Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 9 of 362
Found at i:3006770 original size:46 final size:46
Alignment explanation
Indices: 3006718--3007037 Score: 437
Period size: 46 Copynumber: 7.0 Consensus size: 46
3006708 GGTGTAAACA
** *
3006718 ATGAAAT-ATATAAGACCATGGTTGAAAGATACCATAACAACGTGAC
1 ATGAAATGA-ATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
3006764 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
3006810 ATGAAATGAATAAGACCATGGTTGAAAGATATCATGGCAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* ** * *
3006856 ATAAAATGTGTAAGACTATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
3006902 GGGAAATGAATAAGACCACGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
3006948 ATGAAATGAATAAAACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * *
3006994 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
3007038 TCAAAGATAA
Statistics
Matches: 244, Mismatches: 28, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
45 1 0.00
46 242 0.99
47 1 0.00
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:3010382 original size:131 final size:129
Alignment explanation
Indices: 3009950--3010389 Score: 568
Period size: 127 Copynumber: 3.4 Consensus size: 129
3009940 AACGATAAAT
* * * ** * * *
3009950 CGAAACCCAGCACGATTGGGCACGATTTATCGAA-TTTCCAAATATGAAACATTGCCTCATTTTA
1 CGAAACCCAGCACGATTGGGCACGATCTCTCAAACTCCCCAAATACGAAATATTGCCTCGTTTTA
* * * * * * *
3010014 ATTCAAGAAAACATGGATGAAATGTC-AAAAGA-ATATTCCGTATCTTAGTCGAATGAAAAAAAA
66 ATTTAAGAAAACGTGGATGAAATTTCAAAAAAAGATATTCCATATTTTAGTCGAA-GGAAAAAAA
* * * *
3010077 CGAAACCCAGCACAATTGGGCACGATCTCTCAAACT-TCCAAACACGAAATATGGCCAT-GTTTT
1 CGAAACCCAGCACGATTGGGCACGATCTCTCAAACTCCCCAAATACGAAATATTGCC-TCGTTTT
* * * *
3010140 AGTTTAAGAAAACGTGGATGAAATTTCAAAAAAGGATATTCCATATTGTAGTCGAATGAAAAAAA
65 AATTTAAGAAAACGTGGATGAAATTTCAAAAAAAGATATTCCATATTTTAGTCGAAGGAAAAAAA
*
3010205 -GAAACCCAGCACGATTGAGCACGATCTCTCAAAACTCCCCAAATACGAAATATTGCCTCGTTTT
1 CGAAACCCAGCACGATTGGGCACGATCTCTC-AAACTCCCCAAATACGAAATATTGCCTCGTTTT
3010269 AATTTAAGAAAACGTGGATGAAATTTCAAAAAAAAAGATATTCCATATTTTAGTCGAAGGAAAAA
65 AATTTAAGAAAACGTGGATGAAATTTC--AAAAAAAGATATTCCATATTTTAGTCGAAGGAAAAA
3010334 AA
128 AA
*
3010336 CGAAACCCAGCGCGATTGGGCACGATCTCTCAAACTCCCCAAATACGAAATATT
1 CGAAACCCAGCACGATTGGGCACGATCTCTCAAACTCCCCAAATACGAAATATT
3010390 TCCTTATATT
Statistics
Matches: 272, Mismatches: 31, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
127 101 0.37
128 19 0.07
129 66 0.24
131 58 0.21
132 28 0.10
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (129 bp):
CGAAACCCAGCACGATTGGGCACGATCTCTCAAACTCCCCAAATACGAAATATTGCCTCGTTTTA
ATTTAAGAAAACGTGGATGAAATTTCAAAAAAAGATATTCCATATTTTAGTCGAAGGAAAAAAA
Found at i:3012554 original size:132 final size:132
Alignment explanation
Indices: 3012386--3012860 Score: 464
Period size: 132 Copynumber: 3.6 Consensus size: 132
3012376 ATTTCTGATA
* *
3012386 TGCTCCATAGCCGATACATGGAGATAAGATCCGTAATTTTTAGTCTGTTTCCTGTAACTTCAGGA
1 TGCTCCATAGCCGATACATGGAGATAAGATCCGTAATTTTTAGTCTGCTTCCTGCAACTTCAGGA
* * * * *
3012451 AGATAAGACTAGTATTTTCAACCTGCTCTCTTGCTGCCCCAGAAAGATAAG-GTCGGTGGTTAAA
66 AGATAAGACTACTATGTTCAACCTGCTCTCTTGCTACCCCAGAAAGATAAGACT-AGTGGTTAAA
3012515 ATC
130 ATC
* * *
3012518 TGCTCCATAGCTGATATATGGAGATAAGATCTGTAATTTTTAGTCTGCTTCCTGCAACTTCAGGA
1 TGCTCCATAGCCGATACATGGAGATAAGATCCGTAATTTTTAGTCTGCTTCCTGCAACTTCAGGA
* * *
3012583 AGATAAGACTTCTATGTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGACTAGTGGTTAAAA
66 AGATAAGACTACTATGTTCAACCTGCTCTCTTGCTACCCCAGAAAGATAAGACTAGTGGTTAAAA
3012648 TC
131 TC
* * * * * *
3012650 TGCTCCATAGCCAATACAT-GAGGATAAGACTCAC-CATTTTTTA-TCTACTTCATAGCCAA-TA
1 TGCTCCATAGCCGATACATGGA-GATAAGA-TC-CGTAATTTTTAGTCTGCTTCCT-G-CAACTT
* * * * * **** *
3012711 CATGG-ATATAAGATCTGTAACT-T-TTCAGCCTACT-TCCTGCAATTTTAGGAAGATAAGACTA
61 CA-GGAAGATAAGA-C--T-ACTATGTTCAACCTGCTCTCTTGCTACCCCAGAAAGATAAGACTA
*
3012772 GTGGCTAAAATC
121 GTGGTTAAAATC
* * * *
3012784 TGCTCCATAGCCGTTACATGGAGATAAGATCTGTAACTTTTCAGTCTGCTTCCTACAACTTCAGG
1 TGCTCCATAGCCGATACATGGAGATAAGATCCGTAA-TTTTTAGTCTGCTTCCTGCAACTTCAGG
*
3012849 AAGACAAGACTA
65 AAGATAAGACTA
3012861 GTAGCTGAGA
Statistics
Matches: 280, Mismatches: 46, Indels: 36
0.77 0.13 0.10
Matches are distributed among these distances:
130 1 0.00
131 3 0.01
132 148 0.53
133 30 0.11
134 75 0.27
135 19 0.07
136 2 0.01
137 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (132 bp):
TGCTCCATAGCCGATACATGGAGATAAGATCCGTAATTTTTAGTCTGCTTCCTGCAACTTCAGGA
AGATAAGACTACTATGTTCAACCTGCTCTCTTGCTACCCCAGAAAGATAAGACTAGTGGTTAAAA
TC
Found at i:3012811 original size:89 final size:89
Alignment explanation
Indices: 3012700--3012947 Score: 347
Period size: 89 Copynumber: 2.8 Consensus size: 89
3012690 TTATCTACTT
* * * * * *
3012700 CATAGCCAATACATGGATATAAGATCTGTAACTTTTCAGCCTACTTCCTGCAATTTTAGGAAGAT
1 CATAGCCGATACATGGAGATAAGATCTGTAACTTTTCAGTCTGCTTCCTACAATTTCAGGAAGAT
*
3012765 AAGACTAGTGGCTAAAATCTGCTC
66 AAGACTAGTAGCTAAAATCTGCTC
* * *
3012789 CATAGCCGTTACATGGAGATAAGATCTGTAACTTTTCAGTCTGCTTCCTACAACTTCAGGAAGAC
1 CATAGCCGATACATGGAGATAAGATCTGTAACTTTTCAGTCTGCTTCCTACAATTTCAGGAAGAT
* *
3012854 AAGACTAGTAGCTGAGATCTGCTC
66 AAGACTAGTAGCTAAAATCTGCTC
* *
3012878 CATAGCTGATACATGGAGATAA-AGTCTGTAA-TTTTCAGTCTGCTTCCTACAATTTCAAGAAGA
1 CATAGCCGATACATGGAGATAAGA-TCTGTAACTTTTCAGTCTGCTTCCTACAATTTCAGGAAGA
3012941 TAAGACT
65 TAAGACT
3012948 TGCTATCTTC
Statistics
Matches: 141, Mismatches: 17, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
88 37 0.26
89 104 0.74
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (89 bp):
CATAGCCGATACATGGAGATAAGATCTGTAACTTTTCAGTCTGCTTCCTACAATTTCAGGAAGAT
AAGACTAGTAGCTAAAATCTGCTC
Found at i:3013143 original size:100 final size:100
Alignment explanation
Indices: 3012970--3013162 Score: 341
Period size: 100 Copynumber: 1.9 Consensus size: 100
3012960 TCTGCTCCAC
* *
3012970 TGCAACTTCAGGGAGATAAGACTTGTCATTTTTGATCTACTCCATAGCCGATACATGGAGATAAG
1 TGCAACTTCAGGAAGATAAGACTTGTCATTTTCGATCTACTCCATAGCCGATACATGGAGATAAG
3013035 ATCTGTAAATTTTCAGTCTGCTTCCTGCTGCTTCT
66 ATCTGTAAATTTTCAGTCTGCTTCCTGCTGCTTCT
* * *
3013070 TGCAACTTCAGGAAGATGAGACTTGTCATTTTCGATCTGCTCCATAGCCGATATATGGAGATAAG
1 TGCAACTTCAGGAAGATAAGACTTGTCATTTTCGATCTACTCCATAGCCGATACATGGAGATAAG
3013135 ATCTGTAAATTTTCAGTCTGCTTCCTGC
66 ATCTGTAAATTTTCAGTCTGCTTCCTGC
3013163 AACTTTAGGA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 88 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (100 bp):
TGCAACTTCAGGAAGATAAGACTTGTCATTTTCGATCTACTCCATAGCCGATACATGGAGATAAG
ATCTGTAAATTTTCAGTCTGCTTCCTGCTGCTTCT
Found at i:3024862 original size:130 final size:129
Alignment explanation
Indices: 3024534--3024974 Score: 572
Period size: 127 Copynumber: 3.4 Consensus size: 129
3024524 AACGATAAAT
* * * * ** *
3024534 CGAAACCCAGCACGATTGAGAACGATTTATCGAA-TTTCCAAATACGAAATATTGCCTCATTTTA
1 CGAAACCCAGCACGATTGAGCACGATCTCTCAAACTCCCCAAATACGAAATATTGCCTCGTTTTA
* * * * *
3024598 ATTCAAGAAAACATGGATGAAATGTC--AAAAGGATATTCCGTATCTTAGTCAAATGAAAAAAAA
66 GTTTAAGAAAACATGGATGAAATTTCAAAAAAGGATATTCCATAT-TTAGTCGAATGAAAAAAAA
* * * * * * *
3024661 CGAAACCCAACACGATTGGGCACGATCTCTCGAACT-TCCAAACACGAAATATTGTCTTGTTTTA
1 CGAAACCCAGCACGATTGAGCACGATCTCTCAAACTCCCCAAATACGAAATATTGCCTCGTTTTA
3024725 GTTTAAGAAAACATGGATGAAATTTCAAAAAAGGATATTCCATATTGTAGTCGAATG-AAAAAAA
66 GTTTAAGAAAACATGGATGAAATTTCAAAAAAGGATATTCCATATT-TAGTCGAATGAAAAAAAA
3024789 CGAAACCCAGCACGATTGAGCACGATCTCTCAAAACTCCCCAAATACGAAATATTGCCTCGTTTT
1 CGAAACCCAGCACGATTGAGCACGATCTCTC-AAACTCCCCAAATACGAAATATTGCCTCGTTTT
* *
3024854 AGTTTAAGAAAA-AGTGGATGAAATTTCAAAAAAAAGGAT-TTCCATATTTTACTCGAAGGAAAA
65 AGTTTAAGAAAACA-TGGATGAAATTTC--AAAAAAGGATATTCCATA-TTTAGTCGAATGAAAA
3024917 AAAA
126 AAAA
*
3024921 AGAAACCCAGCACGATTGAGCACGATCTCTCAAACTCCCCAAATACGAAATATT
1 CGAAACCCAGCACGATTGAGCACGATCTCTCAAACTCCCCAAATACGAAATATT
3024975 TCCTTATATT
Statistics
Matches: 279, Mismatches: 24, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
127 76 0.27
128 38 0.14
129 30 0.11
130 48 0.17
131 38 0.14
132 49 0.18
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (129 bp):
CGAAACCCAGCACGATTGAGCACGATCTCTCAAACTCCCCAAATACGAAATATTGCCTCGTTTTA
GTTTAAGAAAACATGGATGAAATTTCAAAAAAGGATATTCCATATTTAGTCGAATGAAAAAAAA
Found at i:3028616 original size:15 final size:15
Alignment explanation
Indices: 3028596--3028629 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3028586 TTAATCATAA
3028596 TTAATTAATAAAAAC
1 TTAATTAATAAAAAC
* *
3028611 TTAATTAATTAAACC
1 TTAATTAATAAAAAC
3028626 TTAA
1 TTAA
3028630 GTGTAATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAATTAATAAAAAC
Found at i:3031166 original size:8 final size:8
Alignment explanation
Indices: 3031149--3031195 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
3031139 TTTAAATTTT
*
3031149 TTTTAGAA
1 TTTTATAA
3031157 TTTTATAA
1 TTTTATAA
3031165 TTTTATAA
1 TTTTATAA
*
3031173 TTATAT-A
1 TTTTATAA
*
3031180 TTTTAGAA
1 TTTTATAA
*
3031188 TTTCATAA
1 TTTTATAA
3031196 AAAATAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
7 5 0.16
8 27 0.84
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (8 bp):
TTTTATAA
Found at i:3031215 original size:31 final size:32
Alignment explanation
Indices: 3031180--3031247 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 32
3031170 TAATTATATA
*
3031180 TTTTAGAATTTCATAAAA-AATAATTTA-ATTT
1 TTTTAAAATTT-ATAAAATAATAATTTACATTT
* **
3031211 TTTTAAAATTTTTAAAATAATTTTTTACATTT
1 TTTTAAAATTTATAAAATAATAATTTACATTT
3031243 TTTTA
1 TTTTA
3031248 CACTTTTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 5 0.16
31 17 0.55
32 9 0.29
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (32 bp):
TTTTAAAATTTATAAAATAATAATTTACATTT
Found at i:3036940 original size:12 final size:12
Alignment explanation
Indices: 3036923--3036947 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3036913 ACTATCAACC
3036923 AACCAACCCGAG
1 AACCAACCCGAG
3036935 AACCAACCCGAG
1 AACCAACCCGAG
3036947 A
1 A
3036948 TATATATATA
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:0.44, C:0.40, G:0.16, T:0.00
Consensus pattern (12 bp):
AACCAACCCGAG
Found at i:3037211 original size:27 final size:27
Alignment explanation
Indices: 3037171--3037232 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
3037161 TGGGCCCTAC
* * *
3037171 TATTAGAGAGTATTTTTTTAATAATTT
1 TATTATAGACTATTTTTTTAACAATTT
3037198 TATTATAGACTATTTTTTTAACAATTT
1 TATTATAGACTATTTTTTTAACAATTT
3037225 TATTATAG
1 TATTATAG
3037233 GTTTAGTCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (27 bp):
TATTATAGACTATTTTTTTAACAATTT
Found at i:3042073 original size:2 final size:2
Alignment explanation
Indices: 3042066--3042093 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3042056 ATTGCAAGTA
3042066 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3042094 GCATATGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3045739 original size:29 final size:29
Alignment explanation
Indices: 3045669--3045740 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 29
3045659 GTATTAGTAA
*
3045669 TCACTCAATT-TTAGTAAATTTTTTTTTGG
1 TCAC-CAATTATTAGTAAATTTTGTTTTGG
*
3045698 TCACCCATCTATTAGTAAA-TTTGTTTTGG
1 TCACCAAT-TATTAGTAAATTTTGTTTTGG
3045727 TCATCCAATTATTA
1 TCA-CCAATTATTA
3045741 AAAGTTATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 3 0.08
29 22 0.59
30 12 0.32
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (29 bp):
TCACCAATTATTAGTAAATTTTGTTTTGG
Found at i:3054305 original size:24 final size:24
Alignment explanation
Indices: 3054274--3054332 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 24
3054264 ATTGTAAATT
*
3054274 AATAAAATTAATACAAT-TCTTTAA
1 AATAAAATTAACACAATAT-TTTAA
*
3054298 AATAAAATTAGCACAATATTTTAA
1 AATAAAATTAACACAATATTTTAA
3054322 AATAATAATTA
1 AATAA-AATTA
3054333 TGAATTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 25 0.81
25 6 0.19
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (24 bp):
AATAAAATTAACACAATATTTTAA
Found at i:3057359 original size:25 final size:25
Alignment explanation
Indices: 3057329--3057416 Score: 88
Period size: 25 Copynumber: 3.5 Consensus size: 25
3057319 ATGAAATTAC
3057329 AATGAGTATAATTGAGATCTTGGTA
1 AATGAGTATAATTGAGATCTTGGTA
* * *****
3057354 AATGAGTTTGA-TGAGATGAAATTA
1 AATGAGTATAATTGAGATCTTGGTA
3057378 CAATGAGTATAATTGAGATCTTGGTA
1 -AATGAGTATAATTGAGATCTTGGTA
*
3057404 AATGAGTTTAATT
1 AATGAGTATAATT
3057417 ATTTTTGGGG
Statistics
Matches: 46, Mismatches: 15, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
24 8 0.17
25 30 0.65
26 8 0.17
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (25 bp):
AATGAGTATAATTGAGATCTTGGTA
Found at i:3057387 original size:50 final size:50
Alignment explanation
Indices: 3057312--3057412 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
3057302 CATTGACAGA
3057312 TGATGAGATGAAATTACAATGAGTATAATTGAGATCTTGGTAAATGAGTT
1 TGATGAGATGAAATTACAATGAGTATAATTGAGATCTTGGTAAATGAGTT
3057362 TGATGAGATGAAATTACAATGAGTATAATTGAGATCTTGGTAAATGAGTT
1 TGATGAGATGAAATTACAATGAGTATAATTGAGATCTTGGTAAATGAGTT
3057412 T
1 T
3057413 AATTATTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.35
Consensus pattern (50 bp):
TGATGAGATGAAATTACAATGAGTATAATTGAGATCTTGGTAAATGAGTT
Found at i:3061104 original size:21 final size:21
Alignment explanation
Indices: 3061071--3061119 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
3061061 TTTTTTTTTC
*
3061071 AAATT-GAATCGAGTGAAATG
1 AAATTCGAATCGAGTGAAATA
*
3061091 AAATTCGAGTCGAGTGAAATA
1 AAATTCGAATCGAGTGAAATA
3061112 AAATTCGA
1 AAATTCGA
3061120 CTGAAATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.24
Consensus pattern (21 bp):
AAATTCGAATCGAGTGAAATA
Found at i:3061410 original size:19 final size:19
Alignment explanation
Indices: 3061389--3061435 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
3061379 AGAAATAAAA
3061389 TTTGAAATTTTTATAAATAT
1 TTTG-AATTTTTATAAATAT
3061409 TTTGAATTTTT-TAAATTAT
1 TTTGAATTTTTATAAA-TAT
*
3061428 TCTGAATT
1 TTTGAATT
3061436 ATCTTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 4 0.16
19 17 0.68
20 4 0.16
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.57
Consensus pattern (19 bp):
TTTGAATTTTTATAAATAT
Found at i:3075306 original size:19 final size:19
Alignment explanation
Indices: 3075284--3075321 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3075274 AATTTTTATG
*
3075284 TTTAA-ATTTATTTTTTAAA
1 TTTAATATTT-TTATTTAAA
3075303 TTTAATATTTTTATTTAAA
1 TTTAATATTTTTATTTAAA
3075322 CTTGTTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTAATATTTTTATTTAAA
Found at i:3079561 original size:28 final size:29
Alignment explanation
Indices: 3079514--3079570 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
3079504 AATACACTTC
* * *
3079514 AAGACTCAAGAGAGAGATATCCAAGTATT
1 AAGACTCAAGAGAAAAATATCCAAATATT
*
3079543 AAGA-TCAAGAGAAAAATATTCAAATATT
1 AAGACTCAAGAGAAAAATATCCAAATATT
3079571 TATTATTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.23
Consensus pattern (29 bp):
AAGACTCAAGAGAAAAATATCCAAATATT
Found at i:3080439 original size:29 final size:29
Alignment explanation
Indices: 3080404--3080459 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
3080394 CATTAAGGGC
*
3080404 TCACCTATAAGGT-TTCACATGCAAGGGGT
1 TCACCTAT-AGGTGTTCACATACAAGGGGT
*
3080433 TCACCTATAGGTGTTCGCATACAAGGG
1 TCACCTATAGGTGTTCACATACAAGGG
3080460 TTTTACATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (29 bp):
TCACCTATAGGTGTTCACATACAAGGGGT
Found at i:3080461 original size:28 final size:28
Alignment explanation
Indices: 3080398--3080461 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
3080388 AGCTTGCATT
* *
3080398 AAGGGCTCACCTATAAGGTTTCACATGC
1 AAGGGTTCACCTATAAGGTTTCACATAC
*
3080426 AAGGGGTTCACCTAT-AGGTGTTCGCATAC
1 AA-GGGTTCACCTATAAGGT-TTCACATAC
3080455 AAGGGTT
1 AAGGGTT
3080462 TTACATGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 11 0.35
29 20 0.65
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (28 bp):
AAGGGTTCACCTATAAGGTTTCACATAC
Found at i:3080611 original size:23 final size:22
Alignment explanation
Indices: 3080579--3080634 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
3080569 GTAGGGTTCC
*
3080579 CATAA-TAAACAAGTATGTTTCG
1 CATAACTAAACAACT-TGTTTCG
*
3080601 CATAACTAAACAACTTGTTTTG
1 CATAACTAAACAACTTGTTTCG
3080623 CATAACTAAACA
1 CATAACTAAACA
3080635 TGTACAGTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 23 0.74
23 8 0.26
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (22 bp):
CATAACTAAACAACTTGTTTCG
Found at i:3081377 original size:19 final size:18
Alignment explanation
Indices: 3081336--3081380 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
3081326 TACAACTTAT
*
3081336 TTTCTAATATAATTCTAAT
1 TTTCT-ATATAATTCTAAA
*
3081355 TTTCTATATAATTTTTAAA
1 TTTCTATATAA-TTCTAAA
3081374 TTTCTAT
1 TTTCTAT
3081381 TTATAGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTCTATATAATTCTAAA
Found at i:3082143 original size:21 final size:22
Alignment explanation
Indices: 3082119--3082175 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
3082109 CATACTTTTA
3082119 AATATATAAATAATATAA-TAT
1 AATATATAAATAATATAATTAT
* *
3082140 AATATAAAAATAAAAATAATTAT
1 AATATATAAAT-AATATAATTAT
*
3082163 AAT-TATAATTAAT
1 AATATATAAATAAT
3082176 TTATTAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
21 12 0.41
22 11 0.38
23 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AATATATAAATAATATAATTAT
Found at i:3082147 original size:27 final size:29
Alignment explanation
Indices: 3082117--3082171 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 29
3082107 CTCATACTTT
* * *
3082117 TAAATATATAAATAA-TATAATA-TAATA
1 TAAAAATAAAAATAATTATAATTATAATA
3082144 TAAAAATAAAAATAATTATAATTATAAT
1 TAAAAATAAAAATAATTATAATTATAAT
3082172 TAATTTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 13 0.57
28 6 0.26
29 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
TAAAAATAAAAATAATTATAATTATAATA
Found at i:3082628 original size:25 final size:26
Alignment explanation
Indices: 3082567--3082647 Score: 78
Period size: 25 Copynumber: 3.1 Consensus size: 26
3082557 GTAAGTACGA
3082567 AATTAAAAATAGAAA-T-ATTAATAATT
1 AATT-AAAATA-AAATTAATTAATAATT
*
3082593 AAATTAGAAATAAAATTATTTAATAATT
1 -AATTA-AAATAAAATTAATTAATAATT
* *
3082621 AATT-AAATAGAATTAATTAGTAATT
1 AATTAAAATAAAATTAATTAATAATT
3082646 AA
1 AA
3082648 ATTGTTGAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
25 20 0.43
26 4 0.09
27 14 0.30
28 9 0.19
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (26 bp):
AATTAAAATAAAATTAATTAATAATT
Found at i:3084405 original size:31 final size:30
Alignment explanation
Indices: 3084364--3084425 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
3084354 TAATGCAAAA
*
3084364 AAATTC-AAAAAAAAGTTGTTAAAAATTCAAT
1 AAATTCAAAAAAAAAATTG-TAAAAATT-AAT
*
3084395 AAATTTAAAAAAAAAATTGTAAAAATTAAT
1 AAATTCAAAAAAAAAATTGTAAAAATTAAT
3084425 A
1 A
3084426 TATATATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 4 0.14
31 13 0.46
32 11 0.39
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (30 bp):
AAATTCAAAAAAAAAATTGTAAAAATTAAT
Found at i:3089242 original size:30 final size:30
Alignment explanation
Indices: 3089206--3089265 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
3089196 GATGAACATA
3089206 TCTTAAAGGAAAAGTAATCAAAATTGTTGC
1 TCTTAAAGGAAAAGTAATCAAAATTGTTGC
3089236 TCTTAAAGGAAAAGTAATCAAAATTGTTGC
1 TCTTAAAGGAAAAGTAATCAAAATTGTTGC
3089266 CCAACAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (30 bp):
TCTTAAAGGAAAAGTAATCAAAATTGTTGC
Found at i:3095053 original size:6 final size:6
Alignment explanation
Indices: 3095044--3095070 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3095034 TTCATTTTCC
3095044 AATATT AATATT AATATT AATATT AAT
1 AATATT AATATT AATATT AATATT AAT
3095071 GATTGGTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATATT
Found at i:3095260 original size:7 final size:7
Alignment explanation
Indices: 3095248--3095283 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
3095238 AGATGCATTC
3095248 TTTTCTT
1 TTTTCTT
3095255 TTTTCTT
1 TTTTCTT
3095262 TTTTCTT
1 TTTTCTT
*
3095269 TTTCCTT
1 TTTTCTT
3095276 TTTT-TT
1 TTTTCTT
3095282 TT
1 TT
3095284 AAATAGAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 4 0.15
7 23 0.85
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTCTT
Found at i:3100774 original size:24 final size:23
Alignment explanation
Indices: 3100746--3100799 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
3100736 TAAAATTTTA
3100746 ATAAATAAAAAATATATAAA-AAT
1 ATAAATAAAAAAT-TATAAATAAT
**
3100769 ATTAAATATTAAATTATAAATAAT
1 A-TAAATAAAAAATTATAAATAAT
3100793 ATAAATA
1 ATAAATA
3100800 TTTTAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 13 0.48
24 14 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATAAATAAAAAATTATAAATAAT
Found at i:3102854 original size:11 final size:10
Alignment explanation
Indices: 3102833--3102863 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
3102823 CTGAGATTGC
3102833 CTTTTTTTTT
1 CTTTTTTTTT
3102843 CTTTTCTTTTT
1 CTTTT-TTTTT
3102854 CTTTTTTTTT
1 CTTTTTTTTT
3102864 GGGGGGGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:3104715 original size:18 final size:18
Alignment explanation
Indices: 3104692--3104728 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3104682 CTACTTGTCT
3104692 GAAGAAAGTTATTAGATC
1 GAAGAAAGTTATTAGATC
3104710 GAAGAAAGTTATTAGATC
1 GAAGAAAGTTATTAGATC
3104728 G
1 G
3104729 GTTGATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.27
Consensus pattern (18 bp):
GAAGAAAGTTATTAGATC
Found at i:3104984 original size:17 final size:16
Alignment explanation
Indices: 3104958--3104996 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3104948 CTTTTGGATT
*
3104958 AGTTTGAGTTACTTTTA
1 AGTTTAAGTTA-TTTTA
*
3104975 TGTTTAAGTTATTTTA
1 AGTTTAAGTTATTTTA
3104991 AGTTTA
1 AGTTTA
3104997 GATAAATTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.26, C:0.03, G:0.15, T:0.56
Consensus pattern (16 bp):
AGTTTAAGTTATTTTA
Found at i:3107535 original size:15 final size:14
Alignment explanation
Indices: 3107473--3107536 Score: 53
Period size: 15 Copynumber: 4.6 Consensus size: 14
3107463 CAAAATATTT
3107473 TTATATTTTATTAA
1 TTATATTTTATTAA
*
3107487 -TA-ATTTGAATATAA
1 TTATATTT-TAT-TAA
* *
3107501 ATATA-ATTATTAA
1 TTATATTTTATTAA
3107514 TTATATTTTATTATA
1 TTATATTTTATTA-A
3107529 TTATATTT
1 TTATATTT
3107537 AATCTTTCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
12 4 0.10
13 11 0.28
14 11 0.28
15 12 0.31
16 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
TTATATTTTATTAA
Found at i:3110531 original size:16 final size:16
Alignment explanation
Indices: 3110510--3110540 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3110500 AATCATTGAA
3110510 AAATGATATGAATCTT
1 AAATGATATGAATCTT
*
3110526 AAATGATTTGAATCT
1 AAATGATATGAATCT
3110541 GAAAATAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (16 bp):
AAATGATATGAATCTT
Found at i:3111126 original size:22 final size:23
Alignment explanation
Indices: 3111082--3111126 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
3111072 TCAAAACAAT
* *
3111082 TTGAAATTTGAAATGATCCAAAC
1 TTGAAATTCGAAATGATACAAAC
*
3111105 TTGAAA-TCGAAATGATATAAAC
1 TTGAAATTCGAAATGATACAAAC
3111127 AATAAACTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (23 bp):
TTGAAATTCGAAATGATACAAAC
Found at i:3113871 original size:30 final size:30
Alignment explanation
Indices: 3113808--3113870 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
3113798 AGTTTATATC
* *
3113808 TTTATAATTTTTAAAGGATTAAATTAAATT
1 TTTATAATTTTTAAAGGATCAAAGTAAATT
* *
3113838 TTTATCATTTTTAAAGGATCATAGTATAATT
1 TTTATAATTTTTAAAGGATCAAAGTA-AATT
3113869 TT
1 TT
3113871 ACTATGTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 22 0.79
31 6 0.21
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (30 bp):
TTTATAATTTTTAAAGGATCAAAGTAAATT
Found at i:3116369 original size:12 final size:12
Alignment explanation
Indices: 3116352--3116384 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3116342 CGGCCCGCCC
3116352 ATATTAATTTTT
1 ATATTAATTTTT
3116364 ATATT-ATTTTT
1 ATATTAATTTTT
3116375 ATA-TAATTTT
1 ATATTAATTTT
3116385 AAATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:3116540 original size:30 final size:30
Alignment explanation
Indices: 3116504--3116561 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
3116494 CAATTTAACA
*
3116504 AGCAAATGCCTCTAAAATAATAACAAAATT
1 AGCAAATGCCTCTAAAATAATAAAAAAATT
** *
3116534 AGCAAATGTTTTTAAAATAATAAAAAAA
1 AGCAAATGCCTCTAAAATAATAAAAAAA
3116562 AGTAACAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.26
Consensus pattern (30 bp):
AGCAAATGCCTCTAAAATAATAAAAAAATT
Found at i:3116624 original size:22 final size:22
Alignment explanation
Indices: 3116599--3116641 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3116589 TATCCAAACA
3116599 ATAACAACAAAATAGTAGCAAT
1 ATAACAACAAAATAGTAGCAAT
* **
3116621 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
3116642 AATAGGAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAT
Found at i:3116645 original size:11 final size:11
Alignment explanation
Indices: 3116606--3116646 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
3116596 ACAATAACAA
3116606 CAAAATAGTAG
1 CAAAATAGTAG
* *
3116617 CAATATAATAG
1 CAAAATAGTAG
*
3116628 TAAAATAGTAG
1 CAAAATAGTAG
3116639 CAAAATAG
1 CAAAATAG
3116647 GAAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:3124715 original size:19 final size:20
Alignment explanation
Indices: 3124674--3124718 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
3124664 CTTTAGATTT
*
3124674 TTTTCTTTTATGTTTTTTAA
1 TTTTCTTTTATCTTTTTTAA
3124694 TTTTCTTTT-TCTTTTTCT-A
1 TTTTCTTTTATCTTTTT-TAA
3124713 TTTTCT
1 TTTTCT
3124719 ATCCTCTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTCTTTTATCTTTTTTAA
Found at i:3138168 original size:16 final size:17
Alignment explanation
Indices: 3138147--3138179 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3138137 TTATGACATA
*
3138147 TATTAACCTTA-ATTAT
1 TATTAACATTAGATTAT
3138163 TATTAACATTAGATTAT
1 TATTAACATTAGATTAT
3138180 CACATTCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.48
Consensus pattern (17 bp):
TATTAACATTAGATTAT
Found at i:3138249 original size:21 final size:20
Alignment explanation
Indices: 3138203--3138250 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
3138193 CTCAATATAT
** *
3138203 AAAAATAATAATTATTTTAT
1 AAAAATAATAATTAGGTTAG
3138223 ACAAAATAATAATTAGGGTTAG
1 A-AAAATAATAATTA-GGTTAG
3138245 AAAAAT
1 AAAAAT
3138251 CTAAAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 18 0.78
22 4 0.17
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.33
Consensus pattern (20 bp):
AAAAATAATAATTAGGTTAG
Found at i:3143746 original size:16 final size:17
Alignment explanation
Indices: 3143714--3143746 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3143704 TTAACTGAAC
*
3143714 TTATGTAGTACTTTTAA
1 TTATGTAATACTTTTAA
3143731 TTATGTAATA-TTTTAA
1 TTATGTAATACTTTTAA
3143747 GACTTGAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (17 bp):
TTATGTAATACTTTTAA
Found at i:3152511 original size:23 final size:23
Alignment explanation
Indices: 3152485--3152528 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3152475 ATTACGAATG
3152485 AAAATATATATTATT-TTTAATAT
1 AAAATATATATT-TTATTTAATAT
*
3152508 AAAATATTTATTTTATTTAAT
1 AAAATATATATTTTATTTAAT
3152529 TTTAGCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AAAATATATATTTTATTTAATAT
Found at i:3156754 original size:9 final size:9
Alignment explanation
Indices: 3156740--3156771 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
3156730 AACTGGTCAT
*
3156740 TCCACCATC
1 TCCACCACC
3156749 TCCACCACC
1 TCCACCACC
3156758 TCCACCACC
1 TCCACCACC
3156767 TCCAC
1 TCCAC
3156772 AGCCAAGGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.22, C:0.62, G:0.00, T:0.16
Consensus pattern (9 bp):
TCCACCACC
Found at i:3159533 original size:13 final size:13
Alignment explanation
Indices: 3159515--3159539 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3159505 AGCGACAGAT
3159515 GGGATATGTTTAC
1 GGGATATGTTTAC
3159528 GGGATATGTTTA
1 GGGATATGTTTA
3159540 TATTTGTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.04, G:0.32, T:0.40
Consensus pattern (13 bp):
GGGATATGTTTAC
Found at i:3161227 original size:9 final size:9
Alignment explanation
Indices: 3161213--3161244 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
3161203 AACTGGTCAT
*
3161213 TCCACCATC
1 TCCACCACC
3161222 TCCACCACC
1 TCCACCACC
3161231 TCCACCACC
1 TCCACCACC
3161240 TCCAC
1 TCCAC
3161245 AGCCAAGGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.22, C:0.62, G:0.00, T:0.16
Consensus pattern (9 bp):
TCCACCACC
Found at i:3167403 original size:42 final size:42
Alignment explanation
Indices: 3167324--3167404 Score: 108
Period size: 43 Copynumber: 1.9 Consensus size: 42
3167314 TAGTGTTGTC
*
3167324 TCTAATTTATAATTATTTTATTTTGAATAAAATTTTTTATTA
1 TCTAATTTATAATTAATTTATTTTGAATAAAATTTTTTATTA
* ** *
3167366 TCTAATTTATGATTAAATTTATTTTTTATAATATTTTTT
1 TCTAATTTATAATT-AATTTATTTTGAATAAAATTTTTT
3167405 TGGCCAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
42 13 0.39
43 20 0.61
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (42 bp):
TCTAATTTATAATTAATTTATTTTGAATAAAATTTTTTATTA
Found at i:3176461 original size:9 final size:9
Alignment explanation
Indices: 3176397--3176474 Score: 77
Period size: 9 Copynumber: 8.4 Consensus size: 9
3176387 ACATGTAACA
3176397 AAAAATTAT
1 AAAAATTAT
*
3176406 AAAAA-AAT
1 AAAAATTAT
3176414 AAAAATTAAT
1 AAAAATT-AT
*
3176424 AAAAGTTAT
1 AAAAATTAT
3176433 AAAAATTAT
1 AAAAATTAT
**
3176442 AAATTTTAT
1 AAAAATTAT
*
3176451 AAAAATCATAA
1 AAAAAT--TAT
3176462 AAAAATTAT
1 AAAAATTAT
3176471 AAAA
1 AAAA
3176475 TGCATAAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
8 7 0.13
9 32 0.58
10 8 0.15
11 8 0.15
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:3176472 original size:20 final size:20
Alignment explanation
Indices: 3176447--3176486 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3176437 ATTATAAATT
3176447 TTATAAAAAT-CATAAAAAAA
1 TTAT-AAAATGCATAAAAAAA
3176467 TTATAAAATGCATAAAAAAA
1 TTATAAAATGCATAAAAAAA
3176487 GCCCTTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (20 bp):
TTATAAAATGCATAAAAAAA
Found at i:3176584 original size:20 final size:20
Alignment explanation
Indices: 3176561--3176617 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
3176551 TAATTTTTTC
3176561 TATATTTTTATAAAAAAATT
1 TATATTTTTATAAAAAAATT
* *
3176581 TATAATTTT-TAATAAAATT
1 TATATTTTTATAAAAAAATT
3176600 TAAATATTTTTATTAAAA
1 T--ATATTTTTA-TAAAA
3176618 GTTAATATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 10 0.34
20 8 0.28
21 7 0.24
23 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATATTTTTATAAAAAAATT
Found at i:3176610 original size:21 final size:20
Alignment explanation
Indices: 3176562--3176631 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
3176552 AATTTTTTCT
*
3176562 ATATTTTTATAAAAAAATTT-
1 ATATTTTT-TAATAAAATTTA
*
3176582 ATAATTTTTAATAAAATTTA
1 ATATTTTTTAATAAAATTTA
* *
3176602 A-ATATTTTTATTAAAAGTTA
1 ATAT-TTTTTAATAAAATTTA
3176622 ATATTTTTTA
1 ATATTTTTTA
3176632 TTTTTATCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
19 11 0.26
20 29 0.69
21 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (20 bp):
ATATTTTTTAATAAAATTTA
Found at i:3198239 original size:31 final size:31
Alignment explanation
Indices: 3198196--3198258 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
3198186 CGTAAATGAG
* **
3198196 TATTGATTCATTTACTGATTATCATAGTATA
1 TATTGATCCATTTACCCATTATCATAGTATA
3198227 TATTGATCCATTTACCCATTATCATAGTATA
1 TATTGATCCATTTACCCATTATCATAGTATA
3198258 T
1 T
3198259 TTTTTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (31 bp):
TATTGATCCATTTACCCATTATCATAGTATA
Found at i:3198320 original size:2 final size:2
Alignment explanation
Indices: 3198313--3198337 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3198303 ATTCCTGTTT
3198313 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3198338 TTTAATTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3200758 original size:7 final size:7
Alignment explanation
Indices: 3200746--3200772 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3200736 CATAGGATTC
3200746 ATAAAAA
1 ATAAAAA
3200753 ATAAAAA
1 ATAAAAA
3200760 ATAAAAA
1 ATAAAAA
3200767 ATAAAA
1 ATAAAA
3200773 TAAAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
ATAAAAA
Found at i:3204737 original size:18 final size:18
Alignment explanation
Indices: 3204698--3204738 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
3204688 TTGTGTGTGT
3204698 TATTTTAAGATTTTTTGC
1 TATTTTAAGATTTTTTGC
*
3204716 -ATTTTAATTATTTTTT-C
1 TATTTTAA-GATTTTTTGC
3204733 TATTTT
1 TATTTT
3204739 TTGTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (18 bp):
TATTTTAAGATTTTTTGC
Found at i:3213191 original size:14 final size:15
Alignment explanation
Indices: 3213163--3213191 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3213153 AACCCATTAT
3213163 CATTTAAATATTTTA
1 CATTTAAATATTTTA
3213178 CATTTAAA-ATTTTA
1 CATTTAAATATTTTA
3213192 AAAATTACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (15 bp):
CATTTAAATATTTTA
Found at i:3213266 original size:14 final size:14
Alignment explanation
Indices: 3213229--3213273 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
3213219 TATATCTCAC
*
3213229 AACAAATTAAATAT
1 AACAAATTAAATTT
*
3213243 ACCAAA-TAAATTT
1 AACAAATTAAATTT
*
3213256 AACAAATTAAATTC
1 AACAAATTAAATTT
3213270 AACA
1 AACA
3213274 CTCCTTAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (14 bp):
AACAAATTAAATTT
Found at i:3215639 original size:6 final size:6
Alignment explanation
Indices: 3215628--3215728 Score: 202
Period size: 6 Copynumber: 16.8 Consensus size: 6
3215618 TCTGAAATTG
3215628 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
3215676 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
3215724 ATATA
1 ATATA
3215729 TATGTATAAC
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 95 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:3217365 original size:31 final size:30
Alignment explanation
Indices: 3217315--3217382 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
3217305 TTATAAAATT
*
3217315 ATAAT-AAAATTATATTTTAATCTTTTAAAA
1 ATAATAAAAATTATAATTTAAT-TTTTAAAA
*
3217345 ATAATAAAAATTCTAATTTAATTTTTAAAA
1 ATAATAAAAATTATAATTTAATTTTTAAAA
*
3217375 ATTATAAA
1 ATAATAAA
3217383 TATTTTTACT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 20 0.59
31 14 0.41
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (30 bp):
ATAATAAAAATTATAATTTAATTTTTAAAA
Found at i:3223403 original size:9 final size:9
Alignment explanation
Indices: 3223389--3223438 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
3223379 TTTATACAAA
3223389 TAATTCGGT
1 TAATTCGGT
*
3223398 TAATTCGGG
1 TAATTCGGT
*
3223407 TAATTCAGT
1 TAATTCGGT
*
3223416 TAATTCGAT
1 TAATTCGGT
*
3223425 AAATTCGGT
1 TAATTCGGT
3223434 TAATT
1 TAATT
3223439 TTATACTTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (9 bp):
TAATTCGGT
Found at i:3243969 original size:28 final size:29
Alignment explanation
Indices: 3243935--3244010 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
3243925 TTCAGAAAAA
*
3243935 TTTTAAAATTTT-AATTTTATTTAT-ATAT
1 TTTTAAAATTTTAAAATTT-TTTATAATAT
3243963 TTTTAAAATTTTAAAATTTTTTATAATAT
1 TTTTAAAATTTTAAAATTTTTTATAATAT
* * *
3243992 TTTAAAAAATATAAAATTT
1 TTTTAAAATTTTAAAATTT
3244011 AGAATTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 17 0.40
29 25 0.60
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TTTTAAAATTTTAAAATTTTTTATAATAT
Found at i:3243995 original size:20 final size:18
Alignment explanation
Indices: 3243962--3243998 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
3243952 TATTTATATA
3243962 TTTTTAAAATTTTAAAAT
1 TTTTTAAAATTTTAAAAT
3243980 TTTTTATAATATTTTAAAA
1 TTTTTA-AA-ATTTTAAAA
3243999 AATATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTTAAAATTTTAAAAT
Found at i:3244028 original size:18 final size:18
Alignment explanation
Indices: 3244001--3244036 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3243991 TTTTAAAAAA
3244001 TATAAAATTTAGAATTTT
1 TATAAAATTTAGAATTTT
* *
3244019 TATAATATTTTGAATTTT
1 TATAAAATTTAGAATTTT
3244037 AAAAATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
TATAAAATTTAGAATTTT
Found at i:3244982 original size:30 final size:30
Alignment explanation
Indices: 3244948--3245072 Score: 196
Period size: 30 Copynumber: 4.2 Consensus size: 30
3244938 AATAAAAAAA
*
3244948 CACCAACTCCACTAGCCACATTTGCTCCAC
1 CACCAACTCCACTAGCCACACTTGCTCCAC
* *
3244978 CACCAACTCTACTAGCCACACTCGCTCCAC
1 CACCAACTCCACTAGCCACACTTGCTCCAC
*
3245008 CACCTACTCCACTAGCCACACTTGCTCCAC
1 CACCAACTCCACTAGCCACACTTGCTCCAC
* *
3245038 CACCTACTCCATTAGCCACACTTGCTCCAC
1 CACCAACTCCACTAGCCACACTTGCTCCAC
3245068 CACCA
1 CACCA
3245073 CTTGTACCTA
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 87 1.00
ACGTcount: A:0.26, C:0.49, G:0.06, T:0.19
Consensus pattern (30 bp):
CACCAACTCCACTAGCCACACTTGCTCCAC
Found at i:3245605 original size:46 final size:48
Alignment explanation
Indices: 3245540--3245668 Score: 140
Period size: 46 Copynumber: 2.8 Consensus size: 48
3245530 TTGTTATTAT
* *
3245540 TATATTTCTT-AATATTATATTATGTATATATTTTTTAATATATTAGG
1 TATATATCTTAAATACTATATTATGTATATATTTTTTAATATATTAGG
* * * * * * *
3245587 TATAT-TC-TAAATTCTATATTACGTATATATATTATACTATTTTATG
1 TATATATCTTAAATACTATATTATGTATATATTTTTTAATATATTAGG
*
3245633 TATATATCTTTAATACTATATTAT-TATATATTTTTT
1 TATATATCTTAAATACTATATTATGTATATATTTTTT
3245669 TCTACATGTT
Statistics
Matches: 66, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
45 1 0.02
46 36 0.55
47 17 0.26
48 12 0.18
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.57
Consensus pattern (48 bp):
TATATATCTTAAATACTATATTATGTATATATTTTTTAATATATTAGG
Found at i:3245638 original size:25 final size:24
Alignment explanation
Indices: 3245600--3245663 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
3245590 ATTCTAAATT
*
3245600 CTATATTACGTATATATA-TT-ATA
1 CTATATTA-TTATATATATTTAATA
* *
3245623 CTATTTTATGTATATATCTTTAATA
1 CTATATTAT-TATATATATTTAATA
3245648 CTATATTATTATATAT
1 CTATATTATTATATAT
3245664 TTTTTTCTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 14 0.41
24 9 0.26
25 11 0.32
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.53
Consensus pattern (24 bp):
CTATATTATTATATATATTTAATA
Found at i:3245727 original size:76 final size:81
Alignment explanation
Indices: 3245609--3245779 Score: 199
Period size: 76 Copynumber: 2.2 Consensus size: 81
3245599 TCTATATTAC
* * * * *
3245609 GTATATATATTATACTATTTTATGTATATATCTTTAATACTATATTAT-TATATATTTTTTTCTA
1 GTATATATTTTATACTATATTATGTATATATCTTTAACACTATATTATGTACATATTTTTTTATA
*
3245673 -C-ATGTTAT-CTTAT
66 TCTATGTTATACATAT
* * * *
3245686 GTATATATTTTA-ATTATATTATGTATGTATTTTTTACACTATATTATGTACATATTTTTTTATA
1 GTATATATTTTATACTATATTATGTATATATCTTTAACACTATATTATGTACATATTTTTTTATA
*
3245750 TCTATTTTATACATAT
66 TCTATGTTATACATAT
*
3245766 GTATATATTATATA
1 GTATATATTTTATA
3245780 TATCTTAACA
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
76 29 0.38
77 25 0.32
78 1 0.01
79 6 0.08
80 15 0.19
81 1 0.01
ACGTcount: A:0.32, C:0.06, G:0.05, T:0.57
Consensus pattern (81 bp):
GTATATATTTTATACTATATTATGTATATATCTTTAACACTATATTATGTACATATTTTTTTATA
TCTATGTTATACATAT
Found at i:3245733 original size:25 final size:25
Alignment explanation
Indices: 3245555--3245745 Score: 105
Period size: 25 Copynumber: 7.8 Consensus size: 25
3245545 TTCTTAATAT
3245555 TATATTATGTATATATTTTTTA-A-
1 TATATTATGTATATATTTTTTACAC
* * ** **
3245578 TATATTA-G-GTATATTCTAAATTC
1 TATATTATGTATATATTTTTTACAC
* * *
3245601 TATATTACGTATATA--TATTATAC
1 TATATTATGTATATATTTTTTACAC
* * * *
3245624 TATTTTATGTATATATCTTTAATAC
1 TATATTATGTATATATTTTTTACAC
*
3245649 TATATTAT-TATATATTTTTTTCTACATGT
1 TATATTATGTATATA--TTTTT-TACA--C
* *
3245678 TATCTTATGTATATA--TTTTA-AT
1 TATATTATGTATATATTTTTTACAC
*
3245700 TATATTATGTATGTATTTTTTACAC
1 TATATTATGTATATATTTTTTACAC
*
3245725 TATATTATGTACATATTTTTT
1 TATATTATGTATATATTTTTT
3245746 TATATCTATT
Statistics
Matches: 127, Mismatches: 26, Indels: 28
0.70 0.14 0.15
Matches are distributed among these distances:
21 8 0.06
22 15 0.12
23 30 0.24
24 13 0.10
25 39 0.31
26 7 0.06
27 2 0.02
29 7 0.06
30 6 0.05
ACGTcount: A:0.32, C:0.06, G:0.05, T:0.57
Consensus pattern (25 bp):
TATATTATGTATATATTTTTTACAC
Found at i:3245754 original size:27 final size:25
Alignment explanation
Indices: 3245541--3245759 Score: 68
Period size: 23 Copynumber: 8.8 Consensus size: 25
3245531 TGTTATTATT
* * *
3245541 ATATTTCTTAATATTATATTATGTAT
1 ATATTTTTTAAT-CTATATTATGTAC
*
3245567 ATATTTTTTAA--TATATTAGGT--
1 ATATTTTTTAATCTATATTATGTAC
* * * *
3245588 ATA-TTCTAAATTCTATATTACGTAT
1 ATATTTTTTAA-TCTATATTATGTAC
* * * *
3245613 ATATATTAT-A-CTATTTTATGTAT
1 ATATTTTTTAATCTATATTATGTAC
* *
3245636 ATA-TCTTTAATACTATATTAT-TAT
1 ATATTTTTTAAT-CTATATTATGTAC
* *
3245660 ATATTTTTTTCTACATGTTATCTTATGT--
1 ATA--TTTTT-TA-AT-CTATATTATGTAC
* *
3245688 ATATATTTTAAT-TATATTATGTAT
1 ATATTTTTTAATCTATATTATGTAC
*
3245712 GTATTTTTTACA-CTATATTATGTAC
1 ATATTTTTTA-ATCTATATTATGTAC
*
3245737 ATATTTTTTTATATCTATTTTAT
1 ATA-TTTTTTA-ATCTATATTAT
3245760 ACATATGTAT
Statistics
Matches: 145, Mismatches: 27, Indels: 41
0.68 0.13 0.19
Matches are distributed among these distances:
20 5 0.03
21 3 0.02
22 11 0.08
23 33 0.23
24 16 0.11
25 28 0.19
26 23 0.16
27 11 0.08
28 5 0.03
29 9 0.06
30 1 0.01
ACGTcount: A:0.32, C:0.06, G:0.05, T:0.57
Consensus pattern (25 bp):
ATATTTTTTAATCTATATTATGTAC
Found at i:3256902 original size:13 final size:14
Alignment explanation
Indices: 3256885--3256919 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
3256875 GGCATCTTAA
3256885 AAAAAGAGAAAAAG
1 AAAAAGAGAAAAAG
3256899 -AAAAGA-AAAAAG
1 AAAAAGAGAAAAAG
3256911 AAAAAGAGA
1 AAAAAGAGA
3256920 GAGGGGTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 6 0.32
13 12 0.63
14 1 0.05
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AAAAAGAGAAAAAG
Found at i:3257963 original size:13 final size:13
Alignment explanation
Indices: 3257929--3257964 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
3257919 GCCGATGTAT
*
3257929 TTTTAATTTCTGT
1 TTTTAATTTCTGC
3257942 TTTTCAATTTCTGC
1 TTTT-AATTTCTGC
3257956 TTTTAATTT
1 TTTTAATTT
3257965 ATGTTTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.67
Consensus pattern (13 bp):
TTTTAATTTCTGC
Found at i:3257972 original size:13 final size:13
Alignment explanation
Indices: 3257928--3257972 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
3257918 CGCCGATGTA
3257928 TTTTTAATTTCTG
1 TTTTTAATTTCTG
3257941 TTTTTCAATTTCTG
1 TTTTT-AATTTCTG
* *
3257955 CTTTTAATTTATG
1 TTTTTAATTTCTG
3257968 TTTTT
1 TTTTT
3257973 CAAAAATCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.16, C:0.09, G:0.07, T:0.69
Consensus pattern (13 bp):
TTTTTAATTTCTG
Found at i:3258079 original size:99 final size:99
Alignment explanation
Indices: 3257864--3258236 Score: 380
Period size: 99 Copynumber: 3.9 Consensus size: 99
3257854 TTTTTTCAAT
* * *
3257864 TTATGCTTTTCAAAAATCAACTCATATTGCGA-AGAGTGAGCTGAGCCTC-GGGCACGCCGATGT
1 TTATGCTTTTC-AAAATCAACTCATATTGCGAGAG-GTGAGTTGAGCCTCAGGGCACGCTGAGGT
** *
3257927 ATTTTTAATTTCTGTTTTTCAATTTCTGCTTTTAAT
64 ATTTTTAATTTCTGTTTTTCAATTTCTGCTTACAAA
*
3257963 TTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTA
1 TTATGCTTTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTA
*
3258028 TTTTTAATTTCTGTTTTTCAATTTTTGCCTTACAAA
65 TTTTTAATTTCTGTTTTTCAATTTCTG-CTTACAAA
* * * *
3258064 TTCTGCTTTTC-AAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTAT
1 TTATGCTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTAT
* * * * *
3258128 TTTCAATTT-TCGTTTTTTTAATTTATG-TTTCTAA
66 TTTTAATTTCT-G-TTTTTCAATTTCTGCTTACAAA
* * *
3258162 --A--------AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAA
1 TTATGCTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTAT
* * *
3258217 TTTCAATTTTTGTTTGTCAA
66 TTTTAATTTCTGTTTTTCAA
3258237 AACTCAACTC
Statistics
Matches: 242, Mismatches: 25, Indels: 25
0.83 0.09 0.09
Matches are distributed among these distances:
88 6 0.02
89 59 0.24
90 1 0.00
98 6 0.02
99 103 0.43
100 53 0.22
101 14 0.06
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.39
Consensus pattern (99 bp):
TTATGCTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTAT
TTTTAATTTCTGTTTTTCAATTTCTGCTTACAAA
Found at i:3258338 original size:148 final size:148
Alignment explanation
Indices: 3258142--3258982 Score: 1012
Period size: 148 Copynumber: 5.6 Consensus size: 148
3258132 AATTTTCGTT
* * * * *
3258142 TTTTTAATTTATGTTTCT-AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* *
3258206 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAACTCAACTCATATTGCAAGAGGTGAGTTGAGCC
66 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
*
3258271 TCAAGACACGTTGAGGTG
131 TCAAGACACGTTGAGGTA
* *
3258289 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGTGATAGGTGAGTTGAGCCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
3258354 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
66 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
3258419 TCAAGACACGTTGAGGTA
131 TCAAGACACGTTGAGGTA
* * * *
3258437 TTTTTAATTTCTGTCTTTAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* * * * * *
3258502 CGTTGAGGTATTTTTAATTTCTGTCTT-TAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGA
66 CGCTGAGGTAATTTCAATTTTTGT-TTGT--CAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
* * *
3258566 ACTTCAAGACACATTGAGGTA
128 GCCTCAAGACACGTTGAGGTA
* * *
3258587 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTTCGATAGGTGAGTTGAACCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
3258652 --CTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCC
66 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
3258715 TCAAGACACGTTGAGGTA
131 TCAAGACACGTTGAGGTA
* * * *
3258733 TTTTCAATTTTTGTCTTTTAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG--
1 TTTTCAATTTCTGT-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAC
* * *
3258796 ACGCTGAAGTGTTTTCCATTTCTGTTCTTCAATTTCTGTGTT-TCAAAAAAATCAGCTCATATTG
65 ACGCTG-AG-G---T--A------AT-TTCAATTTTTGT-TTGTC--AAAAATCAACTCATATTG
* * ** **
3258860 CGAGTGGTGAGTTGAGCCTTGACTCACACACTGAGGTA
113 CGAGAGGTGAGTTGAGCC-TCA-AGACACGTTGAGGTA
* * * *
3258898 TTTTCAAATTCTGTTTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* *
3258963 CGCTGAGATATTTTCAATTT
66 CGCTGAGGTAATTTCAATTT
3258983 CTTTTTTTTT
Statistics
Matches: 599, Mismatches: 66, Indels: 53
0.83 0.09 0.07
Matches are distributed among these distances:
145 1 0.00
146 62 0.10
147 64 0.11
148 223 0.37
149 3 0.01
150 108 0.18
152 9 0.02
153 2 0.00
154 1 0.00
159 1 0.00
160 1 0.00
161 14 0.02
162 2 0.00
163 33 0.06
164 44 0.07
165 25 0.04
166 6 0.01
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (148 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
TCAAGACACGTTGAGGTA
Found at i:3258350 original size:75 final size:75
Alignment explanation
Indices: 3258142--3258827 Score: 881
Period size: 75 Copynumber: 9.3 Consensus size: 75
3258132 AATTTTCGTT
* * * * *
3258142 TTTTTAATTTATGTTTCT-AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
3258206 CGCTGAGGTA
66 CGTTGAGGTA
* * * * *
3258216 ATTTCAATTTTTGTTTGTC--AAAACTCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
3258279 CGTTGAGGTG
66 CGTTGAGGTA
* *
3258289 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGTGATAGGTGAGTTGAGCCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
3258354 CGCTGAGGTA
66 CGTTGAGGTA
* * *
3258364 ATTTCAATTTTTGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
3258427 CGTTGAGGTA
66 CGTTGAGGTA
* * * *
3258437 TTTTTAATTTCTGTCTTTAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
3258502 CGTTGAGGTA
66 CGTTGAGGTA
* * * * * *
3258512 TTTTTAATTTCTGTCTTTAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACTTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
3258577 CATTGAGGTA
66 CGTTGAGGTA
* * *
3258587 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTTCGATAGGTGAGTTGAACCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
3258652 C--TGAGGTA
66 CGTTGAGGTA
* * * *
3258660 ATTTCAATTTTTGTTTGTC--AAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
3258723 CGTTGAGGTA
66 CGTTGAGGTA
* * * *
3258733 TTTTCAATTTTTGTCTTTTAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG--
1 TTTTCAATTTCTGT-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAC
* * *
3258796 ACGCTGAAGTG
65 ACGTTGAGGTA
* *
3258807 TTTTCCATTTCTGTTCTTCAA
1 TTTTCAATTTCTGTTTTTCAA
3258828 TTTCTGTGTT
Statistics
Matches: 540, Mismatches: 62, Indels: 21
0.87 0.10 0.03
Matches are distributed among these distances:
71 41 0.08
73 176 0.33
74 37 0.07
75 248 0.46
76 38 0.07
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (75 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
CGTTGAGGTA
Found at i:3258992 original size:77 final size:77
Alignment explanation
Indices: 3258823--3258990 Score: 205
Period size: 77 Copynumber: 2.2 Consensus size: 77
3258813 ATTTCTGTTC
* * * * * * *
3258823 TTCAATTTCTGTGTTTCAAAAAAATCAGCTCATATTGCGAGTGGTGAGTTGAGCCTTGACTCACA
1 TTCAAATTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTTCACGCACA
*
3258888 CACTGAGGTATT
66 CACTGAGATATT
* *
3258900 TTCAAATTCTGTTTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCC-TCA-GGACA
1 TTCAAATTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTTCACGCACA
*
3258963 CGCTGAGATATT
66 CACTGAGATATT
* *
3258975 TTCAATTTCTTTTTTT
1 TTCAAATTCTGTTTTT
3258991 TTTCAATTTA
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
75 27 0.35
76 2 0.03
77 49 0.63
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (77 bp):
TTCAAATTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTTCACGCACA
CACTGAGATATT
Found at i:3259040 original size:169 final size:164
Alignment explanation
Indices: 3258661--3259070 Score: 472
Period size: 169 Copynumber: 2.5 Consensus size: 164
3258651 ACTGAGGTAA
* * * **
3258661 TTTCAATTTTTGTTTGTC--AAAAATCAACTCATATTGCGAGATGTGAGTTGAGCC-TCAAGACA
1 TTTCAATTTATGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGATCACA
* * * * *
3258723 CGTTGAGGTATTTTCAATTTTTGTCTTTTAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGA
66 CGCTGAGGTATTTTCAAATTCTGTCTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTCA
* * *
3258788 ACCTCAAGACGCTGAAGTGTTTTCCATTTCTGTT
131 ACCTCAACACGCTGAAGTATTTTCAATTTCTGTT
* * * *
3258822 CTTCAATTTCTGTGTT-TCAAAAAAATCAGCTCATATTGCGAGTGGTGAGTTGAGCCTTGACTCA
1 TTTCAATTTATGT-TTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGA-TCA
* **
3258886 CACACTGAGGTATTTTCAAATTCTGT-TTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTT
64 CACGCTGAGGTATTTTCAAATTCTGTCTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
* *
3258950 CAGCCTCAGGACACGCTG-AGATATTTTCAATTTCTTTTTTT
129 CAACCTCA--ACACGCTGAAG-TATTTTCAATTTC---TGTT
* *
3258991 TTTCAATTTATGTTTGTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGATCAC
1 TTTCAATTTATGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGATCAC
*
3259056 ACGCCGAGGTATTTT
65 ACGCTGAGGTATTTT
3259071 TAATTGATTT
Statistics
Matches: 207, Mismatches: 29, Indels: 18
0.81 0.11 0.07
Matches are distributed among these distances:
161 13 0.06
162 2 0.01
163 33 0.16
164 43 0.21
165 25 0.12
166 18 0.09
168 2 0.01
169 69 0.33
170 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (164 bp):
TTTCAATTTATGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGATCACA
CGCTGAGGTATTTTCAAATTCTGTCTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTCA
ACCTCAACACGCTGAAGTATTTTCAATTTCTGTT
Found at i:3259129 original size:91 final size:88
Alignment explanation
Indices: 3258919--3259225 Score: 334
Period size: 91 Copynumber: 3.4 Consensus size: 88
3258909 TGTTTTTCCA
* * * *
3258919 AAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCAG-GACACGCTGAGATATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGTCACACGCCGAGGTATTTTCAA-TT
**
3258983 CTTTTTTTTTTCAATTTATGTTTGTC
65 AATTTTTTTTTCAA-TTATGTTTG-C
* *
3259009 AAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGATCACACGCCGAGGTATTTTTAA
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG-TCACACGCCGAGGTATTTTCAA
*
3259074 TTGATTTTTTTTTCAATTCATGCTTTGC
63 TTAATTTTTTTTTCAATT-ATG-TTTGC
* * **
3259102 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATACCGAGGTATTTTCAA--
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGTCACACGCCGAGGTATTTTCAATT
* * * *
3259165 AATTTGTTTTACAAATTTTGTTT-T
65 AATTTTTTTTTC-AATTATGTTTGC
*
3259189 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
3259226 TGGCTCACGT
Statistics
Matches: 188, Mismatches: 21, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
87 35 0.19
88 3 0.02
89 11 0.06
90 4 0.02
91 55 0.29
92 41 0.22
93 18 0.10
94 21 0.11
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (88 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGTCACACGCCGAGGTATTTTCAATTA
ATTTTTTTTTCAATTATGTTTGC
Found at i:3259247 original size:87 final size:87
Alignment explanation
Indices: 3259011--3259307 Score: 235
Period size: 87 Copynumber: 3.4 Consensus size: 87
3259001 TGTTTGTCAA
* * * * ** * *
3259011 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGATCACACGCCGAGGTATTTTTAATT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAA--
* * * *
3259076 GATTTTTTTTTCAAT-TC-ATGCTTTGC
64 -ATTCTGTTTTAAATGTCTA-G-TTT-T
* * * *
3259102 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATACCGAGGTATTTTCAAAA
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTC-AAA
*
3259167 TT-TGTTTTACAAAT-T-TTGTTTT
65 TTCTGTTTT--AAATGTCTAGTTTT
* * * * *
3259189 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAAAT
*
3259254 TCTGTTTTTAATGTCTAGTTTT
66 TCTGTTTTAAATGTCTAGTTTT
* * *
3259276 AAAGAGTCAATTCATATTGCGAGAAATGAGTT
1 AAA-AATCAACTCATATTGCGAGAAGTGAGTT
3259308 AAGCTCAGGA
Statistics
Matches: 173, Mismatches: 25, Indels: 19
0.80 0.12 0.09
Matches are distributed among these distances:
85 3 0.02
86 5 0.03
87 68 0.39
88 33 0.19
89 4 0.02
90 4 0.02
91 54 0.31
92 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.36
Consensus pattern (87 bp):
AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAAAT
TCTGTTTTAAATGTCTAGTTTT
Found at i:3259903 original size:18 final size:18
Alignment explanation
Indices: 3259880--3259933 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
3259870 CCACCACCAA
3259880 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
*
3259898 CTCCACCA-CCA-A----
1 CTCCACTAGCCACACTTG
3259910 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
3259928 CTCCAC
1 CTCCAC
3259934 CACCTACTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 7 0.25
13 3 0.11
14 1 0.04
16 1 0.04
17 3 0.11
18 13 0.46
ACGTcount: A:0.24, C:0.50, G:0.07, T:0.19
Consensus pattern (18 bp):
CTCCACTAGCCACACTTG
Found at i:3259906 original size:30 final size:30
Alignment explanation
Indices: 3259870--3259998 Score: 204
Period size: 30 Copynumber: 4.3 Consensus size: 30
3259860 CTAGCCTTTG
3259870 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
3259900 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* * *
3259930 CCACCACCTACTCTACTAGCCACATTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* * *
3259960 CTACCACCTACTCCATTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
3259990 CCACCACCA
1 CCACCACCA
3259999 CTTGTACCTA
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 90 1.00
ACGTcount: A:0.26, C:0.48, G:0.06, T:0.20
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:3260573 original size:23 final size:25
Alignment explanation
Indices: 3260480--3260611 Score: 100
Period size: 23 Copynumber: 5.6 Consensus size: 25
3260470 TTTTTTTGGT
* *
3260480 TATTAT-TATATTTC-TTAATATTA
1 TATTATGTATATATCATTAATACTA
* *
3260503 TATTATGTATATATTC-TT-TTAATA
1 TATTATGTATATA-TCATTAATACTA
* * *
3260527 TATTAGGTATAT-TC-TAAATTCTA
1 TATTATGTATATATCATTAATACTA
*
3260550 TATTACGTATATAT-ATT-ATACTA
1 TATTATGTATATATCATTAATACTA
* *
3260573 TTTTATGTATATATCTTTAATACTA
1 TATTATGTATATATCATTAATACTA
*
3260598 TATTATTTATATAT
1 TATTATGTATATAT
3260612 TTTTTCTACA
Statistics
Matches: 86, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
22 3 0.03
23 37 0.43
24 24 0.28
25 22 0.26
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (25 bp):
TATTATGTATATATCATTAATACTA
Found at i:3260585 original size:25 final size:25
Alignment explanation
Indices: 3260494--3260704 Score: 100
Period size: 25 Copynumber: 8.6 Consensus size: 25
3260484 ATTATATTTC
*
3260494 TTAATATTATATTATGTATATAT-T
1 TTAATACTATATTATGTATATATAT
* * * *
3260518 CTT-TTAATATATTAGGTATAT-T-C
1 -TTAATACTATATTATGTATATATAT
* * *
3260541 TAAATTCTATATTACGTATATATA-
1 TTAATACTATATTATGTATATATAT
* *
3260565 TT-ATACTATTTTATGTATATATCT
1 TTAATACTATATTATGTATATATAT
* *
3260589 TTAATACTATATTATTTATATATTTTT
1 TTAATACTATATTATGTATATA--TAT
** *
3260616 TCTACATGTTATCTTATGTATATAT-T
1 T-TA-ATACTATATTATGTATATATAT
* *
3260642 TTAAT--TATATTATGTATGTATTT
1 TTAATACTATATTATGTATATATAT
* * * *
3260665 TTTACACTATATTATGTACATATTT
1 TTAATACTATATTATGTATATATAT
*
3260690 TTTATATCTAT-TTAT
1 TTAATA-CTATATTAT
3260705 ACATATGTAT
Statistics
Matches: 145, Mismatches: 28, Indels: 26
0.73 0.14 0.13
Matches are distributed among these distances:
22 15 0.10
23 36 0.25
24 21 0.14
25 46 0.32
26 6 0.04
27 4 0.03
28 2 0.01
29 15 0.10
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (25 bp):
TTAATACTATATTATGTATATATAT
Found at i:3260674 original size:76 final size:79
Alignment explanation
Indices: 3260556--3260724 Score: 193
Period size: 76 Copynumber: 2.2 Consensus size: 79
3260546 TCTATATTAC
* * * * * *
3260556 GTATATATATTATACTATTTTATGTATATATCTTTAATACTATATTATTTATATATTTTTTCTA-
1 GTATATATTTTATACTATATTATGTATATATCTTTAACACTATATTATGTACATATTTTTTATAT
*
3260620 C-ATGTTAT-CTTAT
66 CTAT-TTATACATAT
* * * *
3260633 GTATATATTTTA-ATTATATTATGTATGTATTTTTTACACTATATTATGTACATATTTTTTATAT
1 GTATATATTTTATACTATATTATGTATATATCTTTAACACTATATTATGTACATATTTTTTATAT
3260697 CTATTTATACATAT
66 CTATTTATACATAT
*
3260711 GTATATATTATATA
1 GTATATATTTTATA
3260725 TATCTTAACA
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
76 42 0.55
77 16 0.21
78 17 0.22
79 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (79 bp):
GTATATATTTTATACTATATTATGTATATATCTTTAACACTATATTATGTACATATTTTTTATAT
CTATTTATACATAT
Found at i:3260779 original size:25 final size:24
Alignment explanation
Indices: 3260751--3260806 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
3260741 GTTATATTTT
*
3260751 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
3260776 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
3260799 CACTATTA
1 CACTATTA
3260807 CTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:3262677 original size:4 final size:4
Alignment explanation
Indices: 3262668--3262702 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
3262658 GGTCCATAAC
3262668 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
3262703 ATGAAGTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:3266125 original size:21 final size:22
Alignment explanation
Indices: 3266096--3266142 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
3266086 CAGAAGGAGT
*
3266096 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
3266118 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
3266139 GAGT
1 GAGT
3266143 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:3267391 original size:10 final size:10
Alignment explanation
Indices: 3267360--3267393 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3267350 CTTCAAAGAC
3267360 ATATACATAT
1 ATATACATAT
*
3267370 ACATACATAT
1 ATATACATAT
*
3267380 ATATATATAT
1 ATATACATAT
3267390 ATAT
1 ATAT
3267394 GCAAAATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATACATAT
Found at i:3267695 original size:193 final size:193
Alignment explanation
Indices: 3267368--3267869 Score: 833
Period size: 193 Copynumber: 2.6 Consensus size: 193
3267358 ACATATACAT
* * *
3267368 ATACATACATATATATATATATATATGCAAAATGATATTTAAGAAAAACCCAAAGAGGTGATTAA
1 ATACATACATATATATATATATA-A-GCAAAATGATATTTAAGGAAAACCCAAAGAGCTGGTTAA
* *
3267433 TTTAAAACTTAAGACAGATCACAAATATCACTTAATAATTAAGATGGCAGAAAGGAATATCAAAG
64 TGTAAACCTTAAGACAGATCACAAATATCACTTAATAATTAAGATGGCAGAAAGGAATATCAAAG
*
3267498 TAAAAAGGGTTATCAATGGCTGTCATGCAATGTGAGGCACATATTAAGGCCATACCTGCAAATAC
129 TAAAAAGGGTTATCAATGGCTGTCATGCAATGTGAGACACATATTAAGGCCATACCTGCAAATAC
* * **
3267563 ATACACACATATATATATATCTAAGCAAAATGATATTTAAGGAAAACCCAAAGCTCTGGTTAATG
1 ATACATACATATATATATATATAAGCAAAATGATATTTAAGGAAAACCCAAAGAGCTGGTTAATG
*
3267628 TAAACCTTAAGACAGATCACAAATATCACTTAATAATTAAGATTGCAGAAAGGAATATCAAAGTA
66 TAAACCTTAAGACAGATCACAAATATCACTTAATAATTAAGATGGCAGAAAGGAATATCAAAGTA
3267693 AAAAGGGTTATCAATGGCTGTCATGCAATGTGAGACACATATTAAGGCCATACCTGCAAATAC
131 AAAAGGGTTATCAATGGCTGTCATGCAATGTGAGACACATATTAAGGCCATACCTGCAAATAC
* *
3267756 ATACATATATATATATGCAAATATATATGCAAAATGATATTTAAGGAAAACCCAAAGAGCTGGTT
1 ATACATACATATATAT----ATATATAAGCAAAATGATATTTAAGGAAAACCCAAAGAGCTGGTT
3267821 AATGTAAACCTTAAGACAGATCACAAATATCACTTAATAATTAAGATGG
62 AATGTAAACCTTAAGACAGATCACAAATATCACTTAATAATTAAGATGG
3267870 AAGCAAGGTA
Statistics
Matches: 285, Mismatches: 18, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
193 174 0.61
194 1 0.00
195 21 0.07
197 89 0.31
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (193 bp):
ATACATACATATATATATATATAAGCAAAATGATATTTAAGGAAAACCCAAAGAGCTGGTTAATG
TAAACCTTAAGACAGATCACAAATATCACTTAATAATTAAGATGGCAGAAAGGAATATCAAAGTA
AAAAGGGTTATCAATGGCTGTCATGCAATGTGAGACACATATTAAGGCCATACCTGCAAATAC
Found at i:3267795 original size:14 final size:12
Alignment explanation
Indices: 3267764--3267788 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3267754 ACATACATAT
3267764 ATATATATGCAA
1 ATATATATGCAA
3267776 ATATATATGCAA
1 ATATATATGCAA
3267788 A
1 A
3267789 ATGATATTTA
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:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (12 bp):
ATATATATGCAA
Found at i:3281723 original size:16 final size:18
Alignment explanation
Indices: 3281696--3281728 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3281686 TGAAAATAAG
3281696 TTTAATTAAAAT-ATTAT
1 TTTAATTAAAATGATTAT
3281713 TTTAA-TAAAATGATTA
1 TTTAATTAAAATGATTA
3281729 AATTCCATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (18 bp):
TTTAATTAAAATGATTAT
Found at i:3281943 original size:21 final size:21
Alignment explanation
Indices: 3281899--3281941 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3281889 TAATAACTAA
3281899 TGATAAATTAATTAATTAATT
1 TGATAAATTAATTAATTAATT
* *
3281920 TGATAACTTATATTTATTAATT
1 TGATAAATTA-ATTAATTAATT
3281942 GAACTTGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (21 bp):
TGATAAATTAATTAATTAATT
Found at i:3283307 original size:23 final size:23
Alignment explanation
Indices: 3283281--3283337 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 23
3283271 GTATAGTGTG
*
3283281 TAGTGTAGGCAGAGAGAGCTTTT
1 TAGTTTAGGCAGAGAGAGCTTTT
3283304 TAGTTTAGGGCAGAGAGAGCTTTT
1 TAGTTTA-GGCAGAGAGAGCTTTT
3283328 TAGTTTAGGC
1 TAGTTTAGGC
3283338 TTAGGGTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 9 0.28
24 23 0.72
ACGTcount: A:0.25, C:0.09, G:0.33, T:0.33
Consensus pattern (23 bp):
TAGTTTAGGCAGAGAGAGCTTTT
Found at i:3283319 original size:24 final size:24
Alignment explanation
Indices: 3283288--3283336 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
3283278 GTGTAGTGTA
3283288 GGCAGAGAGAGCTTTTTAGTTTAG
1 GGCAGAGAGAGCTTTTTAGTTTAG
3283312 GGCAGAGAGAGCTTTTTAGTTTAG
1 GGCAGAGAGAGCTTTTTAGTTTAG
3283336 G
1 G
3283337 CTTAGGGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.35, T:0.33
Consensus pattern (24 bp):
GGCAGAGAGAGCTTTTTAGTTTAG
Found at i:3286082 original size:6 final size:6
Alignment explanation
Indices: 3286071--3286095 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3286061 AATCAAAATT
3286071 ATTATA ATTATA ATTATA ATTATA A
1 ATTATA ATTATA ATTATA ATTATA A
3286096 AAATAAAACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTATA
Found at i:3292993 original size:9 final size:9
Alignment explanation
Indices: 3292981--3293030 Score: 75
Period size: 9 Copynumber: 5.6 Consensus size: 9
3292971 AATAAATTTT
3292981 ATAATTCAA
1 ATAATTCAA
3292990 ATAATTCAA
1 ATAATTCAA
3292999 ATAACTT-AA
1 ATAA-TTCAA
*
3293008 ATACTTCAA
1 ATAATTCAA
3293017 ATAATTCAA
1 ATAATTCAA
3293026 ATAAT
1 ATAAT
3293031 AGATTGATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
8 2 0.05
9 33 0.89
10 2 0.05
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (9 bp):
ATAATTCAA
Found at i:3293000 original size:27 final size:27
Alignment explanation
Indices: 3292970--3293029 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
3292960 CAATTTTTTA
**
3292970 AAATAAATTTTATAATTCAAATAATTC
1 AAATAAATTAAATAATTCAAATAATTC
* *
3292997 AAATAACTTAAATACTTCAAATAATTC
1 AAATAAATTAAATAATTCAAATAATTC
3293024 AAATAA
1 AAATAA
3293030 TAGATTGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (27 bp):
AAATAAATTAAATAATTCAAATAATTC
Found at i:3298472 original size:26 final size:26
Alignment explanation
Indices: 3298442--3298494 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
3298432 TGGCCAATGT
*
3298442 ACATGGACTGCATAGATAACTTATGC
1 ACATGGACTGCATACATAACTTATGC
3298468 ACATGGACTGCATACATAACTTATGC
1 ACATGGACTGCATACATAACTTATGC
3298494 A
1 A
3298495 TAGTGTAGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (26 bp):
ACATGGACTGCATACATAACTTATGC
Found at i:3302364 original size:22 final size:22
Alignment explanation
Indices: 3302337--3302379 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3302327 CCCTCGATTG
3302337 AATTAATT-AACTAAATTCAGTC
1 AATTAATTGAA-TAAATTCAGTC
*
3302359 AATTAATTGAATTAATTCAGT
1 AATTAATTGAATAAATTCAGT
3302380 TTTACCTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (22 bp):
AATTAATTGAATAAATTCAGTC
Found at i:3302715 original size:15 final size:15
Alignment explanation
Indices: 3302695--3302735 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
3302685 ATATTTGAGT
3302695 AAAAATATAAATTTA
1 AAAAATATAAATTTA
*
3302710 AAAAATAT-ATTTTA
1 AAAAATATAAATTTA
3302724 AAAAATA-AAATT
1 AAAAATATAAATT
3302736 CTTTTGAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAATATAAATTTA
Found at i:3307967 original size:12 final size:12
Alignment explanation
Indices: 3307947--3307979 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3307937 ATACATATTA
3307947 TATGTGTATGCG
1 TATGTGTATGCG
*
3307959 TATGCGTATGCG
1 TATGTGTATGCG
3307971 TATGTGTAT
1 TATGTGTAT
3307980 ATATATGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.18, C:0.09, G:0.30, T:0.42
Consensus pattern (12 bp):
TATGTGTATGCG
Found at i:3309094 original size:13 final size:12
Alignment explanation
Indices: 3309076--3309106 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
3309066 AAAGACTGTC
3309076 ATTTTTTTTAAAT
1 ATTTTTTTT-AAT
3309089 ATTTTTTTTAAT
1 ATTTTTTTTAAT
3309101 ATTTTT
1 ATTTTT
3309107 AATATTATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
ATTTTTTTTAAT
Found at i:3309543 original size:4 final size:4
Alignment explanation
Indices: 3309536--3309562 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3309526 TTCATTATAC
3309536 ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATG
3309563 AGTCATGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:3313396 original size:25 final size:28
Alignment explanation
Indices: 3313326--3313399 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 28
3313316 TCTTTTTAAT
* *
3313326 TAATAACTCTTTTATTTATATAAATAAAA
1 TAATAAATATTTTA-TTATATAAATAAAA
* *
3313355 TAATAAATATGTAATTATAT-AAT-AAA
1 TAATAAATATTTTATTATATAAATAAAA
*
3313381 -AATATATATTTTATTATAT
1 TAATAAATATTTTATTATAT
3313400 CATTATGTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 16 0.42
26 3 0.08
27 3 0.08
28 6 0.16
29 10 0.26
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (28 bp):
TAATAAATATTTTATTATATAAATAAAA
Found at i:3313505 original size:21 final size:18
Alignment explanation
Indices: 3313481--3313519 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 18
3313471 TATATGTTTT
3313481 TATATTTATCATTATTTTAAA
1 TATATTT-T-ATT-TTTTAAA
3313502 TATATTTTATTTTTTAAA
1 TATATTTTATTTTTTAAA
3313520 ACATCAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 3 0.17
20 1 0.06
21 7 0.39
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATTTTATTTTTTAAA
Found at i:3313921 original size:19 final size:19
Alignment explanation
Indices: 3313884--3313929 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
3313874 CATAATGATA
* *
3313884 TATATAA-TATATTTTTAT
1 TATATAATTACATATTTAT
3313902 TATATAATTACATATTTAT
1 TATATAATTACATATTTAT
*
3313921 TATTTAATT
1 TATATAATT
3313930 TTTATAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TATATAATTACATATTTAT
Found at i:3313923 original size:90 final size:90
Alignment explanation
Indices: 3313771--3313959 Score: 197
Period size: 90 Copynumber: 2.0 Consensus size: 90
3313761 TTCAAAAAAT
3313771 AAAATATATTTAACATAATGATAAATATCAAATATATATTCCAATTATATAATTATTAATTATAT
1 AAAATATATTTAACATAATGATAAATAT-AAATATATATTCCAATTATATAATTATTAATTATAT
* *
3313836 AA-ATAAATAAAGGAGTTATTAATTA
65 AATATAAATAAAAGAATTATTAATTA
* * ** *
3313861 AAAATATTTTTAACATAATGATATATAT-AATATAT-TT-TTATTATATAATTACATATTTATTA
1 AAAATATATTTAACATAATGATAAATATAAATATATATTCCAATTATATAA-T---TATTAATTA
*
3313923 TTTAATTTTTATAAATAAAAGAATTATTAATTA
62 TATAA----TATAAATAAAAGAATTATTAATTA
3313956 AAAA
1 AAAA
3313960 GATGAATTAA
Statistics
Matches: 82, Mismatches: 8, Indels: 13
0.80 0.08 0.13
Matches are distributed among these distances:
86 9 0.11
87 3 0.04
88 7 0.09
90 38 0.46
95 25 0.30
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (90 bp):
AAAATATATTTAACATAATGATAAATATAAATATATATTCCAATTATATAATTATTAATTATATA
ATATAAATAAAAGAATTATTAATTA
Found at i:3314048 original size:14 final size:14
Alignment explanation
Indices: 3314031--3314057 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3314021 TAAAAAATAT
3314031 AAAAAGCATTATTC
1 AAAAAGCATTATTC
3314045 AAAAAGCATTATT
1 AAAAAGCATTATT
3314058 AATTAGTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (14 bp):
AAAAAGCATTATTC
Found at i:3326347 original size:76 final size:74
Alignment explanation
Indices: 3326161--3326352 Score: 215
Period size: 76 Copynumber: 2.5 Consensus size: 74
3326151 CATATCAAAG
* * * * *
3326161 CATTAGAGTTATGATTTCACTTTAATTTTATTTTATTTTGGACCCTTTTATTTAAATCTTTTGGT
1 CATTAGAATTATGATTTCACTTGAATTTTATTTTTTTTTGGACCCTTTTATTTAAATCCTTTAGT
3326226 GTTCAATAT
66 GTTCAATAT
* ** * *
3326235 CATTAGAATTGTGGCTTCATTTCGACTTTATATTTTTTTTTGGACCCTTTTATTTAAATCCTTTA
1 CATTAGAATTATGATTTCACTT-GAATTT-TATTTTTTTTTGGACCCTTTTATTTAAATCCTTTA
*
3326300 GTGTT-AGTAGT
64 GTGTTCAATA-T
*
3326311 CATTTCAGAATTATGATTTCACTTGAATTTTGTTTTTCTTTT
1 CA-TT-AGAATTATGATTTCACTTGAATTTTATTTTT-TTTT
3326353 TTTCTTTTTT
Statistics
Matches: 95, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
74 17 0.18
75 7 0.07
76 46 0.48
77 11 0.12
78 14 0.15
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.54
Consensus pattern (74 bp):
CATTAGAATTATGATTTCACTTGAATTTTATTTTTTTTTGGACCCTTTTATTTAAATCCTTTAGT
GTTCAATAT
Found at i:3328896 original size:16 final size:16
Alignment explanation
Indices: 3328875--3328906 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3328865 GCAAACCCTT
*
3328875 TAAATACAAAAAAATC
1 TAAATAAAAAAAAATC
3328891 TAAATAAAAAAAAATC
1 TAAATAAAAAAAAATC
3328907 AACATACACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAATAAAAAAAAATC
Found at i:3354271 original size:69 final size:71
Alignment explanation
Indices: 3354095--3354271 Score: 214
Period size: 72 Copynumber: 2.5 Consensus size: 71
3354085 CTTTCCAAGG
* ** * *
3354095 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAAGTTTA
*
3354160 TTTTTT
66 TGTTTT
* ** *
3354166 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTT-AGTTT
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAAGTTT
3354230 ATGTTTT
65 ATGTTTT
** *
3354237 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
3354272 TTTAATTTCT
Statistics
Matches: 91, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
69 31 0.34
71 9 0.10
72 51 0.56
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAAGTTTA
TGTTTT
Found at i:3354397 original size:76 final size:74
Alignment explanation
Indices: 3354289--3354626 Score: 430
Period size: 76 Copynumber: 4.5 Consensus size: 74
3354279 TCTGTTTTTC
*
3354289 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
3354354 GTTGTTAAAAA
66 GTT-TT-AAAA
**
3354365 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
*
3354430 GTTTT--CA
66 GTTTTAAAA
* * * ** * * *
3354437 AAATTCAACTTATATTGTGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
*
3354502 GTTTCAAAA
66 GTTTTAAAA
* * * *
3354511 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTTAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTAATTTCAATT
*
3354575 TCTGTTTTTAAAG
63 TCTG-TTTTAAAA
*
3354588 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
3354627 ATTACACACT
Statistics
Matches: 231, Mismatches: 24, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
72 64 0.28
73 1 0.00
74 34 0.15
75 2 0.01
76 88 0.38
77 41 0.18
78 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33
Consensus pattern (74 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
GTTTTAAAA
Found at i:3354561 original size:148 final size:147
Alignment explanation
Indices: 3354275--3354621 Score: 423
Period size: 148 Copynumber: 2.3 Consensus size: 147
3354265 TAAGCCTTTT
** *
3354275 AATTTCTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
1 AATTTCTG-TTTTCAAAATCAACTCATATTGCTAGAAATGAGTTGAGCCTCAAGACACGCTGAGG
3354340 TAATTTCAATTTCTGTTGTTAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG
65 TAATTTCAATTTCTGTTGTTAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG
3354405 ACACGCTGAGGTAATTTC
130 ACACGCTGAGGTAATTTC
* *
3354423 AATTTCTGTTTTCAAAATTCAACTTATATTG-TGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
1 AATTTCTGTTTTCAAAA-TCAACTCATATTGCT-AGAAATGAGTTGAGCCTCAAGACACGCTGAG
* * * **
3354487 GTATTTTCAATTTCTG-T-TTCAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-G
64 GTAATTTCAATTTCTGTTGTTAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAG
* * *
3354549 GTTCACATGCTGAGGTATTTTT
129 G---ACACGCTGAGGTAATTTC
* * **
3354571 AATTTCTGTTTTTAAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 AATTTCTG-TTTT---CAAAATCAACTCATATTGCTAGAAATGAGTTGAGC
3354622 TTCAGATTAC
Statistics
Matches: 171, Mismatches: 18, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
145 2 0.01
146 40 0.23
147 11 0.06
148 85 0.50
149 4 0.02
151 25 0.15
152 4 0.02
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (147 bp):
AATTTCTGTTTTCAAAATCAACTCATATTGCTAGAAATGAGTTGAGCCTCAAGACACGCTGAGGT
AATTTCAATTTCTGTTGTTAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGA
CACGCTGAGGTAATTTC
Found at i:3355142 original size:72 final size:72
Alignment explanation
Indices: 3355025--3355277 Score: 391
Period size: 73 Copynumber: 3.5 Consensus size: 72
3355015 TTTGAAAGAA
* *
3355025 TCAACTCATATTGCGAGAAATGAGTTGAGCGTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
3355090 TCAAAAT
66 TCAAAAT
*
3355097 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTG-TT
3355162 TTCAAAAT
65 TTCAAAAT
* * * *
3355170 TCAACTCATATTGCAAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTG
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
*
3355235 TCAAAAAAA
66 TC--AAAAT
3355244 TCAACTCATATTGCGA-AAAGTGAGTTGAGCCTCA
1 TCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCA
3355278 GTTCACATGT
Statistics
Matches: 167, Mismatches: 10, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
72 63 0.38
73 71 0.43
74 33 0.20
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (72 bp):
TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
TCAAAAT
Found at i:3358875 original size:22 final size:22
Alignment explanation
Indices: 3358847--3358899 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
3358837 CAGTCAGACA
3358847 TCGGTGTCGGGACACCTAAGCT
1 TCGGTGTCGGGACACCTAAGCT
*
3358869 TCGGTGTCGTGACACCTAAGCT
1 TCGGTGTCGGGACACCTAAGCT
*
3358891 TTGGTGTCG
1 TCGGTGTCG
3358900 CAACACTCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.15, C:0.25, G:0.32, T:0.28
Consensus pattern (22 bp):
TCGGTGTCGGGACACCTAAGCT
Done.