Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 131 of 136
Found at i:45229977 original size:100 final size:101
Alignment explanation
Indices: 45229820--45230024 Score: 385
Period size: 100 Copynumber: 2.0 Consensus size: 101
45229810 AAATCGAGTG
45229820 AAAAATTTCGAGTTAATTGAGTTCACAAGTCCTATTTTATCATCCTAACTCAATTTTAAATTTTT
1 AAAAATTTCGAG-TAATTGAGTTCACAAGTCCTATTTTATCATCCTAACTCAATTTTAAATTTTT
45229885 TTTAAATTGAGTCAAGTTGAATCGAGTAAAATTATTC
65 TTTAAATTGAGTCAAGTTGAATCGAGTAAAATTATTC
*
45229922 AAAAATTTCGA-TAATTGAGTTCACAAGTCCTATTTTATTATCCTAACTCAATTTTAAATTTTTT
1 AAAAATTTCGAGTAATTGAGTTCACAAGTCCTATTTTATCATCCTAACTCAATTTTAAATTTTTT
45229986 TTAAATTGAGTCAAGTTGAATCGAGTAAAATTATTC
66 TTAAATTGAGTCAAGTTGAATCGAGTAAAATTATTC
45230022 AAA
1 AAA
45230025 TTAAATTCAA
Statistics
Matches: 102, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
100 91 0.89
102 11 0.11
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (101 bp):
AAAAATTTCGAGTAATTGAGTTCACAAGTCCTATTTTATCATCCTAACTCAATTTTAAATTTTTT
TTAAATTGAGTCAAGTTGAATCGAGTAAAATTATTC
Found at i:45230052 original size:13 final size:13
Alignment explanation
Indices: 45230036--45230060 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45230026 TAAATTCAAA
45230036 AAATAAAAATATC
1 AAATAAAAATATC
45230049 AAATAAAAATAT
1 AAATAAAAATAT
45230061 TATTACAATA
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:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAAAATATC
Found at i:45233693 original size:31 final size:30
Alignment explanation
Indices: 45233642--45233780 Score: 115
Period size: 31 Copynumber: 4.6 Consensus size: 30
45233632 TTGTAAGATT
45233642 AAAA-TTATACTTTAAGTTATTAAATTATTA
1 AAAATTTATA-TTTAAGTTATTAAATTATTA
*
45233672 ATAAATTTATATTTTAA-TTATTTAATT-TTA
1 A-AAATTTATA-TTTAAGTTATTAAATTATTA
* **
45233702 AAAATTTGTAAAATAA-TTATTAAATTATTTA
1 AAAATTTAT-ATTTAAGTTATTAAATTA-TTA
* * *
45233733 AAAGTTTTTATTTAAGTTATTAAATTATTTG
1 AAAATTTATATTTAAGTTATTAAATTA-TTA
* *
45233764 AAAGTTTTTATTTAAGT
1 AAAATTTATATTTAAGT
45233781 CATCGAGTTG
Statistics
Matches: 92, Mismatches: 11, Indels: 11
0.81 0.10 0.10
Matches are distributed among these distances:
29 19 0.21
30 10 0.11
31 53 0.58
32 10 0.11
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (30 bp):
AAAATTTATATTTAAGTTATTAAATTATTA
Found at i:45236356 original size:19 final size:18
Alignment explanation
Indices: 45236322--45236359 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
45236312 AACACTTGTC
45236322 TTTTTAATTTTATAATTA
1 TTTTTAATTTTATAATTA
45236340 TTTTTACATCTTT-TAATTA
1 TTTTTA-AT-TTTATAATTA
45236359 T
1 T
45236360 AAATTTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 9 0.50
20 3 0.17
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTTAATTTTATAATTA
Found at i:45242639 original size:17 final size:17
Alignment explanation
Indices: 45242617--45242651 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
45242607 TAAATTAATT
*
45242617 TGAATTGAATTAAAAGA
1 TGAATTAAATTAAAAGA
*
45242634 TGAATTAAATTAATAGA
1 TGAATTAAATTAAAAGA
45242651 T
1 T
45242652 AACACAATCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (17 bp):
TGAATTAAATTAAAAGA
Found at i:45246337 original size:19 final size:19
Alignment explanation
Indices: 45246292--45246329 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
45246282 ACTGTTAAAT
*
45246292 TATATTATTGCCCTTAGTA
1 TATATTATTGCCCTAAGTA
45246311 TATATTATTAGCCCTAAGT
1 TATATTATT-GCCCTAAGT
45246330 TTAATTATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.45
Consensus pattern (19 bp):
TATATTATTGCCCTAAGTA
Found at i:45257851 original size:22 final size:22
Alignment explanation
Indices: 45257826--45257872 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
45257816 TTGATTTTCC
*
45257826 TTAAAATTATTTAAATAATTTA
1 TTAAAATTATTAAAATAATTTA
45257848 TTAAAATTATTAAAATAATTTA
1 TTAAAATTATTAAAATAATTTA
45257870 TTA
1 TTA
45257873 TACTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAAAATTATTAAAATAATTTA
Found at i:45258644 original size:8 final size:8
Alignment explanation
Indices: 45258633--45258663 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
45258623 AATTTTATTA
45258633 TTTTTAAT
1 TTTTTAAT
45258641 TTTTTAAT
1 TTTTTAAT
45258649 TTTTTAAT
1 TTTTTAAT
45258657 TTTTTAA
1 TTTTTAA
45258664 AATTAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTAAT
Found at i:45260764 original size:26 final size:26
Alignment explanation
Indices: 45260734--45260795 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
45260724 TAAAAAAATA
45260734 ACCAAAATATTATAACTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTATTT
* *
45260760 ACCAAATTATTATAATTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTATTT
*
45260786 ATCAAAATAT
1 ACCAAAATAT
45260796 ACAAAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (26 bp):
ACCAAAATATTATAACTTTTTTATTT
Found at i:45274629 original size:28 final size:27
Alignment explanation
Indices: 45274567--45274629 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
45274557 AATTACATTT
**
45274567 AAAATTAAAATATAAAAATTAAGTCTC
1 AAAATTAAAATATAAAAATTAAAACTC
* * *
45274594 AAATTTAAACATATTAAAATTAAAACTG
1 AAAATTAAA-ATATAAAAATTAAAACTC
45274622 AAAATTAA
1 AAAATTAA
45274630 CCATTTTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
27 8 0.28
28 21 0.72
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.30
Consensus pattern (27 bp):
AAAATTAAAATATAAAAATTAAAACTC
Found at i:45275259 original size:14 final size:14
Alignment explanation
Indices: 45275240--45275273 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
45275230 CATGATATAA
*
45275240 TTAAAAAATAGAAT
1 TTAAAAAATAAAAT
45275254 TTAAAAAATAAAAT
1 TTAAAAAATAAAAT
45275268 TCTAAA
1 T-TAAA
45275274 TGAAGTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (14 bp):
TTAAAAAATAAAAT
Found at i:45278567 original size:20 final size:21
Alignment explanation
Indices: 45278519--45278569 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
45278509 TCAATAAATT
*
45278519 ATTTAAATAAATAATAATTAA
1 ATTTAAATAAAAAATAATTAA
* *
45278540 ATTCAAATAAAAAATTATT-A
1 ATTTAAATAAAAAATAATTAA
45278560 ATTTAAATAA
1 ATTTAAATAA
45278570 CTAAAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
ATTTAAATAAAAAATAATTAA
Found at i:45284081 original size:24 final size:24
Alignment explanation
Indices: 45284045--45284095 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
45284035 AACGAAGGAT
*
45284045 GGACCTTTCGGTGATGGAATATCA
1 GGACCTTTAGGTGATGGAATATCA
* *
45284069 GGACTTTTAGGTGGTGGAATATCA
1 GGACCTTTAGGTGATGGAATATCA
45284093 GGA
1 GGA
45284096 GGGATGCTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.12, G:0.33, T:0.29
Consensus pattern (24 bp):
GGACCTTTAGGTGATGGAATATCA
Found at i:45285122 original size:26 final size:27
Alignment explanation
Indices: 45285093--45285145 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
45285083 TATTCTTTAT
*
45285093 ATATG-AAATTTTTATAATTTTT-TAAA
1 ATATGTAAATTTTGA-AATTTTTATAAA
45285119 ATATGTAAATTTTGAAATTTTTATAAA
1 ATATGTAAATTTTGAAATTTTTATAAA
45285146 TATTTTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (27 bp):
ATATGTAAATTTTGAAATTTTTATAAA
Found at i:45288335 original size:20 final size:20
Alignment explanation
Indices: 45288294--45288335 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
45288284 ATTTTTGGAC
* *
45288294 AAAAATCTATTTTATTATTT
1 AAAAATATATTTTATTAATT
45288314 AAAAATATA-TTTATATAATT
1 AAAAATATATTTTAT-TAATT
45288334 AA
1 AA
45288336 TTTTTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
AAAAATATATTTTATTAATT
Found at i:45294186 original size:216 final size:208
Alignment explanation
Indices: 45293793--45294189 Score: 455
Period size: 216 Copynumber: 1.9 Consensus size: 208
45293783 GCCTTGAGAT
* *
45293793 TTTAGGGGGATTTGGATAGGAGGTTGTCATTGGTGAAGTTCAATATGAATTTAATGGTTTTTGTA
1 TTTAGGGGGATTTGGATAGGAGGTTGTCATTGATGAAGTTCAATATGAATTTAATGCTTTTTGTA
* * * * *
45293858 TTGGAGTTCCAAAAATGAATTATCAACAGGTGATCAGAGAAAGTGGCAGTGGACATCTCCCTAGG
66 TTGGAGTTCCAAAAATCAATTACCAACAGGTGATCAAAGAAAGTGGCAGCGGACATCTCCCCAGG
* ** **
45293923 CATTTGGACTGAATTTGAATCTAGGAGTCATCACTATTGGGAGGGCTTTACCTGAATACCACTCT
131 CATTTAGACTGAATTCAAATCTAGGAGTCATCACTATTGAAAGGGCTTTACCTGAATACCACTCT
45293988 GGCCTGAACAAGA
196 GGCCTGAACAAGA
* * *
45294001 TTTAGGGGGATTTGGATATGAGGGGTTGTCATTGATGAAGTTTATATTTGAATTTAATGCTTTTT
1 TTTAGGGGGATTTGGATA-G-GAGGTTGTCATTGATGAAGTTCA-ATATGAATTTAATGCTTTTT
* *
45294066 GTATTGGTGAAGTT-CAGAAGA-CAATTTACCAACAGGTGATCAAA-AGAAGTGGC-GCGGTACT
63 GTATT-G-G-AGTTCCA-AAAATCAA-TTACCAACAGGTGATCAAAGA-AAGTGGCAGCGG-ACA
* *
45294127 TCTTCCCCCGGGCATTTAGA-TTAAGTTCAAATCTTA-GAGTCATCACTATTGAAAGGGCTTTAC
121 TC-T-CCCCAGGCATTTAGACTGAA-TTCAAATC-TAGGAGTCATCACTATTGAAAGGGCTTTAC
45294190 TAAATACTAC
Statistics
Matches: 156, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
208 18 0.12
209 1 0.01
210 20 0.13
211 23 0.15
212 1 0.01
213 9 0.06
214 35 0.22
215 4 0.03
216 43 0.28
217 2 0.01
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.32
Consensus pattern (208 bp):
TTTAGGGGGATTTGGATAGGAGGTTGTCATTGATGAAGTTCAATATGAATTTAATGCTTTTTGTA
TTGGAGTTCCAAAAATCAATTACCAACAGGTGATCAAAGAAAGTGGCAGCGGACATCTCCCCAGG
CATTTAGACTGAATTCAAATCTAGGAGTCATCACTATTGAAAGGGCTTTACCTGAATACCACTCT
GGCCTGAACAAGA
Found at i:45296533 original size:21 final size:20
Alignment explanation
Indices: 45296509--45296551 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
45296499 ATCATTTCTT
* *
45296509 ATTTAATTATTTCATATTAAA
1 ATTTAAATATTT-AAATTAAA
45296530 ATTTAAATATTTAAATTAAA
1 ATTTAAATATTTAAATTAAA
45296550 AT
1 AT
45296552 AAACTAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTAAATATTTAAATTAAA
Found at i:45305652 original size:35 final size:35
Alignment explanation
Indices: 45305606--45305674 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
45305596 GGAAAAAAAG
45305606 TTTACCGCCACCGGAAAACAGAGGAGCTTCAACCT
1 TTTACCGCCACCGGAAAACAGAGGAGCTTCAACCT
*
45305641 TTTACCGCCACCGGAAAACAGAGGAGTTTCAACC
1 TTTACCGCCACCGGAAAACAGAGGAGCTTCAACC
45305675 AGTGTCACTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.32, C:0.30, G:0.20, T:0.17
Consensus pattern (35 bp):
TTTACCGCCACCGGAAAACAGAGGAGCTTCAACCT
Found at i:45309701 original size:20 final size:20
Alignment explanation
Indices: 45309673--45309745 Score: 57
Period size: 20 Copynumber: 3.7 Consensus size: 20
45309663 AGTTTTTTAT
45309673 TTTCTTATAATTTTTTAATAA
1 TTTC-TATAATTTTTTAATAA
45309694 TTTCTAT-A--TTTTAAT-A
1 TTTCTATAATTTTTTAATAA
*
45309710 TTT-TATAATAAATTTTAATAA
1 TTTCTATAAT--TTTTTAATAA
*
45309731 TTTTCTAAAATTTTT
1 -TTTCTATAATTTTT
45309746 ATATATGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 16
0.70 0.03 0.27
Matches are distributed among these distances:
15 3 0.07
16 5 0.12
17 7 0.17
19 1 0.02
20 10 0.24
21 8 0.19
22 3 0.07
23 5 0.12
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTCTATAATTTTTTAATAA
Found at i:45309728 original size:10 final size:9
Alignment explanation
Indices: 45309685--45309734 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
45309675 TCTTATAATT
45309685 TTTTAATAA
1 TTTTAATAA
45309694 TTTCT-AT-A
1 TTT-TAATAA
*
45309702 TTTTAATAT
1 TTTTAATAA
45309711 TTTATAATAAA
1 TTT-TAAT-AA
45309722 TTTTAATAA
1 TTTTAATAA
45309731 TTTT
1 TTTT
45309735 CTAAAATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
7 1 0.03
8 6 0.18
9 14 0.41
10 9 0.26
11 4 0.12
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTTAATAA
Found at i:45309746 original size:20 final size:20
Alignment explanation
Indices: 45309684--45309746 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
45309674 TTCTTATAAT
*
45309684 TTTTTAATAA-TTTCT-ATA
1 TTTTTAATAATTTTCTAAAA
*
45309702 -TTTTAAT-ATTTTATAATAA
1 TTTTTAATAATTTTCTAA-AA
*
45309721 ATTTTAATAATTTTCTAAAA
1 TTTTTAATAATTTTCTAAAA
45309741 TTTTTA
1 TTTTTA
45309747 TATATGTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
16 1 0.03
17 11 0.31
18 1 0.03
19 1 0.03
20 14 0.39
21 8 0.22
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTAATAATTTTCTAAAA
Found at i:45310063 original size:30 final size:32
Alignment explanation
Indices: 45310025--45310099 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
45310015 CTCTTTTATA
45310025 ATAAATTTTAACAAATG-TTT-T-TA-TGTTTT
1 ATAAATTTTAA-AAATGATTTCTATATTGTTTT
*
45310054 TTAATATTTTAAAAATGATTTCTATATTGTTTT
1 ATAA-ATTTTAAAAATGATTTCTATATTGTTTT
45310087 ATAAATTTTAAAA
1 ATAAATTTTAAAA
45310100 TTTTTCTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 8 0.21
30 10 0.26
31 1 0.03
32 11 0.28
33 9 0.23
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (32 bp):
ATAAATTTTAAAAATGATTTCTATATTGTTTT
Found at i:45310096 original size:32 final size:28
Alignment explanation
Indices: 45310025--45310122 Score: 103
Period size: 26 Copynumber: 3.4 Consensus size: 28
45310015 CTCTTTTATA
45310025 ATAAATTTTAACAAATGTTTTTATGTTTT
1 ATAAATTTTAA-AAATGTTTTTATGTTTT
*
45310054 TTAATATTTTAAAAATGATTTCTATATTGTTTT
1 ATAA-ATTTTAAAAATG-TTT-T-TA-TGTTTT
45310087 ATAAATTTT-AAAAT-TTTTCTAT-TTTT
1 ATAAATTTTAAAAATGTTTT-TATGTTTT
45310113 ATAAATTTTA
1 ATAAATTTTA
45310123 TATTTTATAA
Statistics
Matches: 60, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
26 13 0.22
27 1 0.02
28 3 0.05
29 11 0.18
30 10 0.17
31 6 0.10
32 7 0.12
33 9 0.15
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (28 bp):
ATAAATTTTAAAAATGTTTTTATGTTTT
Found at i:45310135 original size:19 final size:17
Alignment explanation
Indices: 45310092--45310151 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
45310082 GTTTTATAAA
*
45310092 TTTTA-AAATTTTTCTAT
1 TTTTATAAA-TTTTATAT
45310109 TTTTATAAATTTTATAT
1 TTTTATAAATTTTATAT
* *
45310126 TTTATAATAAATTTTGTTT
1 TTT-T-ATAAATTTTATAT
45310145 TTTTATA
1 TTTTATA
45310152 TCTCTAACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 18 0.49
18 5 0.14
19 14 0.38
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTATAAATTTTATAT
Found at i:45310278 original size:27 final size:28
Alignment explanation
Indices: 45310247--45310311 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
45310237 TTTTTAAATG
*
45310247 TTTTTATAAATTTTAAA-ATTTTTTATAA
1 TTTTTATAAATTTCAAATATTTTTT-TAA
*
45310275 TTTTT-TATATTTCAAATATTTTTTTAA
1 TTTTTATAAATTTCAAATATTTTTTTAA
45310302 TTTTTATAAA
1 TTTTTATAAA
45310312 AAAAGTATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 17 0.53
28 15 0.47
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (28 bp):
TTTTTATAAATTTCAAATATTTTTTTAA
Found at i:45310279 original size:9 final size:9
Alignment explanation
Indices: 45310225--45310310 Score: 52
Period size: 10 Copynumber: 9.2 Consensus size: 9
45310215 NNNNNTAACA
45310225 AATTTTTAAT
1 AATTTTT-AT
45310235 AATTTTTA-
1 AATTTTTAT
45310243 AATGTTTTTAT
1 AA--TTTTTAT
* *
45310254 AAATTTTAA
1 AATTTTTAT
45310263 AATTTTTTAT
1 AA-TTTTTAT
45310273 AATTTTT-T
1 AATTTTTAT
* *
45310281 -ATATTTCAA
1 AAT-TTTTAT
*
45310290 ATATTTTTTT
1 A-ATTTTTAT
45310300 AATTTTTAT
1 AATTTTTAT
45310309 AA
1 AA
45310311 AAAAAGTATA
Statistics
Matches: 58, Mismatches: 10, Indels: 17
0.68 0.12 0.20
Matches are distributed among these distances:
7 2 0.03
8 6 0.10
9 22 0.38
10 24 0.41
11 4 0.07
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (9 bp):
AATTTTTAT
Found at i:45310280 original size:10 final size:10
Alignment explanation
Indices: 45310225--45310283 Score: 61
Period size: 10 Copynumber: 6.1 Consensus size: 10
45310215 NNNNNTAACA
*
45310225 AATTTTTAAT
1 AATTTTTTAT
45310235 AA-TTTTTA-
1 AATTTTTTAT
45310243 AATGTTTTTAT
1 AAT-TTTTTAT
* *
45310254 AA-ATTTTAA
1 AATTTTTTAT
45310263 AATTTTTTAT
1 AATTTTTTAT
45310273 AATTTTTTAT
1 AATTTTTTAT
45310283 A
1 A
45310284 TTTCAAATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
8 2 0.05
9 12 0.30
10 24 0.60
11 2 0.05
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (10 bp):
AATTTTTTAT
Found at i:45310281 original size:20 final size:19
Alignment explanation
Indices: 45310224--45310279 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
45310214 NNNNNNTAAC
*
45310224 AAATTTTTAATAATTTTT-
1 AAATTTTTTATAATTTTTA
*
45310242 AAATGTTTTTATAAATTTTA
1 AAAT-TTTTTATAATTTTTA
45310262 AAATTTTTTATAATTTTT
1 AAATTTTTTATAATTTTT
45310280 TATATTTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 4 0.12
19 25 0.76
20 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
AAATTTTTTATAATTTTTA
Found at i:45310450 original size:36 final size:36
Alignment explanation
Indices: 45310409--45310478 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
45310399 TGAAGCTCAT
*
45310409 AATAACAAATAAAATACGGCTTGGACGGCTTGGCAA
1 AATAACAAATAAAATACGGCTTGGACAGCTTGGCAA
45310445 AATAACAAATAAAATACGGCTTGGACAGCTTGGC
1 AATAACAAATAAAATACGGCTTGGACAGCTTGGC
45310479 TCGGAAAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.20
Consensus pattern (36 bp):
AATAACAAATAAAATACGGCTTGGACAGCTTGGCAA
Found at i:45317891 original size:11 final size:11
Alignment explanation
Indices: 45317875--45317900 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
45317865 TAAAAATTAA
45317875 AAAAGTATTTT
1 AAAAGTATTTT
45317886 AAAAGTATTTT
1 AAAAGTATTTT
45317897 AAAA
1 AAAA
45317901 ATAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:45327512 original size:1 final size:1
Alignment explanation
Indices: 45327506--45327561 Score: 76
Period size: 1 Copynumber: 56.0 Consensus size: 1
45327496 CCCATCATCC
* * * *
45327506 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAGAAAGAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
45327562 GCTCCCTATT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:45340524 original size:23 final size:23
Alignment explanation
Indices: 45340498--45340543 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
45340488 CTTGGTATTT
*
45340498 CAAGTGGCAGCGATCAGACAACC
1 CAAGTGACAGCGATCAGACAACC
45340521 CAAGTGACAGCGATCAGACAACC
1 CAAGTGACAGCGATCAGACAACC
45340544 GGTTCGAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.30, G:0.24, T:0.09
Consensus pattern (23 bp):
CAAGTGACAGCGATCAGACAACC
Found at i:45342653 original size:50 final size:50
Alignment explanation
Indices: 45342534--45342772 Score: 255
Period size: 50 Copynumber: 4.6 Consensus size: 50
45342524 GGTAAAAACA
* * * ** *
45342534 TGCCAAAGCCATGTCCCATACATGGTCTTACATGGGATGTTCTCATGTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* * *
45342585 TTTCC-ATGCCATGTCCCAGACATGGTCTTACGGGGGACCTTTCATCTCGG
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
45342635 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
45342685 TGCCCATGCCATGTCCCAGACATGGTTTTACAGGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATCTC--GG
* * *
45342740 ATGCCAATGTCATGTCCCAAACATGGTTTTACA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACA
45342773 TGAGATCTCT
Statistics
Matches: 159, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
49 3 0.02
50 89 0.56
51 28 0.18
52 3 0.02
53 5 0.03
55 2 0.01
56 29 0.18
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:45342721 original size:100 final size:105
Alignment explanation
Indices: 45342533--45342779 Score: 306
Period size: 100 Copynumber: 2.4 Consensus size: 105
45342523 TGGTAAAAAC
* ** * **
45342533 ATGCCAAAGCCATGTCCCATACATGGTCTTACATGGGATGTTCTCATGTCGGTTTCCATGCCATG
1 ATGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATCCTCTCATCTCGGTGCCCATGCCATG
*
45342598 TCCCAGACATGGTCTTACGGGGGACCT-T-TCATCTC-GG
66 TCCCAGACATGGTCTTACAGGGGACCTCTATCATCTCAGG
* *
45342635 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATCCTCTCATCTCGGTGCCCATGCCATG
* *
45342698 TCCCAGACATGGTTTTACAGGGGACCTCTCATGATCTCAAGG
66 TCCCAGACATGGTCTTACAGGGGACCTCT-ATCATCTC-AGG
* * * *
45342740 ATGCCAATGTCATGTCCCAAACATGGTTTTACATGAGATC
1 ATGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATC
45342780 TCTTTACCCA
Statistics
Matches: 123, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
100 46 0.37
101 36 0.29
103 6 0.05
105 2 0.02
106 32 0.26
107 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (105 bp):
ATGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATCCTCTCATCTCGGTGCCCATGCCATG
TCCCAGACATGGTCTTACAGGGGACCTCTATCATCTCAGG
Found at i:45343170 original size:29 final size:31
Alignment explanation
Indices: 45343120--45343177 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
45343110 CCTCGACTCT
* *
45343120 AACTTTTTCAAAATTATGA-TTTTGCCCCTA
1 AACTTTTACAAAATTATCATTTTTGCCCCTA
*
45343150 AACTTTTACATAATTA-CATTTTTGCCCC
1 AACTTTTACAAAATTATCATTTTTGCCCC
45343178 CAAGGCTCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.43
Consensus pattern (31 bp):
AACTTTTACAAAATTATCATTTTTGCCCCTA
Found at i:45345648 original size:6 final size:6
Alignment explanation
Indices: 45345637--45345670 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
45345627 TATAACACTA
* *
45345637 AAAATT AAAATT AAAATT AAAATG AAAATG AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAA
45345671 ATGATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (6 bp):
AAAATT
Found at i:45345681 original size:2 final size:2
Alignment explanation
Indices: 45345674--45345703 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
45345664 ATGAAAAATG
45345674 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45345704 CTTCACCTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45353058 original size:15 final size:15
Alignment explanation
Indices: 45353038--45353092 Score: 65
Period size: 15 Copynumber: 3.4 Consensus size: 15
45353028 GGGGAAATTC
45353038 GAGTTAAGTACTAAT
1 GAGTTAAGTACTAAT
45353053 GAGTTAAGTACGACTAAAT
1 GAGTTAAGT---ACT-AAT
*
45353072 GAGTTAAATACTAAT
1 GAGTTAAGTACTAAT
45353087 GAGTTA
1 GAGTTA
45353093 CCCATTAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
15 18 0.51
16 3 0.09
18 3 0.09
19 11 0.31
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (15 bp):
GAGTTAAGTACTAAT
Found at i:45364455 original size:2 final size:2
Alignment explanation
Indices: 45364448--45364490 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
45364438 ATTTGTTATT
* * *
45364448 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA AA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45364490 T
1 T
45364491 TAGATAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45366169 original size:2 final size:2
Alignment explanation
Indices: 45366162--45366190 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
45366152 NNNNNNAATT
45366162 TA TA 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 TA TA T
45366191 TTCCTTGTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45366634 original size:22 final size:24
Alignment explanation
Indices: 45366607--45366658 Score: 81
Period size: 22 Copynumber: 2.2 Consensus size: 24
45366597 AATACTTCTA
45366607 TATTTAGTTTTTAAAAATA-TTTT
1 TATTTAGTTTTTAAAAATAGTTTT
*
45366630 T-TTTATTTTTTAAAAATAGTTTT
1 TATTTAGTTTTTAAAAATAGTTTT
45366653 TATTTA
1 TATTTA
45366659 AAAAAAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 16 0.62
23 6 0.23
24 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (24 bp):
TATTTAGTTTTTAAAAATAGTTTT
Found at i:45378168 original size:24 final size:25
Alignment explanation
Indices: 45378115--45378168 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
45378105 ATTGTAAAAT
* *
45378115 ATAATTTTATTTTACTTATTTTTTT
1 ATAATATTATTTTACTTATTTTTTA
45378140 A-AATATTATTTTA-TT-TTTATTTA
1 ATAATATTATTTTACTTATTT-TTTA
45378163 ATAATA
1 ATAATA
45378169 ATTCTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 3 0.12
23 6 0.24
24 15 0.60
25 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
ATAATATTATTTTACTTATTTTTTA
Found at i:45382446 original size:6 final size:6
Alignment explanation
Indices: 45382435--45382469 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
45382425 AAATATCGTA
45382435 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
45382470 ATATATATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:45387612 original size:19 final size:19
Alignment explanation
Indices: 45387588--45387656 Score: 81
Period size: 19 Copynumber: 3.6 Consensus size: 19
45387578 AAAATATAAA
45387588 ATTTAGAATTTTTATAAA-T
1 ATTTAGAATTTTTA-AAATT
45387607 ATTTAGAA-TTTTAAAATT
1 ATTTAGAATTTTTAAAATT
45387625 ATTTTA-AATTTTTGAAAATT
1 A-TTTAGAATTTTT-AAAATT
*
45387645 ATTTTGAATTTT
1 ATTTAGAATTTT
45387657 GGTTGAGAGA
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
17 3 0.07
18 9 0.20
19 19 0.43
20 13 0.30
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (19 bp):
ATTTAGAATTTTTAAAATT
Found at i:45387644 original size:20 final size:19
Alignment explanation
Indices: 45387589--45387656 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 19
45387579 AAATATAAAA
45387589 TTTAGAATTTTTATAAA-TA-
1 TTTA-AATTTTTA-AAATTAT
45387608 TTTAGAA-TTTTAAAATTAT
1 TTTA-AATTTTTAAAATTAT
45387627 TTTAAATTTTTGAAAATTAT
1 TTTAAATTTTT-AAAATTAT
*
45387647 TTTGAATTTT
1 TTTAAATTTT
45387657 GGTTGAGAGA
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
17 3 0.07
18 9 0.20
19 15 0.34
20 17 0.39
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
TTTAAATTTTTAAAATTAT
Found at i:45393567 original size:19 final size:15
Alignment explanation
Indices: 45393529--45393558 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
45393519 ATGTTTCAAC
45393529 TTAATAATGTTGTTA
1 TTAATAATGTTGTTA
45393544 TTAATGAATGTTGTT
1 TTAAT-AATGTTGTT
45393559 GTATTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (15 bp):
TTAATAATGTTGTTA
Found at i:45396770 original size:21 final size:21
Alignment explanation
Indices: 45396706--45396870 Score: 120
Period size: 21 Copynumber: 7.9 Consensus size: 21
45396696 CCGTGTTTGC
* * *
45396706 TTTCCGTTTAGCTCTCATGAGC
1 TTTCAGTTTAGCTCTTATG-GG
* * *
45396728 TTT-AG-TTAACTCATATGAG
1 TTTCAGTTTAGCTCTTATGGG
*
45396747 TTTCAGTTTAGCCCTTATGGG
1 TTTCAGTTTAGCTCTTATGGG
* *
45396768 TTTCAGTTTAGCTCTTTTGAG
1 TTTCAGTTTAGCTCTTATGGG
* *
45396789 CTTCAGTTTAACTCTTATGGG
1 TTTCAGTTTAGCTCTTATGGG
* *
45396810 TTTCCGTTTAGCTCTTATGAGC
1 TTTCAGTTTAGCTCTTATG-GG
* * * *
45396832 TTTC-GTTTAACCCTTACGGA
1 TTTCAGTTTAGCTCTTATGGG
* *
45396852 TTTCCGTTTAGCACTTATG
1 TTTCAGTTTAGCTCTTATG
45396871 TGCTTCTGTG
Statistics
Matches: 111, Mismatches: 28, Indels: 9
0.75 0.19 0.06
Matches are distributed among these distances:
19 3 0.03
20 16 0.14
21 84 0.76
22 8 0.07
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.44
Consensus pattern (21 bp):
TTTCAGTTTAGCTCTTATGGG
Found at i:45396796 original size:42 final size:42
Alignment explanation
Indices: 45396741--45396876 Score: 175
Period size: 42 Copynumber: 3.2 Consensus size: 42
45396731 AGTTAACTCA
* * *
45396741 TATGAGTTTCAGTTTAGCCCTTATGGGTTTCAGTTTAGCTCT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTTAGCTCT
* *
45396783 TTTGAGCTTCAGTTTAACTCTTATGGGTTTCCGTTTAGCTCT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTTAGCTCT
* * *
45396825 TATGAGCTTTC-GTTTAACCCTTACGGATTTCCGTTTAGCACT
1 TATGAGC-TTCAGTTTAACCCTTATGGGTTTCCGTTTAGCTCT
*
45396867 TATGTGCTTC
1 TATGAGCTTC
45396877 TGTGCAGCCT
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
41 3 0.04
42 76 0.93
43 3 0.04
ACGTcount: A:0.16, C:0.20, G:0.19, T:0.45
Consensus pattern (42 bp):
TATGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTTAGCTCT
Found at i:45396840 original size:63 final size:61
Alignment explanation
Indices: 45396704--45396840 Score: 166
Period size: 63 Copynumber: 2.2 Consensus size: 61
45396694 TTCCGTGTTT
*
45396704 GCTTTCCGTTTAGCTCTCATGAGCTTTAGTTAACTCATATGAGTTTCAGTTTAGCCCTTATG
1 GCTTT-CGTTTAGCTCTCATGAGCTTCAGTTAACTCATATGAGTTTCAGTTTAGCCCTTATG
* ** * * * *
45396766 GGTTTCAGTTTAGCTCTTTTGAGCTTCAGTTTAACTCTTATGGGTTTCCGTTTAGCTCTTATG
1 GCTTTC-GTTTAGCTCTCATGAGCTTCAG-TTAACTCATATGAGTTTCAGTTTAGCCCTTATG
45396829 AGCTTTCGTTTA
1 -GCTTTCGTTTA
45396841 ACCCTTACGG
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
61 1 0.02
62 23 0.37
63 34 0.54
64 5 0.08
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (61 bp):
GCTTTCGTTTAGCTCTCATGAGCTTCAGTTAACTCATATGAGTTTCAGTTTAGCCCTTATG
Found at i:45399050 original size:141 final size:142
Alignment explanation
Indices: 45398890--45399172 Score: 559
Period size: 141 Copynumber: 2.0 Consensus size: 142
45398880 TCATTTAATA
45398890 TTTTATACTCTTTTTAATATTTAAATATTTATTAAAATTAATTATATTTTAAGTTTATCTTAAAT
1 TTTTATACTCTTTTTAATATTTAAATATTTATTAAAATTAATTATATTTTAAGTTTATCTTAAAT
45398955 ATAAAGTTATAGATACAAAATTTTATAATATATTTTAATTAGTAAATATTACATAAAAATGTATG
66 ATAAAGTTATAGATACAAAATTTTATAATATATTTTAATTAGTAAATATTACATAAAAATGTATG
45399020 GGATTGCACAGG
131 GGATTGCACAGG
45399032 TTTTATACTC-TTTTAATATTTAAATATTTATTAAAATTAATTATATTTTAAGTTTATCTTAAAT
1 TTTTATACTCTTTTTAATATTTAAATATTTATTAAAATTAATTATATTTTAAGTTTATCTTAAAT
45399096 ATAAAGTTATAGATACAAAATTTTATAATATATTTTAATTAGTAAATATTACATAAAAATGTATG
66 ATAAAGTTATAGATACAAAATTTTATAATATATTTTAATTAGTAAATATTACATAAAAATGTATG
45399161 GGATTGCACAGG
131 GGATTGCACAGG
45399173 ATATTAAAAA
Statistics
Matches: 141, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
141 131 0.93
142 10 0.07
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.46
Consensus pattern (142 bp):
TTTTATACTCTTTTTAATATTTAAATATTTATTAAAATTAATTATATTTTAAGTTTATCTTAAAT
ATAAAGTTATAGATACAAAATTTTATAATATATTTTAATTAGTAAATATTACATAAAAATGTATG
GGATTGCACAGG
Found at i:45416217 original size:52 final size:52
Alignment explanation
Indices: 45416139--45416243 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
45416129 TTTATTGCCT
45416139 AATAAATTTTCTCAATTATGATATTATTAGACATAGCACCTGTGGAAGTTCA
1 AATAAATTTTCTCAATTATGATATTATTAGACATAGCACCTGTGGAAGTTCA
45416191 AATAAATTTTCTCAATTATGATATTATTAGACATAGCACCTGTGGAAGTTCA
1 AATAAATTTTCTCAATTATGATATTATTAGACATAGCACCTGTGGAAGTTCA
45416243 A
1 A
45416244 TTGCCTGATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (52 bp):
AATAAATTTTCTCAATTATGATATTATTAGACATAGCACCTGTGGAAGTTCA
Found at i:45422013 original size:18 final size:18
Alignment explanation
Indices: 45421992--45422033 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
45421982 TCATGCAATC
*
45421992 CATTTT-TTTACAATTGTT
1 CATTTTCTTTAAAATT-TT
45422010 CATTTTCTTTAAAATTTT
1 CATTTTCTTTAAAATTTT
45422028 CATTTT
1 CATTTT
45422034 GAGCTATACC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.24, C:0.12, G:0.02, T:0.62
Consensus pattern (18 bp):
CATTTTCTTTAAAATTTT
Found at i:45424071 original size:2 final size:2
Alignment explanation
Indices: 45424066--45424092 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
45424056 TATATATATA
45424066 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
45424093 TTGGTCGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:45424942 original size:14 final size:14
Alignment explanation
Indices: 45424923--45424953 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
45424913 AAAATTGTTG
45424923 TATATACATACATA
1 TATATACATACATA
*
45424937 TATATACATATATA
1 TATATACATACATA
45424951 TAT
1 TAT
45424954 GATGACTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (14 bp):
TATATACATACATA
Found at i:45428383 original size:24 final size:24
Alignment explanation
Indices: 45428338--45428383 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
45428328 TCCCCTTAAC
*
45428338 AAATAAACTCAATTTTATAAATAA
1 AAATAAACTAAATTTTATAAATAA
45428362 AAATAAAACTAAATTTTA-AAAT
1 AAAT-AAACTAAATTTTATAAAT
45428384 TTCCACAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (24 bp):
AAATAAACTAAATTTTATAAATAA
Found at i:45431949 original size:22 final size:22
Alignment explanation
Indices: 45431924--45432009 Score: 84
Period size: 22 Copynumber: 3.8 Consensus size: 22
45431914 TAATGAACAA
*
45431924 AGAGCAGTAAAGTGCTATACAG
1 AGAGCACTAAAGTGCTATACAG
*
45431946 AGAGCAC-AAATGTGCTAAACAG
1 AGAGCACTAAA-GTGCTATACAG
* *
45431968 AGAGCACTGACGTGCTAGTAATCAG
1 AGAGCACTAAAGTGCTA-T-A-CAG
*
45431993 AGAGCACTAACGTGCTA
1 AGAGCACTAAAGTGCTA
45432010 ATAATCAGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
21 3 0.06
22 29 0.55
23 1 0.02
24 1 0.02
25 19 0.36
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (22 bp):
AGAGCACTAAAGTGCTATACAG
Found at i:45431996 original size:25 final size:25
Alignment explanation
Indices: 45431943--45432018 Score: 95
Period size: 25 Copynumber: 3.2 Consensus size: 25
45431933 AAGTGCTATA
* *
45431943 CAGAGAGCACAAATGTGCT-A-AA-
1 CAGAGAGCACTAACGTGCTAATAAT
* *
45431965 CAGAGAGCACTGACGTGCTAGTAAT
1 CAGAGAGCACTAACGTGCTAATAAT
45431990 CAGAGAGCACTAACGTGCTAATAAT
1 CAGAGAGCACTAACGTGCTAATAAT
45432015 CAGA
1 CAGA
45432019 AAGCGCGCTA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
22 16 0.36
24 2 0.04
25 27 0.60
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (25 bp):
CAGAGAGCACTAACGTGCTAATAAT
Found at i:45432783 original size:27 final size:26
Alignment explanation
Indices: 45432745--45432801 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
45432735 AAATCCCAAA
* *
45432745 TTTTCTTTCTTTCCTTCCCT-TTTTCT
1 TTTTCTTTCTTT-CTCCCCTGTTTTCG
45432771 TTTTCTTTCCTTTCTCCCCTGTTTTCG
1 TTTTCTTT-CTTTCTCCCCTGTTTTCG
45432798 TTTT
1 TTTT
45432802 GCTATTCTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.00, C:0.30, G:0.04, T:0.67
Consensus pattern (26 bp):
TTTTCTTTCTTTCTCCCCTGTTTTCG
Found at i:45432920 original size:21 final size:22
Alignment explanation
Indices: 45432894--45432936 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
45432884 ATTAATAAGT
45432894 ATGTAT-ATATATTAATTACAA
1 ATGTATAATATATTAATTACAA
*
45432915 ATGTATACATATATTTATTACA
1 ATGTATA-ATATATTAATTACA
45432937 CTTGTCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
23 13 0.68
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (22 bp):
ATGTATAATATATTAATTACAA
Found at i:45443137 original size:20 final size:21
Alignment explanation
Indices: 45443097--45443140 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
45443087 TAATACTCTC
45443097 AAAATAATATTTATTTATTTAT
1 AAAATAATA-TTATTTATTTAT
*
45443119 AAAATAATA-TATTTTTTTAT
1 AAAATAATATTATTTATTTAT
45443139 AA
1 AA
45443141 TTTCACAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
22 9 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AAAATAATATTATTTATTTAT
Found at i:45445440 original size:13 final size:13
Alignment explanation
Indices: 45445422--45445446 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45445412 TTTGTCTCCC
45445422 CCCCCCCCCCCCG
1 CCCCCCCCCCCCG
45445435 CCCCCCCCCCCC
1 CCCCCCCCCCCC
45445447 CAATTTTCAC
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:0.00, C:0.96, G:0.04, T:0.00
Consensus pattern (13 bp):
CCCCCCCCCCCCG
Found at i:45445440 original size:14 final size:14
Alignment explanation
Indices: 45445421--45445447 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
45445411 CTTTGTCTCC
45445421 CCCCCCCCCCCCCG
1 CCCCCCCCCCCCCG
45445435 CCCCCCCCCCCCC
1 CCCCCCCCCCCCC
45445448 AATTTTCACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.96, G:0.04, T:0.00
Consensus pattern (14 bp):
CCCCCCCCCCCCCG
Found at i:45447941 original size:3 final size:3
Alignment explanation
Indices: 45447933--45447962 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
45447923 AAAAAATGTC
45447933 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
45447963 GATTCTTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:45456488 original size:18 final size:21
Alignment explanation
Indices: 45456467--45456513 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 21
45456457 ATTTCTTTAT
*
45456467 TTTTCTTTTT-T-TCTTC-CC
1 TTTTCTTTTTCTCTCTTCTCA
*
45456485 TTTTATTTTTCTCTCTTCTCA
1 TTTTCTTTTTCTCTCTTCTCA
45456506 TTTTCTTT
1 TTTTCTTT
45456514 ACTGAAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 9 0.39
19 1 0.04
20 5 0.22
21 8 0.35
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTCTTTTTCTCTCTTCTCA
Found at i:45457639 original size:15 final size:16
Alignment explanation
Indices: 45457611--45457642 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
45457601 CTGTTTTAGT
45457611 AATTTAACCAAAATAA
1 AATTTAACCAAAATAA
45457627 AATTTAA-CAAAATAA
1 AATTTAACCAAAATAA
45457642 A
1 A
45457643 TCATTAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (16 bp):
AATTTAACCAAAATAA
Found at i:45462132 original size:14 final size:14
Alignment explanation
Indices: 45462115--45462172 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
45462105 ATAATATAAT
45462115 ATTTATAAATATGA
1 ATTTATAAATATGA
*
45462129 ATTTATAACATATAA
1 ATTTATAA-ATATGA
*
45462144 TATTTATAAAAAT-A
1 -ATTTATAAATATGA
45462158 ATTTTATAAAT-TGA
1 A-TTTATAAATATGA
45462172 A
1 A
45462173 CTTTTTATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
13 2 0.05
14 19 0.51
15 8 0.22
16 8 0.22
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (14 bp):
ATTTATAAATATGA
Found at i:45462142 original size:30 final size:30
Alignment explanation
Indices: 45462108--45462166 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
45462098 TTTGTAGATA
*
45462108 ATATAATATTTATAAATATGAA-TTTATAAC
1 ATATAATATTTATAAAAAT-AATTTTATAAC
45462138 ATATAATATTTATAAAAATAATTTTATAA
1 ATATAATATTTATAAAAATAATTTTATAA
45462167 ATTGAACTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (30 bp):
ATATAATATTTATAAAAATAATTTTATAAC
Found at i:45464771 original size:3 final size:3
Alignment explanation
Indices: 45464763--45464788 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
45464753 GTTTGCTTTT
45464763 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
45464789 TTTTGTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:45466605 original size:16 final size:18
Alignment explanation
Indices: 45466584--45466616 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
45466574 AACATTAAAA
45466584 TAATATT-TAA-ATTCAT
1 TAATATTATAAGATTCAT
45466600 TAATATTATAAGATTCA
1 TAATATTATAAGATTCA
45466617 ATAAAAATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (18 bp):
TAATATTATAAGATTCAT
Found at i:45472417 original size:17 final size:18
Alignment explanation
Indices: 45472376--45472418 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
45472366 GTATAAGATA
45472376 ATATAATTATATTAACTT
1 ATATAATTATATTAACTT
**
45472394 ATA-AATTATA-TATTTT
1 ATATAATTATATTAACTT
45472410 ATATAATTA
1 ATATAATTA
45472419 ATAAAATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 12 0.55
18 3 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATAATTATATTAACTT
Found at i:45472480 original size:101 final size:102
Alignment explanation
Indices: 45472361--45472566 Score: 396
Period size: 101 Copynumber: 2.0 Consensus size: 102
45472351 AAATAGATTT
45472361 ATTTTGTATAAGATAATATAATTATATTAACTTATAAATTATATATTTTATATAATTAATAAAAT
1 ATTTTGTATAAGA-AATATAATTATATTAACTTATAAATTATATATTTTATATAATTAATAAAAT
45472426 TTGGAATGGTATGGAGCTAGCCTTACTCTTTGAGAATA
65 TTGGAATGGTATGGAGCTAGCCTTACTCTTTGAGAATA
45472464 ATTTTGTATAAG-AATATAATTATATTAACTTATAAATTATATATTTTATATAATTAATAAAATT
1 ATTTTGTATAAGAAATATAATTATATTAACTTATAAATTATATATTTTATATAATTAATAAAATT
45472528 TGGAATGGTATGGAGCTAGCCTTACTCTTTGAGAATA
66 TGGAATGGTATGGAGCTAGCCTTACTCTTTGAGAATA
45472565 AT
1 AT
45472567 ATCTTTGAGG
Statistics
Matches: 103, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
101 91 0.88
103 12 0.12
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.43
Consensus pattern (102 bp):
ATTTTGTATAAGAAATATAATTATATTAACTTATAAATTATATATTTTATATAATTAATAAAATT
TGGAATGGTATGGAGCTAGCCTTACTCTTTGAGAATA
Found at i:45472518 original size:17 final size:18
Alignment explanation
Indices: 45472477--45472519 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
45472467 TTGTATAAGA
45472477 ATATAATTATATTAACTT
1 ATATAATTATATTAACTT
**
45472495 ATA-AATTATA-TATTTT
1 ATATAATTATATTAACTT
45472511 ATATAATTA
1 ATATAATTA
45472520 ATAAAATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 12 0.55
18 3 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATAATTATATTAACTT
Found at i:45473537 original size:37 final size:36
Alignment explanation
Indices: 45473478--45473550 Score: 87
Period size: 35 Copynumber: 2.0 Consensus size: 36
45473468 CAATTCACCA
*
45473478 AAAAAAAAACATACATATATAAACATGTTTTAAAATAT
1 AAAAAAAAACATACATATATAAA-A-GTTTGAAAATAT
*
45473516 AAAAAAAAAC-TA-ATGTAATAAAAGTTTGAAAATAT
1 AAAAAAAAACATACATAT-ATAAAAGTTTGAAAATAT
45473551 TTCTCTGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 11 0.34
36 4 0.12
37 7 0.22
38 10 0.31
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (36 bp):
AAAAAAAAACATACATATATAAAAGTTTGAAAATAT
Found at i:45478823 original size:22 final size:22
Alignment explanation
Indices: 45478771--45478823 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
45478761 TCTGGAGGGT
* *
45478771 TAAAGTATAATTTTACAATTAC
1 TAAAGTAAAATTTTAAAATTAC
**
45478793 TAATTTAAAATTTTATAAATTA-
1 TAAAGTAAAATTTTA-AAATTAC
45478815 TAAAGTAAA
1 TAAAGTAAA
45478824 GGATTAAATC
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (22 bp):
TAAAGTAAAATTTTAAAATTAC
Found at i:45478832 original size:86 final size:86
Alignment explanation
Indices: 45478733--45478904 Score: 335
Period size: 86 Copynumber: 2.0 Consensus size: 86
45478723 TTTATAATTT
45478733 GTAAAGGAATAAATCAAAATTTTATCATTCTGGAGGGTTAAAGTATAATTTTACAATTACTAATT
1 GTAAAGGAATAAATCAAAATTTTATCATTCTGGAGGGTTAAAGTATAATTTTACAATTACTAATT
45478798 TAAAATTTTATAAATTATAAA
66 TAAAATTTTATAAATTATAAA
*
45478819 GTAAAGGATTAAATCAAAATTTTATCATTCTGGAGGGTTAAAGTATAATTTTACAATTACTAATT
1 GTAAAGGAATAAATCAAAATTTTATCATTCTGGAGGGTTAAAGTATAATTTTACAATTACTAATT
45478884 TAAAATTTTATAAATTATAAA
66 TAAAATTTTATAAATTATAAA
45478905 AAAATCTAAA
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (86 bp):
GTAAAGGAATAAATCAAAATTTTATCATTCTGGAGGGTTAAAGTATAATTTTACAATTACTAATT
TAAAATTTTATAAATTATAAA
Found at i:45490064 original size:2 final size:2
Alignment explanation
Indices: 45490057--45490087 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
45490047 NNNNAAAGGG
45490057 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45490088 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45491906 original size:4 final size:4
Alignment explanation
Indices: 45491892--45491923 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
45491882 TTGAAGACTT
45491892 AGAA AGAAA AGAA AGAA AGAA AGAA AGAA AGA
1 AGAA AG-AA AGAA AGAA AGAA AGAA AGAA AGA
45491924 GGGCAGAGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:45501145 original size:27 final size:28
Alignment explanation
Indices: 45501101--45501154 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
45501091 ATCAATTTTT
* *
45501101 TTTATTAAAATATTTTATTTATTTTTTCG
1 TTTAATAAAATA-TTTATTAATTTTTTCG
45501130 TTTAATAAAATA-TTATTAATTTTTT
1 TTTAATAAAATATTTATTAATTTTTT
45501155 TCTGGATCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 12 0.52
29 11 0.48
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTAATAAAATATTTATTAATTTTTTCG
Found at i:45501272 original size:27 final size:27
Alignment explanation
Indices: 45501212--45501273 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
45501202 GCTATTTCAT
* *
45501212 AGGCGCGACTAGTTGAGCCTATCTGAC
1 AGGCGCGACTAGTTGAGCCTAACTCAC
* * *
45501239 AGCCGCGACTAGTTGTGCCTAACTCAG
1 AGGCGCGACTAGTTGAGCCTAACTCAC
45501266 AGGCGCGA
1 AGGCGCGA
45501274 ATGGTGGTGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.23, C:0.27, G:0.31, T:0.19
Consensus pattern (27 bp):
AGGCGCGACTAGTTGAGCCTAACTCAC
Found at i:45502336 original size:33 final size:33
Alignment explanation
Indices: 45502288--45502369 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
45502278 CCGGGAGGAG
* * *
45502288 TGGAGTACGGCGGTGGATACGGGCT-GGAAAGAGC
1 TGGAGTACTGAGGTGGATACGAGCTAGG-AAGA-C
* *
45502322 -GGAGTACTGAGGTGGATATGAGCTAGGATGAC
1 TGGAGTACTGAGGTGGATACGAGCTAGGAAGAC
45502354 TGGAGTACTGAGGTGG
1 TGGAGTACTGAGGTGG
45502370 TAATGGGCTG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
32 1 0.02
33 38 0.93
34 2 0.05
ACGTcount: A:0.24, C:0.11, G:0.45, T:0.20
Consensus pattern (33 bp):
TGGAGTACTGAGGTGGATACGAGCTAGGAAGAC
Found at i:45505567 original size:20 final size:20
Alignment explanation
Indices: 45505523--45505568 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
45505513 AATACATTAC
*
45505523 TTTT-TCCTTTCTTTCTTCT
1 TTTTCTCCTTTCTCTCTTCT
* *
45505542 TCTTCTCCTTTCTCTCTTTT
1 TTTTCTCCTTTCTCTCTTCT
45505562 TTTTCTC
1 TTTTCTC
45505569 TCCTCCGGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTCTCCTTTCTCTCTTCT
Found at i:45505764 original size:27 final size:27
Alignment explanation
Indices: 45505720--45505792 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
45505710 AACAGACCAT
* * *
45505720 TCGCGCCTACCTGTCAGGCTTGATTAG
1 TCGCGCCTATCTGACAGGCTCGATTAG
*
45505747 TCGCGCCTGTCTGACAGGCTCGATTAG
1 TCGCGCCTATCTGACAGGCTCGATTAG
45505774 TCGCGCCTATCTGACAGGC
1 TCGCGCCTATCTGACAGGC
45505793 ACGACCCGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.15, C:0.32, G:0.27, T:0.26
Consensus pattern (27 bp):
TCGCGCCTATCTGACAGGCTCGATTAG
Found at i:45505913 original size:21 final size:22
Alignment explanation
Indices: 45505880--45505925 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
45505870 ATAAAAAAGT
45505880 AATATTTTATTTAA-ACAAAAA
1 AATATTTTATTTAATACAAAAA
*
45505901 AATATATTT-TTTAATATAAAAA
1 AATAT-TTTATTTAATACAAAAA
45505923 AAT
1 AAT
45505926 TCATTTGCGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AATATTTTATTTAATACAAAAA
Found at i:45505920 original size:26 final size:25
Alignment explanation
Indices: 45505855--45505924 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 25
45505845 ATATATTTAA
45505855 ATATTTTTTAA-A-AAAATAAAAAAGT
1 ATATTTTTTAATATAAAA-AAAAAA-T
* *
45505880 A-ATATTTT-ATTTAAACAAAAAAAT
1 ATATTTTTTAATATAAA-AAAAAAAT
45505904 ATATTTTTTAATATAAAAAAA
1 ATATTTTTTAATATAAAAAAA
45505925 TTCATTTGCG
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
23 1 0.03
24 8 0.22
25 20 0.56
26 7 0.19
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (25 bp):
ATATTTTTTAATATAAAAAAAAAAT
Found at i:45506686 original size:19 final size:17
Alignment explanation
Indices: 45506650--45506696 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
45506640 AAATAAAATT
45506650 CTAAAACCAAAACTAAAA
1 CTAAAA-CAAAACTAAAA
45506668 CTAAAACAAAAGTCTAAAA
1 CTAAAACAAAA--CTAAAA
*
45506687 ATAAAA-AAAA
1 CTAAAACAAAA
45506697 AAACATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 10 0.38
19 11 0.42
ACGTcount: A:0.70, C:0.15, G:0.02, T:0.13
Consensus pattern (17 bp):
CTAAAACAAAACTAAAA
Found at i:45509443 original size:23 final size:23
Alignment explanation
Indices: 45509417--45509460 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
45509407 CCAATTCGAA
*
45509417 AAATACAAAGACAAAAATTAATC
1 AAATAAAAAGACAAAAATTAATC
* *
45509440 AAATAAAAATATAAAAATTAA
1 AAATAAAAAGACAAAAATTAA
45509461 ATTCACAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.20
Consensus pattern (23 bp):
AAATAAAAAGACAAAAATTAATC
Found at i:45516537 original size:69 final size:69
Alignment explanation
Indices: 45516425--45516601 Score: 300
Period size: 69 Copynumber: 2.6 Consensus size: 69
45516415 CCAACAATAC
*
45516425 TAACTACGATTATAAGTAATTTCTAGACATCAGAGACCACTCAGTCGCATTCCAAAATGCAGTCA
1 TAACTACGATTATAAGTAATTTCTAGACATCAGAGACCACTCAGTCGCATTCCAAAATGCAATCA
45516490 ATTA
66 ATTA
* * *
45516494 TAACTATGATTATAAGTAATTTCTAGACATCAGAGACCCCTCAGTTGCATTCCAAAATGCAATCA
1 TAACTACGATTATAAGTAATTTCTAGACATCAGAGACCACTCAGTCGCATTCCAAAATGCAATCA
*
45516559 GTTA
66 ATTA
*
45516563 TAACTACGATTTTAAGTAATTTCTAGACATCAGAGACCA
1 TAACTACGATTATAAGTAATTTCTAGACATCAGAGACCA
45516602 TCAATCACAT
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 100 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.29
Consensus pattern (69 bp):
TAACTACGATTATAAGTAATTTCTAGACATCAGAGACCACTCAGTCGCATTCCAAAATGCAATCA
ATTA
Found at i:45517566 original size:3 final size:3
Alignment explanation
Indices: 45517558--45517595 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
45517548 ACAAATTTGA
45517558 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
45517596 AGGGCCTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:45517635 original size:3 final size:3
Alignment explanation
Indices: 45517627--45517660 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
45517617 AATTTGAAAT
45517627 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
45517661 AGGGCCTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:45517638 original size:65 final size:66
Alignment explanation
Indices: 45517550--45517683 Score: 261
Period size: 65 Copynumber: 2.0 Consensus size: 66
45517540 CTAACAAAAC
45517550 AAATTTGAAATAATAATAATAATAATAATAATAATAATAATAATAAAGGGCCTAATTAATTAAAG
1 AAATTTGAAATAATAATAATAATAATAATAATAATAATAATAATAAAGGGCCTAATTAATTAAAG
45517615 A
66 A
45517616 AAATTTGAAAT-ATAATAATAATAATAATAATAATAATAATAATAAAGGGCCTAATTAATTAAAG
1 AAATTTGAAATAATAATAATAATAATAATAATAATAATAATAATAAAGGGCCTAATTAATTAAAG
45517680 A
66 A
45517681 AAA
1 AAA
45517684 ATCAATAAGA
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
65 57 0.84
66 11 0.16
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (66 bp):
AAATTTGAAATAATAATAATAATAATAATAATAATAATAATAATAAAGGGCCTAATTAATTAAAG
A
Found at i:45519328 original size:84 final size:84
Alignment explanation
Indices: 45519081--45519312 Score: 392
Period size: 84 Copynumber: 2.8 Consensus size: 84
45519071 GTTATAATAT
* * **
45519081 TTGGATAAATCATTTTATTATTCTTCTCAATAAAGCTTTGATCTAATGATCGTCTAAACTTGATC
1 TTGGATAAATCATTTTATTTTTCTCCTTGATAAAGCTTTGATCTAATGATCGTCTAAACTTGATC
*
45519146 TTAGATAAATGTGGGTCGA
66 TTAGATAAATGTGGGCCGA
*
45519165 TTGGATAAATCATTTTATTTTTCTCCTTGATAAAGCTTTGATCTAATGATTGTCTAAACTTGATC
1 TTGGATAAATCATTTTATTTTTCTCCTTGATAAAGCTTTGATCTAATGATCGTCTAAACTTGATC
45519230 TTAGATAAATGTGGGCCGA
66 TTAGATAAATGTGGGCCGA
* *
45519249 TTGGATAAATCATTTTATTTTTCTCCTTGATAAAGCTTTGATCTAATGGTCGTATAAACTTGAT
1 TTGGATAAATCATTTTATTTTTCTCCTTGATAAAGCTTTGATCTAATGATCGTCTAAACTTGAT
45519313 ATTGGATAGA
Statistics
Matches: 139, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 139 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (84 bp):
TTGGATAAATCATTTTATTTTTCTCCTTGATAAAGCTTTGATCTAATGATCGTCTAAACTTGATC
TTAGATAAATGTGGGCCGA
Found at i:45521544 original size:26 final size:26
Alignment explanation
Indices: 45521501--45521550 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
45521491 TAATAACGGA
* *
45521501 TTGCTCTATTCTTATTATTTTGTTAC
1 TTGCTCTATTATTATTATTATGTTAC
*
45521527 TTGCTCTATTATTTTTATTATGTT
1 TTGCTCTATTATTATTATTATGTT
45521551 TTTATAGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.16, C:0.12, G:0.08, T:0.64
Consensus pattern (26 bp):
TTGCTCTATTATTATTATTATGTTAC
Found at i:45525834 original size:25 final size:24
Alignment explanation
Indices: 45525806--45525860 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
45525796 TCCCGATATT
45525806 TGGCTATCTTGAGCTTCCCGATTAA
1 TGGCTATCTTGAGCTTCCCG-TTAA
* *
45525831 TGGCTCTCTTGAGCTTCCCGTTTA
1 TGGCTATCTTGAGCTTCCCGTTAA
45525855 TGGCTA
1 TGGCTA
45525861 GTATGAGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 8 0.30
25 19 0.70
ACGTcount: A:0.15, C:0.25, G:0.22, T:0.38
Consensus pattern (24 bp):
TGGCTATCTTGAGCTTCCCGTTAA
Found at i:45529461 original size:22 final size:22
Alignment explanation
Indices: 45529420--45529486 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
45529410 TGCACTAATG
* *
45529420 AACAAAGAGCACTGAGGTGCTA
1 AACAAAGAGCACTAATGTGCTA
* *
45529442 TACAAAGAGCACAAATGTGCTA
1 AACAAAGAGCACTAATGTGCTA
**
45529464 AACGGAGAGCACTAATGTGCTA
1 AACAAAGAGCACTAATGTGCTA
45529486 A
1 A
45529487 TAATCGGATA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (22 bp):
AACAAAGAGCACTAATGTGCTA
Found at i:45530910 original size:14 final size:14
Alignment explanation
Indices: 45530891--45530929 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
45530881 TTGTTTCACT
*
45530891 GAAAATGGCTTCCG
1 GAAAATGACTTCCG
* *
45530905 GAAAATGATTTCTG
1 GAAAATGACTTCCG
45530919 GAAAATGACTT
1 GAAAATGACTT
45530930 ACTTTTCTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (14 bp):
GAAAATGACTTCCG
Found at i:45531542 original size:5 final size:6
Alignment explanation
Indices: 45531527--45531551 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
45531517 TTTGAAATTA
45531527 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
45531552 TATATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:45538045 original size:21 final size:21
Alignment explanation
Indices: 45538019--45538065 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
45538009 ATGTACATGT
45538019 ATATATTATAAA-ATGTATGCA
1 ATATATTATAAATAT-TATGCA
* *
45538040 TTATATTTTAAATATTATGCA
1 ATATATTATAAATATTATGCA
45538061 ATATA
1 ATATA
45538066 AAAATATATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (21 bp):
ATATATTATAAATATTATGCA
Found at i:45539521 original size:29 final size:31
Alignment explanation
Indices: 45539486--45539553 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 31
45539476 TAATAAATAT
45539486 ATATTTTTATTTTTA-TTTTTAAATTTTAAA
1 ATATTTTTATTTTTATTTTTTAAATTTTAAA
* *
45539516 A-ATTTTTATTTTTATTTTTTTACTTTTAAA
1 ATATTTTTATTTTTATTTTTTAAATTTTAAA
45539546 ATATTTTT
1 ATATTTTT
45539554 TTGTGTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 13 0.38
30 15 0.44
31 6 0.18
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (31 bp):
ATATTTTTATTTTTATTTTTTAAATTTTAAA
Found at i:45544176 original size:5 final size:6
Alignment explanation
Indices: 45544151--45544175 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
45544141 GATAAAATCT
45544151 AATAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA A
45544176 TCCATGTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:45546266 original size:39 final size:39
Alignment explanation
Indices: 45546216--45546294 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
45546206 AAACCCTCTC
45546216 AAAATTTGGGTGAGCCTTCGGGTTTGGATAAATAACTCA
1 AAAATTTGGGTGAGCCTTCGGGTTTGGATAAATAACTCA
* *
45546255 AAAATTTGGGTGGGTCTTCGGGTTTGGATAAATAACTCA
1 AAAATTTGGGTGAGCCTTCGGGTTTGGATAAATAACTCA
45546294 A
1 A
45546295 CCATTGAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.32
Consensus pattern (39 bp):
AAAATTTGGGTGAGCCTTCGGGTTTGGATAAATAACTCA
Found at i:45549625 original size:84 final size:84
Alignment explanation
Indices: 45549513--45549866 Score: 674
Period size: 84 Copynumber: 4.2 Consensus size: 84
45549503 ATCTTTAGCG
45549513 GCTTATTTCACACAAACGCCGCTATAGAACAAGACCTTTAGCGCGCTTTTCCACCAACGCCGCTA
1 GCTT-TTT-ACACAAACGCCGCTATAGAACAAGACCTTTAGCGCGCTTTTCCACCAACGCCGCTA
45549578 AAGATCATGACTTTTAACGGC
64 AAGATCATGACTTTTAACGGC
45549599 GCTTTTTACACAAACGCCGCTATAGAACAAGACCTTTAGCGGCGC-TTTCCACCAACGCCGCTAA
1 GCTTTTTACACAAACGCCGCTATAGAACAAGACCTTTAGC-GCGCTTTTCCACCAACGCCGCTAA
45549663 AGATCATGACTTTTAACGGC
65 AGATCATGACTTTTAACGGC
45549683 GCTTTTTACACAAACGCCGCTATAGAACAAGACCTTTAGCGCGCTTTTCCACCAACGCCGCTAAA
1 GCTTTTTACACAAACGCCGCTATAGAACAAGACCTTTAGCGCGCTTTTCCACCAACGCCGCTAAA
45549748 GATCATGACTTTTAACGGC
66 GATCATGACTTTTAACGGC
45549767 GCTTTTTACACAAACGCCGCTATAGAACAAGACCTTTAGCGCGCTTTTCCACCAACGCCGCTAAA
1 GCTTTTTACACAAACGCCGCTATAGAACAAGACCTTTAGCGCGCTTTTCCACCAACGCCGCTAAA
45549832 GATCATGACTTTTAACGGC
66 GATCATGACTTTTAACGGC
45549851 GCTTTTTACACAAACG
1 GCTTTTTACACAAACG
45549867 TTTAACTTAA
Statistics
Matches: 266, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
83 4 0.02
84 251 0.94
85 7 0.03
86 4 0.02
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.25
Consensus pattern (84 bp):
GCTTTTTACACAAACGCCGCTATAGAACAAGACCTTTAGCGCGCTTTTCCACCAACGCCGCTAAA
GATCATGACTTTTAACGGC
Found at i:45549683 original size:41 final size:42
Alignment explanation
Indices: 45549483--45549866 Score: 391
Period size: 43 Copynumber: 9.1 Consensus size: 42
45549473 TTTTAGCAAT
* * * *
45549483 AAACGCCGCTATAGAACAAGATCTTTAGCGGC-TTATTTCACAC
1 AAACGCCGCTAAAGAACAAGACCTTTAACGGCGCT-TTTC-CAC
* *
45549526 AAACGCCGCTATAGAACAAGACCTTTAGC-GCGCTTTTCCAC
1 AAACGCCGCTAAAGAACAAGACCTTTAACGGCGCTTTTCCAC
* * * * *
45549567 CAACGCCGCTAAAGATCATGACTTTTAACGGCGCTTTTTACAC
1 AAACGCCGCTAAAGAACAAGACCTTTAACGGCGC-TTTTCCAC
* *
45549610 AAACGCCGCTATAGAACAAGACCTTTAGCGGCGC-TTTCCAC
1 AAACGCCGCTAAAGAACAAGACCTTTAACGGCGCTTTTCCAC
* * * * *
45549651 CAACGCCGCTAAAGATCATGACTTTTAACGGCGCTTTTTACAC
1 AAACGCCGCTAAAGAACAAGACCTTTAACGGCGC-TTTTCCAC
* *
45549694 AAACGCCGCTATAGAACAAGACCTTTAGC-GCGCTTTTCCAC
1 AAACGCCGCTAAAGAACAAGACCTTTAACGGCGCTTTTCCAC
* * * * *
45549735 CAACGCCGCTAAAGATCATGACTTTTAACGGCGCTTTTTACAC
1 AAACGCCGCTAAAGAACAAGACCTTTAACGGCGC-TTTTCCAC
* *
45549778 AAACGCCGCTATAGAACAAGACCTTTAGC-GCGCTTTTCCAC
1 AAACGCCGCTAAAGAACAAGACCTTTAACGGCGCTTTTCCAC
* * * * *
45549819 CAACGCCGCTAAAGATCATGACTTTTAACGGCGCTTTTTACAC
1 AAACGCCGCTAAAGAACAAGACCTTTAACGGCGC-TTTTCCAC
45549862 AAACG
1 AAACG
45549867 TTTAACTTAA
Statistics
Matches: 280, Mismatches: 52, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
41 120 0.43
42 26 0.09
43 134 0.48
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACAAGACCTTTAACGGCGCTTTTCCAC
Found at i:45555433 original size:17 final size:19
Alignment explanation
Indices: 45555399--45555435 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
45555389 TTGTATTATG
*
45555399 TTTTAAATATATATTATTT
1 TTTTAAATATATAATATTT
45555418 TTTTAAA-AT-TAATATTT
1 TTTTAAATATATAATATTT
45555435 T
1 T
45555436 AGATGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 2 0.12
19 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTAAATATATAATATTT
Found at i:45555455 original size:2 final size:2
Alignment explanation
Indices: 45555448--45555476 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
45555438 ATGATTTTAA
45555448 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 A
45555477 AAAGCTTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45564253 original size:14 final size:15
Alignment explanation
Indices: 45564231--45564268 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
45564221 CAATCAAACA
45564231 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
45564245 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
45564260 ACAGAAAAT
1 CCAGAAAAT
45564269 TAAAAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:45564442 original size:16 final size:17
Alignment explanation
Indices: 45564407--45564444 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
45564397 ATTAAACCCG
*
45564407 AATAACCCAGAACCCCA
1 AATAACCCAGAACCCAA
*
45564424 AATAACCCA-AACCGAA
1 AATAACCCAGAACCCAA
45564440 AATAA
1 AATAA
45564445 TTGGACCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.55, C:0.32, G:0.05, T:0.08
Consensus pattern (17 bp):
AATAACCCAGAACCCAA
Found at i:45575360 original size:26 final size:26
Alignment explanation
Indices: 45575331--45575400 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 26
45575321 GAAATTTGTA
* *
45575331 ATTTATGTATTTATATA-ATTTTTGAT
1 ATTTATATATTTATATATATTTAT-AT
*
45575357 ATTTTAATATATATATATATATTTATAT
1 A-TTT-ATATATTTATATATATTTATAT
*
45575385 ATTTATATATTCATAT
1 ATTTATATATTTATAT
45575401 TTAATATTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
26 11 0.31
27 6 0.17
28 14 0.39
29 5 0.14
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (26 bp):
ATTTATATATTTATATATATTTATAT
Found at i:45575383 original size:16 final size:16
Alignment explanation
Indices: 45575364--45575400 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
45575354 GATATTTTAA
45575364 TATATATATATATATT
1 TATATATATATATATT
*
45575380 TATATATTTATATATT
1 TATATATATATATATT
*
45575396 CATAT
1 TATAT
45575401 TTAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATATATATATATT
Found at i:45575400 original size:28 final size:27
Alignment explanation
Indices: 45575331--45575410 Score: 67
Period size: 27 Copynumber: 2.9 Consensus size: 27
45575321 GAAATTTGTA
* *
45575331 ATTTATGTATT-TATATAATTTTTGATAT
1 ATTTATATATTATATAT-ATATTT-ATAT
45575359 -TTTA-ATATATATATATATATTTATAT
1 ATTTATATAT-TATATATATATTTATAT
*
45575385 ATTTATATATTCATATTTAATATTTA
1 ATTTATATATT-ATATAT-ATATTTA
45575411 CAAACATTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
26 7 0.16
27 15 0.35
28 14 0.33
29 7 0.16
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.59
Consensus pattern (27 bp):
ATTTATATATTATATATATATTTATAT
Found at i:45578372 original size:22 final size:22
Alignment explanation
Indices: 45578322--45578365 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
45578312 TTGCAAAGGT
* *
45578322 AATTTATGTTTCTTCTTCCATC
1 AATTTCTGCTTCTTCTTCCATC
45578344 AATTTCTGCTTCTTCTTCCATC
1 AATTTCTGCTTCTTCTTCCATC
45578366 GTTTTCTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.05, T:0.52
Consensus pattern (22 bp):
AATTTCTGCTTCTTCTTCCATC
Found at i:45584737 original size:45 final size:44
Alignment explanation
Indices: 45584645--45584740 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 44
45584635 ATTACAACAT
* *
45584645 CATTCCATTCAACCAAACACAAGAATAGTATTACGCCTCTATTC
1 CATTACATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
*
45584689 CATTACATTCAACCAAACA-ATTGAATTACTATT-CTGCCTCTATTC
1 CATTACATTCAACCAAACACA-AGAA-TACTATTAC-GCCTCTATTC
45584734 CATTACA
1 CATTACA
45584741 GCTCTATTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
43 1 0.02
44 22 0.48
45 23 0.50
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTACATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
Found at i:45584747 original size:16 final size:16
Alignment explanation
Indices: 45584726--45584758 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
45584716 ACTATTCTGC
45584726 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
*
45584742 CTCTATTTCATTACAG
1 CTCTATTCCATTACAG
45584758 C
1 C
45584759 GAACCAAACG
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:0.24, C:0.30, G:0.06, T:0.39
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:45598840 original size:2 final size:2
Alignment explanation
Indices: 45598835--45598865 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
45598825 TCTCAAGCTA
*
45598835 AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45598866 CGTATATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45601646 original size:26 final size:28
Alignment explanation
Indices: 45601615--45601679 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 28
45601605 TCTAAGATAA
* * *
45601615 AAATTAAACCCCATGCTCAAT-C-TAAT
1 AAATTAAACCCAATGCCCAATACACAAT
45601641 AAATTAAACCCAATGCCCAATACACAAT
1 AAATTAAACCCAATGCCCAATACACAAT
*
45601669 AAACTAAACCC
1 AAATTAAACCC
45601680 TAGCCCCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 19 0.58
27 1 0.03
28 13 0.39
ACGTcount: A:0.48, C:0.29, G:0.03, T:0.20
Consensus pattern (28 bp):
AAATTAAACCCAATGCCCAATACACAAT
Found at i:45607765 original size:21 final size:21
Alignment explanation
Indices: 45607729--45607779 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
45607719 TATATATTTA
*
45607729 AAATTTAATCTTATTACAATTC
1 AAATTTTATCTTATTA-AATTC
*
45607751 AAATTTTAT-TTATTAAATTT
1 AAATTTTATCTTATTAAATTC
45607771 AAATATTTA
1 AAAT-TTTA
45607780 GACATTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 8 0.31
21 10 0.38
22 8 0.31
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATTTTATCTTATTAAATTC
Found at i:45610273 original size:30 final size:30
Alignment explanation
Indices: 45610237--45610384 Score: 269
Period size: 30 Copynumber: 4.9 Consensus size: 30
45610227 AGGACATATG
* *
45610237 CCCATGTGCTAGGTCGCGTGTCACACACGA
1 CCCATGTGCTAGGCCGTGTGTCACACACGA
45610267 CCCATGTGCTAGGCCGTGTGTCACACACGA
1 CCCATGTGCTAGGCCGTGTGTCACACACGA
45610297 CCCATGTGCTAGGCCGTGTGTCACACACGA
1 CCCATGTGCTAGGCCGTGTGTCACACACGA
45610327 CCCATGTGCTAGGCCGTGTGTCACACACGA
1 CCCATGTGCTAGGCCGTGTGTCACACACGA
*
45610357 CCTATGTGCTAGGCCGTGTGTCACACAC
1 CCCATGTGCTAGGCCGTGTGTCACACAC
45610385 AGCTGAGACA
Statistics
Matches: 115, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 115 1.00
ACGTcount: A:0.20, C:0.33, G:0.26, T:0.21
Consensus pattern (30 bp):
CCCATGTGCTAGGCCGTGTGTCACACACGA
Found at i:45611377 original size:24 final size:25
Alignment explanation
Indices: 45611317--45611378 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
45611307 TCAGGCTTAG
*
45611317 TAACAGGAAGCTCACAAATAGCCTA
1 TAACAGGAAGCTCACAAAGAGCCTA
* * *
45611342 TATCGGGTAGCTC-CAAAGAGCACT-
1 TAACAGGAAGCTCACAAAGAGC-CTA
45611366 TAACAGGAAGCTC
1 TAACAGGAAGCTC
45611379 TGGAGAGCAG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
24 17 0.59
25 12 0.41
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (25 bp):
TAACAGGAAGCTCACAAAGAGCCTA
Found at i:45611979 original size:21 final size:21
Alignment explanation
Indices: 45611953--45612003 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
45611943 TATATGAGTA
45611953 AATTTA-ACTTCAATTTAATAC
1 AATTTACA-TTCAATTTAATAC
* *
45611974 AATTTACATTCAATTTTATCC
1 AATTTACATTCAATTTAATAC
*
45611995 AATTCACAT
1 AATTTACAT
45612004 CTCAGGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTTACATTCAATTTAATAC
Found at i:45616854 original size:2 final size:2
Alignment explanation
Indices: 45616849--45616873 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45616839 AAAAAGTGTG
45616849 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
45616874 TATGTTTTTT
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:45620346 original size:107 final size:108
Alignment explanation
Indices: 45620132--45620346 Score: 423
Period size: 107 Copynumber: 2.0 Consensus size: 108
45620122 AGATTGCTAC
45620132 TAAGTGAATTTTTTTTATTTTATTTTAAAATGTTATACAAATAAATTTAACCAAAAAAAAGTTAA
1 TAAGTGAATTTTTTTTATTTTATTTTAAAATGTTATACAAATAAATTTAACCAAAAAAAAGTTAA
45620197 TATTGTTAAGAATTAGGTCTGAATTTTAAAATCTGAAAAATAG
66 TATTGTTAAGAATTAGGTCTGAATTTTAAAATCTGAAAAATAG
45620240 TAAGTGAA-TTTTTTTATTTTATTTTAAAATGTTATACAAATAAATTTAACCAAAAAAAAGTTAA
1 TAAGTGAATTTTTTTTATTTTATTTTAAAATGTTATACAAATAAATTTAACCAAAAAAAAGTTAA
45620304 TATTGTTAAGAATTAGGTCTGAATTTTAAAATCTGAAAAATAG
66 TATTGTTAAGAATTAGGTCTGAATTTTAAAATCTGAAAAATAG
45620347 AGAGACAAAA
Statistics
Matches: 107, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
107 99 0.93
108 8 0.07
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (108 bp):
TAAGTGAATTTTTTTTATTTTATTTTAAAATGTTATACAAATAAATTTAACCAAAAAAAAGTTAA
TATTGTTAAGAATTAGGTCTGAATTTTAAAATCTGAAAAATAG
Done.