Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 163 of 253
Found at i:52786329 original size:24 final size:25
Alignment explanation
Indices: 52786277--52786323 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
52786267 TTAGTAATGA
*
52786277 ATTTGAAAATATAAAATGTTTTTAG
1 ATTTGAAAATATAAAATATTTTTAG
52786302 ATTTGACAAAT-T-AAATATTTTT
1 ATTTGA-AAATATAAAATATTTTT
52786324 GTATTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 7 0.35
26 4 0.20
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.47
Consensus pattern (25 bp):
ATTTGAAAATATAAAATATTTTTAG
Found at i:52789110 original size:30 final size:30
Alignment explanation
Indices: 52789052--52789110 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
52789042 ATTTTCGAGC
* **
52789052 CTAGGGGCAAAATAGTCATTTTGTCAAAGT
1 CTAGAGGCAAAATAGTCATTTTACCAAAGT
* *
52789082 CTAGAGGCAAAATGGTCGTTTTACCAAAG
1 CTAGAGGCAAAATAGTCATTTTACCAAAG
52789111 ATATGAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (30 bp):
CTAGAGGCAAAATAGTCATTTTACCAAAGT
Found at i:52789598 original size:46 final size:46
Alignment explanation
Indices: 52789449--52789670 Score: 195
Period size: 46 Copynumber: 4.8 Consensus size: 46
52789439 TCACTTGTGT
* * * *
52789449 GAGCTAGTGTAAGACATGTCTGAGACATGCATCGGCCAT--ATTATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCC-TCGA-GACGA
* * * * *
52789495 GAGCTAGTGTAAGACCATGTCTGGGATATGGGATCGGCATTGAGACGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGACGA
* *
52789543 GTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACG-A
* *
52789590 -AGCCAGTGTAAGACATGTTTGGGACATGCATCGG-CTACGAGA--T
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGACGA
* *
52789633 GTGTCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
52789671 ACAGATATGC
Statistics
Matches: 148, Mismatches: 18, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
44 11 0.07
45 15 0.10
46 71 0.48
47 27 0.18
48 23 0.16
49 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGA
Found at i:52798269 original size:30 final size:29
Alignment explanation
Indices: 52798235--52798298 Score: 101
Period size: 30 Copynumber: 2.2 Consensus size: 29
52798225 ATGAGTCGGA
*
52798235 AGCTTTAGCACTAAGTGTGTGATTTAAACT
1 AGCTTTAGCACTAAGTGTGCGATTT-AACT
*
52798265 AGCTTTGGCACTAAGTGTGCGATTTAACT
1 AGCTTTAGCACTAAGTGTGCGATTTAACT
52798294 AGCTT
1 AGCTT
52798299 CGGTTATTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 9 0.28
30 23 0.72
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (29 bp):
AGCTTTAGCACTAAGTGTGCGATTTAACT
Found at i:52806922 original size:45 final size:46
Alignment explanation
Indices: 52806765--52806936 Score: 156
Period size: 45 Copynumber: 3.7 Consensus size: 46
52806755 CACTTGTGTA
*
52806765 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAT-ATTATGAG-
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCC-TCA-TACGAGT
* * * * * *
52806811 AGCTAGTGTAAGACCATGTCTGGGATATGGGATCAGCATTGAGACGAGT
1 AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CTCATACGAGT
*
52806860 -GCTAGTATAAGACATGTCTGGGACATGCATCGGCCTCA-A-GAGT
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCATACGAGT
* **
52806903 AAGCCAGTGTAAGACATGTCTGGGGTATGCATCG
1 -AGCTAGTGTAAGACATGTCTGGGACATGCATCG
52806937 ACTACGGGAC
Statistics
Matches: 103, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
43 4 0.04
44 1 0.01
45 30 0.29
46 19 0.18
47 26 0.25
48 22 0.21
49 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.24
Consensus pattern (46 bp):
AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCATACGAGT
Found at i:52810424 original size:20 final size:20
Alignment explanation
Indices: 52810378--52810418 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
52810368 TCAAACCACC
*
52810378 GATAATGCCATCATTGTGTA
1 GATAGTGCCATCATTGTGTA
*
52810398 GATAGTGCCATCGTTGTGTA
1 GATAGTGCCATCATTGTGTA
52810418 G
1 G
52810419 GAAGTGATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (20 bp):
GATAGTGCCATCATTGTGTA
Found at i:52812705 original size:27 final size:26
Alignment explanation
Indices: 52812654--52812708 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
52812644 TATTTTTAAG
*
52812654 TTTTAAGACTCTGTTTTCAAAATGTGT
1 TTTTAAGA-TCTGTTTTAAAAATGTGT
*
52812681 TTTTAAG-TCTGTTTTAAAAATATGT
1 TTTTAAGATCTGTTTTAAAAATGTGT
52812706 TTT
1 TTT
52812709 ATGCAAGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 19 0.73
27 7 0.27
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (26 bp):
TTTTAAGATCTGTTTTAAAAATGTGT
Found at i:52813179 original size:49 final size:48
Alignment explanation
Indices: 52813122--52813236 Score: 140
Period size: 49 Copynumber: 2.3 Consensus size: 48
52813112 AGGGTAAGCT
* * * *
52813122 TGAACATATCTTATGTTCCTCAGCCATTCTGATAAGTGTGTTAGGTGCG
1 TGAACATAT-TTATGTTCCTCAGCCATTCTCATAAATGTGTTAAGTGCA
* *
52813171 TGAACATATTTAATGTTCTTTAGCCATTCTCATAAATGTGTTAAGTGCA
1 TGAACATATTT-ATGTTCCTCAGCCATTCTCATAAATGTGTTAAGTGCA
*
52813220 AGAACATATTTTATGTT
1 TGAACATA-TTTATGTT
52813237 TCTTAGTCGT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
48 2 0.04
49 52 0.91
50 3 0.05
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (48 bp):
TGAACATATTTATGTTCCTCAGCCATTCTCATAAATGTGTTAAGTGCA
Found at i:52815426 original size:24 final size:24
Alignment explanation
Indices: 52815399--52815444 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
52815389 GAACCTTAAC
52815399 TTGCTCATAATTGACATATGAAAG
1 TTGCTCATAATTGACATATGAAAG
52815423 TTGCTCATAATTGACATATGAA
1 TTGCTCATAATTGACATATGAA
52815445 CCTACCTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (24 bp):
TTGCTCATAATTGACATATGAAAG
Found at i:52816588 original size:13 final size:13
Alignment explanation
Indices: 52816567--52816604 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
52816557 CCTGGCACAT
*
52816567 GCCCATGTCCTTA
1 GCCCGTGTCCTTA
52816580 GCCCGTGTCCTTA
1 GCCCGTGTCCTTA
52816593 GCCCGTGTCCTT
1 GCCCGTGTCCTT
52816605 CACACGGCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.08, C:0.39, G:0.21, T:0.32
Consensus pattern (13 bp):
GCCCGTGTCCTTA
Found at i:52817657 original size:47 final size:49
Alignment explanation
Indices: 52817601--52817717 Score: 141
Period size: 49 Copynumber: 2.4 Consensus size: 49
52817591 GCCATGTCTT
* *
52817601 AGACATGGTCTTACACTGGCTCATC-CATT-AAGTTGATGCCAAGTCCC
1 AGACATGGTCTTACACTGGCTCATCACATTGAAGTCGACGCCAAGTCCC
* * * *
52817648 AGACATGGTCTTACACTGAC-CATCGAGATTGAGGTCGACGCCATGTCCC
1 AGACATGGTCTTACACTGGCTCATC-ACATTGAAGTCGACGCCAAGTCCC
*
52817697 AGACATGGTCTTAGACTGGCT
1 AGACATGGTCTTACACTGGCT
52817718 TACGTCGCGA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
46 4 0.07
47 19 0.33
48 3 0.05
49 32 0.55
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (49 bp):
AGACATGGTCTTACACTGGCTCATCACATTGAAGTCGACGCCAAGTCCC
Found at i:52817787 original size:47 final size:45
Alignment explanation
Indices: 52817728--52817854 Score: 161
Period size: 48 Copynumber: 2.8 Consensus size: 45
52817718 TACGTCGCGA
52817728 GGCCAATGCATGTCCCAGACATGTCTTACACTAGCTCTCATTTCAA-T
1 GGCCAATGCATGTCCCAGACATGTCTTACACTAGCTCTCA--T-AAGT
* *
52817775 -GCCAATGCCATGTCCCAGACATGGTCTTACAATGGCTCTCATAATGT
1 GGCCAATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATAA-GT
52817822 GGCCAATGCATGT-CCAGACATGTCTTACACTAG
1 GGCCAATGCATGTCCCAGACATGTCTTACACTAG
52817855 AGCATAAATG
Statistics
Matches: 71, Mismatches: 4, Indels: 12
0.82 0.05 0.14
Matches are distributed among these distances:
45 12 0.17
46 16 0.23
47 20 0.28
48 23 0.32
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (45 bp):
GGCCAATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAAGT
Found at i:52826884 original size:66 final size:66
Alignment explanation
Indices: 52826772--52826898 Score: 157
Period size: 66 Copynumber: 1.9 Consensus size: 66
52826762 TTATTGCATT
* * *
52826772 AATGTCACTGCATGAGTTAATCTTAGATTGCATCCAGAATTGTTGCCGCACTTGATAGCTGCCCA
1 AATGTCACTGCATGAGTGAATCTTAGATTGCATCCAGAATTGTTGCCGCACCTGACAGCTGCCCA
52826837 C
66 C
* * * * * *
52826838 AATGTCACTGTATTAGTGAAT-TCTAGATTGCGTCTATAATTTTTGCCGCACCTGACAGCTG
1 AATGTCACTGCATGAGTGAATCT-TAGATTGCATCCAGAATTGTTGCCGCACCTGACAGCTG
52826899 TCCGGATAAG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 1 0.02
66 50 0.98
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (66 bp):
AATGTCACTGCATGAGTGAATCTTAGATTGCATCCAGAATTGTTGCCGCACCTGACAGCTGCCCA
C
Found at i:52838284 original size:65 final size:65
Alignment explanation
Indices: 52838180--52838310 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
52838170 ACTATAAGAA
52838180 AATGAAAAATGAGAGGGAGTAAGCATAAAGCTTAGTAAGTTGCACATAAATAAATATACAACTTT
1 AATGAAAAATGAGAGGGAGTAAGCATAAAGCTTAGTAAGTTGCACATAAATAAATATACAACTTT
52838245 AATGAAAAATGAGAGGGAGTAAGCATAAAGCTTAGTAAGTTGCACATAAATAAATATACAACTTT
1 AATGAAAAATGAGAGGGAGTAAGCATAAAGCTTAGTAAGTTGCACATAAATAAATATACAACTTT
52838310 A
1 A
52838311 CCATTCATCA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.24
Consensus pattern (65 bp):
AATGAAAAATGAGAGGGAGTAAGCATAAAGCTTAGTAAGTTGCACATAAATAAATATACAACTTT
Found at i:52838728 original size:46 final size:46
Alignment explanation
Indices: 52838542--52838763 Score: 184
Period size: 46 Copynumber: 4.7 Consensus size: 46
52838532 TGGGGTCAGG
* ** * *
52838542 TGCCGATGCCATGTCCCAGACATGGTCTTACACAAGTTCTAGCATATCTG
1 TGCCGATG-CATGTCCCAGACATGGTCTTACACTAGCACT--CATCTC-A
* * * *
52838592 TGCCGTTGCCATGTTCCAGACATGGTCTTACACT-G-ACACATCTCG
1 TGCCGATG-CATGTCCCAGACATGGTCTTACACTAGCACTCATCTCA
* *
52838637 TAGCCGATGCATGTCCTAGACAT-GTCTTACACTAGC-TTACATCTCA
1 T-GCCGATGCATGTCCCAGACATGGTCTTACACTAGCACT-CATCTCA
* * *
52838683 TGGTCGAAGCATGTCCCAGACAT-GTCTTACACTAGCACTCGTCTCAA
1 T-GCCGATGCATGTCCCAGACATGGTCTTACACTAGCACTCATCTC-A
*
52838730 TGCCGATGTCATGTCCCAGGCATGGTCTTACACT
1 TGCCGATG-CATGTCCCAGACATGGTCTTACACT
52838764 GGATCTCAAA
Statistics
Matches: 143, Mismatches: 21, Indels: 18
0.79 0.12 0.10
Matches are distributed among these distances:
44 10 0.07
45 15 0.10
46 59 0.41
47 16 0.11
48 11 0.08
49 1 0.01
50 31 0.22
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.28
Consensus pattern (46 bp):
TGCCGATGCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCA
Found at i:52842245 original size:49 final size:49
Alignment explanation
Indices: 52842142--52842268 Score: 157
Period size: 49 Copynumber: 2.6 Consensus size: 49
52842132 TAAGATGCTG
* * *
52842142 ATGCCATGTCCCAGACATGGTATTACACTGGCTTTCATATAGCGAGGCCG
1 ATGCCATGTCCCAGACA-GGTCTTACACTGGCTCTCATATAGCGAGGCCA
* * * *
52842192 ATGCCATGTCCTAGACAGGTCTTACACTGGCTCTCATTTATC-AGTGTCA
1 ATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCATATAGCGAG-GCCA
*
52842241 ATGCCATGTCCCAGAGAGGTCTTACACT
1 ATGCCATGTCCCAGACAGGTCTTACACT
52842269 AACACAAAAC
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
48 2 0.03
49 49 0.73
50 16 0.24
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (49 bp):
ATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCATATAGCGAGGCCA
Found at i:52842466 original size:48 final size:48
Alignment explanation
Indices: 52842331--52842466 Score: 154
Period size: 48 Copynumber: 2.9 Consensus size: 48
52842321 TATTGCGACA
* * * *
52842331 CCGATGCATGTCCCAGACATGTCTTACACTAGCTCTC--GTCTCAATG
1 CCGATGCATGTCCCAGACATGTCTTACACTAGCACACATATCTCAAGG
* * * *
52842377 TCGATGCATGTCCCACACATGTCTTACACT-G-ACTTAAATATCTCGAGG
1 CCGATGCATGTCCCAGACATGTCTTACACTAGCAC--ACATATCTCAAGG
52842425 CCGATGCATGTCCCAGACATGTCTTACACTAGCACACATATC
1 CCGATGCATGTCCCAGACATGTCTTACACTAGCACACATATC
52842467 ACCCATTATC
Statistics
Matches: 73, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
44 1 0.01
45 1 0.01
46 28 0.38
48 40 0.55
49 1 0.01
50 2 0.03
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (48 bp):
CCGATGCATGTCCCAGACATGTCTTACACTAGCACACATATCTCAAGG
Found at i:52845985 original size:40 final size:40
Alignment explanation
Indices: 52845930--52846107 Score: 254
Period size: 40 Copynumber: 4.5 Consensus size: 40
52845920 CGGATGGTAA
* **
52845930 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
52845970 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
52846010 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
52846050 CCGGGCTAAGTCCCGAAGGCATTTGAGAGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
52846090 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
52846108 TACTTGGTTT
Statistics
Matches: 128, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
39 17 0.13
40 110 0.86
41 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:52853583 original size:49 final size:49
Alignment explanation
Indices: 52853478--52853792 Score: 176
Period size: 46 Copynumber: 6.7 Consensus size: 49
52853468 GGGTTAAGAT
* *
52853478 GCCGACGTCATGTCCCAGACATGGTCTTACATTGGCTTTCATATAGCGAG
1 GCCGATGTCATGTCCCAGACA-GGTCTTACACTGGCTTTCATATAGCGAG
* *
52853528 GCCGATGTCATGTCCCAGACAGGTCTTACACTGGCTCTT-ATTTATC-AG
1 GCCGATGTCATGTCCCAGACAGGTCTTACACTGGCT-TTCATATAGCGAG
* * * * * * * *
52853576 TGTCGATGCCATGTTCCAGAAAGGTCTTACACTGAC--ACACA-A-C-AA
1 -GCCGATGTCATGTCCCAGACAGGTCTTACACTGGCTTTCATATAGCGAG
* * * * *
52853621 GCTGATGCCATGTCGCAGACAGGTCTTACACTAGCTTGT-ATATCGCGAG
1 GCCGATGTCATGTCCCAGACAGGTCTTACACTGGCTT-TCATATAGCGAG
* * * * * * * * *
52853670 GCCGGTG-CATGTCCTAGACATGTCTTACACTAGCTCTCGTCT--CAAT
1 GCCGATGTCATGTCCCAGACAGGTCTTACACTGGCTTTCATATAGCGAG
* * * * *
52853716 GTCGATG-CATGTCCCAGACATGTCTTACATTGGCTCTCATACTA--TA-
1 GCCGATGTCATGTCCCAGACAGGTCTTACACTGGCTTTCATA-TAGCGAG
* *
52853762 GCTGATG-CATGTCCCAGACATGTCTTACACT
1 GCCGATGTCATGTCCCAGACAGGTCTTACACT
52853793 AGCACACTTA
Statistics
Matches: 208, Mismatches: 45, Indels: 28
0.74 0.16 0.10
Matches are distributed among these distances:
44 28 0.13
45 2 0.01
46 67 0.32
47 4 0.02
48 30 0.14
49 55 0.26
50 22 0.11
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (49 bp):
GCCGATGTCATGTCCCAGACAGGTCTTACACTGGCTTTCATATAGCGAG
Found at i:52857732 original size:14 final size:14
Alignment explanation
Indices: 52857713--52857741 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
52857703 TGATTCAATT
52857713 TCTACTATTTTTGG
1 TCTACTATTTTTGG
52857727 TCTACTATTTTTGG
1 TCTACTATTTTTGG
52857741 T
1 T
52857742 GATTTTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (14 bp):
TCTACTATTTTTGG
Found at i:52866944 original size:30 final size:31
Alignment explanation
Indices: 52866893--52866951 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
52866883 CACCCTTAAA
* * *
52866893 ATATTTGCACTATTAGTCCTTCAACTTTTTC
1 ATATTTACACTATTAATCCTTCAAATTTTTC
52866924 ATATTTACACT-TTAATCCTTCAAATTTT
1 ATATTTACACTATTAATCCTTCAAATTTT
52866952 GAGTATTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.27, C:0.20, G:0.03, T:0.49
Consensus pattern (31 bp):
ATATTTACACTATTAATCCTTCAAATTTTTC
Found at i:52866959 original size:30 final size:31
Alignment explanation
Indices: 52866893--52866961 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
52866883 CACCCTTAAA
* * *
52866893 ATATTTGCACTATTAGTCCTTCAACTTTTTC
1 ATATTTACACTATTAATCCTTCAACATTTTC
*
52866924 ATATTTACACT-TTAATCCTTCAA-ATTTTG
1 ATATTTACACTATTAATCCTTCAACATTTTC
52866953 AGTATTTAC
1 A-TATTTAC
52866962 TCTTGGGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 5 0.15
30 18 0.55
31 10 0.30
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.48
Consensus pattern (31 bp):
ATATTTACACTATTAATCCTTCAACATTTTC
Found at i:52868515 original size:53 final size:53
Alignment explanation
Indices: 52868342--52868548 Score: 175
Period size: 53 Copynumber: 3.8 Consensus size: 53
52868332 ATTAGCGTTT
* * * * * *
52868342 AAGGATTCCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTC-TACTAGGA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGAAATGGTAAGTTCATA--AGGC
* * * * * * * *
52868396 AAGAAAATCATGTAAGACCATGTCAAGACAT-GACATTGATAAACTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGA-AATGGT-AAGTTC-ATAAGGC
* * * *
52868451 AAAGATCCCATGTAAGACCATGCCAAGGCATGGAAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGAAATGGTAAGTTCATAAGGC
* *
52868504 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGAAATGGTAAGTT
52868549 TAAAAAGGAA
Statistics
Matches: 118, Mismatches: 30, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
53 47 0.40
54 32 0.27
55 35 0.30
56 2 0.02
57 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGAAATGGTAAGTTCATAAGGC
Found at i:52876984 original size:61 final size:61
Alignment explanation
Indices: 52876889--52877011 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
52876879 GAGTAATGGA
52876889 ACTTAGATTATGATTCGATTAGATCATGTTATATAGCGAATCAAAACCATGCTCTTTGTAT
1 ACTTAGATTATGATTCGATTAGATCATGTTATATAGCGAATCAAAACCATGCTCTTTGTAT
52876950 ACTTAGATTATGATTCGATTAGATCATGTTATATAGCGAATCAAAACCATGCTCTTTGTAT
1 ACTTAGATTATGATTCGATTAGATCATGTTATATAGCGAATCAAAACCATGCTCTTTGTAT
52877011 A
1 A
52877012 TGGTTATTGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (61 bp):
ACTTAGATTATGATTCGATTAGATCATGTTATATAGCGAATCAAAACCATGCTCTTTGTAT
Found at i:52877203 original size:40 final size:40
Alignment explanation
Indices: 52877134--52877294 Score: 189
Period size: 40 Copynumber: 4.0 Consensus size: 40
52877124 CGGATGATAA
* * * *
52877134 CCGGACTAAGATCCGAAGGCATTCGTGCTAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* * * * * *
52877174 CCAGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATAT
*
52877214 CCGGGCTAAGACCCGAAGGCATTTGTACGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* *
52877254 CCGGGATAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
52877294 C
1 C
52877295 TGGCTAAATC
Statistics
Matches: 101, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
39 2 0.02
40 97 0.96
41 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
Found at i:52879562 original size:120 final size:120
Alignment explanation
Indices: 52879349--52879580 Score: 324
Period size: 120 Copynumber: 1.9 Consensus size: 120
52879339 CATTTGAATG
* * * *
52879349 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCA
* * *
52879414 TTTATGCTAGTGACCATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGAT
66 TTTATGCGAGTGACCATACCCGGGTTAAGACCCGAAGGCAATTGTGCGAGTTGAT
* *
52879469 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TATATCCGGGGTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAG-TGATTATATCCGGGCTAAGACCCGAAGGC
* * *
52879533 ATTTGTGCGAGTTG-CTATCCCCGGGTTAAGACCCGAAGGCAATTGTGC
65 ATTTATGCGAG-TGACCATACCCGGGTTAAGACCCGAAGGCAATTGTGC
52879581 TTGTGGTTAT
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
120 93 0.95
121 5 0.05
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (120 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCA
TTTATGCGAGTGACCATACCCGGGTTAAGACCCGAAGGCAATTGTGCGAGTTGAT
Found at i:52879579 original size:40 final size:40
Alignment explanation
Indices: 52879349--52879580 Score: 288
Period size: 40 Copynumber: 5.8 Consensus size: 40
52879339 CATTTGAATG
* * * *
52879349 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
* * * * * *
52879389 TTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGACC
1 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
52879429 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGAT
*
52879469 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGAT
* *
52879509 ATATCCGGGGTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGAT
** *
52879549 ATCCCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATATCCGGGTTAAGACCCGAAGGCATTTGTGC
52879581 TTGTGGTTAT
Statistics
Matches: 175, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 172 0.98
41 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGAT
Found at i:52882732 original size:40 final size:40
Alignment explanation
Indices: 52882655--52882872 Score: 316
Period size: 40 Copynumber: 5.5 Consensus size: 40
52882645 AAACCAAGTA
* * *
52882655 CCTTCGGGATTTAG-CCGGATATAGCT-ACTTGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
52882694 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
52882734 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
52882774 CCTTCAGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
** *
52882814 CCTTCGGGACTTAGCCCGGA-ATTAGTTGCTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
52882854 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
52882873 TTACCATCCG
Statistics
Matches: 164, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
39 15 0.09
40 149 0.91
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:52890738 original size:40 final size:40
Alignment explanation
Indices: 52890661--52890878 Score: 325
Period size: 40 Copynumber: 5.5 Consensus size: 40
52890651 AAACCAAGTA
* *
52890661 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
52890700 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
52890740 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
52890780 CCTTCGAGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
** *
52890820 CCTTCGGGACTTAGCCCGGA-ATTAGTCGCTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
52890860 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
52890879 TTACCATCCG
Statistics
Matches: 165, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
39 15 0.09
40 150 0.91
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:52901827 original size:40 final size:40
Alignment explanation
Indices: 52901758--52901925 Score: 205
Period size: 40 Copynumber: 4.2 Consensus size: 40
52901748 CGGATGATAA
* * * *
52901758 CCGGACTAAGATCCGAAGGCATTCGTGCTAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* * * * * * *
52901798 CCAGGCTATGTCCTGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATAT
52901838 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
*
52901878 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
52901918 CC-GGCTAA
1 CCGGGCTAA
52901926 ATCCTGAAGA
Statistics
Matches: 109, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
39 8 0.07
40 99 0.91
41 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
Found at i:52902202 original size:22 final size:22
Alignment explanation
Indices: 52902162--52902203 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
52902152 GAATGTGCAT
*
52902162 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
52902184 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
52902204 TCAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Found at i:52904511 original size:25 final size:25
Alignment explanation
Indices: 52904483--52904552 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
52904473 CTCTTTTAAT
* *
52904483 AACTGGGGTAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
52904508 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
52904533 AACTGGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
52904553 AGCACTTCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:52904788 original size:27 final size:27
Alignment explanation
Indices: 52904758--52904918 Score: 187
Period size: 27 Copynumber: 6.0 Consensus size: 27
52904748 GGGAAAAATT
* * *
52904758 GTAATTTTACCCCACAAGGGTATCTCG
1 GTAATTCTACCCTACAAGGGTATTTCG
* * **
52904785 GTAATTCTACCCTATAGGGGTATTTTA
1 GTAATTCTACCCTACAAGGGTATTTCG
52904812 GTAATTCTACCCTACAAGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCG
* * **
52904839 GTAATTCTACCCTATAGGGGTATTTTA
1 GTAATTCTACCCTACAAGGGTATTTCG
* *
52904866 GTAATTCTACCCTATAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCG
* *
52904893 GTAATTCTACCATACAGGGGTATTTC
1 GTAATTCTACCCTACAAGGGTATTTC
52904919 AATAATTTTG
Statistics
Matches: 115, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 115 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.36
Consensus pattern (27 bp):
GTAATTCTACCCTACAAGGGTATTTCG
Found at i:52904924 original size:27 final size:27
Alignment explanation
Indices: 52904775--52904925 Score: 203
Period size: 27 Copynumber: 5.6 Consensus size: 27
52904765 TACCCCACAA
* *
52904775 GGGTATCTCGGTAATTCTACCCTATAG
1 GGGTATTTCAGTAATTCTACCCTATAG
* * *
52904802 GGGTATTTTAGTAATTCTACCCTACAA
1 GGGTATTTCAGTAATTCTACCCTATAG
*
52904829 GGGTATTTCGGTAATTCTACCCTATAG
1 GGGTATTTCAGTAATTCTACCCTATAG
*
52904856 GGGTATTTTAGTAATTCTACCCTATAG
1 GGGTATTTCAGTAATTCTACCCTATAG
* * *
52904883 GGGTATTTCGGTAATTCTACCATACAG
1 GGGTATTTCAGTAATTCTACCCTATAG
*
52904910 GGGTATTTCAATAATT
1 GGGTATTTCAGTAATT
52904926 TTGTAAATCG
Statistics
Matches: 107, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 107 1.00
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (27 bp):
GGGTATTTCAGTAATTCTACCCTATAG
Found at i:52904925 original size:54 final size:54
Alignment explanation
Indices: 52904758--52904917 Score: 257
Period size: 54 Copynumber: 3.0 Consensus size: 54
52904748 GGGAAAAATT
* * *
52904758 GTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTATAGGGGTATTTTA
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTTA
52904812 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTTA
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTTA
* * * *
52904866 GTAATTCTACCCTATAGGGGTATTTCGGTAATTCTACCATACAGGGGTATTT
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTT
52904918 CAATAATTTT
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 99 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (54 bp):
GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTTA
Found at i:52904951 original size:81 final size:81
Alignment explanation
Indices: 52904784--52904955 Score: 184
Period size: 81 Copynumber: 2.1 Consensus size: 81
52904774 AGGGTATCTC
* * **
52904784 GGTAATTCTACCCTATAGGGGTATTTTAGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTAC
1 GGTAATTCTACCCTATAGGGGTATTTCAGTAATTCTACCATACAAGGGTATTTCAATAATTCTAC
** ***
52904849 CCTATAGGGGTATTTT
66 CAAATAGGGGTAAAAT
* * * **
52904865 AGTAATTCTACCCTATAGGGGTATTTCGGTAATTCTACCATACAGGGGTATTTCAATAATT-TTG
1 GGTAATTCTACCCTATAGGGGTATTTCAGTAATTCTACCATACAAGGGTATTTCAATAATTCTAC
* *
52904929 TAAATCGAGGGTAAAAT
66 CAAATAG-GGGTAAAAT
52904946 GGTAATTCTA
1 GGTAATTCTA
52904956 AAAATCAGGG
Statistics
Matches: 73, Mismatches: 17, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
80 4 0.05
81 69 0.95
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (81 bp):
GGTAATTCTACCCTATAGGGGTATTTCAGTAATTCTACCATACAAGGGTATTTCAATAATTCTAC
CAAATAGGGGTAAAAT
Found at i:52905018 original size:27 final size:27
Alignment explanation
Indices: 52904910--52905390 Score: 322
Period size: 27 Copynumber: 17.8 Consensus size: 27
52904900 TACCATACAG
* * **
52904910 GGGTATTTCAATAATTTTGTAAATCGA
1 GGGTATTTTAGTAATTTTACAAATCGA
*** * * *
52904937 GGGTAAAATGGTAATTCTAAAAATC-A
1 GGGTATTTTAGTAATTTTACAAATCGA
* * *
52904963 GGGGTACTTTGGTAATTTTTACAAGTCGA
1 -GGGTATTTTAGTAA-TTTTACAAATCGA
*
52904992 GGGTATTTCAGTAATTTTACAAATCGA
1 GGGTATTTTAGTAATTTTACAAATCGA
* * *
52905019 GGGTATTTCAGAAATTTTGCAAA-CTGA
1 GGGTATTTTAGTAATTTTACAAATC-GA
*
52905046 GGGTATTTTAGTAATTTCACAAATC-A
1 GGGTATTTTAGTAATTTTACAAATCGA
* *
52905072 GGGGTATTTTGGTAATTTTACAAA-CCA
1 -GGGTATTTTAGTAATTTTACAAATCGA
* * * *
52905099 GAAGTATTTTAGTAATTTTATAAACCAA
1 G-GGTATTTTAGTAATTTTACAAATCGA
* *
52905127 GGGTATTTTGGTAATTTTACAAGTCGA
1 GGGTATTTTAGTAATTTTACAAATCGA
* *
52905154 GGGTATTTCAGTAATTTCACAAATC-A
1 GGGTATTTTAGTAATTTTACAAATCGA
* * *
52905180 GGGGTATTTTGGTAATTTTGCAAGTCGA
1 -GGGTATTTTAGTAATTTTACAAATCGA
* * *
52905208 GGGTATTTCAGTAATTTCACAAA-CCA
1 GGGTATTTTAGTAATTTTACAAATCGA
* *
52905234 GGGGTATTTT-GTAATTTCACAAA-CTA
1 -GGGTATTTTAGTAATTTTACAAATCGA
* *
52905260 GGGGTATTTTGGTAATTTTACAAA-CCA
1 -GGGTATTTTAGTAATTTTACAAATCGA
* *
52905287 GGGGTATTTTGGTAATTTTACAAA-CCA
1 -GGGTATTTTAGTAATTTTACAAATCGA
* *
52905314 GTGGTATTTT-GTTAATTTTACGAA-CTA
1 G-GGTATTTTAG-TAATTTTACAAATCGA
* * ** *
52905341 GAGGTATTTTGGTAATTCTACCCTATAG-
1 G-GGTATTTTAGTAATTTTA-CAAATCGA
*
52905369 GGGTATTTTAGTAATTTCACAA
1 GGGTATTTTAGTAATTTTACAA
52905391 TAAAGGGTAA
Statistics
Matches: 367, Mismatches: 69, Indels: 37
0.78 0.15 0.08
Matches are distributed among these distances:
26 36 0.10
27 302 0.82
28 28 0.08
29 1 0.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (27 bp):
GGGTATTTTAGTAATTTTACAAATCGA
Found at i:52905062 original size:54 final size:54
Alignment explanation
Indices: 52904947--52905357 Score: 401
Period size: 54 Copynumber: 7.6 Consensus size: 54
52904937 GGGTAAAATG
* * * * *
52904947 GTAATTCTAAAAATCAGGGGTACTTTGGTAATTTTTAC-AAGTCGAGGGTATTTCA
1 GTAATTTTACAAATCAGGGGTATTTTGGTAA-TTTTACAAACT-GAGGGTATTTTA
** * *
52905002 GTAATTTTACAAATC-GAGGGTATTTCAGAAATTTTGCAAACTGAGGGTATTTTA
1 GTAATTTTACAAATCAG-GGGTATTTTGGTAATTTTACAAACTGAGGGTATTTTA
* * *
52905056 GTAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAAC-CAGAAGTATTTTA
1 GTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACTGAG-GGTATTTTA
* * * * *
52905110 GTAATTTTATAAACCAAGGGTATTTTGGTAATTTTAC-AAGTCGAGGGTATTTCA
1 GTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACT-GAGGGTATTTTA
* * * *
52905164 GTAATTTCACAAATCAGGGGTATTTTGGTAATTTTGC-AAGTCGAGGGTATTTCA
1 GTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACT-GAGGGTATTTTA
* * * *
52905218 GTAATTTCACAAACCAGGGGTATTTT-GTAATTTCACAAACT-AGGGGTATTTTG
1 GTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACTGA-GGGTATTTTA
* *
52905271 GTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAAC-CAGTGGTATTTT-
1 GTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACTGAG-GGTATTTTA
* *
52905324 GTTAATTTTACGAA-CTAGAGGTATTTTGGTAATT
1 G-TAATTTTACAAATC-AGGGGTATTTTGGTAATT
52905358 CTACCCTATA
Statistics
Matches: 304, Mismatches: 39, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
52 1 0.00
53 48 0.16
54 226 0.74
55 29 0.10
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.38
Consensus pattern (54 bp):
GTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACTGAGGGTATTTTA
Found at i:52905426 original size:27 final size:26
Alignment explanation
Indices: 52905394--52905480 Score: 120
Period size: 27 Copynumber: 3.2 Consensus size: 26
52905384 TTCACAATAA
*
52905394 AGGGTAAAACGATAATTTTGTAAATCG
1 AGGGTAAAAC-ATAATTCTGTAAATCG
*
52905421 AGGGTAAAACAATAATTCTGTAAATCA
1 AGGGTAAAAC-ATAATTCTGTAAATCG
*
52905448 AGGGTAAAACAGTAATTCTATAAATCG
1 AGGGTAAAACA-TAATTCTGTAAATCG
52905475 AGGGTA
1 AGGGTA
52905481 CTTTGGTAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
26 1 0.02
27 53 0.98
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (26 bp):
AGGGTAAAACATAATTCTGTAAATCG
Found at i:52910888 original size:24 final size:24
Alignment explanation
Indices: 52910861--52910907 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
52910851 TTATAATATG
* * *
52910861 AAAATGACTATTTTGCCCCTAGGT
1 AAAATGACCATTATACCCCTAGGT
52910885 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
52910908 GTTTAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (24 bp):
AAAATGACCATTATACCCCTAGGT
Found at i:52911056 original size:26 final size:25
Alignment explanation
Indices: 52911019--52911088 Score: 97
Period size: 26 Copynumber: 2.8 Consensus size: 25
52911009 GGAAGTGCAC
*
52911019 AAAGGGCTTTTGCCCCAGTTTACTGA
1 AAAGGGCTTTTGCCCCAGTTT-CTCA
* *
52911045 GAAGGGCTTTTGCCCCAGTTTGTCA
1 AAAGGGCTTTTGCCCCAGTTTCTCA
52911070 AAAGGGC-TTTGCCCCAGTT
1 AAAGGGCTTTTGCCCCAGTT
52911089 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.30
25 8 0.20
26 20 0.50
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (25 bp):
AAAGGGCTTTTGCCCCAGTTTCTCA
Found at i:52911101 original size:24 final size:24
Alignment explanation
Indices: 52911019--52911101 Score: 89
Period size: 26 Copynumber: 3.3 Consensus size: 24
52911009 GGAAGTGCAC
*
52911019 AAAGGGCTTTTGCCCCAGTTTACTGA
1 AAAGGGCTTTTGCCCCAG-TTA-TTA
*
52911045 GAAGGGCTTTTGCCCCAGTT-TGTCA
1 AAAGGGCTTTTGCCCCAGTTAT-T-A
52911070 AAAGGGC-TTTGCCCCAGTTATTA
1 AAAGGGCTTTTGCCCCAGTTATTA
52911093 AAAGAGGCT
1 AAAG-GGCT
52911102 AGGCCTCCAG
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
23 6 0.12
24 16 0.33
25 10 0.20
26 17 0.35
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (24 bp):
AAAGGGCTTTTGCCCCAGTTATTA
Found at i:52911346 original size:31 final size:31
Alignment explanation
Indices: 52911310--52911373 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
52911300 GTTTACAGTG
*
52911310 AAGGCTTCGGCCTAGTAATATGAAATATGAA
1 AAGGCTTCGGCCCAGTAATATGAAATATGAA
* **
52911341 AAGGCTTTGGCCCAGTGTTATGAAATATGAA
1 AAGGCTTCGGCCCAGTAATATGAAATATGAA
52911372 AA
1 AA
52911374 ATGAAAAGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (31 bp):
AAGGCTTCGGCCCAGTAATATGAAATATGAA
Found at i:52916576 original size:43 final size:43
Alignment explanation
Indices: 52916528--52916877 Score: 547
Period size: 43 Copynumber: 8.1 Consensus size: 43
52916518 CCGGCATTAC
*
52916528 GCCTGCTAGGCACGAAGGCCCAAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
52916571 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
52916614 GCCTGCTAGGCACGAAGGCCTGAATACACATCACCAGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
52916657 GCCTGCTAGGCACGAAGGCCCGAATATATATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* * * * *
52916700 GCCTGCTAGGCACGAAAGGCCCGAATATATATCACCAGAACAAA
1 GCCTGCTAGGCACG-AAGGCCCGAATACACATCACCGGCACGAA
*
52916744 GCCTGCTAGGCACGAAGGCCCGAATATACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* * *
52916787 GCCTGCTAGGCATGAAGGCCCGAATACACATCACCGGTATGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
52916830 GCCAGCTAGGCACGAAGGCCCGAATATACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
52916873 GCCTG
1 GCCTG
52916878 TGAGATTTAA
Statistics
Matches: 282, Mismatches: 24, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
43 242 0.86
44 40 0.14
ACGTcount: A:0.32, C:0.32, G:0.25, T:0.12
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:52916806 original size:173 final size:172
Alignment explanation
Indices: 52916528--52916877 Score: 565
Period size: 173 Copynumber: 2.0 Consensus size: 172
52916518 CCGGCATTAC
* * *
52916528 GCCTGCTAGGCACGAAGGCCCAAATACACATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCG
1 GCCTGCTAGGCACGAAGGCCCAAATACACATCACCAGAACAAAGCCTGCTAGGCACGAAGGCCCG
*
52916593 AATACACATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCTGAATACACATCACCAGCACGAAG
66 AATACACATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAAG
* *
52916658 CCTGCTAGGCACGAAGGCCCGAATATATATCACCGGCACGAA
131 CCAGCTAGGCACGAAGGCCCGAATATACATCACCGGCACGAA
* * *
52916700 GCCTGCTAGGCACGAAAGGCCCGAATATATATCACCAGAACAAAGCCTGCTAGGCACGAAGGCCC
1 GCCTGCTAGGCACG-AAGGCCCAAATACACATCACCAGAACAAAGCCTGCTAGGCACGAAGGCCC
* * * * *
52916765 GAATATACATCACCGGCACGAAGCCTGCTAGGCATGAAGGCCCGAATACACATCACCGGTATGAA
65 GAATACACATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
52916830 GCCAGCTAGGCACGAAGGCCCGAATATACATCACCGGCACGAA
130 GCCAGCTAGGCACGAAGGCCCGAATATACATCACCGGCACGAA
52916873 GCCTG
1 GCCTG
52916878 TGAGATTTAA
Statistics
Matches: 163, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
172 14 0.09
173 149 0.91
ACGTcount: A:0.32, C:0.32, G:0.25, T:0.12
Consensus pattern (172 bp):
GCCTGCTAGGCACGAAGGCCCAAATACACATCACCAGAACAAAGCCTGCTAGGCACGAAGGCCCG
AATACACATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAAG
CCAGCTAGGCACGAAGGCCCGAATATACATCACCGGCACGAA
Found at i:52921443 original size:93 final size:93
Alignment explanation
Indices: 52921314--52921485 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
52921304 CGCCCATAAG
* * *
52921314 CGAACTCGGACTCAACTCAACGCGCTCGGGCGTTCGCATCCATAACTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAACTGAACTCGGACTCAACTCA
52921379 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
* *
52921407 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAACTGAACTCGGACTCAACTCA
52921472 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
52921486 TCAACCATCC
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:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAACTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATTTCA
Found at i:52921482 original size:46 final size:46
Alignment explanation
Indices: 52921307--52921482 Score: 191
Period size: 46 Copynumber: 3.8 Consensus size: 46
52921297 TGTAACCCGC
* * * *
52921307 CCATAAGCGAACTCGGACTCAACTCAACGCGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
52921353 CCATAA-CTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGC-GAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
52921403 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
52921446 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
52921483 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:52923117 original size:21 final size:20
Alignment explanation
Indices: 52923094--52923161 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
52923084 GTTGAGAACG
*
52923094 AAGTTGCTACTGCAGAAGAGG
1 AAGTTGCT-CTGCAGAAGAGA
52923115 AAGTT-CT-TGCAGAAGAGA
1 AAGTTGCTCTGCAGAAGAGA
* * *
52923133 AAGTTGTTGCTGAAGAAGAAA
1 AAGTTGCT-CTGCAGAAGAGA
52923154 AAGTTGCT
1 AAGTTGCT
52923162 GAAAATGAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 15 0.38
19 1 0.03
20 2 0.05
21 21 0.54
ACGTcount: A:0.37, C:0.10, G:0.29, T:0.24
Consensus pattern (20 bp):
AAGTTGCTCTGCAGAAGAGA
Found at i:52923127 original size:18 final size:18
Alignment explanation
Indices: 52923104--52923153 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
52923094 AAGTTGCTAC
*
52923104 TGCAGAAGAGGAAGTTCT
1 TGCAGAAGAGAAAGTTCT
*
52923122 TGCAGAAGAGAAAGTTGT
1 TGCAGAAGAGAAAGTTCT
*
52923140 TGCTGAAGAAGAAA
1 TGCAGAAG-AGAAA
52923154 AAGTTGCTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.40, C:0.08, G:0.32, T:0.20
Consensus pattern (18 bp):
TGCAGAAGAGAAAGTTCT
Found at i:52923693 original size:16 final size:16
Alignment explanation
Indices: 52923672--52923726 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
52923662 GTTTGGTTCA
*
52923672 CTGTAATAGAATAGGG
1 CTGTAATAGAATAGAG
**
52923688 CTGTAATTCAATAGAG
1 CTGTAATAGAATAGAG
*
52923704 CTGTAATGGAATAGAG
1 CTGTAATAGAATAGAG
52923720 CTGTAAT
1 CTGTAAT
52923727 CAGTAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.29
Consensus pattern (16 bp):
CTGTAATAGAATAGAG
Found at i:52923794 original size:44 final size:46
Alignment explanation
Indices: 52923708--52923801 Score: 149
Period size: 44 Copynumber: 2.1 Consensus size: 46
52923698 ATAGAGCTGT
52923708 AATGGAATAGAGCTGTAATCAGTAATTCAATTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATCAGTAATTCAATTGTTTGGTTGAATGG
*
52923754 AATGGAATAGAGCTGTAAT-AG-AATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATCAGTAATTCAAT-TGTTTGGTTGAATGG
52923798 AATG
1 AATG
52923802 ATGTTGTAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
43 1 0.02
44 24 0.52
45 2 0.04
46 19 0.41
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (46 bp):
AATGGAATAGAGCTGTAATCAGTAATTCAATTGTTTGGTTGAATGG
Found at i:52924011 original size:12 final size:11
Alignment explanation
Indices: 52923993--52924047 Score: 58
Period size: 12 Copynumber: 4.8 Consensus size: 11
52923983 AATAATATAT
52923993 ATTTTAATAAA
1 ATTTTAATAAA
*
52924004 ATTATTAATAAC
1 ATT-TTAATAAA
*
52924016 ATTATTAATAAT
1 ATT-TTAATAAA
52924028 A-TTTAATAATA
1 ATTTTAATAA-A
52924039 ATTTTAATA
1 ATTTTAATA
52924048 TAAAATTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 26 0.68
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTTTAATAAA
Found at i:52931427 original size:47 final size:47
Alignment explanation
Indices: 52931356--52931570 Score: 340
Period size: 47 Copynumber: 4.6 Consensus size: 47
52931346 CCCTTCGGGA
* * * * * *
52931356 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
52931403 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52931450 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52931497 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52931544 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
52931571 TATTAAAATA
Statistics
Matches: 159, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 159 1.00
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:52931434 original size:25 final size:25
Alignment explanation
Indices: 52931406--52931484 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
52931396 ACTCGGCCCT
52931406 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * * *
52931431 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
52931453 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
52931478 ATCACAT
1 ATCACAT
52931485 CGGCCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:52935633 original size:40 final size:40
Alignment explanation
Indices: 52935578--52936056 Score: 735
Period size: 40 Copynumber: 12.0 Consensus size: 40
52935568 ATTTTGTCCA
* ** * *
52935578 AGCAAGAATGC-CTTCGGGGTTTAGCACGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACT
* * *
52935617 AGCACGGATGCTCTTCGGAACTTAGTCCGGATACATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACT
* * *
52935657 AGCACGAATGCTCTTTGAGCCTTAGCCCGGATACATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACT
* *
52935697 AGCATGAATGCTCTTCGAGACTTAGCCCGGATACATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACT
52935737 AGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACT
* *
52935777 AGCACGAATGCTCTTCGAGACTTGGCCCGGATACATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACT
*
52935817 AGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCATT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACT
* *
52935857 AGCACGAATGCTCTTCGAGACTTGGCCCGGATACATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACT
* *
52935897 AGCACGAATGCTCTTCGAGACTTGGCCCGGATACATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACT
* *
52935937 AGCATGAATGCTCTTCGGGACTTAGCCTGGATACATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACT
*
52935977 AGCACGAATGCTCTTCGGGACTTAGCCCGGATGCATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACT
*
52936017 AGCACAAATGCTCTTCGGGACTTAGCCCGGATACATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACT
52936057 CTCAATTCTC
Statistics
Matches: 403, Mismatches: 36, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
39 9 0.02
40 394 0.98
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
AGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACT
Found at i:52937544 original size:47 final size:47
Alignment explanation
Indices: 52937473--52937687 Score: 295
Period size: 47 Copynumber: 4.6 Consensus size: 47
52937463 CCCTTCGGGA
* * * * * *
52937473 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * * *
52937520 CCTATCACATGTATACACTTTCACATTCATCACATTGGACATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52937567 CTTATCACATATATGCACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
52937614 CTTATCACATATATACACTTTCACATTCATCATATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52937661 CTTATCACACATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
52937688 TATTCAAATA
Statistics
Matches: 152, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 152 1.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:52937551 original size:25 final size:24
Alignment explanation
Indices: 52937523--52937601 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 24
52937513 ACTCGGCCCT
52937523 ATCACATGTATACACTTTCACATTC
1 ATCACAT-TATACACTTTCACATTC
** * *
52937548 ATCACATTGGACA--TTCGGCCTT-
1 ATCACATTATACACTTTC-ACATTC
*
52937570 ATCACATATATGCACTTTCACATTC
1 ATCACAT-TATACACTTTCACATTC
52937595 ATCACAT
1 ATCACAT
52937602 CGGCCATTAG
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
22 10 0.25
23 6 0.15
24 7 0.17
25 17 0.43
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (24 bp):
ATCACATTATACACTTTCACATTC
Found at i:52944954 original size:23 final size:23
Alignment explanation
Indices: 52944928--52944977 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
52944918 ACCCTATGCA
52944928 ATGCAACATA-ATATCATACATGG-
1 ATGCAACATACATAT-A-ACATGGC
52944951 ATGCAACATACATATAACATGGC
1 ATGCAACATACATATAACATGGC
52944974 ATGC
1 ATGC
52944978 TCAAATACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.24
23 15 0.60
24 4 0.16
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (23 bp):
ATGCAACATACATATAACATGGC
Found at i:52945058 original size:27 final size:27
Alignment explanation
Indices: 52945015--52945132 Score: 103
Period size: 27 Copynumber: 4.4 Consensus size: 27
52945005 CAAATTTATC
* * *
52945015 ATTTTACCTTACCGGGGTATTACAGTT
1 ATTTTACCCTACAGGGGTATTTCAGTT
*
52945042 ATTTTACCCTACAGGGGTATTTCGGTT
1 ATTTTACCCTACAGGGGTATTTCAGTT
* ** * *
52945069 ATTCTACCCTATGGGGGTATTTCTGTA
1 ATTTTACCCTACAGGGGTATTTCAGTT
* * * *
52945096 ATTTTACCCTA-TGACGGTATTTCGGTC
1 ATTTTACCCTACAG-GGGTATTTCAGTT
52945123 ATTTTACCCT
1 ATTTTACCCT
52945133 TGAGGGTGTC
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
26 1 0.01
27 75 0.99
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.42
Consensus pattern (27 bp):
ATTTTACCCTACAGGGGTATTTCAGTT
Found at i:52945152 original size:26 final size:27
Alignment explanation
Indices: 52945057--52945152 Score: 86
Period size: 27 Copynumber: 3.6 Consensus size: 27
52945047 ACCCTACAGG
* * * **
52945057 GGTATTTCGGTTATTCTACCCTATGGG
1 GGTATCTCGGTCATTTTACCCTATGAC
* * *
52945084 GGTATTTCTGTAATTTTACCCTATGAC
1 GGTATCTCGGTCATTTTACCCTATGAC
* *
52945111 GGTATTTCGGTCATTTTACCCT-TGAG
1 GGTATCTCGGTCATTTTACCCTATGAC
*
52945137 GGTGTCTCGGTCATTT
1 GGTATCTCGGTCATTT
52945153 GATCACATAA
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
26 17 0.29
27 42 0.71
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.43
Consensus pattern (27 bp):
GGTATCTCGGTCATTTTACCCTATGAC
Found at i:52945185 original size:27 final size:27
Alignment explanation
Indices: 52945146--52945513 Score: 483
Period size: 27 Copynumber: 13.8 Consensus size: 27
52945136 GGGTGTCTCG
* * * * *
52945146 GTCATTTGATCACATAAAGGCAAAATT
1 GTCATTTTATCACATGAGGGTAAAATC
* * *
52945173 ATCATTTTATCACATAAGGGCAAAATC
1 GTCATTTTATCACATGAGGGTAAAATC
* * * *
52945200 ATCATTTTATCATATAAGGGTAAAATT
1 GTCATTTTATCACATGAGGGTAAAATC
* * * * *
52945227 GTCATTTCATTATATAAGGGAAAAATC
1 GTCATTTTATCACATGAGGGTAAAATC
*
52945254 GTCATTTCATCACATGAGGGTAAAATC
1 GTCATTTTATCACATGAGGGTAAAATC
52945281 GTCATTTTATCAC---A-GGTAAAATC
1 GTCATTTTATCACATGAGGGTAAAATC
52945304 GTCATTTTATCACATGAGGGTAAAATC
1 GTCATTTTATCACATGAGGGTAAAATC
*
52945331 GTCATTTTATTACATGAGGGTAAAATC
1 GTCATTTTATCACATGAGGGTAAAATC
*
52945358 ATCATTTTATCACATGAGGGTAAAATC
1 GTCATTTTATCACATGAGGGTAAAATC
*
52945385 GTCATTTTATCACATGAGGGTAAAGTC
1 GTCATTTTATCACATGAGGGTAAAATC
52945412 GTCATTTTATCACATGAGGGTAAAATC
1 GTCATTTTATCACATGAGGGTAAAATC
* *
52945439 GTCATTTTATCACATGAGGGTAAAGTA
1 GTCATTTTATCACATGAGGGTAAAATC
*
52945466 GTCATTTTATCACATGAGGGTAAAATT
1 GTCATTTTATCACATGAGGGTAAAATC
*
52945493 ATCATTTTATCACATGAGGGT
1 GTCATTTTATCACATGAGGGT
52945514 TCAAGTACAC
Statistics
Matches: 309, Mismatches: 28, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
23 22 0.07
24 1 0.00
26 1 0.00
27 285 0.92
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (27 bp):
GTCATTTTATCACATGAGGGTAAAATC
Found at i:52947389 original size:48 final size:48
Alignment explanation
Indices: 52947284--52947416 Score: 151
Period size: 48 Copynumber: 2.8 Consensus size: 48
52947274 CTGTGGGCTT
* * * * *
52947284 GAACATATCTTATGTTCCCCAGCTATTCTAATAAGTGTATTAAGTGCAA
1 GAACATATTTTATGTTCCTCAGCAATTCTGATAAG-ATATTAAGTGCAA
* * *
52947333 GAATATATTTTATGTTCCTCAGCAATGCTGATAA-ATATGTAAGTGCGA
1 GAACATATTTTATGTTCCTCAGCAATTCTGATAAGATAT-TAAGTGCAA
* *
52947381 GAACATATTTTATGTTTCTCAGCCATTCTGATAAGA
1 GAACATATTTTATGTTCCTCAGCAATTCTGATAAGA
52947417 CAAATATGTA
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
47 3 0.04
48 38 0.54
49 29 0.41
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (48 bp):
GAACATATTTTATGTTCCTCAGCAATTCTGATAAGATATTAAGTGCAA
Found at i:52950614 original size:3 final size:3
Alignment explanation
Indices: 52950606--52950637 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
52950596 GTTTGAAAAC
*
52950606 ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
52950638 GAGAGTTGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:52950957 original size:25 final size:25
Alignment explanation
Indices: 52950920--52950986 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
52950910 GTAGAATATT
52950920 TAATATGTAAATTATATTTAAAATAA
1 TAATAT-TAAATTATATTTAAAATAA
* **
52950946 TAATATTAAATTATTTTTTTAATAA
1 TAATATTAAATTATATTTAAAATAA
* *
52950971 TATTGAATAAATTATA
1 TAAT-ATTAAATTATA
52950987 AATTATAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 19 0.56
26 15 0.44
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (25 bp):
TAATATTAAATTATATTTAAAATAA
Found at i:52955160 original size:22 final size:22
Alignment explanation
Indices: 52955120--52955161 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
52955110 ACGGTTTATC
*
52955120 AGGGGTACACGGCTATGTGGAA
1 AGGGGTACACGGCCATGTGGAA
*
52955142 AGGGGTACACGGCCGTGTGG
1 AGGGGTACACGGCCATGTGG
52955162 CTAGGTCCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.17, G:0.45, T:0.17
Consensus pattern (22 bp):
AGGGGTACACGGCCATGTGGAA
Found at i:52956210 original size:3 final size:3
Alignment explanation
Indices: 52956202--52956226 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
52956192 TTATTCGATC
52956202 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
52956227 TTGTAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:52956658 original size:27 final size:27
Alignment explanation
Indices: 52956619--52956682 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
52956609 ATCTAAATCC
*
52956619 AAATGTAAGAACCTTATGGTTTCATTA
1 AAATGTAAAAACCTTATGGTTTCATTA
52956646 AAATGTAAAAACCTTATGGTTTCATTA
1 AAATGTAAAAACCTTATGGTTTCATTA
*
52956673 AATTGTAAAA
1 AAATGTAAAA
52956683 CCTATTTAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (27 bp):
AAATGTAAAAACCTTATGGTTTCATTA
Found at i:52957588 original size:19 final size:20
Alignment explanation
Indices: 52957502--52957598 Score: 58
Period size: 21 Copynumber: 4.7 Consensus size: 20
52957492 GACCCGATTT
*
52957502 TTTTTTTTTGCAAAATT-AAAG
1 TTTTTTTTT--AAAATTAAAAC
52957523 TTTTCTTTTTAAAA--AAATCAC
1 TTTT-TTTTTAAAATTAAA--AC
* *
52957544 TATTTTTCTTAAAGATCAAAAC
1 T-TTTTTTTTAAA-ATTAAAAC
52957566 TTTTTTTTTAAAATTAAAA-
1 TTTTTTTTTAAAATTAAAAC
**
52957585 TTTTCCTTTAAAAT
1 TTTTTTTTTAAAAT
52957599 GACTAAAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
19 14 0.23
20 10 0.16
21 23 0.37
22 12 0.19
24 3 0.05
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (20 bp):
TTTTTTTTTAAAATTAAAAC
Found at i:52958645 original size:42 final size:42
Alignment explanation
Indices: 52958595--52958739 Score: 175
Period size: 42 Copynumber: 3.5 Consensus size: 42
52958585 GCCTTCATAT
* * * *
52958595 AATGCAATGAAAAGTAAATAAACCTCCATACCTGGGCCTTTA
1 AATGCAACGAAAAGTAAACAAACATCCACACCTGGGCCTTTA
* * *
52958637 AATGCAATGCAAAGTAAACGAAA-ATCCCCACCTGGGCCTTTA
1 AATGCAACGAAAAGTAAAC-AAACATCCACACCTGGGCCTTTA
* * * *
52958679 AATGCAACGAAAAGTAAACAGACATCCACACTTGAGCCTCTA
1 AATGCAACGAAAAGTAAACAAACATCCACACCTGGGCCTTTA
52958721 AATGCAACGAAAAGTAAAC
1 AATGCAACGAAAAGTAAAC
52958740 GGACCTCCAC
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
41 2 0.02
42 84 0.94
43 3 0.03
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.19
Consensus pattern (42 bp):
AATGCAACGAAAAGTAAACAAACATCCACACCTGGGCCTTTA
Found at i:52958749 original size:42 final size:42
Alignment explanation
Indices: 52958595--52958769 Score: 172
Period size: 42 Copynumber: 4.2 Consensus size: 42
52958585 GCCTTCATAT
* * * * * *
52958595 AATGCAATGAAAAGTAAATAAACCTCCATACCTGGGCCTTTA
1 AATGCAACGAAAAGTAAACAAACATCCACACCTGAGCCTCTA
* * * * *
52958637 AATGCAATGCAAAGTAAACGAAA-ATCCCCACCTGGGCCTTTA
1 AATGCAACGAAAAGTAAAC-AAACATCCACACCTGAGCCTCTA
* *
52958679 AATGCAACGAAAAGTAAACAGACATCCACACTTGAGCCTCTA
1 AATGCAACGAAAAGTAAACAAACATCCACACCTGAGCCTCTA
** * * *
52958721 AATGCAACGAAAAGTAAACGGACCTCCACACTTGAGTCTCTA
1 AATGCAACGAAAAGTAAACAAACATCCACACCTGAGCCTCTA
52958763 AATGCAA
1 AATGCAA
52958770 TATGAGACAT
Statistics
Matches: 116, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
41 2 0.02
42 111 0.96
43 3 0.03
ACGTcount: A:0.41, C:0.25, G:0.15, T:0.19
Consensus pattern (42 bp):
AATGCAACGAAAAGTAAACAAACATCCACACCTGAGCCTCTA
Found at i:52960503 original size:13 final size:13
Alignment explanation
Indices: 52960485--52960509 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52960475 CGTGAAGTCA
52960485 AATTTCTTGCATC
1 AATTTCTTGCATC
52960498 AATTTCTTGCAT
1 AATTTCTTGCAT
52960510 GTCCAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.08, T:0.48
Consensus pattern (13 bp):
AATTTCTTGCATC
Found at i:52965715 original size:454 final size:457
Alignment explanation
Indices: 52964824--52965738 Score: 1746
Period size: 454 Copynumber: 2.0 Consensus size: 457
52964814 CTTTGATATA
52964824 CAAACTTTTAAAAATGATTACATCTCAGAGGACTCAAGGATAGCAGGTAATGGTATGAGTTGCCA
1 CAAACTTTTAAAAATGATTACATCTCAGAGGACTCAAGGATAGCAGGTAATGGTATGAGTTGCCA
52964889 GTTGTCCAAGGTAGGTGTTATACCAGTGAGCTATCCTTGGTCCTTTTCAAATGGCATTTATTTCC
66 GTTGTCCAAGGTAGGTGTTATACCAGTGAGCTATCCTTGGTCCTTTTCAAATGGCATTTATTTCC
52964954 AAAGTTAGAAAATTATTTGGATTTGTCATAAAAAATGTTTTTTTTTAAATTTTTTTTAAAATAAT
131 AAAGTTAGAAAATTATTTGGATTTGTCATAAAAAATGTTTTTTTTT-AATTTTTTTTAAAATAAT
* *
52965019 GTTTCTGAATAAAAAAATGAGCAAATGACTGAACAAATGGATTAATGACTGTTCGATTTATAATT
195 GTTTCTGAATAAAAAAATGAGCAAATGACTGAACAAATGGATTAATGACTGTTCAACTTATAATT
52965084 TTTTTTTCTATTTTTCATTCATACTTAAGGAAAGTCATAGTCGATCCTATTGCCATAAGGCAAAC
260 TTTTTTTCTATTTTTCATTCATACTTAAGGAAAGTCATAGTCGATCCTATTGCCATAAGGCAAAC
52965149 CTCTACTCGTCGTTCTTCTTCTTCCTCCTCATGAGCTTGATGGAATTTTGGTAATGTGCCTGAGC
325 CTCTACTCGTCGTTCTTCTTCTTCCTCCTCATGAGCTTGATGGAATTTTGGTAATGTGCCTGAGC
* *
52965214 CACCTCCAGAAGTTTCATTGCAAGCTCGTTTCTAGTCGTAAAAGGGGTAGATTCTTTTTTGAGAT
390 CACCTCCAGAAGTTTCATTGCAAGCTCGTTCCTAGTCGTAAAAGGGGTAGATTCTTTTTTAAGAT
52965279 CCT
455 CCT
52965282 CAAACTTTTAAAAATGATTACATCTCAGAGGACTCAAGGATAGCAGGTAATGGTATGAGTTGCCA
1 CAAACTTTTAAAAATGATTACATCTCAGAGGACTCAAGGATAGCAGGTAATGGTATGAGTTGCCA
52965347 GTTGTCCAAGGTAGGTGTTATACCAGTGAGCTATCCTTGGTCCTTTTCAAATGGCATTTATTTCC
66 GTTGTCCAAGGTAGGTGTTATACCAGTGAGCTATCCTTGGTCCTTTTCAAATGGCATTTATTTCC
52965412 AAAGTTAGAAAATTATTTGGATTTGTCATAAAAAATGTTTTTTTTT-A-TTTTTTTAAAATAATG
131 AAAGTTAGAAAATTATTTGGATTTGTCATAAAAAATGTTTTTTTTTAATTTTTTTTAAAATAATG
*
52965475 TTTCTGAATAAAAAAATGAGCGAATGACTGAACAAATGGATTAATGACTGTTCAACTTATAA-TT
196 TTTCTGAATAAAAAAATGAGCAAATGACTGAACAAATGGATTAATGACTGTTCAACTTATAATTT
*
52965539 TTTTTTCTATTTTTCATTCATACTTAAGGAAAGTCATAGTCGATCCTATTGCCATAGGGCAAACC
261 TTTTTTCTATTTTTCATTCATACTTAAGGAAAGTCATAGTCGATCCTATTGCCATAAGGCAAACC
52965604 TCTACTCGTCGTTCTTCTTCTTCCTCCTCATGAGCTTGATGGAATTTTGGTAATGTGCCTGAGCC
326 TCTACTCGTCGTTCTTCTTCTTCCTCCTCATGAGCTTGATGGAATTTTGGTAATGTGCCTGAGCC
52965669 ACCTCCAGAAGTTTCATTGCAAGCTCGTTCCTAGTCGTAAAAGGGGTAGATTCTTTTTTAAGATC
391 ACCTCCAGAAGTTTCATTGCAAGCTCGTTCCTAGTCGTAAAAGGGGTAGATTCTTTTTTAAGATC
52965734 CT
456 CT
52965736 CAA
1 CAA
52965739 TCTATTCAAA
Statistics
Matches: 451, Mismatches: 6, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
454 199 0.44
455 75 0.17
456 1 0.00
458 176 0.39
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.37
Consensus pattern (457 bp):
CAAACTTTTAAAAATGATTACATCTCAGAGGACTCAAGGATAGCAGGTAATGGTATGAGTTGCCA
GTTGTCCAAGGTAGGTGTTATACCAGTGAGCTATCCTTGGTCCTTTTCAAATGGCATTTATTTCC
AAAGTTAGAAAATTATTTGGATTTGTCATAAAAAATGTTTTTTTTTAATTTTTTTTAAAATAATG
TTTCTGAATAAAAAAATGAGCAAATGACTGAACAAATGGATTAATGACTGTTCAACTTATAATTT
TTTTTTCTATTTTTCATTCATACTTAAGGAAAGTCATAGTCGATCCTATTGCCATAAGGCAAACC
TCTACTCGTCGTTCTTCTTCTTCCTCCTCATGAGCTTGATGGAATTTTGGTAATGTGCCTGAGCC
ACCTCCAGAAGTTTCATTGCAAGCTCGTTCCTAGTCGTAAAAGGGGTAGATTCTTTTTTAAGATC
CT
Found at i:52984862 original size:207 final size:207
Alignment explanation
Indices: 52984332--52985232 Score: 1509
Period size: 207 Copynumber: 4.4 Consensus size: 207
52984322 GCAGATCTGG
* * *
52984332 CTGAAGCAAGATCCAAGATGATTTGACATCCTTGTGCTTAAAAGGAATAAATCGAAGACATAGCT
1 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
52984397 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
66 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* * * ** * * **
52984462 AGAGCAGATCGATGTTTGGCGTCTCCATATTCGACTCAGGGTAGACACATAGCAGATCTAACCTT
131 AGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTT
* *
52984527 CAGATGATTAGA
196 CAGATGTTTATA
* * *
52984539 CTGAAGC-AGATCCAATATGATTTGGCATCCTTGTGTTTACAAGAAACAAATCGAA-ATCATAGC
1 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGA-CATAGC
* *
52984602 TGATTTGGCTTTCACGAGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTTTGTATTGTCA
65 TGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCA
* * * *
52984667 GAGAACAAATTGAAGGTTGGCGTCTCCATATTCAACGGAGAGCAGACACATAGTAGATCTGGCCT
130 GAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCT
52984732 TCAGATGTTTATA
195 TCAGATGTTTATA
*
52984745 CTGAAGCAAGATCCAAGATAATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
1 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
*
52984810 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTCGGCATCTCTGTATTGTCAG
66 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
*
52984875 AGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAAAGCAGACACATAGCAGATCTGGCCTT
131 AGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTT
52984940 CAGATGTTTATA
196 CAGATGTTTATA
52984952 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
1 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
52985017 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
66 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* *
52985082 AGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGAGTAGACACATAGCAGATCTGGCCTT
131 AGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTT
52985147 CAGATGTTTATA
196 CAGATGTTTATA
*
52985159 CTGAAGCAAGATCCAAGATAATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
1 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
*
52985224 AATTTGGCT
66 GATTTGGCT
52985233 GAAGCAGACC
Statistics
Matches: 649, Mismatches: 42, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
205 1 0.00
206 181 0.28
207 466 0.72
208 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (207 bp):
CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
AGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTT
CAGATGTTTATA
Found at i:52987236 original size:3 final size:3
Alignment explanation
Indices: 52987224--52987269 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
52987214 TCAATATATA
52987224 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TA- TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
52987267 TAT
1 TAT
52987270 CACATTTGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 6 0.15
3 30 0.77
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:52988695 original size:8 final size:8
Alignment explanation
Indices: 52988684--52988734 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
52988674 GTAAATTAGG
52988684 TAATTAAA
1 TAATTAAA
52988692 TAATTAAA
1 TAATTAAA
*
52988700 TGA-TAAA
1 TAATTAAA
*
52988707 TTAAATAAA
1 -TAATTAAA
52988716 TTAAATTAAA
1 -T-AATTAAA
52988726 TAATTAAA
1 TAATTAAA
52988734 T
1 T
52988735 GATAAATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
7 4 0.11
8 20 0.54
9 7 0.19
10 6 0.16
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (8 bp):
TAATTAAA
Found at i:52988710 original size:12 final size:12
Alignment explanation
Indices: 52988693--52988746 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
52988683 GTAATTAAAT
52988693 AATTAAATGATA
1 AATTAAATGATA
52988705 AATT-AA--ATA
1 AATTAAATGATA
* *
52988714 AATTAAATTAAA
1 AATTAAATGATA
52988726 TAATTAAATGATA
1 -AATTAAATGATA
52988739 AATTAAAT
1 AATTAAAT
52988747 AAAATAAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
9 7 0.20
10 2 0.06
11 2 0.06
12 14 0.40
13 10 0.29
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (12 bp):
AATTAAATGATA
Found at i:52988710 original size:20 final size:20
Alignment explanation
Indices: 52988685--52988748 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
52988675 TAAATTAGGT
52988685 AATTAAATAATTAAATGATA
1 AATTAAATAATTAAATGATA
52988705 AATT--A-AA-TAAAT--TA
1 AATTAAATAATTAAATGATA
52988719 AATTAAATAATTAAATGATA
1 AATTAAATAATTAAATGATA
52988739 AATTAAATAA
1 AATTAAATAA
52988749 AATAAAACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
14 6 0.16
16 6 0.16
17 4 0.11
18 6 0.16
20 16 0.42
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
AATTAAATAATTAAATGATA
Found at i:52988720 original size:5 final size:5
Alignment explanation
Indices: 52988685--52988751 Score: 54
Period size: 5 Copynumber: 13.6 Consensus size: 5
52988675 TAAATTAGGT
52988685 AATTA AA-T- AATTA AATGATA AATTA AA-TA AATTA AATTA AA-T- AATTA
1 AATTA AATTA AATTA AAT--TA AATTA AATTA AATTA AATTA AATTA AATTA
*
52988732 AATGATA AATTA AATAA AAT
1 AAT--TA AATTA AATTA AAT
52988752 AAAACAAGCT
Statistics
Matches: 52, Mismatches: 1, Indels: 18
0.73 0.01 0.25
Matches are distributed among these distances:
3 4 0.08
4 8 0.15
5 30 0.58
7 10 0.19
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (5 bp):
AATTA
Found at i:52988725 original size:34 final size:34
Alignment explanation
Indices: 52988685--52988754 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
52988675 TAAATTAGGT
*
52988685 AATTAAATAATTAAATGATAAATTAAATAAATTA
1 AATTAAATAATTAAATGATAAATTAAATAAAATA
52988719 AATTAAATAATTAAATGATAAATTAAATAAAATA
1 AATTAAATAATTAAATGATAAATTAAATAAAATA
52988753 AA
1 AA
52988755 ACAAGCTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (34 bp):
AATTAAATAATTAAATGATAAATTAAATAAAATA
Found at i:52991073 original size:5 final size:5
Alignment explanation
Indices: 52991059--52991117 Score: 52
Period size: 5 Copynumber: 11.6 Consensus size: 5
52991049 AGCTTGTTTT
*
52991059 ATTTT ATTTA ATTTA TCATTTA A-TT- ATTTA ATTTA ATTT- ATTTA ATTTA
1 ATTTA ATTTA ATTTA --ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
52991108 TCATTTA ATT
1 --ATTTA ATT
52991118 ATTTAATCAC
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
3 1 0.02
4 8 0.17
5 27 0.59
7 10 0.22
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (5 bp):
ATTTA
Found at i:52991081 original size:12 final size:12
Alignment explanation
Indices: 52991064--52991117 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
52991054 GTTTTATTTT
52991064 ATTTAATTTATC
1 ATTTAATTTATC
* *
52991076 ATTTAATTATTTA
1 ATTTAATT-TATC
52991089 ATTTAA-TT-T-
1 ATTTAATTTATC
52991098 ATTTAATTTATC
1 ATTTAATTTATC
52991110 ATTTAATT
1 ATTTAATT
52991118 ATTTAATCAC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
9 6 0.17
10 3 0.08
11 2 0.06
12 17 0.47
13 8 0.22
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTTAATTTATC
Found at i:52991087 original size:20 final size:20
Alignment explanation
Indices: 52991062--52991124 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
52991052 TTGTTTTATT
52991062 TTATTTAATTTATCATTTAA
1 TTATTTAATTTATCATTTAA
52991082 TTATTTAATTTA--A--T--
1 TTATTTAATTTATCATTTAA
52991096 TTATTTAATTTATCATTTAA
1 TTATTTAATTTATCATTTAA
52991116 TTATTTAAT
1 TTATTTAAT
52991125 CACCTAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
14 12 0.32
16 2 0.05
18 2 0.05
20 21 0.57
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTAATTTATCATTTAA
Found at i:52991103 original size:34 final size:34
Alignment explanation
Indices: 52991056--52991124 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
52991046 GAAAGCTTGT
*
52991056 TTTATTTTATTTAATTTATCATTTAATTATTTAA
1 TTTAATTTATTTAATTTATCATTTAATTATTTAA
52991090 TTTAATTTATTTAATTTATCATTTAATTATTTAA
1 TTTAATTTATTTAATTTATCATTTAATTATTTAA
52991124 T
1 T
52991125 CACCTAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (34 bp):
TTTAATTTATTTAATTTATCATTTAATTATTTAA
Found at i:52991554 original size:16 final size:18
Alignment explanation
Indices: 52991517--52991556 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
52991507 GTTTTTTTAG
52991517 TATTTGTGCATATTATATT
1 TATTTGTG-ATATTATATT
52991536 TATTTGTG-TATTA-ATT
1 TATTTGTGATATTATATT
52991552 TATTT
1 TATTT
52991557 AGTTGTCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
17 5 0.24
19 8 0.38
ACGTcount: A:0.25, C:0.03, G:0.10, T:0.62
Consensus pattern (18 bp):
TATTTGTGATATTATATT
Found at i:52996721 original size:14 final size:14
Alignment explanation
Indices: 52996702--52996731 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
52996692 TATCTTATAA
52996702 ATATGCGTGAATCT
1 ATATGCGTGAATCT
*
52996716 ATATGCGTTAATCT
1 ATATGCGTGAATCT
52996730 AT
1 AT
52996732 CTTGAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (14 bp):
ATATGCGTGAATCT
Found at i:53007346 original size:93 final size:93
Alignment explanation
Indices: 53007240--53007412 Score: 274
Period size: 93 Copynumber: 1.9 Consensus size: 93
53007230 CGCCCATAAG
* * *
53007240 CGAACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGAACTCAACTCAACGAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
53007305 ACGAGCTCGGATGCCTAGTTACATCTCT
66 ACGAGCTCGGATGCCTAGTTACATCTCT
* * *
53007333 CGAACTCGGACTCAACTCAACGAATTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGAACTCAACTCAACGAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
* *
53007398 ATGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
53007413 CAAATATCCT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
CGAACTCGAACTCAACTCAACGAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCT
Found at i:53007408 original size:46 final size:46
Alignment explanation
Indices: 53007233--53007408 Score: 171
Period size: 46 Copynumber: 3.8 Consensus size: 46
53007223 TGTAACCCGC
* * * *
53007233 CCATAAGCGAACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
* * *
53007279 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA---C-ATTTGCAT
**
53007329 CTC-T---CGAACTCGGACTCAACTCAACGAATTCGGACATTTGCAT
1 C-CATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
* * *
53007372 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
53007409 TGCCCAAATA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 1 0.01
43 8 0.08
44 1 0.01
46 61 0.58
47 27 0.25
49 1 0.01
50 6 0.06
51 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
Found at i:53019172 original size:207 final size:207
Alignment explanation
Indices: 53018663--53019563 Score: 1509
Period size: 207 Copynumber: 4.4 Consensus size: 207
53018653 GCAGATCTGG
53018663 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
1 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
* *
53018728 GATTTGGCTTTCACGTGCTTACTATGAAGCAAATCTAAGATGATTTGGCATCTTTGTATTGTCAG
66 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* * * ** *
53018793 AGAGCAGATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTG
131 AGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTT
* *
53018858 CAGATGATTAGA
196 CAGATGTTTATA
* * * *
53018870 CTAAAGC-AGATCCAATATGATTTGGCATCCTTGTGTTTACAAGAAACAAATCGAA-ATCATAGC
1 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGA-CATAGC
** *
53018933 TGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGATATCTCTGTATTGTTA
65 TGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCA
* *
53018998 GAGAACAAATCGAAGGTTGGCGTATCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCT
130 GAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCT
*
53019063 TCAGATGTTAATA
195 TCAGATGTTTATA
*
53019076 CTGAAGCAAGATCCAAGATAATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
1 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
*
53019141 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAC
66 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* * * *
53019206 AGAACAAATCGAAGTTTGGCATCTCCATATTCGACGGAAAGCAGACATATAGCAGATCTGGTCTT
131 AGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTT
53019271 CAGATGTTTATA
196 CAGATGTTTATA
*
53019283 CTGAACCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
1 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
53019348 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
66 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* *
53019413 AGAACAAATCGAAGTTTGGCGTCTCCATATTCGATGGAGAGTAGACACATAGCAGATCTGGCCTT
131 AGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTT
53019478 CAGATGTTTATA
196 CAGATGTTTATA
*
53019490 CTGAAGCAAGATCCAAGATAATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
1 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
53019555 GATTTGGCT
66 GATTTGGCT
53019564 GAAGCAGACC
Statistics
Matches: 644, Mismatches: 47, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
205 1 0.00
206 184 0.29
207 458 0.71
208 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (207 bp):
CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
AGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTT
CAGATGTTTATA
Found at i:53021488 original size:3 final size:3
Alignment explanation
Indices: 53021476--53021515 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
53021466 TCAATATATA
53021476 TAT T-T TAT TAT TAT TAT TAT TAT TAT T-T TA- TAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
53021516 CACATTTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
2 6 0.18
3 24 0.73
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:53022940 original size:8 final size:8
Alignment explanation
Indices: 53022929--53022979 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
53022919 GTAAATTAGG
53022929 TAATTAAA
1 TAATTAAA
53022937 TAATTAAA
1 TAATTAAA
*
53022945 TGA-TAAA
1 TAATTAAA
*
53022952 TTAAATAAA
1 -TAATTAAA
53022961 TTAAATTAAA
1 -T-AATTAAA
53022971 TAATTAAA
1 TAATTAAA
53022979 T
1 T
53022980 GATAAATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
7 4 0.11
8 20 0.54
9 7 0.19
10 6 0.16
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (8 bp):
TAATTAAA
Found at i:53022955 original size:12 final size:12
Alignment explanation
Indices: 53022938--53022991 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
53022928 GTAATTAAAT
53022938 AATTAAATGATA
1 AATTAAATGATA
53022950 AATT-AA--ATA
1 AATTAAATGATA
* *
53022959 AATTAAATTAAA
1 AATTAAATGATA
53022971 TAATTAAATGATA
1 -AATTAAATGATA
53022984 AATTAAAT
1 AATTAAAT
53022992 AAAATAAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
9 7 0.20
10 2 0.06
11 2 0.06
12 14 0.40
13 10 0.29
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (12 bp):
AATTAAATGATA
Found at i:53022955 original size:20 final size:20
Alignment explanation
Indices: 53022930--53022993 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
53022920 TAAATTAGGT
53022930 AATTAAATAATTAAATGATA
1 AATTAAATAATTAAATGATA
53022950 AATT--A-AA-TAAAT--TA
1 AATTAAATAATTAAATGATA
53022964 AATTAAATAATTAAATGATA
1 AATTAAATAATTAAATGATA
53022984 AATTAAATAA
1 AATTAAATAA
53022994 AATAAAACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
14 6 0.16
16 6 0.16
17 4 0.11
18 6 0.16
20 16 0.42
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
AATTAAATAATTAAATGATA
Found at i:53022965 original size:5 final size:5
Alignment explanation
Indices: 53022930--53022996 Score: 54
Period size: 5 Copynumber: 13.6 Consensus size: 5
53022920 TAAATTAGGT
53022930 AATTA AA-T- AATTA AATGATA AATTA AA-TA AATTA AATTA AA-T- AATTA
1 AATTA AATTA AATTA AAT--TA AATTA AATTA AATTA AATTA AATTA AATTA
*
53022977 AATGATA AATTA AATAA AAT
1 AAT--TA AATTA AATTA AAT
53022997 AAAACAAGCT
Statistics
Matches: 52, Mismatches: 1, Indels: 18
0.73 0.01 0.25
Matches are distributed among these distances:
3 4 0.08
4 8 0.15
5 30 0.58
7 10 0.19
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (5 bp):
AATTA
Found at i:53022970 original size:34 final size:34
Alignment explanation
Indices: 53022930--53022999 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
53022920 TAAATTAGGT
*
53022930 AATTAAATAATTAAATGATAAATTAAATAAATTA
1 AATTAAATAATTAAATGATAAATTAAATAAAATA
53022964 AATTAAATAATTAAATGATAAATTAAATAAAATA
1 AATTAAATAATTAAATGATAAATTAAATAAAATA
53022998 AA
1 AA
53023000 ACAAGCTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (34 bp):
AATTAAATAATTAAATGATAAATTAAATAAAATA
Found at i:53025683 original size:5 final size:5
Alignment explanation
Indices: 53025669--53025735 Score: 54
Period size: 5 Copynumber: 13.6 Consensus size: 5
53025659 AGCTTGTTTT
*
53025669 ATTTT ATTTA ATTTA TCATTTA A-TT- ATTTA ATTTA ATTT- ATTTA ATTTA
1 ATTTA ATTTA ATTTA --ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
53025718 TCATTTA A-TT- ATTTA ATT
1 --ATTTA ATTTA ATTTA ATT
53025736 ACCTAATTTA
Statistics
Matches: 52, Mismatches: 1, Indels: 18
0.73 0.01 0.25
Matches are distributed among these distances:
3 2 0.04
4 12 0.23
5 28 0.54
7 10 0.19
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (5 bp):
ATTTA
Found at i:53025691 original size:12 final size:12
Alignment explanation
Indices: 53025674--53025727 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
53025664 GTTTTATTTT
53025674 ATTTAATTTATC
1 ATTTAATTTATC
* *
53025686 ATTTAATTATTTA
1 ATTTAATT-TATC
53025699 ATTTAA-TT-T-
1 ATTTAATTTATC
53025708 ATTTAATTTATC
1 ATTTAATTTATC
53025720 ATTTAATT
1 ATTTAATT
53025728 ATTTAATTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
9 6 0.17
10 3 0.08
11 2 0.06
12 17 0.47
13 8 0.22
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTTAATTTATC
Found at i:53025697 original size:20 final size:20
Alignment explanation
Indices: 53025672--53025735 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
53025662 TTGTTTTATT
53025672 TTATTTAATTTATCATTTAA
1 TTATTTAATTTATCATTTAA
53025692 TTATTTAATTTA--A--T--
1 TTATTTAATTTATCATTTAA
53025706 TTATTTAATTTATCATTTAA
1 TTATTTAATTTATCATTTAA
53025726 TTATTTAATT
1 TTATTTAATT
53025736 ACCTAATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
14 12 0.32
16 2 0.05
18 2 0.05
20 22 0.58
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTAATTTATCATTTAA
Found at i:53025699 original size:8 final size:8
Alignment explanation
Indices: 53025686--53025736 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
53025676 TTAATTTATC
53025686 ATTTAATT
1 ATTTAATT
53025694 ATTTAATTT
1 ATTTAA-TT
*
53025703 AATTTATTT
1 -ATTTAATT
*
53025712 AATTT-ATC
1 -ATTTAATT
53025720 ATTTAATT
1 ATTTAATT
53025728 ATTTAATT
1 ATTTAATT
53025736 A
1 A
53025737 CCTAATTTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 4 0.11
8 18 0.50
9 9 0.25
10 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (8 bp):
ATTTAATT
Found at i:53025713 original size:34 final size:34
Alignment explanation
Indices: 53025666--53025735 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
53025656 GAAAGCTTGT
*
53025666 TTTATTTTATTTAATTTATCATTTAATTATTTAA
1 TTTAATTTATTTAATTTATCATTTAATTATTTAA
53025700 TTTAATTTATTTAATTTATCATTTAATTATTTAA
1 TTTAATTTATTTAATTTATCATTTAATTATTTAA
53025734 TT
1 TT
53025736 ACCTAATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (34 bp):
TTTAATTTATTTAATTTATCATTTAATTATTTAA
Found at i:53026164 original size:16 final size:18
Alignment explanation
Indices: 53026127--53026166 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
53026117 GTTTTTTTAG
53026127 TATTTGTGCATATTATATT
1 TATTTGTGCA-ATTATATT
53026146 TATTTGTGC-ATTA-ATT
1 TATTTGTGCAATTATATT
53026162 TATTT
1 TATTT
53026167 AGTTGTCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
17 4 0.19
19 9 0.43
ACGTcount: A:0.25, C:0.05, G:0.10, T:0.60
Consensus pattern (18 bp):
TATTTGTGCAATTATATT
Found at i:53026172 original size:20 final size:19
Alignment explanation
Indices: 53026130--53026172 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
53026120 TTTTTAGTAT
*
53026130 TTGTGCATATTATATTTAT
1 TTGTGCATATTATATTTAG
53026149 TTGTGCATTAATT-TATTTAG
1 TTGTGCA-T-ATTATATTTAG
53026169 TTGT
1 TTGT
53026173 CTAATGTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 11 0.52
21 3 0.14
ACGTcount: A:0.23, C:0.05, G:0.14, T:0.58
Consensus pattern (19 bp):
TTGTGCATATTATATTTAG
Found at i:53032959 original size:40 final size:40
Alignment explanation
Indices: 53032904--53033165 Score: 438
Period size: 40 Copynumber: 6.5 Consensus size: 40
53032894 ATGATAATCA
* *
53032904 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCG
53032944 GGCTAAG-CTCCGAAGGCATTTGTGCGAGTTACTATATCCG
1 GGCTAAGTC-CCGAAGGCATTTGTGCGAGTTACTATATCCG
*
53032984 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCA
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
*
53033024 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATACCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
53033064 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
* *
53033104 GGCTAAGACCCGAAGGCATTTGTGCGAGTTACTATAACCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
53033144 GGCTAAGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
53033166 AGCAAGTAGT
Statistics
Matches: 210, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
39 1 0.00
40 207 0.99
41 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
Found at i:53033464 original size:22 final size:21
Alignment explanation
Indices: 53033423--53033466 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
53033413 GAATGTGCAT
53033423 ATATGAAGTTATCCATTTAGCC
1 ATATGAAGTTATCCA-TTAGCC
53033445 ATATGAATGTTATACC-TTAGCC
1 ATATGAA-GTTAT-CCATTAGCC
53033467 GAAACTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.65
23 5 0.25
24 2 0.10
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (21 bp):
ATATGAAGTTATCCATTAGCC
Found at i:53034589 original size:14 final size:14
Alignment explanation
Indices: 53034570--53034599 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53034560 TATCTTATAA
53034570 ATATGCGTGAATCT
1 ATATGCGTGAATCT
*
53034584 ATATGCGTTAATCT
1 ATATGCGTGAATCT
53034598 AT
1 AT
53034600 CTTAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (14 bp):
ATATGCGTGAATCT
Found at i:53047288 original size:17 final size:17
Alignment explanation
Indices: 53047266--53047298 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
53047256 TTAAATCAAG
53047266 AAAAAA-AACAATAAAAC
1 AAAAAAGAA-AATAAAAC
53047283 AAAAAAGAAAATAAAA
1 AAAAAAGAAAATAAAA
53047299 AGTAAAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.85, C:0.06, G:0.03, T:0.06
Consensus pattern (17 bp):
AAAAAAGAAAATAAAAC
Found at i:53047549 original size:13 final size:13
Alignment explanation
Indices: 53047531--53047555 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53047521 TTTTTTGGAC
53047531 ATGCAAGAAATTG
1 ATGCAAGAAATTG
53047544 ATGCAAGAAATT
1 ATGCAAGAAATT
53047556 TGACTTCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (13 bp):
ATGCAAGAAATTG
Found at i:53049038 original size:16 final size:17
Alignment explanation
Indices: 53049008--53049040 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
53048998 TAGAGTCACC
53049008 TTCATAATGATCATGAA
1 TTCATAATGATCATGAA
53049025 TTCATAAT-ATCATGAA
1 TTCATAATGATCATGAA
53049041 GCCAATGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (17 bp):
TTCATAATGATCATGAA
Found at i:53049395 original size:50 final size:50
Alignment explanation
Indices: 53049277--53049511 Score: 289
Period size: 50 Copynumber: 4.7 Consensus size: 50
53049267 TCTCGTATTG
* * ** * *
53049277 ATGCCATGTCCCAGACATGGTCTTATACGAAAT-A-ATATATCGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATATCTATGCTA
* * *
53049325 ATGCCATATCCCAGATATGGTCTTACATGGGATCATATATAT-TGATGCTA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATATCT-ATGCTA
* ** *
53049375 ATACCATGTCTTAGACATGGTCTTACATGGGATCACATATATCTATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATATCTATGCTA
* *
53049425 ATGCCATGTCCCAGACATTGTCTTACATAGGATCACATATATCTATG-TCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATATCTATGCT-A
53049475 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACA
53049512 CATAACCCTA
Statistics
Matches: 159, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
48 27 0.17
49 1 0.01
50 130 0.82
51 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (50 bp):
ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATATCTATGCTA
Found at i:53061965 original size:25 final size:25
Alignment explanation
Indices: 53061926--53062019 Score: 73
Period size: 25 Copynumber: 3.8 Consensus size: 25
53061916 GTTTCGACCC
*
53061926 ACAGCTCGTGTGAGCATACCAATTT
1 ACAGCTCGTGAGAGCATACCAATTT
* * *
53061951 ACAGCTTGTGAGAGCATATCGATTT
1 ACAGCTCGTGAGAGCATACCAATTT
* * * * * *
53061976 ACAACTAGAGTGAGCATACCGATTC
1 ACAGCTCGTGAGAGCATACCAATTT
*
53062001 ACAGTTCGT-ATGAGCATAC
1 ACAGCTCGTGA-GAGCATAC
53062020 ATGTACATGA
Statistics
Matches: 53, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (25 bp):
ACAGCTCGTGAGAGCATACCAATTT
Found at i:53064202 original size:23 final size:23
Alignment explanation
Indices: 53064171--53064215 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
53064161 AGAACTTTTA
*
53064171 ATCGAGAAGCTCACCAAGAGCCT
1 ATCGAGAAGCTCACAAAGAGCCT
*
53064194 ATCGGGAAGCTCACAAAGAGCC
1 ATCGAGAAGCTCACAAAGAGCC
53064216 ATGTAACAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.29, G:0.24, T:0.11
Consensus pattern (23 bp):
ATCGAGAAGCTCACAAAGAGCCT
Found at i:53078296 original size:41 final size:40
Alignment explanation
Indices: 53078197--53078300 Score: 111
Period size: 40 Copynumber: 2.6 Consensus size: 40
53078187 CTTTTATCAA
** *
53078197 ATCACCGGCATTTAGCCTGCTAGGTTTTAAACTCGAATTC
1 ATCACCGGCATTTAGCCTGCTAGACTTTAAACTCGAACTC
*** *
53078237 ATCACCGGCACGAAGCCTGCTAGACTTT-AAGTCTGAACTC
1 ATCACCGGCATTTAGCCTGCTAGACTTTAAACTC-GAACTC
*
53078277 ATTCACCGGCATTTTGCCTGCTAG
1 A-TCACCGGCATTTAGCCTGCTAG
53078301 GCTTGAAGCC
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
39 4 0.08
40 29 0.57
41 18 0.35
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (40 bp):
ATCACCGGCATTTAGCCTGCTAGACTTTAAACTCGAACTC
Found at i:53078345 original size:43 final size:43
Alignment explanation
Indices: 53078278--53078448 Score: 170
Period size: 43 Copynumber: 4.0 Consensus size: 43
53078268 TCTGAACTCA
* *
53078278 TTCACCGGCATT-TTGCCTGCTAGGCTTGAAGCCCAATATCAT
1 TTCACCGGCATTATAGCCTGCTAGGCCTGAAGCCCAATATCAT
* * * *
53078320 TTCACTGGCATTATAGCCTGCTAGGCCGGAAGCCCGATATTAT
1 TTCACCGGCATTATAGCCTGCTAGGCCTGAAGCCCAATATCAT
* *
53078363 CTCACCGGCATTATAGCCTGCTAGGCCTGAAGCCCGATAAT-ATT
1 TTCACCGGCATTATAGCCTGCTAGGCCTGAAGCCCAAT-ATCA-T
* * * *
53078407 ATTCACCAGC-TTAAAGCTTGCTAGGCC-GAGGCCCGAATATCA
1 -TTCACCGGCATTATAGCCTGCTAGGCCTGAAGCCC-AATATCA
53078449 CATTTCGATA
Statistics
Matches: 108, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
42 11 0.10
43 69 0.64
44 21 0.19
45 7 0.06
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (43 bp):
TTCACCGGCATTATAGCCTGCTAGGCCTGAAGCCCAATATCAT
Found at i:53078441 original size:86 final size:85
Alignment explanation
Indices: 53078279--53078442 Score: 199
Period size: 86 Copynumber: 1.9 Consensus size: 85
53078269 CTGAACTCAT
* * ** *
53078279 TCACCGGCATTTTGCCTGCTAGGCTTGAAGCCCAATATCATTTCACTGGCATTATAGCCTGCTAG
1 TCACCGGCATTTAGCCTGCTAGGCCTGAAGCCCAATATCATTTCACCAGCATTAAAGCCTGCTAG
53078344 GCCGGAAGCCCGATATTATC
66 GCCGGAAGCCCGATATTATC
* *
53078364 TCACCGGCATTATAGCCTGCTAGGCCTGAAGCCCGATAAT-ATTATTCACCAGC-TTAAAGCTTG
1 TCACCGGCATT-TAGCCTGCTAGGCCTGAAGCCCAAT-ATCA-T-TTCACCAGCATTAAAGCCTG
*
53078427 CTAGGCC-GAGGCCCGA
62 CTAGGCCGGAAGCCCGA
53078443 ATATCACATT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
85 11 0.16
86 31 0.46
87 18 0.27
88 7 0.10
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.26
Consensus pattern (85 bp):
TCACCGGCATTTAGCCTGCTAGGCCTGAAGCCCAATATCATTTCACCAGCATTAAAGCCTGCTAG
GCCGGAAGCCCGATATTATC
Found at i:53079588 original size:29 final size:28
Alignment explanation
Indices: 53079547--53079614 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
53079537 ACACTCACAC
* *
53079547 AACCATATATTTC-ACAATTTCACATTTT
1 AACCATAAATTTCTAC-ATTTCACAATTT
53079575 AACCACTAAATTTCTACATTTCACAATTT
1 AACCA-TAAATTTCTACATTTCACAATTT
53079604 AATCCA-AAATT
1 AA-CCATAAATT
53079615 GACATTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 10 0.29
29 20 0.57
30 5 0.14
ACGTcount: A:0.40, C:0.22, G:0.00, T:0.38
Consensus pattern (28 bp):
AACCATAAATTTCTACATTTCACAATTT
Found at i:53088311 original size:18 final size:19
Alignment explanation
Indices: 53088285--53088339 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 19
53088275 CTTGGCCCAT
*
53088285 TGCAATAACAGTAAAT-AG
1 TGCAGTAACAGTAAATCAG
*
53088303 TGCAGTAACAAT-AATCAG
1 TGCAGTAACAGTAAATCAG
53088321 TGCAGTAACAGTAAA-CAG
1 TGCAGTAACAGTAAATCAG
53088339 T
1 T
53088340 ATGCAAATCC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 3 0.09
18 27 0.84
19 2 0.06
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (19 bp):
TGCAGTAACAGTAAATCAG
Found at i:53088702 original size:27 final size:28
Alignment explanation
Indices: 53088664--53088943 Score: 265
Period size: 27 Copynumber: 10.4 Consensus size: 28
53088654 ACACAAACAT
*
53088664 CACATAGGGGCAAAA-CAGTCATTTTAC
1 CACATAAGGGCAAAATCAGTCATTTTAC
* * *
53088691 CTCATAAGGGCAAAA-CCGTCATGTTAC
1 CACATAAGGGCAAAATCAGTCATTTTAC
** * *
53088718 CTTATAAGGGAAAAATCA-TCATTTTAT
1 CACATAAGGGCAAAATCAGTCATTTTAC
* *
53088745 CACATAAGGACAAAAT-AGTCATTTTGC
1 CACATAAGGGCAAAATCAGTCATTTTAC
* *
53088772 CACATAAGGG-AAAAACTGTCATTTTAC
1 CACATAAGGGCAAAATCAGTCATTTTAC
* * *
53088799 CTCATAAAGGCAAAATC-GTCATTTTAT
1 CACATAAGGGCAAAATCAGTCATTTTAC
* *
53088826 CACATAAGGGCAAAA-CTGTCATTTTGC
1 CACATAAGGGCAAAATCAGTCATTTTAC
* *
53088853 CACATAAGGGAAAAATC-GTCATTTTAA
1 CACATAAGGGCAAAATCAGTCATTTTAC
* *
53088880 CTCATAAGGGCAAAATC-GTCATTTTAT
1 CACATAAGGGCAAAATCAGTCATTTTAC
* * *
53088907 CAAATAAGGG-AAAAGCAGTCATTTTAT
1 CACATAAGGGCAAAATCAGTCATTTTAC
*
53088934 CTCATAAGGG
1 CACATAAGGG
53088944 TTCAGGTACA
Statistics
Matches: 208, Mismatches: 38, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
26 11 0.05
27 190 0.91
28 7 0.03
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (28 bp):
CACATAAGGGCAAAATCAGTCATTTTAC
Found at i:53088799 original size:81 final size:81
Alignment explanation
Indices: 53088662--53088931 Score: 357
Period size: 81 Copynumber: 3.3 Consensus size: 81
53088652 ATACACAAAC
* * * * * * * *
53088662 ATCACATAGGGGCAAAACAGTCATTTTACCTCATAAGGGCAAAACCGTCATGTTACCTTATAAGG
1 ATCACATAAGGGCAAAATAGTCATTTTGCCACATAAGGGAAAAACTGTCATTTTACCTCATAAGG
* *
53088727 GAAAAATCATCATTTT
66 GCAAAATCGTCATTTT
* *
53088743 ATCACATAAGGACAAAATAGTCATTTTGCCACATAAGGGAAAAACTGTCATTTTACCTCATAAAG
1 ATCACATAAGGGCAAAATAGTCATTTTGCCACATAAGGGAAAAACTGTCATTTTACCTCATAAGG
53088808 GCAAAATCGTCATTTT
66 GCAAAATCGTCATTTT
*
53088824 ATCACATAAGGGCAAAACT-GTCATTTTGCCACATAAGGGAAAAA-TCGTCATTTTAACTCATAA
1 ATCACATAAGGGCAAAA-TAGTCATTTTGCCACATAAGGGAAAAACT-GTCATTTTACCTCATAA
53088887 GGGCAAAATCGTCATTTT
64 GGGCAAAATCGTCATTTT
* *
53088905 ATCAAATAAGGG-AAAAGCAGTCATTTT
1 ATCACATAAGGGCAAAA-TAGTCATTTT
53088932 ATCTCATAAG
Statistics
Matches: 168, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
80 5 0.03
81 162 0.96
82 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.28
Consensus pattern (81 bp):
ATCACATAAGGGCAAAATAGTCATTTTGCCACATAAGGGAAAAACTGTCATTTTACCTCATAAGG
GCAAAATCGTCATTTT
Found at i:53092188 original size:39 final size:39
Alignment explanation
Indices: 53092134--53092245 Score: 188
Period size: 39 Copynumber: 2.9 Consensus size: 39
53092124 TGCATGATAT
53092134 TGGGAATATATCCGGACATGAGGTCCGCAGGCTATATGC
1 TGGGAATATATCCGGACATGAGGTCCGCAGGCTATATGC
*
53092173 TGGGAATATACCCGGACATGAGGTCCGCAGGCTATATGC
1 TGGGAATATATCCGGACATGAGGTCCGCAGGCTATATGC
* * *
53092212 TGGAAATATATCCTGACATGAGGTCTGCAGGCTA
1 TGGGAATATATCCGGACATGAGGTCCGCAGGCTA
53092246 CGTGCTGAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 68 1.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (39 bp):
TGGGAATATATCCGGACATGAGGTCCGCAGGCTATATGC
Found at i:53098775 original size:22 final size:22
Alignment explanation
Indices: 53098728--53098776 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
53098718 TGCAAGAAAA
*
53098728 ACCAACCCAACCATCCAATCAT
1 ACCAACCCAACCATCCAATCAC
* *
53098750 ACCAACTCCATCCATCCTA-CAC
1 ACCAAC-CCAACCATCCAATCAC
53098772 ACCAA
1 ACCAA
53098777 AAAGGGTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.39, C:0.47, G:0.00, T:0.14
Consensus pattern (22 bp):
ACCAACCCAACCATCCAATCAC
Found at i:53100229 original size:15 final size:15
Alignment explanation
Indices: 53100206--53100236 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53100196 TAATTTTCAA
53100206 AAAAAAAAACAAAAT
1 AAAAAAAAACAAAAT
*
53100221 AAAACAAAACAAAAT
1 AAAAAAAAACAAAAT
53100236 A
1 A
53100237 CTCTAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.10, G:0.00, T:0.06
Consensus pattern (15 bp):
AAAAAAAAACAAAAT
Done.