Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 10 of 175
Found at i:3001424 original size:29 final size:31
Alignment explanation
Indices: 3001381--3001461 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
3001371 AAATTGAATC
3001381 AAATCAAAATTTCATGTA-AAAAAT-TACATA
1 AAATCAAAA-TTCATGTATAAAAATCTACATA
* * *
3001411 AAATCAAAATTCATGCATAAAACTCTACATC
1 AAATCAAAATTCATGTATAAAAATCTACATA
**
3001442 GGATCAAAATTCATGTATAA
1 AAATCAAAATTCATGTATAA
3001462 TTTTAAGATT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
29 7 0.16
30 14 0.33
31 22 0.51
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (31 bp):
AAATCAAAATTCATGTATAAAAATCTACATA
Found at i:3005256 original size:14 final size:14
Alignment explanation
Indices: 3005239--3005301 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 14
3005229 TAAATATACG
3005239 TATTTAATTATTTA
1 TATTTAATTATTTA
*
3005253 TATTT-ATTCATATA
1 TATTTAATT-ATTTA
*
3005267 -ATTT-ATTATTTT
1 TATTTAATTATTTA
* *
3005279 TAATAAATTATTTAA
1 TATTTAATTATTT-A
3005294 TATTTAAT
1 TATTTAAT
3005302 AGTAATTTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
12 3 0.08
13 12 0.32
14 16 0.43
15 6 0.16
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTTAATTATTTA
Found at i:3005334 original size:16 final size:17
Alignment explanation
Indices: 3005298--3005334 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3005288 ATTTAATATT
*
3005298 TAATAGTAATTTTTAAA
1 TAATAATAATTTTTAAA
3005315 -AATAATAA-TTTTAAA
1 TAATAATAATTTTTAAA
3005330 TAATA
1 TAATA
3005335 TTATTCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
TAATAATAATTTTTAAA
Found at i:3006869 original size:4 final size:4
Alignment explanation
Indices: 3006822--3006884 Score: 56
Period size: 4 Copynumber: 15.8 Consensus size: 4
3006812 AATTATTTCT
* * * * * *
3006822 TTTA TTTT TTTA -TTA GTTA TTTA TATA TATA TTTG TTGTT TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TTTA
3006870 TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTT
3006885 TAAACAAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
3 3 0.06
4 43 0.88
5 3 0.06
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:3015583 original size:32 final size:35
Alignment explanation
Indices: 3015537--3015603 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 35
3015527 GTTAATTATA
*
3015537 ATAATATTTAATATT-T-AATATATT-AATAACGT
1 ATAATATTTAATATTATCAATAAATTAAATAACGT
3015569 ATAAT-TTTACATATTATCAATAAATTAAATAACGT
1 ATAATATTTA-ATATTATCAATAAATTAAATAACGT
3015604 TGCATCTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 4 0.13
32 10 0.33
33 1 0.03
34 7 0.23
35 8 0.27
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (35 bp):
ATAATATTTAATATTATCAATAAATTAAATAACGT
Found at i:3018447 original size:6 final size:6
Alignment explanation
Indices: 3018438--3018463 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3018428 CTTAATTCTA
3018438 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
3018464 AAAACCCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:3021875 original size:3 final size:3
Alignment explanation
Indices: 3021861--3021901 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
3021851 GAGTTGATAA
*
3021861 TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3021902 GCAACCACTC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3023142 original size:61 final size:60
Alignment explanation
Indices: 3023055--3023168 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
3023045 AATATTCAAC
* *
3023055 AAATATAGCCCTCAATGTTTACAAAAAAAATT-ATTTTAGTTTGAATTCTAAAAAAGTTAAT
1 AAATATAGCCCTCAATGTTTAC--AAAAAATTCAATTTAGTTTCAATTCTAAAAAAGTTAAT
* * *
3023116 AAATTTAGCCCTCAAAT-TTTATAAAAATTTCAATTTAGTTTCAATTCTAAAAA
1 AAATATAGCCCTC-AATGTTTACAAAAAATTCAATTTAGTTTCAATTCTAAAAA
3023169 TTTTAATGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
59 7 0.15
60 20 0.43
61 16 0.35
62 3 0.07
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (60 bp):
AAATATAGCCCTCAATGTTTACAAAAAATTCAATTTAGTTTCAATTCTAAAAAAGTTAAT
Found at i:3035560 original size:12 final size:12
Alignment explanation
Indices: 3035543--3035577 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
3035533 AAATGATGAT
*
3035543 ATGTATGTATGC
1 ATGTATGCATGC
3035555 ATGTATGCATGC
1 ATGTATGCATGC
*
3035567 ATGCATGCATG
1 ATGTATGCATG
3035578 TATTCCTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (12 bp):
ATGTATGCATGC
Found at i:3040146 original size:18 final size:19
Alignment explanation
Indices: 3040103--3040152 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
3040093 AACTATATTA
3040103 AAAAATATTTTATTAATTTTT
1 AAAAATA-TTTA-TAATTTTT
*
3040124 -TAAATATTTAT-ATTTTT
1 AAAAATATTTATAATTTTT
3040141 AAAAATATTTAT
1 AAAAATATTTAT
3040153 CAATAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 6 0.23
18 11 0.42
19 4 0.15
20 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AAAAATATTTATAATTTTT
Found at i:3046572 original size:21 final size:21
Alignment explanation
Indices: 3046548--3046591 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3046538 TATTTTCTAT
*
3046548 AATTTTTTTA-ATATTATTATA
1 AATTTTTTTATATAATATT-TA
3046569 AATTTTTTTATATAATATTTA
1 AATTTTTTTATATAATATTTA
3046590 AA
1 AA
3046592 ACTACCCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AATTTTTTTATATAATATTTA
Found at i:3048476 original size:16 final size:16
Alignment explanation
Indices: 3048455--3048506 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
3048445 TTTGGTTCGC
3048455 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3048471 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* * *
3048487 TGTAATGGAATAGATG
1 TGTATTGGATTAGAGG
3048503 TGTA
1 TGTA
3048507 ATAGCAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:3048553 original size:45 final size:44
Alignment explanation
Indices: 3048487--3048581 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 44
3048477 GGATTAGAGG
* * *
3048487 TGTAATGGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
3048532 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
3048576 TGTAAT
1 TGTAAT
3048582 AGAGGTGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.41
45 26 0.59
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:3048764 original size:18 final size:17
Alignment explanation
Indices: 3048743--3048777 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3048733 TTATTATTTA
*
3048743 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
3048761 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
3048778 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:3048771 original size:28 final size:27
Alignment explanation
Indices: 3048701--3048773 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
3048691 TTTATTATCA
*
3048701 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
3048729 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
3048756 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
3048774 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:3049001 original size:147 final size:147
Alignment explanation
Indices: 3048680--3048981 Score: 329
Period size: 147 Copynumber: 2.0 Consensus size: 147
3048670 ATTTAAATTT
* * *
3048680 TAATAAGATTATTTATTATCAAA-AATAAATAATTTAATCATATTTAAACATAATTATTATTTAA
1 TAATAAGATTA-TAAATAT-AAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAA
* * * * **
3048744 TATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAGAAATTTGTTTTGGTA
64 TATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACACAAATATGATTTACTA
* ** * * *
3048809 AATTATTTTATTTAAATTT
129 AATCATAATATTGAAACTG
* * *
3048828 TAATAAGATTATTAATATCAATAATAAATAATTTACTCATATTTAAACATAATTATTATTAAATA
1 TAATAAGATTATAAATATAAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATA
* **
3048893 TATTTTAATTAAAATATATAATTTAAT-AAATTCTTAATAATTAATATTCTTATATGAATTTACT
66 TATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACA--CAAATATG-ATTTACT
*
3048957 CAAATCATAATATATGATACTG
128 -AAATCATAATAT-TGAAACTG
3048979 TAA
1 TAA
3048982 AATATAAATT
Statistics
Matches: 128, Mismatches: 20, Indels: 9
0.82 0.13 0.06
Matches are distributed among these distances:
146 19 0.15
147 74 0.58
148 15 0.12
149 4 0.03
150 9 0.07
151 7 0.05
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.45
Consensus pattern (147 bp):
TAATAAGATTATAAATATAAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATA
TATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACACAAATATGATTTACTAAA
TCATAATATTGAAACTG
Found at i:3049031 original size:18 final size:17
Alignment explanation
Indices: 3048991--3049043 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
3048981 AAATATAAAT
3048991 TAAAATA-ATAA-TT-A
1 TAAAATATATAATTTAA
*
3049005 TTAAATATAT--TTTAA
1 TAAAATATATAATTTAA
3049020 TTAAAATATATAATTTAA
1 -TAAAATATATAATTTAA
3049038 TAAAAT
1 TAAAAT
3049044 TCTAATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.26
15 3 0.10
16 9 0.29
17 6 0.19
18 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATATATAATTTAA
Found at i:3049089 original size:60 final size:58
Alignment explanation
Indices: 3048899--3049090 Score: 157
Period size: 56 Copynumber: 3.2 Consensus size: 58
3048889 AATATATTTT
3048899 AATTAAAATATATAATTTAAT-AAATTCTTAATAATTAATATTCTTATATGAATTTACTCA
1 AATTAAAATATATAATTTAATAAAATTC-TAATAA-TAATATTCTTATATGAATTTACT-A
* * * * *
3048959 AATCATAATATATGATACTGTAAAATATAAA-T-TAA-AATAATAATTATTAAAT-ATATTT--T
1 AAT--TAAAATAT-ATAAT-T-TAATA-AAATTCTAATAATAAT-ATTCTTATATGA-ATTTACT
3049018 -
58 A
3049018 AATTAAAATATATAATTTAATAAAATTCTAATAATCAATATTCTTATATGAATTTACTAA
1 AATTAAAATATATAATTTAATAAAATTCTAATAAT-AATATTCTTATATGAATTTACT-A
*
3049078 AATTATAATATAT
1 AATTAAAATATAT
3049091 GATACTATAA
Statistics
Matches: 103, Mismatches: 11, Indels: 36
0.69 0.07 0.24
Matches are distributed among these distances:
53 3 0.03
54 5 0.05
55 4 0.04
56 19 0.18
57 11 0.11
58 1 0.01
59 3 0.03
60 15 0.15
61 1 0.01
62 12 0.12
63 18 0.17
64 4 0.04
65 3 0.03
66 1 0.01
67 3 0.03
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (58 bp):
AATTAAAATATATAATTTAATAAAATTCTAATAATAATATTCTTATATGAATTTACTA
Found at i:3049101 original size:60 final size:59
Alignment explanation
Indices: 3048920--3049103 Score: 151
Period size: 60 Copynumber: 3.1 Consensus size: 59
3048910 ATAATTTAAT
* * *
3048920 AAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTA
1 AAATTC-TAATAA-TAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATA
* ** * * * ** * * *
3048981 AAATAT-AAATTAA-AATAATAATTAT-TAAATATATTTTAATTAAAATATATAAT-TTAATA
1 AAAT-TCTAA-TAATAAT-ATTCTTATATGAATTTACTAAAATTATAATATATGATACT-ATA
3049040 AAATTCTAATAATCAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATA
1 AAATTCTAATAAT-AATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATA
3049100 AAAT
1 AAAT
3049104 ATAATTTGAA
Statistics
Matches: 90, Mismatches: 24, Indels: 19
0.68 0.18 0.14
Matches are distributed among these distances:
58 5 0.06
59 37 0.41
60 39 0.43
61 8 0.09
62 1 0.01
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (59 bp):
AAATTCTAATAATAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATA
Found at i:3049160 original size:59 final size:58
Alignment explanation
Indices: 3048876--3049162 Score: 169
Period size: 59 Copynumber: 4.8 Consensus size: 58
3048866 ATATTTAAAC
* * *
3048876 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAAT-AAAT-T--CTT-A
1 ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATATAATTTAA
** * * * * *
3048929 ATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT-GTAAAATATAAATTA
1 ATAATTAATATT-AAATAT--ATTT--T--AATTAAAATATATGAT-TTAATAAAATAT-AATTT
3048993 AA
57 AA
* * * *
3048995 ATAA-TAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTAATAATCA
1 ATAATTAA-TATTAAATATATTTTAATTAAAATATATGATTTAATAAAA-TATAAT-TTAA
** * * * ** * *
3049055 AT-ATTCTTATATGAATTTACTAAAATTATAATATATGATACT-ATAAAATATAATTTGAA
1 ATAATTAATAT-TAAATATATTTTAATTAAAATATATGAT-TTAATAAAATATAATTT-AA
3049114 ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAAT
1 ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAAT
3049163 TTAAAATAAT
Statistics
Matches: 167, Mismatches: 43, Indels: 42
0.66 0.17 0.17
Matches are distributed among these distances:
53 11 0.07
54 4 0.02
56 4 0.02
58 4 0.02
59 62 0.37
60 53 0.32
61 7 0.04
62 1 0.01
63 4 0.02
65 8 0.05
66 9 0.05
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (58 bp):
ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATATAATTTAA
Found at i:3049161 original size:119 final size:120
Alignment explanation
Indices: 3048870--3049163 Score: 477
Period size: 119 Copynumber: 2.5 Consensus size: 120
3048860 TTACTCATAT
*
3048870 TTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAAT-AAATTCTTAATAAT
1 TTAAA-ATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
* * *
3048934 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA
65 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
3048990 TTAAAATAA-TAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC-TAATAAT
1 TTAAAATAATTAA-TATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
* *
3049053 CAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATAAAATATAAT
65 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
* *
3049109 TTGAAATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 TTAAAATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
3049164 TAAAATAATT
Statistics
Matches: 163, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
118 2 0.01
119 147 0.90
120 14 0.09
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (120 bp):
TTAAAATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATC
AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
Found at i:3054442 original size:36 final size:36
Alignment explanation
Indices: 3054378--3054451 Score: 98
Period size: 38 Copynumber: 2.1 Consensus size: 36
3054368 TTGTTTTTTT
3054378 ATTTATTTTATATAAAAATAAGAAAAAATTATAATATA
1 ATTTATTTTATATAAAAATAAGAAAAAATTA-AAT-TA
**
3054416 ATTTATTTTATA-AAAAATAA-TCAAAATTAAATTA
1 ATTTATTTTATATAAAAATAAGAAAAAATTAAATTA
3054450 AT
1 AT
3054452 GCTTAATCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 4 0.12
35 3 0.09
36 7 0.21
37 8 0.24
38 12 0.35
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (36 bp):
ATTTATTTTATATAAAAATAAGAAAAAATTAAATTA
Found at i:3054684 original size:22 final size:22
Alignment explanation
Indices: 3054656--3054699 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3054646 CAAAAAAAAA
* *
3054656 ATTGTTGTTTTCTTATTGTTTT
1 ATTGTTGTTTTCTCACTGTTTT
3054678 ATTGTTGTTTTCTCACTGTTTT
1 ATTGTTGTTTTCTCACTGTTTT
3054700 GTTATCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.09, G:0.14, T:0.68
Consensus pattern (22 bp):
ATTGTTGTTTTCTCACTGTTTT
Found at i:3058907 original size:265 final size:265
Alignment explanation
Indices: 3058434--3058964 Score: 1035
Period size: 265 Copynumber: 2.0 Consensus size: 265
3058424 GCTTTTTGGG
3058434 TTCATGGATTTTCAGTTTTTACTTACTAATTACCATCACATGTTACGAGAATAAATTTGTTATGA
1 TTCATGGATTTTCAGTTTTTACTTACTAATTACCATCACATGTTACGAGAATAAATTTGTTATGA
3058499 TGTTTATAACAAGATGTTACAGCTTTCCTTCATGTTTTTTGTTGATTCGTAATCTTCCATATAAG
66 TGTTTATAACAAGATGTTACAGCTTTCCTTCATGTTTTTTGTTGATTCGTAATCTTCCATATAAG
3058564 TTGATGGTTTTAAGTGTGCCTAATTTATTTGTTTTAGATGGCTATGATTTCTTAATTTCTATTTT
131 TTGATGGTTTTAAGTGTGCCTAATTTATTTGTTTTAGATGGCTATGATTTCTTAATTTCTATTTT
3058629 TGTTCACTCTTTATCCTTAGTTAAAAATATTTGTGGCTTGCAGGCGAGAGCTGGTCTAGATTATG
196 TGTTCACTCTTTATCCTTAGTTAAAAATATTTGTGGCTTGCAGGCGAGAGCTGGTCTAGATTATG
3058694 AATCC
261 AATCC
3058699 TTCATGGATTTTCAGTTTTTACTTACTAATTACCATCACATGTTACGAGAATAAATTTGTTATGA
1 TTCATGGATTTTCAGTTTTTACTTACTAATTACCATCACATGTTACGAGAATAAATTTGTTATGA
*
3058764 TGTTTATAACAAGATGTTACAGCTTTTCTTCATGTTTTTTGTTGATTCGTAATCTTCCATATAAG
66 TGTTTATAACAAGATGTTACAGCTTTCCTTCATGTTTTTTGTTGATTCGTAATCTTCCATATAAG
3058829 TTGATGGTTTTAAGTGTGCCTAATTTATTTGTTTTAGATGGCTATGATTTCTTAATTTCTATTTT
131 TTGATGGTTTTAAGTGTGCCTAATTTATTTGTTTTAGATGGCTATGATTTCTTAATTTCTATTTT
* *
3058894 TGTTCTCTCTTTATCCTTGGTTAAAAATATTTGTGGCTTGCAGGCGAGAGCTGGTCTAGATTATG
196 TGTTCACTCTTTATCCTTAGTTAAAAATATTTGTGGCTTGCAGGCGAGAGCTGGTCTAGATTATG
3058959 AATCC
261 AATCC
3058964 T
1 T
3058965 CATATGGGAA
Statistics
Matches: 263, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
265 263 1.00
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.46
Consensus pattern (265 bp):
TTCATGGATTTTCAGTTTTTACTTACTAATTACCATCACATGTTACGAGAATAAATTTGTTATGA
TGTTTATAACAAGATGTTACAGCTTTCCTTCATGTTTTTTGTTGATTCGTAATCTTCCATATAAG
TTGATGGTTTTAAGTGTGCCTAATTTATTTGTTTTAGATGGCTATGATTTCTTAATTTCTATTTT
TGTTCACTCTTTATCCTTAGTTAAAAATATTTGTGGCTTGCAGGCGAGAGCTGGTCTAGATTATG
AATCC
Found at i:3060120 original size:3 final size:3
Alignment explanation
Indices: 3060112--3060144 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3060102 AGGCTCTGCC
3060112 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
3060145 GCAGCGCCCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:3069207 original size:23 final size:22
Alignment explanation
Indices: 3069162--3069208 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
3069152 CGAAAATATA
*
3069162 TTAAATATATATATTTTTATTT
1 TTAAATATATATAGTTTTATTT
*
3069184 TTAAA-ATATACTAGTTTTAGTT
1 TTAAATATATA-TAGTTTTATTT
3069206 TTA
1 TTA
3069209 TTTTAAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (22 bp):
TTAAATATATATAGTTTTATTT
Found at i:3069364 original size:92 final size:93
Alignment explanation
Indices: 3069257--3069437 Score: 319
Period size: 93 Copynumber: 2.0 Consensus size: 93
3069247 AACAATTAAT
* *
3069257 ACAATTAACAATTAATAATTTGATAT-ATTTGATAATTTTACTAACAATTAATACAATTAACAAT
1 ACAATTAACAATTAATAATTTGATATAATTTGATAATTTTAATAACAATTAATACAATTAAAAAT
3069321 TAATAATTTTACTAACAAAATGTTAGTA
66 TAATAATTTTACTAACAAAATGTTAGTA
*
3069349 ACAATTAAGAATTAATAATTTGATATAATTTGATAATTTTAATAACAATTAATACAATTAAAAAT
1 ACAATTAACAATTAATAATTTGATATAATTTGATAATTTTAATAACAATTAATACAATTAAAAAT
*
3069414 TAATAATTTTACTTACAAAATGTT
66 TAATAATTTTACTAACAAAATGTT
3069438 GATTGGTACA
Statistics
Matches: 84, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
92 25 0.30
93 59 0.70
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (93 bp):
ACAATTAACAATTAATAATTTGATATAATTTGATAATTTTAATAACAATTAATACAATTAAAAAT
TAATAATTTTACTAACAAAATGTTAGTA
Found at i:3069460 original size:93 final size:92
Alignment explanation
Indices: 3069269--3069472 Score: 281
Period size: 93 Copynumber: 2.2 Consensus size: 92
3069259 AATTAACAAT
* *
3069269 TAATAATTTGATAT-ATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTAC
1 TAATAATTTGATATAATTTGATAATTTTAATAACAATTAATACAATTAAAAATTAATAATTTTAC
* *
3069333 TAACAAAATGTTAGTAACAATTAAGAAT
66 TAACAAAATGTTAGTAACAA-TAAAAAA
3069361 TAATAATTTGATATAATTTGATAATTTTAATAACAATTAATACAATTAAAAATTAATAATTTTAC
1 TAATAATTTGATATAATTTGATAATTTTAATAACAATTAATACAATTAAAAATTAATAATTTTAC
*
3069426 TTACAAAATGTTGATTGGT-ACAA-AAAAAA
66 TAACAAAATGTT-A---GTAACAATAAAAAA
*
3069455 T-ATAATTTGATACAATTT
1 TAATAATTTGATATAATTT
3069473 TAATAACAAT
Statistics
Matches: 101, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
92 14 0.14
93 75 0.74
94 6 0.06
96 4 0.04
97 2 0.02
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (92 bp):
TAATAATTTGATATAATTTGATAATTTTAATAACAATTAATACAATTAAAAATTAATAATTTTAC
TAACAAAATGTTAGTAACAATAAAAAA
Found at i:3069487 original size:16 final size:16
Alignment explanation
Indices: 3069468--3069508 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
3069458 AATTTGATAC
3069468 AATTTTAATAACAATT
1 AATTTTAATAACAATT
*
3069484 AATTTTGATAACAATT
1 AATTTTAATAACAATT
*
3069500 AGTTTTAAT
1 AATTTTAAT
3069509 TTTAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (16 bp):
AATTTTAATAACAATT
Found at i:3069510 original size:22 final size:23
Alignment explanation
Indices: 3069482--3069543 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
3069472 TTAATAACAA
* * *
3069482 TTAATTTTGATAACAAT-TAGTT
1 TTAATTTTAATAAAAATATAATT
3069504 TTAATTTTAATAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
3069527 TTAATTTTAATTAAAAA
1 TTAATTTTAA-TAAAAA
3069544 ATAGGCCGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 15 0.43
23 14 0.40
24 6 0.17
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:3069682 original size:20 final size:20
Alignment explanation
Indices: 3069657--3069694 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3069647 AGCCTCCTTG
3069657 TATAAATATCCCATCATTAC
1 TATAAATATCCCATCATTAC
*
3069677 TATAAATATCCCCTCATT
1 TATAAATATCCCATCATT
3069695 CTTCAACTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (20 bp):
TATAAATATCCCATCATTAC
Found at i:3069899 original size:22 final size:22
Alignment explanation
Indices: 3069858--3069900 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
3069848 GGGAAAATGA
3069858 TTTTTAGAAAATAACTTATTTAT
1 TTTTTAGAAAATAAC-TATTTAT
3069881 TTTTTAGAAAACTAA-TATTT
1 TTTTTAGAAAA-TAACTATTT
3069901 TCTAGTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 11 0.58
24 3 0.16
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTTTAGAAAATAACTATTTAT
Found at i:3074814 original size:24 final size:24
Alignment explanation
Indices: 3074782--3074831 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
3074772 GTAAAAGTAT
3074782 CATGGAGGTACTTGTATTAGGAGA
1 CATGGAGGTACTTGTATTAGGAGA
3074806 CATGGAGGTACTTGTATTAGGAGA
1 CATGGAGGTACTTGTATTAGGAGA
3074830 CA
1 CA
3074832 GATTATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.10, G:0.32, T:0.28
Consensus pattern (24 bp):
CATGGAGGTACTTGTATTAGGAGA
Found at i:3081038 original size:20 final size:22
Alignment explanation
Indices: 3081010--3081054 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
3081000 GTATGAAAGC
*
3081010 ATATTTTTATATGTAAGTATAT
1 ATATTTATATATGTAAGTATAT
3081032 ATATTTATATATGTAAGTATAT
1 ATATTTATATATGTAAGTATAT
3081054 A
1 A
3081055 ATAAAGGCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
ATATTTATATATGTAAGTATAT
Found at i:3081116 original size:63 final size:61
Alignment explanation
Indices: 3080976--3081117 Score: 162
Period size: 63 Copynumber: 2.3 Consensus size: 61
3080966 TGAAAGTATA
* * * *
3080976 TATATATGTATATATAATAAAGGCGTATGAAAGCATATTTTTATATGTAAGTATATATATT
1 TATATATGTATATATAATAAAGGCGTATGAAAGCATATTTTTACATGTAAGTATAAAAATG
* *
3081037 TATATATGTAAGTATATAATAAAGGCGTATGAAAGCATATTTATGTACATGT-ATTTTAAAAAAT
1 TATATATGT-A-TATATAATAAAGGCGTATGAAAGCATATTT-T-TACATGTAAGTAT-AAAAAT
3081101 G
61 G
3081102 TATATA-GATATATATA
1 TATATATG-TATATATA
3081118 GATGTGCAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
61 9 0.13
62 1 0.01
63 36 0.52
64 6 0.09
65 17 0.25
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.40
Consensus pattern (61 bp):
TATATATGTATATATAATAAAGGCGTATGAAAGCATATTTTTACATGTAAGTATAAAAATG
Found at i:3081334 original size:3 final size:3
Alignment explanation
Indices: 3081326--3081357 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3081316 AAAAAGGGAA
3081326 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3081358 GCTAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3090872 original size:31 final size:31
Alignment explanation
Indices: 3090832--3090896 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
3090822 ATGACCTGCT
* * * *
3090832 ACCCTGGATTGCCCGACGACGATGGCTTACC
1 ACCCCGGATTACCCGACAACGATGGCCTACC
3090863 ACCCCGGATTACCCGACAACGATGGCCTACC
1 ACCCCGGATTACCCGACAACGATGGCCTACC
3090894 ACC
1 ACC
3090897 AGGTTGTCCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.40, G:0.22, T:0.15
Consensus pattern (31 bp):
ACCCCGGATTACCCGACAACGATGGCCTACC
Found at i:3098373 original size:29 final size:30
Alignment explanation
Indices: 3098338--3098411 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 30
3098328 AGACATTTTA
*
3098338 TAAAAATACATGTACCACATTAAATATTT-
1 TAAAAATATATGTACCACATTAAATATTTG
* **
3098367 TCAAAATATAAATACCACATTAAATATTTG
1 TAAAAATATATGTACCACATTAAATATTTG
3098397 TAAAAATATATGTAC
1 TAAAAATATATGTAC
3098412 AAAATGTAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 25 0.68
30 12 0.32
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.34
Consensus pattern (30 bp):
TAAAAATATATGTACCACATTAAATATTTG
Found at i:3099239 original size:29 final size:31
Alignment explanation
Indices: 3099178--3099239 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 31
3099168 ACAATTTAAT
* **
3099178 TTGGTCATTTTGAATTTTTGTATTTTTTGAA
1 TTGGTCATTTTGAATTTCTGTATTTTTCAAA
*
3099209 TTGGTCATTTT-TA-TTCTGTATTTTTCAAA
1 TTGGTCATTTTGAATTTCTGTATTTTTCAAA
3099238 TT
1 TT
3099240 TTAAACTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 15 0.56
30 1 0.04
31 11 0.41
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (31 bp):
TTGGTCATTTTGAATTTCTGTATTTTTCAAA
Found at i:3102213 original size:23 final size:23
Alignment explanation
Indices: 3102173--3102217 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3102163 ATAGAAAAAG
*
3102173 ATATATATGCAACGATATATATT
1 ATATATATGAAACGATATATATT
3102196 ATATATTATGAAAC-ATATATAT
1 ATATA-TATGAAACGATATATAT
3102218 ATTAATATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (23 bp):
ATATATATGAAACGATATATATT
Found at i:3104267 original size:41 final size:41
Alignment explanation
Indices: 3104222--3104366 Score: 121
Period size: 41 Copynumber: 3.3 Consensus size: 41
3104212 CTATATTTAA
3104222 ATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACT
1 ATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACT
* * * ** *
3104263 ATTTTTTTAATATTATACATATATTCATTTACGTATGTAAGCTATATTTA-A
1 ATTTTATTAATA--ATA-A-AT-TT-A-TAACTTAAATAAG---TA-TTACT
3104314 ATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACT
1 ATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACT
*
3104355 ATTTTTTTAATA
1 ATTTTATTAATA
3104367 TTATACATAT
Statistics
Matches: 79, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
40 3 0.04
41 24 0.30
43 3 0.04
44 10 0.13
45 3 0.04
46 4 0.05
47 3 0.04
48 10 0.13
49 3 0.04
51 13 0.16
52 3 0.04
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (41 bp):
ATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACT
Found at i:3104293 original size:51 final size:51
Alignment explanation
Indices: 3104238--3104385 Score: 140
Period size: 42 Copynumber: 3.1 Consensus size: 51
3104228 TTAATAATAA
3104238 ATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTC
1 ATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTC
* * * * **
3104289 A-TT-T-ACGT--AT--GTA--AGCTA-TATTTAAATTTTATTA-ATA-ATAA
1 ATTTATAACTTAAATAAGTATTA-CTATTTTTTTAATATTA-TACATATATTC
3104330 ATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTC
1 ATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTC
3104381 ATTTA
1 ATTTA
3104386 CATAACACAT
Statistics
Matches: 71, Mismatches: 12, Indels: 28
0.64 0.11 0.25
Matches are distributed among these distances:
41 3 0.04
42 16 0.23
43 6 0.08
44 6 0.08
46 4 0.06
48 6 0.08
49 6 0.08
50 16 0.23
51 8 0.11
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (51 bp):
ATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTC
Found at i:3104350 original size:92 final size:92
Alignment explanation
Indices: 3104193--3104386 Score: 388
Period size: 92 Copynumber: 2.1 Consensus size: 92
3104183 GTTTAAAAGC
3104193 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
3104258 TTACTATTTTTTTAATATTATACATAT
66 TTACTATTTTTTTAATATTATACATAT
3104285 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
3104350 TTACTATTTTTTTAATATTATACATAT
66 TTACTATTTTTTTAATATTATACATAT
3104377 ATTCATTTAC
1 ATTCATTTAC
3104387 ATAACACATA
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 102 1.00
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (92 bp):
ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
TTACTATTTTTTTAATATTATACATAT
Found at i:3104406 original size:9 final size:9
Alignment explanation
Indices: 3104383--3104766 Score: 129
Period size: 9 Copynumber: 44.9 Consensus size: 9
3104373 ATATATTCAT
3104383 TTACATAAC
1 TTACATAAC
3104392 --ACATAAC
1 TTACATAAC
3104399 TTACATAAC
1 TTACATAAC
* *
3104408 CTACTTAA-
1 TTACATAAC
*
3104416 -TATATAAC
1 TTACATAAC
*
3104424 TTGCATAAC
1 TTACATAAC
* *
3104433 TTAAATAAG
1 TTACATAAC
*
3104442 TTACGTAA-
1 TTACATAAC
3104450 TAATACATAA-
1 T--TACATAAC
*
3104460 -TACACAAC
1 TTACATAAC
*
3104468 TTACAT-TC
1 TTACATAAC
* *
3104476 GTAAATAA-
1 TTACATAAC
* *
3104484 -TACAGAGC
1 TTACATAAC
3104492 TTACATAAC
1 TTACATAAC
*
3104501 TTACATACC
1 TTACATAAC
* *
3104510 CTACATAAA
1 TTACATAAC
* *
3104519 TTAAATAAG
1 TTACATAAC
3104528 TTACATAA-
1 TTACATAAC
*
3104536 TAATACATACC
1 T--TACATAAC
* *
3104547 CTACATAAA
1 TTACATAAC
* *
3104556 TTAAATAAG
1 TTACATAAC
3104565 TTACATAA-
1 TTACATAAC
*
3104573 TAATACATACC
1 T--TACATAAC
*
3104584 CTACATAAC
1 TTACATAAC
3104593 TTACATAA-
1 TTACATAAC
*
3104601 -GACATAA-
1 TTACATAAC
*
3104608 TTTCATAA-
1 TTACATAAC
*
3104616 -TACACAAC
1 TTACATAAC
**
3104624 TTACGCAAC
1 TTACATAAC
3104633 TTACATAA-
1 TTACATAAC
*
3104641 -GACATAAC
1 TTACATAAC
*
3104649 TTACAT--G
1 TTACATAAC
*
3104656 TGTAAATAA-
1 T-TACATAAC
**
3104665 -TACATATT
1 TTACATAAC
3104673 TTACATAAC
1 TTACATAAC
3104682 TTACATAA-
1 TTACATAAC
*
3104690 -GACATAAC
1 TTACATAAC
*
3104698 TTACATAAG
1 TTACATAAC
*
3104707 TTTCATAA-
1 TTACATAAC
* *
3104715 -TACACATC
1 TTACATAAC
**
3104723 TTACGCAAC
1 TTACATAAC
*
3104732 TTACACAAC
1 TTACATAAC
3104741 TTACATAAC
1 TTACATAAC
3104750 TTACATAAC
1 TTACATAAC
3104759 TTACATAA
1 TTACATAA
3104767 TGTATATCTT
Statistics
Matches: 274, Mismatches: 70, Indels: 62
0.67 0.17 0.15
Matches are distributed among these distances:
7 55 0.20
8 17 0.06
9 184 0.67
10 18 0.07
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (9 bp):
TTACATAAC
Found at i:3104416 original size:92 final size:90
Alignment explanation
Indices: 3104193--3104442 Score: 272
Period size: 92 Copynumber: 2.7 Consensus size: 90
3104183 GTTTAAAAGC
* * ***
3104193 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
1 ATTCATTTACG-A-GTAAACTATACTTAAAACCTATTAATAATAAATTTATAACTTAAATAAGTA
3104258 TTACTATTTTTTTAATATTATACATAT
64 TTACTATTTTTTTAATATTATACATAT
* * ***
3104285 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
1 ATTCATTTACG-A-GTAAACTATACTTAAAACCTATTAATAATAAATTTATAACTTAAATAAGTA
3104350 TTACTATTTTTTTAATATTATACATAT
64 TTACTATTTTTTTAATATTATACATAT
* *
3104377 ATTCATTTAC-A-TAACAC-ATAACTTACATAACCTACTTAATATATAACTTGCATAACTTAAAT
1 ATTCATTTACGAGTAA-ACTAT-ACTTA-A-AACCTA-TTAATA-ATAAATT-TATAACTTAAAT
3104439 AAGT
59 AAGT
3104443 TACGTAATAA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
88 5 0.03
89 5 0.03
90 2 0.01
91 3 0.02
92 108 0.75
93 6 0.04
94 15 0.10
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (90 bp):
ATTCATTTACGAGTAAACTATACTTAAAACCTATTAATAATAAATTTATAACTTAAATAAGTATT
ACTATTTTTTTAATATTATACATAT
Found at i:3104546 original size:37 final size:37
Alignment explanation
Indices: 3104502--3104608 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
3104492 TTACATAACT
3104502 TACATACCCTACATAAATTAAATAAGTTACATAATAA
1 TACATACCCTACATAAATTAAATAAGTTACATAATAA
3104539 TACATACCCTACATAAATTAAATAAGTTACATAATAA
1 TACATACCCTACATAAATTAAATAAGTTACATAATAA
* *
3104576 TACATACCCTACATAACTTACATAAG--ACATAAT
1 TACATACCCTACATAAATTAAATAAGTTACATAAT
3104609 TTCATAATAC
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
35 7 0.10
37 61 0.90
ACGTcount: A:0.50, C:0.19, G:0.03, T:0.29
Consensus pattern (37 bp):
TACATACCCTACATAAATTAAATAAGTTACATAATAA
Found at i:3104605 original size:16 final size:16
Alignment explanation
Indices: 3104586--3104706 Score: 73
Period size: 16 Copynumber: 8.0 Consensus size: 16
3104576 TACATACCCT
3104586 ACATAACTTACATAAG
1 ACATAACTTACATAAG
* *
3104602 ACATAA-TTTCATAAT
1 ACATAACTTACATAAG
*
3104617 ACACAACTTAC----G
1 ACATAACTTACATAAG
3104629 -C--AACTTACATAAG
1 ACATAACTTACATAAG
**
3104642 ACATAACTTACATGTG
1 ACATAACTTACATAAG
* **
3104658 TAAATAA--TACATATTTT
1 -ACATAACTTACATA--AG
3104675 ACATAACTTACATAAG
1 ACATAACTTACATAAG
3104691 ACATAACTTACATAAG
1 ACATAACTTACATAAG
3104707 TTTCATAATA
Statistics
Matches: 79, Mismatches: 13, Indels: 26
0.67 0.11 0.22
Matches are distributed among these distances:
9 7 0.09
11 1 0.01
13 1 0.01
14 1 0.01
15 17 0.22
16 40 0.51
17 6 0.08
18 6 0.08
ACGTcount: A:0.46, C:0.18, G:0.06, T:0.30
Consensus pattern (16 bp):
ACATAACTTACATAAG
Found at i:3104616 original size:40 final size:40
Alignment explanation
Indices: 3104572--3104647 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
3104562 AAGTTACATA
* * *
3104572 ATAATACATACCCTACATAACTTACATAAGACATAATTTC
1 ATAATACACAACCTACACAACTTACATAAGACATAATTTC
* *
3104612 ATAATACACAACTTACGCAACTTACATAAGACATAA
1 ATAATACACAACCTACACAACTTACATAAGACATAA
3104648 CTTACATGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.47, C:0.22, G:0.04, T:0.26
Consensus pattern (40 bp):
ATAATACACAACCTACACAACTTACATAAGACATAATTTC
Found at i:3104639 original size:25 final size:25
Alignment explanation
Indices: 3104611--3104767 Score: 111
Period size: 25 Copynumber: 6.2 Consensus size: 25
3104601 GACATAATTT
* *
3104611 CATAATACACAACTTACGCAACTTA
1 CATAATACATAACTTACACAACTTA
* **
3104636 CATAAGACATAACTT--ACATGTGTA
1 CATAATACATAACTTACACAACT-TA
* ** *
3104660 AATAATACATATTTTACATAACTTA
1 CATAATACATAACTTACACAACTTA
* * * *
3104685 CATAAGACATAACTTACATAAGTTT
1 CATAATACATAACTTACACAACTTA
* * *
3104710 CATAATACACATCTTACGCAACTTA
1 CATAATACATAACTTACACAACTTA
* *
3104735 CACAACTTACATAACTTACATAACTTA
1 CATAA--TACATAACTTACACAACTTA
3104762 CATAAT
1 CATAAT
3104768 GTATATCTTG
Statistics
Matches: 96, Mismatches: 31, Indels: 10
0.70 0.23 0.07
Matches are distributed among these distances:
23 3 0.03
24 13 0.14
25 57 0.59
26 3 0.03
27 20 0.21
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.31
Consensus pattern (25 bp):
CATAATACATAACTTACACAACTTA
Found at i:3104640 original size:49 final size:46
Alignment explanation
Indices: 3104595--3104736 Score: 133
Period size: 49 Copynumber: 2.9 Consensus size: 46
3104585 TACATAACTT
*
3104595 ACATAAGACATAATTTCATAATACACAACTTACGCAACTTACATAAG
1 ACATAA-ACATAATTTCATAATACACATCTTACGCAACTTACATAAG
* * * * **
3104642 ACAT-AACTTACATGTGTAAATAATACATATTTTACATAACTTACATAAG
1 ACATAAACATA-AT-T-T-CATAATACACATCTTACGCAACTTACATAAG
3104691 ACATAACTTACATAAGTTTCATAATACACATCTTACGCAACTTACA
1 ACATAA---ACATAA-TTTCATAATACACATCTTACGCAACTTACA
3104737 CAACTTACAT
Statistics
Matches: 73, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
45 4 0.05
46 3 0.04
47 5 0.07
48 1 0.01
49 29 0.40
50 23 0.32
51 1 0.01
52 2 0.03
53 5 0.07
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (46 bp):
ACATAAACATAATTTCATAATACACATCTTACGCAACTTACATAAG
Found at i:3108990 original size:21 final size:21
Alignment explanation
Indices: 3108917--3109025 Score: 119
Period size: 21 Copynumber: 5.2 Consensus size: 21
3108907 CAGCAACTTA
* * * *
3108917 AAGCAGATGCGGCAGCAAGAG
1 AAGCAGAGGCTGCAGCGAGGG
* *
3108938 AAGCAGAGGCGGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
* *
3108959 AAGTACAGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
** *
3108980 AAGCAGAGGCTAAAGTGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
3109001 AAGCAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
3109022 AAGC
1 AAGC
3109026 CGAGCAGCGT
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 74 1.00
ACGTcount: A:0.34, C:0.17, G:0.43, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:3109415 original size:43 final size:42
Alignment explanation
Indices: 3109381--3109779 Score: 216
Period size: 43 Copynumber: 9.3 Consensus size: 42
3109371 AGGTGTTGGC
* * *
3109381 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGAT-ATGGT
* ** *
3109424 CTTTAGCGGCGTTTGTAGAAAAAGCGCCACTAAAGATCATGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGAT-ATGGT
** *
3109467 CTTTAGCGGCGTTTGTGGGGAAAACGCCGCTAAAGAT-TAGGTT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATAT-GG-T
* * * * *
3109510 CTTTAGTGGCGTTTTGTTGTCGAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCG-TTTGTGGTCAAAGCGCCGCTAAAGAT-ATGGT
* ** *
3109554 CTATT-GCGGCGTTTGAGGGGAAAGTGCCGCTAAAGAT-TAGGTT
1 CT-TTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATAT-GG-T
* * * * * *
3109597 CTTTCGTGGCGTTTGTGATCAAAGTGCCGCTATAGATTAGGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGA-TATGGT
* * *** * ** *
3109640 -TTATTGCGGCGTTTGAGAAAAAAACGCCGCTAAAGACCCTGAT
1 CTT-TAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGA-TATGGT
* ** * * * *
3109683 CTTTAGCGGCGCTTGT-CCCAAAAACGCCGCTAAAGGTCTTAGT
1 CTTTAGCGGCGTTTGTGGTC-AAAGCGCCGCTAAAGAT-ATGGT
* * *
3109726 CTTCAGCGGCGTTTGTGCT-AGAAGCGCCGCTAAAGATCAGGGT
1 CTTTAGCGGCGTTTGTGGTCA-AAGCGCCGCTAAAGAT-ATGGT
3109769 CTTTAGCGGCG
1 CTTTAGCGGCG
3109780 CATTCATTAG
Statistics
Matches: 269, Mismatches: 70, Indels: 34
0.72 0.19 0.09
Matches are distributed among these distances:
41 1 0.00
42 9 0.03
43 221 0.82
44 34 0.13
45 4 0.01
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (42 bp):
CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATATGGT
Found at i:3109495 original size:86 final size:85
Alignment explanation
Indices: 3109381--3109779 Score: 293
Period size: 86 Copynumber: 4.6 Consensus size: 85
3109371 AGGTGTTGGC
* * ** *
3109381 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTAGAAAA
1 CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGT-GAAAA
*
3109446 AGCGCCACTAAAGATCATGGT
65 AGCGCCGCTAAAGATCATGGT
* * * * ***
3109467 CTTTAGCGGCGTTTGTGGGGAAAACGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTTGTCG
1 CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCG-TTTG-TGAAA
* *
3109532 AAGCGCCGCTATAGATCAGGGT
64 AAGCGCCGCTAAAGATCATGGT
* * * * * * *
3109554 CTATT-GCGGCGTTTGAGGGGAAAGTGCCGCTAAAGATTAGGTTCTTTCGTGGCGTTTGTGATCA
1 CT-TTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTGA-AA
* * * *
3109618 AAGTGCCGCTATAGATTAGGGT
64 AAGCGCCGCTAAAGATCATGGT
* * *** * * ** * * *
3109640 -TTATTGCGGCGTTTGAGAAAAAAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTGTCCCAA
1 CTT-TAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGT--GAA
* * *
3109704 AAA-CGCCGCTAAAGGTCTTAGT
63 AAAGCGCCGCTAAAGATCATGGT
* **
3109726 CTTCAGCGGCGTTTGT-GCTAGAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCG
1 CTTTAGCGGCGTTTGTGGGGA-AAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCG
3109780 CATTCATTAG
Statistics
Matches: 248, Mismatches: 55, Indels: 20
0.77 0.17 0.06
Matches are distributed among these distances:
84 1 0.00
85 5 0.02
86 162 0.65
87 76 0.31
88 4 0.02
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (85 bp):
CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTGAAAAA
GCGCCGCTAAAGATCATGGT
Found at i:3109626 original size:130 final size:129
Alignment explanation
Indices: 3109381--3109637 Score: 304
Period size: 130 Copynumber: 2.0 Consensus size: 129
3109371 AGGTGTTGGC
3109381 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTAGAAAA
1 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTAGAAAA
* *
3109446 AGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGGGGAAAACGCCGCTAAAGATTAGGTT
66 AGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGAGCAAAACGCCGCTAAAGATTAGGTT
* * * * *
3109510 CTTTAGTGGCGTTTTGTTGTCGAAGCGCCGCTATAGATCAGGGTCTATT-GCGGCGTTTG-AGGG
1 CTTTAGTGGCGTTTT-TGGTCAAAGCGCCGCTAAAGATAAGGGTCT-TTAGCGGCGTTTGTA-GA
* * * * * * * ** *
3109573 GAAAGTGCCGCTAAAGATTA-GGTTCTTTCGTGGCGTTTGTGATCAAAGTGCCGCTATAGATTAG
63 AAAAGCGCCACTAAAGATCATGG-TCTTTAGCGGCGTTTGTGAGCAAAACGCCGCTAAAGATTAG
3109637 G
127 G
3109638 GTTTATTGCG
Statistics
Matches: 107, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
129 18 0.17
130 87 0.81
131 2 0.02
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.30
Consensus pattern (129 bp):
CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTAGAAAA
AGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGAGCAAAACGCCGCTAAAGATTAGGTT
Found at i:3109651 original size:130 final size:129
Alignment explanation
Indices: 3109381--3109779 Score: 292
Period size: 130 Copynumber: 3.1 Consensus size: 129
3109371 AGGTGTTGGC
*
3109381 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTAGAAAA
1 CTTTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTAGAAAA
* *
3109446 AGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGGGGAAAACGCCGCTAAAGATTAGGTT
66 AGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGAGCAAAACGCCGCTAAAGATTAGGTT
* * * * * *
3109510 CTTTAGTGGCGTTTTGTTGTCGAAGCGCCGCTATAGATCAGGGTCTATT-GCGGCGTTTG-AGGG
1 CTTTAGCGGCGTTTT-TGGTCAAAGCGCCGCTAAAGATAAGGGTCT-TTAGCGGCGTTTGTA-GA
* * * * * * * ** *
3109573 GAAAGTGCCGCTAAAGATTA-GGTTCTTTCGTGGCGTTTGTGATCAAAGTGCCGCTATAGATTAG
63 AAAAGCGCCACTAAAGATCATGG-TCTTTAGCGGCGTTTGTGAGCAAAACGCCGCTAAAGATTA-
3109637 GGTT
126 GGTT
** *** * **** * * **
3109641 -TATT-GCGGCGTTTGAGAAAAAAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTGTCCCAA
1 CT-TTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGT-AGAA
* * * * * * *
3109704 AAA-CGCCGCTAAAGGTCTTAGTCTTCAGCGGCGTTTGT--GCTAGAAGCGCCGCTAAAGATCAG
64 AAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGAGC-A-AAACGCCGCTAAAGATTAG
*
3109766 GGT
127 GTT
3109769 CTTTAGCGGCG
1 CTTTAGCGGCG
3109780 CATTCATTAG
Statistics
Matches: 207, Mismatches: 49, Indels: 28
0.73 0.17 0.10
Matches are distributed among these distances:
127 1 0.00
128 8 0.04
129 92 0.44
130 98 0.47
131 8 0.04
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (129 bp):
CTTTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTAGAAAA
AGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGAGCAAAACGCCGCTAAAGATTAGGTT
Found at i:3110168 original size:3 final size:3
Alignment explanation
Indices: 3110162--3110191 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3110152 AACAATAGGG
3110162 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3110192 AGTTCACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3111940 original size:21 final size:21
Alignment explanation
Indices: 3111887--3111942 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
3111877 CGCCCAGTAA
*
3111887 CTGCTGCTACGCT-G--CTCT
1 CTGCTGCTACGCTGGTTCCCT
3111905 CTGCT-CT-CTGCTGGTTCCCT
1 CTGCTGCTAC-GCTGGTTCCCT
3111925 CTGCTGCTACGCTGGTTC
1 CTGCTGCTACGCTGGTTC
3111943 TTTGCCCTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
16 1 0.03
17 5 0.16
18 6 0.19
20 8 0.26
21 10 0.32
22 1 0.03
ACGTcount: A:0.04, C:0.38, G:0.23, T:0.36
Consensus pattern (21 bp):
CTGCTGCTACGCTGGTTCCCT
Found at i:3113747 original size:9 final size:9
Alignment explanation
Indices: 3113731--3113791 Score: 95
Period size: 9 Copynumber: 6.8 Consensus size: 9
3113721 GGTATTTTTT
3113731 GGTAATTCG
1 GGTAATTCG
*
3113740 GTTAATTCG
1 GGTAATTCG
*
3113749 GTTAATTCG
1 GGTAATTCG
3113758 GGTAATTCG
1 GGTAATTCG
*
3113767 GGTAATTCT
1 GGTAATTCG
3113776 GGTAATTCG
1 GGTAATTCG
3113785 GGTAATT
1 GGTAATT
3113792 TTTAACCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 48 1.00
ACGTcount: A:0.23, C:0.10, G:0.28, T:0.39
Consensus pattern (9 bp):
GGTAATTCG
Found at i:3113969 original size:12 final size:12
Alignment explanation
Indices: 3113952--3113976 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3113942 AGTAATTTCG
3113952 GGTCGGTTAACC
1 GGTCGGTTAACC
3113964 GGTCGGTTAACC
1 GGTCGGTTAACC
3113976 G
1 G
3113977 AATGAACACC
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:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:3114977 original size:18 final size:18
Alignment explanation
Indices: 3114954--3115001 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
3114944 AAAATATGAG
*
3114954 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTC
3114972 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
3114990 AAATGATGTTCA
1 AAATGATGTTCA
3115002 AATTGATGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:3117262 original size:8 final size:8
Alignment explanation
Indices: 3117245--3117292 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
3117235 TATACGAAAT
3117245 AAAATGAAA
1 AAAAT-AAA
3117254 AAAATAAAA
1 AAAAT-AAA
3117263 GAAAATAAA
1 -AAAATAAA
*
3117272 AACATAAA
1 AAAATAAA
*
3117280 TAAATAAA
1 AAAATAAA
3117288 AAAAT
1 AAAAT
3117293 GGACATTGCG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
8 17 0.52
9 11 0.33
10 5 0.15
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.15
Consensus pattern (8 bp):
AAAATAAA
Found at i:3129386 original size:24 final size:24
Alignment explanation
Indices: 3129331--3129386 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
3129321 TATATTGATG
* *
3129331 TATATAGACATAAATTAAAATATG
1 TATATATACATAAATTAAAATATA
* *
3129355 TGTGTATACATAAATTACAAA-ATA
1 TATATATACATAAATTA-AAATATA
3129379 TATATATA
1 TATATATA
3129387 GTATATTTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (24 bp):
TATATATACATAAATTAAAATATA
Found at i:3129436 original size:18 final size:18
Alignment explanation
Indices: 3129415--3129449 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3129405 AGAAAAAAAT
*
3129415 AAATATGTATATATATAA
1 AAATATGTACATATATAA
3129433 AAATATGTACATATATA
1 AAATATGTACATATATA
3129450 TAGGTGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (18 bp):
AAATATGTACATATATAA
Found at i:3129710 original size:36 final size:37
Alignment explanation
Indices: 3129670--3129759 Score: 98
Period size: 36 Copynumber: 2.5 Consensus size: 37
3129660 ACACATCTAA
*
3129670 ATATATATACT-TATAAAAATAA-AAATAT-GTATATGT
1 ATATATATA-TATATAAAAA-AAGAAATATAGTATACGT
*
3129706 ATATAGATATATATAAAAAAAGAAATATGAGTATACGT
1 ATATATATATATATAAAAAAAGAAATAT-AGTATACGT
*
3129744 ATATATAT-TAAATAAA
1 ATATATATATATATAAA
3129760 TTATATGTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
35 3 0.07
36 22 0.48
37 7 0.15
38 14 0.30
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.34
Consensus pattern (37 bp):
ATATATATATATATAAAAAAAGAAATATAGTATACGT
Found at i:3129892 original size:3 final size:3
Alignment explanation
Indices: 3129884--3129921 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3129874 ATAATACCAA
3129884 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
3129922 ATAATAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:3131332 original size:44 final size:42
Alignment explanation
Indices: 3131253--3131339 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 42
3131243 ATCTTGGAAA
* * **
3131253 GATAAGATTTACCATCTTTGATCTGCTCCACTACTGCATAGG
1 GATAAGATTTACAATCTTTGACCTAATCCACTACTGCATAGG
* *
3131295 GATACAGATTCTACAATCTTTGACCTAATCCATTACTGCTTAGG
1 GATA-AGATT-TACAATCTTTGACCTAATCCACTACTGCATAGG
3131339 G
1 G
3131340 TGATAGGACT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
42 4 0.11
43 5 0.14
44 28 0.76
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (42 bp):
GATAAGATTTACAATCTTTGACCTAATCCACTACTGCATAGG
Found at i:3131407 original size:132 final size:132
Alignment explanation
Indices: 3131246--3132068 Score: 1283
Period size: 132 Copynumber: 6.2 Consensus size: 132
3131236 CCTTGCTATC
* * * * * *
3131246 TTGGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCATAGGGAT-ACAGATTCTACA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGG-TGACAGAATCTGCA
** * * *
3131310 ATCTTTGACCTAATCCATTACTGCTTAGGGTGATAGGACTAATGG-TTAAAATCTGCTTCTCTAC
65 ATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTT-AAATCTGCTTCTCCAC
3131374 TGTA
129 TGTA
* * *
3131378 TTGGGAAGATAAGATTCACCATATTTGATCTGCTCCACTACTGCTCAGGGTGACAGAATCTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* * *
3131443 TCTTTAACCTATTCCATTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
66 TCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
3131508 TA
131 TA
* *
3131510 TTGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAAGGTGACAGAATCTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
*
3131575 TCTTCAACCTACTCCACTATTGCTTAGGGTGATAGGACTAATGG-TGTAAATCTGCTTCTCCACT
66 TCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCT-TAAATCTGCTTCTCCACT
3131639 GTA
130 GTA
*
3131642 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGATAGAATCTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* ** *
3131707 TCTTCAACCTACTCCACTATTGCTTAGGGTGATAGGACTAATGGAGTAAATCAGCTTCTCCACTG
66 TCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
3131772 TA
131 TA
* *
3131774 TTGGGAAGATAAGATTCACCATCTTCGATCTTCTCCACTACTGCTTAGGGTGATAGAATCTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* * *
3131839 TATTCAACCTACTCCACTACTGCTTAGGGTGATATGACTAATGGCTTAAATATGCTTCTCCACTG
66 TCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
3131904 TA
131 TA
3131906 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* * * *
3131971 TCTTCAACCTACTCCACTATTGCTTAGGGTGATAGGACTAATGGTTTAAATTTGCTTCTCAACTG
66 TCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
3132036 TA
131 TA
*
3132038 TTGGGAAGATAAGATTCACCATCTTCAATCT
1 TTGGGAAGATAAGATTCACCATCTTCGATCT
3132069 CTTCCGCTGC
Statistics
Matches: 648, Mismatches: 39, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
131 2 0.00
132 644 0.99
133 2 0.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (132 bp):
TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
TCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
TA
Found at i:3131725 original size:44 final size:44
Alignment explanation
Indices: 3131405--3132005 Score: 193
Period size: 44 Copynumber: 13.7 Consensus size: 44
3131395 ACCATATTTG
* * * *
3131405 ATCTGCTCCACTACTGCTCAGGGTGACAGAATCTGCAATCTTTA
1 ATCTACTCCACTACTGCTTAGGGTGATAGAATCTGCAATCTTCA
* * * * *
3131449 ACCTATTCCATTACTGCTTAGGGTGATAGGA-CT--AATGGCTTAA
1 ATCTACTCCACTACTGCTTAGGGTGATAGAATCTGCAAT--CTTCA
* * * * * * * * * **
3131492 ATCTGCTTCTCCACTG-TATTGGGAAGATAAGATTC-ACCATCTTTG
1 ATCTACTCCACTACTGCT-TAGGG-TGAT-AGAATCTGCAATCTTCA
* * *
3131537 ATCTGCTCCACTACTGCTTAAGGTGACAGAATCTGCAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGTGATAGAATCTGCAATCTTCA
* * * * *
3131581 ACCTACTCCACTATTGCTTAGGGTGATAGGA-CT--AATGGTGTAA
1 ATCTACTCCACTACTGCTTAGGGTGATAGAATCTGCAAT-CT-TCA
* * * * * * * * * *
3131624 ATCTGCTTCTCCACTG-TATTGGGAAGATAAGATTC-ACCATCTTCG
1 ATCTACTCCACTACTGCT-TAGGG-TGAT-AGAATCTGCAATCTTCA
*
3131669 ATCTGCTCCACTACTGCTTAGGGTGATAGAATCTGCAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGTGATAGAATCTGCAATCTTCA
* * * ** *
3131713 ACCTACTCCACTATTGCTTAGGGTGATAGGA-CT--AATGGAGTAA
1 ATCTACTCCACTACTGCTTAGGGTGATAGAATCTGCAAT--CTTCA
* * * * * * * * *
3131756 ATC-AGCTTCTCCACTG-TATTGGGAAGATAAGATTC-ACCATCTTCG
1 ATCTA-CTCCACTACTGCT-TAGGG-TGAT-AGAATCTGCAATCTTCA
* *
3131801 ATCTTCTCCACTACTGCTTAGGGTGATAGAATCTGCAATATTCA
1 ATCTACTCCACTACTGCTTAGGGTGATAGAATCTGCAATCTTCA
* *
3131845 ACCTACTCCACTACTGCTTAGGGTGATATG-A-CT--AATGGCTTAA
1 ATCTACTCCACTACTGCTTAGGGTGATA-GAATCTGCAAT--CTTCA
* * * * * * * * * * *
3131888 ATATGCTTCTCCACTG-TATTGGGAAGATAAGATTC-ACCATCTTCG
1 ATCTACTCCACTACTGCT-TAGGG-TGAT-AGAATCTGCAATCTTCA
* *
3131933 ATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGTGATAGAATCTGCAATCTTCA
* *
3131977 ACCTACTCCACTATTGCTTAGGGTGATAG
1 ATCTACTCCACTACTGCTTAGGGTGATAG
3132006 GACTAATGGT
Statistics
Matches: 385, Mismatches: 128, Indels: 88
0.64 0.21 0.15
Matches are distributed among these distances:
41 12 0.03
42 6 0.02
43 93 0.24
44 177 0.46
45 80 0.21
46 9 0.02
47 8 0.02
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (44 bp):
ATCTACTCCACTACTGCTTAGGGTGATAGAATCTGCAATCTTCA
Found at i:3132108 original size:46 final size:46
Alignment explanation
Indices: 3132041--3132343 Score: 423
Period size: 46 Copynumber: 6.6 Consensus size: 46
3132031 AACTGTATTG
* * * *
3132041 GGAAGATAAGAT-TCACCATCTTCAATCTCTTCCGCTGCCAAATACA
1 GGAAGACAAGATCT-ACTATCTTCGATCTCCTCCGCTGCCAAATACA
*
3132087 GGAAGACAAGATCTACTATCTTCGATCTCCTCCGCTGCCAAATATA
1 GGAAGACAAGATCTACTATCTTCGATCTCCTCCGCTGCCAAATACA
* * *
3132133 GGAAGATAAGATCTGCTATCTTTGATCTCCTCCGCTGCCAAATACA
1 GGAAGACAAGATCTACTATCTTCGATCTCCTCCGCTGCCAAATACA
* * *
3132179 GAAAGACAAGATCTGCTATCTTCGATCTCCTCTGCTGCCAAATACA
1 GGAAGACAAGATCTACTATCTTCGATCTCCTCCGCTGCCAAATACA
* **
3132225 GGAAGACAAGATCTACTATCTTTGATCTCCTTGGCTGCCAAATACA
1 GGAAGACAAGATCTACTATCTTCGATCTCCTCCGCTGCCAAATACA
*
3132271 GGAAGACAAGATCTGCTATCTTCGATCTCCTCTC-CTGCCAAATACA
1 GGAAGACAAGATCTACTATCTTCGATCTCCTC-CGCTGCCAAATACA
3132317 GGAAGACAAGATCTGA-TATCTTCGATC
1 GGAAGACAAGATCT-ACTATCTTCGATC
3132344 AATACAGGAA
Statistics
Matches: 231, Mismatches: 23, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
46 230 1.00
47 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (46 bp):
GGAAGACAAGATCTACTATCTTCGATCTCCTCCGCTGCCAAATACA
Found at i:3132298 original size:138 final size:134
Alignment explanation
Indices: 3132058--3132466 Score: 525
Period size: 138 Copynumber: 3.1 Consensus size: 134
3132048 AAGATTCACC
3132058 ATCTTCAATCTCTTCCGCTGCCAAATACAGGAAGACAAGATCTACTATCTTCGATCTCCTCCGCT
1 ATCTTC-ATCTC-T-CGCTGCCAAATACAGGAAGACAAGATCTACTATCTTCGATCTCCTCCGCT
* * *
3132123 GCCAAATATAGGAAGATAAGATCTGCTATCTTTGATCTCCTCCGCTGCCAAATACAGAAAGACAA
63 GCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCC-CTGCCAAATACAGAAAGACAA
3132188 GATCTGCT
127 GATCTGCT
* **
3132196 ATCTTCGATCTCCTCTGCTGCCAAATACAGGAAGACAAGATCTACTATCTTTGATCTCCTTGGCT
1 ATCTTC-ATCT-CTC-GCTGCCAAATACAGGAAGACAAGATCTACTATCTTCGATCTCCTCCGCT
*
3132261 GCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCTCCTGCCAAATACAGGAAGACAA
63 GCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC-CCTGCCAAATACAGAAAGACAA
3132326 GATCTG--
127 GATCTGCT
* * * *
3132332 A---T-ATCT-TCGAT--C-AATACAGGAAGAGAAGATCTGCTATCTTCGATCTCCTCCGTTGCC
1 ATCTTCATCTCTCGCTGCCAAATACAGGAAGACAAGATCTACTATCTTCGATCTCCTCCGCTGCC
* * *
3132389 AAATACAGGAAGACAAGATTTGCTATCTTCGATCTCATCCACTGCCAAATACA-AGAAGATAAGA
66 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCC-CTGCCAAATACAGA-AAGACAAGA
3132453 TCTGCT
129 TCTGCT
3132459 ATCTTCAT
1 ATCTTCAT
3132467 TGATCTGTTC
Statistics
Matches: 241, Mismatches: 19, Indels: 29
0.83 0.07 0.10
Matches are distributed among these distances:
124 1 0.00
125 100 0.41
126 1 0.00
127 1 0.00
128 2 0.01
129 2 0.01
130 1 0.00
131 6 0.02
133 1 0.00
136 1 0.00
137 1 0.00
138 122 0.51
139 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (134 bp):
ATCTTCATCTCTCGCTGCCAAATACAGGAAGACAAGATCTACTATCTTCGATCTCCTCCGCTGCC
AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCCTGCCAAATACAGAAAGACAAGATC
TGCT
Found at i:3132348 original size:33 final size:33
Alignment explanation
Indices: 3132311--3132376 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
3132301 TCTCCTGCCA
3132311 AATACAGGAAGACAAGATCTGATATCTTCGATC
1 AATACAGGAAGACAAGATCTGATATCTTCGATC
* *
3132344 AATACAGGAAGAGAAGATCTGCTATCTTCGATC
1 AATACAGGAAGACAAGATCTGATATCTTCGATC
3132377 TCCTCCGTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (33 bp):
AATACAGGAAGACAAGATCTGATATCTTCGATC
Found at i:3132397 original size:46 final size:46
Alignment explanation
Indices: 3132344--3132464 Score: 179
Period size: 46 Copynumber: 2.6 Consensus size: 46
3132334 ATCTTCGATC
* * **
3132344 AATACAGGAAGAGAAGATCTGCTATCTTCGATCTCCTCCGTTGCCA
1 AATACAGGAAGACAAGATCTGCTATCTTCGATCTCATCCACTGCCA
*
3132390 AATACAGGAAGACAAGATTTGCTATCTTCGATCTCATCCACTGCCA
1 AATACAGGAAGACAAGATCTGCTATCTTCGATCTCATCCACTGCCA
* *
3132436 AATACAAGAAGATAAGATCTGCTATCTTC
1 AATACAGGAAGACAAGATCTGCTATCTTC
3132465 ATTGATCTGT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 67 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (46 bp):
AATACAGGAAGACAAGATCTGCTATCTTCGATCTCATCCACTGCCA
Found at i:3133552 original size:21 final size:21
Alignment explanation
Indices: 3133526--3133572 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3133516 GGTATAGCAA
3133526 GATCACCACATGCCCCAATCT
1 GATCACCACATGCCCCAATCT
** *
3133547 GATCACTTCATGCCCCATTCT
1 GATCACCACATGCCCCAATCT
3133568 GATCA
1 GATCA
3133573 ATATTTGAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.38, G:0.11, T:0.26
Consensus pattern (21 bp):
GATCACCACATGCCCCAATCT
Found at i:3136623 original size:62 final size:57
Alignment explanation
Indices: 3136547--3136694 Score: 190
Period size: 57 Copynumber: 2.5 Consensus size: 57
3136537 AATTGACGGT
*
3136547 AAAAAGGATCTAGCCCGGATGGGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGTG
1 AAAAA-GATCTAGCCCGGACGGGTGATCC--T--TGATATAGCCCTCCCGAAGAATATGTG-G
*
3136610 AAAAAGATCTAGCCCGGACAGGTGAT-CTTGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGATCCTTGATATAGCCCTCCCGAAGAATATGTGG
* *
3136666 AAAATAGATTTAGCCCGGACGGGTAATCC
1 AAAA-AGATCTAGCCCGGACGGGTGATCC
3136695 GAATTAGGGT
Statistics
Matches: 78, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
56 5 0.06
57 46 0.59
58 1 0.01
59 1 0.01
61 1 0.01
62 19 0.24
63 5 0.06
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (57 bp):
AAAAAGATCTAGCCCGGACGGGTGATCCTTGATATAGCCCTCCCGAAGAATATGTGG
Found at i:3136919 original size:66 final size:66
Alignment explanation
Indices: 3136813--3136941 Score: 249
Period size: 66 Copynumber: 2.0 Consensus size: 66
3136803 TGAGTTTATA
3136813 TTGCAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGGATGAGGTTCGCGGGAGTGTGCTAT
1 TTGCAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGGATGAGGTTCGCGGGAGTGTGCTAT
3136878 C
66 C
*
3136879 TTGCAGGGGATTTAGCCTGGACTGGTAATCCTGCTGTAAGGATGAGGTTCGCGGGAGTGTGCT
1 TTGCAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGGATGAGGTTCGCGGGAGTGTGCT
3136942 CTCTGAAATG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.18, C:0.17, G:0.37, T:0.28
Consensus pattern (66 bp):
TTGCAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGGATGAGGTTCGCGGGAGTGTGCTAT
C
Found at i:3137553 original size:6 final size:6
Alignment explanation
Indices: 3137542--3137589 Score: 51
Period size: 6 Copynumber: 7.3 Consensus size: 6
3137532 TTGACCTCTC
*
3137542 CTTTTT CTTTTT CTTCTTTT TTTTTCT CTTTTT CTTCTTT CTTTTT CT
1 CTTTTT CTTTTT C-T-TTTT CTTTT-T CTTTTT CTT-TTT CTTTTT CT
3137590 CCTATTTTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
6 19 0.53
7 13 0.36
8 4 0.11
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
CTTTTT
Found at i:3137573 original size:21 final size:21
Alignment explanation
Indices: 3137543--3137590 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
3137533 TGACCTCTCC
*
3137543 TTTT-TCTTTTTCTTCTTTTT
1 TTTTCTCTTTTTCTTCTTTCT
3137563 TTTTCTCTTTTTCTTCTTTCT
1 TTTTCTCTTTTTCTTCTTTCT
3137584 TTTTCTC
1 TTTTCTC
3137591 CTATTTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTCTCTTTTTCTTCTTTCT
Found at i:3137588 original size:13 final size:12
Alignment explanation
Indices: 3137546--3137589 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
3137536 CCTCTCCTTT
3137546 TTCTTTTTCTTC
1 TTCTTTTTCTTC
3137558 TT-TTTTT-TTC
1 TTCTTTTTCTTC
3137568 -TCTTTTTCTTC
1 TTCTTTTTCTTC
3137579 TTTCTTTTTCT
1 -TTCTTTTTCT
3137590 CCTATTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
9 1 0.04
10 8 0.29
11 8 0.29
12 2 0.07
13 9 0.32
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTCTTTTTCTTC
Found at i:3137637 original size:16 final size:15
Alignment explanation
Indices: 3137602--3137648 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 15
3137592 TATTTTTGAC
3137602 TTTGATTTTTTGATTT-
1 TTTGATTTTTT--TTTA
3137618 TTTGATTTATTTTTTA
1 TTTGATTT-TTTTTTA
3137634 TTTGAATTTTTTTTT
1 TTTG-ATTTTTTTTT
3137649 GAGTCTAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 3 0.11
16 18 0.64
17 7 0.25
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.77
Consensus pattern (15 bp):
TTTGATTTTTTTTTA
Found at i:3137643 original size:12 final size:12
Alignment explanation
Indices: 3137610--3137650 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
3137600 ACTTTGATTT
3137610 TTTGATTTTTTGA
1 TTTGATTTTTT-A
3137623 TTT-ATTTTTTA
1 TTTGATTTTTTA
3137634 TTTGAATTTTTT-
1 TTTG-ATTTTTTA
3137646 TTTGA
1 TTTGA
3137651 GTCTAAACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 5 0.19
12 11 0.42
13 10 0.38
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (12 bp):
TTTGATTTTTTA
Found at i:3141949 original size:13 final size:13
Alignment explanation
Indices: 3141928--3142004 Score: 75
Period size: 13 Copynumber: 5.9 Consensus size: 13
3141918 ATACTCAAAA
3141928 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
3141941 TTCTCAAAAGTAC
1 TTTTCAAAAGCAC
* *
3141954 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
* *
3141967 TTTTTCACAA-CCC
1 -TTTTCAAAAGCAC
*
3141980 TTTTCAAAAGCAA
1 TTTTCAAAAGCAC
3141993 TTTTCAAAAGCA
1 TTTTCAAAAGCA
3142005 ATGAAGAACT
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
12 8 0.16
13 35 0.71
14 6 0.12
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:3144936 original size:42 final size:42
Alignment explanation
Indices: 3144885--3144969 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
3144875 GTTTACAAAC
*
3144885 AAAAACGCCGTTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
*
3144927 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
3144969 A
1 A
3144970 TGTTCTTTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
Found at i:3144972 original size:23 final size:23
Alignment explanation
Indices: 3144946--3144992 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
3144936 GCTAAAGATC
3144946 ATGTTCTTTAGCGGCGCTTAGAA
1 ATGTTCTTTAGCGGCGCTTAGAA
3144969 ATGTTCTTTAGCGGCGCTTAGAA
1 ATGTTCTTTAGCGGCGCTTAGAA
3144992 A
1 A
3144993 AAAACGCCGC
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:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (23 bp):
ATGTTCTTTAGCGGCGCTTAGAA
Found at i:3145008 original size:65 final size:65
Alignment explanation
Indices: 3144904--3145026 Score: 237
Period size: 65 Copynumber: 1.9 Consensus size: 65
3144894 GTTAAAGACC
*
3144904 ATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 ATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
3144969 ATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG
1 ATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG
3145027 TTTGTAAAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (65 bp):
ATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
Found at i:3145036 original size:42 final size:42
Alignment explanation
Indices: 3144965--3145296 Score: 300
Period size: 42 Copynumber: 7.9 Consensus size: 42
3144955 AGCGGCGCTT
**
3144965 AGAA-ATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAA
1 AGAACATGTTCTTTAGCGGCGCTTTTAAAAAAACGCCGCTAA
* *
3145006 AGAACATGTTCTTTAGCGGCG-TTTGTAAAAAAATGCCACTAA
1 AGAACATGTTCTTTAGCGGCGCTTT-TAAAAAAACGCCGCTAA
* * ***
3145048 AGACCATGTTCTTTAGCAGCGCTTAGGAAAAAACGCCGCTAA
1 AGAACATGTTCTTTAGCGGCGCTTTTAAAAAAACGCCGCTAA
*
3145090 AGAACATGTTCTTTAGCGGCGC--TTAAGGGAAAACGCCGCTAA
1 AGAACATGTTCTTTAGCGGCGCTTTTAA--AAAAACGCCGCTAA
* * *
3145132 AGAACATATTCTTTAGCGGCGC--TTAAGGGAAAACGCCCCTAA
1 AGAACATGTTCTTTAGCGGCGCTTTTAA--AAAAACGCCGCTAA
* * **** *
3145174 AGATCATGTTCTTTAGCGGCGTTTTTTTTCTAATCGCCGCTAA
1 AGAACATGTTCTTTAGCGGCG-CTTTTAAAAAAACGCCGCTAA
* * ** * *
3145217 AGAACATGTTCTTTAGTGGC-ATTTTTTACAAACGCCGCAAA
1 AGAACATGTTCTTTAGCGGCGCTTTTAAAAAAACGCCGCTAA
*
3145258 AGAACATGTTCTTTAGTGGCGCTTTTATACAAAAACGCC
1 AGAACATGTTCTTTAGCGGCGCTTTTA-A-AAAAACGCC
3145297 ACTATTTTGG
Statistics
Matches: 241, Mismatches: 39, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
40 1 0.00
41 42 0.17
42 158 0.66
43 30 0.12
44 8 0.03
45 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.27
Consensus pattern (42 bp):
AGAACATGTTCTTTAGCGGCGCTTTTAAAAAAACGCCGCTAA
Found at i:3145110 original size:84 final size:84
Alignment explanation
Indices: 3144965--3145300 Score: 331
Period size: 84 Copynumber: 4.0 Consensus size: 84
3144955 AGCGGCGCTT
*
3144965 AGAA-ATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTT
1 AGAACATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTT
*
3145029 TGTAA-AAAAATGCCACTAA
66 T-TAAGAAAAACGCCACTAA
* * *
3145048 AGACCATGTTCTTTAGCAGCGCTTAGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG-C
1 AGAACATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTT
* *
3145112 TTAAGGGAAAACGCCGCTAA
66 TTAA-GAAAAACGCCACTAA
* * * *
3145132 AGAACATATTCTTTAGCGGCGCTTAAGG-GAAAACGCCCCTAAAGATCATGTTCTTTAGCGGCGT
1 AGAACATGTTCTTTAGCGGCGCTT-AGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG-
***** * *
3145196 TTTTTTTCTAATCGCCGCTAA
64 TTTTAAGAAAAACGCCACTAA
* * **** * * *
3145217 AGAACATGTTCTTTAGTGGC-ATTTTTTACAAACGCCGCAAAAGAACATGTTCTTTAGTGGCGCT
1 AGAACATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG-T
*
3145281 TTTATACAAAAACGCCACTA
65 TTTA-AGAAAAACGCCACTA
3145301 TTTTGGGGAT
Statistics
Matches: 205, Mismatches: 40, Indels: 14
0.79 0.15 0.05
Matches are distributed among these distances:
82 3 0.01
83 4 0.02
84 155 0.76
85 41 0.20
86 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (84 bp):
AGAACATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTT
TTAAGAAAAACGCCACTAA
Found at i:3145675 original size:21 final size:21
Alignment explanation
Indices: 3145607--3145677 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
3145597 TTTTGCTCTG
* *
3145607 CTCTGCTTCTCTTGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
3145628 CTCCGCTTCCCTCGCTGCAGT
1 CTCTGCTTCCCTCGCTGCAGC
* * *
3145649 CGCTGCTTCCCTCGCTTCCGC
1 CTCTGCTTCCCTCGCTGCAGC
3145670 CTCTGCTT
1 CTCTGCTT
3145678 TAAGTTGTAG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.03, C:0.45, G:0.18, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:3148774 original size:23 final size:23
Alignment explanation
Indices: 3148748--3148823 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
3148738 ATAAGTGCCA
3148748 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
3148771 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
3148794 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
3148817 CACTGAT
1 CACTGAT
3148824 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:3153742 original size:11 final size:9
Alignment explanation
Indices: 3153694--3154228 Score: 84
Period size: 7 Copynumber: 62.0 Consensus size: 9
3153684 AATTGCAATG
3153694 GTAAGTTAT
1 GTAAGTTAT
3153703 GTAAGTTAT
1 GTAAGTTAT
3153712 GTAAGTTAAAT
1 GTAAGTT--AT
3153723 GT-A-TTAT
1 GTAAGTTAT
3153730 GTAAGTTAAAT
1 GTAAGTT--AT
3153741 GTAAG-T-T
1 GTAAGTTAT
3153748 GTAAGTTAT
1 GTAAGTTAT
*
3153757 -TATGTATTAT
1 GTAAG--TTAT
3153767 GTAAG-T-T
1 GTAAGTTAT
3153774 GTAAGTTAAAT
1 GTAAGTT--AT
*
3153785 GT-A-TTGT
1 GTAAGTTAT
3153792 GTAAG-T-T
1 GTAAGTTAT
3153799 GTAAGTTAAAT
1 GTAAGTT--AT
3153810 GT-A-TTAT
1 GTAAGTTAT
3153817 GTAAG-T-T
1 GTAAGTTAT
3153824 GTAAGTTAT
1 GTAAGTTAT
*
3153833 -TATGTATTAT
1 GTAAG--TTAT
3153843 GTAAG-T-T
1 GTAAGTTAT
3153850 GTAAGTTAT
1 GTAAGTTAT
* *
3153859 -TATGTATTGT
1 GTAAG--TTAT
3153869 GTAAG-T-T
1 GTAAGTTAT
3153876 GTAAGTTAT
1 GTAAGTTAT
* *
3153885 -TATGTATTGT
1 GTAAG--TTAT
3153895 GTAAG-T-T
1 GTAAGTTAT
3153902 GTAAGTTAAAT
1 GTAAGTT--AT
3153913 GT-A-TTAT
1 GTAAGTTAT
3153920 GTAAGTTAAAT
1 GTAAGTT--AT
3153931 GT-A-TTAT
1 GTAAGTTAT
3153938 GTAAG-T-T
1 GTAAGTTAT
3153945 GTAAGTTAAAT
1 GTAAGTT--AT
3153956 GT-A-TTAT
1 GTAAGTTAT
3153963 GTAAG-T-T
1 GTAAGTTAT
3153970 GTAAGTTAAAT
1 GTAAGTT--AT
3153981 GT-A-TTAT
1 GTAAGTTAT
3153988 GTAAG-T-T
1 GTAAGTTAT
3153995 GTAAGTTAT
1 GTAAGTTAT
*
3154004 -TATGTATTAT
1 GTAAG--TTAT
3154014 GTAAG-T-T
1 GTAAGTTAT
3154021 GTAAGTTAT
1 GTAAGTTAT
* *
3154030 -TATGTATTGT
1 GTAAG--TTAT
3154040 GTAAG-T-T
1 GTAAGTTAT
3154047 GTAAGTTAT
1 GTAAGTTAT
* *
3154056 -TATGTATTGT
1 GTAAG--TTAT
3154066 GTAAG-T-T
1 GTAAGTTAT
3154073 GTAAGTTAT
1 GTAAGTTAT
* *
3154082 -TATGTATTGT
1 GTAAG--TTAT
3154092 GTAAG-T-T
1 GTAAGTTAT
3154099 GTAAGTTAAAT
1 GTAAGTT--AT
3154110 GT-A-TTAT
1 GTAAGTTAT
*
3154117 GTCAGTTAAAT
1 GTAAGTT--AT
3154128 GT-A-TTAT
1 GTAAGTTAT
3154135 GTAAG-T-T
1 GTAAGTTAT
3154142 GTAAGTTAAAT
1 GTAAGTT--AT
3154153 GT-A-TTAT
1 GTAAGTTAT
3154160 GTAAG-T-T
1 GTAAGTTAT
3154167 GTAAGTTAT
1 GTAAGTTAT
*
3154176 -TATGTATTAT
1 GTAAG--TTAT
*
3154186 GTAAGTAAT
1 GTAAGTTAT
3154195 GTAAGTTAAAT
1 GTAAGTT--AT
3154206 GT-A-TTAT
1 GTAAGTTAT
3154213 GTAAG-T-T
1 GTAAGTTAT
3154220 GTAAGTTAT
1 GTAAGTTAT
3154229 TATGTATTAT
Statistics
Matches: 393, Mismatches: 26, Indels: 214
0.62 0.04 0.34
Matches are distributed among these distances:
7 145 0.37
8 71 0.18
9 63 0.16
10 43 0.11
11 71 0.18
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:3153773 original size:26 final size:25
Alignment explanation
Indices: 3153739--3154238 Score: 659
Period size: 26 Copynumber: 20.1 Consensus size: 25
3153729 TGTAAGTTAA
3153739 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-TATGTATT
*
3153765 ATGTAAGTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTATATGTATT
* *
3153790 GTGTAAGTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTATATGTATT
3153815 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-TATGTATT
3153841 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-TATGTATT
*
3153867 GTGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-TATGTATT
* *
3153893 GTGTAAGTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTATATGTATT
3153918 ATGTAAG-T-T-A---A-ATGTATT
1 ATGTAAGTTGTAAGTTATATGTATT
*
3153936 ATGTAAGTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTATATGTATT
*
3153961 ATGTAAGTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTATATGTATT
3153986 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-TATGTATT
3154012 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-TATGTATT
*
3154038 GTGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-TATGTATT
*
3154064 GTGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-TATGTATT
* *
3154090 GTGTAAGTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTATATGTATT
*
3154115 ATGTCAG-T-T-A---A-ATGTATT
1 ATGTAAGTTGTAAGTTATATGTATT
*
3154133 ATGTAAGTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTATATGTATT
3154158 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-TATGTATT
*
3154184 ATGTAAGTAATGTAAGTTAAATGTATT
1 ATGTAAGT--TGTAAGTTATATGTATT
3154211 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-TATGTATT
3154237 AT
1 AT
3154239 TTAATAAAAT
Statistics
Matches: 438, Mismatches: 16, Indels: 40
0.89 0.03 0.08
Matches are distributed among these distances:
18 27 0.06
19 4 0.01
20 2 0.00
21 2 0.00
22 2 0.00
23 2 0.00
24 4 0.01
25 154 0.35
26 217 0.50
27 15 0.03
28 9 0.02
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.47
Consensus pattern (25 bp):
ATGTAAGTTGTAAGTTATATGTATT
Found at i:3154063 original size:197 final size:196
Alignment explanation
Indices: 3153702--3154238 Score: 908
Period size: 197 Copynumber: 2.7 Consensus size: 196
3153692 TGGTAAGTTA
*
3153702 TGTAAGTTATGTAAGTTAAATGTATTATGTAAGTT--A---A--ATGTAAGTTGTAAGTTATTAT
1 TGTAAG-T-TGTAAGTTAAATGTATTATGTAAGTTAAATGTATTATGTAAGTTGTAAGTTA-AAT
*
3153760 GTATTATGTAAGTTGTAAGTTAAATGTATTGTGTAAGTTGTAAGTTAAATGTATTATGTAAGTTG
63 GTATTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTG
3153825 TAAGTTATTATGTATTATGTAAGTTGTAAGTTATTATGTATTGTGTAAGTTGTAAGTTATTATGT
128 TAAGTTATTATGTATTATGTAAGTTGTAAGTTATTATGTATTGTGTAAGTTGTAAGTTATTATGT
3153890 ATTG
193 ATTG
3153894 TGTAAGTTGTAAGTTAAATGTATTATGTAAGTTAAATGTATTATGTAAGTTGTAAGTTAAATGTA
1 TGTAAGTTGTAAGTTAAATGTATTATGTAAGTTAAATGTATTATGTAAGTTGTAAGTTAAATGTA
*
3153959 TTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTA
66 TTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTA
*
3154024 AGTTATTATGTATTGTGTAAGTTGTAAGTTATTATGTATTGTGTAAGTTGTAAGTTATTATGTAT
130 AGTTATTATGTATTATGTAAGTTGTAAGTTATTATGTATTGTGTAAGTTGTAAGTTATTATGTAT
3154089 TG
195 TG
*
3154091 TGTAAGTTGTAAGTTAAATGTATTATGTCAGTTAAATGTATTATGTAAGTTGTAAGTTAAATGTA
1 TGTAAGTTGTAAGTTAAATGTATTATGTAAGTTAAATGTATTATGTAAGTTGTAAGTTAAATGTA
*
3154156 TTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTAATGTAAGTTAAATGTATTATGTAAGTTG
66 TTATGTAAGTTGTAAGTTA-AATGTATTATGTAAGT--TGTAAGTTAAATGTATTATGTAAGTTG
3154221 TAAGTTATTATGTATTAT
128 TAAGTTATTATGTATTAT
3154239 TTAATAAAAT
Statistics
Matches: 326, Mismatches: 8, Indels: 15
0.93 0.02 0.04
Matches are distributed among these distances:
190 26 0.08
191 1 0.00
192 7 0.02
195 1 0.00
196 48 0.15
197 185 0.57
198 15 0.05
199 34 0.10
200 9 0.03
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (196 bp):
TGTAAGTTGTAAGTTAAATGTATTATGTAAGTTAAATGTATTATGTAAGTTGTAAGTTAAATGTA
TTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAA
GTTATTATGTATTATGTAAGTTGTAAGTTATTATGTATTGTGTAAGTTGTAAGTTATTATGTATT
G
Found at i:3154330 original size:34 final size:34
Alignment explanation
Indices: 3154292--3154404 Score: 106
Period size: 34 Copynumber: 3.2 Consensus size: 34
3154282 ATTAATAATA
3154292 TTTAATAAAATAACATTTTATTTTAATAGTCAAT
1 TTTAATAAAATAACATTTTATTTTAATAGTCAAT
* * * *
3154326 TTTAAT--ATTCCACATATTT-TTTATAATTATTAATAAT
1 TTTAATAAAAT-AACAT-TTTATTT-TAA-TAGT--CAAT
3154363 ATTTAATAAAATAACATTTTATTTTAATAGTCAAT
1 -TTTAATAAAATAACATTTTATTTTAATAGTCAAT
3154398 TTTAATA
1 TTTAATA
3154405 TTCCACATAT
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
32 2 0.03
33 7 0.11
34 19 0.31
35 6 0.10
37 6 0.10
38 12 0.20
39 7 0.11
40 2 0.03
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (34 bp):
TTTAATAAAATAACATTTTATTTTAATAGTCAAT
Found at i:3154357 original size:72 final size:72
Alignment explanation
Indices: 3154275--3154419 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
3154265 ACATTACTAA
3154275 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
3154340 TATTTTT
66 TATTTTT
3154347 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
3154412 TATTTTT
66 TATTTTT
3154419 T
1 T
3154420 TATATTTTAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.50
Consensus pattern (72 bp):
TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
TATTTTT
Found at i:3154422 original size:38 final size:38
Alignment explanation
Indices: 3154307--3154422 Score: 111
Period size: 38 Copynumber: 3.2 Consensus size: 38
3154297 TAAAATAACA
3154307 TTTTATTTTAATAGTCAATTTTAATATTCCACATATTT
1 TTTTATTTTAATAGTCAATTTTAATATTCCACATATTT
* * ***
3154345 TTTATAATTATTAATAAT--A-TTTAATA----AAATAACA
1 TTT-T-ATT-TTAATAGTCAATTTTAATATTCCACATATTT
3154379 TTTTATTTTAATAGTCAATTTTAATATTCCACATATTT
1 TTTTATTTTAATAGTCAATTTTAATATTCCACATATTT
3154417 TTTTAT
1 TTTTAT
3154423 ATTTTATTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 20
0.66 0.11 0.23
Matches are distributed among these distances:
31 7 0.12
32 3 0.05
33 2 0.03
34 14 0.24
38 20 0.34
39 2 0.03
40 3 0.05
41 7 0.12
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (38 bp):
TTTTATTTTAATAGTCAATTTTAATATTCCACATATTT
Found at i:3154588 original size:13 final size:13
Alignment explanation
Indices: 3154570--3154640 Score: 106
Period size: 13 Copynumber: 5.5 Consensus size: 13
3154560 ATTTATAATT
3154570 ATTTAAGTAATAA
1 ATTTAAGTAATAA
* *
3154583 ATTTAAGTAACAT
1 ATTTAAGTAATAA
3154596 ATTTAAGTAATAA
1 ATTTAAGTAATAA
* *
3154609 ATTTAAGTAACAT
1 ATTTAAGTAATAA
3154622 ATTTAAGTAATAA
1 ATTTAAGTAATAA
3154635 ATTTAA
1 ATTTAA
3154641 ACAAATTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 50 1.00
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAAGTAATAA
Found at i:3154599 original size:26 final size:26
Alignment explanation
Indices: 3154569--3154640 Score: 144
Period size: 26 Copynumber: 2.8 Consensus size: 26
3154559 TATTTATAAT
3154569 TATTTAAGTAATAAATTTAAGTAACA
1 TATTTAAGTAATAAATTTAAGTAACA
3154595 TATTTAAGTAATAAATTTAAGTAACA
1 TATTTAAGTAATAAATTTAAGTAACA
3154621 TATTTAAGTAATAAATTTAA
1 TATTTAAGTAATAAATTTAA
3154641 ACAAATTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (26 bp):
TATTTAAGTAATAAATTTAAGTAACA
Found at i:3154671 original size:40 final size:40
Alignment explanation
Indices: 3154612--3154755 Score: 216
Period size: 40 Copynumber: 3.5 Consensus size: 40
3154602 GTAATAAATT
** *
3154612 TAAGTAACATATTTAAGTAATAAATTTAAACAAATTTTAG
1 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAG
3154652 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAG
1 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAG
*
3154692 TAAGTAATGTATTTAAGTAATTAATAAATTTAAACAAATTTTAG
1 TAAGTAATGTATTT---T-AGTAATAAATTTAAACAAATTTTAG
3154736 TAAGTAATGTATTTTAGTAA
1 TAAGTAATGTATTTTAGTAA
3154756 GTAATGTATT
Statistics
Matches: 95, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
40 55 0.58
41 1 0.01
43 1 0.01
44 38 0.40
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.41
Consensus pattern (40 bp):
TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAG
Found at i:3154751 original size:17 final size:17
Alignment explanation
Indices: 3154729--3154926 Score: 132
Period size: 17 Copynumber: 10.6 Consensus size: 17
3154719 ATTTAAACAA
3154729 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
3154746 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
*
3154763 ATTTTAGTAA-TAAATTT
1 ATTTTAGTAAGT-AATGT
3154780 AAACAAATTTTAGTAAGTAATGT
1 ------ATTTTAGTAAGTAATGT
* *
3154803 ATTTTAG-AAATAAATTT
1 ATTTTAGTAAGT-AATGT
*
3154820 AAACAAATTTATGTAAGTAATGT
1 -----ATTTTA-GTAAGTAATGT
3154843 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
*
3154860 ATTTTAGTAA-TAAATTT
1 ATTTTAGTAAGT-AATGT
*
3154877 AAACAAATTTTAGTAAGTAATTT
1 ------ATTTTAGTAAGTAATGT
3154900 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
3154917 ATTTTAGTAA
1 ATTTTAGTAA
3154927 TAAATTTAAC
Statistics
Matches: 147, Mismatches: 10, Indels: 48
0.72 0.05 0.23
Matches are distributed among these distances:
16 5 0.03
17 93 0.63
18 5 0.03
22 5 0.03
23 34 0.23
24 5 0.03
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (17 bp):
ATTTTAGTAAGTAATGT
Found at i:3154755 original size:57 final size:57
Alignment explanation
Indices: 3154685--3154809 Score: 178
Period size: 57 Copynumber: 2.1 Consensus size: 57
3154675 ATTTAAACAA
*
3154685 ATTTTAGTAAGTAATGTATTTAAGTAATTAATAAATTTAAACAAATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATG----TAAGTAAGTAATAAATTTAAACAAATTTTAGTAAGTAATGT
** *
3154746 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGTAAGTAAGTAATAAATTTAAACAAATTTTAGTAAGTAATGT
3154803 ATTTTAG
1 ATTTTAG
3154810 AAATAAATTT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
57 44 0.73
61 16 0.27
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (57 bp):
ATTTTAGTAAGTAATGTAAGTAAGTAATAAATTTAAACAAATTTTAGTAAGTAATGT
Found at i:3154793 original size:40 final size:40
Alignment explanation
Indices: 3154746--3154852 Score: 189
Period size: 40 Copynumber: 2.7 Consensus size: 40
3154736 TAAGTAATGT
3154746 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
*
3154786 ATTTTAGTAAGTAATGTATTTTAGAAATAAATTTAAACAA
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
3154826 A-TTTATGTAAGTAATGTATTTTAGTAA
1 ATTTTA-GTAAGTAATGTATTTTAGTAA
3154853 GTAATGTATT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
39 4 0.06
40 60 0.94
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (40 bp):
ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
Found at i:3154839 original size:97 final size:99
Alignment explanation
Indices: 3154645--3154906 Score: 458
Period size: 97 Copynumber: 2.6 Consensus size: 99
3154635 ATTTAAACAA
*
3154645 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTAAGT
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG-
3154710 AATTAATAAATTTAAACAAATTTTAGTAAGTAATGT
65 AA-TAATAAATTTAAACAAATTTTAGTAAGTAATGT
3154746 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG-
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGA
3154810 A-AATAAATTTAAACAAA-TTTATGTAAGTAATGT
66 ATAATAAATTTAAACAAATTTTA-GTAAGTAATGT
*
3154843 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATTTATTTTAG
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
3154907 TAAGTAATGT
Statistics
Matches: 158, Mismatches: 2, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
96 4 0.03
97 90 0.57
99 1 0.01
101 63 0.40
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.44
Consensus pattern (99 bp):
ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGA
ATAATAAATTTAAACAAATTTTAGTAAGTAATGT
Found at i:3154847 original size:57 final size:57
Alignment explanation
Indices: 3154786--3154935 Score: 266
Period size: 57 Copynumber: 2.6 Consensus size: 57
3154776 ATTTAAACAA
*
3154786 ATTTTAGTAAGTAATGTATTTTAGAAATAAATTTAAACAAA-TTTATGTAAGTAATGT
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTA-GTAAGTAATGT
*
3154843 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATTT
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGT
3154900 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAA
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAA
3154936 CATTCAATCG
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
57 86 0.96
58 4 0.04
ACGTcount: A:0.43, C:0.01, G:0.11, T:0.45
Consensus pattern (57 bp):
ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGT
Found at i:3156284 original size:11 final size:11
Alignment explanation
Indices: 3156268--3156307 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
3156258 GATGATAATA
3156268 CATTAGTTACC
1 CATTAGTTACC
3156279 CATTAGTTACC
1 CATTAGTTACC
*
3156290 CACTAGTTACC
1 CATTAGTTACC
3156301 CA-TAGTT
1 CATTAGTT
3156308 TGAGATATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 5 0.18
11 23 0.82
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.35
Consensus pattern (11 bp):
CATTAGTTACC
Found at i:3157398 original size:84 final size:83
Alignment explanation
Indices: 3157291--3157491 Score: 330
Period size: 84 Copynumber: 2.4 Consensus size: 83
3157281 ATTAACACCG
3157291 TTTTGTGGCGTTTTTGGTAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACAACACCGTTT
1 TTTTGTGGCGTTTTT-G-AAAAACGCCACTAAATATTACAGCTGTGAACAGAAACAACACCGTTT
3157356 TCGTGGTCTGGAATTGCATT
64 TCGTGGTCTGGAATTGCATT
*
3157376 TTTTGTGGCGTTTTTAGAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACGACACCGTTTT
1 TTTTGTGGCGTTTTT-GAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACAACACCGTTTT
3157441 CGTGGTCTGGAATTGCATT
65 CGTGGTCTGGAATTGCATT
* * *
3157460 ATTTGTGGCATTTTCTTAAAAACGCCACTAAA
1 TTTTGTGGCGTTTT-TGAAAAACGCCACTAAA
3157492 AGTTTAACTA
Statistics
Matches: 110, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
84 93 0.85
85 17 0.15
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (83 bp):
TTTTGTGGCGTTTTTGAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACAACACCGTTTTC
GTGGTCTGGAATTGCATT
Found at i:3157894 original size:12 final size:12
Alignment explanation
Indices: 3157877--3157902 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3157867 TTAAAATAGC
3157877 ACGACCTCTTTT
1 ACGACCTCTTTT
3157889 ACGACCTCTTTT
1 ACGACCTCTTTT
3157901 AC
1 AC
3157903 AATTATATAT
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:0.19, C:0.35, G:0.08, T:0.38
Consensus pattern (12 bp):
ACGACCTCTTTT
Found at i:3158831 original size:111 final size:112
Alignment explanation
Indices: 3158515--3159215 Score: 1183
Period size: 112 Copynumber: 6.3 Consensus size: 112
3158505 AACACCTAGA
* *
3158515 TTAGCGGCGCTTTACAAAAAACGCCACTAA-TGCCCCCCCAAAGGACACAAAACGGCACCGTCTG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGT-CCCCCCCAAAGGCCACAAAACGGCACCGTCTG
* * * * * ** *
3158579 GGAGTATTATTTGCGGCATTTTTTTATAAGCGCTGCTAATGTTCACTCT
65 GGTGTATTATTTGCGGC-GTTATCTATAAACGCCACTAATGCTCACTCT
*
3158628 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCATAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
*
3158693 GTGTATTATTTGCGGCGTTATTTATAAACGCCACTAATGCTCACTCT
66 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
3158740 TTAGCGGCGCTTTACAATAAACGCCACTAAGT-CCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
3158804 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
66 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
*
3158851 TTAGCGGCGCTTTGCAATAAACGCCACTAAGT-CCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
* *
3158915 GTGTATTATTTGCGGCGTTATTTATAAACGCCGCTAATGCTCACTCT
66 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
*
3158962 TTAGCGGCGCTTTACAATAAATGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
*
3159027 GTGTATTGTTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
66 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
3159074 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
3159139 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
66 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
* **
3159186 TTAGCGGCGCTTTTCCTTAAACGCCACTAA
1 TTAGCGGCGCTTTACAATAAACGCCACTAA
3159216 TGCTCACTCT
Statistics
Matches: 561, Mismatches: 25, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
111 215 0.38
112 270 0.48
113 75 0.13
114 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.25
Consensus pattern (112 bp):
TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
Found at i:3159016 original size:223 final size:224
Alignment explanation
Indices: 3158515--3159215 Score: 1192
Period size: 223 Copynumber: 3.1 Consensus size: 224
3158505 AACACCTAGA
* *
3158515 TTAGCGGCGCTTTACAAAAAACGCCACTAA-TGCCCCCCCAAAGGACACAAAACGGCACCGTCTG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGT-CCCCCCCAAAGGCCACAAAACGGCACCGTCTG
* * * * * ** *
3158579 GGAGTATTATTTGCGGCATTTTTTTATAAGCGCTGCTAATGTTCACTCTTTAGCGGCGCTTTACA
65 GGTGTATTATTTGCGGC-GTTATCTATAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTACA
*
3158644 ATAAACGCCACTAAGTCCCCCCCAAAGGCCATAAAACGGCACCGTCTGGGTGTATTATTTGCGGC
129 ATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATTATTTGCGGC
3158709 GTTATTTATAAACGCCACTAATGCTCACTCT
194 GTTATTTATAAACGCCACTAATGCTCACTCT
3158740 TTAGCGGCGCTTTACAATAAACGCCACTAAGT-CCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
*
3158804 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTGCAAT
66 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTACAAT
3158869 AAACGCCACTAAGT-CCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATTATTTGCGGCGT
131 AAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATTATTTGCGGCGT
*
3158933 TATTTATAAACGCCGCTAATGCTCACTCT
196 TATTTATAAACGCCACTAATGCTCACTCT
*
3158962 TTAGCGGCGCTTTACAATAAATGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
*
3159027 GTGTATTGTTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTACAAT
66 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTACAAT
3159092 AAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATTATTTGCGGCGT
131 AAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATTATTTGCGGCGT
*
3159157 TATCTATAAACGCCACTAATGCTCACTCT
196 TATTTATAAACGCCACTAATGCTCACTCT
* **
3159186 TTAGCGGCGCTTTTCCTTAAACGCCACTAA
1 TTAGCGGCGCTTTACAATAAACGCCACTAA
3159216 TGCTCACTCT
Statistics
Matches: 451, Mismatches: 22, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
222 108 0.24
223 164 0.36
224 149 0.33
225 29 0.06
226 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.25
Consensus pattern (224 bp):
TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTACAAT
AAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATTATTTGCGGCGT
TATTTATAAACGCCACTAATGCTCACTCT
Found at i:3159208 original size:40 final size:40
Alignment explanation
Indices: 3159163--3159279 Score: 189
Period size: 40 Copynumber: 2.9 Consensus size: 40
3159153 GCGTTATCTA
**
3159163 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTCCT
1 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTAAT
3159203 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTAAT
1 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTAAT
* * *
3159243 TAAACGCCGCTATTGCTCACTCTTTACCGGCGCTTTT
1 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTT
3159280 GCTCCAAACG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 72 1.00
ACGTcount: A:0.21, C:0.31, G:0.15, T:0.33
Consensus pattern (40 bp):
TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTAAT
Found at i:3160536 original size:18 final size:16
Alignment explanation
Indices: 3160505--3160538 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
3160495 GTTGATTTGG
3160505 AATTAAACAAATTTAT
1 AATTAAACAAATTTAT
3160521 AATTAATACTAAATTTAT
1 AATTAA-AC-AAATTTAT
3160539 TCTATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTAAACAAATTTAT
Found at i:3168542 original size:51 final size:51
Alignment explanation
Indices: 3168466--3168589 Score: 203
Period size: 51 Copynumber: 2.4 Consensus size: 51
3168456 CGGATCACAT
* *
3168466 TTATCACTTGTCACTTGTCCCTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGCAGCTAAAGCTACCAC
* * *
3168517 TTATCACTTGTCACCTGTCACTGATCAGATAAGTGCAGCTAAAGTTACTAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGCAGCTAAAGCTACCAC
3168568 TTATCACTTGTCACTTGTCACT
1 TTATCACTTGTCACTTGTCACT
3168590 TGCCACTGAT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 67 1.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.34
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAGATAAGTGCAGCTAAAGCTACCAC
Found at i:3189079 original size:18 final size:19
Alignment explanation
Indices: 3189056--3189094 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3189046 AAACGGATGG
3189056 TTTAATCTATTAT-GAATT
1 TTTAATCTATTATGGAATT
* *
3189074 TTTAATTTTTTATGGAATT
1 TTTAATCTATTATGGAATT
3189093 TT
1 TT
3189095 AATTTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (19 bp):
TTTAATCTATTATGGAATT
Found at i:3189093 original size:19 final size:17
Alignment explanation
Indices: 3189065--3189100 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 17
3189055 GTTTAATCTA
3189065 TTATGAATTTTTAATTTT
1 TTATGAA-TTTTAATTTT
3189083 TTATGGAATTTTAATTTT
1 TTAT-GAATTTTAATTTT
3189101 AATTTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (17 bp):
TTATGAATTTTAATTTT
Found at i:3189098 original size:6 final size:6
Alignment explanation
Indices: 3189089--3189113 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3189079 TTTTTTATGG
3189089 AATTTT AATTTT AATTTT AATTTT A
1 AATTTT AATTTT AATTTT AATTTT A
3189114 GTTATTGCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
AATTTT
Found at i:3189526 original size:7 final size:7
Alignment explanation
Indices: 3189483--3189507 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3189473 AAACGTTTCG
3189483 TTTTTAT
1 TTTTTAT
3189490 TTTTTAT
1 TTTTTAT
3189497 TTTTTAT
1 TTTTTAT
3189504 TTTT
1 TTTT
3189508 ATGTTTAATT
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:3194061 original size:63 final size:63
Alignment explanation
Indices: 3193988--3194161 Score: 224
Period size: 63 Copynumber: 2.8 Consensus size: 63
3193978 ACACACGTCC
* * * * **
3193988 GTGTCTCTAGCTCATATGTCTCTAATTCTAAAATAGTGAGTTACACAATTTGGACACATGC-T
1 GTGTCTCTAGCTCGTATGCCTCTAATTCTAAAACAGTGAGTTACACAATCTGGACACACACAT
* * * *
3194050 AGTGTCCCTAGCCCGTATGCCTCTAATTCTAAAACAGCGAGTTACACGATCTGGACACACACAT
1 -GTGTCTCTAGCTCGTATGCCTCTAATTCTAAAACAGTGAGTTACACAATCTGGACACACACAT
* *
3194114 GTGTCTCTAGCTTGTGTGCCTCTAATTCTAAAACAGTGAGTTACACAA
1 GTGTCTCTAGCTCGTATGCCTCTAATTCTAAAACAGTGAGTTACACAA
3194162 CCTACTATAT
Statistics
Matches: 94, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
63 93 0.99
64 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (63 bp):
GTGTCTCTAGCTCGTATGCCTCTAATTCTAAAACAGTGAGTTACACAATCTGGACACACACAT
Found at i:3194776 original size:15 final size:13
Alignment explanation
Indices: 3194733--3194770 Score: 60
Period size: 12 Copynumber: 2.9 Consensus size: 13
3194723 ATGAAGTAAC
3194733 AAAGAAAAGAAGAA
1 AAAG-AAAGAAGAA
3194747 AAAGAAA-AAGAA
1 AAAGAAAGAAGAA
3194759 AAAGAAAGAAGA
1 AAAGAAAGAAGA
3194771 GGAAAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.52
13 7 0.30
14 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAGAA
Found at i:3196013 original size:28 final size:28
Alignment explanation
Indices: 3195973--3196030 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
3195963 AGCCAAGCAA
3195973 GAATTCTATGAAGACTTTCAATGTGATC
1 GAATTCTATGAAGACTTTCAATGTGATC
3196001 GAATTCTATGAAGACTTTCAATGTGATC
1 GAATTCTATGAAGACTTTCAATGTGATC
3196029 GA
1 GA
3196031 GTTTTCTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (28 bp):
GAATTCTATGAAGACTTTCAATGTGATC
Found at i:3202413 original size:126 final size:125
Alignment explanation
Indices: 3202099--3202468 Score: 458
Period size: 122 Copynumber: 3.0 Consensus size: 125
3202089 ACACAAATAC
* * *
3202099 ATATTTTCAACTCAGACGAGCAATTGATATATCGAAGATACTTGTGACACAGGTTTAGCCTTA-A
1 ATATTTTCAGCTCGGACGAGCAATTGATATATCGAAGATACTTGTGACACAGGTTTAGCCTGAGA
* *
3202163 TTGGTAACCTGATGCCAATTTAAAGGTTTAGCTTGGACG-GATAACTTGACA-TG--TATAT
66 CTGGTAA-CTGATGTCAATTTAAAGGTTTAGCTTGGACGAG-TAACTTGACATTGTATATAT
* * * * *
3202221 ATATTTTCAGCTTGGATGAGCAATTGATATATCGAATATACTTATGACACATGTTTAGCCTG-GA
1 ATATTTTCAGCTCGGACGAGCAATTGATATATCGAAGATACTTGTGACACAGGTTTAGCCTGAGA
**
3202285 CTGGTAACTTGATGTCAATTTAAAGGTTTAGCCCGGACGAGTAACTTGACATTTGTATATAT
66 CTGGTAAC-TGATGTCAATTTAAAGGTTTAGCTTGGACGAGTAACTTGACA-TTGTATATAT
* * *
3202347 ATATTTTTAGCTCGGACGAGTAATTGATGTATCGAAGATACTTGTGACACAGGTTTAGCC-GAGA
1 ATATTTTCAGCTCGGACGAGCAATTGATATATCGAAGATACTTGTGACACAGGTTTAGCCTGAGA
* *
3202411 CTGGTAAC----CT-AATTTAAAGGTTTAGCTTGGACGAGTAACCTGACATGTGTATATAT
66 CTGGTAACTGATGTCAATTTAAAGGTTTAGCTTGGACGAGTAACTTGACAT-TGTATATAT
3202467 AT
1 AT
3202469 TTAGCTCAAA
Statistics
Matches: 215, Mismatches: 24, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
119 1 0.00
120 43 0.20
121 2 0.01
122 98 0.46
123 1 0.00
124 2 0.01
125 1 0.00
126 67 0.31
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.34
Consensus pattern (125 bp):
ATATTTTCAGCTCGGACGAGCAATTGATATATCGAAGATACTTGTGACACAGGTTTAGCCTGAGA
CTGGTAACTGATGTCAATTTAAAGGTTTAGCTTGGACGAGTAACTTGACATTGTATATAT
Found at i:3210411 original size:15 final size:15
Alignment explanation
Indices: 3210391--3210421 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3210381 CTATTATCTT
3210391 TAACTGCTAACAGAC
1 TAACTGCTAACAGAC
3210406 TAACTGCTAACAGAC
1 TAACTGCTAACAGAC
3210421 T
1 T
3210422 TACAACGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.23
Consensus pattern (15 bp):
TAACTGCTAACAGAC
Found at i:3210455 original size:20 final size:20
Alignment explanation
Indices: 3210430--3210471 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3210420 CTTACAACGG
*
3210430 TACAACGGTTTTGACTATAT
1 TACAACGGCTTTGACTATAT
* *
3210450 TACAACTGCTTTGACTGTAT
1 TACAACGGCTTTGACTATAT
3210470 TA
1 TA
3210472 ACTCTAACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (20 bp):
TACAACGGCTTTGACTATAT
Done.