
Indices: 39701615--39701690 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 23
39701605 AACAAAATTT
39701615 TTTTAGATA-GATTATTACTATTAAA
1 TTTTA-ATAGGATTATTA-T-TTAAA
*
39701640 TTTTAAT-GTGAATATTATTT-AA
1 TTTTAATAG-GATTATTATTTAAA
*
39701662 TTTTAATAGGATTATTATTAAATA
1 TTTTAATAGGATTATTATTTAA-A
39701686 TTTTA
1 TTTTA
39701691 TATTAATTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
22 18 0.42
23 4 0.09
24 9 0.21
25 12 0.28
ACGTcount: A:0.38, C:0.01, G:0.08, T:0.53
Consensus pattern (23 bp):
TTTTAATAGGATTATTATTTAAA
Found at i:39701706 original size:24 final size:24
Alignment explanation
Indices: 39701679--39701752 Score: 71
Period size: 23 Copynumber: 3.1 Consensus size: 24
39701669 AGGATTATTA
39701679 TTAAATATTTTATATTAATTTAAT
1 TTAAATATTTTATATTAATTTAAT
* * *
39701703 TT-AATGTTTTATAATAAATTATAT
1 TTAAATATTTTATATTAATTTA-AT
* * *
39701727 TAAAATATTTTAT-TTATTTTATT
1 TTAAATATTTTATATTAATTTAAT
39701750 TTA
1 TTA
39701753 TATTTTTTGA
Statistics
Matches: 38, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
23 19 0.50
24 10 0.26
25 9 0.24
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (24 bp):
TTAAATATTTTATATTAATTTAAT
Found at i:39701729 original size:23 final size:23
Alignment explanation
Indices: 39701672--39701739 Score: 57
Period size: 23 Copynumber: 2.8 Consensus size: 23
39701662 TTTTAATAGG
*
39701672 ATTATTATTAAATATTTTATATTAA
1 ATTA-TATT-AATATTTTATAATAA
* *
39701697 TTTA-ATTTAATGTTTTATAATAA
1 ATTATA-TTAATATTTTATAATAA
39701720 ATTATATTAAAATATTTTAT
1 ATTATATT--AATATTTTAT
39701740 TTATTTTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
23 19 0.56
24 3 0.09
25 12 0.35
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (23 bp):
ATTATATTAATATTTTATAATAA
Found at i:39710568 original size:40 final size:40
Alignment explanation
Indices: 39710523--39710647 Score: 134
Period size: 40 Copynumber: 3.1 Consensus size: 40
39710513 GCGTTATACT
*
39710523 TTCTGTTTGGCGTGATTCGAATGGATCAACTCTTATGAGC
1 TTCTGTTTGGCATGATTCGAATGGATCAACTCTTATGAGC
* * *
39710563 TTCTG-TTGGCATGTTTC-AAGTGGACCAGCTCTTATGAGC
1 TTCTGTTTGGCATGATTCGAA-TGGATCAACTCTTATGAGC
*
39710602 TTCTGTTTGGCAT-ATTTACG-TTGGAT-AAGCTCTTATGAGC
1 TTCTGTTTGGCATGA-TT-CGAATGGATCAA-CTCTTATGAGC
39710642 TTCTGT
1 TTCTGT
39710648 CTGGTGTGTT
Statistics
Matches: 71, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
38 2 0.03
39 33 0.46
40 35 0.49
41 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (40 bp):
TTCTGTTTGGCATGATTCGAATGGATCAACTCTTATGAGC
Found at i:39711374 original size:12 final size:13
Alignment explanation
Indices: 39711350--39711383 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
39711340 GATTAATGTC
39711350 ATTTTGAGTTGGT
1 ATTTTGAGTTGGT
39711363 ATTTTG-GTTGGT
1 ATTTTGAGTTGGT
39711375 A-TTTGAGTT
1 ATTTTGAGTT
39711384 TTTTAAGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 10 0.50
13 6 0.30
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (13 bp):
ATTTTGAGTTGGT
Found at i:39717556 original size:19 final size:19
Alignment explanation
Indices: 39717509--39717546 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
39717499 AAATTTCTCA
39717509 ATTACTTTTGTTTAAGATT
1 ATTACTTTTGTTTAAGATT
39717528 ATTACTTTTGTTTAAGATT
1 ATTACTTTTGTTTAAGATT
39717547 TTTTGTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.11, T:0.58
Consensus pattern (19 bp):
ATTACTTTTGTTTAAGATT
Found at i:39721997 original size:3 final size:3
Alignment explanation
Indices: 39721989--39722015 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
39721979 ATTTTCTTAC
39721989 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT
39722016 TGCATGTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:39728081 original size:386 final size:386
Alignment explanation
Indices: 39727368--39728145 Score: 1556
Period size: 386 Copynumber: 2.0 Consensus size: 386
39727358 TCTTGTGACA
39727368 GCTACCTCAAAATGAGTACTGCATTTGTTCTTGCAATTGCCCACTTAACTATATGCATTCATGTA
1 GCTACCTCAAAATGAGTACTGCATTTGTTCTTGCAATTGCCCACTTAACTATATGCATTCATGTA
39727433 ATTACATGTAAGAACAGGCATGAAGTAGCTTTGAAGCAGTGAGCAAGCTATTTGGCTTGAATTAA
66 ATTACATGTAAGAACAGGCATGAAGTAGCTTTGAAGCAGTGAGCAAGCTATTTGGCTTGAATTAA
39727498 GCCATAGCTATTCATACATATTTTAATCTAAACACAGGCACATCTGTATGTATATAAGAAAGATG
131 GCCATAGCTATTCATACATATTTTAATCTAAACACAGGCACATCTGTATGTATATAAGAAAGATG
39727563 AAGAAAGAATGTCTACCCCTGCTGCAATGAGGTCTGATTGCAAATTATAGTCACTGCTGTTATAT
196 AAGAAAGAATGTCTACCCCTGCTGCAATGAGGTCTGATTGCAAATTATAGTCACTGCTGTTATAT
39727628 TCACGTAGGATGAATATGAAATTCTGGTGGAGCTTAATCATTTGATTATTTGATGAACTGTTTGA
261 TCACGTAGGATGAATATGAAATTCTGGTGGAGCTTAATCATTTGATTATTTGATGAACTGTTTGA
39727693 TATTTATCTGAAGTAGGATGGAGTTTTGGCTTAAAAAATTCCTACTCTTAACATGTAAAGT
326 TATTTATCTGAAGTAGGATGGAGTTTTGGCTTAAAAAATTCCTACTCTTAACATGTAAAGT
39727754 GCTACCTCAAAATGAGTACTGCATTTGTTCTTGCAATTGCCCACTTAACTATATGCATTCATGTA
1 GCTACCTCAAAATGAGTACTGCATTTGTTCTTGCAATTGCCCACTTAACTATATGCATTCATGTA
39727819 ATTACATGTAAGAACAGGCATGAAGTAGCTTTGAAGCAGTGAGCAAGCTATTTGGCTTGAATTAA
66 ATTACATGTAAGAACAGGCATGAAGTAGCTTTGAAGCAGTGAGCAAGCTATTTGGCTTGAATTAA
39727884 GCCATAGCTATTCATACATATTTTAATCTAAACACAGGCACATCTGTATGTATATAAGAAAGATG
131 GCCATAGCTATTCATACATATTTTAATCTAAACACAGGCACATCTGTATGTATATAAGAAAGATG
39727949 AAGAAAGAATGTCTACCCCTGCTGCAATGAGGTCTGATTGCAAATTATAGTCACTGCTGTTATAT
196 AAGAAAGAATGTCTACCCCTGCTGCAATGAGGTCTGATTGCAAATTATAGTCACTGCTGTTATAT
39728014 TCACGTAGGATGAATATGAAATTCTGGTGGAGCTTAATCATTTGATTATTTGATGAACTGTTTGA
261 TCACGTAGGATGAATATGAAATTCTGGTGGAGCTTAATCATTTGATTATTTGATGAACTGTTTGA
39728079 TATTTATCTGAAGTAGGATGGAGTTTTGGCTTAAAAAATTCCTACTCTTAACATGTAAAGT
326 TATTTATCTGAAGTAGGATGGAGTTTTGGCTTAAAAAATTCCTACTCTTAACATGTAAAGT
39728140 GCTACC
1 GCTACC
39728146 ATACTAGGGA
Statistics
Matches: 392, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
386 392 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (386 bp):
GCTACCTCAAAATGAGTACTGCATTTGTTCTTGCAATTGCCCACTTAACTATATGCATTCATGTA
ATTACATGTAAGAACAGGCATGAAGTAGCTTTGAAGCAGTGAGCAAGCTATTTGGCTTGAATTAA
GCCATAGCTATTCATACATATTTTAATCTAAACACAGGCACATCTGTATGTATATAAGAAAGATG
AAGAAAGAATGTCTACCCCTGCTGCAATGAGGTCTGATTGCAAATTATAGTCACTGCTGTTATAT
TCACGTAGGATGAATATGAAATTCTGGTGGAGCTTAATCATTTGATTATTTGATGAACTGTTTGA
TATTTATCTGAAGTAGGATGGAGTTTTGGCTTAAAAAATTCCTACTCTTAACATGTAAAGT
Found at i:39728919 original size:24 final size:24
Alignment explanation
Indices: 39728892--39728940 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
39728882 AAAGAAGTAA
39728892 GATTATAAGATAAGAACATAAGGC
1 GATTATAAGATAAGAACATAAGGC
*
39728916 GATTATAAGATAGGAACATAAGGC
1 GATTATAAGATAAGAACATAAGGC
39728940 G
1 G
39728941 TGCGAGTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.47, C:0.08, G:0.24, T:0.20
Consensus pattern (24 bp):
GATTATAAGATAAGAACATAAGGC
Found at i:39732050 original size:43 final size:43
Alignment explanation
Indices: 39731746--39732037 Score: 451
Period size: 43 Copynumber: 6.8 Consensus size: 43
39731736 GCGTCGCTAA
* *
39731746 CTTTAGCGGCGCGTATACCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCAAGAC
* * *
39731789 CTTTAGCGGCGCTTTTCCCAC-AACGCCGCTAAAGACCAGGTC
1 CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCAAGAC
* *
39731831 CTTTAGCGGCGCTTTTTCCACAAACACCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCAAGAC
* *
39731874 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCAAGAC
* *
39731917 CTTTAGCGGCGCTTATACCACAAACGCCGCTAAAGACTAAGAC
1 CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCAAGAC
*
39731960 CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCAAAAC
1 CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCAAGAC
*
39732003 CTTTAGCGGCGCTTTTTATCACAAACGCCGCTAAA
1 CTTTAGCGGCGC-TTTTACCACAAACGCCGCTAAA
39732038 AACATAATCT
Statistics
Matches: 227, Mismatches: 20, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
42 39 0.17
43 167 0.74
44 21 0.09
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.20
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCAAGAC
Found at i:39732808 original size:23 final size:23
Alignment explanation
Indices: 39732758--39732809 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
39732748 GTTAGGTGTC
* *
39732758 AGTATAAAGACATGTCAGATATG
1 AGTATGAAGACATGTCAGAGATG
* * *
39732781 GGTATGAAGGCATGTCTGAGATG
1 AGTATGAAGACATGTCAGAGATG
39732804 AGTATG
1 AGTATG
39732810 TTCAATTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.27
Consensus pattern (23 bp):
AGTATGAAGACATGTCAGAGATG
Found at i:39733286 original size:12 final size:12
Alignment explanation
Indices: 39733269--39733298 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
39733259 CAAGACAGAT
39733269 CAAATTTTAAAG
1 CAAATTTTAAAG
39733281 CAAATTTTAAAG
1 CAAATTTTAAAG
39733293 CAAATT
1 CAAATT
39733299 GCTGCTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (12 bp):
CAAATTTTAAAG
Found at i:39735751 original size:145 final size:143
Alignment explanation
Indices: 39735490--39735775 Score: 527
Period size: 145 Copynumber: 2.0 Consensus size: 143
39735480 GGAGGGGGGT
39735490 AGGGAATTAAAAAAAATGGCGCTATTTTTTTAAAAGTAAATTTTATTTTGTGGCGTTTTTTTATA
1 AGGGAATTAAAAAAAATGGCGCTATTTTTTTAAAAGTAAATTTTATTTTGTGGCGTTTTTTTATA
*
39735555 AAAACGCCGCTATTGTTTATCTATTGCGGCGTTTTTTACACAAACGCCGCAAAAAATTATTTTAT
66 AAAACGCCGCTATTGCTTATCTATTGCGGCGTTTTTTACACAAACGCCGCAAAAAATTATTTTAT
39735620 TTGGAATAAAACG
131 TTGGAATAAAACG
*
39735633 AGGGAATTTAAAAAAATGGCGCTATTTTTTTAAAAGTAAATTTTATTTTGTGGCGTTTTTTTTTA
1 AGGGAATTAAAAAAAATGGCGCTATTTTTTTAAAAGTAAATTTTATTTTGTGGCG--TTTTTTTA
*
39735698 TAAAAACGCCGCTATTGCTTATCTATTGCGGCGTTTTTTACAGAAACGCCGCAAAAAATTATTTT
64 TAAAAACGCCGCTATTGCTTATCTATTGCGGCGTTTTTTACACAAACGCCGCAAAAAATTATTTT
39735763 ATTTGGAATAAAA
129 ATTTGGAATAAAA
39735776 TGACACTGTT
Statistics
Matches: 138, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
143 54 0.39
145 84 0.61
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (143 bp):
AGGGAATTAAAAAAAATGGCGCTATTTTTTTAAAAGTAAATTTTATTTTGTGGCGTTTTTTTATA
AAAACGCCGCTATTGCTTATCTATTGCGGCGTTTTTTACACAAACGCCGCAAAAAATTATTTTAT
TTGGAATAAAACG
Found at i:39736762 original size:28 final size:29
Alignment explanation
Indices: 39736720--39736774 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
39736710 TCAAATCTCT
* * *
39736720 AAACCCTAAATCACTAA-CTCTTAACCCC
1 AAACCCCAAACCACTAACCTCTAAACCCC
39736748 AAACCCCAAACCACTAACCTCTAAACC
1 AAACCCCAAACCACTAACCTCTAAACC
39736775 TTATTTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (29 bp):
AAACCCCAAACCACTAACCTCTAAACCCC
Found at i:39736847 original size:82 final size:82
Alignment explanation
Indices: 39736750--39736909 Score: 243
Period size: 82 Copynumber: 2.0 Consensus size: 82
39736740 TTAACCCCAA
*
39736750 ACCCCAAACCACTAAC-CTCTAAACCTTATTTAATATAGAAATTAAAAAACACTAATTAATCTAA
1 ACCCCAAACCACTAACTC-CTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAA
*
39736814 ATCATAAACCCTAACATG
65 ACCATAAACCCTAACATG
* *
39736832 ACCCCAAATCC-CTAACTCCTAAACATTATTTAATATATAAATTAAAACACACTAATTAATCTAA
1 ACCCCAAA-CCACTAACTCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAA
*
39736896 ACCCTAAACCCTAA
65 ACCATAAACCCTAA
39736910 ACTAACACTA
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
82 68 0.96
83 3 0.04
ACGTcount: A:0.47, C:0.26, G:0.01, T:0.26
Consensus pattern (82 bp):
ACCCCAAACCACTAACTCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAA
CCATAAACCCTAACATG
Found at i:39736935 original size:82 final size:81
Alignment explanation
Indices: 39736753--39736936 Score: 219
Period size: 82 Copynumber: 2.2 Consensus size: 81
39736743 ACCCCAAACC
* *
39736753 CCAAA-CCACTAACCTCTAAACCTTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAATC
1 CCAAATCCA-TAACC-CTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAACC
* *
39736817 ATAAACCCTAACATGACC
64 ATAAACCCTAACATAACA
* * * *
39736835 CCAAATCCCTAACTCCTAAACATTATTTAATATATAAATTAAAACACACTAATTAATCTAAACCC
1 CCAAATCCATAAC-CCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAACCA
39736900 TAAACCCTAA-ACTAACA
65 TAAACCCTAACA-TAACA
* *
39736917 CTAAATCTATAAACCCTAAA
1 CCAAATCCAT-AACCCTAAA
39736937 TTCCTAACTC
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
81 1 0.01
82 80 0.92
83 6 0.07
ACGTcount: A:0.48, C:0.25, G:0.01, T:0.26
Consensus pattern (81 bp):
CCAAATCCATAACCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAACCAT
AAACCCTAACATAACA
Found at i:39737030 original size:14 final size:15
Alignment explanation
Indices: 39737011--39737042 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
39737001 CTTAAATTAG
39737011 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
39737025 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
39737040 AAT
1 AAT
39737043 TTATAAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:39737466 original size:41 final size:41
Alignment explanation
Indices: 39737409--39737772 Score: 550
Period size: 41 Copynumber: 8.9 Consensus size: 41
39737399 AAATGTTTTT
39737409 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
*
39737450 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* *
39737491 GCGGCGCTTTTTTAAAAACACCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* * * *
39737532 GTGGTGCTTTCTCAAAAATGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* * *
39737573 GCGGCGTTTTTTTAAAAATGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* * *
39737614 GCGGCGTTTTTTTAAAAATGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
*
39737655 GCGGCGCTTTCTCAAAAAGCGCCGCTAAAGA-CTTGAGCATTA
1 GCGGCGCTTTTTCAAAAA-CGCCGCTAAAGATC-TGAGCATTA
*
39737697 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* *
39737738 GCAGCGCTTTTTTAAAAACGCCGCTAAAGATCTGA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGA
39737773 AAGGTACAAA
Statistics
Matches: 298, Mismatches: 22, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
41 259 0.87
42 39 0.13
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.26
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:39737847 original size:39 final size:39
Alignment explanation
Indices: 39737817--39737894 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
39737807 TTGCGGCATT
39737817 TTTCCAAAAAACGCCGCTAATGCTAATTTTTAGCGGCGC
1 TTTCCAAAAAACGCCGCTAATGCTAATTTTTAGCGGCGC
* * * *
39737856 TTTCCTAGAAACGCCGCTAATGCTCGATCTTTAGCGGCG
1 TTTCCAAAAAACGCCGCTAATGCT-AATTTTTAGCGGCG
39737895 TTTTACGTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 22 0.65
40 12 0.35
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (39 bp):
TTTCCAAAAAACGCCGCTAATGCTAATTTTTAGCGGCGC
Found at i:39737935 original size:40 final size:40
Alignment explanation
Indices: 39737816--39737938 Score: 142
Period size: 40 Copynumber: 3.1 Consensus size: 40
39737806 TTTGCGGCAT
* * *
39737816 TTTTCCAAAAAACGCCGCTAATGCT-AATTTTTAGCGGCG
1 TTTTCCTAGAAACGCCGCTAATGCTCGATTTTTAGCGGCG
* *
39737855 CTTTCCTAGAAACGCCGCTAATGCTCGATCTTTAGCGGCG
1 TTTTCCTAGAAACGCCGCTAATGCTCGATTTTTAGCGGCG
* * * *
39737895 TTTTACGT-TAAGCGCCGCTAATGCTCGATTTTTAGTGGCG
1 TTTT-CCTAGAAACGCCGCTAATGCTCGATTTTTAGCGGCG
39737935 TTTT
1 TTTT
39737939 TTGTCCAAAC
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
39 22 0.31
40 47 0.66
41 2 0.03
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (40 bp):
TTTTCCTAGAAACGCCGCTAATGCTCGATTTTTAGCGGCG
Found at i:39744778 original size:21 final size:21
Alignment explanation
Indices: 39744753--39744803 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
39744743 CAAGCTATAG
39744753 GGGTATCGCGATATCCTTTTA
1 GGGTATCGCGATATCCTTTTA
* *
39744774 GGGTATCGTGATATCTTTTTA
1 GGGTATCGCGATATCCTTTTA
39744795 GGGTATCGC
1 GGGTATCGC
39744804 AATACCCACC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (21 bp):
GGGTATCGCGATATCCTTTTA
Found at i:39748002 original size:19 final size:19
Alignment explanation
Indices: 39747987--39748024 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
39747977 AAGAAAATAG
39747987 CAACAAAACAGTAAAAAAA
1 CAACAAAACAGTAAAAAAA
* *
39748006 CAAGAAAATAGTAAAAAAA
1 CAACAAAACAGTAAAAAAA
39748025 ATAATAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.11, G:0.08, T:0.08
Consensus pattern (19 bp):
CAACAAAACAGTAAAAAAA
Found at i:39748005 original size:30 final size:31
Alignment explanation
Indices: 39747959--39748016 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
39747949 GAAATGGTAG
*
39747959 CAAAATAGTGAAAAAAACAAGAAAATAGCAA
1 CAAAACAGTGAAAAAAACAAGAAAATAGCAA
39747990 CAAAACAGT-AAAAAAACAAGAAAATAG
1 CAAAACAGTGAAAAAAACAAGAAAATAG
39748017 TAAAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.69, C:0.10, G:0.12, T:0.09
Consensus pattern (31 bp):
CAAAACAGTGAAAAAAACAAGAAAATAGCAA
Found at i:39752996 original size:37 final size:36
Alignment explanation
Indices: 39752934--39753009 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
39752924 GATAACCACT
*
39752934 TTAATATTAAATTAATAAAATACTATTAAGATAAGTA
1 TTAATATTAAATTAATAAAATACTATTAAAATAA-TA
*
39752971 TTAA-ATTAAATTTAATATTAA-ACTATTAAAATAATA
1 TTAATATTAAA-TTAATA-AAATACTATTAAAATAATA
39753007 TTA
1 TTA
39753010 TTTTTGGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 11 0.31
37 22 0.63
38 2 0.06
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (36 bp):
TTAATATTAAATTAATAAAATACTATTAAAATAATA
Found at i:39753407 original size:19 final size:19
Alignment explanation
Indices: 39753383--39753425 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
39753373 AAAATATCAT
39753383 ATTAATTTTAATTGATTTG
1 ATTAATTTTAATTGATTTG
* *
39753402 ATTAATTTTATTTTATTTG
1 ATTAATTTTAATTGATTTG
39753421 ATTAA
1 ATTAA
39753426 AATTAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (19 bp):
ATTAATTTTAATTGATTTG
Found at i:39754604 original size:15 final size:14
Alignment explanation
Indices: 39754578--39754613 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
39754568 GCTATGCATG
*
39754578 CAAAATATAAAAGA
1 CAAAATACAAAAGA
39754592 CATAAATACAAAAGA
1 CA-AAATACAAAAGA
39754607 CAAAATA
1 CAAAATA
39754614 GTGAAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.69, C:0.11, G:0.06, T:0.14
Consensus pattern (14 bp):
CAAAATACAAAAGA
Found at i:39759143 original size:5 final size:5
Alignment explanation
Indices: 39759133--39759159 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
39759123 AAAATGACAG
39759133 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
39759160 GTTTAACACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:39760769 original size:16 final size:16
Alignment explanation
Indices: 39760748--39760780 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39760738 TAGAAGAAAG
39760748 TGTTGGTTGAGAAAAA
1 TGTTGGTTGAGAAAAA
39760764 TGTTGGTTGAGAAAAA
1 TGTTGGTTGAGAAAAA
39760780 T
1 T
39760781 CAGCTCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.33
Consensus pattern (16 bp):
TGTTGGTTGAGAAAAA
Found at i:39760778 original size:15 final size:15
Alignment explanation
Indices: 39760742--39760778 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
39760732 AAGTGATAGA
*
39760742 AGAAAGTGTTGGTTG
1 AGAAAATGTTGGTTG
39760757 AGAAAAATGTTGGTTG
1 AG-AAAATGTTGGTTG
39760773 AGAAAA
1 AGAAAA
39760779 ATCAGCTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.41, C:0.00, G:0.32, T:0.27
Consensus pattern (15 bp):
AGAAAATGTTGGTTG
Found at i:39780667 original size:20 final size:20
Alignment explanation
Indices: 39780644--39780688 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
39780634 GACCAAGCCA
*
39780644 CCAGTAATACAGATAAATTG
1 CCAGTAATACAGATAAACTG
* *
39780664 CCAGTATTGCAGATAAACTG
1 CCAGTAATACAGATAAACTG
39780684 CCAGT
1 CCAGT
39780689 TGCAAACAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (20 bp):
CCAGTAATACAGATAAACTG
Found at i:39785796 original size:19 final size:19
Alignment explanation
Indices: 39785749--39785802 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
39785739 ATGCAAAAAA
* *
39785749 AGTTTGTTGTTTTTTTATT
1 AGTTTGTTGCTTTTTTACT
* *
39785768 GGTTTCTTGCTTTTTTACT
1 AGTTTGTTGCTTTTTTACT
*
39785787 ATTTTGTTGCTATTTT
1 AGTTTGTTGCT-TTTT
39785803 CTTGTTTTCT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 23 0.85
20 4 0.15
ACGTcount: A:0.09, C:0.07, G:0.15, T:0.69
Consensus pattern (19 bp):
AGTTTGTTGCTTTTTTACT
Found at i:39786424 original size:40 final size:40
Alignment explanation
Indices: 39786334--39786446 Score: 113
Period size: 40 Copynumber: 2.8 Consensus size: 40
39786324 ACACACCAGT
*
39786334 TTGTGGACAAGCCACCAGTAATGCAGAAAAACTGCTAGAA
1 TTGTGGACAAGCCACCAGTAATGCAGAAAAACTACTAGAA
* * * * *
39786374 TTGTGTACAAGCCACTAGTATTGCA-AACGAGCTACTAGTAA
1 TTGTGGACAAGCCACCAGTAATGCAGAA-AAACTACTAG-AA
* * *
39786415 -TGTGGACAAGCCAGCAATAATGCAGATAAACT
1 TTGTGGACAAGCCACCAGTAATGCAGAAAAACT
39786447 GCCAATATTG
Statistics
Matches: 56, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
39 2 0.04
40 51 0.91
41 3 0.05
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (40 bp):
TTGTGGACAAGCCACCAGTAATGCAGAAAAACTACTAGAA
Found at i:39786452 original size:20 final size:20
Alignment explanation
Indices: 39786429--39786473 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
39786419 GACAAGCCAG
* *
39786429 CAATAATGCAGATAAACTGC
1 CAATAATGCAAACAAACTGC
* *
39786449 CAATATTGCAAACAAGCTGC
1 CAATAATGCAAACAAACTGC
39786469 CAATA
1 CAATA
39786474 TTGTGGACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.22, G:0.13, T:0.20
Consensus pattern (20 bp):
CAATAATGCAAACAAACTGC
Found at i:39788096 original size:9 final size:9
Alignment explanation
Indices: 39788082--39788148 Score: 98
Period size: 9 Copynumber: 7.4 Consensus size: 9
39788072 GTAGTGATTC
*
39788082 AATTCGGTT
1 AATTCGGGT
*
39788091 AATTCGAGT
1 AATTCGGGT
39788100 AATTCGGGT
1 AATTCGGGT
39788109 AATTCGGGT
1 AATTCGGGT
39788118 AATTCGGGT
1 AATTCGGGT
*
39788127 AATTCGGTT
1 AATTCGGGT
*
39788136 AATTCGGTT
1 AATTCGGGT
39788145 AATT
1 AATT
39788149 TTTAACAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 54 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.39
Consensus pattern (9 bp):
AATTCGGGT
Found at i:39788270 original size:28 final size:27
Alignment explanation
Indices: 39788211--39788270 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 27
39788201 CGAATTAACC
* ***
39788211 AAAAAAAATTCGGTTTGGTTAATTTTTT
1 AAAAAAAATTCGGTTCGGTTAA-CGGTT
*
39788239 AAAAAAATTTCGGTTCGGTTAACGGTT
1 AAAAAAAATTCGGTTCGGTTAACGGTT
39788266 AAAAA
1 AAAAA
39788271 TTTTCAAAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 7 0.26
28 20 0.74
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.37
Consensus pattern (27 bp):
AAAAAAAATTCGGTTCGGTTAACGGTT
Found at i:39791502 original size:21 final size:21
Alignment explanation
Indices: 39791461--39791503 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
39791451 TTTAATATAT
*
39791461 TAATTAAAATTTTACTGAATA
1 TAATTAAAATTTTACTAAATA
*
39791482 TAATTAGATATTTTA-TAAATA
1 TAATTA-AAATTTTACTAAATA
39791503 T
1 T
39791504 GAAATATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (21 bp):
TAATTAAAATTTTACTAAATA
Found at i:39794833 original size:19 final size:19
Alignment explanation
Indices: 39794809--39794941 Score: 185
Period size: 19 Copynumber: 6.8 Consensus size: 19
39794799 AATCTTCAGG
39794809 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
39794828 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
39794847 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
39794866 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
39794885 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
39794904 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTT---AGATAT
39794926 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
39794942 AGATATGATT
Statistics
Matches: 101, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
19 82 0.81
22 19 0.19
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:39794883 original size:57 final size:58
Alignment explanation
Indices: 39794809--39794964 Score: 206
Period size: 57 Copynumber: 2.6 Consensus size: 58
39794799 AATCTTCAGG
*
39794809 GATATGCAATCTTAGATATGATATGTAATCTTAGATATAATATATAATCTT-AGATAT
1 GATATGCAATCTTAGATATGATATGTAATCTTAGATATAATATACAATCTTAAGATAT
* * *
39794866 GATATGCAATCTTAGATATGATATATAATCTTAGATATGATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGATATGATATGTAATCTTAGATATAATATACAATCTT--AAGATAT
*
39794926 GATATGCAATCTTAGAAGATATGATTTTGTAATCTTAGA
1 GATATGCAATCTT---AGATATGA-TATGTAATCTTAGA
39794965 GATTTAATTT
Statistics
Matches: 86, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
57 47 0.55
60 19 0.22
63 8 0.09
64 12 0.14
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (58 bp):
GATATGCAATCTTAGATATGATATGTAATCTTAGATATAATATACAATCTTAAGATAT
Found at i:39794967 original size:22 final size:22
Alignment explanation
Indices: 39794809--39794964 Score: 128
Period size: 19 Copynumber: 7.7 Consensus size: 22
39794799 AATCTTCAGG
39794809 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
* *
39794828 GATATGTAATCTTAG-ATATAAT
1 GATATGCAATCTTAGAAGAT-AT
39794850 -ATAT--AATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
39794866 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
**
39794885 GATATATAATCTTAG---ATAT
1 GATATGCAATCTTAGAAGATAT
39794904 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
39794926 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
39794948 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
39794965 GATTTAATTT
Statistics
Matches: 116, Mismatches: 9, Indels: 20
0.80 0.06 0.14
Matches are distributed among these distances:
16 2 0.02
17 7 0.06
19 58 0.50
21 7 0.06
22 30 0.26
23 12 0.10
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:39795500 original size:31 final size:31
Alignment explanation
Indices: 39795433--39795500 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
39795423 CAAATTAGTC
*
39795433 TTTTTTCATTTTCTTTATTTTTTATTAATTA
1 TTTTTTCATATTCTTTATTTTTTATTAATTA
* *
39795464 GTTTTTC-TATTCTTT-TTTTTATATTTAGTTA
1 TTTTTTCATATTCTTTATTTTT-TA-TTAATTA
39795495 TTTTTT
1 TTTTTT
39795501 TAAAAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 5 0.16
30 9 0.29
31 17 0.55
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (31 bp):
TTTTTTCATATTCTTTATTTTTTATTAATTA
Found at i:39795630 original size:22 final size:22
Alignment explanation
Indices: 39795567--39795625 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 22
39795557 TAATATAATT
*
39795567 ATTATTTTTATTTATTTATATGTA
1 ATTA-TTTT-TTTATCTATATGTA
39795591 ATTATTTTTTTATCTATATGT-
1 ATTATTTTTTTATCTATATGTA
39795612 ATATATTTATTTTA
1 AT-TATTT-TTTTA
39795626 GTATACATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 2 0.06
22 17 0.53
23 9 0.28
24 4 0.12
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (22 bp):
ATTATTTTTTTATCTATATGTA
Found at i:39808184 original size:19 final size:19
Alignment explanation
Indices: 39808155--39808246 Score: 130
Period size: 19 Copynumber: 4.8 Consensus size: 19
39808145 AATCTTCAGG
*
39808155 GATATGCAATCTTAGATAT
1 GATATACAATCTTAGATAT
* *
39808174 AATATATAATCTTAGATAT
1 GATATACAATCTTAGATAT
*
39808193 GATATGCAATCTTAGATAT
1 GATATACAATCTTAGATAT
*
39808212 GATATATAATCTTAGATAT
1 GATATACAATCTTAGATAT
*
39808231 GATATGCAATCTTAGA
1 GATATACAATCTTAGA
39808247 AGATATGGTT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 63 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (19 bp):
GATATACAATCTTAGATAT
Found at i:39808200 original size:38 final size:38
Alignment explanation
Indices: 39808155--39808246 Score: 175
Period size: 38 Copynumber: 2.4 Consensus size: 38
39808145 AATCTTCAGG
39808155 GATATGCAATCTTAGATATAATATATAATCTTAGATAT
1 GATATGCAATCTTAGATATAATATATAATCTTAGATAT
*
39808193 GATATGCAATCTTAGATATGATATATAATCTTAGATAT
1 GATATGCAATCTTAGATATAATATATAATCTTAGATAT
39808231 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
39808247 AGATATGGTT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (38 bp):
GATATGCAATCTTAGATATAATATATAATCTTAGATAT
Found at i:39808806 original size:10 final size:10
Alignment explanation
Indices: 39808766--39808819 Score: 58
Period size: 10 Copynumber: 5.3 Consensus size: 10
39808756 AAATTAGTCT
39808766 TTTTTTCATT-
1 TTTTTT-ATTA
*
39808776 TTCTTTATT-
1 TTTTTTATTA
39808785 TTTTATTAATTA
1 TTTT-TT-ATTA
39808797 TTTTTTATTA
1 TTTTTTATTA
39808807 TTTTTTATTA
1 TTTTTTATTA
39808817 TTT
1 TTT
39808820 AGTTANNNNN
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
9 6 0.15
10 24 0.62
11 5 0.13
12 4 0.10
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTTATTA
Found at i:39820395 original size:2 final size:2
Alignment explanation
Indices: 39820390--39820431 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
39820380 TTATCCATAA
39820390 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39820431 A
1 A
39820432 ACATAATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39828973 original size:30 final size:30
Alignment explanation
Indices: 39828937--39828996 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
39828927 CAACTATGTC
39828937 TTTCTCATATTATGAGACCTACTGATTGGA
1 TTTCTCATATTATGAGACCTACTGATTGGA
*
39828967 TTTCTCATATTATGAGAGCTACTGATTGGA
1 TTTCTCATATTATGAGACCTACTGATTGGA
39828997 CTTTTTTAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (30 bp):
TTTCTCATATTATGAGACCTACTGATTGGA
Found at i:39829127 original size:19 final size:19
Alignment explanation
Indices: 39829103--39829140 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
39829093 CTACAGTGCA
39829103 TTTCTCCAACACATGAGCC
1 TTTCTCCAACACATGAGCC
39829122 TTTCTCCAACACATGAGCC
1 TTTCTCCAACACATGAGCC
39829141 ACGTGTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.37, G:0.11, T:0.26
Consensus pattern (19 bp):
TTTCTCCAACACATGAGCC
Found at i:39834377 original size:56 final size:50
Alignment explanation
Indices: 39834207--39834400 Score: 237
Period size: 50 Copynumber: 3.8 Consensus size: 50
39834197 TCATCATAAC
* * * *
39834207 ATGCCAAAGCCATGTCCCAGACATGGTCTTAC-GGAGGACCTCTCATCTCG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATG-GGACTTCTAATCTCG
*
39834257 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACTTCTAATCTCG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACTTCTAATCTCG
* *
39834307 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACATCTCATGATCTCAATG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAC-T-TC-TAATCTC---G
* *
39834363 ATGCCAATGTCATGTCCCAGACATGGTCTTACATGGGA
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
39834401 TCTCTTTACC
Statistics
Matches: 128, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
50 82 0.64
51 2 0.02
52 2 0.02
53 6 0.05
56 36 0.28
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (50 bp):
ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACTTCTAATCTCG
Found at i:39837487 original size:33 final size:32
Alignment explanation
Indices: 39837450--39837551 Score: 86
Period size: 33 Copynumber: 3.2 Consensus size: 32
39837440 TACAGTATAA
39837450 ACTAATTCTTGGTTGAAAACTAATTATTCACGT
1 ACTAA-TCTTGGTTGAAAACTAATTATTCACGT
* ** * *
39837483 ACTAAACTATTTTTGAATAACTACAGTA-T-A--A
1 ACTAATCT-TGGTTGAA-AACTA-ATTATTCACGT
39837514 ACTAAGTCTTGGTTGAAAACTAATTATTCACGT
1 ACTAA-TCTTGGTTGAAAACTAATTATTCACGT
39837547 ACTAA
1 ACTAA
39837552 ACTATTTTTG
Statistics
Matches: 51, Mismatches: 10, Indels: 16
0.66 0.13 0.21
Matches are distributed among these distances:
29 3 0.06
30 6 0.12
31 12 0.24
32 4 0.08
33 17 0.33
34 6 0.12
35 3 0.06
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (32 bp):
ACTAATCTTGGTTGAAAACTAATTATTCACGT
Found at i:39837532 original size:64 final size:64
Alignment explanation
Indices: 39837431--39837581 Score: 293
Period size: 64 Copynumber: 2.4 Consensus size: 64
39837421 GATGGTGTTC
*
39837431 TTGAATAACTACAGTATAAACTAATTCTTGGTTGAAAACTAATTATTCACGTACTAAACTATTT
1 TTGAATAACTACAGTATAAACTAAGTCTTGGTTGAAAACTAATTATTCACGTACTAAACTATTT
39837495 TTGAATAACTACAGTATAAACTAAGTCTTGGTTGAAAACTAATTATTCACGTACTAAACTATTT
1 TTGAATAACTACAGTATAAACTAAGTCTTGGTTGAAAACTAATTATTCACGTACTAAACTATTT
39837559 TTGAATAACTACAGTATAAACTA
1 TTGAATAACTACAGTATAAACTA
39837582 TTAAAGCAAG
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 86 1.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (64 bp):
TTGAATAACTACAGTATAAACTAAGTCTTGGTTGAAAACTAATTATTCACGTACTAAACTATTT
Found at i:39850390 original size:50 final size:50
Alignment explanation
Indices: 39850281--39850528 Score: 280
Period size: 50 Copynumber: 4.8 Consensus size: 50
39850271 ATTTGGGTAA
*
39850281 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGA-C--G
* *
39850337 AGAGGTCCCATGTAAGACCCTGTCTGGGAAATGGCATTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* *
39850387 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
*** * * * * *
39850437 AGAGGTCCCCCATAAGACTATGTCTGGGACATGGCATGGGCACCAATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
** * * *
39850487 AGAACTCCCATGTAAGACCATATCTGGGATATGACATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
39850529 GTACAAGAAA
Statistics
Matches: 167, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
50 121 0.72
52 1 0.01
53 4 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
Found at i:39853243 original size:24 final size:22
Alignment explanation
Indices: 39853197--39853243 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
39853187 TAAATTCGGT
*
39853197 AGCAGCTTCTTTAATGCATTCC
1 AGCAGCTTCTTTAATGCAGTCC
*
39853219 AGCATGCTTCCTTTAATGCCGTCC
1 AGCA-GCTT-CTTTAATGCAGTCC
39853243 A
1 A
39853244 AGGGAGTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.19
23 4 0.19
24 13 0.62
ACGTcount: A:0.21, C:0.30, G:0.15, T:0.34
Consensus pattern (22 bp):
AGCAGCTTCTTTAATGCAGTCC
Found at i:39856097 original size:20 final size:20
Alignment explanation
Indices: 39856072--39856110 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
39856062 AATGTATTTG
39856072 TTTGCACTTCAGTGCCTCTA
1 TTTGCACTTCAGTGCCTCTA
*
39856092 TTTGCACTTCGGTGCCTCT
1 TTTGCACTTCAGTGCCTCT
39856111 GTATGAACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.10, C:0.31, G:0.18, T:0.41
Consensus pattern (20 bp):
TTTGCACTTCAGTGCCTCTA
Found at i:39861276 original size:3 final size:3
Alignment explanation
Indices: 39861268--39861349 Score: 164
Period size: 3 Copynumber: 27.3 Consensus size: 3
39861258 TTTTATAGTC
39861268 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
39861316 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
39861350 TGTTATTAAG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:39863395 original size:14 final size:14
Alignment explanation
Indices: 39863374--39863407 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 14
39863364 CATGAATATA
39863374 AAAAAAAAGAAAAAAG
1 AAAAAAAAG--AAAAG
39863390 AAAAAAAAGAAAAG
1 AAAAAAAAGAAAAG
39863404 AAAA
1 AAAA
39863408 CAGCGAGCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
16 9 0.50
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAAG
Found at i:39872840 original size:28 final size:27
Alignment explanation
Indices: 39872790--39872842 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
39872780 TAGGTTTATT
* * *
39872790 AAAATTAAAAATTTTAAATTTAAATTC
1 AAAAATAAAAATTTAAAAATTAAATTC
39872817 AAAAATAAAAATATTAAAAATTAAAT
1 AAAAATAAAAAT-TTAAAAATTAAAT
39872843 ATTTTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (27 bp):
AAAAATAAAAATTTAAAAATTAAATTC
Found at i:39878130 original size:27 final size:29
Alignment explanation
Indices: 39878100--39878162 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 29
39878090 TTAAATATCA
39878100 TTTATTATAT-TTAAGTTTTAAAAAT-A-T
1 TTTATTATATATTAA-TTTTAAAAATAATT
*
39878127 TTTA-TATATCATTAATTTTACAAATAATT
1 TTTATTATAT-ATTAATTTTAAAAATAATT
39878156 TTTATTA
1 TTTATTA
39878163 ATTGCTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 5 0.17
27 13 0.43
28 5 0.17
29 5 0.17
30 2 0.07
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (29 bp):
TTTATTATATATTAATTTTAAAAATAATT
Found at i:39886985 original size:16 final size:15
Alignment explanation
Indices: 39886964--39886997 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
39886954 AAAGTTGATA
39886964 ATAATTAATATATATT
1 ATAATTAATATA-ATT
39886980 ATAATTAATATAATT
1 ATAATTAATATAATT
39886995 ATA
1 ATA
39886998 TACTAGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATAATTAATATAATT
Found at i:39901795 original size:68 final size:68
Alignment explanation
Indices: 39901684--39901813 Score: 199
Period size: 68 Copynumber: 1.9 Consensus size: 68
39901674 TAAACTTAAT
** *
39901684 CACTTTAATATTAAATTTAATTTAATTTATCAAGATAAATATTAGATTAAATTTAATATTAAGAT
1 CACTTTAATATTAAATTTAATAAAATTTATCAAGATAAATATTAAATTAAATTTAATATTAAGAT
39901749 AAC
66 AAC
* *
39901752 CACTTTAATATTAAA-TTAATAAAATATTATTAAGATAAGTATTAAATTAAATTTAATATTAA
1 CACTTTAATATTAAATTTAATAAAAT-TTATCAAGATAAATATTAAATTAAATTTAATATTAA
39901814 ACTATTAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
67 8 0.14
68 48 0.86
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (68 bp):
CACTTTAATATTAAATTTAATAAAATTTATCAAGATAAATATTAAATTAAATTTAATATTAAGAT
AAC
Found at i:39905530 original size:19 final size:21
Alignment explanation
Indices: 39905508--39905549 Score: 70
Period size: 19 Copynumber: 2.1 Consensus size: 21
39905498 ATAGTTAAAA
39905508 TTAATTAATTA-AC-TTAATC
1 TTAATTAATTATACATTAATC
39905527 TTAATTAATTATACATTAATC
1 TTAATTAATTATACATTAATC
39905548 TT
1 TT
39905550 CAAGTAGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 11 0.52
20 2 0.10
21 8 0.38
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAATTAATTATACATTAATC
Found at i:39910891 original size:26 final size:27
Alignment explanation
Indices: 39910849--39910912 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
39910839 CTAGAATCTC
* *
39910849 AAACCCTAAACAAAAAATAA-AAGCAT
1 AAACCCTAAACAAAAAACAATAACCAT
*
39910875 AAACCCTAAA-ATCAAAACAATAACCAT
1 AAACCCTAAACA-AAAAACAATAACCAT
*
39910902 AAACCATAAAC
1 AAACCCTAAAC
39910913 CCAAAATCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 1 0.03
26 16 0.52
27 14 0.45
ACGTcount: A:0.62, C:0.23, G:0.02, T:0.12
Consensus pattern (27 bp):
AAACCCTAAACAAAAAACAATAACCAT
Found at i:39910955 original size:21 final size:20
Alignment explanation
Indices: 39910930--39910978 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
39910920 CATAAATCTA
*
39910930 AAATCTCAAGCCATGAACCCT
1 AAATCTCAAG-CATAAACCCT
39910951 AAATC-CTAAGCATAAACCCT
1 AAATCTC-AAGCATAAACCCT
39910971 AAA-CTCAA
1 AAATCTCAA
39910979 ACCCAAAACC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 3 0.12
20 14 0.56
21 8 0.32
ACGTcount: A:0.45, C:0.31, G:0.06, T:0.18
Consensus pattern (20 bp):
AAATCTCAAGCATAAACCCT
Found at i:39911072 original size:13 final size:14
Alignment explanation
Indices: 39911054--39911092 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
39911044 CCCTTGAACC
39911054 TTAAACCC-AAATA
1 TTAAACCCTAAATA
*
39911067 TTAAACCCTAAATC
1 TTAAACCCTAAATA
39911081 TTAAACCCTAAA
1 TTAAACCCTAAA
39911093 CCTAAACCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (14 bp):
TTAAACCCTAAATA
Done.