Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 142 of 189
Found at i:43184655 original size:25 final size:26
Alignment explanation
Indices: 43184622--43184672 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
43184612 ATACATCGCA
*
43184622 TAAATTAAAAATATT-TTTAAATAAT
1 TAAAATAAAAATATTATTTAAATAAT
*
43184647 TAAAATAAAAATATTATTTTAATAAT
1 TAAAATAAAAATATTATTTAAATAAT
43184673 ATTACATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
TAAAATAAAAATATTATTTAAATAAT
Found at i:43185161 original size:39 final size:40
Alignment explanation
Indices: 43185118--43185222 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
43185108 TTCCATTATG
43185118 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
43185157 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
43185202 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
43185223 ACACCTTTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:43185216 original size:45 final size:44
Alignment explanation
Indices: 43185116--43185225 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
43185106 TTTTCCATTA
43185116 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
43185155 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
43185200 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
43185226 CCTTTAATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:43185225 original size:16 final size:16
Alignment explanation
Indices: 43185206--43185257 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
43185196 GATTTGCTAT
* *
43185206 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
*
43185222 TACACCTTTAATCCAA
1 TACACCTCTAATCCAA
43185238 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
43185254 TACA
1 TACA
43185258 GCGAACCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:43189939 original size:50 final size:50
Alignment explanation
Indices: 43189697--43189939 Score: 324
Period size: 50 Copynumber: 4.9 Consensus size: 50
43189687 TTTTTTGTAT
* * * ** * *
43189697 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTTATCTCGG
* * ** * * *
43189747 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTTATCTCGG
* *
43189797 TGCCAACGCCATCTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTTATCTCGG
*
43189847 TGCCAACGCCATGTCCCAGACATGGTCTTTCATGAGACCTCTTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTTATCTCGG
*
43189897 TGCCAACGCCATGCCCCAGACATGGTCTTACATGAGACCTCTT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTT
43189940 TACCCAAATG
Statistics
Matches: 171, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 171 1.00
ACGTcount: A:0.21, C:0.32, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTTATCTCGG
Found at i:43195383 original size:23 final size:23
Alignment explanation
Indices: 43195353--43195396 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
43195343 ATTAGTACAG
*
43195353 TTTATTAGTTAAAGTCTCCCCCA
1 TTTATTAGTTAAAGGCTCCCCCA
43195376 TTTATTAGTTAAAGGCTCCCC
1 TTTATTAGTTAAAGGCTCCCC
43195397 TGTTTCACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (23 bp):
TTTATTAGTTAAAGGCTCCCCCA
Found at i:43197776 original size:50 final size:50
Alignment explanation
Indices: 43197711--43198147 Score: 486
Period size: 50 Copynumber: 8.8 Consensus size: 50
43197701 ATTATAAGAT
*
43197711 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAG
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAG
* * * *
43197761 GTCCCACGTAAGACCATGTCTTGAACATGGCGTTGGCACCGAGATAAGAG
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAG
* *
43197811 GTCCCATATAAGACCATGTCTGGGACATGGTC-TTGGCACCAAGATGAGAG
1 GTCCCATGTAAGACCATGTCTGGGACATGG-CGTTGGCACCGAGATGAGAG
*
43197861 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAAAG
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAG
* * ** * *
43197911 GTCCTATGTAAGACCATGTTTGATACATGGCGTTGACACCGAGATGAAAG
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAG
* * *
43197961 GACCCATGTAAGACTATGTCTGGGACATGGCGTTGGCACCGAGATTAGAG
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAG
* * * * * * *
43198011 GTCCTC-CGTAAGACCATGTTTGGGACATGACATGGGCACCGATATGAGAA
1 GTCC-CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAG
* ** * * * * * *
43198061 CTCCCATGTAAGACCATACCTGGGATATGGCATTGGCA--GTACAGGAAAC
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCG-AGATGAGAG
* * * *
43198110 ATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
43198148 TGTTATATTC
Statistics
Matches: 325, Mismatches: 57, Indels: 11
0.83 0.15 0.03
Matches are distributed among these distances:
48 1 0.00
49 38 0.12
50 284 0.87
51 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAG
Found at i:43203956 original size:20 final size:20
Alignment explanation
Indices: 43203930--43203992 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
43203920 CTTGTACAAG
43203930 ATTTGCACTTTGGTGCCCCT
1 ATTTGCACTTTGGTGCCCCT
* **
43203950 GTTTGCACATTT-GTGAACCT
1 ATTTGCAC-TTTGGTGCCCCT
*
43203970 ATCTGCACTTTGGTGCCCCT
1 ATTTGCACTTTGGTGCCCCT
43203990 ATT
1 ATT
43203993 ATTCATCTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 3 0.09
20 27 0.82
21 3 0.09
ACGTcount: A:0.14, C:0.27, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTTGCACTTTGGTGCCCCT
Found at i:43226250 original size:56 final size:50
Alignment explanation
Indices: 43226190--43226375 Score: 176
Period size: 50 Copynumber: 3.6 Consensus size: 50
43226180 AGATCCCATG
**
43226190 TAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGGTCCCACA
1 TAAGACCATGTCTGGGACATGGCATTGGC---ACCGA-G--ATGAGAGGTCCCACA
* * * *
43226246 TAAGACCATTTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCACA
* * * ** *
43226296 TAAGACCATGTCTGGGACATGCCA-TGGACACCGATATTAGAACTCCCATA
1 TAAGACCATGTCTGGGACATGGCATTGG-CACCGAGATGAGAGGTCCCACA
* *
43226346 TAAGACCATATCTGGGATATGGCATTGGCA
1 TAAGACCATGTCTGGGACATGGCATTGGCA
43226376 GTACAGGAAA
Statistics
Matches: 109, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
49 3 0.03
50 72 0.66
51 3 0.03
52 1 0.01
53 3 0.03
56 27 0.25
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCACA
Found at i:43226652 original size:20 final size:20
Alignment explanation
Indices: 43226627--43226675 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
43226617 TGAGTTATTA
43226627 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
43226647 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
43226667 AAG-AAGCAA
1 AAGTAAGCAA
43226676 AGACCATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:43226804 original size:14 final size:14
Alignment explanation
Indices: 43226785--43226811 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43226775 TTTATTTTCT
43226785 TTCTTTTCTTATAC
1 TTCTTTTCTTATAC
43226799 TTCTTTTCTTATA
1 TTCTTTTCTTATA
43226812 GTATGGCCAA
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:0.15, C:0.19, G:0.00, T:0.67
Consensus pattern (14 bp):
TTCTTTTCTTATAC
Found at i:43231431 original size:22 final size:22
Alignment explanation
Indices: 43231403--43231524 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
43231393 TTCCACATCC
43231403 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
43231425 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
43231449 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
43231472 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
43231496 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
43231519 ATCACA
1 ATCACA
43231525 CATACACATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:43231438 original size:47 final size:47
Alignment explanation
Indices: 43231375--43231925 Score: 761
Period size: 47 Copynumber: 11.6 Consensus size: 47
43231365 CCCTTCGGGA
* * *
43231375 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
43231422 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
43231469 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
43231516 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
43231563 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * * *
43231610 CTTATCTCACATACACATGTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACA-CTTTCACATTCATCACATTGGCCATTCGGC
43231658 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
43231707 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
43231754 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
43231803 CTTATCACATATACACACTTTCACATTCATCAC-TTCGCACATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGC-CATTCGGC
* *
43231850 CTTATCACTTATATACA-TATTCACATTCATCACATTCGGCACATTAGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATT-GGC-CATTCGGC
43231899 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
43231926 TATTCAAATA
Statistics
Matches: 469, Mismatches: 23, Indels: 22
0.91 0.04 0.04
Matches are distributed among these distances:
46 5 0.01
47 299 0.64
48 37 0.08
49 120 0.26
50 8 0.02
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:43233449 original size:56 final size:56
Alignment explanation
Indices: 43233382--43233501 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
43233372 TATTAGTTTA
43233382 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
43233438 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
43233494 TTGCCCAT
1 TTGCCCAT
43233502 CATCCCTGTC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:43234953 original size:40 final size:40
Alignment explanation
Indices: 43234854--43235331 Score: 811
Period size: 40 Copynumber: 12.0 Consensus size: 40
43234844 CTCCGGAATA
*
43234854 GATACATCACTAGCATGAATGCTCTTCGGGACTTAG-CCA
1 GATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCG
* *
43234893 GATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCG
1 GATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCG
43234933 GATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCG
1 GATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCG
*
43234973 GATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCG
1 GATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCG
* *
43235013 GATACATCACTAGCAGGAATGCTCTTCGGAACTTAGCCCG
1 GATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCG
43235053 GATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCG
1 GATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCG
*
43235093 GATACATCACTAGCATGAATGCTCTTCGGGACTTAACCCG
1 GATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCG
*
43235133 GATACATCACTAGCATGAATGTCTCTTCGGAACTTA-CCCG
1 GATACATCACTAGCATGAATG-CTCTTCGGGACTTAGCCCG
43235173 GATACATCACTAGCATGAATGCTCTTCGGGAC-TAGCCCG
1 GATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCG
*
43235212 GATACATCACTAGCATGAATGCTCTTCGGAACTTAGCCCG
1 GATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCG
*
43235252 GATACATCACTAGCATGAATGCTCTTCGGAACTTAGCCCG
1 GATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCG
*
43235292 GATTACATCACTAGCATGAATGCTCTTC-GGACTTAACCCG
1 GA-TACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCG
43235332 ATTTAGTAAC
Statistics
Matches: 418, Mismatches: 16, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
38 2 0.00
39 79 0.19
40 299 0.72
41 38 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
GATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCG
Found at i:43235377 original size:39 final size:39
Alignment explanation
Indices: 43235310--43235450 Score: 126
Period size: 39 Copynumber: 3.6 Consensus size: 39
43235300 CACTAGCATG
* * *
43235310 AATGCTCTTCGGACTTAACCC-GATTTAGTAACTCGCACC
1 AATGC-CTTCGGGCTTAGCCCGGAATTAGTAACTCGCACC
*
43235349 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACA
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACC
** * * * *
43235388 AATGCCTTCGATCTTAGTCCGG-ATATGGTCACTTAGCA-C
1 AATGCCTTCGGGCTTAGCCCGGAAT-TAGTAAC-TCGCACC
*
43235427 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGG-CTTAGCCCGGA
43235451 CATCATTCGA
Statistics
Matches: 82, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
38 15 0.18
39 54 0.66
40 13 0.16
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACC
Found at i:43237792 original size:47 final size:47
Alignment explanation
Indices: 43237729--43238276 Score: 798
Period size: 47 Copynumber: 11.6 Consensus size: 47
43237719 CCCTTCGGGA
* * *
43237729 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
43237776 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCAGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
43237823 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
43237870 CTTCTCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
43237917 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
43237964 CTTATCTCACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
43238011 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
43238060 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
43238107 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
43238154 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
43238201 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
43238250 CTTATCACATATACACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
43238277 TATTCAAATA
Statistics
Matches: 474, Mismatches: 21, Indels: 12
0.93 0.04 0.02
Matches are distributed among these distances:
46 1 0.00
47 383 0.81
49 89 0.19
50 1 0.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:43238110 original size:190 final size:190
Alignment explanation
Indices: 43237729--43238276 Score: 811
Period size: 190 Copynumber: 2.9 Consensus size: 190
43237719 CCCTTCGGGA
** * * *
43237729 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACACATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
* * *
43237794 TTTCACATTCATCACATTGGCCATTCAGCCTTATCTC--ATATATGCA-TGTTCACATTCATCAC
66 TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACT-TTCACATTCATCAC
* * * *
43237856 ATTGGCCATTCGGCCTTCTCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
130 ATTGGCCATTCGGCCTTATCACATATACACACT-TTCACATTCATCACATCGGCCATTAGGC
* * *
43237917 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCACATACACA
1 CTTATCACACATACACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACA
43237981 -TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCA
65 CT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCA
*
43238045 CATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
129 CATTGGCCATTCGGCCTTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
43238107 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACACATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
* *
43238172 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCACA
*
43238237 TTGGCCATTAGGCCTTATCACATATACACACTTTCACATT
131 TTGGCCATTCGGCCTTATCACATATACACACTTTCACATT
43238277 TATTCAAATA
Statistics
Matches: 325, Mismatches: 27, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
187 2 0.01
188 88 0.27
190 231 0.71
191 4 0.01
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (190 bp):
CTTATCACACATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCACA
TTGGCCATTCGGCCTTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:43239792 original size:56 final size:56
Alignment explanation
Indices: 43239725--43239844 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
43239715 TATTAGTTTA
43239725 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
43239781 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
43239837 TTGCCCAT
1 TTGCCCAT
43239845 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:43244641 original size:20 final size:21
Alignment explanation
Indices: 43244618--43244658 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43244608 ATCACTTTAA
*
43244618 TATCAA-ATTAATATAATATT
1 TATCAAGATAAATATAATATT
*
43244638 TATCAAGATAAATATTATATT
1 TATCAAGATAAATATAATATT
43244659 GAATTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (21 bp):
TATCAAGATAAATATAATATT
Found at i:43254699 original size:36 final size:36
Alignment explanation
Indices: 43254643--43254763 Score: 120
Period size: 36 Copynumber: 3.4 Consensus size: 36
43254633 TACTCTCTAT
*
43254643 TTTAGTGTG-TTTCGATTGGATTAGCTCTTCCGAGCCA
1 TTTAGTGTGTTTTCGA-TGGATTAGCTCTTACGAG-CA
* * *
43254680 -TTAGTGTGTTTTTGATGGATTAGCTCGTATGAGCA
1 TTTAGTGTGTTTTCGATGGATTAGCTCTTACGAGCA
* * * *
43254715 TTTGGTGTGTTTTGGATGGACTAGCTCTTATGAGCA
1 TTTAGTGTGTTTTCGATGGATTAGCTCTTACGAGCA
* *
43254751 TCTGGTGTGTTTT
1 TTTAGTGTGTTTT
43254764 GGTGGGATTA
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
35 2 0.03
36 66 0.90
37 5 0.07
ACGTcount: A:0.16, C:0.12, G:0.28, T:0.44
Consensus pattern (36 bp):
TTTAGTGTGTTTTCGATGGATTAGCTCTTACGAGCA
Found at i:43254764 original size:36 final size:36
Alignment explanation
Indices: 43254683--43254765 Score: 130
Period size: 36 Copynumber: 2.3 Consensus size: 36
43254673 CGAGCCATTA
* * *
43254683 GTGTGTTTTTGATGGATTAGCTCGTATGAGCATTTG
1 GTGTGTTTTGGATGGACTAGCTCGTATGAGCATCTG
*
43254719 GTGTGTTTTGGATGGACTAGCTCTTATGAGCATCTG
1 GTGTGTTTTGGATGGACTAGCTCGTATGAGCATCTG
43254755 GTGTGTTTTGG
1 GTGTGTTTTGG
43254766 TGGGATTACC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.14, C:0.10, G:0.33, T:0.43
Consensus pattern (36 bp):
GTGTGTTTTGGATGGACTAGCTCGTATGAGCATCTG
Found at i:43259924 original size:22 final size:22
Alignment explanation
Indices: 43259899--43259958 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
43259889 TTAATCCAGC
*
43259899 CCAATACATAATTTTCTATTTT
1 CCAATAAATAATTTTCTATTTT
* *
43259921 CCAA-AAATAATATT-AATTTT
1 CCAATAAATAATTTTCTATTTT
*
43259941 CTAATTAAATAATTTTCT
1 CCAA-TAAATAATTTTCT
43259959 CATCTCAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 8 0.28
21 8 0.28
22 13 0.45
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (22 bp):
CCAATAAATAATTTTCTATTTT
Found at i:43260178 original size:6 final size:6
Alignment explanation
Indices: 43260163--43260217 Score: 83
Period size: 6 Copynumber: 9.0 Consensus size: 6
43260153 CAAAAATGAA
* *
43260163 TCATTT CTCATTC TCATTT TCATTT TCATTT TCATTT TCAATT TCATTT
1 TCATTT -TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT
43260212 TCATTT
1 TCATTT
43260218 CAAGAAAACC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
6 39 0.89
7 5 0.11
ACGTcount: A:0.18, C:0.20, G:0.00, T:0.62
Consensus pattern (6 bp):
TCATTT
Found at i:43260845 original size:6 final size:6
Alignment explanation
Indices: 43260828--43260866 Score: 69
Period size: 6 Copynumber: 6.3 Consensus size: 6
43260818 ACACACCATC
43260828 TTTCAGT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TT
1 TTTCA-T TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TT
43260867 CAAGAAAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 27 0.84
7 5 0.16
ACGTcount: A:0.15, C:0.15, G:0.03, T:0.67
Consensus pattern (6 bp):
TTTCAT
Found at i:43272787 original size:20 final size:20
Alignment explanation
Indices: 43272750--43272798 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
43272740 CATATCATGC
*
43272750 ATTCATTTGTGATCTCATAT
1 ATTCATTTTTGATCTCATAT
* *
43272770 ATTCATTTTTTATTTCATAT
1 ATTCATTTTTGATCTCATAT
43272790 ATTCATTTT
1 ATTCATTTT
43272799 CAACCAGATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.24, C:0.12, G:0.04, T:0.59
Consensus pattern (20 bp):
ATTCATTTTTGATCTCATAT
Found at i:43272872 original size:24 final size:24
Alignment explanation
Indices: 43272844--43272890 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
43272834 ATGCAAGATA
* *
43272844 ATAATGCTCATATGAGCTATGAAT
1 ATAATGCTCACACGAGCTATGAAT
43272868 ATAATGCTCACACGAGCTATGAA
1 ATAATGCTCACACGAGCTATGAA
43272891 ATGGGCTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (24 bp):
ATAATGCTCACACGAGCTATGAAT
Found at i:43274553 original size:14 final size:13
Alignment explanation
Indices: 43274529--43274562 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
43274519 AATCACTATT
*
43274529 CATATATAGCTCA
1 CATATAGAGCTCA
43274542 CAATATAGAGCTCA
1 C-ATATAGAGCTCA
43274556 CATATAG
1 CATATAG
43274563 TTTAACACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (13 bp):
CATATAGAGCTCA
Found at i:43275026 original size:18 final size:18
Alignment explanation
Indices: 43275005--43275042 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
43274995 CATTCAAAAG
43275005 AATATGAAATTTCAATAA
1 AATATGAAATTTCAATAA
*
43275023 AATATGAAATTTTAATAA
1 AATATGAAATTTCAATAA
43275041 AA
1 AA
43275043 AATAGTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (18 bp):
AATATGAAATTTCAATAA
Found at i:43275046 original size:20 final size:20
Alignment explanation
Indices: 43275000--43275046 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 20
43274990 TTTGTCATTC
43275000 AAAAGAATATGAAATTTCAAT
1 AAAA-AATATGAAATTTCAAT
*
43275021 --AAAATATGAAATTTTAAT
1 AAAAAATATGAAATTTCAAT
43275039 AAAAAATA
1 AAAAAATA
43275047 GTTTAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 15 0.65
19 2 0.09
20 6 0.26
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (20 bp):
AAAAAATATGAAATTTCAAT
Found at i:43275313 original size:26 final size:27
Alignment explanation
Indices: 43275284--43275348 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 27
43275274 ATGATTGCAA
*
43275284 CTCGCCAAGCCCACTGGC-GAC-CTCAG
1 CTCGCCAAGCCCACTAGCAGACACT-AG
*
43275310 CTCGCC-AGACCCACTAGCATACACTAG
1 CTCGCCAAG-CCCACTAGCAGACACTAG
43275337 CTCGCCAAGCCC
1 CTCGCCAAGCCC
43275349 CTAACTCCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
25 2 0.06
26 14 0.42
27 13 0.39
28 4 0.12
ACGTcount: A:0.23, C:0.46, G:0.18, T:0.12
Consensus pattern (27 bp):
CTCGCCAAGCCCACTAGCAGACACTAG
Found at i:43276598 original size:13 final size:13
Alignment explanation
Indices: 43276580--43276613 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
43276570 ACCTCATTGG
43276580 ATTAAATTATTAA
1 ATTAAATTATTAA
43276593 ATTAAAATTATTAA
1 ATT-AAATTATTAA
43276607 A-TAAATT
1 ATTAAATT
43276614 GAAATTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 4 0.20
14 11 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTAAATTATTAA
Found at i:43281897 original size:24 final size:24
Alignment explanation
Indices: 43281870--43281921 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
43281860 TTAGTAAGTC
*
43281870 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
43281894 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
43281918 AAAT
1 AAAT
43281922 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:43286054 original size:25 final size:25
Alignment explanation
Indices: 43286022--43286076 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
43286012 TAATTTAATC
*
43286022 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
43286046 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
43286071 ATATAT
1 ATATAT
43286077 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:43290667 original size:19 final size:19
Alignment explanation
Indices: 43290625--43290684 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
43290615 CATGGGCTTA
*
43290625 GGCCGAAATGGGCCACGT-TG
1 GGCCGAAATGGG-C-TGTGTG
43290645 GGCCGAAATGGGCTGTGTG
1 GGCCGAAATGGGCTGTGTG
*
43290664 GGCC-TAATGGGCT-TGTG
1 GGCCGAAATGGGCTGTGTG
43290681 GGCC
1 GGCC
43290685 TACACGGATG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
17 8 0.22
18 10 0.27
19 7 0.19
20 12 0.32
ACGTcount: A:0.15, C:0.22, G:0.43, T:0.20
Consensus pattern (19 bp):
GGCCGAAATGGGCTGTGTG
Found at i:43290682 original size:17 final size:18
Alignment explanation
Indices: 43290651--43290686 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
43290641 GTTGGGCCGA
43290651 AATGGGCTGTGTGGGCCT
1 AATGGGCTGTGTGGGCCT
43290669 AATGGGCT-TGTGGGCCT
1 AATGGGCTGTGTGGGCCT
43290686 A
1 A
43290687 CACGGATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.14, C:0.17, G:0.42, T:0.28
Consensus pattern (18 bp):
AATGGGCTGTGTGGGCCT
Found at i:43290973 original size:28 final size:27
Alignment explanation
Indices: 43290899--43291127 Score: 124
Period size: 27 Copynumber: 8.4 Consensus size: 27
43290889 CTCCAAAATA
* *
43290899 GGTAATATGACCAAAATACCCCTGA-AG
1 GGTAAAATGACTAAAATACCCCT-ACAG
* * ***
43290926 GATAAAATAACTATTTTACCCCTAACA-
1 GGTAAAATGACTAAAATACCCCT-ACAG
* *
43290953 GATGAAAATGACTAAAATACCCCTATAG
1 GGT-AAAATGACTAAAATACCCCTACAG
* * * *
43290981 GGTAAAATGACTGAAATACCCCCATAA
1 GGTAAAATGACTAAAATACCCCTACAG
* ** * * *
43291008 GGTAACATGACCGAAATACCCCCATAA
1 GGTAAAATGACTAAAATACCCCTACAG
* *
43291035 GGTAAAATGA-TCGAAATACCCCTATAG
1 GGTAAAATGACT-AAAATACCCCTACAG
* * *
43291062 GGTAAAATGA-TCGAAATACCCCCATAG
1 GGTAAAATGACT-AAAATACCCCTACAG
** * * *
43291089 GGTAAAATGACCGAAATAACCTTATAG
1 GGTAAAATGACTAAAATACCCCTACAG
43291116 GGTAAAATGACT
1 GGTAAAATGACT
43291128 TTTATACCCC
Statistics
Matches: 168, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
27 149 0.89
28 19 0.11
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.21
Consensus pattern (27 bp):
GGTAAAATGACTAAAATACCCCTACAG
Found at i:43290997 original size:27 final size:27
Alignment explanation
Indices: 43290957--43291127 Score: 211
Period size: 27 Copynumber: 6.3 Consensus size: 27
43290947 CTAACAGATG
* *
43290957 AAAATGACTAAAATACCCCTATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
*
43290984 AAAATGACTGAAATACCCCCATAAGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* * *
43291011 AACATGACCGAAATACCCCCATAAGGT
1 AAAATGACTGAAATACCCCCATAGGGT
*
43291038 AAAATGA-TCGAAATACCCCTATAGGGT
1 AAAATGACT-GAAATACCCCCATAGGGT
43291065 AAAATGA-TCGAAATACCCCCATAGGGT
1 AAAATGACT-GAAATACCCCCATAGGGT
* * **
43291092 AAAATGACCGAAATAACCTTATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
43291119 AAAATGACT
1 AAAATGACT
43291128 TTTATACCCC
Statistics
Matches: 127, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
27 127 1.00
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.20
Consensus pattern (27 bp):
AAAATGACTGAAATACCCCCATAGGGT
Found at i:43291139 original size:81 final size:81
Alignment explanation
Indices: 43290967--43291125 Score: 248
Period size: 81 Copynumber: 2.0 Consensus size: 81
43290957 AAAATGACTA
* *
43290967 AAATACCCCTATAGGGTAAAATGACTGAAATACCCCCATAAGGTAACATGACCGAAATACCCCCA
1 AAATACCCCTATAGGGTAAAATGACTGAAATACCCCCATAAGGTAAAATGACCGAAATAACCCCA
43291032 TAAGGTAAAATGATCG
66 TAAGGTAAAATGATCG
* **
43291048 AAATACCCCTATAGGGTAAAATGA-TCGAAATACCCCCATAGGGTAAAATGACCGAAATAACCTT
1 AAATACCCCTATAGGGTAAAATGACT-GAAATACCCCCATAAGGTAAAATGACCGAAATAACCCC
*
43291112 ATAGGGTAAAATGA
65 ATAAGGTAAAATGA
43291126 CTTTTATACC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
80 1 0.01
81 70 0.99
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (81 bp):
AAATACCCCTATAGGGTAAAATGACTGAAATACCCCCATAAGGTAAAATGACCGAAATAACCCCA
TAAGGTAAAATGATCG
Found at i:43291396 original size:26 final size:26
Alignment explanation
Indices: 43291360--43291414 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
43291350 TTTGCCACAT
*
43291360 ATACTGTTACTAGCAGCTTTGCTACG
1 ATACTGATACTAGCAGCTTTGCTACG
* * *
43291386 ATACTGATACTGGTAGCTTTGCTGCG
1 ATACTGATACTAGCAGCTTTGCTACG
43291412 ATA
1 ATA
43291415 TTAGTGTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (26 bp):
ATACTGATACTAGCAGCTTTGCTACG
Found at i:43291574 original size:33 final size:33
Alignment explanation
Indices: 43291532--43291614 Score: 130
Period size: 33 Copynumber: 2.5 Consensus size: 33
43291522 ACTGTATTGG
43291532 GCTAAGGCCCACACTGTACTATCACTTCATAGA
1 GCTAAGGCCCACACTGTACTATCACTTCATAGA
* *
43291565 GCTAAGGCCCACACTGTACTGTCACTTCATAGG
1 GCTAAGGCCCACACTGTACTATCACTTCATAGA
* *
43291598 GCTCAGGCCCAGACTGT
1 GCTAAGGCCCACACTGT
43291615 TACTGCATGC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.23
Consensus pattern (33 bp):
GCTAAGGCCCACACTGTACTATCACTTCATAGA
Found at i:43292687 original size:29 final size:30
Alignment explanation
Indices: 43292629--43292687 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
43292619 TAAGTTAGAT
*
43292629 AAAGAAATTCGACACAAGCAGAATTAAAGA
1 AAAGAAATTCGACACAAGCAGAATAAAAGA
43292659 AAAGAAATT-GACAACAAGCA-AATAAAAGA
1 AAAGAAATTCGAC-ACAAGCAGAATAAAAGA
43292688 TAAGTCCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.61, C:0.12, G:0.15, T:0.12
Consensus pattern (30 bp):
AAAGAAATTCGACACAAGCAGAATAAAAGA
Found at i:43297453 original size:16 final size:16
Alignment explanation
Indices: 43297432--43297465 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
43297422 CTACTGAAAC
43297432 AAAGTAAATGTTCCTA
1 AAAGTAAATGTTCCTA
*
43297448 AAAGTAAATGTTTCTA
1 AAAGTAAATGTTCCTA
43297464 AA
1 AA
43297466 TATTTTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (16 bp):
AAAGTAAATGTTCCTA
Found at i:43300815 original size:25 final size:25
Alignment explanation
Indices: 43300787--43300838 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
43300777 CACTGACCAA
*
43300787 TCCTTGCATTTGAGATTGACAGCTT
1 TCCTTGCATTTGAGATTGACAACTT
43300812 TCCTTGCATTTGAGATTGACAACTT
1 TCCTTGCATTTGAGATTGACAACTT
43300837 TC
1 TC
43300839 TCTAGAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (25 bp):
TCCTTGCATTTGAGATTGACAACTT
Found at i:43302002 original size:25 final size:25
Alignment explanation
Indices: 43301972--43302020 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
43301962 AGTGCTCTGA
43301972 CAGCAAAGTCACTTGCATAACACAG
1 CAGCAAAGTCACTTGCATAACACAG
43301997 CAGCAAAGTCACTTGCATAACACA
1 CAGCAAAGTCACTTGCATAACACA
43302021 ATAGTTCGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.29, G:0.14, T:0.16
Consensus pattern (25 bp):
CAGCAAAGTCACTTGCATAACACAG
Found at i:43308246 original size:41 final size:41
Alignment explanation
Indices: 43308179--43308311 Score: 187
Period size: 41 Copynumber: 3.2 Consensus size: 41
43308169 TTTATGGTTT
* * *
43308179 CCTTTTCATTTGTTGTCATTTTTGGATAACATCCATTTCAA
1 CCTTTTCATTTGTTATCCTTTCTGGATAACATCCATTTCAA
*
43308220 CCTTTTCATTTGATATCCTTTCTGGATAACAT-CATTTTCAA
1 CCTTTTCATTTGTTATCCTTTCTGGATAACATCCA-TTTCAA
* *
43308261 CCTTTTTATTTGTTATCCTTTCTGGATAACATCCTTTTCAA
1 CCTTTTCATTTGTTATCCTTTCTGGATAACATCCATTTCAA
*
43308302 TCTTTTCATT
1 CCTTTTCATT
43308312 GATTCAGAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
40 2 0.02
41 78 0.96
42 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.08, T:0.50
Consensus pattern (41 bp):
CCTTTTCATTTGTTATCCTTTCTGGATAACATCCATTTCAA
Found at i:43312343 original size:25 final size:25
Alignment explanation
Indices: 43312315--43312376 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
43312305 ATATTACATT
43312315 ATTTAAATATAATATATATCAATAA
1 ATTTAAATATAATATATATCAATAA
* * *
43312340 ATTTATAA-ATAATTTATATTAATTA
1 ATTTA-AATATAATATATATCAATAA
*
43312365 ATTAAAAT-TAAT
1 ATTTAAATATAAT
43312377 TAAAATTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
24 6 0.19
25 23 0.74
26 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTTAAATATAATATATATCAATAA
Found at i:43317043 original size:56 final size:56
Alignment explanation
Indices: 43316957--43317076 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
43316947 ACAAGGGATG
43316957 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
43317013 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
43317069 ATGGGCAA
1 ATGGGCAA
43317077 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:43318302 original size:42 final size:41
Alignment explanation
Indices: 43318203--43318350 Score: 176
Period size: 40 Copynumber: 3.6 Consensus size: 41
43318193 TCGAATGATG
* * *
43318203 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTTACTATA
* * *
43318243 TCCGGACTAAGAT-CCGAAGGCATTTGGTGCGAAGTTAGTACA
1 TCCGGGCTAAG-TCCCGAAGGCATTT-GTGCGAAGTTACTATA
*
43318285 TCCGGGTTAAGTCCCGAAGGCATTTGTGCG-AGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTTACTATA
* *
43318325 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
43318351 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
40 49 0.54
41 10 0.11
42 32 0.35
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTTACTATA
Found at i:43318330 original size:40 final size:40
Alignment explanation
Indices: 43318203--43318369 Score: 169
Period size: 40 Copynumber: 4.1 Consensus size: 40
43318193 TCGAATGATG
* * *
43318203 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATA
* * *
43318243 TCCGGACTAAGAT-CCGAAGGCATTTGGTGCGAAGTTAGTACA
1 TCCGGGCTAAG-TCCCGAAGGCATTT-GTGCG-AGTTACTATA
*
43318285 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
* * **
43318325 ACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATA
43318365 TCCGG
1 TCCGG
43318370 TTAAATTCCG
Statistics
Matches: 105, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
39 2 0.02
40 62 0.59
41 10 0.10
42 31 0.30
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
Found at i:43324946 original size:57 final size:56
Alignment explanation
Indices: 43324835--43324955 Score: 224
Period size: 57 Copynumber: 2.1 Consensus size: 56
43324825 ACAAGGGATG
43324835 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
43324891 ATGGGCAAAACATGTCATGAAACATGTGTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGT-TGTGTTAATGGAAAAATAAAATAAGAAGC
43324948 ATGGGCAA
1 ATGGGCAA
43324956 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 27 0.43
57 36 0.57
ACGTcount: A:0.45, C:0.09, G:0.24, T:0.22
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:43326235 original size:40 final size:40
Alignment explanation
Indices: 43326083--43326228 Score: 181
Period size: 40 Copynumber: 3.6 Consensus size: 40
43326073 TCGAATGATG
* * * *
43326083 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
43326123 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
43326163 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
43326204 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
43326229 AACGAGTAGC
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
39 1 0.01
40 82 0.88
41 10 0.11
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:43326235 original size:80 final size:80
Alignment explanation
Indices: 43326083--43326261 Score: 195
Period size: 80 Copynumber: 2.2 Consensus size: 80
43326073 TCGAATGATG
* *
43326083 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
**
43326148 GTGCGAGTTA-CTAAA
66 GAACGAG-TAGCTAAA
* * * * *
43326163 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
*
43326226 TTGAACGAGTAGCTATA
64 TTGAACGAGTAGCTAAA
* *
43326243 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
43326262 TACGTGATTT
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
79 17 0.20
80 60 0.71
81 7 0.08
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGTAGCTAAA
Found at i:43330119 original size:16 final size:16
Alignment explanation
Indices: 43330095--43330148 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
43330085 TTTGGTTCAC
* *
43330095 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
43330111 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
43330127 TGTAATAGAATAGAGG
1 TGTAATGGAATAGAGG
43330143 TGTAAT
1 TGTAAT
43330149 AGCAAATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:43330149 original size:16 final size:16
Alignment explanation
Indices: 43330105--43330150 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
43330095 TGTATTGGAT
*
43330105 TAGAGGTGTAATGGAA
1 TAGAGGTGTAATAGAA
43330121 TAGAGGTGTAATAGAA
1 TAGAGGTGTAATAGAA
43330137 TAGAGGTGTAATAG
1 TAGAGGTGTAATAG
43330151 CAAATCAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.35, T:0.26
Consensus pattern (16 bp):
TAGAGGTGTAATAGAA
Found at i:43330193 original size:45 final size:44
Alignment explanation
Indices: 43330127--43330224 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
43330117 GGAATAGAGG
*
43330127 TGTAATAGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATAGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* * ***
43330172 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATAGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
*
43330216 TGGAATAGA
1 TGTAATAGA
43330225 GGTGTAATAG
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 23 0.51
45 22 0.49
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.33
Consensus pattern (44 bp):
TGTAATAGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:43330390 original size:25 final size:25
Alignment explanation
Indices: 43330358--43330412 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
43330348 TAATTTAATC
*
43330358 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
43330382 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
43330407 ATATAT
1 ATATAT
43330413 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:43334736 original size:50 final size:50
Alignment explanation
Indices: 43334682--43335367 Score: 832
Period size: 50 Copynumber: 13.5 Consensus size: 50
43334672 TATCCCAAGT
* * ** * * *
43334682 ATGGTTTTACATGAGAGTTCTCATATCGGTGCCCATGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
*** *
43334732 ATGGTCTTATGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
*
43334782 ATGGTCTTACATGGGACCTCTCATCTCGGTGTCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
* * *
43334832 ATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGACATGTCCCAAAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
* ** * * * *
43334882 ATGGTCTTACATGGTAGTTCTCATATCAGTGCCCATGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
***
43334932 ATGGTCTTATGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
* *
43334982 ATGGTCTTACATGGGACCTCTCATCTCGGTGTCAACGTCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
* * * *
43335032 ATGGTCTTACATGGGATCTCTCATCTCAGTGCCAACGTCATGTCCCAAAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
* ** * * *
43335082 ATGGTCTTACATGGTAGTTCTCATATCGGTGCCCATGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
***
43335132 ATGGTCTTATGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
* * *
43335182 ATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGCCATGTCCCAAAT
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
*
43335232 ATGGTCTTACATGGGACCTCTCATCGGACCTCTCATCTTGGTGCCAACGCCATGTTCCAGAC
1 ATGGTCTTACATGGGA-C-CTC-TC--A----TC-TC--GGTGCCAACGCCATGTCCCAGAC
* * *
43335294 ATGGTCTTACATGAGACCTCTCATCTTGGTGCCAACGCCATATCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
*
43335344 ATGGTCTTACATGAGACCTCTCAT
1 ATGGTCTTACATGGGACCTCTCAT
43335368 AATTTCAATA
Statistics
Matches: 545, Mismatches: 79, Indels: 24
0.84 0.12 0.04
Matches are distributed among these distances:
50 490 0.90
51 1 0.00
52 4 0.01
53 4 0.01
55 1 0.00
57 1 0.00
59 4 0.01
60 5 0.01
61 1 0.00
62 34 0.06
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.27
Consensus pattern (50 bp):
ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
Found at i:43334965 original size:200 final size:200
Alignment explanation
Indices: 43334682--43335256 Score: 1044
Period size: 200 Copynumber: 2.9 Consensus size: 200
43334672 TATCCCAAGT
*
43334682 ATGGTTTTACATGAG-AGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTATGGGG
1 ATGGTCTTACATG-GTAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTATGGGG
*
43334746 GACCTCTCATCTCGGTGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
65 GACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
43334811 TGTCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGACATGTC
130 TGTCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGACATGTC
43334876 CCAAAC
195 CCAAAC
*
43334882 ATGGTCTTACATGGTAGTTCTCATATCAGTGCCCATGCCATGTCCCAGACATGGTCTTATGGGGG
1 ATGGTCTTACATGGTAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTATGGGGG
43334947 ACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
66 ACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
* * *
43335012 GTCAACGTCATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCAGTGCCAACGTCATGTCC
131 GTCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGACATGTCC
43335077 CAAAC
196 CAAAC
43335082 ATGGTCTTACATGGTAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTATGGGGG
1 ATGGTCTTACATGGTAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTATGGGGG
*
43335147 ACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGT
66 ACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
* * *
43335212 GCCAACGCCATGTCCCAAATATGGTCTTACATGGGACCTCTCATC
131 GTCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATC
43335257 GGACCTCTCA
Statistics
Matches: 361, Mismatches: 13, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
199 1 0.00
200 360 1.00
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (200 bp):
ATGGTCTTACATGGTAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTATGGGGG
ACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
GTCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGACATGTCC
CAAAC
Found at i:43335276 original size:62 final size:62
Alignment explanation
Indices: 43335195--43335318 Score: 194
Period size: 62 Copynumber: 2.0 Consensus size: 62
43335185 GTCTTACATG
* *
43335195 GGACCTCTCATCTCAGTGCCAACGCCATGTCCCAAATATGGTCTTACATGGGACCTCTCATC
1 GGACCTCTCATCTCAGTGCCAACGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATC
** * *
43335257 GGACCTCTCATCTTGGTGCCAACGCCATGTTCCAGACATGGTCTTACATGAGACCTCTCATC
1 GGACCTCTCATCTCAGTGCCAACGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATC
43335319 TTGGTGCCAA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.27
Consensus pattern (62 bp):
GGACCTCTCATCTCAGTGCCAACGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATC
Found at i:43335280 original size:112 final size:112
Alignment explanation
Indices: 43335145--43335367 Score: 365
Period size: 112 Copynumber: 2.0 Consensus size: 112
43335135 GTCTTATGGG
*
43335145 GGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCA
1 GGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCA
* * *
43335210 GTGCCAACGCCATGTCCCAAATATGGTCTTACATGGGACCTCTCATC
66 GTGCCAACGCCATATCCCAAACATGGTCTTACATGAGACCTCTCATC
* * **
43335257 GGACCTCTCATCTTGGTGCCAACGCCATGTTCCAGACATGGTCTTACATGAGACCTCTCATCTTG
1 GGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCA
*
43335322 GTGCCAACGCCATATCCCAGACATGGTCTTACATGAGACCTCTCAT
66 GTGCCAACGCCATATCCCAAACATGGTCTTACATGAGACCTCTCAT
43335368 AATTTCAATA
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
112 102 1.00
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.26
Consensus pattern (112 bp):
GGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCA
GTGCCAACGCCATATCCCAAACATGGTCTTACATGAGACCTCTCATC
Found at i:43340137 original size:39 final size:40
Alignment explanation
Indices: 43340070--43340180 Score: 111
Period size: 39 Copynumber: 2.8 Consensus size: 40
43340060 TTTAAGTATA
* * * * **
43340070 TAATTATGTCATAATCTGAACATATTTAATA-AGATTTTT
1 TAATTATGTCATAGTTTGGACATATTTAATATACATAATT
43340109 TAATTATGTCATAGTTTAGGACAT-TTTAA-ATACATAATT
1 TAATTATGTCATAGTTT-GGACATATTTAATATACATAATT
* * *
43340148 TAATTATGTCCTAGTTTGGAAATCTTTAATATA
1 TAATTATGTCATAGTTTGGACATATTTAATATA
43340181 TGTGTTTAGT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
38 6 0.10
39 46 0.77
40 8 0.13
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (40 bp):
TAATTATGTCATAGTTTGGACATATTTAATATACATAATT
Found at i:43346318 original size:28 final size:28
Alignment explanation
Indices: 43346266--43346360 Score: 113
Period size: 29 Copynumber: 3.3 Consensus size: 28
43346256 AGAAGAAAAT
43346266 CCTTTGTGGCAAAACTTTGGAAAGGCAAG
1 CCTTTGTGGCAAAACTTT-GAAAGGCAAG
* *
43346295 CCTTTGTGGCAAACCTATT-AAAGG-ATAA
1 CCTTTGTGGCAAAACT-TTGAAAGGCA-AG
*
43346323 CCTTTGTTGCAAAACTTTAGAAAGGCAAG
1 CCTTTGTGGCAAAACTTT-GAAAGGCAAG
43346352 CCTTTGTGG
1 CCTTTGTGG
43346361 TGAACCTATT
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
27 3 0.05
28 20 0.36
29 29 0.53
30 3 0.05
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (28 bp):
CCTTTGTGGCAAAACTTTGAAAGGCAAG
Found at i:43346354 original size:57 final size:57
Alignment explanation
Indices: 43346266--43346386 Score: 188
Period size: 57 Copynumber: 2.1 Consensus size: 57
43346256 AGAAGAAAAT
* *
43346266 CCTTTGTGGCAAAACTTTGGAAAGGCAAGCCTTTGTGGCAAACCTATTAAAGGATAA
1 CCTTTGTGGCAAAACTTTAGAAAGGCAAGCCTTTGTGGCAAACCTATTAAAGGACAA
* **
43346323 CCTTTGTTGCAAAACTTTAGAAAGGCAAGCCTTTGTGGTGAACCTATTAAAGGACAA
1 CCTTTGTGGCAAAACTTTAGAAAGGCAAGCCTTTGTGGCAAACCTATTAAAGGACAA
*
43346380 CTTTTGT
1 CCTTTGT
43346387 AGCAGTGGTG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (57 bp):
CCTTTGTGGCAAAACTTTAGAAAGGCAAGCCTTTGTGGCAAACCTATTAAAGGACAA
Found at i:43350891 original size:232 final size:232
Alignment explanation
Indices: 43350485--43350937 Score: 906
Period size: 232 Copynumber: 2.0 Consensus size: 232
43350475 GAACTGTTTT
43350485 TATATACGAACTCTACTGAGGGCAAAAATCATTCCCAGCTTCCTGCGAATTCCACCACATGGCTT
1 TATATACGAACTCTACTGAGGGCAAAAATCATTCCCAGCTTCCTGCGAATTCCACCACATGGCTT
43350550 GGTTGCATGTCTTCTAGTACTTGGATCACCCTCTCTTATTGACCATCTATCTATAAATGATAAGA
66 GGTTGCATGTCTTCTAGTACTTGGATCACCCTCTCTTATTGACCATCTATCTATAAATGATAAGA
43350615 AGTACTGAAATTCAATTTCCAACCCAAGGGTTCTTATAAAATTTTCCAAAATCTCGATGTGGATC
131 AGTACTGAAATTCAATTTCCAACCCAAGGGTTCTTATAAAATTTTCCAAAATCTCGATGTGGATC
43350680 GTGGATCTTGATCGACGGTAATGAAATCATTCCCATC
196 GTGGATCTTGATCGACGGTAATGAAATCATTCCCATC
43350717 TATATACGAACTCTACTGAGGGCAAAAATCATTCCCAGCTTCCTGCGAATTCCACCACATGGCTT
1 TATATACGAACTCTACTGAGGGCAAAAATCATTCCCAGCTTCCTGCGAATTCCACCACATGGCTT
43350782 GGTTGCATGTCTTCTAGTACTTGGATCACCCTCTCTTATTGACCATCTATCTATAAATGATAAGA
66 GGTTGCATGTCTTCTAGTACTTGGATCACCCTCTCTTATTGACCATCTATCTATAAATGATAAGA
43350847 AGTACTGAAATTCAATTTCCAACCCAAGGGTTCTTATAAAATTTTCCAAAATCTCGATGTGGATC
131 AGTACTGAAATTCAATTTCCAACCCAAGGGTTCTTATAAAATTTTCCAAAATCTCGATGTGGATC
43350912 GTGGATCTTGATCGACGGTAATGAAA
196 GTGGATCTTGATCGACGGTAATGAAA
43350938 ACGAGCACGC
Statistics
Matches: 221, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
232 221 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (232 bp):
TATATACGAACTCTACTGAGGGCAAAAATCATTCCCAGCTTCCTGCGAATTCCACCACATGGCTT
GGTTGCATGTCTTCTAGTACTTGGATCACCCTCTCTTATTGACCATCTATCTATAAATGATAAGA
AGTACTGAAATTCAATTTCCAACCCAAGGGTTCTTATAAAATTTTCCAAAATCTCGATGTGGATC
GTGGATCTTGATCGACGGTAATGAAATCATTCCCATC
Found at i:43355473 original size:48 final size:48
Alignment explanation
Indices: 43355405--43355601 Score: 232
Period size: 48 Copynumber: 4.1 Consensus size: 48
43355395 AATAGATTTC
* * * *
43355405 TCGGTGGCCTGCACACAGTCCGTACCACCTTTGTGTAATAACAGATTC
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
* * * * * *
43355453 TCGGTGGCCTGCACATAGTCCATGTCACCCTTGTATCTTAACAAATTA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
* * * * * * *
43355501 TTGGTGGCCTACACATACTCTGTGCCACCCTTGTGTCACAACAGAATA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
*
43355549 TCGGTGGCTTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
43355597 TCGGT
1 TCGGT
43355602 ACGGATAGTA
Statistics
Matches: 120, Mismatches: 29, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 120 1.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (48 bp):
TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
Found at i:43373963 original size:82 final size:82
Alignment explanation
Indices: 43373853--43374089 Score: 311
Period size: 82 Copynumber: 2.9 Consensus size: 82
43373843 ATGATTGTCG
* * *
43373853 TTCAATAGATTTTATTCCT-TTTTTATTTTGTTTCCAAACAAGAATTAATTGAATAATTCTATTT
1 TTCAACAGATTTTATT-CTATTTTGATTTTGTTTCCAAACAAGAATTAATTAAATAATTCTATTT
*
43373917 C-AGAATTTATTCTCG-CA
65 CGAG-ATTTATTCCCGCCA
* *
43373934 TCTCAACAGATTTTATTCTATTTTGATTTTGTTTCCAAACAATAATTAAATAAATAATTCTATTT
1 T-TCAACAGATTTTATTCTATTTTGATTTTGTTTCCAAACAAGAATTAATTAAATAATTCTATTT
43373999 CGAGATTTATTCCCGCCA
65 CGAGATTTATTCCCGCCA
* * * *
43374017 TTTAACAGATTTTATT-TGATTTTGATTTTGTTTCCAAACAAGATTTAATTAAATAATTTTGTTT
1 TTCAACAGATTTTATTCT-ATTTTGATTTTGTTTCCAAACAAGAATTAATTAAATAATTCTATTT
*
43374081 CAAGATTTA
65 CGAGATTTA
43374090 ATCCTGTCGG
Statistics
Matches: 138, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
81 4 0.03
82 129 0.93
83 5 0.04
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (82 bp):
TTCAACAGATTTTATTCTATTTTGATTTTGTTTCCAAACAAGAATTAATTAAATAATTCTATTTC
GAGATTTATTCCCGCCA
Found at i:43374212 original size:12 final size:13
Alignment explanation
Indices: 43374195--43374225 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
43374185 TTTTTTATTT
43374195 ATTGTGGCTTT-A
1 ATTGTGGCTTTAA
43374207 ATTGTGGCTTTAA
1 ATTGTGGCTTTAA
43374220 ATTGTG
1 ATTGTG
43374226 AAAGCTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.19, C:0.06, G:0.26, T:0.48
Consensus pattern (13 bp):
ATTGTGGCTTTAA
Found at i:43374232 original size:28 final size:29
Alignment explanation
Indices: 43374201--43374255 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
43374191 ATTTATTGTG
* * *
43374201 GCTTTAATTGTGGCTTTAAA-TTGTGAAA
1 GCTTAAATTGTAGCTTCAAACTTGTGAAA
43374229 GCTTAAATTGTAGCTTCAAACTTGTGA
1 GCTTAAATTGTAGCTTCAAACTTGTGA
43374256 CATCAAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (29 bp):
GCTTAAATTGTAGCTTCAAACTTGTGAAA
Found at i:43379188 original size:50 final size:48
Alignment explanation
Indices: 43379073--43379189 Score: 146
Period size: 51 Copynumber: 2.4 Consensus size: 48
43379063 CAAGATCTTG
*
43379073 TTTATTTAATTATTT-TTTAGATATGATGTTTTAAATAAATATAAATA
1 TTTATTTAATTATTTGTTTAGATACGATGTTTTAAATAAATATAAATA
* * *
43379120 TTTATTTAATTGATTTTGTTTAGATCCGGTGTTTTTACATAAATATAAATA
1 TTTATTTAATT-A-TTTGTTTAGATACGATG-TTTTAAATAAATATAAATA
*
43379171 TTTGTTTATATTATTTGTT
1 TTTATTTA-ATTATTTGTT
43379190 CAAAATCTTG
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
47 11 0.18
48 1 0.02
49 3 0.05
50 16 0.27
51 26 0.43
52 3 0.05
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (48 bp):
TTTATTTAATTATTTGTTTAGATACGATGTTTTAAATAAATATAAATA
Found at i:43383746 original size:19 final size:19
Alignment explanation
Indices: 43383722--43383765 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
43383712 CTTCTCAGAA
43383722 GTATTTTTTAAGATAAAAT
1 GTATTTTTTAAGATAAAAT
*
43383741 GTA-TTTTTGAGATAAAAT
1 GTATTTTTTAAGATAAAAT
*
43383759 ATATTTT
1 GTATTTT
43383766 AAAAAAGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (19 bp):
GTATTTTTTAAGATAAAAT
Found at i:43386356 original size:31 final size:32
Alignment explanation
Indices: 43386299--43386363 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 32
43386289 AAAATAATAA
*
43386299 ATAATAACATGTAATTACCATTATTATTATAT
1 ATAATAACATATAATTACCATTATTATTATAT
* *
43386331 ATAATAATATATAA-TACTATTATTATTATAT
1 ATAATAACATATAATTACCATTATTATTATAT
43386362 AT
1 AT
43386364 GTAATGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 18 0.60
32 12 0.40
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (32 bp):
ATAATAACATATAATTACCATTATTATTATAT
Found at i:43386652 original size:22 final size:23
Alignment explanation
Indices: 43386617--43386660 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
43386607 AAATAATGGT
43386617 TTAAAACATGTAAAACATTTTTC
1 TTAAAACATGTAAAACATTTTTC
* *
43386640 TTAAAAC-TTTAAAATATTTTT
1 TTAAAACATGTAAAACATTTTT
43386661 AAATTACATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (23 bp):
TTAAAACATGTAAAACATTTTTC
Found at i:43387974 original size:18 final size:18
Alignment explanation
Indices: 43387939--43387973 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
43387929 TTATATTTAT
43387939 TTTAAAAATAATAAAAAA
1 TTTAAAAATAATAAAAAA
43387957 TTTAAAAA-AATAAAAAA
1 TTTAAAAATAATAAAAAA
43387974 AGGCATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TTTAAAAATAATAAAAAA
Found at i:43388200 original size:26 final size:25
Alignment explanation
Indices: 43388152--43388244 Score: 86
Period size: 25 Copynumber: 3.7 Consensus size: 25
43388142 AATATAATTT
*
43388152 TTAAAAATTATAAAAAATGGAAATA
1 TTAAAAATTATAAAAAATAGAAATA
43388177 TTAAAATATTA-AAAATAATAGAAATCA
1 TTAAAA-ATTATAAAA-AATAGAAAT-A
* *
43388204 TTTAGAAA--ATAAAATATA-AAATA
1 -TTAAAAATTATAAAAAATAGAAATA
43388227 TTTAAAAATTATAAAAAA
1 -TTAAAAATTATAAAAAA
43388245 ATTTAAAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
23 8 0.14
24 4 0.07
25 21 0.38
26 16 0.29
27 2 0.04
28 5 0.09
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (25 bp):
TTAAAAATTATAAAAAATAGAAATA
Found at i:43388229 original size:23 final size:25
Alignment explanation
Indices: 43388188--43388235 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 25
43388178 TAAAATATTA
43388188 AAAATAATAGAAATCATTTAGAAAAT
1 AAAATAATAGAAATCATTTA-AAAAT
43388214 AAAAT-ATA-AAAT-ATTTAAAAAT
1 AAAATAATAGAAATCATTTAAAAAT
43388236 TATAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.23
23 5 0.23
24 4 0.18
25 3 0.14
26 5 0.23
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (25 bp):
AAAATAATAGAAATCATTTAAAAAT
Found at i:43388249 original size:42 final size:44
Alignment explanation
Indices: 43388154--43388255 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 44
43388144 TATAATTTTT
*
43388154 AAAAATTATAAAAAATGGAAATATTAAAATATTAAAAATAATAGA
1 AAAAATT-TAAAAAATGAAAATATTAAAATATTAAAAATAATAGA
** * *
43388199 AATCATTTAGAAAAT-AAAATA-TAAAATATTTAAAAATTATA-A
1 AAAAATTTAAAAAATGAAAATATTAAAATA-TTAAAAATAATAGA
43388241 AAAAATTTAAAAAAT
1 AAAAATTTAAAAAAT
43388256 TAGATATTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
42 20 0.42
43 16 0.33
44 7 0.15
45 5 0.10
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (44 bp):
AAAAATTTAAAAAATGAAAATATTAAAATATTAAAAATAATAGA
Found at i:43393007 original size:30 final size:31
Alignment explanation
Indices: 43392950--43393009 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
43392940 ATAAATGCCA
* *
43392950 AAAAAAATTACGTGAATAGATCAATTTTTTT
1 AAAAAAATTACGGGAATAGAGCAATTTTTTT
* *
43392981 AAAAAAATTATGGGAATA-AGCTATTTTTT
1 AAAAAAATTACGGGAATAGAGCAATTTTTT
43393010 GGAAATCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (31 bp):
AAAAAAATTACGGGAATAGAGCAATTTTTTT
Found at i:43393150 original size:66 final size:66
Alignment explanation
Indices: 43393036--43393172 Score: 202
Period size: 66 Copynumber: 2.1 Consensus size: 66
43393026 TTGCAGGGAA
* * * * *
43393036 ACTTGGAAGCGTTTTCAGCATGTTGCATTGAAAACGCTTCCAGCTAGAATCGCTTTCTACTAAGT
1 ACTTGGAAGCATTTTCAACATATTGCATGGAAAACGCTTCCAGCTAGAATCACTTTCTACTAAGT
43393101 C
66 C
* * *
43393102 ACTTGGAAGCATTTTCAACATATTGCATGGAAAACGCTTTCAGTTAGAATCACTTTCTGCTAAGT
1 ACTTGGAAGCATTTTCAACATATTGCATGGAAAACGCTTCCAGCTAGAATCACTTTCTACTAAGT
43393167 C
66 C
43393168 ACTTG
1 ACTTG
43393173 AAAATGCTTC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (66 bp):
ACTTGGAAGCATTTTCAACATATTGCATGGAAAACGCTTCCAGCTAGAATCACTTTCTACTAAGT
C
Found at i:43396012 original size:12 final size:13
Alignment explanation
Indices: 43395995--43396025 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
43395985 ACTTAATCAC
43395995 TTTAATATT-AAT
1 TTTAATATTAAAT
43396007 TTTAATATTAAAT
1 TTTAATATTAAAT
43396020 TTTAAT
1 TTTAAT
43396026 TAATAGAATA
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TTTAATATTAAAT
Found at i:43396101 original size:20 final size:18
Alignment explanation
Indices: 43396051--43396102 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
43396041 CTACAAGATA
43396051 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
43396068 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
*
43396088 GATATTAAATTAATA
1 AATATTAAATTAATA
43396103 AAATATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 11 0.38
18 1 0.03
19 3 0.10
20 14 0.48
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:43399746 original size:89 final size:89
Alignment explanation
Indices: 43399590--43399767 Score: 311
Period size: 89 Copynumber: 2.0 Consensus size: 89
43399580 GCTGAAGCTT
*
43399590 CCTCTCGAGCACAGATCGCATAAGCTTTAGTCGACACTGGTGCCTCAAATCTCACAGTAGAGCCT
1 CCTCTCGAGCACAGATCGCATAAGCTTTAGTCGACACTGGTGCCTCAAATCTCACAGCAGAGCCT
43399655 TTCGTTCCACTACGACTATTACCC
66 TTCGTTCCACTACGACTATTACCC
* * * *
43399679 CCTCTCGAGCACGGATCGCATGAGCTTTAGTCGACACTGGTGCCTCAGATCTCACAGCAGAGTCT
1 CCTCTCGAGCACAGATCGCATAAGCTTTAGTCGACACTGGTGCCTCAAATCTCACAGCAGAGCCT
43399744 TTCGTTCCACTACGACTATTACCC
66 TTCGTTCCACTACGACTATTACCC
43399768 GCATTACCAG
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 84 1.00
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.26
Consensus pattern (89 bp):
CCTCTCGAGCACAGATCGCATAAGCTTTAGTCGACACTGGTGCCTCAAATCTCACAGCAGAGCCT
TTCGTTCCACTACGACTATTACCC
Found at i:43413412 original size:15 final size:16
Alignment explanation
Indices: 43413392--43413432 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
43413382 TTTAAAAACA
* *
43413392 CATATCATAT-TATAT
1 CATATCATATACAGAT
43413407 CATATCA-ATACAGAT
1 CATATCATATACAGAT
43413422 CATATCATATA
1 CATATCATATA
43413433 ATAAATATGC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 2 0.09
15 17 0.77
16 3 0.14
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.37
Consensus pattern (16 bp):
CATATCATATACAGAT
Found at i:43419295 original size:20 final size:19
Alignment explanation
Indices: 43419248--43419297 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
43419238 CAATATAAAC
43419248 ATTAAATT-A-AATTTAAT
1 ATTAAATTAATAATTTAAT
43419265 ATTAAGA-TAATAACTTTAAT
1 ATTAA-ATTAATAA-TTTAAT
43419285 ATTAAATTAATAA
1 ATTAAATTAATAA
43419298 AATACTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.21
18 2 0.07
19 3 0.11
20 17 0.61
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
ATTAAATTAATAATTTAAT
Found at i:43426863 original size:39 final size:39
Alignment explanation
Indices: 43426779--43426888 Score: 150
Period size: 39 Copynumber: 2.8 Consensus size: 39
43426769 TTATCGAAAT
* *
43426779 CATTGTTATAATTGTTGTAATTATAA-TTTACGATCGAA
1 CATTATTATAATTGTTGTAATTATAATTTTACGATCAAA
* * *
43426817 TATTATTATAATTATTGTAATTATAATTTTTCGATCAAA
1 CATTATTATAATTGTTGTAATTATAATTTTACGATCAAA
*
43426856 CATTATTATAATTGTGGTAATTATAATTATTAC
1 CATTATTATAATTGTTGTAATTATAATT-TTAC
43426889 ATTCGGTTAA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 23 0.38
39 35 0.57
40 3 0.05
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (39 bp):
CATTATTATAATTGTTGTAATTATAATTTTACGATCAAA
Found at i:43433759 original size:26 final size:26
Alignment explanation
Indices: 43433699--43433759 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
43433689 TATCCGGAGC
* *
43433699 TCCTGATTAAAAGCTCTTCGTGAGCT
1 TCCTGATTAAAAGCTCTTCATGAACT
* * * *
43433725 TCTTAATTAAAAGTTCTTTATGAACT
1 TCCTGATTAAAAGCTCTTCATGAACT
43433751 TCCTGATTA
1 TCCTGATTA
43433760 TTACTCTTAT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (26 bp):
TCCTGATTAAAAGCTCTTCATGAACT
Found at i:43437887 original size:39 final size:39
Alignment explanation
Indices: 43437683--43437905 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
43437673 TTGAATGCTG
* * * * * *
43437683 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
43437723 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
43437763 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
*
43437803 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
43437843 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
43437882 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
43437906 TGAACGAGGA
Statistics
Matches: 154, Mismatches: 22, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
39 38 0.25
40 106 0.69
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:43437925 original size:79 final size:80
Alignment explanation
Indices: 43437763--43437940 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
43437753 AGATACAAGT
* * * *
43437763 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
43437828 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
43437843 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
43437907 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
43437922 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
43437941 TATGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:43450881 original size:41 final size:43
Alignment explanation
Indices: 43450768--43450900 Score: 164
Period size: 45 Copynumber: 3.0 Consensus size: 43
43450758 AGGATTTTTG
* *
43450768 ATATGTGTTCTCGTGTAAGACCACGTCTGGGACGATGGCATCGAT
1 ATATGTGAT-TCGTGTAAGACCATGTCTGGGAC-ATGGCATCGAT
*
43450813 ATATGTGATTACGTGTAAGACCATGTCTAGGACATTGGCATCG-T
1 ATATGTGATT-CGTGTAAGACCATGTCTGGGACA-TGGCATCGAT
*
43450857 AT-T-TGATTCGTGTAAGACCTTGTCTGGGACAGTGGCATCGAT
1 ATATGTGATTCGTGTAAGACCATGTCTGGGACA-TGGCATCGAT
43450899 AT
1 AT
43450901 GAGATAGCAT
Statistics
Matches: 79, Mismatches: 6, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
41 29 0.37
42 8 0.10
43 1 0.01
44 5 0.06
45 36 0.46
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
ATATGTGATTCGTGTAAGACCATGTCTGGGACATGGCATCGAT
Found at i:43460257 original size:46 final size:46
Alignment explanation
Indices: 43460148--43460281 Score: 112
Period size: 46 Copynumber: 2.9 Consensus size: 46
43460138 CAGGTGAAAG
* * * ** *
43460148 TAATAGTGCCCGGTTACCCGTTTGGGTTAAACCTACACGAATAAT-GAA
1 TAATAGTGCCAGGTCACCCATTAAGGTTGAACCTACAC--A-AATCGAA
* * *
43460196 TCATAGTGTCAGGTCA-CC-TGTAAGGGTTGAACCTATACAAATCGAA
1 TAATAGTGCCAGGTCACCCAT-TAA-GGTTGAACCTACACAAATCGAA
*
43460242 TAATAGTGCCTGGTCACCCATTAAGGTTGAACCTACACAA
1 TAATAGTGCCAGGTCACCCATTAAGGTTGAACCTACACAA
43460282 CAAATTGTCT
Statistics
Matches: 69, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
45 3 0.04
46 33 0.48
47 8 0.12
48 25 0.36
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (46 bp):
TAATAGTGCCAGGTCACCCATTAAGGTTGAACCTACACAAATCGAA
Found at i:43464202 original size:36 final size:36
Alignment explanation
Indices: 43464150--43464226 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 36
43464140 AATCCCAATA
*
43464150 AAAATCTAATAATAATTA-AAAATTAAAAATGTTAAT
1 AAAATCTAATAATAATTATAAAA-TAAAAACGTTAAT
* *
43464186 GAAAATCTCA-AATAATTATAAAATAATAACGTTAAT
1 -AAAATCTAATAATAATTATAAAATAAAAACGTTAAT
43464222 AAAAT
1 AAAAT
43464227 TTTAAAATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 5 0.14
36 19 0.53
37 12 0.33
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (36 bp):
AAAATCTAATAATAATTATAAAATAAAAACGTTAAT
Found at i:43465201 original size:22 final size:22
Alignment explanation
Indices: 43465176--43465219 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
43465166 CTTCTTCAAA
43465176 AAAGAAAAGATCTTTTCCAGAT
1 AAAGAAAAGATCTTTTCCAGAT
43465198 AAAGAAAAGATCTTTTCCAGAT
1 AAAGAAAAGATCTTTTCCAGAT
43465220 TTATTTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (22 bp):
AAAGAAAAGATCTTTTCCAGAT
Found at i:43477563 original size:86 final size:86
Alignment explanation
Indices: 43477473--43477653 Score: 355
Period size: 86 Copynumber: 2.1 Consensus size: 86
43477463 AATATAATTG
43477473 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
1 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
43477538 TGTTAAGTATTAATGTTGATA
66 TGTTAAGTATTAATGTTGATA
43477559 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
1 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
43477624 TGTTAAGTATTAATGTTGATA
66 TGTTAAGTATTAATGTTGATA
43477645 TAATT-TTAT
1 TAATTATTAT
43477654 GTGGAGAGAA
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 4 0.04
86 91 0.96
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (86 bp):
TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
TGTTAAGTATTAATGTTGATA
Found at i:43477795 original size:51 final size:51
Alignment explanation
Indices: 43477720--43477924 Score: 378
Period size: 51 Copynumber: 4.0 Consensus size: 51
43477710 TATACGTAAA
43477720 AATTAT-CATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAAC
1 AATTATACATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAAC
43477770 AATTATACATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAAC
1 AATTATACATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAAC
*
43477821 AATTATACATACACCAACAATATTTTTTAGGGTAAATAACATTAAACCAAC
1 AATTATACATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAAC
43477872 AATTATACATACACCAACAATGTTTTTTAGGG-ACAATAACATTAAACCAAC
1 AATTATACATACACCAACAATGTTTTTTAGGGTA-AATAACATTAAACCAAC
43477923 AA
1 AA
43477925 GTAATTTTGG
Statistics
Matches: 151, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
50 7 0.05
51 144 0.95
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.29
Consensus pattern (51 bp):
AATTATACATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAAC
Found at i:43477975 original size:33 final size:33
Alignment explanation
Indices: 43477871--43477979 Score: 127
Period size: 33 Copynumber: 3.3 Consensus size: 33
43477861 ATTAAACCAA
* *
43477871 CAATTATACATACACCAACAATGT-TTTTTAGGGA
1 CAATTATACATACACCAACAAT-TAATTTTA-GGT
* *
43477905 CAA-TA-ACATTAAACCAACAAGTAATTTT-GGT
1 CAATTATACA-TACACCAACAATTAATTTTAGGT
43477936 CAATTATACATACACCAACAATTAATTTTAGGT
1 CAATTATACATACACCAACAATTAATTTTAGGT
43477969 CAATTATACAT
1 CAATTATACAT
43477980 GCTTTATAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
31 5 0.08
32 23 0.36
33 33 0.52
34 3 0.05
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.32
Consensus pattern (33 bp):
CAATTATACATACACCAACAATTAATTTTAGGT
Found at i:43481063 original size:29 final size:28
Alignment explanation
Indices: 43481030--43481116 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
43481020 TCATAAGAAC
43481030 ATTTTATGAAATTATATTTAATAATAATT
1 ATTTTAT-AAATTATATTTAATAATAATT
* * *
43481059 A-TTT-TAAATTGTATTAAATCAT-A-T
1 ATTTTATAAATTATATTTAATAATAATT
* *
43481083 ATTTTAATTAAAATATATTTAATATTAATT
1 ATTTT-A-TAAATTATATTTAATAATAATT
43481113 ATTT
1 ATTT
43481117 CAAATTTTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
24 2 0.05
25 4 0.09
26 14 0.32
27 1 0.02
28 16 0.36
29 2 0.05
30 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (28 bp):
ATTTTATAAATTATATTTAATAATAATT
Found at i:43481292 original size:67 final size:66
Alignment explanation
Indices: 43481217--43481429 Score: 161
Period size: 67 Copynumber: 3.2 Consensus size: 66
43481207 ATTATAATGT
*
43481217 ATTT-AATAATAATTTTGTTTAAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTA
1 ATTTAAATAATAATTATGTTTAAATATGATTAAA-TATTTATTATTGATATTAATAATCTTATTA
43481281 AA
65 AA
* * * * * * *
43481283 ATTTAAATAACAA-TATG--TAATTTCTGCTAATTATAAGAATT-TTATT-AAATT-ATATATTT
1 ATTTAAATAATAATTATGTTTAA-ATATG---ATTA-AATATTTATTATTGATATTAATA-ATCT
43481342 TAATTAAAA
60 T-ATT-AAA
* * * *
43481351 TATATTTAATAATAATTATATTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTAT
1 -AT-TTAAATAATAATTATGTTTAAATATGATT-AAATATTTATTATTGATATTAATAATCTTAT
43481416 TAAA
63 TAAA
43481420 ATTTAAATAA
1 ATTTAAATAA
43481430 CATTAACAAT
Statistics
Matches: 109, Mismatches: 20, Indels: 35
0.66 0.12 0.21
Matches are distributed among these distances:
64 3 0.03
65 6 0.06
66 15 0.14
67 22 0.20
68 12 0.11
69 15 0.14
70 17 0.16
71 10 0.09
72 6 0.06
73 3 0.03
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (66 bp):
ATTTAAATAATAATTATGTTTAAATATGATTAAATATTTATTATTGATATTAATAATCTTATTAA
A
Found at i:43481327 original size:137 final size:138
Alignment explanation
Indices: 43481173--43481431 Score: 412
Period size: 137 Copynumber: 1.9 Consensus size: 138
43481163 TAAGAATATG
* * * *
43481173 AATTATTAAGAATTTTATTAAATTATATACCAAAATTATAATGTATTTAATAATAATTTTGTTTA
1 AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAATTATATTTA
* * *
43481238 AATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATATGTAA
66 AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATATGTAA
43481303 TTTCTGCT
131 TTTCTGCT
****
43481311 AATTA-TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATATTTA
1 AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAATTATATTTA
43481375 AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACA
66 AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACA
43481432 TTAACAATAA
Statistics
Matches: 110, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
137 105 0.95
138 5 0.05
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (138 bp):
AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAATTATATTTA
AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATATGTAA
TTTCTGCT
Found at i:43481349 original size:18 final size:18
Alignment explanation
Indices: 43481321--43481371 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
43481311 AATTATAAGA
43481321 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
43481338 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
*
43481354 A-TTTAATAATAATTATAT
1 ATTTTAATTA-AATTATAT
43481372 TTAAATATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 7 0.24
16 7 0.24
17 5 0.17
18 10 0.34
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:43481471 original size:137 final size:139
Alignment explanation
Indices: 43481206--43481524 Score: 332
Period size: 137 Copynumber: 2.3 Consensus size: 139
43481196 TATATACCAA
* * * * * * *
43481206 AATTATAATGTATTTAATAATAATTTTGTTTAAATATGATTAAATTATTTATTATTGATATTAAT
1 AATTAAAATATATTTAATAATAATTATATTTAAATATGATTAAAATATTTATTACTGATAATAAT
** * ** * *
43481271 AATCTTATTAAAATTTAAATAACAATATGTAATTTCTGCTAATTATAAGAATTTTATTAAATTAT
66 AATCTTATTAAAATTTAAATAACAATATACAATATCTGCTAACCAAAACAATTTTATTAAATTAT
*
43481336 -A-TATTTT
131 AAGCATTTT
43481343 AATTAAAATATATTTAATAATAATTATATTTAAATATGATTAAAATATTTATTACTGATAATAAT
1 AATTAAAATATATTTAATAATAATTATATTTAAATATGATTAAAATATTTATTACTGATAATAAT
* *
43481408 AATCTTATTAAAATTTAAATAACATTA-ACAATAATCAT-CT-ACCAAAACAATTTTCTGCT-AA
66 AATCTTATTAAAATTTAAATAACAATATACAAT-ATC-TGCTAACCAAAACAATTTTAT--TAAA
43481469 TTATAAGCATTTT
127 TTATAAGCATTTT
* *
43481482 -ATTAAATTATATATTTTAATTAA-AA-TATATTTAATTATAATTA
1 AATTAAA--ATATA-TTTAA-TAATAATTATATTTAAATATGATTA
43481525 TGTTTAAATA
Statistics
Matches: 153, Mismatches: 19, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
136 14 0.09
137 94 0.61
138 9 0.06
139 5 0.03
140 21 0.14
141 7 0.05
142 3 0.02
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.46
Consensus pattern (139 bp):
AATTAAAATATATTTAATAATAATTATATTTAAATATGATTAAAATATTTATTACTGATAATAAT
AATCTTATTAAAATTTAAATAACAATATACAATATCTGCTAACCAAAACAATTTTATTAAATTAT
AAGCATTTT
Found at i:43481481 original size:156 final size:156
Alignment explanation
Indices: 43481303--43481624 Score: 572
Period size: 156 Copynumber: 2.1 Consensus size: 156
43481293 CAATATGTAA
43481303 TTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATT
1 TTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATT
*
43481368 ATATTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAT
66 ATATTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAA
43481433 TAACAATAATCATCTACCAAAACAAT
131 TAACAATAATCATCTACCAAAACAAT
* *
43481459 TTTCTGCTAATTATAAGCATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTATAATT
1 TTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATT
* *
43481524 ATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTTTTAAAATTTAAATAACAA
66 ATATTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAA
* *
43481589 TAACAATAATCATTTACCAAAATAAT
131 TAACAATAATCATCTACCAAAACAAT
*
43481615 TTTATGCTAA
1 TTTCTGCTAA
43481625 GGGTATTCTA
Statistics
Matches: 158, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
156 158 1.00
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (156 bp):
TTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATT
ATATTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAA
TAACAATAATCATCTACCAAAACAAT
Found at i:43481505 original size:18 final size:18
Alignment explanation
Indices: 43481477--43481525 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 18
43481467 AATTATAAGC
43481477 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
43481494 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
43481510 A-TTTAATTATAATTAT
1 ATTTTAATTA-AATTAT
43481526 GTTTAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 8 0.29
16 7 0.25
17 5 0.18
18 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:43481511 original size:16 final size:16
Alignment explanation
Indices: 43481477--43481531 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
43481467 AATTATAAGC
43481477 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
43481494 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
43481510 A-TTTAATTATAAT-T
1 ATTTTAATTAAAATAT
43481524 ATGTTTAA
1 AT-TTTAA
43481532 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:43481768 original size:16 final size:16
Alignment explanation
Indices: 43481747--43481782 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
43481737 AATTGGCTAT
43481747 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
43481763 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
43481779 TACA
1 TACA
43481783 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:43482814 original size:18 final size:18
Alignment explanation
Indices: 43482788--43482825 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
43482778 AAATAATTTT
*
43482788 AATATTAAATAATTAATG
1 AATAGTAAATAATTAATG
43482806 AATAGTAAATAATTAATG
1 AATAGTAAATAATTAATG
43482824 AA
1 AA
43482826 AAACATACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (18 bp):
AATAGTAAATAATTAATG
Found at i:43486542 original size:5 final size:5
Alignment explanation
Indices: 43486534--43486562 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
43486524 CATATCATCA
43486534 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
43486563 AGCTGTCTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:43495469 original size:15 final size:15
Alignment explanation
Indices: 43495449--43495480 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
43495439 CATTTCACTA
*
43495449 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
43495464 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
43495479 TT
1 TT
43495481 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:43496610 original size:15 final size:14
Alignment explanation
Indices: 43496582--43496608 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43496572 GAATTTTGTT
43496582 GAAAAATTAATTTG
1 GAAAAATTAATTTG
43496596 GAAAAATTAATTT
1 GAAAAATTAATTT
43496609 TGATCAAGTA
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:0.00, G:0.11, T:0.37
Consensus pattern (14 bp):
GAAAAATTAATTTG
Found at i:43497249 original size:59 final size:61
Alignment explanation
Indices: 43497133--43497249 Score: 157
Period size: 62 Copynumber: 1.9 Consensus size: 61
43497123 AATAATTATA
* * *
43497133 TTAATATTAAATTTAATTTAATGTTTATCTATAAGATAAACATTATATTATTTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTTA-CTATAAGATAAACATTATATTAATTTAATAAGAT
* * *
43497195 TTAATATTAAATTTAATCTGATATTTA-TAT-TGATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTACTATAAGATAAACATTATATTAATTTAATA
43497250 TTAAAGTAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 22 0.45
60 3 0.06
62 24 0.49
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.50
Consensus pattern (61 bp):
TTAATATTAAATTTAATCTAATATTTACTATAAGATAAACATTATATTAATTTAATAAGAT
Found at i:43499457 original size:22 final size:21
Alignment explanation
Indices: 43499408--43499461 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
43499398 CTAATAATTT
* *
43499408 TTTTTTCATTTTTTAAAAATTA
1 TTTTTT-ATTTTTAAAAAATCA
*
43499430 TCTTTTATTTTTAAAAAATACA
1 TTTTTTATTTTTAAAAAAT-CA
43499452 TTTTTTATTT
1 TTTTTTATTT
43499462 CTCAAGATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTTTATTTTTAAAAAATCA
Found at i:43502044 original size:2 final size:2
Alignment explanation
Indices: 43502037--43502063 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43502027 TCGCAAATCA
43502037 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
43502064 TGACGATGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:43507835 original size:12 final size:12
Alignment explanation
Indices: 43507818--43507848 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
43507808 ATAATTTCTT
43507818 TTTTATTTTAAA
1 TTTTATTTTAAA
43507830 TTTTATTTTAAA
1 TTTTATTTTAAA
43507842 TTTTATT
1 TTTTATT
43507849 ATTTTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTATTTTAAA
Found at i:43518539 original size:45 final size:44
Alignment explanation
Indices: 43518473--43518627 Score: 220
Period size: 45 Copynumber: 3.4 Consensus size: 44
43518463 AGTATACAGT
* * *
43518473 AATCAGTAACGGTAGCAGTAACAGTATTCAACACACAAAGTGCTG
1 AATC-GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTG
* * *
43518518 AATCTGTAACAGTAACGGTAACGGTATTCGACACACAAAGTGCCG
1 AATC-GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTG
43518563 AATCGATAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTG
1 AATCG-TAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTG
43518608 AATCAGTAACAGTAACAGTA
1 AATC-GTAACAGTAACAGTA
43518628 GTCGGCACAT
Statistics
Matches: 98, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
44 1 0.01
45 96 0.98
46 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (44 bp):
AATCGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTG
Found at i:43518578 original size:39 final size:40
Alignment explanation
Indices: 43518488--43518654 Score: 142
Period size: 45 Copynumber: 4.0 Consensus size: 40
43518478 GTAACGGTAG
* *
43518488 CAGTAACAGTATTCAACACACAAAGTGCTGAATCTGTAACAGTAA
1 CAGTAACAGTATTCGACACACAAAGTGCCGAATC-G----AGTAA
* *
43518533 CGGTAACGGTATTCGACACACAAAGTGCCGAATCGATAACAGTAA
1 CAGTAACAGTATTCGACACACAAAGTGCCGAATCG-----AGTAA
*
43518578 CAGTAACAGTATTCGACACACAAAGTGCTGAATC-AGTAA
1 CAGTAACAGTATTCGACACACAAAGTGCCGAATCGAGTAA
* * * *
43518617 CAGTAACAGTAGTCGGCACA-TAAGTGCCTAATC-AGTAA
1 CAGTAACAGTATTCGACACACAAAGTGCCGAATCGAGTAA
43518655 GCCGGCAAAT
Statistics
Matches: 109, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
38 15 0.14
39 23 0.21
44 1 0.01
45 70 0.64
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (40 bp):
CAGTAACAGTATTCGACACACAAAGTGCCGAATCGAGTAA
Found at i:43520165 original size:18 final size:18
Alignment explanation
Indices: 43520144--43520180 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
43520134 AAAGGAAGAC
43520144 AGAAAAAGA-AATCGAAAA
1 AGAAAAAGAGAAT-GAAAA
43520162 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
43520180 A
1 A
43520181 AGAGCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.73, C:0.03, G:0.19, T:0.05
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:43521987 original size:33 final size:35
Alignment explanation
Indices: 43521950--43522021 Score: 105
Period size: 33 Copynumber: 2.1 Consensus size: 35
43521940 GAGTTAGTTT
*
43521950 ATTAAATTTT-GTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTTAGTTCAGCTCAAATAAGTGCTAGTA
*
43521983 ATT-AATTTTAGTTCAGCTTAAATAAGTGCTAGTA
1 ATTAAATTTTAGTTCAGCTCAAATAAGTGCTAGTA
43522017 ATTAA
1 ATTAA
43522022 TTTGTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 6 0.18
33 23 0.68
34 4 0.12
35 1 0.03
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (35 bp):
ATTAAATTTTAGTTCAGCTCAAATAAGTGCTAGTA
Found at i:43533258 original size:41 final size:43
Alignment explanation
Indices: 43533182--43533274 Score: 136
Period size: 41 Copynumber: 2.2 Consensus size: 43
43533172 TCCCAGACGT
* * *
43533182 GGTCTTACATGTAATCACATATCGATGCCACTGTCCTAGACAG
1 GGTCTTACACGTAATCAAATATCGATGCCAATGTCCTAGACAG
*
43533225 GGTCTTACACG-AATCAAATA-CGATGCCAATGTCCTAGACAT
1 GGTCTTACACGTAATCAAATATCGATGCCAATGTCCTAGACAG
43533266 GGTCTTACA
1 GGTCTTACA
43533275 TGAAAACACA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 28 0.61
42 8 0.17
43 10 0.22
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (43 bp):
GGTCTTACACGTAATCAAATATCGATGCCAATGTCCTAGACAG
Found at i:43534217 original size:15 final size:14
Alignment explanation
Indices: 43534180--43534223 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
43534170 TTTTATTATA
43534180 ATAACTTTATAATAT
1 ATAACTTTATAAT-T
*
43534195 ATAA-TTTATTATT
1 ATAACTTTATAATT
43534208 ATAACCTTTATAATT
1 ATAA-CTTTATAATT
43534223 A
1 A
43534224 ATATAAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 5 0.20
14 7 0.28
15 13 0.52
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAACTTTATAATT
Found at i:43548488 original size:40 final size:40
Alignment explanation
Indices: 43548392--43548509 Score: 116
Period size: 40 Copynumber: 3.0 Consensus size: 40
43548382 AGATGCATAA
* *
43548392 CAGAGGCATCGAAGTGCGAACAGAGGCA-CGAATGTGCAGG
1 CAGAGGCATCGAAGTGCGAATAGAGACACCGAA-GTGCAGG
* * * * *
43548432 TAGAGGCA-CCATAGTGCGATTAGAGACACCGAAGTGTATG
1 CAGAGGCATCGA-AGTGCGAATAGAGACACCGAAGTGCAGG
*
43548472 CAGAGGCATCGAAGTGCAAATAGAGGA-ACCGAAGTGCA
1 CAGAGGCATCGAAGTGCGAATAGA-GACACCGAAGTGCA
43548510 AACCCGTACA
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
39 2 0.03
40 52 0.84
41 8 0.13
ACGTcount: A:0.35, C:0.19, G:0.33, T:0.14
Consensus pattern (40 bp):
CAGAGGCATCGAAGTGCGAATAGAGACACCGAAGTGCAGG
Found at i:43548496 original size:20 final size:19
Alignment explanation
Indices: 43548393--43548511 Score: 67
Period size: 20 Copynumber: 5.9 Consensus size: 19
43548383 GATGCATAAC
* *
43548393 AGAGGCATCGAAGTGCGAAC
1 AGAGGCA-CGAAGTGCAAAT
**
43548413 AGAGGCACGAATGTGCAGGT
1 AGAGGCACGAA-GTGCAAAT
* * *
43548433 AGAGGCACCATAGTGCGATT
1 AGAGGCACGA-AGTGCAAAT
* * ***
43548453 AGAGACACCGAAGTGTATGC
1 AGAGGCA-CGAAGTGCAAAT
43548473 AGAGGCATCGAAGTGCAAAT
1 AGAGGCA-CGAAGTGCAAAT
*
43548493 AGAGGAACCGAAGTGCAAA
1 AGAGGCA-CGAAGTGCAAA
43548512 CCCGTACAAG
Statistics
Matches: 73, Mismatches: 23, Indels: 6
0.72 0.23 0.06
Matches are distributed among these distances:
19 4 0.05
20 66 0.90
21 3 0.04
ACGTcount: A:0.36, C:0.18, G:0.33, T:0.13
Consensus pattern (19 bp):
AGAGGCACGAAGTGCAAAT
Done.