Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold114
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: 3219552
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Warning! 36736 characters in sequence are not A, C, G, or T
File 9 of 13
Found at i:2125448 original size:36 final size:35
Alignment explanation
Indices: 2125402--2125473 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 35
2125392 AATAAATATT
* *
2125402 ATTATCATAAATATCGATCATCAAATATCAATAATA
1 ATTATAATAAATATCAATCA-CAAATATCAATAATA
* *
2125438 ATTATAATAAATATCAATCACAATTATTAATAATA
1 ATTATAATAAATATCAATCACAAATATCAATAATA
2125473 A
1 A
2125474 AAAAATTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 14 0.44
36 18 0.56
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.35
Consensus pattern (35 bp):
ATTATAATAAATATCAATCACAAATATCAATAATA
Found at i:2125452 original size:22 final size:23
Alignment explanation
Indices: 2125424--2125470 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
2125414 ATCGATCATC
*
2125424 AAATATCAATAATAATTA-TAAT
1 AAATATCAATAACAATTATTAAT
*
2125446 AAATATCAATCACAATTATTAAT
1 AAATATCAATAACAATTATTAAT
2125469 AA
1 AA
2125471 TAAAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (23 bp):
AAATATCAATAACAATTATTAAT
Found at i:2125488 original size:17 final size:17
Alignment explanation
Indices: 2125466--2125499 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2125456 CACAATTATT
2125466 AATAATAAAAAAATTAA
1 AATAATAAAAAAATTAA
2125483 AATAATAAAAAAATTAA
1 AATAATAAAAAAATTAA
2125500 TTATGATATT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AATAATAAAAAAATTAA
Found at i:2125492 original size:15 final size:15
Alignment explanation
Indices: 2125463--2125500 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 15
2125453 AATCACAATT
2125463 ATTAATAATAAAAAA
1 ATTAATAATAAAAAA
2125478 ATTAAAATAATAAAAAA
1 ATT--AATAATAAAAAA
2125495 ATTAAT
1 ATTAAT
2125501 TATGATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 6 0.29
17 15 0.71
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
ATTAATAATAAAAAA
Found at i:2125721 original size:23 final size:24
Alignment explanation
Indices: 2125685--2125730 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
2125675 TTTTAGATTT
2125685 TGGGAGCCATGGCAATACCAGTGG
1 TGGGAGCCATGGCAATACCAGTGG
2125709 TGGGAG-CATGGCAATACCAGTG
1 TGGGAGCCATGGCAATACCAGTG
2125731 CTGGAATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.26, C:0.20, G:0.37, T:0.17
Consensus pattern (24 bp):
TGGGAGCCATGGCAATACCAGTGG
Found at i:2126070 original size:25 final size:22
Alignment explanation
Indices: 2126030--2126075 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
2126020 TTAATATTCT
2126030 CTTAATAAATTGATTTTTAAAAA
1 CTTAATAAATTGA-TTTTAAAAA
*
2126053 CTTAATAATTATTTATTTTAAAA
1 CTTAATAA--ATTGATTTTAAAA
2126076 TAATCAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 8 0.40
25 4 0.20
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (22 bp):
CTTAATAAATTGATTTTAAAAA
Found at i:2127419 original size:11 final size:11
Alignment explanation
Indices: 2127381--2127429 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
2127371 TTTAATGAAA
2127381 AATAATATTTT
1 AATAATATTTT
*
2127392 ATTTAA-A-TTT
1 A-ATAATATTTT
2127402 AAT--TATTTT
1 AATAATATTTT
2127411 AATAATATTTT
1 AATAATATTTT
2127422 AATAATAT
1 AATAATAT
2127430 AATAAATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
8 1 0.03
9 7 0.23
10 4 0.13
11 16 0.52
12 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
AATAATATTTT
Found at i:2127785 original size:16 final size:15
Alignment explanation
Indices: 2127764--2127799 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
2127754 CCTTTTGTCA
*
2127764 AATAATAATACTTAAT
1 AATAATAATAATT-AT
2127780 AATAATAATAATTAT
1 AATAATAATAATTAT
2127795 AATAA
1 AATAA
2127800 AAAGGCCAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (15 bp):
AATAATAATAATTAT
Found at i:2129432 original size:13 final size:13
Alignment explanation
Indices: 2129414--2129438 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2129404 AAATTTAGAC
2129414 TTAATTTAATTAA
1 TTAATTTAATTAA
2129427 TTAATTTAATTA
1 TTAATTTAATTA
2129439 TTATTAAAAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAATTTAATTAA
Found at i:2130343 original size:13 final size:13
Alignment explanation
Indices: 2130325--2130350 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2130315 TACGTATTAC
2130325 TTTATAAATTTTA
1 TTTATAAATTTTA
2130338 TTTATAAATTTTA
1 TTTATAAATTTTA
2130351 AAAAAAATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTATAAATTTTA
Found at i:2135106 original size:2 final size:2
Alignment explanation
Indices: 2135099--2135133 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2135089 ACAAAACTGT
*
2135099 GA GA GA GA GA GA GA GA GA GA GA GC GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2135134 TGGGAAACAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2136716 original size:2 final size:2
Alignment explanation
Indices: 2136709--2136740 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2136699 AGGAAAGGGC
2136709 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2136741 TTCAGCAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2138095 original size:2 final size:2
Alignment explanation
Indices: 2138088--2138124 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2138078 TTGTTAGATT
2138088 TA TA TA TA 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 TA TA TA TA T
2138125 GTTAGATAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2139065 original size:17 final size:16
Alignment explanation
Indices: 2139039--2139074 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
2139029 TTATATTCAC
*
2139039 ATTATTTTTTATATATA
1 ATTATATTTTATATA-A
2139056 ATTATATTTTATATAA
1 ATTATATTTTATATAA
2139072 ATT
1 ATT
2139075 TTAATACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTATATTTTATATAA
Found at i:2139384 original size:2 final size:2
Alignment explanation
Indices: 2139377--2139427 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
2139367 AAAACAACTG
* * * *
2139377 TA TA TA TA TA TA TA TA TA TA GA -A CA CA AA TA TA TA 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
*
2139418 TA TA CA TA TA
1 TA TA TA TA TA
2139428 AATGTTATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (2 bp):
TA
Found at i:2139873 original size:27 final size:25
Alignment explanation
Indices: 2139805--2139873 Score: 66
Period size: 27 Copynumber: 2.6 Consensus size: 25
2139795 TACACACATG
2139805 AATTGATATTTATTTATATTAATATA
1 AATT-ATATTTATTTATATTAATATA
* * **
2139831 AATTTTATATATTTTATAATTGTTATAA
1 AATTATATTTA-TTTAT-ATTAATAT-A
2139859 AATTATATTTATTTA
1 AATTATATTTATTTA
2139874 ATTTAATTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
25 5 0.15
26 9 0.26
27 10 0.29
28 10 0.29
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (25 bp):
AATTATATTTATTTATATTAATATA
Found at i:2140723 original size:16 final size:16
Alignment explanation
Indices: 2140702--2140734 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2140692 TGAAATTAAA
2140702 AATTAATATA-AATTAT
1 AATTAAT-TACAATTAT
2140718 AATTAATTACAATTAT
1 AATTAATTACAATTAT
2140734 A
1 A
2140735 TTATTCTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 14 0.88
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTAATTACAATTAT
Found at i:2142087 original size:2 final size:2
Alignment explanation
Indices: 2142080--2142119 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2142070 TCCTTTTATC
*
2142080 AT AT AT AT AT AT AT AC 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 AT AT AT AT AT
2142120 TGAAAAATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2142853 original size:54 final size:54
Alignment explanation
Indices: 2142771--2142877 Score: 214
Period size: 54 Copynumber: 2.0 Consensus size: 54
2142761 AGCAAAATGG
2142771 AAATATGGAATATGTGTATGAGTTTCATTTAAGGGAGCATTAATTTATCTTTTT
1 AAATATGGAATATGTGTATGAGTTTCATTTAAGGGAGCATTAATTTATCTTTTT
2142825 AAATATGGAATATGTGTATGAGTTTCATTTAAGGGAGCATTAATTTATCTTTT
1 AAATATGGAATATGTGTATGAGTTTCATTTAAGGGAGCATTAATTTATCTTTT
2142878 AATTTTGATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.44
Consensus pattern (54 bp):
AAATATGGAATATGTGTATGAGTTTCATTTAAGGGAGCATTAATTTATCTTTTT
Found at i:2145179 original size:2 final size:2
Alignment explanation
Indices: 2145172--2145203 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2145162 ACTTCGGAAT
*
2145172 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2145204 CACTTGTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2145705 original size:3 final size:3
Alignment explanation
Indices: 2145697--2145728 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2145687 AAGTTAGATA
*
2145697 TCT TCT TCT TCC TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
2145729 AATGCCTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:2147910 original size:2 final size:2
Alignment explanation
Indices: 2147903--2147927 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2147893 GTATGAATTT
2147903 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
2147928 GTAAGTTCAC
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:2148817 original size:2 final size:2
Alignment explanation
Indices: 2148810--2148857 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2148800 CAATGCTAAA
2148810 AT AT AT AT AT AT 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 AT AT AT AT AT AT
2148852 AT AT AT
1 AT AT AT
2148858 TCTTTTAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2149755 original size:22 final size:22
Alignment explanation
Indices: 2149727--2149768 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2149717 AAATTATAAA
2149727 TATTAAA-ATTTAATTTTAAATT
1 TATTAAATA-TTAATTTTAAATT
*
2149749 TATTAAATATTATTTTTAAA
1 TATTAAATATTAATTTTAAA
2149769 AAATAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTAAATATTAATTTTAAATT
Found at i:2151686 original size:6 final size:6
Alignment explanation
Indices: 2151670--2151700 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2151660 CAATTTATTT
*
2151670 TTTTAA ATTTAA TTTTAA TTTTAA TTTTAA T
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA T
2151701 AATAATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
TTTTAA
Found at i:2152718 original size:3 final size:3
Alignment explanation
Indices: 2152712--2152771 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
2152702 TCTCGCCATT
* * * * * *
2152712 GAA GAA GAA GAG GAG GAG GAA GAA GAA GAA GAA GTA GTA GAG GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
2152760 GAA GAA GAA GAA
1 GAA GAA GAA GAA
2152772 CATCATCTGG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:2152744 original size:24 final size:23
Alignment explanation
Indices: 2152712--2152770 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 23
2152702 TCTCGCCATT
2152712 GAAGAAGAAGAGGAGGAGGAAGAA
1 GAAGAAGAAGAGGA-GAGGAAGAA
*
2152736 GAAGAAGAAGTAGTAGAGGAAGAA
1 GAAGAAGAAG-AGGAGAGGAAGAA
2152760 GAAGAAGAAGA
1 GAAGAAGAAGA
2152771 ACATCATCTG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 1 0.03
24 29 0.88
25 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.41, T:0.03
Consensus pattern (23 bp):
GAAGAAGAAGAGGAGAGGAAGAA
Found at i:2157044 original size:141 final size:141
Alignment explanation
Indices: 2156872--2157147 Score: 525
Period size: 141 Copynumber: 2.0 Consensus size: 141
2156862 GGAGCTATAC
2156872 GCAACGCCGAAAAGATGATCAATCGAGACCAAAGTGAAGAATGTTTTGCAAGAAATTCTTCAGTT
1 GCAACGCCGAAAAGATGATCAATCGAGACCAAAGTGAAGAATGTTTTGCAAGAAATTCTTCAGTT
2156937 CTTCTGTTGCATTCCAGGCTGCTCATGACCCAGATGGATACTCGCAAAATTTTGATCAAGGAACA
66 CTTCTGTTGCATTCCAGGCTGCTCATGACCCAGATGGATACTCGCAAAATTTTGATCAAGGAACA
2157002 GGATGCTACAT
131 GGATGCTACAT
* * *
2157013 GCAACGCGGCAAAGATGATCAATCGAGACCAAAGTGGAGAATGTTTTGCAAGAAATTCTTCAGTT
1 GCAACGCCGAAAAGATGATCAATCGAGACCAAAGTGAAGAATGTTTTGCAAGAAATTCTTCAGTT
2157078 CTTCTGTTGCATTCCAGGCTGCTCATGACCCAGATGGATACTCGCAAAATTTTGATCAAGGAACA
66 CTTCTGTTGCATTCCAGGCTGCTCATGACCCAGATGGATACTCGCAAAATTTTGATCAAGGAACA
2157143 GGATG
131 GGATG
2157148 GTTGGAGCCT
Statistics
Matches: 132, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
141 132 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.25
Consensus pattern (141 bp):
GCAACGCCGAAAAGATGATCAATCGAGACCAAAGTGAAGAATGTTTTGCAAGAAATTCTTCAGTT
CTTCTGTTGCATTCCAGGCTGCTCATGACCCAGATGGATACTCGCAAAATTTTGATCAAGGAACA
GGATGCTACAT
Found at i:2159835 original size:2 final size:2
Alignment explanation
Indices: 2159828--2159852 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2159818 TTCCTCATAC
2159828 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 A
2159853 AAAAGAAAGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2161963 original size:31 final size:31
Alignment explanation
Indices: 2161925--2161983 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2161915 CCTTTTATAT
**
2161925 CCTTCAAGTGTGCTAGCTGTTGTTTTGACAC
1 CCTTCAAGAATGCTAGCTGTTGTTTTGACAC
2161956 CCTTCAAGAATGCTAGCTGTTGTTTTGA
1 CCTTCAAGAATGCTAGCTGTTGTTTTGA
2161984 TACATTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (31 bp):
CCTTCAAGAATGCTAGCTGTTGTTTTGACAC
Found at i:2169082 original size:2 final size:2
Alignment explanation
Indices: 2169075--2169113 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2169065 TAAATATGAT
*
2169075 TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2169114 TTTCTATAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2177113 original size:20 final size:21
Alignment explanation
Indices: 2177077--2177117 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
2177067 AGATATCTAA
2177077 TAAAAGATTAATTTTCTTTTTT
1 TAAAAGATT-ATTTTCTTTTTT
2177099 TAAAAGATT-TTTTCTTTTT
1 TAAAAGATTATTTTCTTTTT
2177118 CTTGGCCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (21 bp):
TAAAAGATTATTTTCTTTTTT
Found at i:2183105 original size:6 final size:6
Alignment explanation
Indices: 2183094--2183120 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2183084 TCTTTCTTTT
2183094 TTTTAA TTTTAA TTTTAA TTTTAA TTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTT
2183121 ATTTATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTAA
Found at i:2183166 original size:16 final size:16
Alignment explanation
Indices: 2183138--2183170 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2183128 TAAAATACAT
2183138 ATTTGAAAAATATAAA
1 ATTTGAAAAATATAAA
2183154 ATTT-AAAATATATAAA
1 ATTTGAAAA-ATATAAA
2183170 A
1 A
2183171 AAATTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
ATTTGAAAAATATAAA
Found at i:2184011 original size:20 final size:20
Alignment explanation
Indices: 2183986--2184026 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2183976 GTATGATCCT
2183986 ATATTATATATATAAGAGCC
1 ATATTATATATATAAGAGCC
2184006 ATATTATATATATAAGAGCC
1 ATATTATATATATAAGAGCC
2184026 A
1 A
2184027 CGGAACGCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (20 bp):
ATATTATATATATAAGAGCC
Found at i:2188711 original size:2 final size:2
Alignment explanation
Indices: 2188704--2188734 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2188694 ACTAAGTTAC
*
2188704 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2188735 CACTAGTTTT
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:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2191941 original size:2 final size:2
Alignment explanation
Indices: 2191928--2191962 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2191918 TTCATCCATT
*
2191928 TA TA TT 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 TA TA TA T
2191963 CCAAAAATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2198200 original size:34 final size:34
Alignment explanation
Indices: 2198144--2198258 Score: 142
Period size: 34 Copynumber: 3.4 Consensus size: 34
2198134 ACCATGTTTT
2198144 TTGTTGATTAAAT-GGTGATTTGATAGTTTATCA
1 TTGTTGATTAAATGGGTGATTTGATAGTTTATCA
* *
2198177 TTGTTGATTAAATGGGTGATTTGATTGTTTGTCA
1 TTGTTGATTAAATGGGTGATTTGATAGTTTATCA
* * ** ** *
2198211 TTTTTGACTAAATGGAAGATTTGATAACTTACCA
1 TTGTTGATTAAATGGGTGATTTGATAGTTTATCA
2198245 TTGTTGATTAAATG
1 TTGTTGATTAAATG
2198259 AGAAATTTAG
Statistics
Matches: 68, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
33 13 0.19
34 55 0.81
ACGTcount: A:0.28, C:0.05, G:0.21, T:0.46
Consensus pattern (34 bp):
TTGTTGATTAAATGGGTGATTTGATAGTTTATCA
Found at i:2201356 original size:13 final size:13
Alignment explanation
Indices: 2201338--2201362 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2201328 TGGCTGCCAA
2201338 AAAAAGAAAGAAG
1 AAAAAGAAAGAAG
2201351 AAAAAGAAAGAA
1 AAAAAGAAAGAA
2201363 AATAATAAAT
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:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAGAAG
Found at i:2201710 original size:2 final size:2
Alignment explanation
Indices: 2201703--2201731 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2201693 AGGTAAACGA
2201703 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2201732 GGATTCGGTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2206071 original size:2 final size:2
Alignment explanation
Indices: 2206064--2206113 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
2206054 GTTCACTTAC
*
2206064 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2206106 AT AT AT AT
1 AT AT AT AT
2206114 TTGCATGCAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2214307 original size:21 final size:21
Alignment explanation
Indices: 2214281--2214320 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2214271 GAAATAGCAG
2214281 TGCCATTTTC-CGCTAATTTGC
1 TGCCATTTTCTCG-TAATTTGC
2214302 TGCCATTTTCTCGTAATTT
1 TGCCATTTTCTCGTAATTT
2214321 ATTCTGACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.15, C:0.25, G:0.12, T:0.47
Consensus pattern (21 bp):
TGCCATTTTCTCGTAATTTGC
Found at i:2223210 original size:39 final size:39
Alignment explanation
Indices: 2223143--2223217 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 39
2223133 TCCATAGTTA
* **** *
2223143 AAATTAATTTTCTTTTATTTGTGTGTAAGAAGATTCATT
1 AAATCAATTTTCTTTTATTTAAAAGTAAGAAAATTCATT
2223182 AAATCAATTTTCTTTTATTTAAAAGTAAGAAAATTC
1 AAATCAATTTTCTTTTATTTAAAAGTAAGAAAATTC
2223218 TAATCTAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 30 1.00
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (39 bp):
AAATCAATTTTCTTTTATTTAAAAGTAAGAAAATTCATT
Found at i:2224026 original size:54 final size:54
Alignment explanation
Indices: 2223960--2224068 Score: 182
Period size: 54 Copynumber: 2.0 Consensus size: 54
2223950 TTAGTGCCTC
* * *
2223960 GCTCTCCGTCTTCTTCATTGCCGGGGCATCTTTTTCCTTGGGCATTGGAAGTTT
1 GCTCTCCATCTTCTTCATTGCCAGGGCATCTTTTTCCTTAGGCATTGGAAGTTT
*
2224014 GCTCTCCATCTTCTTTATTGCCAGGGCATCTTTTTCCTTAGGCATTGGAAGTTT
1 GCTCTCCATCTTCTTCATTGCCAGGGCATCTTTTTCCTTAGGCATTGGAAGTTT
2224068 G
1 G
2224069 AACCTCTCGC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.41
Consensus pattern (54 bp):
GCTCTCCATCTTCTTCATTGCCAGGGCATCTTTTTCCTTAGGCATTGGAAGTTT
Found at i:2227611 original size:20 final size:20
Alignment explanation
Indices: 2227562--2227603 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2227552 TCAAATGAAA
2227562 ACACAATTAACAGGTTTTAT
1 ACACAATTAACAGGTTTTAT
*
2227582 ACACAATTAACATGTTTTAT
1 ACACAATTAACAGGTTTTAT
2227602 AC
1 AC
2227604 CCATTTAAAC
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:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (20 bp):
ACACAATTAACAGGTTTTAT
Found at i:2233475 original size:2 final size:2
Alignment explanation
Indices: 2233468--2233494 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2233458 TCATTTTGGG
2233468 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 T
2233495 GGAAATTTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2233690 original size:13 final size:12
Alignment explanation
Indices: 2233660--2233697 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
2233650 GCTCCTTAAT
2233660 TAAAAGGAAACTA
1 TAAAAGGAAA-TA
2233673 T-AAAGGAAATA
1 TAAAAGGAAATA
2233684 GTAAAAGGAAATA
1 -TAAAAGGAAATA
2233697 T
1 T
2233698 CTAAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 2 0.09
12 10 0.43
13 11 0.48
ACGTcount: A:0.61, C:0.03, G:0.18, T:0.18
Consensus pattern (12 bp):
TAAAAGGAAATA
Found at i:2237043 original size:2 final size:2
Alignment explanation
Indices: 2237036--2237074 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2237026 TTTATGCCTT
2237036 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2237075 ATATATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2238361 original size:29 final size:30
Alignment explanation
Indices: 2238329--2238398 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 30
2238319 TTTTTTAAAA
* * * *
2238329 AAAAAATTGAATTTTTTA-ATTTTATTTAT
1 AAAAAATTAAATTTTTTATAATTAATATAT
*
2238358 -AAAATTTAAATTTTTTATAATTAATATAT
1 AAAAAATTAAATTTTTTATAATTAATATAT
2238387 AAAAAAATTAAA
1 -AAAAAATTAAA
2238399 ATTAAATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
28 15 0.47
29 8 0.25
31 9 0.28
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (30 bp):
AAAAAATTAAATTTTTTATAATTAATATAT
Found at i:2239639 original size:2 final size:2
Alignment explanation
Indices: 2239634--2239667 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2239624 TTCACTCTCA
2239634 AT AT 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 AT AT
2239668 GATAACTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2239933 original size:31 final size:31
Alignment explanation
Indices: 2239898--2239961 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
2239888 AACTCTATGC
2239898 ATAAAAAATATAAATATATATGTAAATATAT
1 ATAAAAAATATAAATATATATGTAAATATAT
2239929 ATAAAAAATATAAATATATATGTAAATATAT
1 ATAAAAAATATAAATATATATGTAAATATAT
2239960 AT
1 AT
2239962 GTATATGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (31 bp):
ATAAAAAATATAAATATATATGTAAATATAT
Found at i:2239973 original size:12 final size:12
Alignment explanation
Indices: 2239908--2239964 Score: 70
Period size: 12 Copynumber: 5.2 Consensus size: 12
2239898 ATAAAAAATA
2239908 TAAATATATATG
1 TAAATATATATG
2239920 TAAATATATA--
1 TAAATATATATG
*
2239930 TAAA-A-A-ATA
1 TAAATATATATG
2239939 TAAATATATATG
1 TAAATATATATG
2239951 TAAATATATATG
1 TAAATATATATG
2239963 TA
1 TA
2239965 TATGTATATT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 5 0.13
10 5 0.13
11 1 0.03
12 26 0.67
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (12 bp):
TAAATATATATG
Found at i:2240567 original size:36 final size:39
Alignment explanation
Indices: 2240494--2240568 Score: 104
Period size: 37 Copynumber: 2.0 Consensus size: 39
2240484 ATAATTAGTA
*
2240494 AATTTGATTATTAATAAATTATTTTTTAAAATTTAATAT
1 AATTTGATTATTAATAAATTATTTTTTAAAATATAATAT
2240533 AATTT-ATT-TTATATAAA-TATTTTTTAAAA-ATAATAT
1 AATTTGATTATTA-ATAAATTATTTTTTAAAATATAATAT
2240569 CTGATCGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 6 0.18
37 15 0.44
38 8 0.24
39 5 0.15
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (39 bp):
AATTTGATTATTAATAAATTATTTTTTAAAATATAATAT
Found at i:2241644 original size:18 final size:18
Alignment explanation
Indices: 2241621--2241659 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
2241611 GTTATATATA
2241621 TATATATATGTATGTATG
1 TATATATATGTATGTATG
2241639 TATATATATGTATGTATG
1 TATATATATGTATGTATG
2241657 TAT
1 TAT
2241660 GCCAGATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (18 bp):
TATATATATGTATGTATG
Found at i:2247956 original size:24 final size:23
Alignment explanation
Indices: 2247912--2247956 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2247902 ATATAGATAA
*
2247912 TTAAATTTAATATTAATTTTTAT
1 TTAAATTTAATATTAAATTTTAT
*
2247935 TTAAATTATATTATTAAATTTT
1 TTAAATT-TAATATTAAATTTT
2247957 TATTATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTAAATTTAATATTAAATTTTAT
Found at i:2247960 original size:14 final size:14
Alignment explanation
Indices: 2247917--2247965 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
2247907 GATAATTAAA
*
2247917 TTTAATATT-AATT
1 TTTATTATTAAATT
2247930 TTTA-T-TTAAA-T
1 TTTATTATTAAATT
*
2247941 TATATTATTAAATT
1 TTTATTATTAAATT
2247955 TTTATTATTAA
1 TTTATTATTAA
2247966 TAAATTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
11 6 0.20
12 4 0.13
13 9 0.30
14 11 0.37
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTATTATTAAATT
Found at i:2247961 original size:11 final size:12
Alignment explanation
Indices: 2247911--2247961 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 12
2247901 TATATAGATA
*
2247911 ATTAAATTTAAT
1 ATTAAATTTATT
2247923 ATT-AATTT-TT
1 ATTAAATTTATT
2247933 ATTTAAATTATATT
1 A-TTAAATT-TATT
2247947 ATTAAATTT-TT
1 ATTAAATTTATT
2247958 ATTA
1 ATTA
2247962 TTAATAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
10 2 0.06
11 13 0.38
12 8 0.24
13 8 0.24
14 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTAAATTTATT
Found at i:2247972 original size:22 final size:22
Alignment explanation
Indices: 2247947--2247988 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2247937 AAATTATATT
2247947 ATTAAATT-TTTATTATTAATAA
1 ATTAAATTATTTA-TATTAATAA
2247969 ATTAAATTATTTATATTAAT
1 ATTAAATTATTTATATTAAT
2247989 TTTATCAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTAAATTATTTATATTAATAA
Found at i:2247972 original size:25 final size:24
Alignment explanation
Indices: 2247912--2247960 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
2247902 ATATAGATAA
*
2247912 TTAAATTTAA-TATTAATTTTTAT
1 TTAAATTAAATTATTAATTTTTAT
*
2247935 TTAAATTATATTATTAAATTTTTAT
1 TTAAATTAAATTATT-AATTTTTAT
2247960 T
1 T
2247961 ATTAATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 8 0.36
24 4 0.18
25 10 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTAAATTAAATTATTAATTTTTAT
Found at i:2248195 original size:26 final size:25
Alignment explanation
Indices: 2248149--2248205 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 25
2248139 AATAAAAATT
2248149 TATTAATATACTTTAATAAAATTAA
1 TATTAATATACTTTAATAAAATTAA
2248174 TAATTAATA-A-TTTATATCAAAATTAA
1 T-ATTAATATACTTTA-AT-AAAATTAA
2248200 TATTAA
1 TATTAA
2248206 ATTTAATGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 4 0.14
25 9 0.31
26 16 0.55
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (25 bp):
TATTAATATACTTTAATAAAATTAA
Found at i:2248202 original size:12 final size:12
Alignment explanation
Indices: 2248165--2248212 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
2248155 TATACTTTAA
2248165 TAAAATTAATAAT
1 TAAAATTAAT-AT
*
2248178 TAATAATTTATAT
1 TAA-AATTAATAT
*
2248191 CAAAATTAATAT
1 TAAAATTAATAT
*
2248203 TAAATTTAAT
1 TAAAATTAAT
2248213 GATTTAAAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 16 0.55
13 7 0.24
14 6 0.21
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAATTAATAT
Found at i:2248757 original size:2 final size:2
Alignment explanation
Indices: 2248752--2248809 Score: 68
Period size: 2 Copynumber: 29.5 Consensus size: 2
2248742 TGTGTGTGTG
*
2248752 TA TA TA TA TA TA TA TA CA TA TA -A TA TGA T- TCA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T-A TA TA TA TA TA
2248794 TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA T
2248810 GATTCAGCTA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
1 3 0.06
2 43 0.88
3 3 0.06
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2248793 original size:32 final size:32
Alignment explanation
Indices: 2248752--2248815 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
2248742 TGTGTGTGTG
2248752 TATATATATATATATACATATAATATGATTCA
1 TATATATATATATATACATATAATATGATTCA
*
2248784 TATATATATATATATATATATAATATGATTCA
1 TATATATATATATATACATATAATATGATTCA
2248816 GCTAAAGTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (32 bp):
TATATATATATATATACATATAATATGATTCA
Found at i:2252343 original size:2 final size:2
Alignment explanation
Indices: 2252331--2252374 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
2252321 TCGAACCTTT
2252331 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2252371 TA TA
1 TA TA
2252375 ATTGTAATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2252805 original size:26 final size:27
Alignment explanation
Indices: 2252775--2252829 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
2252765 TAGTATAATT
*
2252775 TATTTATTTAA-TTATTTT-AATTTTAA
1 TATTTATTTAACTT-TTTTAAACTTTAA
2252801 TATTTATTTAACTTTTTTAAACTTTAA
1 TATTTATTTAACTTTTTTAAACTTTAA
2252828 TA
1 TA
2252830 ATTAGCAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (27 bp):
TATTTATTTAACTTTTTTAAACTTTAA
Found at i:2253044 original size:22 final size:22
Alignment explanation
Indices: 2253028--2253139 Score: 67
Period size: 23 Copynumber: 5.2 Consensus size: 22
2253018 CTATTTTACT
2253028 ATTATATAATATATATTATATA
1 ATTATATAATATATATTATATA
* * *
2253050 ATTTTATAATATAAAAATATATA
1 ATTATATAATAT-ATATTATATA
*
2253073 A-TATTATAATATAAATATTA-AAA
1 ATTA-TATAATAT--ATATTATATA
*
2253096 ATTATATTATAT-TATT-TAT-
1 ATTATATAATATATATTATATA
* * *
2253115 ATT-TTTAA-ATATAATAAATA
1 ATTATATAATATATATTATATA
2253135 ATTAT
1 ATTAT
2253140 TAAATTAATT
Statistics
Matches: 68, Mismatches: 13, Indels: 19
0.68 0.13 0.19
Matches are distributed among these distances:
17 2 0.03
18 6 0.09
19 5 0.07
20 8 0.12
21 1 0.01
22 12 0.18
23 27 0.40
24 7 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTATATAATATATATTATATA
Found at i:2253074 original size:23 final size:23
Alignment explanation
Indices: 2253044--2253087 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2253034 TAATATATAT
*
2253044 TATATAATTTTATAATATAAAAA
1 TATATAATATTATAATATAAAAA
2253067 TATATAATATTATAATATAAA
1 TATATAATATTATAATATAAA
2253088 TATTAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATATAATATTATAATATAAAAA
Found at i:2253168 original size:15 final size:15
Alignment explanation
Indices: 2253150--2253185 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
2253140 TAAATTAATT
*
2253150 AAAATAAAATTTTAA
1 AAAATAAAATTATAA
2253165 AAAAT-AAATTATAA
1 AAAATAAAATTATAA
2253179 AAAATAA
1 AAAATAA
2253186 TATAAATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAATAAAATTATAA
Found at i:2253213 original size:23 final size:23
Alignment explanation
Indices: 2253153--2253217 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
2253143 ATTAATTAAA
* *
2253153 ATAAAATTTTAAAAAATAAATTAT
1 ATAAAA-TTTAATAAATCAATTAT
* *
2253177 A-AAAAATAATATAAATCAATTAT
1 ATAAAATTTA-ATAAATCAATTAT
2253200 ATAAAATTTAATAAATCA
1 ATAAAATTTAATAAATCA
2253218 CATTTTAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
22 2 0.06
23 24 0.73
24 7 0.21
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (23 bp):
ATAAAATTTAATAAATCAATTAT
Found at i:2255723 original size:13 final size:13
Alignment explanation
Indices: 2255707--2255736 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2255697 GCCGGTAAGT
2255707 AATGGATTCAGTC
1 AATGGATTCAGTC
2255720 AATGGATTCAGTC
1 AATGGATTCAGTC
2255733 AATG
1 AATG
2255737 TGTTTTGCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.30
Consensus pattern (13 bp):
AATGGATTCAGTC
Found at i:2259539 original size:36 final size:34
Alignment explanation
Indices: 2259457--2259542 Score: 102
Period size: 36 Copynumber: 2.5 Consensus size: 34
2259447 AAAAAATTAT
* *
2259457 ATATCTATA-TAAATTTAATATATATAAGTATTTT
1 ATAT-TATATTAATTTTAATATATATAAGTATTTC
*
2259491 ATATTATATTAATTTTAATATGTATATAATTATTTC
1 ATATTATATTAATTTTAATA--TATATAAGTATTTC
*
2259527 ATATTTTATTAATTTT
1 ATATTATATTAATTTT
2259543 TTTTTTCCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
33 4 0.09
34 14 0.31
36 27 0.60
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (34 bp):
ATATTATATTAATTTTAATATATATAAGTATTTC
Found at i:2259824 original size:19 final size:18
Alignment explanation
Indices: 2259797--2259832 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2259787 TGTTCAAGTG
*
2259797 AAAACAAAAGCAAAAAAAA
1 AAAAAAAAAG-AAAAAAAA
2259816 AAAAAAAAAGAAAAAAA
1 AAAAAAAAAGAAAAAAA
2259833 CACATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.89, C:0.06, G:0.06, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAGAAAAAAAA
Found at i:2261363 original size:25 final size:25
Alignment explanation
Indices: 2261335--2261382 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
2261325 TTATTTTAAA
2261335 TAATATTAATGTAAAAATAAAATTT
1 TAATATTAATGTAAAAATAAAATTT
* *
2261360 TAATATTATTTTAAAAATAAAAT
1 TAATATTAATGTAAAAATAAAAT
2261383 AAACTTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
TAATATTAATGTAAAAATAAAATTT
Found at i:2265327 original size:13 final size:13
Alignment explanation
Indices: 2265309--2265333 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2265299 TATTAAAAAA
2265309 ATTAAATTTAATT
1 ATTAAATTTAATT
2265322 ATTAAATTTAAT
1 ATTAAATTTAAT
2265334 ATTTGATTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTAAATTTAATT
Found at i:2265416 original size:6 final size:6
Alignment explanation
Indices: 2265407--2265460 Score: 54
Period size: 6 Copynumber: 8.5 Consensus size: 6
2265397 TAATATTTAA
* * *
2265407 AAATTT AAATTT AAATTT AAATTC ACATTT AAATAT AGAATAATT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT A-AAT--TT AAATTT
2265458 AAA
1 AAA
2265461 ATTATACATA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
6 31 0.79
7 3 0.08
8 3 0.08
9 2 0.05
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (6 bp):
AAATTT
Found at i:2267609 original size:5 final size:5
Alignment explanation
Indices: 2267601--2267627 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2267591 TTAGAAGATT
2267601 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
2267628 GTAAATTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:2267903 original size:20 final size:20
Alignment explanation
Indices: 2267875--2267913 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2267865 AATTTGATTC
*
2267875 AATTTTATATTAAATTATTT
1 AATTATATATTAAATTATTT
*
2267895 AATTATATATTAATTTATT
1 AATTATATATTAAATTATT
2267914 GATTGATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
AATTATATATTAAATTATTT
Found at i:2267942 original size:14 final size:14
Alignment explanation
Indices: 2267916--2267952 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
2267906 AATTTATTGA
2267916 TTGATTT-ATTTAT
1 TTGATTTAATTTAT
2267929 TTGATTTAATTTAT
1 TTGATTTAATTTAT
*
2267943 TTAATTTAAT
1 TTGATTTAAT
2267953 AATTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (14 bp):
TTGATTTAATTTAT
Found at i:2267952 original size:5 final size:4
Alignment explanation
Indices: 2267889--2267950 Score: 52
Period size: 4 Copynumber: 14.8 Consensus size: 4
2267879 TTATATTAAA
* * * * *
2267889 TTAT TTAA TTAT ATAT TAAT TTAT TGAT TGAT TTAT TTAT TTGAT TTAAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT-AT TT-AT
2267939 TTAT TTAAT TTA
1 TTAT TT-AT TTA
2267951 ATAATTTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
4 35 0.74
5 12 0.26
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (4 bp):
TTAT
Found at i:2268255 original size:7 final size:7
Alignment explanation
Indices: 2268219--2268294 Score: 75
Period size: 7 Copynumber: 10.9 Consensus size: 7
2268209 ACCGTAATCA
*
2268219 TATATTT
1 TATATAT
2268226 TATATAT
1 TATATAT
2268233 T-TATAT
1 TATATAT
* *
2268239 TATTTTT
1 TATATAT
2268246 TATATAT
1 TATATAT
2268253 TATATAT
1 TATATAT
2268260 TATATAT
1 TATATAT
*
2268267 TATTTAT
1 TATATAT
2268274 TA-ATTATT
1 TATA-TA-T
*
2268282 TTTATAT
1 TATATAT
2268289 TATATA
1 TATATA
2268295 ATTTTATTCT
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
6 6 0.11
7 45 0.80
8 4 0.07
9 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TATATAT
Found at i:2268266 original size:36 final size:36
Alignment explanation
Indices: 2268218--2268294 Score: 104
Period size: 36 Copynumber: 2.1 Consensus size: 36
2268208 AACCGTAATC
* *
2268218 ATATATTTTATA-TATTTATATTATT-TTTTATATATT
1 ATATATTATATATTATTTAT-TAATTATTTT-TATATT
2268254 ATATATTATATATTATTTATTAATTATTTTTATATT
1 ATATATTATATATTATTTATTAATTATTTTTATATT
2268290 ATATA
1 ATATA
2268295 ATTTTATTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
36 26 0.70
37 11 0.30
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (36 bp):
ATATATTATATATTATTTATTAATTATTTTTATATT
Found at i:2268279 original size:11 final size:11
Alignment explanation
Indices: 2268223--2268291 Score: 54
Period size: 11 Copynumber: 6.0 Consensus size: 11
2268213 TAATCATATA
2268223 TTTTATA-TAT
1 TTTTATATTAT
*
2268233 TTATATTATT-T
1 TTTTA-TATTAT
2268244 TTTATATATTAT
1 TTT-TATATTAT
2268256 ATATTATATATTAT
1 -T-TT-TATATTAT
2268270 TTATTA-ATTAT
1 TT-TTATATTAT
2268281 TTTTATATTAT
1 TTTTATATTAT
2268292 ATAATTTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
10 7 0.14
11 21 0.43
12 7 0.14
13 3 0.06
14 11 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTATATTAT
Found at i:2268487 original size:2 final size:2
Alignment explanation
Indices: 2268480--2268504 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2268470 ACTTAGCATG
2268480 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
2268505 TATTTTTTAT
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:2268734 original size:21 final size:21
Alignment explanation
Indices: 2268709--2268754 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2268699 ATAATATATC
2268709 TTTAAAA-TAAATTTTAATAAA
1 TTTAAAATTAAA-TTTAATAAA
* *
2268730 TTTAAAATTTAATTTAATTAA
1 TTTAAAATTAAATTTAATAAA
2268751 TTTA
1 TTTA
2268755 TATAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTAAAATTAAATTTAATAAA
Found at i:2269989 original size:14 final size:13
Alignment explanation
Indices: 2269972--2270005 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
2269962 AAATTTAATT
2269972 ATAAAAATATATAA
1 ATAAAAATATA-AA
*
2269986 ATAATAATATAAA
1 ATAAAAATATAAA
2269999 ATAAAAA
1 ATAAAAA
2270006 AGTTTCATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
ATAAAAATATAAA
Found at i:2282138 original size:13 final size:13
Alignment explanation
Indices: 2282114--2282148 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2282104 TATTTTCATA
2282114 TTAAATTT-ATAT
1 TTAAATTTAATAT
*
2282126 TTATATTTAATAT
1 TTAAATTTAATAT
2282139 TTAAATTTAA
1 TTAAATTTAA
2282149 ATAATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTAAATTTAATAT
Found at i:2288559 original size:51 final size:51
Alignment explanation
Indices: 2288504--2288658 Score: 166
Period size: 57 Copynumber: 2.9 Consensus size: 51
2288494 CAGGAGATCT
*
2288504 AGCTCTAAAAGGTGGAGGAGGAGGTGGAGGGGCTACAAGAGACCCAGCACC
1 AGCTCTAAAAGGTGGAGGAGGAGGTGGAGGGGCTACAGGAGACCCAGCACC
* * *
2288555 AGCTCTAACAGATGCTGGAGGAGGAGGAGGTGGAGGAGCTACAGGAGACCCAGCTCC
1 AGCTCTAA-A-A----GGTGGAGGAGGAGGTGGAGGGGCTACAGGAGACCCAGCACC
* ** * * *
2288612 AGCTCTAATAGGTGCTGGAGGAGGAGGAGAGGCTATAGGAGACCCAG
1 AGCTCTAAAAGGTGGAGGAGGAGGTGGAGGGGCTACAGGAGACCCAG
2288659 GTCCAATAGG
Statistics
Matches: 86, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
51 38 0.44
52 1 0.01
53 1 0.01
55 1 0.01
57 45 0.52
ACGTcount: A:0.30, C:0.19, G:0.39, T:0.12
Consensus pattern (51 bp):
AGCTCTAAAAGGTGGAGGAGGAGGTGGAGGGGCTACAGGAGACCCAGCACC
Found at i:2288584 original size:57 final size:57
Alignment explanation
Indices: 2288517--2288640 Score: 203
Period size: 57 Copynumber: 2.2 Consensus size: 57
2288507 TCTAAAAGGT
*
2288517 GGAGGAGGAGGTGGAGGGGCTACAAGAGACCCAGCACCAGCTCTAACAGATGCTGGA
1 GGAGGAGGAGGTGGAGGAGCTACAAGAGACCCAGCACCAGCTCTAACAGATGCTGGA
* * * *
2288574 GGAGGAGGAGGTGGAGGAGCTACAGGAGACCCAGCTCCAGCTCTAATAGGTGCTGGA
1 GGAGGAGGAGGTGGAGGAGCTACAAGAGACCCAGCACCAGCTCTAACAGATGCTGGA
2288631 GGAGGAGGAG
1 GGAGGAGGAG
2288641 AGGCTATAGG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.28, C:0.19, G:0.42, T:0.11
Consensus pattern (57 bp):
GGAGGAGGAGGTGGAGGAGCTACAAGAGACCCAGCACCAGCTCTAACAGATGCTGGA
Found at i:2296280 original size:21 final size:22
Alignment explanation
Indices: 2296251--2296296 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2296241 TGTTCAGACA
** *
2296251 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2296273 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2296294 AGT
1 AGT
2296297 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:2298213 original size:27 final size:27
Alignment explanation
Indices: 2298175--2298242 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
2298165 AACCACCCAT
* *
2298175 TGTTTGTAAAAAATTGTGGTTACTTTG
1 TGTTTGTCAAAAATGGTGGTTACTTTG
* *
2298202 TGTTTGTCAAAAATGGTGGTTTCTTTT
1 TGTTTGTCAAAAATGGTGGTTACTTTG
*
2298229 TATTTGTCAAAAAT
1 TGTTTGTCAAAAAT
2298243 AGTGACATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.49
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTACTTTG
Found at i:2301653 original size:2 final size:2
Alignment explanation
Indices: 2301646--2301686 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2301636 TTACAAGGAA
*
2301646 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2301687 ATAGCAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2306151 original size:23 final size:25
Alignment explanation
Indices: 2306107--2306160 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 25
2306097 AGTTTGAAAG
* *
2306107 TATT-TTTAATTTTTAAATTTG-AT
1 TATTATTTAATTTATAAAGTTGAAT
*
2306130 T-TTATTTAATTTATAAGGTTGAAT
1 TATTATTTAATTTATAAAGTTGAAT
2306154 TATTATT
1 TATTATT
2306161 AAAAGATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 2 0.08
23 15 0.60
24 3 0.12
25 5 0.20
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.61
Consensus pattern (25 bp):
TATTATTTAATTTATAAAGTTGAAT
Found at i:2307124 original size:5 final size:5
Alignment explanation
Indices: 2307106--2307144 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
2307096 TTTTTCATTC
* *
2307106 AAATT AAGATT AAATT AAATT AAATC AATTT AAATT AAA
1 AAATT AA-ATT AAATT AAATT AAATT AAATT AAATT AAA
2307145 ATTTTTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:2312398 original size:17 final size:17
Alignment explanation
Indices: 2312376--2312409 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2312366 GGAGCCCTTA
2312376 CTAGATGCATTATGTTG
1 CTAGATGCATTATGTTG
*
2312393 CTAGATGTATTATGTTG
1 CTAGATGCATTATGTTG
2312410 GATCTAGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.44
Consensus pattern (17 bp):
CTAGATGCATTATGTTG
Found at i:2315374 original size:16 final size:16
Alignment explanation
Indices: 2315349--2315393 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 16
2315339 TATCAAAAAT
2315349 ATTAAATAAAT-TTTA
1 ATTAAATAAATATTTA
2315364 ATTATAATAAATATTTA
1 ATTA-AATAAATATTTA
2315381 A-T-AA-AAATATTTA
1 ATTAAATAAATATTTA
2315394 TTTGGCTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 9 0.32
14 2 0.07
15 4 0.14
16 8 0.29
17 5 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTAAATAAATATTTA
Found at i:2315382 original size:17 final size:15
Alignment explanation
Indices: 2315349--2315382 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 15
2315339 TATCAAAAAT
2315349 ATTAAATAAATTTTA
1 ATTAAATAAATTTTA
2315364 ATTATAATAAATATTTA
1 ATTA-AATAAAT-TTTA
2315381 AT
1 AT
2315383 AAAAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 7 0.41
17 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTAAATAAATTTTA
Found at i:2316049 original size:2 final size:2
Alignment explanation
Indices: 2316042--2316079 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2316032 CCATAATCTT
2316042 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2316080 AAATTAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2321574 original size:2 final size:2
Alignment explanation
Indices: 2321567--2321608 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
2321557 ATTTTATAAA
* *
2321567 AT AT AT AT AT AT AT AT CAA AT -T GT 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 AT AT AT AT AT AT
2321609 CAAAATAAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.94
3 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2323862 original size:2 final size:2
Alignment explanation
Indices: 2323849--2323878 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2323839 TCTCCTCCAC
*
2323849 AT AT AT AA 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
2323879 TTTTATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2324346 original size:19 final size:18
Alignment explanation
Indices: 2324290--2324346 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
2324280 ATTTAATTTT
**
2324290 TTTAAAATTTTTTATATA
1 TTTAAAATAATTTATATA
2324308 TTTAAAATAATATTATATA
1 TTTAAAATAAT-TTATATA
2324327 TTTAAATATAAATTTA-ATA
1 TTTAAA-AT-AATTTATATA
2324346 T
1 T
2324347 AAATATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 9 0.26
19 17 0.50
20 5 0.15
21 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAAAATAATTTATATA
Found at i:2324570 original size:14 final size:14
Alignment explanation
Indices: 2324548--2324590 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2324538 TTAATTTAAT
2324548 AAAATAATATATTA
1 AAAATAATATATTA
** *
2324562 AGTATAATATTTTA
1 AAAATAATATATTA
2324576 AAAATAATA-ATTA
1 AAAATAATATATTA
2324589 AA
1 AA
2324591 TAATTTTTAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (14 bp):
AAAATAATATATTA
Found at i:2324606 original size:25 final size:27
Alignment explanation
Indices: 2324548--2324600 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
2324538 TTAATTTAAT
2324548 AAAATAATATATTAAGTATAATATTTTA
1 AAAATAATATATTAAG-ATAATATTTTA
2324576 AAAATAATA-ATTAA-ATAAT-TTTTA
1 AAAATAATATATTAAGATAATATTTTA
2324600 A
1 A
2324601 TTAATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 6 0.24
25 5 0.20
27 5 0.20
28 9 0.36
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (27 bp):
AAAATAATATATTAAGATAATATTTTA
Found at i:2325133 original size:12 final size:12
Alignment explanation
Indices: 2325118--2325143 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2325108 AGAGGGGGAA
2325118 GAGGAGGAAGAT
1 GAGGAGGAAGAT
2325130 GAGGAGGAAGAT
1 GAGGAGGAAGAT
2325142 GA
1 GA
2325144 AGAAGAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.50, T:0.08
Consensus pattern (12 bp):
GAGGAGGAAGAT
Found at i:2328981 original size:20 final size:20
Alignment explanation
Indices: 2328956--2328999 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
2328946 TTGTATATTC
2328956 ATGTCCATGTAGTTTTCGTA
1 ATGTCCATGTAGTTTTCGTA
2328976 ATGTCCATGTAGTTTTCGTA
1 ATGTCCATGTAGTTTTCGTA
2328996 ATGT
1 ATGT
2329000 AGTTTTCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.45
Consensus pattern (20 bp):
ATGTCCATGTAGTTTTCGTA
Found at i:2329001 original size:14 final size:14
Alignment explanation
Indices: 2328982--2329009 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2328972 CGTAATGTCC
2328982 ATGTAGTTTTCGTA
1 ATGTAGTTTTCGTA
2328996 ATGTAGTTTTCGTA
1 ATGTAGTTTTCGTA
2329010 TTATTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.50
Consensus pattern (14 bp):
ATGTAGTTTTCGTA
Found at i:2329047 original size:2 final size:2
Alignment explanation
Indices: 2329040--2329074 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2329030 AAATTTCCTT
2329040 TA TA TA 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 TA TA TA T
2329075 GGCATGAGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2335439 original size:20 final size:21
Alignment explanation
Indices: 2335407--2335445 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2335397 ATAAATATTT
2335407 TATATTAAAATTTA-ATTAAA
1 TATATTAAAATTTATATTAAA
2335427 TATA-TAAATATTTATATTA
1 TATATTAAA-ATTTATATTA
2335446 TTTTTAATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TATATTAAAATTTATATTAAA
Found at i:2336938 original size:21 final size:21
Alignment explanation
Indices: 2336913--2336963 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2336903 TACACAATTA
* *
2336913 TATAATTTAATTTTTTTA-TTT
1 TATAATTT-ATCTATTTATTTT
2336934 TATAATTCTATCTATTTATTTT
1 TATAATT-TATCTATTTATTTT
2336956 TATAATTT
1 TATAATTT
2336964 CACAAATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (21 bp):
TATAATTTATCTATTTATTTT
Found at i:2345589 original size:42 final size:42
Alignment explanation
Indices: 2345542--2345626 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
2345532 CGTGTGCAGA
2345542 GAGCATGGTGTGGTGGGAGACATGAGGGATGTGTGGCCTAAT
1 GAGCATGGTGTGGTGGGAGACATGAGGGATGTGTGGCCTAAT
2345584 GAGCATGGTGTGGTGGGAGACATGAGGGATGTGTGGCCTAAT
1 GAGCATGGTGTGGTGGGAGACATGAGGGATGTGTGGCCTAAT
2345626 G
1 G
2345627 CTCGGGTGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.21, C:0.09, G:0.46, T:0.24
Consensus pattern (42 bp):
GAGCATGGTGTGGTGGGAGACATGAGGGATGTGTGGCCTAAT
Found at i:2345608 original size:23 final size:23
Alignment explanation
Indices: 2345542--2345609 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
2345532 CGTGTGCAGA
2345542 GAGCATGGTGTGGTGGGAGACAT
1 GAGCATGGTGTGGTGGGAGACAT
***
2345565 GAG---GGATGT-GTGGCCTA-AT
1 GAGCATGG-TGTGGTGGGAGACAT
2345584 GAGCATGGTGTGGTGGGAGACAT
1 GAGCATGGTGTGGTGGGAGACAT
2345607 GAG
1 GAG
2345610 GGATGTGTGG
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
19 5 0.15
20 7 0.21
21 6 0.18
22 7 0.21
23 8 0.24
ACGTcount: A:0.22, C:0.09, G:0.47, T:0.22
Consensus pattern (23 bp):
GAGCATGGTGTGGTGGGAGACAT
Found at i:2345617 original size:23 final size:23
Alignment explanation
Indices: 2345549--2345619 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
2345539 AGAGAGCATG
2345549 GTGTGGTGGGAGACATGAGGGA-
1 GTGTGGTGGGAGACATGAGGGAT
*** *
2345571 -TGT-GTGGCCTA-ATGA-GCAT
1 GTGTGGTGGGAGACATGAGGGAT
2345590 GGTGTGGTGGGAGACATGAGGGAT
1 -GTGTGGTGGGAGACATGAGGGAT
2345614 GTGTGG
1 GTGTGG
2345620 CCTAATGCTC
Statistics
Matches: 35, Mismatches: 8, Indels: 11
0.65 0.15 0.20
Matches are distributed among these distances:
18 2 0.06
19 4 0.11
20 5 0.14
21 6 0.17
22 5 0.14
23 10 0.29
24 3 0.09
ACGTcount: A:0.20, C:0.07, G:0.49, T:0.24
Consensus pattern (23 bp):
GTGTGGTGGGAGACATGAGGGAT
Found at i:2347013 original size:6 final size:6
Alignment explanation
Indices: 2346991--2347034 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
2346981 AGTATAATTA
* * * *
2346991 ATATAT ATACAT ATATAT GTATAT ATAAAT ATATAT GTATAT AT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT AT
2347035 GCATGGAAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (6 bp):
ATATAT
Found at i:2347015 original size:18 final size:18
Alignment explanation
Indices: 2346992--2347034 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
2346982 GTATAATTAA
*
2346992 TATATATACATATATATG
1 TATATATAAATATATATG
2347010 TATATATAAATATATATG
1 TATATATAAATATATATG
2347028 TATATAT
1 TATATAT
2347035 GCATGGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (18 bp):
TATATATAAATATATATG
Found at i:2348056 original size:3 final size:3
Alignment explanation
Indices: 2348048--2348073 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2348038 TAATGTATGT
2348048 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
2348074 GTATTTTGGA
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:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:2353376 original size:168 final size:167
Alignment explanation
Indices: 2353099--2353432 Score: 632
Period size: 168 Copynumber: 2.0 Consensus size: 167
2353089 AAATTTTCAA
2353099 AAAAAATATATAAATATTTTATAAATTTAATAAGAAAATCAATAATTAAAATAAAATAATTAATT
1 AAAAAATATATAAATATTTTATAAATTTAATAAGAAAATCAATAATTAAAATAAAATAATTAATT
*
2353164 TAATAAATTATTAAGAACATATATATCTTTCGTTGTTTGTGTTTTATACATTTTTATATTTAATA
66 TAATAAATTATTAAGAACATATATATCTTTCATTGTTTGTGTTTTATACATTTTTATATTTAATA
*
2353229 AATTATATATACAATAATTTTATATAATAATATAATT
131 AATAATATATACAATAATTTTATATAATAATATAATT
2353266 AAAAAATATATAAATATTTTATAAATTTAATAAGAAAATCAATAATTAAAAATAAAATAATTAAT
1 AAAAAATATATAAATATTTTATAAATTTAATAAGAAAATCAATAATT-AAAATAAAATAATTAAT
2353331 TTAATAAATTATTAAGAACATATATATCTTTCATTGTTTGTGTTTTATACATTTTTATATTTAAT
65 TTAATAAATTATTAAGAACATATATATCTTTCATTGTTTGTGTTTTATACATTTTTATATTTAAT
*
2353396 AAATAATATATCCAATAATTTTATATAATAATATAAT
130 AAATAATATATACAATAATTTTATATAATAATATAAT
2353433 AATTTGTTTT
Statistics
Matches: 163, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
167 47 0.29
168 116 0.71
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (167 bp):
AAAAAATATATAAATATTTTATAAATTTAATAAGAAAATCAATAATTAAAATAAAATAATTAATT
TAATAAATTATTAAGAACATATATATCTTTCATTGTTTGTGTTTTATACATTTTTATATTTAATA
AATAATATATACAATAATTTTATATAATAATATAATT
Found at i:2358577 original size:2 final size:2
Alignment explanation
Indices: 2358572--2358596 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2358562 ATGTATATAG
2358572 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
2358597 AAACATGGCT
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2363218 original size:2 final size:2
Alignment explanation
Indices: 2363211--2363237 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2363201 GAAATAAGCA
2363211 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 A
2363238 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2368780 original size:2 final size:2
Alignment explanation
Indices: 2368773--2368804 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2368763 GCTCCCCTCC
*
2368773 CT CT CT CT CT CT CT AT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2368805 TTTTTTTTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2369254 original size:26 final size:28
Alignment explanation
Indices: 2369206--2369263 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
2369196 AATTTTTTTA
* *
2369206 TTTTAATTTTATTAAAATAAAC-ATTAT
1 TTTTAATTTTAATAAAATAAACAATAAT
2369233 TTTTAA-TTTAATAATAAT-AACAATAAT
1 TTTTAATTTTAATAA-AATAAACAATAAT
2369260 TTTT
1 TTTT
2369264 TTTAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 10 0.37
27 17 0.63
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (28 bp):
TTTTAATTTTAATAAAATAAACAATAAT
Found at i:2369302 original size:20 final size:20
Alignment explanation
Indices: 2369279--2369317 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2369269 AATTTAATTT
2369279 TAAAAAATAATTATTAAAAA
1 TAAAAAATAATTATTAAAAA
* *
2369299 TAAAAAATTATTTTTAAAA
1 TAAAAAATAATTATTAAAA
2369318 TTTTAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAAAATAATTATTAAAAA
Done.