Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 171 of 211
Found at i:53310035 original size:44 final size:44
Alignment explanation
Indices: 53309939--53310060 Score: 131
Period size: 44 Copynumber: 2.8 Consensus size: 44
53309929 ATATCGGTCA
* * * *
53309939 TATCTCCCTAGATAGCAGTGGAATAGGTTGAAAATTATGAGTCC
1 TATCTCCCTAGACAGCAGTGGAATAGGTCGAAGATTAAGAGTCC
*
53309983 TATCTCCCTAGACAGCAGTGGAATAGGTCGAAGATTACAGA-TCT
1 TATCTCCCTAGACAGCAGTGGAATAGGTCGAAGATTA-AGAGTCC
* * * *
53310027 TATTTCCCTA-AGCAGTAGTGGAGTAGATCGAAGA
1 TATCTCCCTAGA-CAGCAGTGGAATAGGTCGAAGA
53310061 CCGCAGCCTT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
43 1 0.01
44 64 0.96
45 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (44 bp):
TATCTCCCTAGACAGCAGTGGAATAGGTCGAAGATTAAGAGTCC
Found at i:53310285 original size:76 final size:76
Alignment explanation
Indices: 53310139--53310287 Score: 203
Period size: 76 Copynumber: 2.0 Consensus size: 76
53310129 GCAGTGAAGC
* * * * * * *
53310139 AGATTGAAGACACCAGTCTTGCCTCTTTGGGTTGACAGCGGAGCAGACTGAAGATAGCAGATATT
1 AGATCGAAGACACCAGCCTTGCCTCTCTGGGTTGACAGCGGAGCAAACTAAAGAAAGCAGATACT
53310204 GCCTTCCTGTT
66 GCCTTCCTGTT
53310215 AGATCGAAGACACCAGCCTTGCCTCTCTGGGTTTG-CAGCGGAGCAAACTAAAGAAAGCAGAT-C
1 AGATCGAAGACACCAGCCTTGCCTCTCTGGG-TTGACAGCGGAGCAAACTAAAGAAAGCAGATAC
53310278 TGACCTTCCT
65 TG-CCTTCCT
53310288 ATACTGACAG
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
75 2 0.03
76 59 0.92
77 3 0.05
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (76 bp):
AGATCGAAGACACCAGCCTTGCCTCTCTGGGTTGACAGCGGAGCAAACTAAAGAAAGCAGATACT
GCCTTCCTGTT
Found at i:53310366 original size:89 final size:87
Alignment explanation
Indices: 53310215--53310496 Score: 350
Period size: 89 Copynumber: 3.2 Consensus size: 87
53310205 CCTTCCTGTT
* * *
53310215 AGATCGAAGACACCAGCCTTGCCT-CTCTGGGTTTGCAGCGGAGCAAACTAAAGAAAGCAGATCT
1 AGATCGAAGACACCAGCCTTGCCTCCT-TGGG-TTGCAGCGGAGCAGACTGAAGAAAGTAGATCT
*
53310279 GACCTTCCTATACTGACAGCGAAGC
64 G-CCTTCCTGTACTGACAGCGAAGC
* *
53310304 AGATCGAAGACACAAGCCTTGCCTCCTTGGGATTGCAGTGGAGCAGACTGAAGAAAGTAGATCTC
1 AGATCGAAGACACCAGCCTTGCCTCCTTGGG-TTGCAGCGGAGCAGACTGAAGAAAGTAGATCT-
*
53310369 GTCTTCCTGTACTGACAGCGAAGC
64 GCCTTCCTGTACTGACAGCGAAGC
* * * ** *
53310393 AGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGCCAGCGGAGCAGACTGAATATTGTAGATTTT
1 AGATCGAAGACACCAGCCTTGCCTCCTTGGGTTG-CAGCGGAGCAGACTGAAGAAAGTAGA-TCT
* *
53310458 GCCTTCCTGTACTGACAGTGAAAC
64 GCCTTCCTGTACTGACAGCGAAGC
*
53310482 AGATCGAAAACACCA
1 AGATCGAAGACACCA
53310497 ACTTTGTGTC
Statistics
Matches: 168, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
88 3 0.02
89 160 0.95
90 5 0.03
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.21
Consensus pattern (87 bp):
AGATCGAAGACACCAGCCTTGCCTCCTTGGGTTGCAGCGGAGCAGACTGAAGAAAGTAGATCTGC
CTTCCTGTACTGACAGCGAAGC
Found at i:53310509 original size:89 final size:88
Alignment explanation
Indices: 53310215--53310528 Score: 344
Period size: 89 Copynumber: 3.5 Consensus size: 88
53310205 CCTTCCTGTT
* * * * *
53310215 AGATCGAAGACACCAGCCTTGCCTCTCTGGGTTTGCAGCGGAGCAAACTAAAGAAAGCAGATCT-
1 AGATCGAAGACACCAACCTTGCCTCCCTGGG-TTGCAGCGGAGCAGACTGAAGAAAGTAGATCTC
*
53310279 GACCTTCCTATACTGACAGCGAAGC
65 G-CCTTCCTGTACTGACAGCGAAGC
* *
53310304 AGATCGAAGACA-CAAGCCTTGCCTCCTTGGGATTGCAGTGGAGCAGACTGAAGAAAGTAGATCT
1 AGATCGAAGACACCAA-CCTTGCCTCCCTGGG-TTGCAGCGGAGCAGACTGAAGAAAGTAGATCT
*
53310368 CGTCTTCCTGTACTGACAGCGAAGC
64 CGCCTTCCTGTACTGACAGCGAAGC
* * * ** * *
53310393 AGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGCCAGCGGAGCAGACTGAATATTGTAGATTTT
1 AGATCGAAGACACCAACCTTGCCTCCCTGGGTTG-CAGCGGAGCAGACTGAAGAAAGTAGATCTC
* *
53310458 GCCTTCCTGTACTGACAGTGAAAC
65 GCCTTCCTGTACTGACAGCGAAGC
* * ** * *
53310482 AGATCGAAAACACCAACTTTGTGTCCCTGTCGTTACAGCGGAGCAGA
1 AGATCGAAGACACCAACCTTGCCTCCCTG-GGTTGCAGCGGAGCAGA
53310529 TTAAAGCTGA
Statistics
Matches: 190, Mismatches: 30, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
88 5 0.03
89 179 0.94
90 6 0.03
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (88 bp):
AGATCGAAGACACCAACCTTGCCTCCCTGGGTTGCAGCGGAGCAGACTGAAGAAAGTAGATCTCG
CCTTCCTGTACTGACAGCGAAGC
Found at i:53312791 original size:3 final size:3
Alignment explanation
Indices: 53312769--53312839 Score: 115
Period size: 3 Copynumber: 23.3 Consensus size: 3
53312759 TGAATCTTCA
*
53312769 TAT TAT CTAT TAT AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
53312815 AAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
53312840 TTGTCATGAG
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
3 60 0.95
4 3 0.05
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:53314908 original size:46 final size:46
Alignment explanation
Indices: 53314845--53314956 Score: 161
Period size: 46 Copynumber: 2.4 Consensus size: 46
53314835 CACTAATATG
*
53314845 TAGCCCAAGCTACCACTGATACGTAGCCATAGCTACCACTGAAATA
1 TAGCCGAAGCTACCACTGATACGTAGCCATAGCTACCACTGAAATA
* * * * *
53314891 TAGTCGAAGCTACCACTGATATGTAGTCGTAGCTACCACTGAAATG
1 TAGCCGAAGCTACCACTGATACGTAGCCATAGCTACCACTGAAATA
*
53314937 TTGCCGAAGCTACCACTGAT
1 TAGCCGAAGCTACCACTGAT
53314957 CAATAACACC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (46 bp):
TAGCCGAAGCTACCACTGATACGTAGCCATAGCTACCACTGAAATA
Found at i:53314954 original size:23 final size:23
Alignment explanation
Indices: 53314842--53314955 Score: 131
Period size: 23 Copynumber: 5.0 Consensus size: 23
53314832 CCACACTAAT
* *
53314842 ATGTAGCCCAAGCTACCACTGAT
1 ATGTAGCCGAAGCTACCACTGAA
*
53314865 ACGTAGCC-ATAGCTACCACTGAA
1 ATGTAGCCGA-AGCTACCACTGAA
* * *
53314888 ATATAGTCGAAGCTACCACTGAT
1 ATGTAGCCGAAGCTACCACTGAA
* *
53314911 ATGTAGTCGTAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGAA
*
53314934 ATGTTGCCGAAGCTACCACTGA
1 ATGTAGCCGAAGCTACCACTGA
53314956 TCAATAACAC
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
22 1 0.01
23 75 0.97
24 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (23 bp):
ATGTAGCCGAAGCTACCACTGAA
Found at i:53321761 original size:11 final size:11
Alignment explanation
Indices: 53321747--53321773 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
53321737 TTATTTTTAT
53321747 TTTTAAAATAA
1 TTTTAAAATAA
53321758 TTTTAAAATAA
1 TTTTAAAATAA
53321769 TTTTA
1 TTTTA
53321774 TTTTTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTTAAAATAA
Found at i:53331573 original size:3 final size:3
Alignment explanation
Indices: 53331565--53331607 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
53331555 TGGAGAGTTT
53331565 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
53331608 TGGTAAAAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:53336373 original size:8 final size:8
Alignment explanation
Indices: 53336360--53336398 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
53336350 TGTTTAAGTT
53336360 TTGGGCTA
1 TTGGGCTA
53336368 TTGGGCTA
1 TTGGGCTA
*
53336376 TTGGGCTG
1 TTGGGCTA
53336384 TTGGG-TA
1 TTGGGCTA
53336391 TTTGGGCT
1 -TTGGGCT
53336399 TTAGGGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
7 1 0.04
8 25 0.93
9 1 0.04
ACGTcount: A:0.08, C:0.10, G:0.41, T:0.41
Consensus pattern (8 bp):
TTGGGCTA
Found at i:53336617 original size:94 final size:94
Alignment explanation
Indices: 53336519--53336699 Score: 238
Period size: 94 Copynumber: 1.9 Consensus size: 94
53336509 AAGATTTGTT
* *
53336519 GTTGTAGCTTCAATCCGACCCACTACAACTTCA-GAGGTATAAGATTTGTAGCTTCAAACTGCTC
1 GTTGTAGCTTCAATCCGACCCACTACAACTTCATG-GGTATAAGATTTGCAGCTTCAAACTACTC
*
53336583 CATTGCAACTTCAGGGAGATAAGGTTCACC
65 CACTGCAACTTCAGGGAGATAAGGTTCACC
* * * * * * **
53336613 GTTGTAGTTTCAATCCGACCTACTGCAATTTTATGGGTATAGGATTTGCAGCTTCAATTTACTCC
1 GTTGTAGCTTCAATCCGACCCACTACAACTTCATGGGTATAAGATTTGCAGCTTCAAACTACTCC
*
53336678 ACTGCAACTTTAGGGAGATAAG
66 ACTGCAACTTCAGGGAGATAAG
53336700 ATTCGTACTG
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
94 73 0.99
95 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (94 bp):
GTTGTAGCTTCAATCCGACCCACTACAACTTCATGGGTATAAGATTTGCAGCTTCAAACTACTCC
ACTGCAACTTCAGGGAGATAAGGTTCACC
Found at i:53342991 original size:64 final size:61
Alignment explanation
Indices: 53342919--53343138 Score: 265
Period size: 64 Copynumber: 3.6 Consensus size: 61
53342909 ATGCAAGCAT
*
53342919 GTATATATATATGAAAATTAATAATATGTATATAAAGATATATAGATAAATAAGATAT-AA
1 GTATATATATATGAAAATTAATAATATGTATATAAAGATATATATATAAATAAGATATAAA
*
53342979 GTGTATATATAT--AAATTGAA-AATACT-TATATAAAGATATATATATATATAATAAGATATAA
1 GTATATATATATGAAAATT-AATAATA-TGTATATAAAG--ATATATATATA-AATAAGATATAA
53343040 A
61 A
* * *
53343041 GTATATATATATGAAAATTTAAACAACACGTATATAAAGATATATATATAATATAAGATATAAA
1 GTATATATATATGAAAA-TT-AATAATATGTATATAAAGATATATATATAA-ATAAGATATAAA
*
53343105 GCATATATATATGAAAATTAA-AA-ATGTATATAAA
1 GTATATATATATGAAAATTAATAATATGTATATAAA
53343139 TGTGTAGATA
Statistics
Matches: 140, Mismatches: 8, Indels: 24
0.81 0.05 0.14
Matches are distributed among these distances:
58 18 0.13
59 3 0.02
60 31 0.22
61 12 0.09
62 15 0.11
63 3 0.02
64 42 0.30
65 4 0.03
66 12 0.09
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.35
Consensus pattern (61 bp):
GTATATATATATGAAAATTAATAATATGTATATAAAGATATATATATAAATAAGATATAAA
Found at i:53343050 original size:29 final size:28
Alignment explanation
Indices: 53342956--53343052 Score: 88
Period size: 29 Copynumber: 3.3 Consensus size: 28
53342946 GTATATAAAG
* *
53342956 ATATATAGATAAATAAGATATAAGTGTAT
1 ATATATATATAAATAAGATATAA-AGTAT
* **
53342985 ATATATAAATTGAAAATACTTATATAAAG-AT
1 ATATATATA-T--AAATA-AGATATAAAGTAT
53343016 ATATATATATATAATAAGATATAAAGTAT
1 ATATATATATA-AATAAGATATAAAGTAT
53343045 ATATATAT
1 ATATATAT
53343053 GAAAATTTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
28 9 0.16
29 22 0.40
30 2 0.04
31 10 0.18
32 6 0.11
33 6 0.11
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.37
Consensus pattern (28 bp):
ATATATATATAAATAAGATATAAAGTAT
Found at i:53343052 original size:66 final size:64
Alignment explanation
Indices: 53342920--53343125 Score: 211
Period size: 66 Copynumber: 3.3 Consensus size: 64
53342910 TGCAAGCATG
* *
53342920 TATATATATATGAAAATTAATAATA-TGTATATAAAG--ATATATAGATA-AATAAGATAT-AAG
1 TATATATATAT-AAAATTAACAATACT-TATATAAAGATATATATATATATAATAAGATATAAAG
53342980 -
64 A
*
53342980 TGTATATATAT-AAATTGAA-AATACTTATATAAAGATATATATATATATAATAAGATATAAAG-
1 TATATATATATAAAATT-AACAATACTTATATAAAGATATATATATATATAATAAGATATAAAGA
* *
53343042 TATATATATATGAAAATTTAAACAACACGTATATAAAGATATATATATA-AT-ATAAGATATAAA
1 TATATATATAT-AAAA-TT-AACAATACTTATATAAAGATATATATATATATAATAAGATATAAA
53343105 GCA
63 G-A
*
53343108 TATATATAT-GAAAATTAA
1 TATATATATATAAAATTAA
53343126 AAATGTATAT
Statistics
Matches: 127, Mismatches: 7, Indels: 22
0.81 0.04 0.14
Matches are distributed among these distances:
58 18 0.14
59 3 0.02
60 20 0.16
61 10 0.08
62 15 0.12
63 2 0.02
64 20 0.16
65 6 0.05
66 33 0.26
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.35
Consensus pattern (64 bp):
TATATATATATAAAATTAACAATACTTATATAAAGATATATATATATATAATAAGATATAAAGA
Found at i:53344787 original size:44 final size:45
Alignment explanation
Indices: 53344715--53344823 Score: 112
Period size: 45 Copynumber: 2.4 Consensus size: 45
53344705 TTAAATCTTT
* ** * * *
53344715 CTCCACTGTAACTTCAAAGAGATAAGATTT-GTATCATCAATCTG
1 CTCCACTGCAACTTCAGGGAAATAAGATTTACTATCATCAAGCTG
* * * *
53344759 CTCCACTGCAACTTCAGGGAAATGAGATTTACTTTCTTCAGGCTG
1 CTCCACTGCAACTTCAGGGAAATAAGATTTACTATCATCAAGCTG
*
53344804 CTCCATTGCAACTTCAGGGA
1 CTCCACTGCAACTTCAGGGA
53344824 GATAGGACTT
Statistics
Matches: 53, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
44 25 0.47
45 28 0.53
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (45 bp):
CTCCACTGCAACTTCAGGGAAATAAGATTTACTATCATCAAGCTG
Found at i:53344883 original size:86 final size:86
Alignment explanation
Indices: 53344754--53344921 Score: 210
Period size: 86 Copynumber: 2.0 Consensus size: 86
53344744 TGTATCATCA
* * * * * * *
53344754 ATCTGCTCCACTGCAACTTCAGGGAAATGAGATTTACTTTCTTCAGGCTGCTCCATTGCAACTTC
1 ATCTGCTCCACTGCAACTTCAGAGAAATAAGATCTACTATCTTCAGGCTACTCCACTGCAACCTC
*
53344819 AGGGAGATAGGACTTGTCGTG
66 AAGGAGATAGGACTTGTCGTG
* * * * *
53344840 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCTATCTTCAGTCTACTCTACTGCAACCTC
1 ATCTGCTCCACTGCAACTTCAGAGAAATAAGATCTACTATCTTCAGGCTACTCCACTGCAACCTC
*
53344905 AATGAGATAGGACTTGT
66 AAGGAGATAGGACTTGT
53344922 AGCTTCAATA
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
86 68 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (86 bp):
ATCTGCTCCACTGCAACTTCAGAGAAATAAGATCTACTATCTTCAGGCTACTCCACTGCAACCTC
AAGGAGATAGGACTTGTCGTG
Found at i:53345158 original size:45 final size:44
Alignment explanation
Indices: 53345082--53345195 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 44
53345072 TTATAGCCTT
* * *
53345082 AATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGTTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGACTCGTAAT-TTC
* * ** *
53345127 AGTCTGCTCCACTGTAACTTTGGGGAGATAAGACTCGTAATTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGACTCGTAATTTC
* *
53345171 AACCTGCCCCACTGCAACTTCAGGG
1 AATCTGCTCCACTGCAACTTCAGGG
53345196 GGACGAGCTT
Statistics
Matches: 55, Mismatches: 14, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
44 22 0.40
45 33 0.60
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAAATAAGACTCGTAATTTC
Found at i:53345158 original size:96 final size:95
Alignment explanation
Indices: 53344942--53345169 Score: 220
Period size: 96 Copynumber: 2.5 Consensus size: 95
53344932 AAGTCTGATG
* * * *
53344942 CAATCTGCTCTACTGCAACTTCAGAGAGATAAGA-T--TCA-TCAT---TTTAATCCGCTCCACT
1 CAATCTGCTCCACTGCAACTTCAGAGAGATAAGACTCGTAATTTATAGCCTTAATCCGCTCCACT
* * * * *
53345000 GTAATTTCAGGGAGATAGGATTGGTTTCTT
66 GCAACTTCAGGGAAATAAGATTCGTTTCTT
* * * *
53345030 TAATCTTCTCCACTGCAACTTCAGAGAGATAAGA-TCTGTAATTTATAGCCTTAATCTGTTCCAC
1 CAATCTGCTCCACTGCAACTTCAGAGAGATAAGACTC-GTAATTTATAGCCTTAATCCGCTCCAC
53345094 TGCAACTTCAGGGAAATAAGATTCGTTATCTT
65 TGCAACTTCAGGGAAATAAGATTCGTT-TCTT
* * ** *
53345126 CAGTCTGCTCCACTGTAACTTTGGGGAGATAAGACTCGTAATTT
1 CAATCTGCTCCACTGCAACTTCAGAGAGATAAGACTCGTAATTT
53345170 CAACCTGCCC
Statistics
Matches: 111, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
88 32 0.29
91 2 0.02
92 3 0.03
95 34 0.31
96 38 0.34
97 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.34
Consensus pattern (95 bp):
CAATCTGCTCCACTGCAACTTCAGAGAGATAAGACTCGTAATTTATAGCCTTAATCCGCTCCACT
GCAACTTCAGGGAAATAAGATTCGTTTCTT
Found at i:53345485 original size:44 final size:44
Alignment explanation
Indices: 53345416--53345530 Score: 119
Period size: 44 Copynumber: 2.6 Consensus size: 44
53345406 ATTTTGACTA
* * *
53345416 GCTCCACTGCAACTTC-AGGGAGATAAGACTCA-T-ATCTTCAACTT
1 GCTCTACTGCAACTTCAAAGG-GATAAG-CTCAGTGA-CTTCAACCT
* * *
53345460 GTTCTACTGCAACTTCAAAGGGATAAGGTTAGTGACTTCAACCT
1 GCTCTACTGCAACTTCAAAGGGATAAGCTCAGTGACTTCAACCT
*
53345504 GCTCTACTGCAACTTCAAAGAGATAAG
1 GCTCTACTGCAACTTCAAAGGGATAAG
53345531 GTTTGTGACT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
43 2 0.03
44 54 0.90
45 4 0.07
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.27
Consensus pattern (44 bp):
GCTCTACTGCAACTTCAAAGGGATAAGCTCAGTGACTTCAACCT
Found at i:53345531 original size:44 final size:44
Alignment explanation
Indices: 53345451--53345543 Score: 150
Period size: 44 Copynumber: 2.1 Consensus size: 44
53345441 AGACTCATAT
* * *
53345451 CTTCAACTTGTTCTACTGCAACTTCAAAGGGATAAGGTTAGTGA
1 CTTCAACCTGCTCTACTGCAACTTCAAAGAGATAAGGTTAGTGA
*
53345495 CTTCAACCTGCTCTACTGCAACTTCAAAGAGATAAGGTTTGTGA
1 CTTCAACCTGCTCTACTGCAACTTCAAAGAGATAAGGTTAGTGA
53345539 CTTCA
1 CTTCA
53345544 CTGATCTGTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (44 bp):
CTTCAACCTGCTCTACTGCAACTTCAAAGAGATAAGGTTAGTGA
Found at i:53346433 original size:18 final size:16
Alignment explanation
Indices: 53346412--53346452 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
53346402 CCTTTCCTTC
53346412 TTCTTTTTTCTTTTCTTT
1 TTCTTTTTTC-TTT-TTT
*
53346430 TTCTTCTTTCTTTTTT
1 TTCTTTTTTCTTTTTT
53346446 TTCTTTT
1 TTCTTTT
53346453 CCTTTTTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 9 0.43
17 3 0.14
18 9 0.43
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTCTTTTTTCTTTTTT
Found at i:53346445 original size:27 final size:30
Alignment explanation
Indices: 53346409--53346476 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
53346399 TGGCCTTTCC
53346409 TTCTTCTTTTTTCTTTT-C-TTTTT-CTTCT
1 TTCTT-TTTTTTCTTTTCCTTTTTTCCTTCT
53346437 TTCTTTTTTTTCTTTTCCTTTTTTCCTTCT
1 TTCTTTTTTTTCTTTTCCTTTTTTCCTTCT
*
53346467 TTCCTTTTTT
1 TTCTTTTTTT
53346477 ATGAAACATT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
27 11 0.31
28 6 0.17
29 5 0.14
30 14 0.39
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (30 bp):
TTCTTTTTTTTCTTTTCCTTTTTTCCTTCT
Found at i:53346450 original size:22 final size:22
Alignment explanation
Indices: 53346409--53346475 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 22
53346399 TGGCCTTTCC
53346409 TTCTTCTTT-TTTCTTTTCTTT
1 TTCTTCTTTCTTTCTTTTCTTT
*
53346430 TTCTTCTTTCTTTTTTTTCTTT
1 TTCTTCTTTCTTTCTTTTCTTT
* * * *
53346452 TCCTTTTTTCCTTCTTTCCTTT
1 TTCTTCTTTCTTTCTTTTCTTT
53346474 TT
1 TT
53346476 TATGAAACAT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 9 0.24
22 29 0.76
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (22 bp):
TTCTTCTTTCTTTCTTTTCTTT
Found at i:53346460 original size:17 final size:16
Alignment explanation
Indices: 53346427--53346476 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
53346417 TTTTCTTTTC
53346427 TTTTT-CTTCTTT-CT
1 TTTTTCCTTCTTTCCT
53346441 TTTTT--TTCTTTTCCT
1 TTTTTCCTTC-TTTCCT
53346456 TTTTTCCTTCTTTCCT
1 TTTTTCCTTCTTTCCT
53346472 TTTTT
1 TTTTT
53346477 ATGAAACATT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
13 3 0.09
14 8 0.25
15 7 0.22
16 11 0.34
17 3 0.09
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTCCTTCTTTCCT
Found at i:53351066 original size:6 final size:6
Alignment explanation
Indices: 53351055--53351084 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
53351045 ATGCAAAAGG
53351055 GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT
53351085 AAAGTATAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
GTATAT
Found at i:53351165 original size:66 final size:61
Alignment explanation
Indices: 53351075--53351275 Score: 241
Period size: 64 Copynumber: 3.2 Consensus size: 61
53351065 ATGTATATGT
*
53351075 ATATGTATATAAAG-TATAAGATATAATAAGGAATATGCAAGCATGTATATATATATGAAAATTA
1 ATATGTATATAAAGATAT-ATATATAATAA-G-ATAT--AAG-ATGTATATATATATGAAAATTA
53351139 AA
60 AA
*
53351141 ATATGTATATAAAGATATATATATAATAAGATATAAAGTATATATATATATATGAAAATTGAAA
1 ATATGTATATAAAGATATATATATAATAAGATAT-AAG-ATGTATATATATATGAAAATT-AAA
* *
53351205 ATACGTATATAAAGATATATATA-ATATAAGATATAA-A-GCATATATATATGAAAATTAAA
1 ATATGTATATAAAGATATATATATA-ATAAGATATAAGATGTATATATATATGAAAATTAAA
53351264 A-ATGTATATAAA
1 ATATGTATATAAA
53351276 TGTGTAGATA
Statistics
Matches: 124, Mismatches: 8, Indels: 14
0.85 0.05 0.10
Matches are distributed among these distances:
58 10 0.08
59 4 0.03
60 17 0.14
61 1 0.01
63 26 0.21
64 38 0.31
65 1 0.01
66 24 0.19
67 3 0.02
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.33
Consensus pattern (61 bp):
ATATGTATATAAAGATATATATATAATAAGATATAAGATGTATATATATATGAAAATTAAA
Found at i:53355195 original size:23 final size:23
Alignment explanation
Indices: 53355165--53355215 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
53355155 GTCTTGTTGT
*
53355165 TGTAATATCCCGAAAATTTCTAC
1 TGTAATATCCCGAAAATTACTAC
*
53355188 TGTAATATCCTGAAAATTACTAC
1 TGTAATATCCCGAAAATTACTAC
*
53355211 AGTAA
1 TGTAA
53355216 GAAAGTAGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (23 bp):
TGTAATATCCCGAAAATTACTAC
Found at i:53358090 original size:25 final size:25
Alignment explanation
Indices: 53358062--53358209 Score: 106
Period size: 25 Copynumber: 6.4 Consensus size: 25
53358052 GGAGTTTAGC
53358062 GTGCTCTCTGATTATTAGCACGTCA
1 GTGCTCTCTGATTATTAGCACGTCA
*
53358087 GTGCTCTCTGATTACTAGCA---C-
1 GTGCTCTCTGATTATTAGCACGTCA
* * *
53358108 --GCTCTCTGATTACTAGCATGTTA
1 GTGCTCTCTGATTATTAGCACGTCA
* * *
53358131 GTGCTCTCCGATTATTAGCACATTA
1 GTGCTCTCTGATTATTAGCACGTCA
*
53358156 GTGCTCTCTG--T-TTAGCACATTC-
1 GTGCTCTCTGATTATTAGCAC-GTCA
* *
53358178 GTGCTCTCTG--TA-TAGCACTTTA
1 GTGCTCTCTGATTATTAGCACGTCA
53358200 GTGCTCTCTG
1 GTGCTCTCTG
53358210 TTTAATAGTG
Statistics
Matches: 104, Mismatches: 10, Indels: 21
0.77 0.07 0.16
Matches are distributed among these distances:
19 18 0.17
21 2 0.02
22 35 0.34
23 2 0.02
25 47 0.45
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (25 bp):
GTGCTCTCTGATTATTAGCACGTCA
Found at i:53358112 original size:44 final size:44
Alignment explanation
Indices: 53358064--53358151 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
53358054 AGTTTAGCGT
* *
53358064 GCTCTCTGATTATTAGCACGTCAGTGCTCTCTGATTACTAGCAC
1 GCTCTCTGATTACTAGCACGTCAGTGCTCTCCGATTACTAGCAC
* * *
53358108 GCTCTCTGATTACTAGCATGTTAGTGCTCTCCGATTATTAGCAC
1 GCTCTCTGATTACTAGCACGTCAGTGCTCTCCGATTACTAGCAC
53358152 ATTAGTGCTC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.35
Consensus pattern (44 bp):
GCTCTCTGATTACTAGCACGTCAGTGCTCTCCGATTACTAGCAC
Found at i:53358113 original size:19 final size:19
Alignment explanation
Indices: 53358089--53358125 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
53358079 GCACGTCAGT
53358089 GCTCTCTGATTACTAGCAC
1 GCTCTCTGATTACTAGCAC
53358108 GCTCTCTGATTACTAGCA
1 GCTCTCTGATTACTAGCA
53358126 TGTTAGTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.32
Consensus pattern (19 bp):
GCTCTCTGATTACTAGCAC
Found at i:53358173 original size:22 final size:22
Alignment explanation
Indices: 53358145--53358213 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
53358135 TCTCCGATTA
53358145 TTAGCACATTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
*
53358167 TTAGCACATTCGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
* *
53358189 ATAGCACTTTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
53358211 TTA
1 TTA
53358214 ATAGTGCATA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCTGT
Found at i:53358194 original size:69 final size:68
Alignment explanation
Indices: 53358062--53358207 Score: 158
Period size: 69 Copynumber: 2.1 Consensus size: 68
53358052 GGAGTTTAGC
* *
53358062 GTGCTCTCTGATTATTAGCACGTCAGTGCTCTCTGATTACTAGCACGCTCTCTGATTACTAGCA-
1 GTGCTCTCCGATTATTAGCACATCAGTGCTCTCTGATTACTAGCACGCTCTCTGA-TACTAGCAC
53358126 TGTTA
65 T-TTA
* *
53358131 GTGCTCTCCGATTATTAGCACATTAGTGCTCTCTGTTTAGC-A-CATTCGTGCTCTCTG-TA-TA
1 GTGCTCTCCGATTATTAGCACATCAGTGCTCTCTGATTA-CTAGCA--C--GCTCTCTGATACTA
53358192 GCACTTTA
61 GCACTTTA
53358200 GTGCTCTC
1 GTGCTCTC
53358208 TGTTTAATAG
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
68 2 0.03
69 52 0.78
70 5 0.07
72 8 0.12
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.38
Consensus pattern (68 bp):
GTGCTCTCCGATTATTAGCACATCAGTGCTCTCTGATTACTAGCACGCTCTCTGATACTAGCACT
TTA
Found at i:53368698 original size:23 final size:23
Alignment explanation
Indices: 53368662--53368705 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
53368652 GAGAGAAATG
*
53368662 TAATATCCCAAAAATTTCTACTA
1 TAATATCCCAAAAATTACTACTA
**
53368685 TAATATCCTGAAAATTACTAC
1 TAATATCCCAAAAATTACTAC
53368706 AGTAAGAAAG
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:0.43, C:0.20, G:0.02, T:0.34
Consensus pattern (23 bp):
TAATATCCCAAAAATTACTACTA
Found at i:53377041 original size:38 final size:38
Alignment explanation
Indices: 53376997--53377073 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
53376987 TGATTTAGGC
*
53376997 AAGGACCCACAAATATAAATAGAGGTCAAACTACGCAA
1 AAGGACCCACAAACATAAATAGAGGTCAAACTACGCAA
*
53377035 AAGGACCCACAAACATAGATAGAGGTCAAACTACGCAA
1 AAGGACCCACAAACATAAATAGAGGTCAAACTACGCAA
53377073 A
1 A
53377074 CTATCTTGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (38 bp):
AAGGACCCACAAACATAAATAGAGGTCAAACTACGCAA
Found at i:53378416 original size:29 final size:31
Alignment explanation
Indices: 53378362--53378426 Score: 100
Period size: 29 Copynumber: 2.2 Consensus size: 31
53378352 ATTGGACTTG
53378362 AATT-TTGAAATATAAAAAGTAAATAGACTA
1 AATTCTTGAAATATAAAAAGTAAATAGACTA
*
53378392 AATTCTTGAAA-ATAAAAA-TACATAGACTA
1 AATTCTTGAAATATAAAAAGTAAATAGACTA
53378421 AATTCT
1 AATTCT
53378427 AAATTTGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 16 0.48
30 11 0.33
31 6 0.18
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (31 bp):
AATTCTTGAAATATAAAAAGTAAATAGACTA
Found at i:53380289 original size:3 final size:3
Alignment explanation
Indices: 53380281--53380326 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
53380271 GTCAAAGCAA
53380281 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
53380327 AACCTTAACT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:53395147 original size:15 final size:15
Alignment explanation
Indices: 53395127--53395155 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
53395117 AAACAAAAAT
53395127 TTGGAGTTTACTTTG
1 TTGGAGTTTACTTTG
53395142 TTGGAGTTTACTTT
1 TTGGAGTTTACTTT
53395156 TTATCTAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.24, T:0.55
Consensus pattern (15 bp):
TTGGAGTTTACTTTG
Found at i:53397200 original size:19 final size:19
Alignment explanation
Indices: 53397172--53397209 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
53397162 TCACTACCAC
53397172 CCACCATAATCAAATTTGT
1 CCACCATAATCAAATTTGT
*
53397191 CCACCGTAATCAAATTTGT
1 CCACCATAATCAAATTTGT
53397210 TATTAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (19 bp):
CCACCATAATCAAATTTGT
Found at i:53397632 original size:54 final size:55
Alignment explanation
Indices: 53397540--53397673 Score: 161
Period size: 54 Copynumber: 2.5 Consensus size: 55
53397530 AAAGTTTTGG
* *
53397540 GGGTTTGAGAGGAAATAAAAGTTTT-AGGGGAAAGCAAAAGG-GAAAAAAATTGAA
1 GGGTTTG-GAGGAAGTAAAAGTTTTGAGGGGAAAGCAAAAGGAAAAAAAAATTGAA
* * *
53397594 GGGTTTGGAGGAAGTAGAAGTTTTGGGAGGGAAA-CAAAAGGAAAAAAAAATTGGA
1 GGGTTTGGAGGAAGTAAAAGTTTTGAG-GGGAAAGCAAAAGGAAAAAAAAATTGAA
53397649 -GGTTTGG-GGAAAGTAAAAGTTTTGA
1 GGGTTTGGAGG-AAGTAAAAGTTTTGA
53397674 AGAAAAAGTA
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
53 17 0.25
54 35 0.51
55 17 0.25
ACGTcount: A:0.43, C:0.01, G:0.34, T:0.21
Consensus pattern (55 bp):
GGGTTTGGAGGAAGTAAAAGTTTTGAGGGGAAAGCAAAAGGAAAAAAAAATTGAA
Found at i:53399352 original size:33 final size:33
Alignment explanation
Indices: 53399288--53399352 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
53399278 AAAGTTCAAG
* *
53399288 ATAAAAAAATTACTAAAATTATGTGTTAATAAC
1 ATAAAAAAATTACTAAAATTATATGTAAATAAC
53399321 ATAAAAAAATTTACTAAAA-TATCAT-TAAATAA
1 ATAAAAAAA-TTACTAAAATTAT-ATGTAAATAA
53399353 TTGAGGAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.32
Consensus pattern (33 bp):
ATAAAAAAATTACTAAAATTATATGTAAATAAC
Found at i:53405712 original size:21 final size:19
Alignment explanation
Indices: 53405688--53405727 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
53405678 CATAAGAATT
53405688 TTAAAAAATATATATTAAAAA
1 TTAAAAAA-AT-TATTAAAAA
*
53405709 TTAATAAAATTATTAAAAA
1 TTAAAAAAATTATTAAAAA
53405728 CGAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 2 0.11
21 7 0.39
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TTAAAAAAATTATTAAAAA
Found at i:53405736 original size:19 final size:20
Alignment explanation
Indices: 53405690--53405736 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
53405680 TAAGAATTTT
**
53405690 AAAAAATATATATTAAAAATT
1 AAAAAA-ATATATTAAAAACG
*
53405711 AATAAAAT-TATTAAAAACG
1 AAAAAAATATATTAAAAACG
53405730 AAAAAAA
1 AAAAAAA
53405737 AGTGAACACA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 15 0.68
20 2 0.09
21 5 0.23
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAAAAATATATTAAAAACG
Found at i:53406868 original size:7 final size:7
Alignment explanation
Indices: 53406858--53406882 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53406848 TTTTTCATTT
53406858 TTTAAAA
1 TTTAAAA
53406865 TTTAAAA
1 TTTAAAA
53406872 TTTAAAA
1 TTTAAAA
53406879 TTTA
1 TTTA
53406883 TTTTTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
TTTAAAA
Found at i:53407148 original size:21 final size:22
Alignment explanation
Indices: 53407124--53407182 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 22
53407114 TTTTAAAAAA
53407124 TAAAATAAAATTATAA-ATTTT
1 TAAAATAAAATTATAATATTTT
*
53407145 TAAAATAAAAAACTTATAATTTTTT
1 TAAAAT--AAAA-TTATAATATTTT
53407170 TAAAA-AAAATTAT
1 TAAAATAAAATTAT
53407183 GAAAATATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 10 0.30
22 4 0.12
23 4 0.12
24 6 0.18
25 9 0.27
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAAATAAAATTATAATATTTT
Found at i:53407149 original size:26 final size:27
Alignment explanation
Indices: 53407120--53407179 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 27
53407110 ATGATTTTAA
53407120 AAAATAAAATAAAATTATAA-ATTTTT
1 AAAATAAAATAAAATTATAATATTTTT
* *
53407146 AAAAT-AAA-AAACTTATAATTTTTTT
1 AAAATAAAATAAAATTATAATATTTTT
53407171 AAAA-AAAAT
1 AAAATAAAAT
53407180 TATGAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 9 0.31
25 15 0.52
26 5 0.17
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (27 bp):
AAAATAAAATAAAATTATAATATTTTT
Found at i:53407249 original size:19 final size:19
Alignment explanation
Indices: 53407209--53407250 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
53407199 TTTCAAATTC
* *
53407209 AAAAAATAAAAATAATTTT
1 AAAAAATAAAAATAAATCT
53407228 AAAAATATAAAAA-AAATCT
1 AAAAA-ATAAAAATAAATCT
53407247 AAAA
1 AAAA
53407251 TCCAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAAAATAAAAATAAATCT
Found at i:53420919 original size:42 final size:41
Alignment explanation
Indices: 53420787--53420943 Score: 145
Period size: 42 Copynumber: 3.8 Consensus size: 41
53420777 AGTACACTCA
* * *
53420787 TATGAG-TTTCAGTTTAACCCTTCTAGGTTTCAGTTCAGCTTT
1 TATGAGCTTT-AGTTTAACCCTTATGGGTTTCAGTTCAGC-TC
* ** *
53420829 TTTGAGCTTTAGTTTAACCCCAATGGGTTTCAGTTTAGCTC
1 TATGAGCTTTAGTTTAACCCTTATGGGTTTCAGTTCAGCTC
* * *
53420870 TTCTGAGCTTTAGATTAACCCTTATGGGTTTCTGTTCAGCTGC
1 -TATGAGCTTTAGTTTAACCCTTATGGGTTTCAGTTCAGCT-C
** * *
53420913 TATGAGCTTCCGTTTAGCCCTTACGGGTTTC
1 TATGAGCTTTAGTTTAACCCTTATGGGTTTC
53420944 CGTTTAGAAC
Statistics
Matches: 93, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
41 1 0.01
42 88 0.95
43 4 0.04
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.42
Consensus pattern (41 bp):
TATGAGCTTTAGTTTAACCCTTATGGGTTTCAGTTCAGCTC
Found at i:53428784 original size:17 final size:18
Alignment explanation
Indices: 53428749--53428783 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
53428739 TGTTTAAGCC
53428749 TAAACCTAGCCTATATTT
1 TAAACCTAGCCTATATTT
53428767 TAAACC-AGCCTA-ATTT
1 TAAACCTAGCCTATATTT
53428783 T
1 T
53428784 TCCCCAAGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 6 0.35
18 6 0.35
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.37
Consensus pattern (18 bp):
TAAACCTAGCCTATATTT
Found at i:53429331 original size:16 final size:16
Alignment explanation
Indices: 53429293--53429331 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
53429283 AAAATATAGA
*
53429293 TTGAAATTAACCAAGT
1 TTGAAATTAACCAAAT
* *
53429309 TTAAAATTGACCAAAT
1 TTGAAATTAACCAAAT
53429325 TTGAAAT
1 TTGAAAT
53429332 AAATACTATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (16 bp):
TTGAAATTAACCAAAT
Found at i:53438040 original size:18 final size:18
Alignment explanation
Indices: 53437997--53438039 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
53437987 TAAAAATTAT
53437997 TTTTAAAATTTAATAAAA
1 TTTTAAAATTTAATAAAA
**
53438015 CATTAAAATTTAA-AAAA
1 TTTTAAAATTTAATAAAA
53438032 TTTTAAAA
1 TTTTAAAA
53438040 AATTAATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
TTTTAAAATTTAATAAAA
Found at i:53447822 original size:28 final size:30
Alignment explanation
Indices: 53447798--53447855 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
53447788 TAATTATTGC
53447798 ATAAAAATAAATT-TTATATATTTATTATGTA
1 ATAAAAATAAATTATTATATATTTA-T-TGTA
* *
53447829 ATAAACATAATTTATTATATATTTATT
1 ATAAAAATAAATTATTATATATTTATT
53447856 TCTTAAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.04
31 12 0.50
32 11 0.46
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (30 bp):
ATAAAAATAAATTATTATATATTTATTGTA
Found at i:53459151 original size:13 final size:13
Alignment explanation
Indices: 53459133--53459160 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53459123 ACTAAATTGG
53459133 AAAGATGATAAAT
1 AAAGATGATAAAT
53459146 AAAGATGATAAAT
1 AAAGATGATAAAT
53459159 AA
1 AA
53459161 TAAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (13 bp):
AAAGATGATAAAT
Found at i:53459735 original size:26 final size:26
Alignment explanation
Indices: 53459686--53459758 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
53459676 CCCTATATAT
* *
53459686 GGCTTTTTGTGAGCTT-CTCGATTAAA
1 GGCTATTTGTGAGCTTCCT-AATTAAA
* *
53459712 GGCTCTTTGTGAGCTTCCTAATTAAT
1 GGCTATTTGTGAGCTTCCTAATTAAA
*
53459738 GGCTATCTG-GAGCTTCCTAAT
1 GGCTATTTGTGAGCTTCCTAAT
53459759 ATGACTCACT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
25 12 0.29
26 27 0.66
27 2 0.05
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (26 bp):
GGCTATTTGTGAGCTTCCTAATTAAA
Found at i:53462941 original size:39 final size:39
Alignment explanation
Indices: 53462898--53462988 Score: 146
Period size: 39 Copynumber: 2.3 Consensus size: 39
53462888 CATATTCACT
* *
53462898 TTTAAGCATATATCACATTACACGTATAATCACACAACA
1 TTTAAGCATATATCACAATACACATATAATCACACAACA
*
53462937 TTTAAGCATATATCACAATACACATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACACAACA
*
53462976 TTCAAGCATATAT
1 TTTAAGCATATAT
53462989 TACCATACTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.30
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACACATATAATCACACAACA
Found at i:53467297 original size:31 final size:31
Alignment explanation
Indices: 53467240--53467305 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
53467230 TTTAAAATAT
* * *
53467240 TTTTAAAATACTTTTTTATATTTTTTTTAAA
1 TTTTAAAATACTTTTTAAAATCTTTTTTAAA
*
53467271 TTTTAAAATA-TTTTTAAAATACTTTTTTTAA
1 TTTTAAAATACTTTTTAAAAT-CTTTTTTAAA
53467302 TTTT
1 TTTT
53467306 TTTAATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 8 0.27
31 22 0.73
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (31 bp):
TTTTAAAATACTTTTTAAAATCTTTTTTAAA
Found at i:53467317 original size:40 final size:40
Alignment explanation
Indices: 53467219--53467401 Score: 278
Period size: 40 Copynumber: 4.5 Consensus size: 40
53467209 AAATATATTT
*
53467219 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTATA
1 ATTTTTTTAATTTTAAAATATTTTAAAAATACTTTTTT-TA
* *
53467260 TTTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTT-AATTTTAAAATATTTTAAAAATACTTTTTTTA
53467301 ATTTTTTTAATTTTAAAATATTTTAAAAATACTTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTAAAAATACTTTTTTTA
*
53467341 AATTTTTTAATTTTAAAATATTTTAAAAATAC-TTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTAAAAATACTTTTTTTA
*
53467380 ATTTTTTAAAATTTTTAAAATA
1 ATTTTTT-TAA-TTTTAAAATA
53467402 AAAATGGGCC
Statistics
Matches: 133, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
39 13 0.10
40 64 0.48
41 26 0.20
42 30 0.23
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (40 bp):
ATTTTTTTAATTTTAAAATATTTTAAAAATACTTTTTTTA
Found at i:53467324 original size:16 final size:16
Alignment explanation
Indices: 53467305--53467366 Score: 50
Period size: 16 Copynumber: 4.4 Consensus size: 16
53467295 TTTTTAATTT
53467305 TTTTAATTTTAAAATA
1 TTTTAATTTTAAAATA
53467321 TTTT-A----AAAATA
1 TTTTAATTTTAAAATA
* *
53467332 CTTT--TTTT-AAATT
1 TTTTAATTTTAAAATA
53467345 TTTTAATTTTAAAATA
1 TTTTAATTTTAAAATA
53467361 TTTTAA
1 TTTTAA
53467367 AAATACTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
11 9 0.26
13 7 0.20
15 5 0.14
16 14 0.40
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTAATTTTAAAATA
Found at i:53468962 original size:20 final size:19
Alignment explanation
Indices: 53468919--53468964 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
53468909 GCAAAATAAA
*
53468919 TCAAAATAATTTTTAAAAT
1 TCAAAATAATTTATAAAAT
53468938 TCAAAAT-ATTTATATAAAT
1 TCAAAATAATTTATA-AAAT
53468957 TCCAAAAT
1 T-CAAAAT
53468965 TTATATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 6 0.25
19 12 0.50
20 6 0.25
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (19 bp):
TCAAAATAATTTATAAAAT
Found at i:53468966 original size:18 final size:19
Alignment explanation
Indices: 53468914--53468970 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 19
53468904 AAAATGCAAA
*
53468914 ATAAA-TCAAAATAATTTTT
1 ATAAATTCAAAAT-ATTTAT
53468933 A-AAATTCAAAATATTTAT
1 ATAAATTCAAAATATTTAT
*
53468951 ATAAATTCCAAA-ATTTAT
1 ATAAATTCAAAATATTTAT
53468969 AT
1 AT
53468971 TTTAAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 17 0.50
19 17 0.50
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAATTCAAAATATTTAT
Found at i:53491454 original size:16 final size:16
Alignment explanation
Indices: 53491429--53491461 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
53491419 CCATATTTAA
53491429 TTTTCTTTTTCACTTTT
1 TTTTCTTTTTCA-TTTT
53491446 TTTTC-TTTTCATTTT
1 TTTTCTTTTTCATTTT
53491461 T
1 T
53491462 AAAATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 6 0.38
17 5 0.31
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTCTTTTTCATTTT
Found at i:53493086 original size:18 final size:18
Alignment explanation
Indices: 53493065--53493115 Score: 77
Period size: 18 Copynumber: 2.8 Consensus size: 18
53493055 TTTTTTGACA
53493065 TTTTAA-ATTTTTATAAAT
1 TTTTAATATTTTTAT-AAT
53493083 TTTTAATATTTTTATAAT
1 TTTTAATATTTTTATAAT
*
53493101 TTCTAATATTTTTAT
1 TTTTAATATTTTTAT
53493116 TTATTTTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 23 0.74
19 8 0.26
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTAATATTTTTATAAT
Found at i:53493121 original size:19 final size:19
Alignment explanation
Indices: 53493071--53493121 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
53493061 GACATTTTAA
* *
53493071 ATTTTTATAAATTTTTAAT
1 ATTTTTATTAATTTCTAAT
53493090 ATTTTTA-TAATTTCTAAT
1 ATTTTTATTAATTTCTAAT
*
53493108 ATTTTTATTTATTT
1 ATTTTTATTAATTT
53493122 TTGAAGTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 16 0.57
19 12 0.43
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTTTATTAATTTCTAAT
Found at i:53493309 original size:20 final size:20
Alignment explanation
Indices: 53493243--53493309 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
53493233 CTTCATATTT
* * *
53493243 TATTTTTATAATATTTTAGAA
1 TATTTTAATAAT-TATTAAAA
* *
53493264 TCTTTTAATAATTATTAATA
1 TATTTTAATAATTATTAAAA
*
53493284 TTTTTTAATAATT-TTAAAA
1 TATTTTAATAATTATTAAAA
53493303 GTATTTT
1 -TATTTT
53493310 TAGTTTTGCA
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
19 5 0.14
20 22 0.59
21 10 0.27
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.58
Consensus pattern (20 bp):
TATTTTAATAATTATTAAAA
Found at i:53497423 original size:23 final size:23
Alignment explanation
Indices: 53497393--53497439 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
53497383 TAGGTATTAC
53497393 CTATAAAAAAGTGTTCTCTTTTT
1 CTATAAAAAAGTGTTCTCTTTTT
53497416 CTATAAAAAAGTGTTCTCTTTTT
1 CTATAAAAAAGTGTTCTCTTTTT
53497439 C
1 C
53497440 ATTGGAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.47
Consensus pattern (23 bp):
CTATAAAAAAGTGTTCTCTTTTT
Found at i:53505317 original size:25 final size:25
Alignment explanation
Indices: 53505276--53505390 Score: 90
Period size: 25 Copynumber: 4.6 Consensus size: 25
53505266 TCATATACAT
*
53505276 GTATGCTCATACAAGCTATGAATCG
1 GTATGCTCATACGAGCTATGAATCG
*
53505301 GTATGCTC-TCACGAGCTGTGAATCG
1 GTATGCTCAT-ACGAGCTATGAATCG
* *
53505326 GTAAT-CTCATACGAGTTAAGAATCG
1 GT-ATGCTCATACGAGCTATGAATCG
* * * * *
53505351 GTAAGCTCTTACAAGCTGTAAATCG
1 GTATGCTCATACGAGCTATGAATCG
* **
53505376 GGAAACTCATACGAG
1 GTATGCTCATACGAG
53505391 TCGTGTTGTG
Statistics
Matches: 70, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
24 2 0.03
25 65 0.93
26 3 0.04
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (25 bp):
GTATGCTCATACGAGCTATGAATCG
Found at i:53505359 original size:50 final size:50
Alignment explanation
Indices: 53505281--53505391 Score: 141
Period size: 50 Copynumber: 2.2 Consensus size: 50
53505271 TACATGTATG
* * * * * * * *
53505281 CTCATACAAGCTATGAATCGGTATGCTCTCACGAGCTGTGAATCGGTAAT
1 CTCATACGAGTTAAGAATCGGTAAGCTCTCACAAGCTGTAAATCGGGAAA
*
53505331 CTCATACGAGTTAAGAATCGGTAAGCTCTTACAAGCTGTAAATCGGGAAA
1 CTCATACGAGTTAAGAATCGGTAAGCTCTCACAAGCTGTAAATCGGGAAA
53505381 CTCATACGAGT
1 CTCATACGAGT
53505392 CGTGTTGTGT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.26
Consensus pattern (50 bp):
CTCATACGAGTTAAGAATCGGTAAGCTCTCACAAGCTGTAAATCGGGAAA
Found at i:53505717 original size:15 final size:15
Alignment explanation
Indices: 53505697--53505735 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
53505687 TATACGAATG
53505697 AATTTAA-CTCATTTC
1 AATTTAATCTCA-TTC
53505712 AATTTAATTCTCATTC
1 AATTTAA-TCTCATTC
53505728 AATTTAAT
1 AATTTAAT
53505736 TCAACATGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 8 0.36
16 10 0.45
17 4 0.18
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (15 bp):
AATTTAATCTCATTC
Found at i:53505730 original size:16 final size:17
Alignment explanation
Indices: 53505704--53505737 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
53505694 ATGAATTTAA
53505704 CTCATTTCAATTTAATT
1 CTCATTTCAATTTAATT
53505721 CTCA-TTCAATTTAATT
1 CTCATTTCAATTTAATT
53505737 C
1 C
53505738 AACATGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (17 bp):
CTCATTTCAATTTAATT
Found at i:53513562 original size:31 final size:31
Alignment explanation
Indices: 53513503--53513563 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
53513493 CTGACAATGT
* *
53513503 TTGCTGAAAAATTACTCCACTTGTCACATGC
1 TTGCTAAAAAATTACTCCACTTGCCACATGC
**
53513534 TTGCTAAAAAATTACTCCTTTTGCCACATG
1 TTGCTAAAAAATTACTCCACTTGCCACATG
53513564 TATCTATTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (31 bp):
TTGCTAAAAAATTACTCCACTTGCCACATGC
Found at i:53518933 original size:30 final size:30
Alignment explanation
Indices: 53518899--53518960 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
53518889 CTTAACAAGA
53518899 AAATGCCTCTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
* *
53518929 AAATGCCTTTAATATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
53518959 AA
1 AA
53518961 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.56, C:0.15, G:0.03, T:0.26
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAC
Found at i:53521327 original size:3 final size:3
Alignment explanation
Indices: 53521319--53521357 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
53521309 ATAAATTTCA
*
53521319 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
53521358 AATCGTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:53521452 original size:35 final size:35
Alignment explanation
Indices: 53521408--53521478 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
53521398 TACATACACT
* * *
53521408 TATACACATACCTTTTTTTGTAATATATATATACA
1 TATAAACATACCTATTTTTATAATATATATATACA
*
53521443 TATAAACATACCTATTTTTATAATATATTTATACA
1 TATAAACATACCTATTTTTATAATATATATATACA
53521478 T
1 T
53521479 GTATATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.39, C:0.13, G:0.01, T:0.46
Consensus pattern (35 bp):
TATAAACATACCTATTTTTATAATATATATATACA
Found at i:53521573 original size:44 final size:43
Alignment explanation
Indices: 53521497--53521581 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 43
53521487 TTTAATACAC
* *
53521497 GCACATATTTCCTATTTTTATAAACCTATATGTATATATACTT
1 GCACATATTTCATATTTTTATAAACATATATGTATATATACTT
* * *
53521540 GCACATATTTCATAATTTTTATATATATCTATGTATATATAC
1 GCACATATTTCAT-ATTTTTATAAACATATATGTATATATAC
53521582 ATATTTTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 12 0.33
44 24 0.67
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.47
Consensus pattern (43 bp):
GCACATATTTCATATTTTTATAAACATATATGTATATATACTT
Found at i:53526093 original size:534 final size:534
Alignment explanation
Indices: 53525085--53526154 Score: 2086
Period size: 534 Copynumber: 2.0 Consensus size: 534
53525075 CCAAAGTGGA
* *
53525085 ATGATGCAAATGCACAATGTGACTACCATGCAGGAATTACGGGGCACTCAATAGAGAATTGCATC
1 ATGATGCAAACGCACAATGTGACTAACATGCAGGAATTACGGGGCACTCAATAGAGAATTGCATC
53525150 ACCTTCAAAAAGCTAGTTGAAAAACTCATCAACATGGGTATTGTCAAGTTGGGTGACTCATCTAC
66 ACCTTCAAAAAGCTAGTTGAAAAACTCATCAACATGGGTATTGTCAAGTTGGGTGACTCATCTAC
53525215 TGCAGAAAATCCGCTACCCAATCATGGTTGACAATAGGGTGAATGTGATGTATGAAGAGATGTTG
131 TGCAGAAAATCCGCTACCCAATCATGGTTGACAATAGGGTGAATGTGATGTATGAAGAGATGTTG
*
53525280 GGAAATGTTCACATCAACGACGTGTCTGAAGACACAATTGCGAAGGGACCTTGTTAGATGTTCGC
196 GGAAATGTTCACATCAACGACGTGCCTGAAGACACAATTGCGAAGGGACCTTGTTAGATGTTCGC
53525345 CCTTATGAATTCCAGAGTGTTCTAAACAATTAGACTGCGGAAGAAATCCCTATAGTTTTTAGAGC
261 CCTTATGAATTCCAGAGTGTTCTAAACAATTAGACTGCGGAAGAAATCCCTATAGTTTTTAGAGC
53525410 TTTTCTAGAGTAATGTTCAGAACATTTTTGTTGTTTTTAGCCTAAAAGTGATGGAAATTCCTTTG
326 TTTTCTAGAGTAATGTTCAGAACATTTTTGTTGTTTTTAGCCTAAAAGTGATGGAAATTCCTTTG
53525475 TGAAATAGGCTCATATTTGAACGTTATTATTCTAATGAAATACATATTTGCGATCATTTTTGAGC
391 TGAAATAGGCTCATATTTGAACGTTATTATTCTAATGAAATACATATTTGCGATCATTTTTGAGC
*
53525540 AAATCTTCTTTCATAATTATTTCTGATTATTTTATTCTTTTGGATCTTCTTCCACATCATTCATT
456 AAATCTTCTTTCATAATTATTTCTGATTATTTCATTCTTTTGGATCTTCTTCCACATCATTCATT
53525605 CATAATCATATTGT
521 CATAATCATATTGT
53525619 ATGATGCAAACGCACAATGTGACTAACATGCAGGAATTACGGGGCACTCAATAGAGAATTGCATC
1 ATGATGCAAACGCACAATGTGACTAACATGCAGGAATTACGGGGCACTCAATAGAGAATTGCATC
53525684 ACCTTCAAAAAGCTAGTTGAAAAACTCATCAACATGGGTATTGTCAAGTTGGGTGACTCATCTAC
66 ACCTTCAAAAAGCTAGTTGAAAAACTCATCAACATGGGTATTGTCAAGTTGGGTGACTCATCTAC
*
53525749 TGCAGAAAATCCGCTACCCAATCATGGTTGACAATAGGGTGAATGTGATGTATGAAGAGGTGTTG
131 TGCAGAAAATCCGCTACCCAATCATGGTTGACAATAGGGTGAATGTGATGTATGAAGAGATGTTG
*
53525814 GGAAATGTTCACATCAACGATGTGCCTGAAGACACAATTGCGAAGGGACCTTGTTAGATGTTCGC
196 GGAAATGTTCACATCAACGACGTGCCTGAAGACACAATTGCGAAGGGACCTTGTTAGATGTTCGC
53525879 CCTTATGAATTCCAGAGTGTTCTAAACAATTAGACTGCGGAAGAAATCCCTATAGTTTTTAGAGC
261 CCTTATGAATTCCAGAGTGTTCTAAACAATTAGACTGCGGAAGAAATCCCTATAGTTTTTAGAGC
53525944 TTTTCTAGAGTAATGTTCAGAACATTTTTGTTGTTTTTAGCCTAAAAGTGATGGAAATTCCTTTG
326 TTTTCTAGAGTAATGTTCAGAACATTTTTGTTGTTTTTAGCCTAAAAGTGATGGAAATTCCTTTG
53526009 TGAAATAGGCTCATATTTGAACGTTATTATTCTAATGAAATACATATTTGCGATCATTTTTGAGC
391 TGAAATAGGCTCATATTTGAACGTTATTATTCTAATGAAATACATATTTGCGATCATTTTTGAGC
53526074 AAATCTTCTTTCATAATTATTTCTGATTATTTCATTCTTTTGGATCTTCTTCCACATCATTCATT
456 AAATCTTCTTTCATAATTATTTCTGATTATTTCATTCTTTTGGATCTTCTTCCACATCATTCATT
53526139 CATAATCATATTGT
521 CATAATCATATTGT
53526153 AT
1 AT
53526155 AAATAATTGT
Statistics
Matches: 530, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
534 530 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (534 bp):
ATGATGCAAACGCACAATGTGACTAACATGCAGGAATTACGGGGCACTCAATAGAGAATTGCATC
ACCTTCAAAAAGCTAGTTGAAAAACTCATCAACATGGGTATTGTCAAGTTGGGTGACTCATCTAC
TGCAGAAAATCCGCTACCCAATCATGGTTGACAATAGGGTGAATGTGATGTATGAAGAGATGTTG
GGAAATGTTCACATCAACGACGTGCCTGAAGACACAATTGCGAAGGGACCTTGTTAGATGTTCGC
CCTTATGAATTCCAGAGTGTTCTAAACAATTAGACTGCGGAAGAAATCCCTATAGTTTTTAGAGC
TTTTCTAGAGTAATGTTCAGAACATTTTTGTTGTTTTTAGCCTAAAAGTGATGGAAATTCCTTTG
TGAAATAGGCTCATATTTGAACGTTATTATTCTAATGAAATACATATTTGCGATCATTTTTGAGC
AAATCTTCTTTCATAATTATTTCTGATTATTTCATTCTTTTGGATCTTCTTCCACATCATTCATT
CATAATCATATTGT
Found at i:53526880 original size:26 final size:26
Alignment explanation
Indices: 53526837--53526887 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
53526827 GGGAAAAGAA
* *
53526837 AAAAGAAGAATAAAAAAATCAAAAAT
1 AAAAGAAAAAGAAAAAAATCAAAAAT
* *
53526863 AAAAGAAAAAGAAGAAAATGAAAAA
1 AAAAGAAAAAGAAAAAAATCAAAAA
53526888 AGGAAAGGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.78, C:0.02, G:0.12, T:0.08
Consensus pattern (26 bp):
AAAAGAAAAAGAAAAAAATCAAAAAT
Found at i:53527771 original size:14 final size:15
Alignment explanation
Indices: 53527752--53527781 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53527742 TTGAGTCAAA
53527752 AAAAATG-AAAATGG
1 AAAAATGAAAAATGG
53527766 AAAAATGAAAAATGG
1 AAAAATGAAAAATGG
53527781 A
1 A
53527782 GAGGTTAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (15 bp):
AAAAATGAAAAATGG
Found at i:53529337 original size:175 final size:175
Alignment explanation
Indices: 53529040--53529892 Score: 1388
Period size: 175 Copynumber: 4.9 Consensus size: 175
53529030 CGGAACGGAC
*
53529040 CGAAAAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATC
1 CGAAAGATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATC
*
53529105 TCCCTGAGATTACAGTGGAGCGGATTAAAATAAATGATCTTATCT-TTCTGAAGTTACAGTAGAG
66 TCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTT-TGAAGTTACAGTAGAG
*
53529169 TAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGAA
130 TAGATCGTATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGAA
* *
53529215 TGAAAGATTTCAGATCTTATCTTCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATC
1 CGAAAGATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATC
53529280 TCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTTTGAAGTTACAGTAGAGT
66 TCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTTTGAAGTTACAGTAGAGT
*
53529345 AGATCGTATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGAC
131 AGATCGTATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGAA
* *
53529390 CGAAAGATTTCAGGTCTTATCTCCCTGATATTACAGCGGAGCAGATTGAAGATAGTAATCCTATC
1 CGAAAGATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATC
* * * *
53529455 TACTTGAGATTACAGTGGAGCGGATTAAAATAAAGAATCTTATCTCTCTGAAGTTACAGTAGAGT
66 TCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTTTGAAGTTACAGTAGAGT
* *
53529520 AGATCGTATCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGAC
131 AGATCGTATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGAA
*
53529565 CGAAAGATTTTAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATC
1 CGAAAGATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATC
53529630 TCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTTTGAAGTTACAGTAGAGT
66 TCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTTTGAAGTTACAGTAGAGT
** *
53529695 AGATCACATCAAGTCTTATCTCCCTGAGATTACAGTGGAGCAG-A
131 AGATCGTATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGAA
* * * *
53529739 CCAAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGTAAATTGAAGCTAGTAATCCTAT
1 CGAAAG-ATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTAT
* * * * * *
53529804 CTCTCTGAGATTACAGTGGAACGAATTAAAATAAAGGATCTTATCTCTCT-AAGGTTATAATAGA
65 CTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTTTGAA-GTTACAGTAGA
* *
53529868 GTAGATCGTTTCAGATCTTATCTCC
129 GTAGATCGTATCAGGTCTTATCTCC
53529893 TAAAGTGGAG
Statistics
Matches: 632, Mismatches: 43, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
174 7 0.01
175 623 0.99
176 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (175 bp):
CGAAAGATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATC
TCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTTTGAAGTTACAGTAGAGT
AGATCGTATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGAA
Found at i:53531526 original size:3 final size:3
Alignment explanation
Indices: 53531518--53531559 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
53531508 AAATTTCATA
*
53531518 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
53531560 AATTGTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:53531680 original size:36 final size:37
Alignment explanation
Indices: 53531604--53531681 Score: 104
Period size: 36 Copynumber: 2.1 Consensus size: 37
53531594 ATTTTTGTAC
* * * *
53531604 ATACACTTATACACATACCTTTTTTTGTAATATATAT
1 ATACACATATAAACATACCTTATTTTATAATATATAT
*
53531641 ATACACATATAAACATACC-TATTTTATAATATATTT
1 ATACACATATAAACATACCTTATTTTATAATATATAT
53531677 ATACA
1 ATACA
53531682 TGTATATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 19 0.53
37 17 0.47
ACGTcount: A:0.41, C:0.15, G:0.01, T:0.42
Consensus pattern (37 bp):
ATACACATATAAACATACCTTATTTTATAATATATAT
Found at i:53531732 original size:44 final size:44
Alignment explanation
Indices: 53531684--53531785 Score: 98
Period size: 44 Copynumber: 2.3 Consensus size: 44
53531674 TTTATACATG
* * *
53531684 TATATATTTATAATACACGCACATATTTCCT-ATTTTTATAAACC
1 TATATATATAT-ATACACACACATATTTCATAATTTTTATAAACC
* ** *
53531728 TATATGTATATATACTTACACATATTTCATAATTTTTATATATATC
1 TATATATATATATACACACACATATTTCATAATTTTTATA-A-ACC
*
53531774 TATGTATATATA
1 TATATATATATA
53531786 CATATTTTAA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
43 15 0.33
44 18 0.39
45 1 0.02
46 12 0.26
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.47
Consensus pattern (44 bp):
TATATATATATATACACACACATATTTCATAATTTTTATAAACC
Found at i:53531786 original size:44 final size:43
Alignment explanation
Indices: 53531703--53531786 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 43
53531693 ATAATACACG
* *
53531703 CACATATTTCCTATTTTTATAAACCTATATGTATATATACTTA
1 CACATATTTCATATTTTTATAAACATATATGTATATATACTTA
* * *
53531746 CACATATTTCATAATTTTTATATATATCTATGTATATATAC
1 CACATATTTCAT-ATTTTTATAAACATATATGTATATATAC
53531787 ATATTTTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 11 0.31
44 24 0.69
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (43 bp):
CACATATTTCATATTTTTATAAACATATATGTATATATACTTA
Found at i:53537078 original size:9 final size:10
Alignment explanation
Indices: 53537059--53537088 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
53537049 AGAGATCACC
53537059 TTTTAATTTT
1 TTTTAATTTT
53537069 TTTTAATTTT
1 TTTTAATTTT
53537079 TTTTCAATTT
1 TTTT-AATTT
53537089 CTATTTTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.74
11 5 0.26
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTAATTTT
Found at i:53538006 original size:28 final size:28
Alignment explanation
Indices: 53537975--53538039 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
53537965 AGCTTTTGGC
* * *
53537975 TTTAGGGTTTATTATTTAATATTTTAAG
1 TTTAGGGTTTAGTATTTAAGATTTAAAG
* * * *
53538003 TTTAAGGTGTAGTGTTTAAGGTTTAAAG
1 TTTAGGGTTTAGTATTTAAGATTTAAAG
53538031 TTTAGGGTT
1 TTTAGGGTT
53538040 CATGTGTTTT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (28 bp):
TTTAGGGTTTAGTATTTAAGATTTAAAG
Found at i:53538632 original size:20 final size:21
Alignment explanation
Indices: 53538595--53538639 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
53538585 GAGGTCAAGA
*
53538595 TTTATGGTTTCATGTTTTGGG
1 TTTATGGTTTCATGTTTTGAG
* *
53538616 TTTAT-GTTTTATTTTTTGAG
1 TTTATGGTTTCATGTTTTGAG
53538636 TTTA
1 TTTA
53538640 AAGTTTTGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.13, C:0.02, G:0.20, T:0.64
Consensus pattern (21 bp):
TTTATGGTTTCATGTTTTGAG
Found at i:53544485 original size:13 final size:13
Alignment explanation
Indices: 53544467--53544494 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53544457 TGAACATGCT
53544467 TTGTAATAATTAA
1 TTGTAATAATTAA
53544480 TTGTAATAATTAA
1 TTGTAATAATTAA
53544493 TT
1 TT
53544495 TTTATAGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (13 bp):
TTGTAATAATTAA
Found at i:53559700 original size:16 final size:16
Alignment explanation
Indices: 53559679--53559709 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53559669 TAAAATTTTT
53559679 AAATAAAAAATAACAA
1 AAATAAAAAATAACAA
*
53559695 AAATAAAGAATAACA
1 AAATAAAAAATAACA
53559710 TTTATTCACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.13
Consensus pattern (16 bp):
AAATAAAAAATAACAA
Found at i:53575507 original size:23 final size:23
Alignment explanation
Indices: 53575481--53575578 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
53575471 ATAAGTGCCA
53575481 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
53575504 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
53575527 CACTGA-ATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
53575549 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
53575572 CACTGAT
1 CACTGAT
53575579 CAATAACACT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
22 21 0.30
23 50 0.70
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:53575546 original size:45 final size:46
Alignment explanation
Indices: 53575481--53575578 Score: 171
Period size: 45 Copynumber: 2.2 Consensus size: 46
53575471 ATAAGTGCCA
* *
53575481 CACTGATATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTAC
53575527 CACTGA-ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTAC
53575572 CACTGAT
1 CACTGAT
53575579 CAATAACACT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 43 0.88
46 6 0.12
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (46 bp):
CACTGATATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTAC
Found at i:53575678 original size:8 final size:8
Alignment explanation
Indices: 53575665--53575693 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
53575655 ACCCGGGACT
53575665 CACTGTAA
1 CACTGTAA
53575673 CACTGTAA
1 CACTGTAA
53575681 CACTGTAA
1 CACTGTAA
53575689 CACTG
1 CACTG
53575694 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:53578133 original size:31 final size:31
Alignment explanation
Indices: 53578100--53578157 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
53578090 GCATAGACCA
*
53578100 AAAATGGAGAAAAT-TG-ATACTTTAGATATC
1 AAAAT-GAGAAAATAAGTATACTTTAGATATC
53578130 AAAATGAGAAAATAAGTATACTTTAGAT
1 AAAATGAGAAAATAAGTATACTTTAGAT
53578158 GCTTAATCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 8 0.32
30 6 0.24
31 11 0.44
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (31 bp):
AAAATGAGAAAATAAGTATACTTTAGATATC
Found at i:53578647 original size:12 final size:13
Alignment explanation
Indices: 53578628--53578668 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 13
53578618 GCAATACGCG
*
53578628 AGGCAGTAAGCGC
1 AGGCAGTAAGCGA
53578641 A-GCAGTAAGC-A
1 AGGCAGTAAGCGA
53578652 AGGCAGTAAGCG-
1 AGGCAGTAAGCGA
53578664 AGGCA
1 AGGCA
53578669 TCGCCTCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 1 0.04
12 23 0.92
13 1 0.04
ACGTcount: A:0.37, C:0.20, G:0.37, T:0.07
Consensus pattern (13 bp):
AGGCAGTAAGCGA
Found at i:53582610 original size:10 final size:10
Alignment explanation
Indices: 53582591--53582621 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
53582581 ACTCTAAAGA
53582591 ATTT-AAAAT
1 ATTTCAAAAT
53582600 ATTTCAAAAT
1 ATTTCAAAAT
53582610 ATTTCAAAAT
1 ATTTCAAAAT
53582620 AT
1 AT
53582622 CTTTGTAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.19
10 17 0.81
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (10 bp):
ATTTCAAAAT
Found at i:53585358 original size:41 final size:41
Alignment explanation
Indices: 53585311--53585415 Score: 192
Period size: 41 Copynumber: 2.6 Consensus size: 41
53585301 CAGACGTTAC
53585311 GTCTAGCAGGCTAAATGCCGGTGATACATTTCAGACTATAT
1 GTCTAGCAGGCTAAATGCCGGTGATACATTTCAGACTATAT
*
53585352 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAT
1 GTCTAGCAGGCTAAATGCCGGTGATACATTTCAGACTATAT
*
53585393 GTCTAGCAGGCTAAGTGCCGGTG
1 GTCTAGCAGGCTAAATGCCGGTG
53585416 TACTGAATCA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (41 bp):
GTCTAGCAGGCTAAATGCCGGTGATACATTTCAGACTATAT
Found at i:53588407 original size:12 final size:12
Alignment explanation
Indices: 53588390--53588414 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53588380 TACGGATCAA
53588390 TCAGACAGAAAT
1 TCAGACAGAAAT
53588402 TCAGACAGAAAT
1 TCAGACAGAAAT
53588414 T
1 T
53588415 TCAAGCGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (12 bp):
TCAGACAGAAAT
Found at i:53589224 original size:22 final size:22
Alignment explanation
Indices: 53589199--53589269 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
53589189 ATTATTCGTA
53589199 ATATTTACATAAACTAACTTTG
1 ATATTTACATAAACTAACTTTG
* * * * *
53589221 ATATATAAACAAAATATTA-TTCGTA
1 ATATTTACATAAACTA--ACTT--TG
53589246 ATATTTACATAAACTAACTTTG
1 ATATTTACATAAACTAACTTTG
53589268 AT
1 AT
53589270 GAAGTCCATA
Statistics
Matches: 34, Mismatches: 10, Indels: 10
0.63 0.19 0.19
Matches are distributed among these distances:
22 15 0.44
23 3 0.09
24 3 0.09
25 13 0.38
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.39
Consensus pattern (22 bp):
ATATTTACATAAACTAACTTTG
Found at i:53589243 original size:47 final size:47
Alignment explanation
Indices: 53589175--53589269 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
53589165 GTATGTTGGT
53589175 TATATAAACAAAATATTATTCGTAATATTTACATAAACTAACTTTGA
1 TATATAAACAAAATATTATTCGTAATATTTACATAAACTAACTTTGA
53589222 TATATAAACAAAATATTATTCGTAATATTTACATAAACTAACTTTGA
1 TATATAAACAAAATATTATTCGTAATATTTACATAAACTAACTTTGA
53589269 T
1 T
53589270 GAAGTCCATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (47 bp):
TATATAAACAAAATATTATTCGTAATATTTACATAAACTAACTTTGA
Found at i:53589249 original size:23 final size:23
Alignment explanation
Indices: 53589176--53589249 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
53589166 TATGTTGGTT
53589176 ATATAAACAAAATATTATTCGTA
1 ATATAAACAAAATATTATTCGTA
** *
53589199 ATATTTACATAAACTA--ACTTTG-A
1 ATATAAACA-AAA-TATTA-TTCGTA
53589222 TATATAAACAAAATATTATTCGTA
1 -ATATAAACAAAATATTATTCGTA
53589246 ATAT
1 ATAT
53589250 TTACATAAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
22 2 0.05
23 19 0.50
24 15 0.39
25 2 0.05
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (23 bp):
ATATAAACAAAATATTATTCGTA
Found at i:53589249 original size:25 final size:25
Alignment explanation
Indices: 53589175--53589249 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
53589165 GTATGTTGGT
53589175 TATATAAACAAAATATTATTCGTAA
1 TATATAAACAAAATATTATTCGTAA
* * * * *
53589200 TATTTACATAAACTA--ACTT--TGA
1 TATATAAACAAAATATTA-TTCGTAA
53589222 TATATAAACAAAATATTATTCGTAA
1 TATATAAACAAAATATTATTCGTAA
53589247 TAT
1 TAT
53589250 TTACATAAAC
Statistics
Matches: 35, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
22 13 0.37
23 3 0.09
24 3 0.09
25 16 0.46
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (25 bp):
TATATAAACAAAATATTATTCGTAA
Found at i:53589527 original size:21 final size:20
Alignment explanation
Indices: 53589494--53589543 Score: 82
Period size: 21 Copynumber: 2.5 Consensus size: 20
53589484 ATAAATAAAA
53589494 TCATTCATGTCAATTCCCTG
1 TCATTCATGTCAATTCCCTG
*
53589514 TCATTCACTGTCAATTTCCTG
1 TCATTCA-TGTCAATTCCCTG
53589535 TCATTCATG
1 TCATTCATG
53589544 ACTTCTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.20, C:0.28, G:0.10, T:0.42
Consensus pattern (20 bp):
TCATTCATGTCAATTCCCTG
Found at i:53592374 original size:17 final size:16
Alignment explanation
Indices: 53592346--53592398 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
53592336 TTTGGTTCGC
53592346 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
53592362 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
53592379 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
53592395 TGTA
1 TGTA
53592399 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:53592463 original size:44 final size:45
Alignment explanation
Indices: 53592379--53592469 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
53592369 GGATTAGAGG
* * *
53592379 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
53592424 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
53592468 TG
1 TG
53592470 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:53592655 original size:18 final size:17
Alignment explanation
Indices: 53592634--53592668 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53592624 TTATTATTAA
*
53592634 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
53592652 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
53592669 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:53592830 original size:120 final size:120
Alignment explanation
Indices: 53592617--53593316 Score: 1037
Period size: 120 Copynumber: 5.8 Consensus size: 120
53592607 ATCATATTTA
53592617 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
53592682 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
53592737 AACATAATTATTATTAAATATATTTTAATTAAAGTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
53592802 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
53592857 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
53592922 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
53592977 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
53593042 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
53593097 AACATAATTATTATTAAATATATTTTAATTAAAATATAT--TTTAATTAAATATAAT-TTAATAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAA-TAAA-AT--TCTTAATAA
* * * * * * * *
53593159 -TAATATATAATT-TCATAAAATT-CTTGATAAT-A-AATTTTCTTATA-TG-AATTTATATAAT
62 TTAATAT-T-CTTAT-ATTAATTTAC-TGA-AATCATAA-TATATGATACTGTAA--AATATAAA
53593217 TT
119 TT
* * * * * *
53593219 AAAATAATTAATATTAAATATAATTTAA-TAATGATATATAATTTCATAAAATTCTTAATAATAA
1 AACATAATTATTATTAAATATATTTTAATTAA-AATATATAATTTAATAAAATTCTTAATAATTA
*
53593283 ATATTCTTATA-TAATTTACTAAAATCATAATATA
65 ATATTCTTATATTAATTTACTGAAATCATAATATA
53593317 ATTTGAGAAT
Statistics
Matches: 533, Mismatches: 26, Indels: 43
0.89 0.04 0.07
Matches are distributed among these distances:
118 8 0.02
119 13 0.02
120 410 0.77
121 26 0.05
122 65 0.12
123 7 0.01
124 4 0.01
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:53593127 original size:15 final size:15
Alignment explanation
Indices: 53593109--53593166 Score: 80
Period size: 16 Copynumber: 3.7 Consensus size: 15
53593099 CATAATTATT
53593109 ATTAAATATATTTTA
1 ATTAAATATATTTTA
53593124 ATTAAAATATATTTTA
1 ATT-AAATATATTTTA
*
53593140 ATTAAATATAATTTA
1 ATTAAATATATTTTA
*
53593155 ATAATAATATAT
1 ATTA-AATATAT
53593167 AATTTCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
15 17 0.45
16 21 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTAAATATATTTTA
Found at i:53593147 original size:31 final size:31
Alignment explanation
Indices: 53593093--53593166 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
53593083 GTAAAATATA
* *
53593093 AATTAACATA-ATTATTATTAAATATATTTT
1 AATTAAAATATATTATTATTAAATATAATTT
53593123 AATTAAAATATATT-TTAATTAAATATAATTT
1 AATTAAAATATATTATT-ATTAAATATAATTT
53593154 AA-TAATAATATAT
1 AATTAA-AATATAT
53593167 AATTTCATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 14 0.36
31 25 0.64
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (31 bp):
AATTAAAATATATTATTATTAAATATAATTT
Found at i:53593168 original size:18 final size:18
Alignment explanation
Indices: 53593114--53593176 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 18
53593104 TTATTATTAA
*
53593114 ATATATTTTAATTAA-AAT
1 ATATAATTTAA-TAATAAT
53593132 ATAT--TTTAAT--TAA-
1 ATATAATTTAATAATAAT
53593145 ATATAATTTAATAATAAT
1 ATATAATTTAATAATAAT
*
53593163 ATATAATTTCATAA
1 ATATAATTTAATAA
53593177 AATTCTTGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 4 0.11
14 2 0.05
15 7 0.18
16 5 0.13
17 3 0.08
18 17 0.45
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
ATATAATTTAATAATAAT
Found at i:53593193 original size:47 final size:46
Alignment explanation
Indices: 53593142--53593286 Score: 156
Period size: 47 Copynumber: 3.2 Consensus size: 46
53593132 ATATTTTAAT
*
53593142 TAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAA
1 TAAATATAATTTAATAAT-ATATATAATTTCATAAAATTCTTAATAA
* * ** *
53593189 TAAAT-T-TTCTTATATGAATTTATATAA-TT--TAAAATAATTAATAT
1 TAAATATAAT-TTA-AT-AATATATATAATTTCATAAAATTCTTAATAA
53593233 TAAATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAA
1 TAAATATAATTTAATAAT-ATATATAATTTCATAAAATTCTTAATAA
53593280 TAAATAT
1 TAAATAT
53593287 TCTTATATAA
Statistics
Matches: 78, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
43 3 0.04
44 25 0.32
45 7 0.09
46 7 0.09
47 33 0.42
48 3 0.04
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (46 bp):
TAAATATAATTTAATAATATATATAATTTCATAAAATTCTTAATAA
Found at i:53593257 original size:44 final size:43
Alignment explanation
Indices: 53593140--53593262 Score: 106
Period size: 44 Copynumber: 2.7 Consensus size: 43
53593130 ATATATTTTA
** *
53593140 ATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTGAT
1 ATTAAATATAATTTAATAAT-ATATATAA-TT--TAAAATAATTAAT
* * *
53593187 AATAAAT-T-TTCTTATATGAATTTATATAATTTAAAATAATTAAT
1 ATTAAATATAAT-TTA-AT-AATATATATAATTTAAAATAATTAAT
53593231 ATTAAATATAATTTAATAATGATATATAATTT
1 ATTAAATATAATTTAATAAT-ATATATAATTT
53593263 CATAAAATTC
Statistics
Matches: 61, Mismatches: 9, Indels: 15
0.72 0.11 0.18
Matches are distributed among these distances:
43 3 0.05
44 28 0.46
45 5 0.08
46 7 0.11
47 15 0.25
48 3 0.05
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (43 bp):
ATTAAATATAATTTAATAATATATATAATTTAAAATAATTAAT
Found at i:53593290 original size:16 final size:16
Alignment explanation
Indices: 53593264--53593297 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
53593254 ATATAATTTC
53593264 ATAAAATTCTTA-ATA
1 ATAAAATTCTTATATA
53593279 ATAAATATTCTTATATA
1 ATAAA-ATTCTTATATA
53593296 AT
1 AT
53593298 TTACTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 7 0.41
17 5 0.29
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAAAATTCTTATATA
Found at i:53593644 original size:66 final size:66
Alignment explanation
Indices: 53593538--53593668 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 66
53593528 CGCAAATGTG
* *
53593538 ATTTGAGTTCAAATTAGATTCATAGTAAGCTCAAATTTTTATTAATGCCAATGCCAACACTACCA
1 ATTTGAGTTCAAATTAGACTCATAGTAAGCTCAAACTTTTATTAATGCCAATGCCAACACTACCA
53593603 C
66 C
* *
53593604 ATTTGGGTTCAAATTATACTCATAGTAAGCTCAAACTTTTATTAATGCCAATGCCAACACTACCA
1 ATTTGAGTTCAAATTAGACTCATAGTAAGCTCAAACTTTTATTAATGCCAATGCCAACACTACCA
53593669 AAACCTTTTG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.33
Consensus pattern (66 bp):
ATTTGAGTTCAAATTAGACTCATAGTAAGCTCAAACTTTTATTAATGCCAATGCCAACACTACCA
C
Found at i:53598660 original size:23 final size:23
Alignment explanation
Indices: 53598633--53598676 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
53598623 AAAATTTTCT
* *
53598633 AATTTAGTATCTAAGTTTGATTC
1 AATTTAGAATCTAAATTTGATTC
*
53598656 AATTTAGAATTTAAATTTGAT
1 AATTTAGAATCTAAATTTGAT
53598677 AATTTTTTTA
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:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (23 bp):
AATTTAGAATCTAAATTTGATTC
Found at i:53598719 original size:18 final size:18
Alignment explanation
Indices: 53598683--53598721 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
53598673 TGATAATTTT
* * *
53598683 TTTAATTTGGTATTTAAA
1 TTTAATTTGATACTCAAA
53598701 TTTAATTTGATACTCAAA
1 TTTAATTTGATACTCAAA
53598719 TTT
1 TTT
53598722 TTTAAATGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.54
Consensus pattern (18 bp):
TTTAATTTGATACTCAAA
Found at i:53600498 original size:17 final size:17
Alignment explanation
Indices: 53600456--53600505 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
53600446 TATATTTTTA
53600456 TAATTTAAATAAAAATT
1 TAATTTAAATAAAAATT
** * *
53600473 TAAGATAAATCAAATTT
1 TAATTTAAATAAAAATT
53600490 TAATTTAAAATAAAAA
1 TAATTT-AAATAAAAA
53600506 ATATTTTTGA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (17 bp):
TAATTTAAATAAAAATT
Found at i:53600511 original size:22 final size:22
Alignment explanation
Indices: 53600469--53600512 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
53600459 TTTAAATAAA
* *
53600469 AATTTAAGATAAATCAAATTTT
1 AATTTAAAATAAATAAAATTTT
53600491 AATTTAAAATAAA-AAATATTTT
1 AATTTAAAATAAATAAA-ATTTT
53600513 TGATATGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
AATTTAAAATAAATAAAATTTT
Found at i:53604745 original size:39 final size:39
Alignment explanation
Indices: 53604700--53604778 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
53604690 TCTTTGTCCC
53604700 TTCCAAGTAAGTAATTTGTTAATTTCGTGCAGATATATT
1 TTCCAAGTAAGTAATTTGTTAATTTCGTGCAGATATATT
*
53604739 TTCCAAGTAAGTAATTTGTTAATTTCTTGCAGATATATT
1 TTCCAAGTAAGTAATTTGTTAATTTCGTGCAGATATATT
53604778 T
1 T
53604779 ACCATCACCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (39 bp):
TTCCAAGTAAGTAATTTGTTAATTTCGTGCAGATATATT
Found at i:53610983 original size:3 final size:3
Alignment explanation
Indices: 53610970--53611003 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
53610960 AAACCCATTC
53610970 ATG AT- ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
53611004 ACAGAGAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:53613691 original size:19 final size:20
Alignment explanation
Indices: 53613662--53613701 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
53613652 TCTATATTCC
53613662 TTTAGCCTTATTTATCAAAA
1 TTTAGCCTTATTTATCAAAA
*
53613682 TTTA-CCTTATTTATCTAAA
1 TTTAGCCTTATTTATCAAAA
53613701 T
1 T
53613702 AATTATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTAGCCTTATTTATCAAAA
Found at i:53627397 original size:121 final size:113
Alignment explanation
Indices: 53627171--53627427 Score: 338
Period size: 121 Copynumber: 2.2 Consensus size: 113
53627161 AAATACGGAT
* *
53627171 ATACGAAAGAAAA-AAAATAAAAAAAAAATTTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGT
1 ATACGAAAAAAAATAAAATAAAATAAAAATTTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGT
* * ** * *
53627235 GTACAGTACCAAAAATTTTTTTTTTATTTTTTTTGTGTCAGAGTCAGATTTAAAA
66 GTACAGTACAAAAAATATTTTTTTTA----TCAT-T-TCAGAATCAGA-TAAAAA
53627290 ATACGAAAAAAAATAAAATAAAATAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAG
1 ATACGAAAAAAAATAAAATAAAATAAAAATTTTT-GGTGCTGGCCTGTCAATGGCCGGCACCCAG
53627355 TGTACAGTACAAAAAAATATTTTTTTT-TCATTTCAGAATCAGATAAAAA
65 TGTACAGTAC-AAAAAATATTTTTTTTATCATTTCAGAATCAGATAAAAA
*
53627404 ATACGAAAAAAAATAAAAAAAAAT
1 ATACGAAAAAAAATAAAATAAAAT
53627428 TTGGGTGCTG
Statistics
Matches: 126, Mismatches: 9, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
114 28 0.22
115 10 0.08
116 1 0.01
117 2 0.02
119 12 0.10
120 19 0.15
121 40 0.32
122 14 0.11
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.29
Consensus pattern (113 bp):
ATACGAAAAAAAATAAAATAAAATAAAAATTTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGT
GTACAGTACAAAAAATATTTTTTTTATCATTTCAGAATCAGATAAAAA
Found at i:53627666 original size:111 final size:110
Alignment explanation
Indices: 53627505--53628028 Score: 610
Period size: 111 Copynumber: 4.6 Consensus size: 110
53627495 ATAAAAAAAA
* *
53627505 TTTTT-GTACTGTACACTGAGTGCCGGCCATTGACAGGCCAGCACCAAAAAACATTTTTTTTATT
1 TTTTTGGTACTGTACACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAA-ATTTTTTTTATT
* *
53627569 TTTTTTCGTATTTTTTTATCTGATTCTGACACTAAAAAAAAT-CTTT
65 TTTTTTCGTATTTTTTTATCTGATTCTAACAC-AAAAAAAATAATTT
* *
53627615 TTTTTGGCACTGTACACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTTTTA-TT
1 TTTTTGGTACTGTACACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATTTTTTTTATTT
*
53627679 TTTTTCGTA-TTTTTTATCTGATTCTGACACGAAAAAAAATAAAATTT
66 TTTTTCGTATTTTTTTATCTGATTCTAACAC-AAAAAAAAT--AATTT
*
53627726 TTTTTAGTACTGTACACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAA-TTTTTTTATTT
1 TTTTTGGTACTGTACACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATTTTTTTTATTT
53627790 TTTTTCGTATTTTTTTATCTGATTCTAACACGAAAAAAGATAATAATAAAAAATT
66 TTTTTCGTATTTTTTTATCTGATTCTAACAC--AAAAA-A-AATAAT------TT
* * ** * * *
53627845 TTCTTCGTACTGTGTACTGGTTGCTGGCCATTGACAGGCCAGCA-CCAAAAATTTTTTTTTTTAT
1 TTTTTGGTACTGTACACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAA--ATTTTTTTTAT
** * ***
53627909 TTTTTTTCGTATTTTTAAATCTGACTCTAACACAAAAAAAATAAAAAAA
64 TTTTTTTCGTATTTTTTTATCTGATTCTAACACAAAAAAAAT--AATTT
** *
53627958 AATTTGGTACTGTACACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATTTTTTTTTTTT
1 TTTTTGGTACTGTACACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATTTTTTTTATTT
53628023 GTTTTT
66 -TTTTT
53628029 TTTCTTTCGT
Statistics
Matches: 358, Mismatches: 34, Indels: 41
0.83 0.08 0.09
Matches are distributed among these distances:
108 30 0.08
109 11 0.03
110 22 0.06
111 107 0.30
112 31 0.09
113 49 0.14
114 8 0.02
115 3 0.01
117 3 0.01
118 8 0.02
119 47 0.13
121 39 0.11
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (110 bp):
TTTTTGGTACTGTACACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATTTTTTTTATTT
TTTTTCGTATTTTTTTATCTGATTCTAACACAAAAAAAATAATTT
Found at i:53629035 original size:19 final size:20
Alignment explanation
Indices: 53628982--53629041 Score: 54
Period size: 19 Copynumber: 3.0 Consensus size: 20
53628972 CTTTATAAAA
53628982 TTTTACAATTTTTTTATATTTC
1 TTTTACAA--TTTTTATATTTC
*
53629004 TTTTACAA-CTTTATATTT-
1 TTTTACAATTTTTATATTTC
53629022 TTTT-CTAATTTTTAATATTT
1 TTTTAC-AATTTTT-ATATTT
53629042 GATTTTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
17 1 0.03
18 6 0.18
19 12 0.36
20 6 0.18
22 8 0.24
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTACAATTTTTATATTTC
Done.