Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 207 of 345
Found at i:59506466 original size:37 final size:37
Alignment explanation
Indices: 59506416--59506498 Score: 139
Period size: 37 Copynumber: 2.2 Consensus size: 37
59506406 GGAATATGTT
* *
59506416 CCGGGTGAGACCCGATGACTACGTGTGGAGATTATGA
1 CCGGGTAAGACCCGATGACTACGTATGGAGATTATGA
*
59506453 CCGGGTAAGACCCGATGACTACGTATGGAGATTATGT
1 CCGGGTAAGACCCGATGACTACGTATGGAGATTATGA
59506490 CCGGGTAAG
1 CCGGGTAAG
59506499 GCTTCTTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.22
Consensus pattern (37 bp):
CCGGGTAAGACCCGATGACTACGTATGGAGATTATGA
Found at i:59511530 original size:31 final size:31
Alignment explanation
Indices: 59511492--59511609 Score: 137
Period size: 31 Copynumber: 3.8 Consensus size: 31
59511482 ACAAATGACA
* **
59511492 AGTGAAAAGTGGTAGCTTTTGCTACCTGATC
1 AGTGAAAAATGGTAGCTTCAGCTACCTGATC
*** *
59511523 AGTGAAAAATGGTAGCCGGAGCTACCTGATT
1 AGTGAAAAATGGTAGCTTCAGCTACCTGATC
*
59511554 AGTGAAAAATGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAATGGTAGCTTCAGCTACCTGATC
* * *
59511585 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAATGGTAGCTTCAGCTAC
59511610 AAGTGACAAG
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 74 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (31 bp):
AGTGAAAAATGGTAGCTTCAGCTACCTGATC
Found at i:59511728 original size:46 final size:46
Alignment explanation
Indices: 59511631--59511797 Score: 176
Period size: 46 Copynumber: 3.6 Consensus size: 46
59511621 GATTTCCGTA
* * * *
59511631 TAAGACCATATCTGGGATATGACAT-AGTGTGATATATGCTATT-GTA
1 TAAGACCATAGCTGGGATATGGCATCAGTGTGATATGTG--ATTCGTG
* * *
59511677 TAAGACCATATCTAGGATATGGCATCAGTGAGATATGTGATTCGTG
1 TAAGACCATAGCTGGGATATGGCATCAGTGTGATATGTGATTCGTG
* * *
59511723 CAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTACGTG
1 TAAGACCATAGCTGGGATATGGCATC-A-GTGTGATATGTGATT-CGTG
*
59511772 TAAGACCATAGCTGGGCTATGGCATC
1 TAAGACCATAGCTGGGATATGGCATC
59511798 GATATATGAA
Statistics
Matches: 104, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
45 3 0.03
46 47 0.45
47 12 0.12
48 13 0.12
49 29 0.28
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (46 bp):
TAAGACCATAGCTGGGATATGGCATCAGTGTGATATGTGATTCGTG
Found at i:59511783 original size:49 final size:48
Alignment explanation
Indices: 59511677--59511812 Score: 177
Period size: 49 Copynumber: 2.8 Consensus size: 48
59511667 TGCTATTGTA
* * * * *
59511677 TAAGACCATATCTAGGATATGGCATC-A-GTGAGATATGTGATTCGTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTCGTG
*
59511723 CAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTACGTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATT-CGTG
*
59511772 TAAGACCATAGCTGGGCTATGGCATCGATATATGAATATGT
1 TAAGACCATAGCTGGGCTATGGCATCGATATGTG-ATATGT
59511813 TTAAGACCAT
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
46 22 0.28
47 1 0.01
48 13 0.17
49 36 0.46
50 6 0.08
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (48 bp):
TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTCGTG
Found at i:59511818 original size:42 final size:42
Alignment explanation
Indices: 59511769--59511882 Score: 149
Period size: 42 Copynumber: 2.7 Consensus size: 42
59511759 ATGTGATTAC
* * *
59511769 GTGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAATAT
1 GTGTAAGACCATAGTTGGACTATGGCATC-ATTATATGAAGAT
* * *
59511811 GTTTAAGACCATAGTTGGCCTATGGCATCATTATGTGAAGAT
1 GTGTAAGACCATAGTTGGACTATGGCATCATTATATGAAGAT
*
59511853 GTGTAAGACCATAGTTGAACTATGGCATCA
1 GTGTAAGACCATAGTTGGACTATGGCATCA
59511883 AGAAAACGAA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 1 0.02
42 62 0.98
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.30
Consensus pattern (42 bp):
GTGTAAGACCATAGTTGGACTATGGCATCATTATATGAAGAT
Found at i:59534823 original size:13 final size:13
Alignment explanation
Indices: 59534805--59534830 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59534795 AGGGATTTGT
59534805 TTATCTAAACTAA
1 TTATCTAAACTAA
59534818 TTATCTAAACTAA
1 TTATCTAAACTAA
59534831 GGGTGCACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:59540514 original size:30 final size:30
Alignment explanation
Indices: 59540459--59540589 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
59540449 ATAGTGAATC
*
59540459 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
*
59540488 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
59540518 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AACT
* * * *
59540546 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAACT
59540576 CGCACACTTAGTGC
1 CGCACACTTAGTGC
59540590 CAATCTTGTC
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 19 0.21
30 48 0.52
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAACT
Found at i:59540569 original size:58 final size:58
Alignment explanation
Indices: 59540458--59540589 Score: 176
Period size: 58 Copynumber: 2.3 Consensus size: 58
59540448 TATAGTGAAT
* * * * *
59540458 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGC
1 CCGCACACTTAGTGCTATATA-TATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
* *
59540517 TCGCACACTTAGTGCTATATA-ATCAAACTCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATATATATC-AACTCGCACACTTAGTGCTATACAATTTTAAAC
59540575 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
59540590 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 2 0.03
58 42 0.66
59 20 0.31
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (58 bp):
CCGCACACTTAGTGCTATATATATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
Found at i:59550130 original size:40 final size:40
Alignment explanation
Indices: 59550022--59550172 Score: 155
Period size: 39 Copynumber: 3.8 Consensus size: 40
59550012 CGAATGGTAT
* * * *
59550022 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAAA
* *
59550063 CCGGG-TCAA-TTCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGCT-AAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* * *
59550102 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCTA-TTAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* * *
59550141 CCGGGCTATGTCCCGAAGGCTTTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
59550173 CGCTATATCC
Statistics
Matches: 92, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
39 45 0.49
40 40 0.43
41 7 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
Found at i:59550142 original size:39 final size:38
Alignment explanation
Indices: 59550022--59550172 Score: 144
Period size: 40 Copynumber: 3.8 Consensus size: 38
59550012 CGAATGGTAT
* *
59550022 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGT-ACTAAA
* *
59550062 TCCGGG-TCAA-TTCCGAAGGCATTTGTGCGAGTTACCAAAA
1 -CCGGGCT-AAGTCCCGAAGGCATTTGTGCGAG-TA-CTAAA
* *
59550102 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCTATTAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTAAA
* * *
59550141 CCGGGCTATGTCCCGAAGGCTTTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
59550173 CGCTATATCC
Statistics
Matches: 93, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
38 1 0.01
39 40 0.43
40 45 0.48
41 7 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTAAA
Found at i:59558127 original size:40 final size:40
Alignment explanation
Indices: 59558031--59558183 Score: 164
Period size: 40 Copynumber: 3.8 Consensus size: 40
59558021 CGAATGGTAT
* * * *
59558031 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAAA
* *
59558072 CCGGG-TCAATTCCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGCT-AAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* * * *
59558112 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCTATTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* * *
59558152 CCGGGCTATGTCCCGAAGGCTTTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
59558184 CGCTATATCC
Statistics
Matches: 94, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 69 0.73
41 25 0.27
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
Found at i:59563750 original size:40 final size:40
Alignment explanation
Indices: 59563695--59563831 Score: 215
Period size: 40 Copynumber: 3.5 Consensus size: 40
59563685 CGGATGATAA
*
59563695 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTGTAT
59563735 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTGTAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTGTAT
* * *
59563775 CCGGGCTAGGACCCGAAGGCAGTTGTGCGAGTTGTTGTAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTGTAT
59563815 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
59563832 ATACTTGGGT
Statistics
Matches: 91, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 78 0.86
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTGTAT
Found at i:59567616 original size:40 final size:41
Alignment explanation
Indices: 59567565--59567672 Score: 132
Period size: 40 Copynumber: 2.7 Consensus size: 41
59567555 TTTAACCGAA
* *
59567565 TATAACGACTCGCTCAAATGCCTTCGGGAC-GAAGCCC-GGT
1 TATAGCGACTCGCACAAATGCCTTCGGGACTGAA-CCCGGGT
* *
59567605 TATAGCGACTCGCACGAATGCCTTCGGGACTTAACCCGGGT
1 TATAGCGACTCGCACAAATGCCTTCGGGACTGAACCCGGGT
**
59567646 T-TAGTAACTCGCACAAATGCCTTCGGG
1 TATAGCGACTCGCACAAATGCCTTCGGG
59567673 CTTAGCCCGG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
40 53 0.90
41 6 0.10
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (41 bp):
TATAGCGACTCGCACAAATGCCTTCGGGACTGAACCCGGGT
Found at i:59567682 original size:79 final size:80
Alignment explanation
Indices: 59567572--59567763 Score: 212
Period size: 79 Copynumber: 2.4 Consensus size: 80
59567562 GAATATAACG
* ** * *
59567572 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGG-TTATAGCGACTCGCACGAATGCCTTCGGGA-C
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGCAACTCGCACGAACGCCTTC-GGATC
* *
59567635 TTAACCCGGGTTTAGTA
64 TTAACCCGGATATAGTA
**
59567652 ACTCGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAACGCCTTCGGATCTT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGCAACTCGCACGAACGCCTTCGGATCTT
** *
59567716 AGTCCGGATATAGTC
66 AACCCGGATATAGTA
*
59567731 ACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
59567764 CATCATTCAA
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 3 0.03
79 51 0.54
80 41 0.43
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.23
Consensus pattern (80 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGCAACTCGCACGAACGCCTTCGGATCTT
AACCCGGATATAGTA
Found at i:59570332 original size:30 final size:30
Alignment explanation
Indices: 59570277--59570436 Score: 222
Period size: 29 Copynumber: 5.5 Consensus size: 30
59570267 ATAGTGAATC
59570277 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
59570306 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
59570336 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
*
59570365 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AGCT
* * * * *
59570393 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
59570423 CGCACACTTAGTGC
1 CGCACACTTAGTGC
59570437 CAATCTTGTC
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.18
29 48 0.40
30 47 0.39
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:59570369 original size:59 final size:57
Alignment explanation
Indices: 59570277--59570436 Score: 223
Period size: 59 Copynumber: 2.8 Consensus size: 57
59570267 ATAGTGAATC
*
59570277 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTC-AGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA---TCAAACT
59570336 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
* * * * *
59570393 CGCACACTTAGTGCTGTACAATTTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATA-TATTTTCAGCTCGCACACTTAGTGC
59570437 CAATCTTGTC
Statistics
Matches: 93, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 21 0.23
59 50 0.54
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (57 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
Found at i:59574302 original size:15 final size:15
Alignment explanation
Indices: 59574278--59574309 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
59574268 TATGCATACA
*
59574278 AAATATAAAAGACAT
1 AAATACAAAAGACAT
59574293 AAATACAAAAGACAT
1 AAATACAAAAGACAT
59574308 AA
1 AA
59574310 TAGTGAAATG
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:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:59574838 original size:45 final size:46
Alignment explanation
Indices: 59574787--59574875 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 46
59574777 TTCCATTTTT
*
59574787 AGAAAACCACATTCATTTCTAAATG-ATTCCATTTCTCCATTTCGG
1 AGAAAACCACAATCATTTCTAAATGTATTCCATTTCTCCATTTCGG
* * * * *
59574832 AGAAAACCATAATCATTTTTTATTGTTTTCCATTTCTCCATTTC
1 AGAAAACCACAATCATTTCTAAATGTATTCCATTTCTCCATTTC
59574876 TATTCATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 20 0.54
46 17 0.46
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (46 bp):
AGAAAACCACAATCATTTCTAAATGTATTCCATTTCTCCATTTCGG
Found at i:59585494 original size:17 final size:17
Alignment explanation
Indices: 59585472--59585505 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
59585462 CACTAACATG
*
59585472 AAAATGTAATGACAATA
1 AAAATGCAATGACAATA
59585489 AAAATGCAATGACAATA
1 AAAATGCAATGACAATA
59585506 TATACTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:59587242 original size:26 final size:26
Alignment explanation
Indices: 59587213--59587263 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
59587203 CCATAAGAGC
* *
59587213 AAAACAATCATTTTACTCTTTAAGGA
1 AAAACAATCATTTTACCCTTCAAGGA
*
59587239 AAAACGATCATTTTACCCTTCAAGG
1 AAAACAATCATTTTACCCTTCAAGG
59587264 GTATTTCAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (26 bp):
AAAACAATCATTTTACCCTTCAAGGA
Found at i:59587318 original size:27 final size:27
Alignment explanation
Indices: 59587287--59587420 Score: 162
Period size: 27 Copynumber: 5.0 Consensus size: 27
59587277 CCTACCCTAT
* *
59587287 AAGGGTATTTTGGTAATTTCACAAATC
1 AAGGGTATTTTAGTAATTTTACAAATC
* * *
59587314 GAGGGTATTTCAATAATTTTACAAATC
1 AAGGGTATTTTAGTAATTTTACAAATC
*
59587341 AAGGGTATTTTGGTAATTTTACAAATC
1 AAGGGTATTTTAGTAATTTTACAAATC
* *
59587368 AAGGGTATCTTAGTAATTTTACAAGT-
1 AAGGGTATTTTAGTAATTTTACAAATC
* *
59587394 AGGGGGTATTTCAGTAATTTTACAAAT
1 A-AGGGTATTTTAGTAATTTTACAAAT
59587421 TAGGGGTTTT
Statistics
Matches: 90, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
26 1 0.01
27 89 0.99
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (27 bp):
AAGGGTATTTTAGTAATTTTACAAATC
Found at i:59587345 original size:81 final size:81
Alignment explanation
Indices: 59587258--59587420 Score: 193
Period size: 81 Copynumber: 2.0 Consensus size: 81
59587248 ATTTTACCCT
** * * *
59587258 TCAAGGGTATTTCAGTAATCCTACCCTAT-AAGGGTATTTTGGTAATTTCACAAATCGAGGGTAT
1 TCAAGGGTATTTCAGTAATCCTA-CAAATCAAGGGTATCTTAGTAATTTCACAAATAGAGGGTAT
59587322 TTCAATAATTTTACAAA
65 TTCAATAATTTTACAAA
** ** * * *
59587339 TCAAGGGTATTTTGGTAATTTTACAAATCAAGGGTATCTTAGTAATTTTACAAGTAGGGGGTATT
1 TCAAGGGTATTTCAGTAATCCTACAAATCAAGGGTATCTTAGTAATTTCACAAATAGAGGGTATT
*
59587404 TCAGTAATTTTACAAA
66 TCAATAATTTTACAAA
59587420 T
1 T
59587421 TAGGGGTTTT
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
80 3 0.04
81 65 0.96
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (81 bp):
TCAAGGGTATTTCAGTAATCCTACAAATCAAGGGTATCTTAGTAATTTCACAAATAGAGGGTATT
TCAATAATTTTACAAA
Found at i:59587385 original size:54 final size:53
Alignment explanation
Indices: 59587258--59587420 Score: 175
Period size: 54 Copynumber: 3.0 Consensus size: 53
59587248 ATTTTACCCT
* ** ** *
59587258 TCAAGGGTATTTCAGTAATCCTACCCTATAAGGGTATTTTGGTAATTTCACAAA
1 TCAAGGGTATTTCAATAATTTTA-CAAATAAGGGTATTTTGGTAATTTTACAAA
*
59587312 TCGAGGGTATTTCAATAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAA
1 TCAAGGGTATTTCAATAATTTTACAAAT-AAGGGTATTTTGGTAATTTTACAAA
* * * **
59587366 TCAAGGGTATCTT-AGTAATTTTACAAGTAGGGGGTATTTCAGTAATTTTACAAA
1 TCAAGGGTAT-TTCAATAATTTTACAAATA-AGGGTATTTTGGTAATTTTACAAA
59587420 T
1 T
59587421 TAGGGGTTTT
Statistics
Matches: 93, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
53 4 0.04
54 87 0.94
55 2 0.02
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (53 bp):
TCAAGGGTATTTCAATAATTTTACAAATAAGGGTATTTTGGTAATTTTACAAA
Found at i:59589085 original size:6 final size:6
Alignment explanation
Indices: 59589065--59589096 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
59589055 CCAACTCCCC
59589065 ATTCAA ATT-AA ATTCAA ATTC-A ATTCAA ATTC
1 ATTCAA ATTCAA ATTCAA ATTCAA ATTCAA ATTC
59589097 TTATGATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.42
6 14 0.58
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.38
Consensus pattern (6 bp):
ATTCAA
Found at i:59589096 original size:11 final size:11
Alignment explanation
Indices: 59589065--59589096 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
59589055 CCAACTCCCC
*
59589065 ATTCAAATTAA
1 ATTCAAATTCA
59589076 ATTCAAATTCA
1 ATTCAAATTCA
59589087 ATTCAAATTC
1 ATTCAAATTC
59589097 TTATGATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTCAAATTCA
Found at i:59589707 original size:21 final size:21
Alignment explanation
Indices: 59589681--59589723 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
59589671 TTCAGTAACT
59589681 TCTTCTGCAGCAGCAACTTCC
1 TCTTCTGCAGCAGCAACTTCC
* *
59589702 TCTTCTGTAGCATCAACTTCC
1 TCTTCTGCAGCAGCAACTTCC
59589723 T
1 T
59589724 TCTCAACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.12, T:0.35
Consensus pattern (21 bp):
TCTTCTGCAGCAGCAACTTCC
Found at i:59594769 original size:9 final size:9
Alignment explanation
Indices: 59594757--59594781 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
59594747 TATTTCATAT
59594757 ATTTATAAA
1 ATTTATAAA
59594766 ATTTATAAA
1 ATTTATAAA
59594775 ATTTATA
1 ATTTATA
59594782 TAATCACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
ATTTATAAA
Found at i:59599465 original size:40 final size:40
Alignment explanation
Indices: 59599420--59599587 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
59599410 CGGAATATAA
59599420 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
59599460 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
59599500 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
59599540 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
59599580 CCGGATAT
1 CCGGATAT
59599588 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:59607478 original size:40 final size:40
Alignment explanation
Indices: 59607433--59607600 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
59607423 CGGAATATAA
59607433 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
59607473 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
59607513 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
59607553 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
59607593 CCGGATAT
1 CCGGATAT
59607601 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:59615897 original size:40 final size:39
Alignment explanation
Indices: 59615852--59615982 Score: 129
Period size: 40 Copynumber: 3.3 Consensus size: 39
59615842 CGGAATATAA
59615852 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
59615892 CCGGATAGAATGTC-CCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA--TCACTGCACAAATGCCTTCGGGTCTTAGC
* ** * * * *
59615932 CCGGATGTAGCCACTAGCGCAATTGCCTTCGGGTCTCAAC
1 CCGGATATAATCACT-GCACAAATGCCTTCGGGTCTTAGC
59615972 CCGGATATAAT
1 CCGGATATAAT
59615983 TTCCAGCATA
Statistics
Matches: 71, Mismatches: 16, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 66 0.93
41 1 0.01
42 2 0.03
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (39 bp):
CCGGATATAATCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:59618213 original size:22 final size:22
Alignment explanation
Indices: 59618185--59618228 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
59618175 ACTCAAGTGT
59618185 TGGTAAAGTTTTTAGTTTGGTC
1 TGGTAAAGTTTTTAGTTTGGTC
59618207 TGGTAAAGTTTTTAGTTTGGTC
1 TGGTAAAGTTTTTAGTTTGGTC
59618229 AGGATATGTA
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:0.18, C:0.05, G:0.27, T:0.50
Consensus pattern (22 bp):
TGGTAAAGTTTTTAGTTTGGTC
Found at i:59630631 original size:71 final size:71
Alignment explanation
Indices: 59630547--59630710 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
59630537 CGATTTGTCT
59630547 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
59630612 CTTTCA
66 CTTTCA
59630618 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
59630683 CTTTCA
66 CTTTCA
59630689 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
59630711 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:59630748 original size:71 final size:70
Alignment explanation
Indices: 59630547--59630744 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
59630537 CGATTTGTCT
* * * *
59630547 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
59630612 CTTTCA
65 CTTTCA
* * * *
59630618 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
59630683 CTTTCA
65 CTTTCA
* *
59630689 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
59630745 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:59638209 original size:71 final size:71
Alignment explanation
Indices: 59638125--59638288 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
59638115 CGATTTGTCT
59638125 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
59638190 CTTTCA
66 CTTTCA
59638196 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
59638261 CTTTCA
66 CTTTCA
59638267 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
59638289 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:59638326 original size:71 final size:70
Alignment explanation
Indices: 59638125--59638322 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
59638115 CGATTTGTCT
* * * *
59638125 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
59638190 CTTTCA
65 CTTTCA
* * * *
59638196 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
59638261 CTTTCA
65 CTTTCA
* *
59638267 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
59638323 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:59643310 original size:21 final size:22
Alignment explanation
Indices: 59643269--59643312 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
59643259 TTACTTACAA
59643269 TTTAATATCTTATTATTAAAAC
1 TTTAATATCTTATTATTAAAAC
* *
59643291 TTTAATTTCTT-TTTTTAAAAC
1 TTTAATATCTTATTATTAAAAC
59643312 T
1 T
59643313 CAAGGTTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTAATATCTTATTATTAAAAC
Found at i:59645134 original size:2 final size:2
Alignment explanation
Indices: 59645127--59645159 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
59645117 ATAATTTCAG
59645127 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
59645160 TTCTTTCGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59646114 original size:21 final size:22
Alignment explanation
Indices: 59646089--59646137 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
59646079 ACAATTTCAA
59646089 ATTTTAAGT-AA-TATCATTAAT
1 ATTTTAAGTAAATTAT-ATTAAT
*
59646110 ATTTT-ATTAAATTATATTAAT
1 ATTTTAAGTAAATTATATTAAT
59646131 ATTTTAA
1 ATTTTAA
59646138 TAGTTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.08
21 18 0.75
22 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTTTAAGTAAATTATATTAAT
Found at i:59651243 original size:46 final size:46
Alignment explanation
Indices: 59651193--59651368 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
59651183 TGTTTGGGCA
59651193 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * *
59651239 TCCGAACTCGTTGAGTTGAGTCCGAGTT--C-GA-GAGATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCAA--ATG
* * *
59651284 CATTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* *
59651332 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
59651369 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 1 0.01
43 7 0.06
44 1 0.01
45 2 0.02
46 63 0.57
47 26 0.24
48 2 0.02
49 1 0.01
50 6 0.05
51 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:59651348 original size:93 final size:93
Alignment explanation
Indices: 59651189--59651360 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
59651179 AGGATGTTTG
*
59651189 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAG
59651254 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * * *
59651282 GGCATTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAG
59651347 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
59651361 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:59654801 original size:20 final size:20
Alignment explanation
Indices: 59654752--59654807 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
59654742 GCTTGTATGG
*
59654752 GTTTGCACTTCAGTGCCTCT
1 GTTTGCACTTTAGTGCCTCT
* * *
59654772 G-TTACACTTTGGTGTCTCT
1 GTTTGCACTTTAGTGCCTCT
59654791 GTTTGCACTTTAGTGCC
1 GTTTGCACTTTAGTGCC
59654808 CTTGATTGCA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.43
Consensus pattern (20 bp):
GTTTGCACTTTAGTGCCTCT
Found at i:59678206 original size:40 final size:40
Alignment explanation
Indices: 59678147--59678288 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
59678137 AAATTGAATG
* * *
59678147 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
59678187 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
59678227 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
59678267 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
59678289 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:59678289 original size:40 final size:39
Alignment explanation
Indices: 59678186--59678314 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
59678176 TGCTGGAAAT
* * *
59678186 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
59678226 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
59678266 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
59678306 TATATCCGG
1 TATATCCGG
59678315 TTATATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:59686210 original size:40 final size:40
Alignment explanation
Indices: 59686144--59686310 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
59686134 AAATTGAATG
* * *
59686144 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
59686183 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
59686223 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
59686263 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
59686303 ATATCCGG
1 ATATCCGG
59686311 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:59693866 original size:80 final size:80
Alignment explanation
Indices: 59693730--59693935 Score: 225
Period size: 80 Copynumber: 2.6 Consensus size: 80
59693720 ATTGAATGAT
* * ** * * * *
59693730 ATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGAGTTAAGACCCGAAGGCAAT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
*
59693795 TGTGCTAGT-GACTAC
66 TGTGCAAGTCG-CTAC
* * * *
59693810 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
* **
59693875 TGTGCAAGTCGTTGT
66 TGTGCAAGTCGCTAC
* * *
59693890 ATCCGGGCTAAGACCTGAAGGCATTCGTGCATGTGGTTATATCCGG
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
59693936 TTGTATTCCG
Statistics
Matches: 105, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
80 104 0.99
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
TGTGCAAGTCGCTAC
Found at i:59693920 original size:40 final size:40
Alignment explanation
Indices: 59693728--59693935 Score: 204
Period size: 40 Copynumber: 5.2 Consensus size: 40
59693718 CAATTGAATG
* * ** * **
59693728 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTT
* * * *
59693768 ATATCCGAGTTAAGACCCGAAGGCAATT-GTGCTAGT-GACT
1 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTCG-TT
* *
59693808 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTT
* * *
59693848 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTT
* * * *
59693888 GTATCCGGGCTAAGACCTGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTT
59693928 ATATCCGG
1 ATATCCGG
59693936 TTGTATTCCG
Statistics
Matches: 140, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
39 3 0.02
40 133 0.95
41 4 0.03
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTT
Found at i:59695785 original size:27 final size:27
Alignment explanation
Indices: 59695745--59695903 Score: 173
Period size: 27 Copynumber: 5.9 Consensus size: 27
59695735 AGGAAGCGTC
*
59695745 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
59695772 CTGGTGGCTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
* *
59695799 CTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
* *
59695826 CTGGTGGCTCTGCCAC-ATATATATGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
59695853 CTGGTGGCTCTGCCACAA-TATCTATAT
1 CTGGTGGCTCTGCCACAATTATCT-GAT
* * *
59695880 CTGGTGACTTTGTCACAA-TATCTG
1 CTGGTGGCTCTGCCACAATTATCTG
59695904 GCAGCCTCGC
Statistics
Matches: 113, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
26 8 0.07
27 102 0.90
28 3 0.03
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.35
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:59695827 original size:54 final size:53
Alignment explanation
Indices: 59695745--59695903 Score: 221
Period size: 54 Copynumber: 3.0 Consensus size: 53
59695735 AGGAAGCGTC
59695745 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
*
59695799 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATATGTT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
* * * * * *
59695853 CTGGTGGCTCTGCCACAATATCTATATCTGGTGACTTTGTCACA-ATATCTG
1 CTGGTGGCTATGCCACATTATCT-GATCTGGTGGCTCTGCCACATATATCTG
59695904 GCAGCCTCGC
Statistics
Matches: 95, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
53 12 0.13
54 83 0.87
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.35
Consensus pattern (53 bp):
CTGGTGGCTATGCCACATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
Found at i:59697372 original size:33 final size:33
Alignment explanation
Indices: 59697335--59697400 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
59697325 ATGTTTCCAA
59697335 GGCTTCTTAGGACTTCTACACGCCACGTTCTAT
1 GGCTTCTTAGGACTTCTACACGCCACGTTCTAT
*
59697368 GGCTTCTTAGGACTTCTATACGCCACGTTCTAT
1 GGCTTCTTAGGACTTCTACACGCCACGTTCTAT
59697401 CTTTTCTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (33 bp):
GGCTTCTTAGGACTTCTACACGCCACGTTCTAT
Found at i:59700431 original size:3 final size:3
Alignment explanation
Indices: 59700423--59700467 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
59700413 TGAATGACCT
59700423 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
59700468 AATTTTGTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:59701242 original size:12 final size:13
Alignment explanation
Indices: 59701204--59701240 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
59701194 TTTGGGTTGT
59701204 AAAGCACTTTTTA
1 AAAGCACTTTTTA
59701217 AAAGCACTTTTTA
1 AAAGCACTTTTTA
59701230 AAAGCACTTTT
1 AAAGCACTTTT
59701241 AACTCAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (13 bp):
AAAGCACTTTTTA
Found at i:59709560 original size:43 final size:43
Alignment explanation
Indices: 59709466--59709644 Score: 200
Period size: 43 Copynumber: 4.2 Consensus size: 43
59709456 TTTAAAAAAT
* * ***
59709466 GCCGCTAAAAGCCATGACTTTTAGCGGCG-TTTGAAAAAAAGC
1 GCCGCTAAAAGTCATGGCTTTTAGCGGCGTTTTTTGAAAAAGC
*
59709508 GCCGCTAAAAGTCATGGTTTTTAGCGGCGTTTTTTGAAAAAGC
1 GCCGCTAAAAGTCATGGCTTTTAGCGGCGTTTTTTGAAAAAGC
* * **
59709551 GCCGCTAAAAGTCATAGCTTTTAGCGGCGTTTGTTGGGAAAGC
1 GCCGCTAAAAGTCATGGCTTTTAGCGGCGTTTTTTGAAAAAGC
* * * * *
59709594 GTCGCTAAAAGACATGGCTTTTAGTGGCGTTTTTCTCACAAA-C
1 GCCGCTAAAAGTCATGGCTTTTAGCGGCGTTTTT-TGAAAAAGC
59709637 GCCGCTAA
1 GCCGCTAA
59709645 TTTTGGCAGA
Statistics
Matches: 115, Mismatches: 20, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
42 26 0.23
43 85 0.74
44 4 0.03
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (43 bp):
GCCGCTAAAAGTCATGGCTTTTAGCGGCGTTTTTTGAAAAAGC
Found at i:59709624 original size:86 final size:85
Alignment explanation
Indices: 59709460--59709644 Score: 221
Period size: 86 Copynumber: 2.2 Consensus size: 85
59709450 CATTTATTTA
* *
59709460 AAAAATGCCGCTAAAAGCCATGACTTTTAGCGGCGTTTGAAAAAAAGCGCCGCTAAAAGTCATGG
1 AAAAACGCCGCTAAAAGCCATGACTTTTAGCGGCGTTTGAAAAAAAGCGCCGCTAAAAGACATGG
* *
59709525 TTTTTAGCGGCGTTTTT-TG
66 CTTTTAGCGGCGTTTTTCTC
* **** *
59709544 AAAAAGCGCCGCTAAAAGTCAT-AGCTTTTAGCGGCGTTTGTTGGGAAAGCGTCGCTAAAAGACA
1 AAAAA-CGCCGCTAAAAGCCATGA-CTTTTAGCGGCGTTTG-AAAAAAAGCGCCGCTAAAAGACA
*
59709608 TGGCTTTTAGTGGCGTTTTTCTC
63 TGGCTTTTAGCGGCGTTTTTCTC
*
59709631 ACAAACGCCGCTAA
1 AAAAACGCCGCTAA
59709645 TTTTGGCAGA
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
84 6 0.07
85 30 0.35
86 44 0.52
87 5 0.06
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (85 bp):
AAAAACGCCGCTAAAAGCCATGACTTTTAGCGGCGTTTGAAAAAAAGCGCCGCTAAAAGACATGG
CTTTTAGCGGCGTTTTTCTC
Found at i:59709774 original size:33 final size:31
Alignment explanation
Indices: 59709716--59709777 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 31
59709706 ACCAATCCAA
* *
59709716 CAAATATAGCATAAAATGCAGCCAAAAACGG
1 CAAATATAGCATAAAATACAACCAAAAACGG
*
59709747 CAAATTTAGCATAAAAAATACAACCAAAAAC
1 CAAATATAGCAT--AAAATACAACCAAAAAC
59709778 ATTAATTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 11 0.42
33 15 0.58
ACGTcount: A:0.56, C:0.19, G:0.10, T:0.15
Consensus pattern (31 bp):
CAAATATAGCATAAAATACAACCAAAAACGG
Found at i:59710061 original size:21 final size:21
Alignment explanation
Indices: 59710010--59710069 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
59710000 TCTGCTGCCA
*
59710010 TTGCTGCTGCCTCTGCCTCCC
1 TTGCTGCTGCCGCTGCCTCCC
** *
59710031 TCACTACTGCCGCTGCCTCCC
1 TTGCTGCTGCCGCTGCCTCCC
59710052 TTGCTGCTGCCGCTGCCT
1 TTGCTGCTGCCGCTGCCT
59710070 AAGTTGTTGC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.03, C:0.47, G:0.20, T:0.30
Consensus pattern (21 bp):
TTGCTGCTGCCGCTGCCTCCC
Found at i:59710080 original size:21 final size:21
Alignment explanation
Indices: 59710010--59710081 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 21
59710000 TCTGCTGCCA
* **
59710010 TTGCTGCTGCCTCTGCCTCCC
1 TTGCTGCTGCCGCTGCCTAAC
** * **
59710031 TCACTACTGCCGCTGCCTCCC
1 TTGCTGCTGCCGCTGCCTAAC
*
59710052 TTGCTGCTGCCGCTGCCTAAG
1 TTGCTGCTGCCGCTGCCTAAC
*
59710073 TTGTTGCTG
1 TTGCTGCTG
59710082 GAGTTCTTCA
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.06, C:0.40, G:0.22, T:0.32
Consensus pattern (21 bp):
TTGCTGCTGCCGCTGCCTAAC
Found at i:59713403 original size:24 final size:24
Alignment explanation
Indices: 59713375--59713422 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
59713365 AACTAGGAGT
59713375 AAATCTTGCATCAAGATGTGGTAA
1 AAATCTTGCATCAAGATGTGGTAA
59713399 AAATCTTGCATCAAGATGTGGTAA
1 AAATCTTGCATCAAGATGTGGTAA
59713423 TCATGTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (24 bp):
AAATCTTGCATCAAGATGTGGTAA
Found at i:59715746 original size:9 final size:9
Alignment explanation
Indices: 59715734--59716021 Score: 208
Period size: 9 Copynumber: 31.6 Consensus size: 9
59715724 AATTATATAT
*
59715734 TTATCTAAG
1 TTATGTAAG
*
59715743 TTATATAAG
1 TTATGTAAG
59715752 TTATGTAAG
1 TTATGTAAG
59715761 TTATGTAAG
1 TTATGTAAG
*
59715770 TTATGTAAA
1 TTATGTAAG
*
59715779 TTATGATATAAAA
1 TTATG---T-AAG
*
59715792 TATATTTAAG
1 T-TATGTAAG
59715802 TATTATGTAAG
1 --TTATGTAAG
59715813 TTATGTAAG
1 TTATGTAAG
*
59715822 TTATGATATG
1 TTATG-TAAG
* * *
59715832 ATATAT-AT
1 TTATGTAAG
59715840 TTATGTAAG
1 TTATGTAAG
*
59715849 TTATAT-A-
1 TTATGTAAG
59715856 TATATGTAAG
1 T-TATGTAAG
*
59715866 TTATATAAG
1 TTATGTAAG
59715875 TTATGTAAG
1 TTATGTAAG
59715884 TTATGTAAG
1 TTATGTAAG
** *
59715893 TTACAT-AT
1 TTATGTAAG
*
59715901 TTATCTAAG
1 TTATGTAAG
*
59715910 TTATATAAG
1 TTATGTAAG
*
59715919 TTATATAAG
1 TTATGTAAG
*
59715928 TTATGTATG
1 TTATGTAAG
*
59715937 TTATATAAG
1 TTATGTAAG
*
59715946 TTATGTAAC
1 TTATGTAAG
*
59715955 TTATATAAG
1 TTATGTAAG
* *
59715964 TTATAT-AT
1 TTATGTAAG
*
59715972 TTATCTAAG
1 TTATGTAAG
**
59715981 TTACATAAG
1 TTATGTAAG
59715990 TTATGTAAG
1 TTATGTAAG
*
59715999 TTTTGTAAG
1 TTATGTAAG
*
59716008 TTATGTAAA
1 TTATGTAAG
59716017 TTATG
1 TTATG
59716022 ATATCAAATA
Statistics
Matches: 222, Mismatches: 43, Indels: 28
0.76 0.15 0.10
Matches are distributed among these distances:
7 1 0.00
8 20 0.09
9 175 0.79
10 9 0.04
11 8 0.04
12 2 0.01
13 4 0.02
14 3 0.01
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:59715811 original size:43 final size:43
Alignment explanation
Indices: 59715761--59715842 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
59715751 GTTATGTAAG
59715761 TTATGTAAGTTATGTAAATTATGATATAAAATATATTTAAGTA
1 TTATGTAAGTTATGTAAATTATGATATAAAATATATTTAAGTA
* * *
59715804 TTATGTAAGTTATGTAAGTTATGATATGATATATATTTA
1 TTATGTAAGTTATGTAAATTATGATATAAAATATATTTA
59715843 TGTAAGTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.46
Consensus pattern (43 bp):
TTATGTAAGTTATGTAAATTATGATATAAAATATATTTAAGTA
Found at i:59715886 original size:71 final size:70
Alignment explanation
Indices: 59715804--59716021 Score: 242
Period size: 71 Copynumber: 3.1 Consensus size: 70
59715794 TATTTAAGTA
* *
59715804 TTATGTAAGTTATGTAAGTTATGATATGATATAT-ATTTATGTAAGTTATATATA-TATGTAAGT
1 TTATGTAAGTTATGTAAGTTAT-ATAT-ATATATAAGTTATATAAGTTATATA-AGTATGTAAGT
59715867 TATATAAG
63 TATATAAG
* * * *
59715875 TTATGTAAGTTATGTAAGTTACATATTTATCTAAGTTATATAAGTTATATAAGTTATGTATGTTA
1 TTATGTAAGTTATGTAAGTTATATATATATATAAGTTATATAAGTTATATAAG-TATGTAAGTTA
59715940 TATAAG
65 TATAAG
* * * * * * *
59715946 TTATGTAACTTATATAAGTTATATATTTATCTAAGTTACATAAGTTATGTAAGTTTTGTAAGTTA
1 TTATGTAAGTTATGTAAGTTATATATATATATAAGTTATATAAGTTATATAAG-TATGTAAGTTA
* *
59716011 TGTAAA
65 TATAAG
59716017 TTATG
1 TTATG
59716022 ATATCAAATA
Statistics
Matches: 129, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
69 5 0.04
70 20 0.16
71 104 0.81
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (70 bp):
TTATGTAAGTTATGTAAGTTATATATATATATAAGTTATATAAGTTATATAAGTATGTAAGTTAT
ATAAG
Found at i:59715888 original size:44 final size:44
Alignment explanation
Indices: 59715734--59716021 Score: 212
Period size: 44 Copynumber: 6.5 Consensus size: 44
59715724 AATTATATAT
* ** *
59715734 TTATCTAAGTTATATAAGTTATGTAAGTTATGTAAGTTATGTAAA
1 TTATATAAGTTATATAAGTTATGTAAGTTACATAAG-TATGTAAG
* * * * **
59715779 TTATGAT-A-TAAAATATATTTAAGT-A-TTATGTAAGTTATGTAAG
1 TTAT-ATAAGTTATATA-AGTTATGTAAGTTACATAAG-TATGTAAG
* * * *
59715822 TTATGATATGATATAT-ATTTATGTAAGTTATATATA-TATGTAAG
1 TTAT-ATAAGTTATATAAGTTATGTAAGTTACATA-AGTATGTAAG
* ** *
59715866 TTATATAAGTTATGTAAGTTATGTAAGTTACATATTTATCTAAG
1 TTATATAAGTTATATAAGTTATGTAAGTTACATAAGTATGTAAG
* * *
59715910 TTATATAAGTTATATAAGTTATGTATGTTATATAAGTTATGTAAC
1 TTATATAAGTTATATAAGTTATGTAAGTTACATAAG-TATGTAAG
* *
59715955 TTATATAAGTTATAT-ATTTATCTAAGTTACATAAGTTATGTAAG
1 TTATATAAGTTATATAAGTTATGTAAGTTACATAAG-TATGTAAG
* * * *
59715999 TTTTGTAAGTTATGTAAATTATG
1 TTATATAAGTTATATAAGTTATG
59716022 ATATCAAATA
Statistics
Matches: 196, Mismatches: 36, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
43 39 0.20
44 109 0.56
45 46 0.23
46 2 0.01
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.46
Consensus pattern (44 bp):
TTATATAAGTTATATAAGTTATGTAAGTTACATAAGTATGTAAG
Found at i:59716146 original size:15 final size:15
Alignment explanation
Indices: 59716126--59716210 Score: 88
Period size: 15 Copynumber: 5.8 Consensus size: 15
59716116 AAGTTGCGGG
59716126 ATTAAATAATATTTA
1 ATTAAATAATATTTA
59716141 ATTAAATAATATTT-
1 ATTAAATAATATTTA
59716155 A-TAAA-AATTATTTTA
1 ATTAAATAA-TA-TTTA
*
59716170 ATTAAATAATATTGA
1 ATTAAATAATATTTA
** *
59716185 AAAAAATTAT-TTTA
1 ATTAAATAATATTTA
59716199 ATTAAATAATAT
1 ATTAAATAATAT
59716211 ACATATCGGT
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
12 2 0.04
13 6 0.11
14 14 0.25
15 26 0.46
16 6 0.11
17 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (15 bp):
ATTAAATAATATTTA
Found at i:59716174 original size:29 final size:29
Alignment explanation
Indices: 59716137--59716210 Score: 130
Period size: 29 Copynumber: 2.6 Consensus size: 29
59716127 TTAAATAATA
* *
59716137 TTTAATTAAATAATATTTATAAAAATTAT
1 TTTAATTAAATAATATTGAAAAAAATTAT
59716166 TTTAATTAAATAATATTGAAAAAAATTAT
1 TTTAATTAAATAATATTGAAAAAAATTAT
59716195 TTTAATTAAATAATAT
1 TTTAATTAAATAATAT
59716211 ACATATCGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (29 bp):
TTTAATTAAATAATATTGAAAAAAATTAT
Found at i:59716414 original size:24 final size:24
Alignment explanation
Indices: 59716382--59716452 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
59716372 TTAACTTAAA
59716382 TGATAAAACGGACGATAATATTTG
1 TGATAAAACGGACGATAATATTTG
* *
59716406 TGATAAAACAGACAATAATATTTG
1 TGATAAAACGGACGATAATATTTG
*
59716430 TGATAAAACGGACGAGAATATTT
1 TGATAAAACGGACGATAATATTT
59716453 CAATAATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.28
Consensus pattern (24 bp):
TGATAAAACGGACGATAATATTTG
Found at i:59716574 original size:64 final size:64
Alignment explanation
Indices: 59716500--59716633 Score: 241
Period size: 64 Copynumber: 2.1 Consensus size: 64
59716490 ATATTTTATT
* * *
59716500 AAATATTTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAACTCGTGATGG
1 AAATATTTGTATATTAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCGTGATAG
59716564 AAATATTTGTATATTAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCGTGATAG
1 AAATATTTGTATATTAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCGTGATAG
59716628 AAATAT
1 AAATAT
59716634 AGAAATATTA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (64 bp):
AAATATTTGTATATTAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCGTGATAG
Found at i:59719947 original size:46 final size:46
Alignment explanation
Indices: 59719897--59720069 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
59719887 TGGTTGAGCA
*
59719897 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
59719943 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* **
59719990 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGTACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
59720036 CCCGAGCTCATTGAGTTGATTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
59720070 GGGGCGGGTT
Statistics
Matches: 104, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 59 0.57
47 29 0.28
48 3 0.03
50 4 0.04
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:59720053 original size:93 final size:93
Alignment explanation
Indices: 59719894--59720064 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
59719884 GGATGGTTGA
* * *
59719894 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCATTGAGT
59719959 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* ** *
59719987 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGTACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCATTGAGT
*
59720052 TGATTCCGAGTTC
66 TGAGTCCGAGTTC
59720065 ACTTAGGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:59727527 original size:46 final size:46
Alignment explanation
Indices: 59727477--59727649 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
59727467 TGGTTGAGCA
* * *
59727477 TCCGAACTCCTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
59727523 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
59727570 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
59727616 CCCGAGCTCGTTGAGTTGATTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
59727650 GGGGCAGGTT
Statistics
Matches: 104, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 58 0.56
47 29 0.28
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:59727633 original size:93 final size:93
Alignment explanation
Indices: 59727474--59727644 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
59727464 GGATGGTTGA
* * *
59727474 GCATCCGAACTCCTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCCTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
59727539 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
59727567 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCCTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
*
59727632 TGATTCCGAGTTC
66 TGAGTCCGAGTTC
59727645 ACTTAGGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCCTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:59730421 original size:16 final size:17
Alignment explanation
Indices: 59730402--59730437 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
59730392 ATTATTTAAT
*
59730402 ATATAAA-TAAAAAATA
1 ATATAAATTAAAAAACA
59730418 ATATAAATTAAAAAACA
1 ATATAAATTAAAAAACA
59730435 ATA
1 ATA
59730438 AGTTATATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (17 bp):
ATATAAATTAAAAAACA
Found at i:59730567 original size:16 final size:16
Alignment explanation
Indices: 59730546--59730599 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
59730536 AGAGCTGCAT
59730546 AAAATTTGAAATCTTG
1 AAAATTTGAAATCTTG
59730562 AAAA-TT---A--TTG
1 AAAATTTGAAATCTTG
59730572 AAAATTTGAAATCATT-
1 AAAATTTGAAATC-TTG
59730588 AAAATTTGAAAT
1 AAAATTTGAAAT
59730600 TATTTAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 14
0.69 0.00 0.31
Matches are distributed among these distances:
10 7 0.23
11 2 0.06
12 1 0.03
14 1 0.03
15 2 0.06
16 16 0.52
17 2 0.06
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (16 bp):
AAAATTTGAAATCTTG
Found at i:59730835 original size:72 final size:72
Alignment explanation
Indices: 59730746--59730915 Score: 243
Period size: 72 Copynumber: 2.4 Consensus size: 72
59730736 TTAACCCCTA
* ** * *
59730746 AACCCCTCAACCCTAAACCATTAACCCTTAATCTTTAAAATTTAAACACTAAACCTTAAACTATG
1 AACCCCTCAACCTTAAACCATTAACCCTTAATCCCTAAAATTTAAACACTAAACCCTAAACTATA
59730811 TCCCTTT
66 TCCCTTT
* *
59730818 AACCCCTCAACCTTAAACCATAAACCCTTAATCCCTAAACTTTAAACACTAAACCCTAAACTATA
1 AACCCCTCAACCTTAAACCATTAACCCTTAATCCCTAAAATTTAAACACTAAACCCTAAACTATA
59730883 TCCCTTT
66 TCCCTTT
* *
59730890 AACCCCTTAACTCTT-AACAATTAACC
1 AACCCCTCAAC-CTTAAACCATTAACC
59730916 ACTAGACCCT
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
72 84 0.97
73 3 0.03
ACGTcount: A:0.38, C:0.33, G:0.01, T:0.28
Consensus pattern (72 bp):
AACCCCTCAACCTTAAACCATTAACCCTTAATCCCTAAAATTTAAACACTAAACCCTAAACTATA
TCCCTTT
Found at i:59730848 original size:29 final size:29
Alignment explanation
Indices: 59730816--59730874 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
59730806 CTATGTCCCT
*
59730816 TTAACCCCTCAACCTTAAAC-CATAAACCC
1 TTAACCCCTAAACCTTAAACAC-TAAACCC
* *
59730845 TTAATCCCTAAACTTTAAACACTAAACCC
1 TTAACCCCTAAACCTTAAACACTAAACCC
59730874 T
1 T
59730875 AAACTATATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (29 bp):
TTAACCCCTAAACCTTAAACACTAAACCC
Found at i:59730998 original size:7 final size:7
Alignment explanation
Indices: 59730986--59731014 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
59730976 TTAGCCCTTG
59730986 AACCATA
1 AACCATA
59730993 AACCATA
1 AACCATA
59731000 AACCATA
1 AACCATA
59731007 AACCATA
1 AACCATA
59731014 A
1 A
59731015 TCCCTAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.28, G:0.00, T:0.14
Consensus pattern (7 bp):
AACCATA
Found at i:59731125 original size:74 final size:75
Alignment explanation
Indices: 59730988--59731199 Score: 209
Period size: 80 Copynumber: 2.7 Consensus size: 75
59730978 AGCCCTTGAA
* *
59730988 CCATAAACCATAAACCATAAACCATAATCCCTAAATCCACAAT-CAATTATCCATAAACCTT-AA
1 CCATAAACCATAAACCCTAAACCATAATCCCT-AA-CC-C-ATGC-ATAATCCATAAACCTTAAA
59731051 -ATTAA-TAT-TAAC
61 TATTAACTATATAAC
59731063 CCATAAACCATAAACCCCTAAACCCATAATCCCTAGACCCATGCATAATCCATAAACCTTAAAAT
1 CCATAAACCATAAA-CCCTAAA-CCATAATCCCTA-ACCCATGCATAATCCATAAACCTT-AAAT
* *
59731128 ATTAACTTGTCATAAT
62 ATTAAC-TAT-ATAAC
* * *
59731144 CCATAAACCATAAACCCTAAACCATATATACCCTAAACCATGCATAAACCTTAAAC
1 CCATAAACCATAAACCCTAAACCATA-AT-CCCTAACCCATGCATAATCCATAAAC
59731200 TATAATAATG
Statistics
Matches: 117, Mismatches: 7, Indels: 21
0.81 0.05 0.14
Matches are distributed among these distances:
74 17 0.15
75 16 0.14
76 11 0.09
77 17 0.15
79 7 0.06
80 27 0.23
81 22 0.19
ACGTcount: A:0.45, C:0.29, G:0.02, T:0.24
Consensus pattern (75 bp):
CCATAAACCATAAACCCTAAACCATAATCCCTAACCCATGCATAATCCATAAACCTTAAATATTA
ACTATATAAC
Found at i:59731178 original size:16 final size:14
Alignment explanation
Indices: 59731147--59731184 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 14
59731137 TCATAATCCA
59731147 TAAACCATAAACCC
1 TAAACCATAAACCC
59731161 TAAACCATATATACCC
1 TAAACCATA-A-ACCC
59731177 TAAACCAT
1 TAAACCAT
59731185 GCATAAACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 9 0.41
15 1 0.05
16 12 0.55
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:59731672 original size:6 final size:6
Alignment explanation
Indices: 59731653--59731683 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
59731643 TTCAGATATG
59731653 ATCAAA AT-AAA ATCAAA ATCAAA ATCAAA AT
1 ATCAAA ATCAAA ATCAAA ATCAAA ATCAAA AT
59731684 AAGACCTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.19
Consensus pattern (6 bp):
ATCAAA
Found at i:59732053 original size:40 final size:40
Alignment explanation
Indices: 59731994--59732084 Score: 121
Period size: 39 Copynumber: 2.2 Consensus size: 40
59731984 TAGATCTATA
59731994 CGGCGTTTTTTCAAAAAGCGCCACTAAAACTCAAATCCATAG
1 CGGCGTTTTTT-AAAAAGCGCCACTAAAACTC-AATCCATAG
* * * *
59732036 CGGTGTTTTTT-AAAAGCGCCGCTAATACTCAATCTATAG
1 CGGCGTTTTTTAAAAAGCGCCACTAAAACTCAATCCATAG
59732075 CGGCGTTTTT
1 CGGCGTTTTT
59732085 GAGGAAGCGC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
39 17 0.39
40 17 0.39
42 10 0.23
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (40 bp):
CGGCGTTTTTTAAAAAGCGCCACTAAAACTCAATCCATAG
Found at i:59732093 original size:40 final size:40
Alignment explanation
Indices: 59731987--59732099 Score: 122
Period size: 40 Copynumber: 2.8 Consensus size: 40
59731977 AATAGTTTAG
*
59731987 ATCTATA-CGGCGTTTTTTCAAAAAGCGCCACTAAAACTCAA
1 ATCTATAGCGGCG-TTTTTC-AAAAGCGCCGCTAAAACTCAA
* * * *
59732028 ATCCATAGCGGTGTTTTTTAAAAGCGCCGCTAATACTC-A
1 ATCTATAGCGGCGTTTTTCAAAAGCGCCGCTAAAACTCAA
* *
59732067 ATCTATAGCGGCGTTTTTGAGGAAGCGCCGCTA
1 ATCTATAGCGGCGTTTTTCA-AAAGCGCCGCTA
59732100 TTGCCACTAA
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
39 18 0.30
40 28 0.46
41 11 0.18
42 4 0.07
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (40 bp):
ATCTATAGCGGCGTTTTTCAAAAGCGCCGCTAAAACTCAA
Found at i:59736077 original size:13 final size:14
Alignment explanation
Indices: 59736054--59736084 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
59736044 TCTAAAAATA
59736054 TAAAAATATATTTT
1 TAAAAATATATTTT
59736068 TAAAAA-ATATTTT
1 TAAAAATATATTTT
59736081 TAAA
1 TAAA
59736085 TATTCCTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAAAATATATTTT
Found at i:59737075 original size:23 final size:23
Alignment explanation
Indices: 59737049--59737096 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
59737039 AGTTTAGAAA
*
59737049 AATTAAATAA-CTAAATAAATAAT
1 AATTAAATAACCAAAATAAA-AAT
*
59737072 AATTAAGTAACCAAAATAAAAAT
1 AATTAAATAACCAAAATAAAAAT
59737095 AA
1 AA
59737097 AGACATAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (23 bp):
AATTAAATAACCAAAATAAAAAT
Found at i:59741978 original size:2 final size:2
Alignment explanation
Indices: 59741971--59742010 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
59741961 AGTATAGTTG
* * *
59741971 AT AT AT AT AT AT AT AT AT AT AG AT AT AT AG AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59742011 TCGGCCATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (2 bp):
AT
Found at i:59742722 original size:29 final size:29
Alignment explanation
Indices: 59742651--59742723 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 29
59742641 GTTGTGAGAT
* *
59742651 TGGCACTAAGTGTGCGGGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAGCTTGAAATACA
*
59742680 TGGCA-TAAGTGTGCGAG-TTTAAAGTACA
1 TGGCACTAAGTGTGCGAGCTTGAAA-TACA
59742708 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
59742724 TGGTTGATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
27 5 0.13
28 19 0.49
29 15 0.38
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATACA
Found at i:59753959 original size:41 final size:41
Alignment explanation
Indices: 59753909--59754043 Score: 135
Period size: 41 Copynumber: 3.3 Consensus size: 41
59753899 GAAGATTTCC
* ** *
59753909 AGGCTCAAAGCCTGATATAATACAGTGGTACGAAGCCTACT
1 AGGCACAAAGCCTGATATAATACACCGGAACGAAGCCTACT
* * *
59753950 AGGCACAAAGCCTAATATACTACACCGGAATGAAGCCTACT
1 AGGCACAAAGCCTGATATAATACACCGGAACGAAGCCTACT
** ** * * *
59753991 AAACACAAAGTTTGATATAATACACCGGCACAAAGCCTGCT
1 AGGCACAAAGCCTGATATAATACACCGGAACGAAGCCTACT
*
59754032 AGGCACAGAGCC
1 AGGCACAAAGCC
59754044 CGAGTATCAC
Statistics
Matches: 72, Mismatches: 22, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (41 bp):
AGGCACAAAGCCTGATATAATACACCGGAACGAAGCCTACT
Found at i:59754062 original size:38 final size:38
Alignment explanation
Indices: 59754009--59754147 Score: 190
Period size: 38 Copynumber: 3.7 Consensus size: 38
59753999 AGTTTGATAT
59754009 AATA-CACCGGCACAAAGCCTGCTAGGCACAGAGCCCG
1 AATATCACCGGCACAAAGCCTGCTAGGCACAGAGCCCG
* ** * *
59754046 AGTATCACCAACACAAAGCCTGCTAGGTACAAAGCCCG
1 AATATCACCGGCACAAAGCCTGCTAGGCACAGAGCCCG
* * *
59754084 AATATCACCGGCACGAAGCCTGCTAGGCAGAGAGCCCA
1 AATATCACCGGCACAAAGCCTGCTAGGCACAGAGCCCG
*
59754122 AATATCACCGGCATAAAGCCTGCTAG
1 AATATCACCGGCACAAAGCCTGCTAG
59754148 ACATAAAGCC
Statistics
Matches: 86, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
37 3 0.03
38 83 0.97
ACGTcount: A:0.34, C:0.32, G:0.22, T:0.12
Consensus pattern (38 bp):
AATATCACCGGCACAAAGCCTGCTAGGCACAGAGCCCG
Found at i:59754156 original size:76 final size:75
Alignment explanation
Indices: 59754009--59754163 Score: 202
Period size: 76 Copynumber: 2.1 Consensus size: 75
59753999 AGTTTGATAT
* * **
59754009 AATACACCGGCACAAAGCCTGCTAGGCACAGAGCCCGAGTATCACCAACACAAAGCCTGCTAGGT
1 AATACACCGGCACAAAGCCTGCTAGGCACAGAGCCCAAATATCACCAACACAAAGCCTGCTAGAC
59754074 ACAAAGCCCG
66 ACAAAGCCCG
* * ** *
59754084 AATATCACCGGCACGAAGCCTGCTAGGCAGAGAGCCCAAATATCACCGGCATAAAGCCTGCTAGA
1 AATA-CACCGGCACAAAGCCTGCTAGGCACAGAGCCCAAATATCACCAACACAAAGCCTGCTAGA
* *
59754149 CATAAAGCCTG
65 CACAAAGCCCG
59754160 AATA
1 AATA
59754164 ACGTTACGTT
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
75 4 0.06
76 64 0.94
ACGTcount: A:0.35, C:0.30, G:0.21, T:0.13
Consensus pattern (75 bp):
AATACACCGGCACAAAGCCTGCTAGGCACAGAGCCCAAATATCACCAACACAAAGCCTGCTAGAC
ACAAAGCCCG
Found at i:59757335 original size:16 final size:16
Alignment explanation
Indices: 59757314--59757344 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
59757304 TTCACTATTA
59757314 TGTCTTTTATATTTTC
1 TGTCTTTTATATTTTC
59757330 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
59757345 GCATGCATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.10, G:0.06, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:59759677 original size:27 final size:28
Alignment explanation
Indices: 59759621--59759690 Score: 124
Period size: 27 Copynumber: 2.5 Consensus size: 28
59759611 AAATTTGTAC
59759621 AGCACTAAGTGTGCGAGTTTGATCATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
59759649 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
59759676 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
59759691 GACTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 24 0.59
28 17 0.41
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:59759701 original size:27 final size:27
Alignment explanation
Indices: 59759621--59759702 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
59759611 AAATTTGTAC
* *
59759621 AGCACTAAGTGTGCGAGTTTGA-TCATAT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
59759649 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
59759676 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
59759703 GCTTTTGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
26 1 0.02
27 30 0.61
28 18 0.37
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:59767501 original size:27 final size:28
Alignment explanation
Indices: 59767445--59767514 Score: 124
Period size: 27 Copynumber: 2.5 Consensus size: 28
59767435 AAATTTGTAC
59767445 AGCACTAAGTGTGCGAGTTTGATCATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
59767473 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
59767500 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
59767515 GACTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 24 0.59
28 17 0.41
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:59767525 original size:27 final size:27
Alignment explanation
Indices: 59767445--59767526 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
59767435 AAATTTGTAC
* *
59767445 AGCACTAAGTGTGCGAGTTTGA-TCATAT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
59767473 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
59767500 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
59767527 GCTTTTGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
26 1 0.02
27 30 0.61
28 18 0.37
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:59769818 original size:25 final size:25
Alignment explanation
Indices: 59769790--59769868 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
59769780 ATAATATTAT
59769790 TTTAATATTTTAATATTAAATTTAA
1 TTTAATATTTTAATATTAAATTTAA
* *
59769815 TTTAATA-CTT-ATCTTAATAATTT--
1 TTTAATATTTTAATATT-A-AATTTAA
59769838 TTTAAT-TGTTTAATATTAAATTTAA
1 TTTAATAT-TTTAATATTAAATTTAA
59769863 TTTAAT
1 TTTAAT
59769869 GTTTATCTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
23 15 0.35
24 6 0.14
25 22 0.51
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (25 bp):
TTTAATATTTTAATATTAAATTTAA
Found at i:59769841 original size:48 final size:48
Alignment explanation
Indices: 59769781--59769878 Score: 146
Period size: 48 Copynumber: 2.0 Consensus size: 48
59769771 TATTCCAAAA
59769781 TAATATTATTTTAATAT-TTTAATATTAAATTTAATTTAATACTTATCT
1 TAATATTATTTTAAT-TGTTTAATATTAAATTTAATTTAATACTTATCT
**
59769829 TAATAATT-TTTTAATTGTTTAATATTAAATTTAATTTAATGTTTATCT
1 TAAT-ATTATTTTAATTGTTTAATATTAAATTTAATTTAATACTTATCT
59769877 TA
1 TA
59769879 TAGATAAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 1 0.02
48 42 0.91
49 3 0.07
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (48 bp):
TAATATTATTTTAATTGTTTAATATTAAATTTAATTTAATACTTATCT
Found at i:59770522 original size:68 final size:67
Alignment explanation
Indices: 59770382--59770680 Score: 260
Period size: 68 Copynumber: 4.4 Consensus size: 67
59770372 CTTAACTATA
** * * *
59770382 GTCTTACACAATATGATGTCATGTTTTACTGTCCTGACGAACTTCATATGTT-ACAATAACCCAG
1 GTCTTACACAATATGATACCATG-TTTACT-TTCTGACGGACTTCATATGTTGTC-ATAACCCAG
* *
59770446 CTGTG
63 ATATG
* * * *
59770451 GTCTTACATAATATGATACCATGTTTATTATTCTGATGGACTTCATATGTTGTCATAGCCCAGAT
1 GTCTTACACAATATGATACCATGTTTACT-TTCTGACGGACTTCATATGTTGTCATAACCCAGAT
59770516 ATG
65 ATG
* * *
59770519 GTCTTACACAATATGATGCCATGTTTACTGTCCTGACGGACTTCATATGTTGGCATAACCCA-AC
1 GTCTTACACAATATGATACCATGTTTACT-TTCTGACGGACTTCATATGTTGTCATAACCCAGA-
59770583 TATG
64 TATG
* * * * * * * * ** * *
59770587 ATATTGCACAATATGATATCATGTTTACTGTCTTGGCGGACTTCATAGGTTGTCGTAGTCTAGCT
1 GTCTTACACAATATGATACCATGTTTACTTTC-TGACGGACTTCATATGTTGTCATAACCCAGAT
59770652 ATG
65 ATG
* **
59770655 GTCTTACACAGTATGATGTCATGTTT
1 GTCTTACACAATATGATACCATGTTT
59770681 TCCCATAGAC
Statistics
Matches: 186, Mismatches: 40, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
67 2 0.01
68 163 0.88
69 21 0.11
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (67 bp):
GTCTTACACAATATGATACCATGTTTACTTTCTGACGGACTTCATATGTTGTCATAACCCAGATA
TG
Found at i:59770610 original size:136 final size:136
Alignment explanation
Indices: 59770382--59770680 Score: 377
Period size: 136 Copynumber: 2.2 Consensus size: 136
59770372 CTTAACTATA
*
59770382 GTCTTACACAATATGATGTCATGTTTTACTGTCCTGACGAACTTCATATGTTACAATAACCCAGC
1 GTCTTACACAATATGATGTCATG-TTTACTGTCCTGACGAACTTCATATGTTACAATAACCCAAC
* * * * * * * *
59770447 TGTGGTCTTACATAATATGATACCATGTTTATTAT-TCTGATGGACTTCATATGTTGTCATAGCC
65 TATGATATTACACAATATGATACCATGTTTACTGTCT-TGACGGACTTCATAGGTTGTCATAGCC
59770511 CAGATATG
129 CAGATATG
* * *
59770519 GTCTTACACAATATGATGCCATGTTTACTGTCCTGACGGACTTCATATGTTGGC-ATAACCCAAC
1 GTCTTACACAATATGATGTCATGTTTACTGTCCTGACGAACTTCATATGTT-ACAATAACCCAAC
* * * * * *
59770583 TATGATATTGCACAATATGATATCATGTTTACTGTCTTGGCGGACTTCATAGGTTGTCGTAGTCT
65 TATGATATTACACAATATGATACCATGTTTACTGTCTTGACGGACTTCATAGGTTGTCATAGCCC
*
59770648 AGCTATG
130 AGATATG
*
59770655 GTCTTACACAGTATGATGTCATGTTT
1 GTCTTACACAATATGATGTCATGTTT
59770681 TCCCATAGAC
Statistics
Matches: 139, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
136 115 0.83
137 24 0.17
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (136 bp):
GTCTTACACAATATGATGTCATGTTTACTGTCCTGACGAACTTCATATGTTACAATAACCCAACT
ATGATATTACACAATATGATACCATGTTTACTGTCTTGACGGACTTCATAGGTTGTCATAGCCCA
GATATG
Found at i:59773186 original size:31 final size:31
Alignment explanation
Indices: 59773151--59773220 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
59773141 TTTAGATCGG
59773151 ATTAAAATTTTAA-AATTTGAAAAACATAAAA
1 ATTAAAATTTTAAGAATTT-AAAAACATAAAA
*
59773182 ATTAAAA--TTAATGAATTTAAAAATATAAAA
1 ATTAAAATTTTAA-GAATTTAAAAACATAAAA
*
59773212 ACTAAAATT
1 ATTAAAATT
59773221 AAATAAATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
29 4 0.12
30 17 0.52
31 12 0.36
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (31 bp):
ATTAAAATTTTAAGAATTTAAAAACATAAAA
Found at i:59773210 original size:30 final size:31
Alignment explanation
Indices: 59773164--59773222 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
59773154 AAAATTTTAA
*
59773164 AATTTGAAAAACATAAAAATTAAAATTAATG
1 AATTTGAAAAACATAAAAACTAAAATTAATG
*
59773195 AATTT-AAAAATATAAAAACTAAAATTAA
1 AATTTGAAAAACATAAAAACTAAAATTAA
59773223 ATAAATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (31 bp):
AATTTGAAAAACATAAAAACTAAAATTAATG
Found at i:59775393 original size:17 final size:18
Alignment explanation
Indices: 59775355--59775397 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
59775345 TATTTTAGCT
59775355 ATTTATTTAATTTTTCAC
1 ATTTATTTAATTTTTCAC
*
59775373 ATTT-TTTAACTTTTTTA-
1 ATTTATTTAA-TTTTTCAC
59775390 ATTTATTT
1 ATTTATTT
59775398 TTTTGTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTATTTAATTTTTCAC
Found at i:59775702 original size:13 final size:13
Alignment explanation
Indices: 59775686--59775715 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
59775676 TAAAAAATGC
59775686 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
*
59775699 AAAAAAGAAAAAG
1 AAAAAAAAAAAAG
59775712 AAAA
1 AAAA
59775716 TATATAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:59780628 original size:8 final size:9
Alignment explanation
Indices: 59780604--59780633 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
59780594 ATTCTGTACC
59780604 TTTAAAAAT
1 TTTAAAAAT
59780613 TTTAAAAAT
1 TTTAAAAAT
59780622 TTTAAAAAT
1 TTTAAAAAT
59780631 TTT
1 TTT
59780634 CAAACTGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TTTAAAAAT
Found at i:59793285 original size:17 final size:18
Alignment explanation
Indices: 59793263--59793308 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
59793253 ACTCATTATA
*
59793263 GCCCGATAAATGAA-AGT
1 GCCCGATAAATGAATAAT
*
59793280 GCCCGATTAAT-AATAAT
1 GCCCGATAAATGAATAAT
*
59793297 GCTCGATAAATG
1 GCCCGATAAATG
59793309 GTAAATGGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 2 0.09
17 21 0.91
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (18 bp):
GCCCGATAAATGAATAAT
Found at i:59800558 original size:47 final size:47
Alignment explanation
Indices: 59800489--59800605 Score: 130
Period size: 47 Copynumber: 2.5 Consensus size: 47
59800479 AAAGAAAAAT
** * * *
59800489 CTTAAAATGGATAATAAATAAAATATTTTAAAAT-AAATA-AATAGAG
1 CTTAAAATATATAATATATAAAACAATTTAAAATAAAATATAA-AGAG
* * *
59800535 TTTAATATATATATATATATAAAACAATTTAAAATAAAATATAAATAG
1 CTTAAAATATATA-ATATATAAAACAATTTAAAATAAAATATAAAGAG
59800583 CTTAAAATATATAATATATAAAA
1 CTTAAAATATATAATATATAAAA
59800606 GGAAATCTGA
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
46 9 0.16
47 28 0.48
48 19 0.33
49 2 0.03
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (47 bp):
CTTAAAATATATAATATATAAAACAATTTAAAATAAAATATAAAGAG
Found at i:59802420 original size:44 final size:44
Alignment explanation
Indices: 59802372--59802525 Score: 136
Period size: 44 Copynumber: 3.5 Consensus size: 44
59802362 CTTTTGCCCT
* *
59802372 CTCCATTGCAATTTCAGGGAGAAGAGATTTGTATCTTCGATCCA
1 CTCCATTGCAATTTCAAGGAGAAGAGATTTGTATCTTCGATCAA
* * ** *
59802416 CTCCACTAG-AATTTCAAGGAGATGAGAATTT-TGGCTTCGAACAA
1 CTCCA-TTGCAATTTCAAGGAGAAGAG-ATTTGTATCTTCGATCAA
* * *
59802460 CTCCAATGCAGTTTCAAGGAGAAGAGATTTGTAGT-TTCGATCTA
1 CTCCATTGCAATTTCAAGGAGAAGAGATTTGTA-TCTTCGATCAA
* *
59802504 CTCCAATGGAAATTT-AAGGAGA
1 CTCC-ATTGCAATTTCAAGGAGA
59802526 TAAAAGCTGA
Statistics
Matches: 85, Mismatches: 19, Indels: 12
0.73 0.16 0.10
Matches are distributed among these distances:
43 5 0.06
44 68 0.80
45 12 0.14
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (44 bp):
CTCCATTGCAATTTCAAGGAGAAGAGATTTGTATCTTCGATCAA
Found at i:59802752 original size:132 final size:133
Alignment explanation
Indices: 59802583--59803015 Score: 484
Period size: 132 Copynumber: 3.3 Consensus size: 133
59802573 AGGCTGGTGG
** * * * *
59802583 CTTCAATCTGCTCCCCTACTACCTC-GGGAAAATAAGAT-TCACCATTTTC-GATCTGCTCCACT
1 CTTCAATCTGCTCTACTGCTACCTCAGGG-AGATAAGATCT-ACCATCTTCAG-CCTGCTCCACT
* * * *
59802645 GTTACTCATGGAGACAAGGCTAGTGGCTTAAATCTGCTCCCTTGCTACCTCAGGGTGATAAGATT
63 GTTGCTCAGGGAAACAAGGCTAGTGGCTTAAATCTGCTCCCTTGCTACCTCAGGGAGATAAGATT
59802710 CGCCGT
128 CGCCGT
* * ** * * * * *
59802716 CTTCAATTTGTTCTACTGCT-GGTTAGGGAGATAAGATCTACAATCTTCAGCCTCCTCTACTGCT
1 CTTCAATCTGCTCTACTGCTACCTCAGGGAGATAAGATCTACCATCTTCAGCCTGCTCCACTGTT
* *
59802780 GCTCAGGGAAACAAGGCTAGTGGCTTAAATCTGCTCCCTT-TTACC-CAGGGAGATAAGATTCAC
66 GCTCAGGGAAACAAGGCTAGTGGCTTAAATCTGCTCCCTTGCTACCTCAGGGAGATAAGATTCGC
59802843 CGT
131 CGT
* * *
59802846 CTTCGATCTGCTCTATTGCTACCTCATGGAGATAAGATCTA-CATCTTCAGCCTGCTCCACTGTT
1 CTTCAATCTGCTCTACTGCTACCTCAGGGAGATAAGATCTACCATCTTCAGCCTGCTCCACTGTT
* * *
59802910 GCTTAGGGAAATAAGGCTAGTAGCTTAAATCTGCTCCCTTGCTACCTCAGGGAGATAAGATTCGC
66 GCTCAGGGAAACAAGGCTAGTGGCTTAAATCTGCTCCCTTGCTACCTCAGGGAGATAAGATTCGC
59802975 CGT
131 CGT
* ** * * **
59802978 CTTCGATCTATTCCATTGCTACCTCATAGAGATAAGAT
1 CTTCAATCTGCTCTACTGCTACCTCAGGGAGATAAGAT
59803016 TTGTGAATTC
Statistics
Matches: 252, Mismatches: 42, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
130 91 0.36
131 24 0.10
132 117 0.46
133 20 0.08
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.30
Consensus pattern (133 bp):
CTTCAATCTGCTCTACTGCTACCTCAGGGAGATAAGATCTACCATCTTCAGCCTGCTCCACTGTT
GCTCAGGGAAACAAGGCTAGTGGCTTAAATCTGCTCCCTTGCTACCTCAGGGAGATAAGATTCGC
CGT
Found at i:59802894 original size:130 final size:133
Alignment explanation
Indices: 59802638--59803015 Score: 512
Period size: 132 Copynumber: 2.9 Consensus size: 133
59802628 TTTCGATCTG
* * * * *
59802638 CTCCACTGTTACTCATGGAGACAAGGCTAGTGGCTTAAATCTGCTCCCTTGCTACCTCAGGGTGA
1 CTCCACTGCTGCTCAGGGAAACAAGGCTAGTGGCTTAAATCTGCTCCCTTGCTACCTCAGGGAGA
* * * ** * *
59802703 TAAGATTCGCCGTCTTCAATTTGTTCTACTGCT-GGTTAGGGAGATAAGATCTACAATCTTCAGC
66 TAAGATTCGCCGTCTTCGATCTGTTCTATTGCTACCTCATGGAGATAAGATCTACAATCTTCAGC
59802767 CTC
131 CTC
* *
59802770 CTCTACTGCTGCTCAGGGAAACAAGGCTAGTGGCTTAAATCTGCTCCCTT-TTACC-CAGGGAGA
1 CTCCACTGCTGCTCAGGGAAACAAGGCTAGTGGCTTAAATCTGCTCCCTTGCTACCTCAGGGAGA
* *
59802833 TAAGATTCACCGTCTTCGATCTGCTCTATTGCTACCTCATGGAGATAAGATCTAC-ATCTTCAGC
66 TAAGATTCGCCGTCTTCGATCTGTTCTATTGCTACCTCATGGAGATAAGATCTACAATCTTCAGC
*
59802897 CTG
131 CTC
* * * *
59802900 CTCCACTGTTGCTTAGGGAAATAAGGCTAGTAGCTTAAATCTGCTCCCTTGCTACCTCAGGGAGA
1 CTCCACTGCTGCTCAGGGAAACAAGGCTAGTGGCTTAAATCTGCTCCCTTGCTACCTCAGGGAGA
* * *
59802965 TAAGATTCGCCGTCTTCGATCTATTCCATTGCTACCTCATAGAGATAAGAT
66 TAAGATTCGCCGTCTTCGATCTGTTCTATTGCTACCTCATGGAGATAAGAT
59803016 TTGTGAATTC
Statistics
Matches: 215, Mismatches: 28, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
130 91 0.42
131 25 0.12
132 99 0.46
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.30
Consensus pattern (133 bp):
CTCCACTGCTGCTCAGGGAAACAAGGCTAGTGGCTTAAATCTGCTCCCTTGCTACCTCAGGGAGA
TAAGATTCGCCGTCTTCGATCTGTTCTATTGCTACCTCATGGAGATAAGATCTACAATCTTCAGC
CTC
Found at i:59804293 original size:15 final size:15
Alignment explanation
Indices: 59804275--59804307 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
59804265 TTCTTTCTTC
59804275 TTTTTTTTTGATTGA
1 TTTTTTTTTGATTGA
*
59804290 TTTTTTTTTTATTGA
1 TTTTTTTTTGATTGA
59804305 TTT
1 TTT
59804308 ATTATTATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (15 bp):
TTTTTTTTTGATTGA
Found at i:59808729 original size:7 final size:7
Alignment explanation
Indices: 59808719--59808751 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
59808709 TCTCTTTCTC
59808719 TTTTTA-
1 TTTTTAT
59808725 TTTTTAT
1 TTTTTAT
59808732 TTTTTATT
1 TTTTTA-T
59808740 TTTTTAT
1 TTTTTAT
59808747 TTTTT
1 TTTTT
59808752 TGTACTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.24
7 12 0.48
8 7 0.28
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:59813008 original size:124 final size:124
Alignment explanation
Indices: 59812786--59813010 Score: 317
Period size: 124 Copynumber: 1.8 Consensus size: 124
59812776 GAATTATGTG
* * ** * * *
59812786 AAATGAAATATGGATGTATATTGATTATTGATTTATGTGTGTATGAGTATTTGAATGATACCCGG
1 AAATGAAATATGAATGTATAATGATTATTGATGCATGTGTGCATGAGCAATTGAATGATACCCGG
* * **
59812851 GCTAAGTCCCGAAGGCGATTATGCTTGTGATTATATTTGCGTTTGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGACGATTATGCTGGAAATTATATTTGCGTTTGAGCCTTAGTAACGA
* *
59812910 AAATGAAATATGAATGTCTAATGATTATTGATGCATGTGTGCATGAGCAATTGAATGATATCCGG
1 AAATGAAATATGAATGTATAATGATTATTGATGCATGTGTGCATGAGCAATTGAATGATACCCGG
59812975 GCTAAGTCCCGAAGAC-ATTTATGCTGGAAATTATAT
66 GCTAAGTCCCGAAGACGA-TTATGCTGGAAATTATAT
59813011 CCGGGTTAAA
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
123 1 0.01
124 86 0.99
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (124 bp):
AAATGAAATATGAATGTATAATGATTATTGATGCATGTGTGCATGAGCAATTGAATGATACCCGG
GCTAAGTCCCGAAGACGATTATGCTGGAAATTATATTTGCGTTTGAGCCTTAGTAACGA
Found at i:59813132 original size:40 final size:40
Alignment explanation
Indices: 59813005--59813134 Score: 156
Period size: 40 Copynumber: 3.2 Consensus size: 40
59812995 ATGCTGGAAA
* * *
59813005 TTATATCCGGGTTAAAACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
59813045 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
59813085 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
59813125 TTATATCCGG
1 TTATATCCGG
59813135 TTGTATTCCG
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
39 4 0.05
40 71 0.95
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:59813133 original size:80 final size:80
Alignment explanation
Indices: 59812967--59813134 Score: 189
Period size: 80 Copynumber: 2.1 Consensus size: 80
59812957 CAATTGAATG
* * *
59812967 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTGGAAATTATATCCGGGTTAAAACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGACATTCATGCTGGAAATTATATCCGGGCTAAAACCCGAAGGCA
59813032 ATTGTGCTAGTGGCT
66 ATTGTGCTAGTGGCT
* * * ** * *
59813047 ACATCCGGGCTAAGACCCGAAGGCATTCGTGC-GAGTCATTCTATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGACATTCATGCTG-GAAATTATATCCGGGCTAAAACCCGAAGGC
*
59813111 -ATTCGTGC-ACGTGGTT
65 AATT-GTGCTA-GTGGCT
59813127 ATATCCGG
1 ATATCCGG
59813135 TTGTATTCCG
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
79 5 0.07
80 68 0.93
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.24
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGACATTCATGCTGGAAATTATATCCGGGCTAAAACCCGAAGGCA
ATTGTGCTAGTGGCT
Found at i:59817074 original size:2 final size:2
Alignment explanation
Indices: 59817067--59817097 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
59817057 AGAGTTTAAA
59817067 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59817098 ACAATTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59824634 original size:31 final size:31
Alignment explanation
Indices: 59824593--59824652 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
59824583 CCTTTTCATA
*
59824593 TTTCATATTTCATAACACTGGGCCGAAGCAT
1 TTTCAAATTTCATAACACTGGGCCGAAGCAT
**
59824624 TTTCAAATTTCATATTACTGGGCCGAAGC
1 TTTCAAATTTCATAACACTGGGCCGAAGC
59824653 CTTTACTGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCAT
Found at i:59824906 original size:24 final size:24
Alignment explanation
Indices: 59824870--59825014 Score: 231
Period size: 24 Copynumber: 6.1 Consensus size: 24
59824860 CCTAGCCTCC
*
59824870 TTTAATAACTGGGGCAAAAGCCCT
1 TTTAATAACTGGGGCATAAGCCCT
*
59824894 TTTTATAACTGGGGCATAAGCCC-
1 TTTAATAACTGGGGCATAAGCCCT
*
59824917 TTTAATAACTGGGGCGTAAGCCCT
1 TTTAATAACTGGGGCATAAGCCCT
*
59824941 TTTGATAACTGGGGCATAAGCCCT
1 TTTAATAACTGGGGCATAAGCCCT
*
59824965 TTTGATAACTGGGGCATAAGCCC-
1 TTTAATAACTGGGGCATAAGCCCT
59824988 TTTAATAACTGGGGCATAAGCCCT
1 TTTAATAACTGGGGCATAAGCCCT
59825012 TTT
1 TTT
59825015 TCACTTCCTC
Statistics
Matches: 112, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
23 43 0.38
24 69 0.62
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (24 bp):
TTTAATAACTGGGGCATAAGCCCT
Found at i:59824952 original size:71 final size:71
Alignment explanation
Indices: 59824874--59825014 Score: 255
Period size: 71 Copynumber: 2.0 Consensus size: 71
59824864 GCCTCCTTTA
* *
59824874 ATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAAGCCCTTTAATAACTGGGGCGTAAGCC
1 ATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
59824939 CTTTTG
66 CTTTTG
*
59824945 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
1 ATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
59825010 CTTTT
66 CTTTT
59825015 TCACTTCCTC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.28
Consensus pattern (71 bp):
ATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
CTTTTG
Found at i:59825014 original size:47 final size:48
Alignment explanation
Indices: 59824870--59825014 Score: 231
Period size: 47 Copynumber: 3.1 Consensus size: 48
59824860 CCTAGCCTCC
* *
59824870 TTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAAGCCC-
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCT
* *
59824917 TTTAATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCCT
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCT
*
59824965 TTTGATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCCT
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCT
59825012 TTT
1 TTT
59825015 TCACTTCCTC
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
47 70 0.77
48 21 0.23
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (48 bp):
TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCT
Found at i:59825087 original size:9 final size:9
Alignment explanation
Indices: 59825073--59825129 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
59825063 ATCTCGTGTG
59825073 CATATCATA
1 CATATCATA
*
59825082 CATATCATGTG
1 CATATCA--TA
59825093 CATATCATA
1 CATATCATA
* *
59825102 CATGTCATGTG
1 CATATCA--TA
59825113 CATATCATA
1 CATATCATA
59825122 CATATCAT
1 CATATCAT
59825130 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:59825092 original size:20 final size:20
Alignment explanation
Indices: 59825069--59825131 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
59825059 GAACATCTCG
59825069 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
59825089 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
59825109 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
59825129 TGT
1 TGT
59825132 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:59825214 original size:25 final size:25
Alignment explanation
Indices: 59825168--59825215 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
59825158 ATATATAAAC
* * * *
59825168 CCTAGGGGTATAATGGTTATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
59825193 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
59825216 CATATTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:59826431 original size:27 final size:27
Alignment explanation
Indices: 59826340--59826423 Score: 116
Period size: 27 Copynumber: 3.1 Consensus size: 27
59826330 GGGCATATTC
*
59826340 GTCATTTTACCATACAGGGG-TATTACG
1 GTCACTTTACCATACAGGGGCT-TTACG
*
59826367 GTCACTTTACCTTACAGGGGCTTTACG
1 GTCACTTTACCATACAGGGGCTTTACG
* *
59826394 GTCACTTTACCCTACAGGGGCTTTATG
1 GTCACTTTACCATACAGGGGCTTTACG
59826421 GTC
1 GTC
59826424 TTTTTACCTA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 51 0.98
28 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.33
Consensus pattern (27 bp):
GTCACTTTACCATACAGGGGCTTTACG
Found at i:59826440 original size:27 final size:26
Alignment explanation
Indices: 59826340--59826433 Score: 109
Period size: 27 Copynumber: 3.5 Consensus size: 26
59826330 GGGCATATTC
*
59826340 GTCATTTTACCATACAGGGG-TATTACG
1 GTCACTTTACC-TACAGGGGCT-TTACG
59826367 GTCACTTTACCTTACAGGGGCTTTACG
1 GTCACTTTACC-TACAGGGGCTTTACG
*
59826394 GTCACTTTACCCTACAGGGGCTTTATG
1 GTCACTTTA-CCTACAGGGGCTTTACG
**
59826421 GTCTTTTTACCTA
1 GTCACTTTACCTA
59826434 ATAGGGGTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.07
27 53 0.88
28 3 0.05
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (26 bp):
GTCACTTTACCTACAGGGGCTTTACG
Done.