Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 11 of 163
Found at i:3232952 original size:18 final size:18
Alignment explanation
Indices: 3232926--3232963 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3232916 AAAGATCGTA
3232926 AAATAATTAA-AAATAAAT
1 AAATAATTAATAAA-AAAT
*
3232944 AAATCATTAATAAAAAAT
1 AAATAATTAATAAAAAAT
3232962 AA
1 AA
3232964 CACTCAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATAATTAATAAAAAAT
Found at i:3234148 original size:20 final size:19
Alignment explanation
Indices: 3234115--3234152 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3234105 TATTATAATC
3234115 TATATTATAGTAATAGTTA
1 TATATTATAGTAATAGTTA
*
3234134 TATATATATATTAATAGTT
1 TATAT-TATAGTAATAGTT
3234153 TTAATAGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (19 bp):
TATATTATAGTAATAGTTA
Found at i:3244838 original size:12 final size:12
Alignment explanation
Indices: 3244821--3244855 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
3244811 AGAACACGTC
3244821 ACCTGTTCCGCG
1 ACCTGTTCCGCG
3244833 ACCTGTTCCGCG
1 ACCTGTTCCGCG
*
3244845 ACCTGTGCCGC
1 ACCTGTTCCGC
3244856 TTTCGAGGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.09, C:0.43, G:0.26, T:0.23
Consensus pattern (12 bp):
ACCTGTTCCGCG
Found at i:3249138 original size:15 final size:16
Alignment explanation
Indices: 3249106--3249140 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3249096 TTGTGTTCTA
3249106 ATCAATTTAAATTTAG
1 ATCAATTTAAATTTAG
*
3249122 ATCAGTTTAAA-TTAG
1 ATCAATTTAAATTTAG
3249137 ATCA
1 ATCA
3249141 TTTTGCATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (16 bp):
ATCAATTTAAATTTAG
Found at i:3250528 original size:30 final size:30
Alignment explanation
Indices: 3250492--3250552 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
3250482 GTTTAACAAA
*
3250492 ACAACAGTTGGTTCTTGATTAATACTCTTC
1 ACAACAGTTGGTTCTTGACTAATACTCTTC
3250522 ACAACAGTTGGTTCTTGACTAATACTCTTC
1 ACAACAGTTGGTTCTTGACTAATACTCTTC
3250552 A
1 A
3250553 GCTTGTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (30 bp):
ACAACAGTTGGTTCTTGACTAATACTCTTC
Found at i:3258866 original size:55 final size:56
Alignment explanation
Indices: 3258752--3258890 Score: 174
Period size: 53 Copynumber: 2.6 Consensus size: 56
3258742 TAAAAAAAGC
3258752 AAAGAAAC--GTT-ACTTTCAAATAAAAAA-TTAAAAATGTATGCATAAAGATATGA
1 AAAGAAACATGTTAACTTTCAAATAAAAAATTTAAAAATGTATGCATAAAGA-ATGA
3258805 AAAGAAA-ATG-TAACTTTCAAATAAAAAATTTAAAAATGTATGCATAAAG-ATGA
1 AAAGAAACATGTTAACTTTCAAATAAAAAATTTAAAAATGTATGCATAAAGAATGA
3258858 AATGAGAAACATGTTAA-TTT--AA-AAAAAATTTAA
1 AA--AGAAACATGTTAACTTTCAAATAAAAAATTTAA
3258891 TTTTGTCGAT
Statistics
Matches: 78, Mismatches: 0, Indels: 16
0.83 0.00 0.17
Matches are distributed among these distances:
53 25 0.32
54 19 0.24
55 25 0.32
56 6 0.08
57 3 0.04
ACGTcount: A:0.56, C:0.06, G:0.11, T:0.27
Consensus pattern (56 bp):
AAAGAAACATGTTAACTTTCAAATAAAAAATTTAAAAATGTATGCATAAAGAATGA
Found at i:3258889 original size:53 final size:53
Alignment explanation
Indices: 3258763--3258890 Score: 158
Period size: 55 Copynumber: 2.4 Consensus size: 53
3258753 AAGAAACGTT
3258763 ACTTTCAAATAAAAAA-TTAAAAATGTATGCATAAAGATATGAAAAGAAAATGTA
1 ACTTT-AAATAAAAAATTTAAAAATGTATGCATAAAGA-ATGAAAAGAAAATGTA
3258817 ACTTTCAAATAAAAAATTTAAAAATGTATGCATAAAG-ATGAAATGAGAAACATGTTA
1 ACTTT-AAATAAAAAATTTAAAAATGTATGCATAAAGAATGAAA--AGAAA-ATG-TA
3258874 A-TTT-AA-AAAAAATTTAA
1 ACTTTAAATAAAAAATTTAA
3258891 TTTTGTCGAT
Statistics
Matches: 69, Mismatches: 0, Indels: 11
0.86 0.00 0.14
Matches are distributed among these distances:
53 17 0.25
54 18 0.26
55 25 0.36
56 6 0.09
57 3 0.04
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.28
Consensus pattern (53 bp):
ACTTTAAATAAAAAATTTAAAAATGTATGCATAAAGAATGAAAAGAAAATGTA
Found at i:3270282 original size:2 final size:2
Alignment explanation
Indices: 3270275--3270307 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3270265 GTAAGCAAGC
3270275 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3270308 CACACATGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3272804 original size:19 final size:20
Alignment explanation
Indices: 3272775--3272812 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3272765 CGATATAACT
3272775 AAATAAACTACCGAAACTTC
1 AAATAAACTACCGAAACTTC
*
3272795 AAAT-AACTACCGATACTT
1 AAATAAACTACCGAAACTT
3272813 AGAAACATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.47, C:0.24, G:0.05, T:0.24
Consensus pattern (20 bp):
AAATAAACTACCGAAACTTC
Found at i:3274687 original size:24 final size:24
Alignment explanation
Indices: 3274655--3274703 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
3274645 ATGTGTGGTC
3274655 TCGAACCACTGTTTTCGACGTCAT
1 TCGAACCACTGTTTTCGACGTCAT
3274679 TCGAACCACTGTTTTCGACGTCAT
1 TCGAACCACTGTTTTCGACGTCAT
3274703 T
1 T
3274704 AAAAATAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (24 bp):
TCGAACCACTGTTTTCGACGTCAT
Found at i:3274832 original size:27 final size:28
Alignment explanation
Indices: 3274797--3274849 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
3274787 ATAAAATTAA
* *
3274797 ATAATTATTTTATAA-TTTTTTAATTGG
1 ATAACTATTTTATAACTTTTATAATTGG
3274824 ATAACTATTTTATAACTTTTATAATT
1 ATAACTATTTTATAACTTTTATAATT
3274850 AAATAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.57
Consensus pattern (28 bp):
ATAACTATTTTATAACTTTTATAATTGG
Found at i:3277605 original size:13 final size:13
Alignment explanation
Indices: 3277587--3277611 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3277577 AGGCATACAC
3277587 ACCTTGCACACAT
1 ACCTTGCACACAT
3277600 ACCTTGCACACA
1 ACCTTGCACACA
3277612 CAGGTGCTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.40, G:0.08, T:0.20
Consensus pattern (13 bp):
ACCTTGCACACAT
Found at i:3278423 original size:101 final size:101
Alignment explanation
Indices: 3278248--3278444 Score: 358
Period size: 101 Copynumber: 2.0 Consensus size: 101
3278238 GATTCCATAA
* *
3278248 ATTTCCACGTGGCCGGAAACAACTTCTTGTCATTGTTATCATTATTATTAATCATACAAATGTGC
1 ATTTCCACGTGGCAGGAAACAACTTCTTATCATTGTTATCATTATTATTAATCATACAAATGTGC
3278313 TTGCACATTTTTATCATTTTTGAAAGATTTAGCAAG
66 TTGCACATTTTTATCATTTTTGAAAGATTTAGCAAG
*
3278349 ATTTCCACTTGGCAGGAAACAACTTCTTATCATTGTTATCATTATTATTAATCATACAAATGTGC
1 ATTTCCACGTGGCAGGAAACAACTTCTTATCATTGTTATCATTATTATTAATCATACAAATGTGC
*
3278414 TTGCACATTTTTATCATTTTTGGAAGATTTA
66 TTGCACATTTTTATCATTTTTGAAAGATTTA
3278445 CTCTTGCTAA
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
101 92 1.00
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (101 bp):
ATTTCCACGTGGCAGGAAACAACTTCTTATCATTGTTATCATTATTATTAATCATACAAATGTGC
TTGCACATTTTTATCATTTTTGAAAGATTTAGCAAG
Found at i:3278701 original size:43 final size:43
Alignment explanation
Indices: 3278634--3278773 Score: 178
Period size: 43 Copynumber: 3.3 Consensus size: 43
3278624 TTATGTGAGA
*
3278634 AAACGTTACTATAGAACATGATCTTTAGA-GGCGCTTTTCTCAC
1 AAACGCTACTATAGAACATGATCTTTA-ACGGCGCTTTTCTCAC
* * *
3278677 AAACGCTATTATAAAACATAATCTTTAACGGCGCTTTTCTCAC
1 AAACGCTACTATAGAACATGATCTTTAACGGCGCTTTTCTCAC
*
3278720 AAACG-TCGCTATAGAACATGATCTTTAACGGCGCTTTTC-CTAC
1 AAACGCT-ACTATAGAACATGATCTTTAACGGCGCTTTTCTC-AC
*
3278763 AAACGCCACTA
1 AAACGCTACTA
3278774 ACATTAACAA
Statistics
Matches: 83, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
42 3 0.04
43 80 0.96
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (43 bp):
AAACGCTACTATAGAACATGATCTTTAACGGCGCTTTTCTCAC
Found at i:3280886 original size:2 final size:2
Alignment explanation
Indices: 3280879--3280903 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3280869 ATAGGTTAAT
3280879 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3280904 TTAAGATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3281740 original size:24 final size:25
Alignment explanation
Indices: 3281704--3281752 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3281694 GTAAATAATT
* *
3281704 AAAAAGTA-TTTTTAATTTTTAAAA
1 AAAAAATACTTTTGAATTTTTAAAA
*
3281728 AAAAAATACTTTTGGATTTTTAAAA
1 AAAAAATACTTTTGAATTTTTAAAA
3281753 TTTTATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (25 bp):
AAAAAATACTTTTGAATTTTTAAAA
Found at i:3281844 original size:17 final size:17
Alignment explanation
Indices: 3281822--3281855 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3281812 CATGCTTTAT
* *
3281822 ATTTTAAGAATTTAAAA
1 ATTTTAAAAATTGAAAA
3281839 ATTTTAAAAATTGAAAA
1 ATTTTAAAAATTGAAAA
3281856 TATTCAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
ATTTTAAAAATTGAAAA
Found at i:3282016 original size:3 final size:3
Alignment explanation
Indices: 3282008--3282032 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3281998 GGGCTAAATT
3282008 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
3282033 AGAATGACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3284335 original size:20 final size:20
Alignment explanation
Indices: 3284310--3284351 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
3284300 AATAAGCACA
3284310 TTATGATGTATTTCAGACAT
1 TTATGATGTATTTCAGACAT
*
3284330 TTATGATGTATTTGAGACAT
1 TTATGATGTATTTCAGACAT
3284350 TT
1 TT
3284352 TTTGTATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.48
Consensus pattern (20 bp):
TTATGATGTATTTCAGACAT
Found at i:3288092 original size:16 final size:16
Alignment explanation
Indices: 3288071--3288103 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3288061 TGATGATTTT
*
3288071 AATGTTAAAGGACTAA
1 AATGTTAAAGGAATAA
3288087 AATGTTAAAGGAATAA
1 AATGTTAAAGGAATAA
3288103 A
1 A
3288104 TTTGTAAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.18, T:0.24
Consensus pattern (16 bp):
AATGTTAAAGGAATAA
Found at i:3288549 original size:16 final size:17
Alignment explanation
Indices: 3288518--3288550 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3288508 TAGTAAATAT
3288518 TAAATTGAGGAATGAAAC
1 TAAATTGA-GAATGAAAC
3288536 TAAATTGA-AATGAAA
1 TAAATTGAGAATGAAA
3288551 TGGTATTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.55, C:0.03, G:0.18, T:0.24
Consensus pattern (17 bp):
TAAATTGAGAATGAAAC
Found at i:3289176 original size:52 final size:52
Alignment explanation
Indices: 3289091--3289382 Score: 440
Period size: 52 Copynumber: 5.6 Consensus size: 52
3289081 ATAAATGCAA
* * *
3289091 AAGGTCTGATGACTATTTGTCATCGTGAGTATATGAATCCTTTACAGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
*
3289143 AAAGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * * *
3289195 AAGGTCCGATGACTATGTCTCATCGTGAGTATATCAATTCTTTACGTATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
** * *
3289247 AAGGTTTGATGACTATGTATCATCATGAGTATATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * *
3289299 GAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTTCGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
*
3289351 GAGGTCCGATGACTATGTGTCATCGTGAGTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTAT
3289383 TAAATGAGAA
Statistics
Matches: 217, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 217 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (52 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
Found at i:3289375 original size:156 final size:156
Alignment explanation
Indices: 3289091--3289382 Score: 485
Period size: 156 Copynumber: 1.9 Consensus size: 156
3289081 ATAAATGCAA
* * *
3289091 AAGGTCTGATGACTATTTGTCATCGTGAGTATATGAATCCTTTACAGATTATAAAGTCCGATGAC
1 AAGGTCTGATGACTATGTATCATCATGAGTATATGAATCCTTTACAGATTATAAAGTCCGATGAC
3289156 TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTCTCATCGT
66 TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTCTCATCGT
3289221 GAGTATATCAATTCTTTACGTATTAT
131 GAGTATATCAATTCTTTACGTATTAT
* * * *
3289247 AAGGTTTGATGACTATGTATCATCATGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGAC
1 AAGGTCTGATGACTATGTATCATCATGAGTATATGAATCCTTTACAGATTATAAAGTCCGATGAC
* * * *
3289312 TATGTGTCATCGTGAGTATATGAATCTTTTTCGGATTATGAGGTCCGATGACTATGTGTCATCGT
66 TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTCTCATCGT
3289377 GAGTAT
131 GAGTAT
3289383 TAAATGAGAA
Statistics
Matches: 125, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
156 125 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (156 bp):
AAGGTCTGATGACTATGTATCATCATGAGTATATGAATCCTTTACAGATTATAAAGTCCGATGAC
TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTCTCATCGT
GAGTATATCAATTCTTTACGTATTAT
Found at i:3289379 original size:26 final size:26
Alignment explanation
Indices: 3289298--3289379 Score: 60
Period size: 26 Copynumber: 3.2 Consensus size: 26
3289288 TTACGGATTA
3289298 TGAGGTCCGATGACTATGTGTCATCG
1 TGAGGTCCGATGACTATGTGTCATCG
** * * * * **
3289324 TGA-GT-ATATGAATCTTTTTCGGATTA
1 TGAGGTCCGATGACTATGTGTC--ATCG
3289350 TGAGGTCCGATGACTATGTGTCATCG
1 TGAGGTCCGATGACTATGTGTCATCG
3289376 TGAG
1 TGAG
3289380 TATTAAATGA
Statistics
Matches: 36, Mismatches: 16, Indels: 8
0.60 0.27 0.13
Matches are distributed among these distances:
24 9 0.25
25 2 0.06
26 14 0.39
27 2 0.06
28 9 0.25
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (26 bp):
TGAGGTCCGATGACTATGTGTCATCG
Found at i:3293539 original size:23 final size:23
Alignment explanation
Indices: 3293492--3293540 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
3293482 TGATCTAAGG
* *
3293492 AAAAATAAAAGAAACTGAATTAA
1 AAAAATAAAAGAAAATGAATCAA
3293515 AAAAATAAAAGAAAATAGAA-CAA
1 AAAAATAAAAGAAAAT-GAATCAA
3293538 AAA
1 AAA
3293541 GAAGTAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.76, C:0.04, G:0.08, T:0.12
Consensus pattern (23 bp):
AAAAATAAAAGAAAATGAATCAA
Found at i:3294380 original size:19 final size:19
Alignment explanation
Indices: 3294356--3294398 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3294346 AAATATAAAT
3294356 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
3294375 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
3294394 TAAAT
1 TAAAT
3294399 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:3294436 original size:5 final size:5
Alignment explanation
Indices: 3294420--3294451 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
3294410 ATATTTTTTA
3294420 AAAAT -AAA- AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
3294452 CCAAGTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 6 0.24
5 19 0.76
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:3295201 original size:103 final size:103
Alignment explanation
Indices: 3294986--3295203 Score: 249
Period size: 103 Copynumber: 2.1 Consensus size: 103
3294976 TATTTTCCTT
* * * * *
3294986 TTTTTTCTTTAAGAATACATTGGACCTTTTGACGCGAAATGAAATGACACCCAAGCACTCCATCC
1 TTTTTT-TTT-AGAATGCATTAGCCCTTTTGACGCGAAATGAAATGACAACCAAGCACTCCACCC
** * * * *
3295051 CGGTTACTCAGCCCAACATGCTCTCAATTTTTTTCTTCTC
64 CGGTTACTCAGCCCAACACACTCTCAATATATTTATTATC
*
3295091 TTTTTTTTTAGAATGCATTAGCCCTTTTGACGCGAAGTGAAATGACAACCAAGCACTCCACCCCG
1 TTTTTTTTTAGAATGCATTAGCCCTTTTGACGCGAAATGAAATGACAACCAAGCACTCCACCCCG
* * * *
3295156 GTTACTCAGTCTAACACATTC-CGAATATATTTATTATT
66 GTTACTCAGCCCAACACACTCTC-AATATATTTATTATC
3295194 TTCTTTTTTT
1 TT-TTTTTTT
3295204 TATTCGGGTT
Statistics
Matches: 95, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
102 1 0.01
103 78 0.82
104 10 0.11
105 6 0.06
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (103 bp):
TTTTTTTTTAGAATGCATTAGCCCTTTTGACGCGAAATGAAATGACAACCAAGCACTCCACCCCG
GTTACTCAGCCCAACACACTCTCAATATATTTATTATC
Found at i:3295860 original size:4 final size:4
Alignment explanation
Indices: 3295851--3295905 Score: 69
Period size: 4 Copynumber: 13.8 Consensus size: 4
3295841 TCCTGGACAA
*
3295851 AAAT AAAT AAAT AAAT AAAT AAAT AAGAT AGAA- AAAT AAAA AAAT AAA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AA-AT A-AAT AAAT AAAT AAAT AAAT
3295899 AAAT AAA
1 AAAT AAA
3295906 AATAATTGGG
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
3 5 0.11
4 35 0.78
5 4 0.09
6 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:3295906 original size:21 final size:21
Alignment explanation
Indices: 3295849--3295910 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
3295839 TTTCCTGGAC
3295849 AAAAATAAATAAAT--AAATAA
1 AAAAATAAA-AAATAAAAATAA
* * * *
3295869 ATAAATAAGATAGAAAAATAA
1 AAAAATAAAAAATAAAAATAA
3295890 AAAAATAAAAAATAAAAATAA
1 AAAAATAAAAAATAAAAATAA
3295911 TTGGGGTTCC
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
19 2 0.06
20 7 0.22
21 23 0.72
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (21 bp):
AAAAATAAAAAATAAAAATAA
Found at i:3298776 original size:21 final size:21
Alignment explanation
Indices: 3298743--3298782 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3298733 ATAGATGCCT
* *
3298743 CAGTTTTCTTTTGAAAATCCA
1 CAGTTTGCCTTTGAAAATCCA
*
3298764 CAGTTTGCCTTTGGAAATC
1 CAGTTTGCCTTTGAAAATC
3298783 TATAGATTGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (21 bp):
CAGTTTGCCTTTGAAAATCCA
Found at i:3300380 original size:23 final size:23
Alignment explanation
Indices: 3300332--3300380 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
3300322 TGATCTAAGG
*
3300332 AAAAATAAAAGAAACTAAATTAA
1 AAAAATAAAAGAAACTAAACTAA
*
3300355 AAAAATAAAAGAAAGTAGAACTAA
1 AAAAATAAAAGAAACTA-AACTAA
3300379 AA
1 AA
3300381 GAAGTAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.14
Consensus pattern (23 bp):
AAAAATAAAAGAAACTAAACTAA
Found at i:3300387 original size:15 final size:16
Alignment explanation
Indices: 3300360--3300389 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3300350 ATTAAAAAAA
3300360 TAAAAGAAAGTAGAAC
1 TAAAAGAAAGTAGAAC
3300376 TAAAAG-AAGTAGAA
1 TAAAAGAAAGTAGAA
3300390 AATAGGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.63, C:0.03, G:0.20, T:0.13
Consensus pattern (16 bp):
TAAAAGAAAGTAGAAC
Found at i:3301221 original size:19 final size:19
Alignment explanation
Indices: 3301197--3301239 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3301187 AAATATAAAT
3301197 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
3301216 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
3301235 TAAAT
1 TAAAT
3301240 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:3304425 original size:10 final size:10
Alignment explanation
Indices: 3304410--3304434 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3304400 GATTATTTCG
3304410 TAATTTTTTA
1 TAATTTTTTA
3304420 TAATTTTTTA
1 TAATTTTTTA
3304430 TAATT
1 TAATT
3304435 AAATAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:3314407 original size:59 final size:60
Alignment explanation
Indices: 3314299--3314785 Score: 635
Period size: 59 Copynumber: 8.3 Consensus size: 60
3314289 TGGATACCCG
* **
3314299 GGGGCAAAATGGTAATTTT-GGTGAAATTAGGGTT-AAAATGGAATTTTGGAAAGTTCGA
1 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA
* * * *
3314357 -GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTTAAAATGGGATTTTGGAAAGTT-TA
1 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA
* * *
3314415 GGGGTAAAATGGTAATTTTCGATGAAATCGTGATTAAAAATGGAATTTTGGAAAGTTCG-
1 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA
*
3314474 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGATTAAAAATGGAATTTTGGAAAGTTC-A
1 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA
* ** *
3314533 GGGGTAAAATGGTAATTTTCGATGAAATCAAGGTTAAAAATGGAATTTTGGAAAGTTTG-
1 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA
* *
3314592 GGGGTAAAATAGTAATTTTCGGTGAAATC-GGGTTAAAAATGGAATTTT-AAAAGATTC-A
1 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG-TTCGA
* * *
3314650 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTT-AAAAGATTCGA
1 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG-TTCGA
* * *
3314710 -GGGTAAAATGGTAA-TTTCGGTGAAATCAGAGTTAAAAATGGAATTTT-AAAAGATTC-A
1 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG-TTCGA
3314767 GGGGTAAAATGGTAATTTT
1 GGGGTAAAATGGTAATTTT
3314786 TGGAAGTTTC
Statistics
Matches: 386, Mismatches: 31, Indels: 23
0.88 0.07 0.05
Matches are distributed among these distances:
57 22 0.06
58 113 0.29
59 250 0.65
60 1 0.00
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.32
Consensus pattern (60 bp):
GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA
Found at i:3314453 original size:30 final size:29
Alignment explanation
Indices: 3314304--3314639 Score: 133
Period size: 29 Copynumber: 11.5 Consensus size: 29
3314294 ACCCGGGGGC
* * *
3314304 AAAATGGTAATTTTGGTGAAATTAGGG-TT
1 AAAATGGTAATTTTCGTGAAA-TCGGGAGT
3314333 AAAATGG-AATTTT-G-GAAAGTTCGAGG-GT
1 AAAATGGTAATTTTCGTGAAA--TCG-GGAGT
*
3314361 AAAATGGTAATTTTTGGTGAAATCGGG-GTTT
1 AAAATGGTAA-TTTTCGTGAAATCGGGAG--T
* *
3314392 AAAATGG-GATTTT-G-GAAAGTTTAGGG-GT
1 AAAATGGTAATTTTCGTGAAA---TCGGGAGT
* *
3314420 AAAATGGTAATTTTCGATGAAATCGTGATT
1 AAAATGGTAATTTTCG-TGAAATCGGGAGT
*
3314450 AAAAATGG-AATTTT-G-GAAAGTTCGGGGGT
1 -AAAATGGTAATTTTCGTGAAA--TCGGGAGT
*
3314479 AAAATGGTAATTTTCGGTGAAATCGGGATT
1 AAAATGGTAATTTTC-GTGAAATCGGGAGT
3314509 AAAAATGG-AATTTT-G-GAAAGTTCAGGG-GT
1 -AAAATGGTAATTTTCGTGAAA--TC-GGGAGT
* *
3314538 AAAATGGTAATTTTCGATGAAATCAAGG-TT
1 AAAATGGTAATTTTCG-TGAAATC-GGGAGT
* *
3314568 AAAAATGG-AATTTT-G-GAAAGTTTGGGGGT
1 -AAAATGGTAATTTTCGTGAAA--TCGGGAGT
* *
3314597 AAAATAGTAATTTTCGGTGAAATCGGG-TT
1 AAAATGGTAATTTTC-GTGAAATCGGGAGT
3314626 AAAAATGG-AATTTT
1 -AAAATGGTAATTTT
3314640 AAAAGATTCA
Statistics
Matches: 244, Mismatches: 23, Indels: 80
0.70 0.07 0.23
Matches are distributed among these distances:
26 4 0.02
27 20 0.08
28 48 0.20
29 61 0.25
30 59 0.24
31 32 0.13
32 20 0.08
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (29 bp):
AAAATGGTAATTTTCGTGAAATCGGGAGT
Found at i:3315872 original size:15 final size:15
Alignment explanation
Indices: 3315852--3315889 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
3315842 TATAAAATAT
* *
3315852 TTATTATTATTACTG
1 TTATTATTATCACTA
3315867 TTATTATTATCACTA
1 TTATTATTATCACTA
3315882 TTATTATT
1 TTATTATT
3315890 GTTATTAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.61
Consensus pattern (15 bp):
TTATTATTATCACTA
Found at i:3315892 original size:24 final size:24
Alignment explanation
Indices: 3315856--3315911 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
3315846 AAATATTTAT
*
3315856 TATTATTACTGTTATT-ATTATCAC
1 TATTATTACTGTTATTAATGAT-AC
*
3315880 TATTATTATTGTTATTAATGATAC
1 TATTATTACTGTTATTAATGATAC
3315904 TATTATTA
1 TATTATTA
3315912 ACCATCCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.55
Consensus pattern (24 bp):
TATTATTACTGTTATTAATGATAC
Found at i:3316592 original size:6 final size:6
Alignment explanation
Indices: 3316573--3316650 Score: 79
Period size: 6 Copynumber: 13.0 Consensus size: 6
3316563 TTTTTTAATG
** * *
3316573 TTAAAT TTTTAT TTAAAT TTAAAT TCAAA- GTAAAT TTAAAT AATTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT
*
3316622 TTAAAT TTAAA- ATAAAT TTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
3316651 AAAATTAAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
5 7 0.12
6 45 0.78
8 6 0.10
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (6 bp):
TTAAAT
Found at i:3316608 original size:17 final size:16
Alignment explanation
Indices: 3316586--3316659 Score: 89
Period size: 17 Copynumber: 4.6 Consensus size: 16
3316576 AATTTTTATT
*
3316586 TAAATTTAAATTCAAA
1 TAAATTTAAATTTAAA
*
3316602 GTAAATTTAAA--TAAT
1 -TAAATTTAAATTTAAA
3316617 TAAATTTAAATTTAAAA
1 TAAATTTAAATTT-AAA
3316634 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
*
3316650 TAAAATTAAA
1 TAAATTTAAA
3316660 GATCAATTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
14 10 0.20
15 2 0.04
16 13 0.26
17 25 0.50
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:3316622 original size:31 final size:31
Alignment explanation
Indices: 3316585--3316644 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
3316575 AAATTTTTAT
*
3316585 TTAAATTTAAATTCAAAGTAAATTTAAATAA
1 TTAAATTTAAATTCAAAATAAATTTAAATAA
*
3316616 TTAAATTTAAATTTAAAATAAATTTAAAT
1 TTAAATTTAAATTCAAAATAAATTTAAAT
3316645 TTAAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (31 bp):
TTAAATTTAAATTCAAAATAAATTTAAATAA
Found at i:3316677 original size:28 final size:27
Alignment explanation
Indices: 3316623--3316678 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
3316613 TAATTAAATT
* *
3316623 TAAATTTAAAATAAATTTAAATTTAAA
1 TAAAATTAAAATAAATTTAAATCTAAA
* *
3316650 TAAAATTAAAGATCAATTTAACTCTAAA
1 TAAAATTAAA-ATAAATTTAAATCTAAA
3316678 T
1 T
3316679 TAAACGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (27 bp):
TAAAATTAAAATAAATTTAAATCTAAA
Found at i:3319241 original size:15 final size:14
Alignment explanation
Indices: 3319190--3319242 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 14
3319180 CATTTGGATC
*
3319190 AAAATTAAAATTTT
1 AAAATTAAAATTAT
*
3319204 AAAATTTAAAATATACA
1 AAAA-TTAAAAT-TA-T
3319221 AAAATTAAAATTGAT
1 AAAATTAAAATT-AT
3319236 AAAATTA
1 AAAATTA
3319243 TATAAAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 4 0.12
15 15 0.47
16 9 0.28
17 4 0.12
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (14 bp):
AAAATTAAAATTAT
Found at i:3320380 original size:3 final size:3
Alignment explanation
Indices: 3320372--3320403 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3320362 ACACTGTTAT
3320372 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3320404 TCGATTCGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3320674 original size:17 final size:18
Alignment explanation
Indices: 3320652--3320686 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3320642 ACTTATGCTA
3320652 CATTGGCT-TGTATTGAC
1 CATTGGCTATGTATTGAC
*
3320669 CATTGGGTATGTATTGAC
1 CATTGGCTATGTATTGAC
3320687 AAAAGCTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.20, C:0.14, G:0.26, T:0.40
Consensus pattern (18 bp):
CATTGGCTATGTATTGAC
Found at i:3323100 original size:19 final size:16
Alignment explanation
Indices: 3323076--3323124 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 16
3323066 TAAAAGTATA
3323076 TTTTTATAATTTCTGAAAT
1 TTTTTATAATTT-T--AAT
3323095 TTTTTATAACTTTTAAT
1 TTTTTATAA-TTTTAAT
*
3323112 TTTTTCTAATTTT
1 TTTTTATAATTTT
3323125 TTAAAATTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 4 0.14
17 11 0.39
19 10 0.36
20 3 0.11
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (16 bp):
TTTTTATAATTTTAAT
Found at i:3323447 original size:3 final size:3
Alignment explanation
Indices: 3323439--3323478 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3323429 GGACACGTAG
3323439 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3323479 GATGATGATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3323483 original size:3 final size:3
Alignment explanation
Indices: 3323477--3323519 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
3323467 AATAATAATA
*
3323477 ATG ATG ATG ATG ATG ATG ATG AT- ATG ATG ATG ATA ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
3323520 AATAATGTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.37, C:0.00, G:0.28, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:3323505 original size:20 final size:20
Alignment explanation
Indices: 3323480--3323520 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3323470 AATAATAATG
*
3323480 ATGATGATGATGATGATGAT
1 ATGATGATGATAATGATGAT
3323500 ATGATGATGATAATGATGAT
1 ATGATGATGATAATGATGAT
3323520 A
1 A
3323521 ATAATGTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (20 bp):
ATGATGATGATAATGATGAT
Found at i:3323520 original size:9 final size:9
Alignment explanation
Indices: 3323474--3323522 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
3323464 AATAATAATA
3323474 ATAATGATG
1 ATAATGATG
*
3323483 ATGATGATG
1 ATAATGATG
*
3323492 ATGATGAT-
1 ATAATGATG
*
3323500 ATGATGATG
1 ATAATGATG
3323509 ATAATGATG
1 ATAATGATG
3323518 ATAAT
1 ATAAT
3323523 AATGTCCAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
8 8 0.22
9 29 0.78
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (9 bp):
ATAATGATG
Found at i:3336901 original size:58 final size:58
Alignment explanation
Indices: 3336804--3336967 Score: 142
Period size: 58 Copynumber: 2.8 Consensus size: 58
3336794 GACACTTGAG
* * * *
3336804 GGGGTAAAATGGTAATATT-GGAAAAGTTCAGGGTTAAAAAT-CAAATTTTAGACA-TCT
1 GGGGTAAAATGGTAATTTTGGGAAAA-ATCAGGATCAAAAATGCAAATTTTAGA-AGTCT
* * * *
3336861 GAGGGTAAAATGGTAATTTTGGGAAAAATC-GAGATCAAAAATGGAATTTTTGGAAGTTT
1 G-GGGTAAAATGGTAATTTTGGGAAAAATCAG-GATCAAAAATGCAAATTTTAGAAGTCT
* * *
3336920 GGGGTAAAATGGTAATTTTGAGAAAAA-CTAGGGTC-AAAATGGAAATTT
1 GGGGTAAAATGGTAATTTTGGGAAAAATC-AGGATCAAAAATGCAAATTT
3336968 AGGAAATTTT
Statistics
Matches: 89, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
57 15 0.17
58 56 0.63
59 18 0.20
ACGTcount: A:0.40, C:0.05, G:0.26, T:0.29
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTGGGAAAAATCAGGATCAAAAATGCAAATTTTAGAAGTCT
Found at i:3336960 original size:30 final size:28
Alignment explanation
Indices: 3336862--3337076 Score: 118
Period size: 29 Copynumber: 7.3 Consensus size: 28
3336852 TAGACATCTG
3336862 AGGGTAAAATGGTAATTTTGGGAAAAA-T
1 AGGGTAAAATGGTAATTTT-GGAAAAATT
* * **
3336890 CGAGATCAAAAATGG-AATTTTTGG-AAGTTT
1 AG-GGT--AAAATGGTAA-TTTTGGAAAAATT
* *
3336920 GGGGTAAAATGGTAATTTTGAGAAAAACT
1 AGGGTAAAATGGTAATTTTG-GAAAAATT
* * **
3336949 AGGGTCAAAATGGAAATTTAGGAAATTTT
1 AGGGT-AAAATGGTAATTTTGGAAAAATT
* **
3336978 AGGGATAAAAAT-GTAATTTTTGAAAGTTT
1 AGGG-T-AAAATGGTAATTTTGGAAAAATT
3337007 GAGGGTAAAATGGTAATTTCTTGGAAAAATT
1 -AGGGTAAAATGGTAA-TT-TTGGAAAAATT
*
3337038 AGGGTCAAAAATGG-AATTTT-GAAAAGTTT
1 AGGGT--AAAATGGTAATTTTGGAAAA-ATT
3337067 AGGGGTAAAA
1 A-GGGTAAAA
3337077 ATATAAATTT
Statistics
Matches: 145, Mismatches: 24, Indels: 36
0.71 0.12 0.18
Matches are distributed among these distances:
27 12 0.08
28 18 0.12
29 45 0.31
30 42 0.29
31 21 0.14
32 7 0.05
ACGTcount: A:0.41, C:0.03, G:0.26, T:0.31
Consensus pattern (28 bp):
AGGGTAAAATGGTAATTTTGGAAAAATT
Found at i:3336961 original size:88 final size:89
Alignment explanation
Indices: 3336862--3337058 Score: 242
Period size: 87 Copynumber: 2.2 Consensus size: 89
3336852 TAGACATCTG
* *
3336862 AGGGT-AAAATGGTAATTTTGGGAAA-AATCGAGATCAAAAATGGAATTTTTGGAAGTTTG-GGG
1 AGGGTCAAAATGG-AATTTTGGGAAATAATAGAGAT-AAAAATGGAATTTTTGAAAGTTTGAGGG
3336924 TAAAATGGTAA-TT-TTGAGAAAAACT
64 TAAAATGGTAATTTCTTG-GAAAAACT
* * ** * *
3336949 AGGGTCAAAATGGAAATTTAGGAAATTTTAGGGATAAAAATGTAATTTTTGAAAGTTTGAGGGTA
1 AGGGTCAAAATGGAATTTTGGGAAATAATAGAGATAAAAATGGAATTTTTGAAAGTTTGAGGGTA
*
3337014 AAATGGTAATTTCTTGGAAAAATT
66 AAATGGTAATTTCTTGGAAAAACT
3337038 AGGGTCAAAAATGGAATTTTG
1 AGGGTC-AAAATGGAATTTTG
3337059 AAAAGTTTAG
Statistics
Matches: 93, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
87 37 0.40
88 26 0.28
89 15 0.16
90 15 0.16
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.31
Consensus pattern (89 bp):
AGGGTCAAAATGGAATTTTGGGAAATAATAGAGATAAAAATGGAATTTTTGAAAGTTTGAGGGTA
AAATGGTAATTTCTTGGAAAAACT
Found at i:3336980 original size:29 final size:29
Alignment explanation
Indices: 3336898--3337100 Score: 110
Period size: 30 Copynumber: 6.9 Consensus size: 29
3336888 ATCGAGATCA
* * *
3336898 AAAATGGAATTTTTGG-AAGTTTGGGGT-
1 AAAATGGAAATTTTGGAAATTTTAGGGTC
* ***
3336925 AAAATGGTAATTTTGAGAAAAACTAGGGTC
1 AAAATGGAAATTTTG-GAAATTTTAGGGTC
* *
3336955 AAAATGGAAATTTAGGAAATTTTAGGGATA
1 AAAATGGAAATTTTGGAAATTTTAGGG-TC
* * *
3336985 AAAAT-GTAATTTTTGAAAGTTTGAGGGT-
1 AAAATGGAAATTTTGGAAA-TTTTAGGGTC
* **
3337013 AAAATGGTAATTTCTTGGAAAAATTAGGGTC
1 AAAATGG-AAATT-TTGGAAATTTTAGGGTC
* * *
3337044 AAAAATGG-AATTTTGAAAAGTTTAGGGGTA
1 -AAAATGGAAATTTTGGAAATTTTA-GGGTC
** * *
3337074 AAAATATAAATTTTGGATAGTTTAGGG
1 AAAATGGAAATTTTGGAAATTTTAGGG
3337101 ACTTTCAAGG
Statistics
Matches: 133, Mismatches: 31, Indels: 22
0.72 0.17 0.12
Matches are distributed among these distances:
27 13 0.10
28 6 0.05
29 45 0.34
30 56 0.42
31 6 0.05
32 7 0.05
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.33
Consensus pattern (29 bp):
AAAATGGAAATTTTGGAAATTTTAGGGTC
Found at i:3337068 original size:89 final size:87
Alignment explanation
Indices: 3336897--3337088 Score: 253
Period size: 89 Copynumber: 2.2 Consensus size: 87
3336887 AATCGAGATC
* *
3336897 AAAAATGGAATTTTTGGAAGTTTGGGGTAAAATGGTAATTTTGAGAAAAACTAGGGTCAAAATGG
1 AAAAATGTAATTTTTGAAAGTTTGGGGTAAAATGGTAATTTTGAGAAAAACTAGGGTCAAAATGG
* *
3336962 AAATTTAGGAAATTTTAGGGAT
66 AAATTTAGAAAAGTTTAGGGAT
*
3336984 AAAAATGTAATTTTTGAAAGTTTGAGGGTAAAATGGTAATTTCTTG-GAAAAATTAGGGTCAAAA
1 AAAAATGTAATTTTTGAAAGTTTG-GGGTAAAATGGTAA-TT-TTGAGAAAAACTAGGGTC-AAA
* *
3337048 ATGG-AATTTTGAAAAGTTTAGGGGT
62 ATGGAAATTTAGAAAAGTTTAGGGAT
* *
3337073 AAAAATATAAATTTTG
1 AAAAATGTAATTTTTG
3337089 GATAGTTTAG
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
87 22 0.24
88 14 0.15
89 46 0.50
90 10 0.11
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (87 bp):
AAAAATGTAATTTTTGAAAGTTTGGGGTAAAATGGTAATTTTGAGAAAAACTAGGGTCAAAATGG
AAATTTAGAAAAGTTTAGGGAT
Found at i:3338118 original size:3 final size:3
Alignment explanation
Indices: 3338110--3338152 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
3338100 TTTTCCCTTT
* *
3338110 TTA TTA TTA TTA ATA TTA TTTA TTA CTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
3338153 GTGCTATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:3338565 original size:25 final size:25
Alignment explanation
Indices: 3338534--3338590 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
3338524 TGGCAGTGGC
* *
3338534 GGTGGCAGAGTAGGTTGAAGCGGGT
1 GGTGGCAGAGCAAGTTGAAGCGGGT
*
3338559 GGTGGCAGAGCAAGTTGAAGCTGGT
1 GGTGGCAGAGCAAGTTGAAGCGGGT
*
3338584 GATGGCA
1 GGTGGCA
3338591 CTGTTGATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.23, C:0.11, G:0.47, T:0.19
Consensus pattern (25 bp):
GGTGGCAGAGCAAGTTGAAGCGGGT
Found at i:3339309 original size:17 final size:17
Alignment explanation
Indices: 3339287--3339325 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
3339277 CTCCGTATCC
3339287 CATCAGGAAGATGATCG
1 CATCAGGAAGATGATCG
3339304 CATCAGGAAGATGATCG
1 CATCAGGAAGATGATCG
3339321 CATCA
1 CATCA
3339326 CTTGTTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.18
Consensus pattern (17 bp):
CATCAGGAAGATGATCG
Found at i:3339787 original size:201 final size:201
Alignment explanation
Indices: 3339304--3339939 Score: 846
Period size: 201 Copynumber: 3.1 Consensus size: 201
3339294 AAGATGATCG
* * * * * *
3339304 CATCAGGAAGATGATCGCATCACTTGTTTTGATCCACTTCTCTATGTTTCATCAGGAAGACGGAT
1 CATCAGGAAGATGACCGCATCACTTGTTTTAATCTACTTCTCTATATCTCATCAGGAAGACGAAT
* * * * * *
3339369 TTGGTTCACTTGTCCGTATCTCATCAAGAAGCTAACCACTTTATTGCTTCGACCTGTTTCTCAGT
66 TTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGT
* * * * * *
3339434 ATCACATCAGGAAGTTT-AGGGTTCGAAGATTTGCTCACATTGAGCGTGGGTTTAATTCGGTCTT
131 ATCTCATCAGGAA-TTTGA-GGTTCGAAGATTTGCTCACATCGAGCGT-CG---AGTT-GGTATA
*
3339498 CTTCTCAGTATCT
189 CTTCTCTGTATCT
* * *
3339511 CATCAGGAAGATGACCGCATCACTTGTTTCAAT-TCGCTTCTCTATATCTCGTCAAGG-AGACGA
1 CATCAGGAAGATGACCGCATCACTTGTTTTAATCT-ACTTCTCTATATCTCATC-AGGAAGACGA
* *
3339574 ATTTGATCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCAACCTGCTTCTCA
64 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCA
* * *
3339639 GTATCTCATCAGGAATTTGAGGTTCGAAGATTTGCTCGCATCAACCGTCGAGTTGGTATACTTCT
129 GTATCTCATCAGGAATTTGAGGTTCGAAGATTTGCTCACATCGAGCGTCGAGTTGGTATACTTCT
3339704 CTGTATCT
194 CTGTATCT
* * *
3339712 CATCAAGAAGATGACCGCCTCACTTGTTTTAATCTACTTCTCTGTATCTCATCAGGAAGACGAAT
1 CATCAGGAAGATGACCGCATCACTTGTTTTAATCTACTTCTCTATATCTCATCAGGAAGACGAAT
*
3339777 TTGGTCCACTTCTCAGTACCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGT
66 TTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGT
** *
3339842 ATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGCGTCAAGTTGGTATACTTCTCT
131 ATCTCATCAGGAATTTGAGGTTCGAAGATTTGCTCACATCGAGCGTCGAGTTGGTATACTTCTCT
3339907 GTATCT
196 GTATCT
* *
3339913 CATCAGGAAGACGACCGCCTCACTTGT
1 CATCAGGAAGATGACCGCATCACTTGT
3339940 GGATAATCGC
Statistics
Matches: 380, Mismatches: 44, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
200 3 0.01
201 221 0.58
202 4 0.01
205 1 0.00
206 27 0.07
207 121 0.32
208 3 0.01
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (201 bp):
CATCAGGAAGATGACCGCATCACTTGTTTTAATCTACTTCTCTATATCTCATCAGGAAGACGAAT
TTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGT
ATCTCATCAGGAATTTGAGGTTCGAAGATTTGCTCACATCGAGCGTCGAGTTGGTATACTTCTCT
GTATCT
Found at i:3340044 original size:39 final size:39
Alignment explanation
Indices: 3339991--3340218 Score: 208
Period size: 39 Copynumber: 5.8 Consensus size: 39
3339981 GTTGATGGTG
* *
3339991 ATCTG-CCCTAGGCTTGGGGTAAAAGATCGAATGGTTGTA
1 ATCTGCCCCT-GGCTCGGGGTAAGAGATCGAATGGTTGTA
* * *
3340030 ATTTGCCCCTGGCTTGGGGTAAGAGATCGAATGGTTGCA
1 ATCTGCCCCTGGCTCGGGGTAAGAGATCGAATGGTTGTA
* * *
3340069 ATCTGCCCCAGGCTCGGGGTAAGAGATCGAATGGCTATA
1 ATCTGCCCCTGGCTCGGGGTAAGAGATCGAATGGTTGTA
* * * * ** *
3340108 ATCTGCCCCTAGCTCGGGGTAAGAGATTG-GTCGACGATG
1 ATCTGCCCCTGGCTCGGGGTAAGAGATCGAATGGTTG-TA
** * * *
3340147 ATCTGCCCCAAGCTTGGGGTAAGAGATCGAATGGCTGCA
1 ATCTGCCCCTGGCTCGGGGTAAGAGATCGAATGGTTGTA
** *
3340186 ATCTGCCCCAAGCTCAGGGTAAGAGATCAGAAT
1 ATCTGCCCCTGGCTCGGGGTAAGAGATC-GAAT
3340219 CTTCATTTTT
Statistics
Matches: 156, Mismatches: 29, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
38 2 0.01
39 143 0.92
40 11 0.07
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (39 bp):
ATCTGCCCCTGGCTCGGGGTAAGAGATCGAATGGTTGTA
Found at i:3340115 original size:78 final size:81
Alignment explanation
Indices: 3339990--3340218 Score: 274
Period size: 78 Copynumber: 2.9 Consensus size: 81
3339980 GGTTGATGGT
* * * * * *
3339990 GATCTGCCCTAGGCTTGGGGTAAAAGATCGAATGGTTGTAATTTGCCCCTGGCTTGGGGTAAGAG
1 GATCTGCCCCAGGCTTGGGGTAAGAGATCGAATGGCTGTAATCTGCCCCTAGCTCGGGGTAAGAG
*
3340055 ATCGAATGGTTG-C-A
66 ATCGAATGGTCGACGA
* *
3340069 -ATCTGCCCCAGGCTCGGGGTAAGAGATCGAATGGCTATAATCTGCCCCTAGCTCGGGGTAAGAG
1 GATCTGCCCCAGGCTTGGGGTAAGAGATCGAATGGCTGTAATCTGCCCCTAGCTCGGGGTAAGAG
3340133 AT----TGGTCGACGA
66 ATCGAATGGTCGACGA
* * * *
3340145 TGATCTGCCCCAAGCTTGGGGTAAGAGATCGAATGGCTGCAATCTGCCCCAAGCTCAGGGTAAGA
1 -GATCTGCCCCAGGCTTGGGGTAAGAGATCGAATGGCTGTAATCTGCCCCTAGCTCGGGGTAAGA
3340210 GATCAGAAT
65 GATC-GAAT
3340219 CTTCATTTTT
Statistics
Matches: 126, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
74 5 0.04
75 1 0.01
76 1 0.01
78 118 0.94
83 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (81 bp):
GATCTGCCCCAGGCTTGGGGTAAGAGATCGAATGGCTGTAATCTGCCCCTAGCTCGGGGTAAGAG
ATCGAATGGTCGACGA
Found at i:3340532 original size:49 final size:49
Alignment explanation
Indices: 3340476--3340687 Score: 257
Period size: 48 Copynumber: 4.3 Consensus size: 49
3340466 GACTTAAACT
** * *
3340476 TTTCCCTTCAAATCTTCGTGGTACTAGATCCGCCGTCGCAGCTTAGATC
1 TTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTTGCAGCTTAGATC
* * **
3340525 TTTCCCTT-ATGTTTTCGCGGTACTGGATCCGCCGTTGCAATATTAGATC
1 TTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTTGC-AGCTTAGATC
* * *
3340574 TTTCCCGTCGTGTCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATC
1 TTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTTGCAGCTTAGATC
* * *
3340623 TTT-CCTTTATGTCTTCGTGGTACTGGATCAGCCGTTGCGGTCTTAGATC
1 TTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTTGCAG-CTTAGATC
*
3340672 TTTCCCGTCATGTCTT
1 TTTCCCTTCATGTCTT
3340688 TGAGGTACAA
Statistics
Matches: 138, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
48 57 0.41
49 44 0.32
50 37 0.27
ACGTcount: A:0.13, C:0.27, G:0.22, T:0.38
Consensus pattern (49 bp):
TTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTTGCAGCTTAGATC
Found at i:3340604 original size:98 final size:98
Alignment explanation
Indices: 3340488--3340687 Score: 301
Period size: 98 Copynumber: 2.0 Consensus size: 98
3340478 TCCCTTCAAA
*
3340488 TCTTCGTGGTACTAGATCCGCCGTCGCAGCTTAGATCTTTCCCTTATGTTTTCGCGGTACTGGAT
1 TCTTCGTGGTACTAGATCCGCCGTCGCAGCTTAGATCTTTCCCTTATGTCTTCGCGGTACTGGAT
* *
3340553 CCGCCGTTGCAATATTAGATCTTTCCCGTCGTG
66 CAGCCGTTGCAATATTAGATCTTTCCCGTCATG
* * * * *
3340586 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCTTTATGTCTTCGTGGTACTGGAT
1 TCTTCGTGGTACTAGATCCGCCGTCGCAGCTTAGATCTTTCCCTTATGTCTTCGCGGTACTGGAT
** *
3340651 CAGCCGTTGCGGTCTTAGATCTTTCCCGTCATG
66 CAGCCGTTGCAATATTAGATCTTTCCCGTCATG
3340684 TCTT
1 TCTT
3340688 TGAGGTACAA
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.12, C:0.27, G:0.23, T:0.38
Consensus pattern (98 bp):
TCTTCGTGGTACTAGATCCGCCGTCGCAGCTTAGATCTTTCCCTTATGTCTTCGCGGTACTGGAT
CAGCCGTTGCAATATTAGATCTTTCCCGTCATG
Found at i:3340709 original size:98 final size:98
Alignment explanation
Indices: 3340488--3340780 Score: 295
Period size: 98 Copynumber: 3.0 Consensus size: 98
3340478 TCCCTTCAAA
* * * * *
3340488 TCTTCGTGGTACTA-GATCCGCCGTCGCAGCTTAGATCTTTCCCTTATGTTTTCGCGGTACTGGA
1 TCTTCGAGGTAC-AGGATCCGCCGTTGCGGCTTAGATCTTTCCTTTATGTCTTCGCGGTACTGGA
* * *
3340552 TCCGCCGTTGCAATATTAGATCTTTCCCGTCGTG
65 TCCGCCGTTGCAGTCTTAGATCTTTCCCGTCATG
* * *
3340586 TCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCTTTATGTCTTCGTGGTACTGGAT
1 TCTTCGAGGTACAGGATCCGCCGTTGCGGCTTAGATCTTTCCTTTATGTCTTCGCGGTACTGGAT
* *
3340651 CAGCCGTTGCGGTCTTAGATCTTTCCCGTCATG
66 CCGCCGTTGCAGTCTTAGATCTTTCCCGTCATG
* ** * ** * * * *
3340684 TCTTTGAGGTACAAGG-TTTGTCGTTGCTACTTAAACCCTTACCTTT-TGTATCTTTGCGGTACT
1 TCTTCGAGGTAC-AGGATCCGCCGTTGCGGCTTAGA-TCTTTCCTTTATG--TCTTCGCGGTACT
* *
3340747 AGATCCGCCGTTGCTGTCTTAGATCTTTCCCGTC
62 GGATCCGCCGTTGCAGTCTTAGATCTTTCCCGTC
3340781 GTGTTTCCTC
Statistics
Matches: 163, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
98 111 0.68
99 10 0.06
100 42 0.26
ACGTcount: A:0.14, C:0.26, G:0.23, T:0.38
Consensus pattern (98 bp):
TCTTCGAGGTACAGGATCCGCCGTTGCGGCTTAGATCTTTCCTTTATGTCTTCGCGGTACTGGAT
CCGCCGTTGCAGTCTTAGATCTTTCCCGTCATG
Found at i:3341777 original size:22 final size:21
Alignment explanation
Indices: 3341715--3341780 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 21
3341705 CCTTTTTCTA
* *
3341715 TTTTTG-TTTT-TCTTCCTGT
1 TTTTTGCTTTTCTTTTCCTTT
3341734 TTTTTGCTTTTCTTTTCTCTTT
1 TTTTTGCTTTTCTTTTC-CTTT
3341756 TCTTTTGC-TTTCTTTTTCCTTT
1 T-TTTTGCTTTTC-TTTTCCTTT
3341778 TTT
1 TTT
3341781 ATTTTTTCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
19 6 0.15
20 4 0.10
21 6 0.15
22 13 0.32
23 11 0.28
ACGTcount: A:0.00, C:0.18, G:0.06, T:0.76
Consensus pattern (21 bp):
TTTTTGCTTTTCTTTTCCTTT
Found at i:3347234 original size:59 final size:58
Alignment explanation
Indices: 3347191--3347341 Score: 198
Period size: 58 Copynumber: 2.6 Consensus size: 58
3347181 TAATTTTTTG
3347191 GAAAAATCAGGATCAAAAATGGAATTTTTGGAAGTTTGGGGTAAAATGGTAATTTCGA
1 GAAAAATCAGGATCAAAAATGGAATTTTTGGAAGTTTGGGGTAAAATGGTAATTTCGA
* * * **
3347249 GAAAAATC-GAGATAAAAAATGGAATTTTTGAAAATTTAAGGTAAAATGGTAATTTCGA
1 GAAAAATCAG-GATCAAAAATGGAATTTTTGGAAGTTTGGGGTAAAATGGTAATTTCGA
* * * *
3347307 GAAAAATTAGGGTC-AAAATAGAATTTTAGGAAGTT
1 GAAAAATCAGGATCAAAAATGGAATTTTTGGAAGTT
3347342 CGAGGGATAA
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
57 18 0.23
58 60 0.76
59 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (58 bp):
GAAAAATCAGGATCAAAAATGGAATTTTTGGAAGTTTGGGGTAAAATGGTAATTTCGA
Found at i:3347310 original size:29 final size:30
Alignment explanation
Indices: 3347233--3347325 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 30
3347223 AGTTTGGGGT
** *
3347233 AAAATGGTAATTTCGAGAAAAATCGAGATAA
1 AAAATGGTAATTTCGAGAAAAATTAAGGT-A
** *
3347264 AAAATGG-AATTT-TTGAAAATTTAAGGT-
1 AAAATGGTAATTTCGAGAAAAATTAAGGTA
* *
3347291 AAAATGGTAATTTCGAGAAAAATTAGGGTC
1 AAAATGGTAATTTCGAGAAAAATTAAGGTA
3347321 AAAAT
1 AAAAT
3347326 AGAATTTTAG
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
27 7 0.14
28 5 0.10
29 20 0.41
30 10 0.20
31 7 0.14
ACGTcount: A:0.48, C:0.04, G:0.19, T:0.28
Consensus pattern (30 bp):
AAAATGGTAATTTCGAGAAAAATTAAGGTA
Found at i:3347347 original size:29 final size:28
Alignment explanation
Indices: 3347315--3347569 Score: 162
Period size: 29 Copynumber: 8.8 Consensus size: 28
3347305 GAGAAAAATT
*
3347315 AGGGTCAAAATAG-AATTTTAGGAAGTTCG
1 AGGGTAAAAAT-GTAATTTT-GGAAGTTCG
3347344 AGGGATAAAAATGTAATTTTTGGAAGTTCG
1 AGGG-TAAAAATGTAA-TTTTGGAAGTTCG
* **
3347374 AGGGT-AAAATGGTAATTTTGAAAAAATC-
1 AGGGTAAAAAT-GTAATTTTG-GAAGTTCG
* **
3347402 AGGGTAAAAATGGAATTTTATAAAGTTCG
1 AGGGTAAAAATGTAATTTT-GGAAGTTCG
**
3347431 AGGGTAAAAATGTAATTTTGGAAAAATCG
1 AGGGTAAAAATGTAATTTTGG-AAGTTCG
* * * *
3347460 A-GATCAAAATGGAATTTTGGAAAGTTTG
1 AGGGTAAAAATGTAATTTTGG-AAGTTCG
* **
3347488 GGGGTAAAAATGTAAATTTTGGGAAAATCG
1 AGGGTAAAAATGT-AATTTT-GGAAGTTCG
**
3347518 A-GGTCAAAAATAG-AATTTTAAAAAGTTCG
1 AGGGT-AAAAAT-GTAATTTT-GGAAGTTCG
*
3347547 GGGGTAAAAATGTAAATTTTGGA
1 AGGGTAAAAATGT-AATTTTGGA
3347570 TAATTTAGGG
Statistics
Matches: 174, Mismatches: 35, Indels: 34
0.72 0.14 0.14
Matches are distributed among these distances:
28 49 0.28
29 72 0.41
30 46 0.26
31 7 0.04
ACGTcount: A:0.42, C:0.04, G:0.25, T:0.29
Consensus pattern (28 bp):
AGGGTAAAAATGTAATTTTGGAAGTTCG
Found at i:3347362 original size:87 final size:86
Alignment explanation
Indices: 3347263--3347476 Score: 254
Period size: 87 Copynumber: 2.5 Consensus size: 86
3347253 AATCGAGATA
* * * *
3347263 AAAAATGGAATTTTTGAAAATT-TAAGGTAAAATGGTAATTTCGAGAAAAATTAGGGTCAAAATA
1 AAAAATGTAATTTTTGAAAATTCGAAGGTAAAATGGTAATTTCGA-AAAAATCAGGGTAAAAATA
*
3347327 GAATTTTAGGAAGTTCGAGGGAT
65 GAATTTTAGAAAGTTCGAGGG-T
* * * * *
3347350 AAAAATGTAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTGAAAAAATCAGGGTAAAAATGG
1 AAAAATGTAATTTTTGAAAATTCGAAGGTAAAATGGTAATTTCGAAAAAATCAGGGTAAAAATAG
*
3347415 AATTTTATAAAGTTCGAGGGT
66 AATTTTAGAAAGTTCGAGGGT
* * *
3347436 AAAAATGTAATTTTGGAAAAATCG-AGATCAAAATGG-AATTT
1 AAAAATGTAATTTTTGAAAATTCGAAGGT-AAAATGGTAATTT
3347477 TGGAAAGTTT
Statistics
Matches: 108, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
85 7 0.06
86 28 0.26
87 54 0.50
88 19 0.18
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.30
Consensus pattern (86 bp):
AAAAATGTAATTTTTGAAAATTCGAAGGTAAAATGGTAATTTCGAAAAAATCAGGGTAAAAATAG
AATTTTAGAAAGTTCGAGGGT
Found at i:3347428 original size:57 final size:57
Alignment explanation
Indices: 3347349--3347569 Score: 250
Period size: 57 Copynumber: 3.8 Consensus size: 57
3347339 GTTCGAGGGA
* * *
3347349 TAAAAATGTAATTTT-TGGAAGTTCGAGGGT-AAAATGGTAATTTTGAAAAAATC-AGGG
1 TAAAAATGGAATTTTAT-AAAGTTCGAGGGTAAAAAT-GTAATTTTGGAAAAATCGA-GG
*
3347406 TAAAAATGGAATTTTATAAAGTTCGAGGGTAAAAATGTAATTTTGGAAAAATCGAGA
1 TAAAAATGGAATTTTATAAAGTTCGAGGGTAAAAATGTAATTTTGGAAAAATCGAGG
* ** * * *
3347463 TCAAAATGGAATTTTGGAAAGTTTGGGGGTAAAAATGTAAATTTTGGGAAAATCGAGG
1 TAAAAATGGAATTTTATAAAGTTCGAGGGTAAAAATGT-AATTTTGGAAAAATCGAGG
* * *
3347521 TCAAAAATAGAATTTTAAAAAGTTCGGGGGTAAAAATGTAAATTTTGGA
1 T-AAAAATGGAATTTTATAAAGTTCGAGGGTAAAAATGT-AATTTTGGA
3347570 TAATTTAGGG
Statistics
Matches: 142, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
57 76 0.54
58 25 0.18
59 41 0.29
ACGTcount: A:0.42, C:0.04, G:0.24, T:0.30
Consensus pattern (57 bp):
TAAAAATGGAATTTTATAAAGTTCGAGGGTAAAAATGTAATTTTGGAAAAATCGAGG
Found at i:3348140 original size:6 final size:6
Alignment explanation
Indices: 3348129--3348226 Score: 60
Period size: 6 Copynumber: 16.5 Consensus size: 6
3348119 TTTTTAATTC
* ** *
3348129 AATTTA AATTTA AACTT- AATTTA AATTTA AACTTT- AATAGA ACTTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AA-TTTA AATTTA AATTTA
** * * *
3348175 AATTTA AATTTA AACTTTA ATAGATA AGTTTA AACTTA AA-TCA AATTTA
1 AATTTA AATTTA AA-TTTA A-ATTTA AATTTA AATTTA AATTTA AATTTA
3348224 AAT
1 AAT
3348227 CCAAAATGAA
Statistics
Matches: 68, Mismatches: 17, Indels: 14
0.69 0.17 0.14
Matches are distributed among these distances:
5 13 0.19
6 43 0.63
7 11 0.16
8 1 0.01
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:3348151 original size:17 final size:17
Alignment explanation
Indices: 3348129--3348162 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3348119 TTTTTAATTC
3348129 AATTTAAATTTAAACTT
1 AATTTAAATTTAAACTT
3348146 AATTTAAATTTAAACTT
1 AATTTAAATTTAAACTT
3348163 TAATAGAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTAAATTTAAACTT
Found at i:3349552 original size:25 final size:26
Alignment explanation
Indices: 3349523--3349571 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
3349513 ATATTAATAT
3349523 TTATATTAATATTAA-ATAAATATAA
1 TTATATTAATATTAATATAAATATAA
* *
3349548 TTATATTCATATTAATATTAATAT
1 TTATATTAATATTAATATAAATAT
3349572 TAAATAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
TTATATTAATATTAATATAAATATAA
Found at i:3349560 original size:37 final size:37
Alignment explanation
Indices: 3349511--3349585 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
3349501 AAATTCAATT
*
3349511 TTATATTAATATTTATATTAATATTAAATAAATATAA
1 TTATATTAATATTAATATTAATATTAAATAAATATAA
*
3349548 TTATATTCATATTAATATTAATATTAAATAAATATAA
1 TTATATTAATATTAATATTAATATTAAATAAATATAA
3349585 T
1 T
3349586 GAATTGTCCG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (37 bp):
TTATATTAATATTAATATTAATATTAAATAAATATAA
Found at i:3349584 original size:6 final size:6
Alignment explanation
Indices: 3349513--3349574 Score: 63
Period size: 6 Copynumber: 10.2 Consensus size: 6
3349503 ATTCAATTTT
* * * *
3349513 ATATTA ATATTT ATATTA ATATTA A-ATAA ATATAATT ATATTC ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATAT--TA ATATTA ATATTA
3349562 ATATTA ATATTA A
1 ATATTA ATATTA A
3349575 ATAAATATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
5 4 0.09
6 38 0.83
8 4 0.09
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTA
Found at i:3360164 original size:29 final size:29
Alignment explanation
Indices: 3360101--3360164 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
3360091 TATTATATGT
3360101 AAAT-ATTGAAATTTGCCGTTATACTTTG
1 AAATCATTGAAATTTGCCGTTATACTTTG
*** * * *
3360129 TTTTCATTGATATTTGTCGTTATATTTTG
1 AAATCATTGAAATTTGCCGTTATACTTTG
3360158 AAATCAT
1 AAATCAT
3360165 GAGTAAATTT
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.28, C:0.09, G:0.12, T:0.50
Consensus pattern (29 bp):
AAATCATTGAAATTTGCCGTTATACTTTG
Found at i:3360274 original size:13 final size:13
Alignment explanation
Indices: 3360256--3360280 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3360246 GATTTTTTAA
3360256 TTAAAATTTACCG
1 TTAAAATTTACCG
3360269 TTAAAATTTACC
1 TTAAAATTTACC
3360281 ACTAATTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (13 bp):
TTAAAATTTACCG
Found at i:3362990 original size:34 final size:34
Alignment explanation
Indices: 3362947--3363013 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
3362937 TAAATAGGAG
3362947 GATAATACGTTTCAGA-GTACTCAAACTCACGTTA
1 GATAATACGTTTCA-ACGTACTCAAACTCACGTTA
*
3362981 GATAATACGTTTCAACGTACTCACACTCACGTT
1 GATAATACGTTTCAACGTACTCAAACTCACGTT
3363014 CTCCTATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 1 0.03
34 30 0.97
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (34 bp):
GATAATACGTTTCAACGTACTCAAACTCACGTTA
Found at i:3369586 original size:25 final size:25
Alignment explanation
Indices: 3369558--3369611 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
3369548 AATTATTGTC
3369558 ACATCATATAACAACACTCTAATTA
1 ACATCATATAACAACACTCTAATTA
3369583 ACATCATATAACAACACTCTAATTA
1 ACATCATATAACAACACTCTAATTA
3369608 ACAT
1 ACAT
3369612 TTTTAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (25 bp):
ACATCATATAACAACACTCTAATTA
Found at i:3378784 original size:15 final size:15
Alignment explanation
Indices: 3378764--3378793 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3378754 CTTCCGAAAT
*
3378764 GTTTAGCTTCTTTCC
1 GTTTAGCCTCTTTCC
3378779 GTTTAGCCTCTTTCC
1 GTTTAGCCTCTTTCC
3378794 TTCTTCGGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.30, G:0.13, T:0.50
Consensus pattern (15 bp):
GTTTAGCCTCTTTCC
Found at i:3383852 original size:21 final size:21
Alignment explanation
Indices: 3383827--3383872 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
3383817 AGATAATTAA
*
3383827 TTTTTCCAATAAAAATCCAAG
1 TTTTTCCAATAAAAATCCAAC
** *
3383848 TTTTTCCTGTAAAATTCCAAC
1 TTTTTCCAATAAAAATCCAAC
3383869 TTTT
1 TTTT
3383873 CCTTCCATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (21 bp):
TTTTTCCAATAAAAATCCAAC
Found at i:3385084 original size:201 final size:200
Alignment explanation
Indices: 3384733--3385253 Score: 772
Period size: 201 Copynumber: 2.6 Consensus size: 200
3384723 AGATTTCTTA
* * *
3384733 TTTGGGCAAGCAGAAGAGATATGACCCTTTTGTCCGCATTCGTAGCACGTCCTTCTCCTCAATTT
1 TTTGGGCAAGCAGAAGAAATATGGCCCTTTTGTCCGCATTCGTAGCACGTCCTTCTCCTCAACTT
* * * * * * * * **
3384798 CCCGCTGCTAACGGTAGAGCCATCGTTAGCAACTTCGTTAACCGTAGGTGCTTCATTAACCGTTG
66 ACCACTG-TAACGCTTGAGCCACCGTTATCAACTTCATTAACCGTAGGTGCTTCATTAACCATCA
* * * * **
3384863 AACCACCGTTGCCAACTTCATTAACTGTAGGTGCTTCGACACTCACAGGTGCTTTGACACTCGTA
130 AACCACCGTTACCAACTTCATTAACTGTAGGTGCTTCCACACTCAAAGGTGCTTCGACACTCACA
3384928 GATCCT
195 GATCCT
* * *
3384934 TTTGGACAAGCAGAAGAAATATGGCCCTTTTGTCCGCACTCGTAGCATGTCCTTCTCCTCAACTT
1 TTTGGGCAAGCAGAAGAAATATGGCCCTTTTGTCCGCATTCGTAGCACGTCCTTCTCCTCAACTT
3384999 ACCACTAGTAACGCTTGAGCCACCGTTATCAACTTCATTAACCGTAGGTGCTTCATTAACCATCA
66 ACCACT-GTAACGCTTGAGCCACCGTTATCAACTTCATTAACCGTAGGTGCTTCATTAACCATCA
* *
3385064 AACCACTGTTACCAACTTCATTAACTGTAGGTGCTTCCACATTCAAAGGTGCTTCGACACTCACA
130 AACCACCGTTACCAACTTCATTAACTGTAGGTGCTTCCACACTCAAAGGTGCTTCGACACTCACA
3385129 GATCCT
195 GATCCT
*
3385135 TTTGGGCAAGCAGAAGAAATATGGCCCTTTTGTCCGCATTCATAGCACGTCCTTCTCCTCAACTT
1 TTTGGGCAAGCAGAAGAAATATGGCCCTTTTGTCCGCATTCGTAGCACGTCCTTCTCCTCAACTT
* *
3385200 ACCACTGGTAACGCTTGAGCCACCATTATCAACTTCATTAACCGTAGCTGCTTC
66 ACCACT-GTAACGCTTGAGCCACCGTTATCAACTTCATTAACCGTAGGTGCTTC
3385254 GACACTCACA
Statistics
Matches: 288, Mismatches: 31, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
201 287 1.00
202 1 0.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.29
Consensus pattern (200 bp):
TTTGGGCAAGCAGAAGAAATATGGCCCTTTTGTCCGCATTCGTAGCACGTCCTTCTCCTCAACTT
ACCACTGTAACGCTTGAGCCACCGTTATCAACTTCATTAACCGTAGGTGCTTCATTAACCATCAA
ACCACCGTTACCAACTTCATTAACTGTAGGTGCTTCCACACTCAAAGGTGCTTCGACACTCACAG
ATCCT
Found at i:3387700 original size:26 final size:25
Alignment explanation
Indices: 3387661--3387740 Score: 88
Period size: 26 Copynumber: 3.1 Consensus size: 25
3387651 TATCAATTAC
** *
3387661 ATCAAGTTGGGTGATTGTTAGTATA
1 ATCAAGTTAAGTGACTGTTAGTATA
* *
3387686 ACTCAAGTTAAGTGACTGTTGGTGTA
1 A-TCAAGTTAAGTGACTGTTAGTATA
*
3387712 ATCAAAGTTAAGTGACTGTTAGTGTA
1 ATC-AAGTTAAGTGACTGTTAGTATA
3387738 ATC
1 ATC
3387741 TACTCTTAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
25 3 0.06
26 44 0.94
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.36
Consensus pattern (25 bp):
ATCAAGTTAAGTGACTGTTAGTATA
Found at i:3389109 original size:22 final size:22
Alignment explanation
Indices: 3389075--3389116 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3389065 CCGATTTTGA
** *
3389075 GTCAGATTTATCTCGAGCTCAG
1 GTCAGATCAATCTCAAGCTCAG
3389097 GTCAGATCAATCTCAAGCTC
1 GTCAGATCAATCTCAAGCTC
3389117 GAATTTATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (22 bp):
GTCAGATCAATCTCAAGCTCAG
Found at i:3392982 original size:23 final size:23
Alignment explanation
Indices: 3392951--3392997 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3392941 ATTATTACAC
*
3392951 TCTTTAAACAATAAAATTCTTAT
1 TCTTCAAACAATAAAATTCTTAT
* *
3392974 TCTTCAAACAATTAAATTTTTAT
1 TCTTCAAACAATAAAATTCTTAT
3392997 T
1 T
3392998 GTTAAACCGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (23 bp):
TCTTCAAACAATAAAATTCTTAT
Found at i:3401266 original size:19 final size:17
Alignment explanation
Indices: 3401242--3401286 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 17
3401232 TAAATTGATT
3401242 TTAAATTTATTTTTAAAAC
1 TTAAATTTA-TTTT-AAAC
*
3401261 TTAAATTTATTTTAAAT
1 TTAAATTTATTTTAAAC
3401278 TTAAATTTA
1 TTAAATTTA
3401287 AATTTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 12 0.48
18 4 0.16
19 9 0.36
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAATTTATTTTAAAC
Found at i:3401277 original size:11 final size:11
Alignment explanation
Indices: 3401230--3401292 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
3401220 TTGTTTTTGG
*
3401230 TTTAAATTGAT
1 TTTAAATTTAT
3401241 TTTAAATTTATT
1 TTTAAATTTA-T
3401253 TTTAAA---A-
1 TTTAAATTTAT
*
3401260 CTTAAATTTAT
1 TTTAAATTTAT
*
3401271 TTTAAATTTAAA
1 TTTAAATTT-AT
3401283 TTTAAATTTA
1 TTTAAATTTA
3401293 AATTTGGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
7 5 0.12
9 1 0.02
10 1 0.02
11 18 0.43
12 17 0.40
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:3401282 original size:6 final size:6
Alignment explanation
Indices: 3401241--3401297 Score: 62
Period size: 6 Copynumber: 9.5 Consensus size: 6
3401231 TTAAATTGAT
** * *
3401241 TTTAAA TTTATT TTTAAAA CTTAAA TTT-AT TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
3401289 TTTAAA TTT
1 TTTAAA TTT
3401298 GGTTTAAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
5 4 0.10
6 34 0.83
7 3 0.07
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:3401287 original size:30 final size:29
Alignment explanation
Indices: 3401231--3401313 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 29
3401221 TGTTTTTGGT
* **
3401231 TTAAATTGATTTTAAATTTATTTTTAAAAC
1 TTAAATTTATTTTAAATTTAAATTT-AAAC
*
3401261 TTAAATTTATTTTAAATTTAAATTTAAAT
1 TTAAATTTATTTTAAATTTAAATTTAAAC
**
3401290 TTAAATTTGGTTTAAATTTGAAAT
1 TTAAATTTATTTTAAATTT-AAAT
3401314 GATTTTAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 20 0.43
30 26 0.57
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (29 bp):
TTAAATTTATTTTAAATTTAAATTTAAAC
Found at i:3402111 original size:18 final size:17
Alignment explanation
Indices: 3402088--3402135 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
3402078 TAATAATAAC
*
3402088 AATAATACT-TTTATT-
1 AATAATAATATTTATTA
3402103 AATAATAATATTTATTA
1 AATAATAATATTTATTA
*
3402120 AATAATTAATAATTAT
1 AATAA-TAATATTTAT
3402136 AAAAAAAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 8 0.29
16 6 0.21
17 5 0.18
18 9 0.32
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
AATAATAATATTTATTA
Found at i:3403070 original size:29 final size:29
Alignment explanation
Indices: 3403038--3403290 Score: 153
Period size: 29 Copynumber: 8.7 Consensus size: 29
3403028 CTCGAACTTC
3403038 CCAAAATCCCATTTTTAACCCTAATTTTA
1 CCAAAATCCCATTTTTAACCCTAATTTTA
* * *
3403067 CCAAAATTACCA-TTTTACCCCTAAACTTT-
1 CCAAAA-TCCCATTTTTAACCCT-AATTTTA
* *
3403096 CCAAAAT-CCATTTTTAA-CCTCGATTTCA
1 CCAAAATCCCATTTTTAACCCT-AATTTTA
* * * *
3403124 CCAAAAATTACC-TTTTTACTCCCGAACTTT-
1 CC-AAAA-TCCCATTTTTA-ACCCTAATTTTA
* * *
3403154 CTAAAATCCCATTTTTAACCCCAATTTCA
1 CCAAAATCCCATTTTTAACCCTAATTTTA
** * * ** *
3403183 CCAAAAATTACAATTTTACCCCTAAACTTC
1 CC-AAAATCCCATTTTTAACCCTAATTTTA
*
3403213 CCAAAATCCCATTTTTAACCCTAATTTCA
1 CCAAAATCCCATTTTTAACCCTAATTTTA
* * *
3403242 CCAAAATTACCA-TTTTACCCCTAAATTT-
1 CCAAAA-TCCCATTTTTAACCCTAATTTTA
*
3403270 CCTAAAATCCCATTTTCAACC
1 CC-AAAATCCCATTTTTAACC
3403291 TCGATTTCAC
Statistics
Matches: 165, Mismatches: 44, Indels: 30
0.69 0.18 0.13
Matches are distributed among these distances:
27 9 0.05
28 24 0.15
29 84 0.51
30 41 0.25
31 5 0.03
32 2 0.01
ACGTcount: A:0.34, C:0.30, G:0.01, T:0.34
Consensus pattern (29 bp):
CCAAAATCCCATTTTTAACCCTAATTTTA
Found at i:3403082 original size:59 final size:58
Alignment explanation
Indices: 3403021--3403433 Score: 464
Period size: 58 Copynumber: 7.1 Consensus size: 58
3403011 TTAAATCAAT
* *
3403021 TTTTACCCTCGAACTTCCCAAAATCCCATTTTTAACCCTAATTTTACC-AAAATTACCA
1 TTTTACCC-CAAACTTCCCAAAATCCCATTTTTAACCCTAATTTCACCAAAAATTACCA
* * *
3403079 TTTTACCCCTAAACTTTCCAAAAT-CCATTTTTAA-CCTCGATTTCACCAAAAATTACCT
1 TTTTACCCC-AAACTTCCCAAAATCCCATTTTTAACCCT-AATTTCACCAAAAATTACCA
* * * * *
3403137 TTTTACTCCCGAACTTTCTAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACAA
1 TTTTAC-CCCAAACTTCCCAAAATCCCATTTTTAACCCTAATTTCACCAAAAATTACCA
3403196 TTTTACCCCTAAACTTCCCAAAATCCCATTTTTAACCCTAATTTCACC-AAAATTACCA
1 TTTTACCCC-AAACTTCCCAAAATCCCATTTTTAACCCTAATTTCACCAAAAATTACCA
* * * *
3403254 TTTTACCCCTAAATTTCCTAAAATCCCATTTTCAA-CCTCGATTTCACCAAAAATTACCA
1 TTTTACCCC-AAACTTCCCAAAATCCCATTTTTAACCCT-AATTTCACCAAAAATTACCA
* * *
3403313 TTTTACCCTCGAACTTCCCCAAAATCTCGTTTTTAA-CCTCAATTTCACC-AAAATTACCA
1 TTTTACCC-CAAACTT-CCCAAAATCCCATTTTTAACCCT-AATTTCACCAAAAATTACCA
* ** * **
3403372 TTTTACCCTCAAATTTCTTAAAATCCCATTTTCAACCCTGGTTTCACCAAAAATTA-CA
1 TTTTACCC-CAAACTTCCCAAAATCCCATTTTTAACCCTAATTTCACCAAAAATTACCA
3403430 TTTT
1 TTTT
3403434 TTCCCCAGAA
Statistics
Matches: 306, Mismatches: 36, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
56 3 0.01
57 21 0.07
58 126 0.41
59 126 0.41
60 30 0.10
ACGTcount: A:0.33, C:0.30, G:0.02, T:0.35
Consensus pattern (58 bp):
TTTTACCCCAAACTTCCCAAAATCCCATTTTTAACCCTAATTTCACCAAAAATTACCA
Found at i:3403094 original size:58 final size:59
Alignment explanation
Indices: 3403032--3403433 Score: 466
Period size: 59 Copynumber: 6.9 Consensus size: 59
3403022 TTTACCCTCG
*
3403032 AACTTCCCAAAATCCCATTTTTAACCCTAATTTTACC-AAAATTACCATTTTACCCCTA
1 AACTTCCCAAAATCCCATTTTTAACCCTAATTTCACCAAAAATTACCATTTTACCCCTA
* * * *
3403090 AACTTTCCAAAAT-CCATTTTTAA-CCTCGATTTCACCAAAAATTACCTTTTTACTCCC-G
1 AACTTCCCAAAATCCCATTTTTAACCCT-AATTTCACCAAAAATTACCATTTTAC-CCCTA
* * * *
3403148 AACTTTCTAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACAATTTTACCCCTA
1 AACTTCCCAAAATCCCATTTTTAACCCTAATTTCACCAAAAATTACCATTTTACCCCTA
3403207 AACTTCCCAAAATCCCATTTTTAACCCTAATTTCACC-AAAATTACCATTTTACCCCTA
1 AACTTCCCAAAATCCCATTTTTAACCCTAATTTCACCAAAAATTACCATTTTACCCCTA
* * * * *
3403265 AATTTCCTAAAATCCCATTTTCAA-CCTCGATTTCACCAAAAATTACCATTTTA-CCCTCG
1 AACTTCCCAAAATCCCATTTTTAACCCT-AATTTCACCAAAAATTACCATTTTACCCCT-A
* *
3403324 AACTTCCCCAAAATCTCGTTTTTAA-CCTCAATTTCACC-AAAATTACCATTTTA-CCCTCA
1 AACTT-CCCAAAATCCCATTTTTAACCCT-AATTTCACCAAAAATTACCATTTTACCCCT-A
* ** * **
3403383 AATTTCTTAAAATCCCATTTTCAACCCTGGTTTCACCAAAAATTA-CATTTT
1 AACTTCCCAAAATCCCATTTTTAACCCTAATTTCACCAAAAATTACCATTTT
3403434 TTCCCCAGAA
Statistics
Matches: 297, Mismatches: 35, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
56 3 0.01
57 20 0.07
58 122 0.41
59 123 0.41
60 29 0.10
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.35
Consensus pattern (59 bp):
AACTTCCCAAAATCCCATTTTTAACCCTAATTTCACCAAAAATTACCATTTTACCCCTA
Found at i:3403305 original size:29 final size:28
Alignment explanation
Indices: 3403021--3403408 Score: 152
Period size: 29 Copynumber: 13.3 Consensus size: 28
3403011 TTAAATCAAT
* *
3403021 TTTTACCCTCGAACTTC-CCAAAATCCCA
1 TTTTAACCTC-AATTTCACCAAAATCCCA
* *
3403049 TTTTTAACC-CTAATTTTACCAAAATTACCA
1 -TTTTAACCTC-AATTTCACCAAAA-TCCCA
* *
3403079 TTTTACCCCTAAACTTT--CCAAAAT-CCA
1 TTTTA-ACCTCAA-TTTCACCAAAATCCCA
* *
3403106 TTTTTAACCTCGATTTCACCAAAAATTACC-
1 -TTTTAACCTCAATTTCACC-AAAA-TCCCA
* * *
3403136 TTTTTACTCCCGAACTTT--CTAAAATCCCA
1 TTTTAAC-CTC-AA-TTTCACCAAAATCCCA
* * *
3403165 TTTTTAACCCCAATTTCACCAAAAATTACAA
1 -TTTTAACCTCAATTTCACC-AAAA-TCCCA
* * *
3403196 TTTTACCCCTAAACTTC-CCAAAATCCCA
1 TTTTA-ACCTCAATTTCACCAAAATCCCA
*
3403224 TTTTTAACC-CTAATTTCACCAAAATTACCA
1 -TTTTAACCTC-AATTTCACCAAAA-TCCCA
* * *
3403254 TTTTACCCCTAAATTTC-CTAAAATCCCA
1 TTTTA-ACCTCAATTTCACCAAAATCCCA
* *
3403282 TTTTCAACCTCGATTTCACCAAAAATTACCA
1 TTTT-AACCTCAATTTCACC-AAAA-TCCCA
* * * **
3403313 TTTTACCCTCGAACTTCCCCAAAATCTCGT
1 TTTTAACCTC-AATTTCACCAAAATC-CCA
*
3403343 TTTTAACCTCAATTTCACCAAAATTACCA
1 TTTTAACCTCAATTTCACCAAAA-TCCCA
* **
3403372 TTTTACCCTCAAATTTC-TTAAAATCCCA
1 TTTTAACCTC-AATTTCACCAAAATCCCA
3403400 TTTTCAACC
1 TTTT-AACC
3403409 CTGGTTTCAC
Statistics
Matches: 267, Mismatches: 56, Indels: 72
0.68 0.14 0.18
Matches are distributed among these distances:
26 3 0.01
27 10 0.04
28 52 0.19
29 98 0.37
30 71 0.27
31 30 0.11
32 3 0.01
ACGTcount: A:0.33, C:0.31, G:0.02, T:0.35
Consensus pattern (28 bp):
TTTTAACCTCAATTTCACCAAAATCCCA
Found at i:3415936 original size:201 final size:201
Alignment explanation
Indices: 3415582--3416188 Score: 883
Period size: 201 Copynumber: 3.0 Consensus size: 201
3415572 GAAGTAGTTC
* * * * *** * * **
3415582 AACAAGCGAGGCGGTCATCTTCTTAATAAGATACAAAGAAGAGCGCCAACTTAGCGCTCAAACAC
1 AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAAATGC
* * * *
3415647 GAGAAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGACGAAGCAATAAAAAGGT
66 GAGCAAATCTTCGAACCCAGCTTCCAGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAAAGGT
* * * * * *
3415712 TAGCTTCCTAATGAGATACAGAGAGGTGGACCAGATTCATTTTCCTGAAGAGATCTAGAGAAGTG
131 TAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCATCTTCCTGAAGAGATCCAGAGAAGCG
*
3415777 AATCAA
196 AATTAA
* *
3415783 AACAAGCGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGAATACCAACTCAACGCCCAAATGC
1 AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAAATGC
* *
3415848 GAGCAAATCTTCGAACTCAGCTTCCAGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAAAAGT
66 GAGCAAATCTTCGAACCCAGCTTCCAGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAAAGGT
* * *
3415913 TAGCTTCCTGATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCG
131 TAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCATCTTCCTGAAGAGATCCAGAGAAGCG
3415978 AATTAA
196 AATTAA
* *
3415984 AACAAGCGAGGCGGTTATATTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAAATGC
1 AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAAATGC
* * *
3416049 GAGCAAATTTTCGAACCCAGCTTCCAGATGAGACACTGAGAAGCAAGTCGAAACAATAAAATGGT
66 GAGCAAATCTTCGAACCCAGCTTCCAGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAAAGGT
*
3416114 TAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTTATCTTCCTG-AGTAGATCCAGAGAAGC
131 TAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCATCTTCCTGAAG-AGATCCAGAGAAGC
3416178 GAATTAA
195 GAATTAA
3416185 AACA
1 AACA
3416189 GATGATTATG
Statistics
Matches: 363, Mismatches: 42, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
200 1 0.00
201 362 1.00
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.19
Consensus pattern (201 bp):
AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAAATGC
GAGCAAATCTTCGAACCCAGCTTCCAGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAAAGGT
TAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCATCTTCCTGAAGAGATCCAGAGAAGCG
AATTAA
Found at i:3416632 original size:6 final size:6
Alignment explanation
Indices: 3416589--3416645 Score: 55
Period size: 6 Copynumber: 9.5 Consensus size: 6
3416579 TTAAATTGAT
** *
3416589 TTTAAA TTTATT TTTAAAA CTTAAA TTT--A TTCTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA
3416637 TTTAAA TTT
1 TTTAAA TTT
3416646 GGTTTAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
4 3 0.07
5 1 0.02
6 31 0.76
7 6 0.15
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:3416635 original size:30 final size:29
Alignment explanation
Indices: 3416579--3416645 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 29
3416569 TATTTTTGGT
* * **
3416579 TTAAATTGATTTTAAATTTATTTTTAAAAC
1 TTAAATTTATTCTAAATTTAAATTT-AAAC
*
3416609 TTAAATTTATTCTAAATTTAAATTTAAAT
1 TTAAATTTATTCTAAATTTAAATTTAAAC
3416638 TTAAATTT
1 TTAAATTT
3416646 GGTTTAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 11 0.34
30 21 0.66
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (29 bp):
TTAAATTTATTCTAAATTTAAATTTAAAC
Found at i:3417460 original size:18 final size:17
Alignment explanation
Indices: 3417437--3417484 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
3417427 TAATAATAAC
*
3417437 AATAATACT-TTTATT-
1 AATAATAATATTTATTA
3417452 AATAATAATATTTATTA
1 AATAATAATATTTATTA
*
3417469 AATAATTAATAATTAT
1 AATAA-TAATATTTAT
3417485 AAAAAAGGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 8 0.29
16 6 0.21
17 5 0.18
18 9 0.32
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
AATAATAATATTTATTA
Found at i:3419601 original size:43 final size:43
Alignment explanation
Indices: 3419523--3419676 Score: 184
Period size: 43 Copynumber: 3.5 Consensus size: 43
3419513 AGAAAGCGCC
*
3419523 GCTAAAGATCATGTTCTTTAGTAGCGGCGTTTGTGGGAAAAGAGCT
1 GCTAAAGACCATGTTC-TT--TAGCGGCGTTTGTGGGAAAAGAGCT
* *
3419569 GCTAAAGAACATGGTCTTTAGCGGCGTTTGTGGGAAAA-ATGCT
1 GCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAAAAGA-GCT
* * * * *
3419612 GCTAAAGACCATGTTCTTTAGCGGCATTTGTTGAAAAAGCGCC
1 GCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAAAAGAGCT
*
3419655 GCTAAAGACCATGTTCTATAGC
1 GCTAAAGACCATGTTCTTTAGC
3419677 AACGTTTTTT
Statistics
Matches: 96, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
42 1 0.01
43 79 0.82
45 2 0.02
46 14 0.15
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.29
Consensus pattern (43 bp):
GCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAAAAGAGCT
Found at i:3427568 original size:26 final size:28
Alignment explanation
Indices: 3427531--3427593 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
3427521 TTTACAAATC
*
3427531 TTTTTAAATAAT-AAATTTA-AATAATTA
1 TTTTTAAATAATCAAATATATAA-AATTA
3427558 TTTTT-AATAATCAAATATATAAAATTA
1 TTTTTAAATAATCAAATATATAAAATTA
*
3427585 TTTATAAAT
1 TTTTTAAAT
3427594 TTGGTAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 6 0.19
27 20 0.65
28 5 0.16
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTTTAAATAATCAAATATATAAAATTA
Found at i:3430378 original size:24 final size:23
Alignment explanation
Indices: 3430342--3430410 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 23
3430332 ATTCAACTGT
*
3430342 TTATTTCAGTTAAACTCTGTTTAA
1 TTATTTCAATTAAA-TCTGTTTAA
* *
3430366 TTATTTCAATTAAAT-TATTTAT
1 TTATTTCAATTAAATCTGTTTAA
*
3430388 TTGTTTCAATTAAATTCTGTTTA
1 TTATTTCAATTAAA-TCTGTTTA
3430411 TTTGTTTTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
22 18 0.47
23 2 0.05
24 18 0.47
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (23 bp):
TTATTTCAATTAAATCTGTTTAA
Found at i:3430415 original size:24 final size:23
Alignment explanation
Indices: 3430345--3430417 Score: 85
Period size: 24 Copynumber: 3.1 Consensus size: 23
3430335 CAACTGTTTA
* * *
3430345 TTTCAGTTAAACTCTGTTTAATTA
1 TTTCAATTAAA-TCTGTTTATTTG
*
3430369 TTTCAATTAAAT-TATTTATTTG
1 TTTCAATTAAATCTGTTTATTTG
3430391 TTTCAATTAAATTCTGTTTATTTG
1 TTTCAATTAAA-TCTGTTTATTTG
3430415 TTT
1 TTT
3430418 TTGAGTCAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
22 18 0.43
23 2 0.05
24 22 0.52
ACGTcount: A:0.27, C:0.08, G:0.07, T:0.58
Consensus pattern (23 bp):
TTTCAATTAAATCTGTTTATTTG
Found at i:3435287 original size:29 final size:28
Alignment explanation
Indices: 3435255--3435326 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
3435245 TAAAATACTA
* *
3435255 TAAAATTATAAATAACTATAGAACTTATT
1 TAAAATTATAAA-AAATATAGAAATTATT
*
3435284 TAAAATTATTAAAAAATATATAAATTATT
1 TAAAATTA-TAAAAAATATAGAAATTATT
*
3435313 AAAATATTATAAAA
1 TAAA-ATTATAAAA
3435327 GTTTACATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 29 0.78
30 8 0.22
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (28 bp):
TAAAATTATAAAAAATATAGAAATTATT
Found at i:3435310 original size:19 final size:18
Alignment explanation
Indices: 3435286--3435325 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
3435276 AACTTATTTA
3435286 AAATTATTAAAAAATATAT
1 AAATTATTAAAAAAT-TAT
*
3435305 AAATTATTAAAATATTAT
1 AAATTATTAAAAAATTAT
3435323 AAA
1 AAA
3435326 AGTTTACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATTATTAAAAAATTAT
Found at i:3436439 original size:18 final size:18
Alignment explanation
Indices: 3436390--3436461 Score: 60
Period size: 18 Copynumber: 4.0 Consensus size: 18
3436380 TGAAAAATCT
*
3436390 TTAAAAATGAA-AAAAATA
1 TTAAAAAT-AATAAAATTA
*
3436408 -TAAAAATTATTAAAATTA
1 TTAAAAA-TAATAAAATTA
3436426 TTAAAAATAATAAAATTA
1 TTAAAAATAATAAAATTA
**
3436444 GAAAAGAAT-ATAAAATTA
1 TTAAA-AATAATAAAATTA
3436462 AAAAAACAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
17 7 0.16
18 29 0.64
19 9 0.20
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (18 bp):
TTAAAAATAATAAAATTA
Found at i:3440263 original size:52 final size:52
Alignment explanation
Indices: 3440175--3440362 Score: 252
Period size: 52 Copynumber: 3.6 Consensus size: 52
3440165 TTCTCATTTA
* * * * **
3440175 ATACTCACGATGACACATTGTCATCAGATCTCATAATCCGAAAAATATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTTATAATCCGTAAAGGATTCAT
* **
3440227 ATACTCACGATGACACATAGTCATCGGACCTTATAATTTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTTATAATCCGTAAAGGATTCAT
* *
3440279 ATACTCACGATGACACATAGTAATCAGACCTTATAATGCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTTATAATCCGTAAAGGATTCAT
*
3440331 ATACTCATGATGACACATAGTCAT-ATGACCTT
1 ATACTCACGATGACACATAGTCATCA-GACCTT
3440363 TTGCATTTAC
Statistics
Matches: 120, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
51 1 0.01
52 119 0.99
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCAGACCTTATAATCCGTAAAGGATTCAT
Found at i:3441859 original size:30 final size:29
Alignment explanation
Indices: 3441824--3442090 Score: 192
Period size: 29 Copynumber: 9.1 Consensus size: 29
3441814 TGAACTTTGT
3441824 AAGTTCGGGGGTAAAATGGTAATTTTTAGG
1 AAGTTC-GGGGTAAAATGGTAATTTTTAGG
*
3441854 AAGTTCGAGGTCAAAAATGG-AATTTTT-GG
1 AAGTTCGGGGT--AAAATGGTAATTTTTAGG
* ** **
3441883 AAGTCCAAAGGTAAAATGGTAATTTTTAAA
1 AAGTTC-GGGGTAAAATGGTAATTTTTAGG
*
3441913 AAGTTCGGGGTCAAAAAT-GTAATTTTTA-A
1 AAGTTCGGGGT--AAAATGGTAATTTTTAGG
* *
3441942 AAGTTCGGGGGTAAAATGGTAATGTTTAGA
1 AAGTTC-GGGGTAAAATGGTAATTTTTAGG
* *
3441972 AAGTTCAGAGTCAAAAATGG-AATTTTT-GG
1 AAGTTCGGGGT--AAAATGGTAATTTTTAGG
* * *
3442001 AAGTTTGGGGGTGAAATGGTAATTTTTAGA
1 AAG-TTCGGGGTAAAATGGTAATTTTTAGG
**
3442031 AAGTTTTGGGTCAAAAATGG-AATTTTTA-G
1 AAGTTCGGGGT--AAAATGGTAATTTTTAGG
* *
3442060 AAGTTAAGGGGTAAGATGGTAATTTTT-GG
1 AAGTT-CGGGGTAAAATGGTAATTTTTAGG
3442089 AA
1 AA
3442091 AATTACGATA
Statistics
Matches: 192, Mismatches: 25, Indels: 41
0.74 0.10 0.16
Matches are distributed among these distances:
28 24 0.12
29 72 0.38
30 71 0.37
31 25 0.13
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (29 bp):
AAGTTCGGGGTAAAATGGTAATTTTTAGG
Found at i:3441870 original size:59 final size:57
Alignment explanation
Indices: 3441770--3442091 Score: 290
Period size: 59 Copynumber: 5.5 Consensus size: 57
3441760 TTTTGGATGC
* * * * *
3441770 TCGGGGGTAAAACGGTAA-TTTTGGACACTTCGAGGTCAAAAAATTGAACTTTGTAAGT
1 TCGGGGGTAAAATGGTAATTTTTAGAAAGTTCGAGGTC-AAAAATGGAA-TTTGTAAGT
* *
3441828 TCGGGGGTAAAATGGTAATTTTTAGGAAGTTCGAGGTCAAAAATGGAATTTTTGGAAGT
1 TCGGGGGTAAAATGGTAATTTTTAGAAAGTTCGAGGTCAAAAATGGAA--TTTGTAAGT
* *** * * * *
3441887 CCAAAGGTAAAATGGTAATTTTTAAAAAGTTCGGGGTCAAAAATGTAATTTTTAAAAGT
1 TCGGGGGTAAAATGGTAATTTTTAGAAAGTTCGAGGTCAAAAATGGAATTTGT--AAGT
* *
3441946 TCGGGGGTAAAATGGTAATGTTTAGAAAGTTC-AGAGTCAAAAATGGAATTTTTGGAAGT
1 TCGGGGGTAAAATGGTAATTTTTAGAAAGTTCGAG-GTCAAAAATGGAA--TTTGTAAGT
* * * *
3442005 TTGGGGGTGAAATGGTAATTTTTAGAAAGTTTTG-GGTCAAAAATGGAATTTTTAGAAGT
1 TCGGGGGTAAAATGGTAATTTTTAGAAAG-TTCGAGGTCAAAAATGGAATTTGT--AAGT
** * *
3442064 TAAGGGGTAAGATGGTAATTTTTGGAAA
1 TCGGGGGTAAAATGGTAATTTTTAGAAA
3442092 ATTACGATAA
Statistics
Matches: 214, Mismatches: 39, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
57 6 0.03
58 27 0.13
59 175 0.82
60 3 0.01
61 3 0.01
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (57 bp):
TCGGGGGTAAAATGGTAATTTTTAGAAAGTTCGAGGTCAAAAATGGAATTTGTAAGT
Found at i:3441976 original size:118 final size:118
Alignment explanation
Indices: 3441824--3442144 Score: 391
Period size: 118 Copynumber: 2.7 Consensus size: 118
3441814 TGAACTTTGT
* *
3441824 AAGTTCGGGGGTAAAATGGTAATTTTTAGGAAGTTCGAGGTCAAAAATGGAATTTTTGGAAGTCC
1 AAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTCGAGGTCAAAAATGGAATTTTTGGAAGTTC
* *
3441889 AAAGGTAAAATGGTAATTTTTAAAAAGTTCGGGGTCAAAAATGTAATTTTTAA
66 AAGGGTAAAATGGTAATTTTTAAAAAGTTCGGGGTCAAAAATGGAATTTTTAA
*
3441942 AAGTTCGGGGGTAAAATGGTAATGTTTAGAAAGTTC-AGAGTCAAAAATGGAATTTTTGGAAGTT
1 AAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTCGAG-GTCAAAAATGGAATTTTTGGAAGTT
*** * * ** *
3442006 TGGGGGTGAAATGGTAATTTTTAGAAAGTTTTGGGTCAAAAATGGAATTTTTAG
65 CAAGGGTAAAATGGTAATTTTTAAAAAGTTCGGGGTCAAAAATGGAATTTTTAA
** * * * * *
3442060 AAGTTAAGGGGTAAGATGGTAATTTTTGGAAAATTACGA--T-AAAAATGTAATTTTTGAAAAGT
1 AAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTT-CGAGGTCAAAAATGGAATTTTTG-GAAGT
3442122 TCAAGGGTCAAAAT-GTAATTTTT
64 TCAAGGGT-AAAATGGTAATTTTT
3442145 GGAAAGTTAA
Statistics
Matches: 173, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
116 15 0.09
117 21 0.12
118 135 0.78
119 1 0.01
120 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (118 bp):
AAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTCGAGGTCAAAAATGGAATTTTTGGAAGTTC
AAGGGTAAAATGGTAATTTTTAAAAAGTTCGGGGTCAAAAATGGAATTTTTAA
Found at i:3442106 original size:88 final size:88
Alignment explanation
Indices: 3441925--3442179 Score: 220
Period size: 88 Copynumber: 2.9 Consensus size: 88
3441915 GTTCGGGGTC
** * * * *
3441925 AAAAATGTAATTTTT-AAAAGTTCGGGGGT-AAAATGGTAATGTTTAGAAAGTTCA-GAGTCAAA
1 AAAAATGTAATTTTTGAAAAGTTCAAGGGTCAAAATGG-AATTTTTAGAAAGTTAAGGGGT-TAA
* ** ** *
3441987 AATGGAATTTTTGGAAGTTTGGGGGT
64 AATGTAATTTTTGGAAAATT-ACGAT
* **
3442013 -GAAATGGTAATTTTT-AGAAAGTT-TTGGGTCAAAAATGGAATTTTTAG-AAGTTAAGGGG-TA
1 AAAAAT-GTAATTTTTGA-AAAGTTCAAGGGTC-AAAATGGAATTTTTAGAAAGTTAAGGGGTTA
*
3442073 AGATGGTAATTTTTGGAAAATTACGAT
63 AAAT-GTAATTTTTGGAAAATTACGAT
* *
3442100 AAAAATGTAATTTTTGAAAAGTTCAAGGGTCAAAATGTAATTTTTGGAAAGTTAAGGGGTTAAAA
1 AAAAATGTAATTTTTGAAAAGTTCAAGGGTCAAAATGGAATTTTTAGAAAGTTAAGGGGTTAAAA
*
3442165 TGTGATTTTTGGAAA
66 TGTAATTTTTGGAAA
3442180 GTTTAGGGGT
Statistics
Matches: 135, Mismatches: 21, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
87 39 0.29
88 68 0.50
89 21 0.16
90 7 0.05
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.35
Consensus pattern (88 bp):
AAAAATGTAATTTTTGAAAAGTTCAAGGGTCAAAATGGAATTTTTAGAAAGTTAAGGGGTTAAAA
TGTAATTTTTGGAAAATTACGAT
Found at i:3442128 original size:59 final size:58
Alignment explanation
Indices: 3441831--3442149 Score: 226
Period size: 59 Copynumber: 5.4 Consensus size: 58
3441821 TGTAAGTTCG
* * ** *
3441831 GGGGT-AAAATGGTAATTTTTAGGAAGTTCGAGGTCAAAAATGGAATTTTTGGAAGTCCAA
1 GGGGTCAAAATGGTAATTTTTAGAAAATTCGA--TCAAAAATGGAATTTTTAAAAGT-TAA
* * * **
3441891 -AGGT-AAAATGGTAATTTTTA-AAAAGTTCGGGGTCAAAAATGTAATTTTTAAAAGTTCG
1 GGGGTCAAAATGGTAATTTTTAGAAAA-TTC--GATCAAAAATGGAATTTTTAAAAGTTAA
* * ** **
3441949 GGGGT-AAAATGGTAATGTTTAGAAAGTTCAGAGTCAAAAATGGAATTTTTGGAAGTTTG
1 GGGGTCAAAATGGTAATTTTTAGAAAATTC-GA-TCAAAAATGGAATTTTTAAAAGTTAA
* * * * *
3442008 GGGGT-GAAATGGTAATTTTTAGAAAGTTTTGGGTCAAAAATGGAATTTTTAGAAGTTAA
1 GGGGTCAAAATGGTAATTTTTAGAAA--ATTCGATCAAAAATGGAATTTTTAAAAGTTAA
* * *
3442067 GGGGT-AAGATGGTAATTTTTGGAAAATTACGAT-AAAAATGTAATTTTTGAAAAGTTCAA
1 GGGGTCAAAATGGTAATTTTTAGAAAATT-CGATCAAAAATGGAATTTTT-AAAAGTT-AA
*
3442126 -GGGTCAAAAT-GTAATTTTTGGAAA
1 GGGGTCAAAATGGTAATTTTTAGAAA
3442150 GTTAAGGGGT
Statistics
Matches: 211, Mismatches: 36, Indels: 26
0.77 0.13 0.10
Matches are distributed among these distances:
57 16 0.08
58 29 0.14
59 159 0.75
60 4 0.02
61 3 0.01
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.33
Consensus pattern (58 bp):
GGGGTCAAAATGGTAATTTTTAGAAAATTCGATCAAAAATGGAATTTTTAAAAGTTAA
Found at i:3442137 original size:30 final size:30
Alignment explanation
Indices: 3441832--3442195 Score: 158
Period size: 30 Copynumber: 12.3 Consensus size: 30
3441822 GTAAGTTCGG
* *
3441832 GGGT-AAAATGGTAATTTTT-AGGAAGTTCGA
1 GGGTCAAAAT-GTAATTTTTGA-AAAGTTCAA
* * *
3441862 -GGTCAAAAATGGAATTTTTG-GAAGTCCAA
1 GGGTC-AAAATGTAATTTTTGAAAAGTTCAA
* * *
3441891 AGGT-AAAATGGTAATTTTTAAAAAGTTC-G
1 GGGTCAAAAT-GTAATTTTTGAAAAGTTCAA
**
3441920 GGGTCAAAAATGTAATTTTT-AAAAGTTCGG
1 GGGTC-AAAATGTAATTTTTGAAAAGTTCAA
*
3441950 GGGT-AAAATGGTAATGTTT-AGAAAGTTC-A
1 GGGTCAAAAT-GTAATTTTTGA-AAAGTTCAA
* * * ***
3441979 GAGTCAAAAATGGAATTTTTG-GAAGTTTGG
1 GGGTC-AAAATGTAATTTTTGAAAAGTTCAA
* **
3442009 GGGT-GAAATGGTAATTTTT-AGAAAGTT-TT
1 GGGTCAAAAT-GTAATTTTTGA-AAAGTTCAA
* *
3442038 GGGTCAAAAATGGAATTTTT-AGAAGTT-AA
1 GGGTC-AAAATGTAATTTTTGAAAAGTTCAA
*
3442067 GGGGT-AAGATGGTAATTTTTGGAAAA-TT--A
1 -GGGTCAAAAT-GTAATTTTT-GAAAAGTTCAA
* * *
3442096 CGATAAAAATGTAATTTTTGAAAAGTTCAA
1 GGGTCAAAATGTAATTTTTGAAAAGTTCAA
*
3442126 GGGTCAAAATGTAATTTTTGGAAAGTT-AA
1 GGGTCAAAATGTAATTTTTGAAAAGTTCAA
* * * * *
3442155 GGGGTTAAAATGTGATTTTTGGAAAGTTTAG
1 -GGGTCAAAATGTAATTTTTGAAAAGTTCAA
3442186 GGGTCAAAAT
1 GGGTCAAAAT
3442196 ATGATTTCTA
Statistics
Matches: 262, Mismatches: 42, Indels: 60
0.72 0.12 0.16
Matches are distributed among these distances:
27 5 0.02
28 31 0.12
29 78 0.30
30 125 0.48
31 23 0.09
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.34
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTTGAAAAGTTCAA
Found at i:3442213 original size:60 final size:60
Alignment explanation
Indices: 3442101--3442217 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
3442091 AATTACGATA
* * *
3442101 AAAATGTAATTTTTGAAAAGTTCAAGGGTCAAAATGTAATTTTTGGAAAGTTAAGGGGTT
1 AAAATGTAATTTTTGAAAAGTTCAAGGGTCAAAATATAATTTCTAGAAAGTTAAGGGGTT
* * * * * *
3442161 AAAATGTGATTTTTGGAAAGTTTAGGGGTCAAAATATGATTTCTAGATAGTTAAGGG
1 AAAATGTAATTTTTGAAAAGTTCAAGGGTCAAAATATAATTTCTAGAAAGTTAAGGG
3442218 ACCTATTAGG
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (60 bp):
AAAATGTAATTTTTGAAAAGTTCAAGGGTCAAAATATAATTTCTAGAAAGTTAAGGGGTT
Found at i:3443852 original size:12 final size:12
Alignment explanation
Indices: 3443837--3443971 Score: 100
Period size: 12 Copynumber: 11.6 Consensus size: 12
3443827 GTATTTGGAC
3443837 TTTAAAATTAAA
1 TTTAAAATTAAA
*
3443849 TTTAAAATTAAG
1 TTTAAAATTAAA
*
3443861 TTTAAAA-T-CA
1 TTTAAAATTAAA
*
3443871 TTTCAAATTTAAA
1 TTT-AAAATTAAA
* *
3443884 -CTAAATTTAAA
1 TTTAAAATTAAA
*
3443895 TTTAAAA-CAAA
1 TTTAAAATTAAA
*
3443906 TTTAAATTTAAA
1 TTTAAAATTAAA
** *
3443918 AATAAATTTAAA
1 TTTAAAATTAAA
*
3443930 TTTAAATTTAAA
1 TTTAAAATTAAA
* *
3443942 -GTAAATTTAAA
1 TTTAAAATTAAA
*
3443953 TTTAAAAATAAA
1 TTTAAAATTAAA
3443965 TTTAAAA
1 TTTAAAA
3443972 CCAATTTAAA
Statistics
Matches: 98, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
10 3 0.03
11 32 0.33
12 62 0.63
13 1 0.01
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (12 bp):
TTTAAAATTAAA
Found at i:3443882 original size:41 final size:38
Alignment explanation
Indices: 3443837--3443999 Score: 129
Period size: 40 Copynumber: 4.2 Consensus size: 38
3443827 GTATTTGGAC
*
3443837 TTTAAAATTAAATTTAAAATTAAGTTTAAAATCATTTCAAA
1 TTTAAAAATAAATTTAAAATTAA-TTTAAAAT-ATTT-AAA
* *
3443878 TTT-AAACTAAATTTAAATTTAA---AACAA-ATTTAAA
1 TTTAAAAATAAATTTAAAATTAATTTAA-AATATTTAAA
* *
3443912 TTTAAAAATAAATTTAAATTTAAATTTAAAGTAAATTTAAA
1 TTTAAAAATAAATTTAAAATT-AATTTAAA--ATATTTAAA
** * *
3443953 TTTAAAAATAAATTTAAAACCAATTTAAACTTAATATAAA
1 TTTAAAAATAAATTTAAAATTAATTTAAA-AT-ATTTAAA
3443993 TTTAAAA
1 TTTAAAA
3444000 TCAAAAGTTT
Statistics
Matches: 102, Mismatches: 10, Indels: 21
0.77 0.08 0.16
Matches are distributed among these distances:
34 6 0.06
35 20 0.20
36 4 0.04
37 2 0.02
38 1 0.01
39 2 0.02
40 39 0.38
41 28 0.27
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (38 bp):
TTTAAAAATAAATTTAAAATTAATTTAAAATATTTAAA
Found at i:3443948 original size:17 final size:17
Alignment explanation
Indices: 3443837--3443998 Score: 121
Period size: 17 Copynumber: 9.4 Consensus size: 17
3443827 GTATTTGGAC
* *
3443837 TTTAAAATTAAATTTAAA
1 TTTAAATTTAAA-ATAAA
* * *
3443855 ATTAAGTTTAAAAT-CA
1 TTTAAATTTAAAATAAA
*
3443871 TTTCAAATTTAAACTAAA
1 TTT-AAATTTAAAATAAA
*
3443889 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
3443906 TTTAAATTTAAAAATAAA
1 TTTAAATTT-AAAATAAA
*
3443924 TTTAAATTTAAATTTAAA
1 TTTAAATTTAAA-ATAAA
* *
3443942 -GTAAATTTAAATTTAAA
1 TTTAAATTTAAA-ATAAA
** **
3443959 AATAAATTTAAAACCAA
1 TTTAAATTTAAAATAAA
* *
3443976 TTTAAACTTAATATAAA
1 TTTAAATTTAAAATAAA
3443993 TTTAAA
1 TTTAAA
3443999 ATCAAAAGTT
Statistics
Matches: 115, Mismatches: 24, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
16 3 0.03
17 69 0.60
18 43 0.37
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:3443964 original size:23 final size:23
Alignment explanation
Indices: 3443920--3443964 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3443910 AATTTAAAAA
**
3443920 TAAATTTAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAAATAAAG
3443943 TAAATTTAAATTTAAAAATAAA
1 TAAATTTAAATTTAAAAATAAA
3443965 TTTAAAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TAAATTTAAATTTAAAAATAAAG
Found at i:3443977 original size:29 final size:29
Alignment explanation
Indices: 3443875--3444004 Score: 113
Period size: 29 Copynumber: 4.5 Consensus size: 29
3443865 AAATCATTTC
*
3443875 AAATTT-AAACTAAATTTAAATTTAAA-AC
1 AAATTTAAAAC-AAATTTAAATTTAAATAT
** ** *
3443903 AAATTTAAATTTAAAAATAAATTTAAATTT
1 AAATTTAAA-ACAAATTTAAATTTAAATAT
** *
3443933 AAATTTAAAGTAAATTTAAATTTAAAAAT
1 AAATTTAAAACAAATTTAAATTTAAATAT
* *
3443962 AAATTTAAAACCAATTTAAACTT-AATAT
1 AAATTTAAAACAAATTTAAATTTAAATAT
3443990 AAATTTAAAATCAAA
1 AAATTTAAAA-CAAA
3444005 AGTTTGATCC
Statistics
Matches: 81, Mismatches: 17, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
28 20 0.25
29 52 0.64
30 9 0.11
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.37
Consensus pattern (29 bp):
AAATTTAAAACAAATTTAAATTTAAATAT
Found at i:3444668 original size:209 final size:209
Alignment explanation
Indices: 3444302--3444915 Score: 996
Period size: 209 Copynumber: 2.9 Consensus size: 209
3444292 TTCCAATGGT
* * *
3444302 TTGGTATCATTGATTTGGTCTACTTCTCAGTGTCTCATCAGGAAGATGACCGT-ATCACTTGTTT
1 TTGGTTTCATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACC-TCATCACTTGTTT
* * ** *
3444366 CAATCCGCTTCTCTATATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGA
65 CAATCCGCTTCTCTGTATCTCATCAGGAAGATGGGTTTGGTCCACTTCTCAGTATCTCATCAGGA
*
3444431 AGCTAACCATTTTACTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGAT
130 AGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGAT
3444496 TTGCTCACTTGGAGC
195 TTGCTCACTTGGAGC
* * *
3444511 TTGGTTTCATTGATCTGGTCTTCTTCTCAGTATCTCATTAGGAAGATGACCTCATCACTTATTTC
1 TTGGTTTCATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCTCATCACTTGTTTC
* *
3444576 AATCCGCTTCTCTGTATCTCATTAGGAAGTTGGGTTTGGTCCACTTCTCAGTATCTCATCAGGAA
66 AATCCGCTTCTCTGTATCTCATCAGGAAGATGGGTTTGGTCCACTTCTCAGTATCTCATCAGGAA
*
3444641 GCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATT
131 GCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATT
3444706 TGCTCACTTGGAGC
196 TGCTCACTTGGAGC
* *
3444720 TTGGTTTCTTTGATTTAGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCTCATCACTTGTTTC
1 TTGGTTTCATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCTCATCACTTGTTTC
* * * *
3444785 AATCCGCTTCTCCGTATCTCATCAAGAAGCTGGGTTTGGTCCACTTCTCAGTATCTCATTAGGAA
66 AATCCGCTTCTCTGTATCTCATCAGGAAGATGGGTTTGGTCCACTTCTCAGTATCTCATCAGGAA
* * *
3444850 GCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGATTCAAAGATT
131 GCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATT
3444915 T
196 T
3444916 TCTCGTATCG
Statistics
Matches: 375, Mismatches: 29, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
208 1 0.00
209 374 1.00
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.36
Consensus pattern (209 bp):
TTGGTTTCATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCTCATCACTTGTTTC
AATCCGCTTCTCTGTATCTCATCAGGAAGATGGGTTTGGTCCACTTCTCAGTATCTCATCAGGAA
GCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATT
TGCTCACTTGGAGC
Done.