Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 121 of 313
Found at i:39111154 original size:17 final size:16
Alignment explanation
Indices: 39111132--39111174 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
39111122 AAGCTCATTC
39111132 AAAAAATAAGAGAGATT
1 AAAAAATAAGAGA-ATT
*
39111149 AAAAAA-AATGAGACTT
1 AAAAAATAA-GAGAATT
39111165 AAAAAATAAG
1 AAAAAATAAG
39111175 TTTGAGTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.14, T:0.16
Consensus pattern (16 bp):
AAAAAATAAGAGAATT
Found at i:39112142 original size:18 final size:21
Alignment explanation
Indices: 39112109--39112151 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
39112099 AATAAAATCT
39112109 AAAATTTTATATAAATAT-TA
1 AAAATTTTATATAAATATATA
39112129 AAAATTTTA-A-AAATATATA
1 AAAATTTTATATAAATATATA
39112148 AAAA
1 AAAA
39112152 AAATTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.27
19 7 0.32
20 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAATTTTATATAAATATATA
Found at i:39114057 original size:26 final size:26
Alignment explanation
Indices: 39113993--39114058 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
39113983 AGTTCTTTAT
*
39113993 TGCTTTTGAAAACTGCTCTTGAAAAG
1 TGCTTTTGAAAAGTGCTCTTGAAAAG
* * *
39114019 TGCTGTGGAAAAGTGC-CTTTAAGAAG
1 TGCTTTTGAAAAGTGCTCTTGAA-AAG
39114045 TGCTTTTGAAAAGT
1 TGCTTTTGAAAAGT
39114059 TTGTTTTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 5 0.15
26 28 0.85
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.33
Consensus pattern (26 bp):
TGCTTTTGAAAAGTGCTCTTGAAAAG
Found at i:39114058 original size:13 final size:13
Alignment explanation
Indices: 39113993--39114058 Score: 71
Period size: 13 Copynumber: 5.1 Consensus size: 13
39113983 AGTTCTTTAT
*
39113993 TGCTTTTGAAAAC
1 TGCTTTTGAAAAG
*
39114006 TGCTCTTGAAAAG
1 TGCTTTTGAAAAG
* *
39114019 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
39114032 TGCCTTT-AAGAAG
1 TGCTTTTGAA-AAG
39114045 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
39114058 T
1 T
39114059 TTGTTTTAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
12 2 0.05
13 39 0.91
14 2 0.05
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.33
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:39114683 original size:13 final size:13
Alignment explanation
Indices: 39114665--39114728 Score: 76
Period size: 13 Copynumber: 4.9 Consensus size: 13
39114655 AGTTCTTCAT
39114665 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
39114678 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
* *
39114691 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
39114704 TACTTTTGAGAAA-
1 TGCTTTTGA-AAAG
39114717 TGCTTTTGAAAA
1 TGCTTTTGAAAA
39114729 TTTTGAATGT
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
12 3 0.07
13 36 0.86
14 3 0.07
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:39114727 original size:26 final size:26
Alignment explanation
Indices: 39114665--39114728 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
39114655 AGTTCTTCAT
* *
39114665 TGCTTTTGAAAAGTGCTTTTGAGAAG
1 TGCTTTTGAAAAGTACTTTTGAGAAA
* *
39114691 TGCTGTGGAAAAGTACTTTTGAGAAA
1 TGCTTTTGAAAAGTACTTTTGAGAAA
39114717 TGCTTTTGAAAA
1 TGCTTTTGAAAA
39114729 TTTTGAATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (26 bp):
TGCTTTTGAAAAGTACTTTTGAGAAA
Found at i:39115298 original size:14 final size:14
Alignment explanation
Indices: 39115279--39115313 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
39115269 AAAGTAAAAT
*
39115279 AATATATACATGTG
1 AATATATACATATG
*
39115293 AATATATATATATG
1 AATATATACATATG
39115307 AATATAT
1 AATATAT
39115314 TTAAAGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.40
Consensus pattern (14 bp):
AATATATACATATG
Found at i:39116069 original size:29 final size:25
Alignment explanation
Indices: 39116017--39116066 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
39116007 TTTTTTAAAT
39116017 TTATTTTTTATAAAAAATATTATTG
1 TTATTTTTTATAAAAAATATTATTG
39116042 TTATTTTTTCGAT-AAAAATATTATT
1 TTATTTTTT--ATAAAAAATATTATT
39116067 ATTTTGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 9 0.39
26 12 0.52
27 2 0.09
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (25 bp):
TTATTTTTTATAAAAAATATTATTG
Found at i:39119322 original size:22 final size:22
Alignment explanation
Indices: 39119274--39119323 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
39119264 ATAATAATTG
* *
39119274 AAAAAGAAATAAAAAATTTCTT
1 AAAAAGAAATAAAAAAATTATT
*
39119296 AAAAATAAATAAAAAAATTATAT
1 AAAAAGAAATAAAAAAATTAT-T
39119319 AAAAA
1 AAAAA
39119324 ATCAATTGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAAAGAAATAAAAAAATTATT
Found at i:39120207 original size:96 final size:95
Alignment explanation
Indices: 39120080--39120387 Score: 314
Period size: 95 Copynumber: 3.2 Consensus size: 95
39120070 TAAGCAAGGG
** ** * * * *
39120080 ATTAGGGTTTAGGGTTTGTCAATTAAATTAATTATAATTTTTTAAAAAATTGGATTA-GTTTTTG
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTAAAAAATT-GATTAGGGTTTAG
* * *
39120144 TGTTTATTGTTTTTTAAGAAAAAATCAATTAA
65 TGTTTA-GGATTTTTAAGAAAAAATCAAATAA
* * * ** *
39120176 CTTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAAATTT-AAAATTTAGATTAGGGTTTAG
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTAAAAAATT-GATTAGGGTTTAG
* * *
39120240 AGTTAAGGGTTTTTAAGAAAAAATCAAATAA
65 TGTTTAGGATTTTTAAGAAAAAATCAAATAA
* * * * *
39120271 ATTAGGGTTCAAGGTTACTTGAGTAAATTAATTATAAATTTTTAATAAATTAATTTAGGGCTTAG
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTAAAAAATTGA-TTAGGGTTTAG
* *
39120336 TGTTTAGGATTTTTAAGTAAAAATTTAAATAA
65 TGTTTAGGATTTTTAAG-AAAAAATCAAATAA
39120368 ATTAGGGTTTAGGGTTACTT
1 ATTAGGGTTTAGGGTTACTT
39120388 AATTTAATAT
Statistics
Matches: 170, Mismatches: 38, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
95 70 0.41
96 70 0.41
97 30 0.18
ACGTcount: A:0.37, C:0.03, G:0.17, T:0.43
Consensus pattern (95 bp):
ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTAAAAAATTGATTAGGGTTTAGT
GTTTAGGATTTTTAAGAAAAAATCAAATAA
Found at i:39120772 original size:126 final size:126
Alignment explanation
Indices: 39120410--39120836 Score: 561
Period size: 126 Copynumber: 3.4 Consensus size: 126
39120400 TTGTTAATTT
* * * * ** *
39120410 AAAGAAGATCCCACGTGGACGCGCTTTTGCTACAATAGGTCCTGAGAAAATAATTTCGAGTAGAC
1 AAAGAAGCTTCCACGTGGACGCACTTTTGCTACAGTAGCCCCTGAAAAAATAATTTCGAGTAGAC
* * * * *
39120475 GTTTCTGAGCAAATAGTGTCAAAAACACTTTAAGAATGATGCTTTGTCAGCAGAAATACTG
66 GTTTCTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
* ** * * * *
39120536 AAAGAAGCTCCCACGTGGACGCGTTTTTACTACAGTATCCCCT-AAAAAATAATTCCGAGTAAAC
1 AAAGAAGCTTCCACGTGGACGCACTTTTGCTACAGTAGCCCCTGAAAAAATAATTTCGAGTAGAC
* *
39120600 GTTTCTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGAATGTTTTGTCAGCAGAAGTACTG
66 GTTTCTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
* * * *
39120661 AAATAAGCTTCCATGTGGACGCATTTTTGCTACAGTAGCCCCTGAAAAAATAATTTTGAGTAGAC
1 AAAGAAGCTTCCACGTGGACGCACTTTTGCTACAGTAGCCCCTGAAAAAATAATTTCGAGTAGAC
* *
39120726 GTTTTTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTG
66 GTTTCTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
* * *
39120787 AAAGAAG-TTCCCACGTGGACGCACATTTGTTACAGTAACCCCTGAAAAAA
1 AAAGAAGCTT-CCACGTGGACGCACTTTTGCTACAGTAGCCCCTGAAAAAA
39120837 GCTCCCACGT
Statistics
Matches: 263, Mismatches: 36, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
125 111 0.42
126 152 0.58
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (126 bp):
AAAGAAGCTTCCACGTGGACGCACTTTTGCTACAGTAGCCCCTGAAAAAATAATTTCGAGTAGAC
GTTTCTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
Found at i:39120843 original size:44 final size:44
Alignment explanation
Indices: 39120784--39120867 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
39120774 AGCAAAAGTA
* * *
39120784 CTGAAAGAAGTTCCCACGTGGACGCACATTTGTTACAGTAACCC
1 CTGAAAAAAGCTCCCACGTGGACGCACATTTGCTACAGTAACCC
*
39120828 CTGAAAAAAGCTCCCACGTGGACGCACTTTTGCTACAGTA
1 CTGAAAAAAGCTCCCACGTGGACGCACATTTGCTACAGTA
39120868 GTGCATGGCC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (44 bp):
CTGAAAAAAGCTCCCACGTGGACGCACATTTGCTACAGTAACCC
Found at i:39123829 original size:20 final size:21
Alignment explanation
Indices: 39123793--39123831 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
39123783 AAATATTGAC
39123793 TTATATAAAAGAAAATCTATT
1 TTATATAAAAGAAAATCTATT
39123814 TTAT-TAAAA-AATAATCTA
1 TTATATAAAAGAA-AATCTA
39123832 GTAAATTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 11 0.65
21 4 0.24
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (21 bp):
TTATATAAAAGAAAATCTATT
Found at i:39126329 original size:11 final size:11
Alignment explanation
Indices: 39126315--39126360 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
39126305 TCTTTTAAAT
*
39126315 AGGAATTTGAG
1 AGGAAATTGAG
39126326 AGGAAATTGAG
1 AGGAAATTGAG
*
39126337 AGCAAATTGAG
1 AGGAAATTGAG
*
39126348 AGGAATTTGAG
1 AGGAAATTGAG
39126359 AG
1 AG
39126361 AATATTAGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.41, C:0.02, G:0.35, T:0.22
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:39126373 original size:12 final size:12
Alignment explanation
Indices: 39126356--39126383 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
39126346 AGAGGAATTT
39126356 GAGAGAATATTA
1 GAGAGAATATTA
39126368 GAGAGAATATTA
1 GAGAGAATATTA
39126380 GAGA
1 GAGA
39126384 AAGGATTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (12 bp):
GAGAGAATATTA
Found at i:39126375 original size:22 final size:21
Alignment explanation
Indices: 39126321--39126385 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
39126311 AAATAGGAAT
*
39126321 TTGAGAGGAAATTGAGAGCAAA
1 TTGAGAGGAATTTGAGAG-AAA
39126343 TTGAGAGGAATTTGAGAGAATA
1 TTGAGAGGAATTTGAGAGAA-A
39126365 TT-AGAGAGAATATT-AGAGAAA
1 TTGAGAG-GAAT-TTGAGAGAAA
39126386 GGATTTAGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
21 7 0.18
22 30 0.77
23 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.29, T:0.23
Consensus pattern (21 bp):
TTGAGAGGAATTTGAGAGAAA
Found at i:39135606 original size:23 final size:23
Alignment explanation
Indices: 39135563--39135608 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
39135553 AAGTTATTGG
* *
39135563 ATGAAATTAAATTGTATATTTTT
1 ATGAAATTAAAATATATATTTTT
*
39135586 ATGAAATTAAAA-ATATAATTTT
1 ATGAAATTAAAATATATATTTTT
39135608 A
1 A
39135609 CTATTTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (23 bp):
ATGAAATTAAAATATATATTTTT
Found at i:39145873 original size:31 final size:31
Alignment explanation
Indices: 39145835--39145897 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
39145825 TGTTTGAGCC
*
39145835 AGGACTAATATTTCAAAAATT-GAAAAGTATA
1 AGGACTAAAATTT-AAAAATTCGAAAAGTATA
**
39145866 AGGACTAAAATTTACCAATTCGAAAAGTATA
1 AGGACTAAAATTTAAAAATTCGAAAAGTATA
39145897 A
1 A
39145898 TGATTGAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.51, C:0.10, G:0.13, T:0.27
Consensus pattern (31 bp):
AGGACTAAAATTTAAAAATTCGAAAAGTATA
Found at i:39146929 original size:20 final size:20
Alignment explanation
Indices: 39146904--39146953 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
39146894 TGGCTTAAAA
39146904 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
39146924 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
39146941 GTGGTAGTGGATT
1 TTGGTAGTGGATT
39146954 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:39151568 original size:20 final size:20
Alignment explanation
Indices: 39151543--39151592 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
39151533 TGGCTTAAAA
39151543 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
39151563 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
39151580 GTGGTAGTGGATT
1 TTGGTAGTGGATT
39151593 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:39152726 original size:17 final size:18
Alignment explanation
Indices: 39152704--39152742 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
39152694 TTACTTTTTT
*
39152704 TTTTAAAGGAAAAA-ACG
1 TTTTAAAAGAAAAATACG
*
39152721 TTTTAAAATAAAAATACG
1 TTTTAAAAGAAAAATACG
39152739 TTTT
1 TTTT
39152743 TTAGAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (18 bp):
TTTTAAAAGAAAAATACG
Found at i:39156128 original size:20 final size:20
Alignment explanation
Indices: 39156095--39156157 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
39156085 TTATTGAAAA
39156095 ATATTTATATTAATATATATAT
1 ATATTTA-A-TAATATATATAT
*
39156117 ATATTTAATAATAAATATGA-
1 ATATTTAATAATATATAT-AT
* *
39156137 ATATTTTAAAAATATAAATAT
1 ATA-TTTAATAATATATATAT
39156158 GAGTATTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
20 13 0.38
21 14 0.41
22 7 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
ATATTTAATAATATATATAT
Found at i:39175771 original size:23 final size:23
Alignment explanation
Indices: 39175711--39175830 Score: 122
Period size: 23 Copynumber: 5.4 Consensus size: 23
39175701 TATGACATAT
* *
39175711 AAGTGCCTGA-A-ACAACACACG
1 AAGTGCCTGAGATACGACACACA
* *
39175732 AGGTGCCT--GATACGACACACG
1 AAGTGCCTGAGATACGACACACA
* * * *
39175753 AGGTGCCTGATATAAGACACATA
1 AAGTGCCTGAGATACGACACACA
*
39175776 AAGTGCCTGAGATACGACACATA
1 AAGTGCCTGAGATACGACACACA
*
39175799 AAGTGCCTGAGATACGACACATA
1 AAGTGCCTGAGATACGACACACA
39175822 AAGTGCCTG
1 AAGTGCCTG
39175831 GTTGGTAAGG
Statistics
Matches: 86, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
20 1 0.01
21 24 0.28
23 61 0.71
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (23 bp):
AAGTGCCTGAGATACGACACACA
Found at i:39175772 original size:21 final size:21
Alignment explanation
Indices: 39175713--39175764 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
39175703 TGACATATAA
*
39175713 GTGCCTGAAACAACACACGAG
1 GTGCCTGATACAACACACGAG
*
39175734 GTGCCTGATACGACACACGAG
1 GTGCCTGATACAACACACGAG
39175755 GTGCCTGATA
1 GTGCCTGATA
39175765 TAAGACACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.27, G:0.27, T:0.15
Consensus pattern (21 bp):
GTGCCTGATACAACACACGAG
Found at i:39175805 original size:46 final size:46
Alignment explanation
Indices: 39175740--39175830 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
39175730 CGAGGTGCCT
* * *
39175740 GATACGACACACGAGGTGCCTGATATAAGACACATAAAGTGCCTGA
1 GATACGACACACAAAGTGCCTGAGATAAGACACATAAAGTGCCTGA
* *
39175786 GATACGACACATAAAGTGCCTGAGATACGACACATAAAGTGCCTG
1 GATACGACACACAAAGTGCCTGAGATAAGACACATAAAGTGCCTG
39175831 GTTGGTAAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (46 bp):
GATACGACACACAAAGTGCCTGAGATAAGACACATAAAGTGCCTGA
Found at i:39177028 original size:5 final size:5
Alignment explanation
Indices: 39177020--39177057 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
39177010 TTTTTAATTT
*
39177020 ATATA ATATA ATACA ATATA ATATA ATA-A A-ATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
39177058 TAAAACATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 1 0.03
4 4 0.14
5 24 0.83
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (5 bp):
ATATA
Found at i:39177040 original size:15 final size:14
Alignment explanation
Indices: 39177020--39177061 Score: 61
Period size: 15 Copynumber: 3.1 Consensus size: 14
39177010 TTTTTAATTT
39177020 ATATAATATAATACA
1 ATATAATATAATA-A
39177035 ATATAATATAATAA
1 ATATAATATAATAA
39177049 A-ATAATAT-ATAA
1 ATATAATATAATAA
39177061 A
1 A
39177062 ACATAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.19
13 7 0.26
14 2 0.07
15 13 0.48
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
ATATAATATAATAA
Found at i:39187893 original size:12 final size:12
Alignment explanation
Indices: 39187861--39187893 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39187851 GAAGGTTGAA
39187861 GAGATGGATGAG
1 GAGATGGATGAG
39187873 GATGA-GGATGAG
1 GA-GATGGATGAG
39187885 GAGATGGAT
1 GAGATGGAT
39187894 ATGTAAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.11
12 15 0.79
13 2 0.11
ACGTcount: A:0.33, C:0.00, G:0.48, T:0.18
Consensus pattern (12 bp):
GAGATGGATGAG
Found at i:39188392 original size:8 final size:9
Alignment explanation
Indices: 39188375--39188399 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
39188365 TCTTCAAAAA
39188375 TAATTTTTT
1 TAATTTTTT
39188384 TAATTTTTT
1 TAATTTTTT
39188393 TAATTTT
1 TAATTTT
39188400 AAGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TAATTTTTT
Found at i:39196104 original size:20 final size:21
Alignment explanation
Indices: 39196070--39196109 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
39196060 TTAATTTAAA
*
39196070 ATTAAATTAAAATATTTTATT
1 ATTAAATTAAAATATCTTATT
*
39196091 ATTAAA-TAATATATCTTAT
1 ATTAAATTAAAATATCTTAT
39196110 CCAAAAAGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTAAATTAAAATATCTTATT
Found at i:39204711 original size:21 final size:21
Alignment explanation
Indices: 39204673--39204712 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39204663 ATTTTAAAAT
**
39204673 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
39204694 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
39204713 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:39204719 original size:22 final size:20
Alignment explanation
Indices: 39204672--39204726 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
39204662 AATTTTAAAA
* *
39204672 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTG
39204692 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTT-G
39204715 TATTTATTAAAA
1 TATTT-TTAAAA
39204727 AATGAGCCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 1 0.03
21 11 0.38
22 10 0.34
23 7 0.24
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTG
Found at i:39205662 original size:15 final size:15
Alignment explanation
Indices: 39205639--39205672 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
39205629 TTGAACTGGT
39205639 TTTGAGGACATTAAG
1 TTTGAGGACATTAAG
*
39205654 TTTGTGGACATTAAG
1 TTTGAGGACATTAAG
39205669 TTTG
1 TTTG
39205673 GACTTTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.26, T:0.41
Consensus pattern (15 bp):
TTTGAGGACATTAAG
Found at i:39212097 original size:5 final size:5
Alignment explanation
Indices: 39212087--39212111 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
39212077 AACGCACTAT
39212087 GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA
39212112 CCTCCAACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:39231607 original size:21 final size:21
Alignment explanation
Indices: 39231570--39231609 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39231560 ATGCCGAAAA
**
39231570 TAATTTTTTTATCAAATTAGG
1 TAATTTTTTTAGAAAATTAGG
39231591 TAATTTTTTTAGAAAATTA
1 TAATTTTTTTAGAAAATTA
39231610 TGGGATTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (21 bp):
TAATTTTTTTAGAAAATTAGG
Found at i:39231765 original size:27 final size:27
Alignment explanation
Indices: 39231705--39231765 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
39231695 TAGGTTAGAT
*
39231705 TTTTTTTTAAATTAGGGTTAGAGTTGA
1 TTTTTTTTAAAGTAGGGTTAGAGTTGA
*** * *
39231732 GAGTTTTTAAAGTAGGGTTAGGGTTTA
1 TTTTTTTTAAAGTAGGGTTAGAGTTGA
39231759 TTTTTTT
1 TTTTTTT
39231766 AAGGTTTAAG
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.52
Consensus pattern (27 bp):
TTTTTTTTAAAGTAGGGTTAGAGTTGA
Found at i:39231816 original size:29 final size:28
Alignment explanation
Indices: 39231783--39231892 Score: 86
Period size: 29 Copynumber: 3.9 Consensus size: 28
39231773 AAGGTTTGTT
39231783 TTTATTATATATTTTTTAATAATTTTTAA
1 TTTATTATATATTTTTT-ATAATTTTTAA
* * * *
39231812 TTTA-TATATA--TTTAATTACTTTTATT
1 TTTATTATATATTTTTTATAATTTTTA-A
* *
39231838 TTTTTTATATATTTTTTAT-TTTTTTAA
1 TTTATTATATATTTTTTATAATTTTTAA
39231865 -TTATATATATTAATTTTTTATAATTTTT
1 TTTAT-TATA-T-ATTTTTTATAATTTTT
39231893 TGAGATGTAA
Statistics
Matches: 62, Mismatches: 11, Indels: 15
0.70 0.12 0.17
Matches are distributed among these distances:
25 8 0.13
26 9 0.15
27 10 0.16
28 12 0.19
29 18 0.29
30 5 0.08
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (28 bp):
TTTATTATATATTTTTTATAATTTTTAA
Found at i:39231868 original size:23 final size:22
Alignment explanation
Indices: 39231831--39231889 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 22
39231821 ATTTAATTAC
*
39231831 TTTTATTTTTTTTA-TATAT-T
1 TTTTATTTTTTTAATTATATAT
39231851 TTTTATTTTTTTAATTATATAT
1 TTTTATTTTTTTAATTATATAT
* *
39231873 ATTAATTTTTTATAATT
1 TTTTATTTTTT-TAATT
39231890 TTTTGAGATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.39
21 5 0.15
22 10 0.30
23 5 0.15
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTATTTTTTTAATTATATAT
Found at i:39231871 original size:25 final size:24
Alignment explanation
Indices: 39231781--39231875 Score: 75
Period size: 25 Copynumber: 3.7 Consensus size: 24
39231771 TTAAGGTTTG
*
39231781 TTTTTATTATATAT-TTTTTAATAAT
1 TTTTTATTATATATATTTTT--TATT
* *
39231806 TTTTAATTTATATATATTTAATTACTT
1 TTTTTA-TTATATATATTT-TTTA-TT
* *
39231833 TTATTTTTTTTATATATTTTTTATT
1 TT-TTTATTATATATATTTTTTATT
39231858 TTTTTAATTATATATATT
1 TTTTT-ATTATATATATT
39231876 AATTTTTTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
24 3 0.05
25 19 0.35
26 13 0.24
27 17 0.31
28 3 0.05
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTTATTATATATATTTTTTATT
Found at i:39236670 original size:15 final size:15
Alignment explanation
Indices: 39236578--39236666 Score: 124
Period size: 15 Copynumber: 5.9 Consensus size: 15
39236568 AGCATTTCTG
*
39236578 CCATAGTCACCACCA
1 CCATAGCCACCACCA
39236593 CCATAGCCACCACCA
1 CCATAGCCACCACCA
* *
39236608 CCATAGCCACCGCCT
1 CCATAGCCACCACCA
*
39236623 CCATAGCCACCACCG
1 CCATAGCCACCACCA
*
39236638 CCATAGCCACCACCC
1 CCATAGCCACCACCA
*
39236653 CCATAGCCGCCACC
1 CCATAGCCACCACC
39236667 CCCAAAGTTA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 67 1.00
ACGTcount: A:0.27, C:0.54, G:0.10, T:0.09
Consensus pattern (15 bp):
CCATAGCCACCACCA
Found at i:39239454 original size:22 final size:22
Alignment explanation
Indices: 39239429--39239482 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
39239419 ATATGACCTT
39239429 TTCATAAAAAATCATAAAAAAA
1 TTCATAAAAAATCATAAAAAAA
* * *
39239451 TTCATTATAACATTATAAAAAAA
1 TTCA-TAAAAAATCATAAAAAAA
39239474 -TCATAAAAA
1 TTCATAAAAA
39239483 TTATTATAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 4 0.15
22 7 0.27
23 15 0.58
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (22 bp):
TTCATAAAAAATCATAAAAAAA
Found at i:39239488 original size:23 final size:23
Alignment explanation
Indices: 39239445--39239506 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
39239435 AAAAATCATA
*
39239445 AAAAAATTCATTATAACATTA-TA-
1 AAAAAA-TCATTA-AAAATTATTAT
39239468 AAAAAATCA-TAAAAATTATTAT
1 AAAAAATCATTAAAAATTATTAT
39239490 AAAAAATCATTAAAAAT
1 AAAAAATCATTAAAAAT
39239507 AATTTAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
20 6 0.17
21 4 0.11
22 12 0.34
23 13 0.37
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAAAATCATTAAAAATTATTAT
Found at i:39239982 original size:24 final size:24
Alignment explanation
Indices: 39239928--39239984 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
39239918 ATATAATTAT
39239928 TATTAA-ATATAATTTAATAAAAA
1 TATTAATATATAATTTAATAAAAA
** *
39239951 TAAAAATATATAATTTAATAAAAT
1 TATTAATATATAATTTAATAAAAA
*
39239975 TTTTAATATA
1 TATTAATATA
39239985 ATTATTTTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TATTAATATATAATTTAATAAAAA
Found at i:39241224 original size:6 final size:6
Alignment explanation
Indices: 39241213--39241243 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
39241203 GTGTTTAATA
*
39241213 TTTATT TTTATT TTTATT ATTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT TTTATT T
39241244 ATGAACCTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:39246333 original size:21 final size:19
Alignment explanation
Indices: 39246277--39246337 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
39246267 TAATTATTTA
39246277 TTAAATT-TAATTAGAATAT
1 TTAAATTATAATTA-AATAT
* *
39246296 ATAAATTATATTTAAATAT
1 TTAAATTATAATTAAATAT
39246315 TTAAATATAATAATTAAATAT
1 TTAAAT-T-ATAATTAAATAT
39246336 TT
1 TT
39246338 GTAATTAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 16 0.46
20 6 0.17
21 13 0.37
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TTAAATTATAATTAAATAT
Found at i:39249489 original size:19 final size:18
Alignment explanation
Indices: 39249467--39249549 Score: 80
Period size: 20 Copynumber: 4.4 Consensus size: 18
39249457 GACACAAAAA
39249467 TTTTGAAACACGAGATTTC
1 TTTTGAAACACGA-ATTTC
39249486 TTTTGAAAACACGAATTTTC
1 TTTTG-AAACACGAA-TTTC
*
39249506 TTTTTGAAACACAAATTT-
1 -TTTTGAAACACGAATTTC
* *
39249524 TTTTAAAACAC-AATTTAT
1 TTTTGAAACACGAATTT-C
39249542 TTTTGAAA
1 TTTTGAAA
39249550 ACATAAAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
16 5 0.09
17 10 0.18
18 7 0.12
19 9 0.16
20 20 0.36
21 5 0.09
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.42
Consensus pattern (18 bp):
TTTTGAAACACGAATTTC
Found at i:39249552 original size:36 final size:35
Alignment explanation
Indices: 39249395--39249549 Score: 116
Period size: 35 Copynumber: 4.3 Consensus size: 35
39249385 AATTTTTCTT
* * * *
39249395 TTTTTGAAAATACGAATTTTTTTTAAAATACAAGAA
1 TTTTTG-AAACACGAAATTTTTTTAAAACACAATAA
* **
39249431 TTTTAGAAACATAAAATTTTTTTAAAGACACAA-AA
1 TTTTTGAAACACGAAATTTTTTTAAA-ACACAATAA
* * **
39249466 ATTTTGAAACACGAGATTTCTTTTGAAAACACGAATTTTC
1 TTTTTGAAACACGAAATTT-TTTT-AAAACAC-AA--TAA
*
39249506 TTTTTGAAACAC-AAATTTTTTTAAAACACAATTTA
1 TTTTTGAAACACGAAATTTTTTTAAAACACAA-TAA
39249541 TTTTTGAAA
1 TTTTTGAAA
39249550 ACATAAAAAT
Statistics
Matches: 96, Mismatches: 16, Indels: 15
0.76 0.13 0.12
Matches are distributed among these distances:
35 44 0.46
36 20 0.21
37 12 0.12
38 4 0.04
39 5 0.05
40 11 0.11
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.40
Consensus pattern (35 bp):
TTTTTGAAACACGAAATTTTTTTAAAACACAATAA
Found at i:39249632 original size:36 final size:36
Alignment explanation
Indices: 39249587--39249682 Score: 108
Period size: 36 Copynumber: 2.7 Consensus size: 36
39249577 CACGAGGATT
*
39249587 TTTTTTG-AAACATGAAAATTTATT-AAAAACGGTCAA
1 TTTTTTGAAAACACGAAAATTT-TTGAAAAACGG-CAA
*
39249623 TTTTTTGAAAACACGAAAATTTTTGAAAGACGGCAA
1 TTTTTTGAAAACACGAAAATTTTTGAAAAACGGCAA
* *
39249659 -TTTTTAAAAACACGGGAAATTTTT
1 TTTTTTGAAAACAC-GAAAATTTTT
39249683 TTGAAAACAC
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
35 12 0.23
36 21 0.40
37 20 0.38
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (36 bp):
TTTTTTGAAAACACGAAAATTTTTGAAAAACGGCAA
Found at i:39249635 original size:37 final size:35
Alignment explanation
Indices: 39249587--39249827 Score: 106
Period size: 36 Copynumber: 6.8 Consensus size: 35
39249577 CACGAGGATT
*
39249587 TTTTTTGAAACATGAAAATTTATT-AAAAACGGTCAA
1 TTTTTTGAAACACGAAAATTT-TTGAAAAACGG-CAA
*
39249623 TTTTTTGAAAACACGAAAATTTTTGAAAGACGGCAA
1 TTTTTTG-AAACACGAAAATTTTTGAAAAACGGCAA
** * **
39249659 TTTTTAAAAACACGGGAAATTTTTTTGAAAACAC-AAAA
1 TTTTTTGAAACAC--GAAA-ATTTTTGAAAA-ACGGCAA
* * *
39249697 ATTTTTGAAACACTG-GAA-TTTTG-AAAAC-ACAGA
1 TTTTTTGAAACAC-GAAAATTTTTGAAAAACGGCA-A
* * *
39249730 -TTTTTGAAACATGAGAATTTTTGAAAACAC-GAAA
1 TTTTTTGAAACACGAAAATTTTTGAAAA-ACGGCAA
* * * * *
39249764 TTTTTTTAAAATAC-AAGAATTTTAGAAACAC-GAAA
1 -TTTTTTGAAACACGAA-AATTTTTGAAAAACGGCAA
* *
39249799 TTTTTTTAGAAACGCGAGAATTTTTGAAA
1 -TTTTTT-GAAACACGAAAATTTTTGAAA
39249828 CGAGAAATTT
Statistics
Matches: 160, Mismatches: 29, Indels: 32
0.72 0.13 0.14
Matches are distributed among these distances:
31 1 0.01
32 18 0.11
33 9 0.06
34 9 0.06
35 23 0.14
36 51 0.32
37 26 0.16
38 21 0.13
39 2 0.01
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.34
Consensus pattern (35 bp):
TTTTTTGAAACACGAAAATTTTTGAAAAACGGCAA
Found at i:39249645 original size:18 final size:18
Alignment explanation
Indices: 39249624--39249827 Score: 129
Period size: 17 Copynumber: 11.5 Consensus size: 18
39249614 AACGGTCAAT
39249624 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* **
39249642 TTTTTG-AAAGACGGCAA
1 TTTTTGAAAACACGAAAA
* *
39249659 TTTTTAAAAACACGGGAAATT
1 TTTTTGAAAACAC--GAAA-A
*
39249680 TTTTTGAAAACACAAAAA
1 TTTTTGAAAACACGAAAA
*
39249698 TTTTTG-AAACACTG-GAA
1 TTTTTGAAAACAC-GAAAA
*
39249715 -TTTTGAAAACAC--AGA
1 TTTTTGAAAACACGAAAA
* *
39249730 TTTTTG-AAACATGAGAA
1 TTTTTGAAAACACGAAAA
*
39249747 TTTTTGAAAACACGAAAT
1 TTTTTGAAAACACGAAAA
* *
39249765 TTTTTTAAAATAC-AAGAA
1 TTTTTGAAAACACGAA-AA
* *
39249783 TTTTAG-AAACACGAAAT
1 TTTTTGAAAACACGAAAA
* * *
39249800 TTTTTTAGAAACGCGAGAA
1 TTTTTGA-AAACACGAAAA
39249819 TTTTTGAAA
1 TTTTTGAAA
39249828 CGAGAAATTT
Statistics
Matches: 138, Mismatches: 34, Indels: 28
0.69 0.17 0.14
Matches are distributed among these distances:
15 6 0.04
16 10 0.07
17 46 0.33
18 45 0.33
19 17 0.12
20 2 0.01
21 12 0.09
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.33
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:39249720 original size:16 final size:16
Alignment explanation
Indices: 39249699--39249755 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
39249689 ACACAAAAAT
39249699 TTTTGAAACACTGGAA
1 TTTTGAAACACTGGAA
* *
39249715 TTTTGAAAACAC-AGAT
1 TTTTG-AAACACTGGAA
39249731 TTTTGAAACA-TGAGAA
1 TTTTGAAACACTG-GAA
39249747 TTTTTGAAA
1 -TTTTGAAA
39249756 ACACGAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
15 5 0.15
16 14 0.42
17 14 0.42
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (16 bp):
TTTTGAAACACTGGAA
Found at i:39249793 original size:35 final size:36
Alignment explanation
Indices: 39249730--39249841 Score: 131
Period size: 36 Copynumber: 3.1 Consensus size: 36
39249720 AAAACACAGA
**
39249730 TTTTT-GAAACATGAGAATTTTTGAAAACACGAAATT
1 TTTTTAGAAACACAAGAATTTTTG-AAACACGAAATT
* *
39249766 TTTTTA-AAATACAAGAATTTTAGAAACACGAAATT
1 TTTTTAGAAACACAAGAATTTTTGAAACACGAAATT
* *
39249801 TTTTTAGAAACGCGAGAATTTTTGAAACGA-GAAATT
1 TTTTTAGAAACACAAGAATTTTTGAAAC-ACGAAATT
39249837 TTTTT
1 TTTTT
39249842 TATAAAAAGT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
35 18 0.28
36 46 0.71
37 1 0.02
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (36 bp):
TTTTTAGAAACACAAGAATTTTTGAAACACGAAATT
Found at i:39249822 original size:20 final size:19
Alignment explanation
Indices: 39249754--39249823 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
39249744 GAATTTTTGA
39249754 AAACACGAAATTTTTTTA-
1 AAACACGAAATTTTTTTAG
* *
39249772 AAATAC-AAGA--ATTTTAG
1 AAACACGAA-ATTTTTTTAG
39249789 AAACACGAAATTTTTTTAG
1 AAACACGAAATTTTTTTAG
*
39249808 AAACGCGAGAATTTTT
1 AAACACGA-AATTTTT
39249824 GAAACGAGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
16 5 0.12
17 8 0.20
18 8 0.20
19 13 0.32
20 7 0.17
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.34
Consensus pattern (19 bp):
AAACACGAAATTTTTTTAG
Found at i:39249839 original size:17 final size:18
Alignment explanation
Indices: 39249783--39249840 Score: 59
Period size: 17 Copynumber: 3.2 Consensus size: 18
39249773 AATACAAGAA
39249783 TTTTAGAAAC-ACGAAATTT
1 TTTTAGAAACGA-GAAA-TT
*
39249802 TTTTAGAAACGCGAGAA-T
1 TTTTAGAAACGAGA-AATT
39249820 TTTT-GAAACGAGAAATT
1 TTTTAGAAACGAGAAATT
39249837 TTTT
1 TTTT
39249841 TTATAAAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
16 2 0.06
17 13 0.38
18 5 0.15
19 12 0.35
20 2 0.06
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (18 bp):
TTTTAGAAACGAGAAATT
Found at i:39249908 original size:17 final size:17
Alignment explanation
Indices: 39249886--39249941 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
39249876 TTATTGTTTT
39249886 TTTTGAAACACGATAAA
1 TTTTGAAACACGATAAA
* *
39249903 TTTTGAGAATATGA-AAA
1 TTTTGA-AACACGATAAA
*
39249920 TTTTTGAAACACGATTAA
1 -TTTTGAAACACGATAAA
39249938 TTTT
1 TTTT
39249942 TTTTTTAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
17 18 0.58
18 13 0.42
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (17 bp):
TTTTGAAACACGATAAA
Found at i:39249939 original size:18 final size:17
Alignment explanation
Indices: 39249885--39249942 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 17
39249875 ATTATTGTTT
39249885 TTTTTGAAACACGATAA
1 TTTTTGAAACACGATAA
* * * *
39249902 ATTTTGAGAATATGAAAA
1 TTTTTGA-AACACGATAA
39249920 TTTTTGAAACACGATTAA
1 TTTTTGAAACACGA-TAA
39249938 TTTTT
1 TTTTT
39249943 TTTTTAAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
17 11 0.35
18 20 0.65
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (17 bp):
TTTTTGAAACACGATAA
Found at i:39250643 original size:13 final size:13
Alignment explanation
Indices: 39250627--39250682 Score: 78
Period size: 13 Copynumber: 4.3 Consensus size: 13
39250617 TTCCTTTCCC
39250627 TTTCTTCTTCCTT
1 TTTCTTCTTCCTT
39250640 TTTCTTCTTCCTT
1 TTTCTTCTTCCTT
* *
39250653 TTTTTTCTCTCTTT
1 TTTCTTCT-TCCTT
39250667 TTTCTTCTT-CTT
1 TTTCTTCTTCCTT
39250679 TTTC
1 TTTC
39250683 AGCAACCCTG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
12 6 0.16
13 21 0.55
14 11 0.29
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTCTTCTTCCTT
Found at i:39250651 original size:30 final size:27
Alignment explanation
Indices: 39250631--39250681 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
39250621 TTTCCCTTTC
39250631 TTCT-TCCTTTTTCTTCTTCCTTTTTT
1 TTCTCTCCTTTTTCTTCTTCCTTTTTT
*
39250657 TTCTCTCTTTTTTCTTCTT-CTTTTT
1 TTCTCTCCTTTTTCTTCTTCCTTTTT
39250682 CAGCAACCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (27 bp):
TTCTCTCCTTTTTCTTCTTCCTTTTTT
Found at i:39250785 original size:15 final size:16
Alignment explanation
Indices: 39250761--39250804 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
39250751 TCTCCTCCCC
*
39250761 TTTTCCTTTTCTT-CT
1 TTTTCTTTTTCTTCCT
39250776 TTTTCTTTTTCTTCCT
1 TTTTCTTTTTCTTCCT
* *
39250792 TTGTCTTTCTCTT
1 TTTTCTTTTTCTT
39250805 TTATTTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTTCTTTTTCTTCCT
Found at i:39251331 original size:30 final size:30
Alignment explanation
Indices: 39251201--39251336 Score: 101
Period size: 30 Copynumber: 4.5 Consensus size: 30
39251191 AGGAAAATAT
* *** *
39251201 GGGGCCAAAATATAATTTTTGGAAAGTTTA
1 GGGGCCAAAATATAAATTTAAAAAAATTTA
* * * *
39251231 GAGGCCCAAATGTAATTTATAAAAAAATTTA
1 GGGGCCAAAATATAAATT-TAAAAAAATTTA
* * *
39251262 GGGGTCAAGATACAAATTTAAAAAAATTTA
1 GGGGCCAAAATATAAATTTAAAAAAATTTA
* * * ** *
39251292 AGGGTCAAAATGTAAATTTGGAAAAGTTTA
1 GGGGCCAAAATATAAATTTAAAAAAATTTA
39251322 GGGGCCAAAATATAA
1 GGGGCCAAAATATAA
39251337 TTTTTTATAT
Statistics
Matches: 81, Mismatches: 24, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
30 62 0.77
31 19 0.23
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.28
Consensus pattern (30 bp):
GGGGCCAAAATATAAATTTAAAAAAATTTA
Found at i:39255235 original size:75 final size:75
Alignment explanation
Indices: 39255111--39256313 Score: 1245
Period size: 75 Copynumber: 15.7 Consensus size: 75
39255101 CAAGAATTAT
* * *
39255111 TTTTCAATTTCTGTTTTTTCAAAAATCAACCCATAATGCGAGAGGTGAGTTGAGCCTCTGG-CAC
1 TTTTCAATTTCTG-TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
39255175 ACGCCGAGGTA
65 ACGCTGAGGTA
* * * *
39255186 GTTTTCAATTGCTGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCGC
1 -TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
39255251 ACGCTGAGGTA
65 ACGCTGAGGTA
* * * * *
39255262 TTTT-AAGTTTCTGTTTTTCAAAACTCAACTCATATTGCTAGAAGTTAGTTGGGCCTCGGGTCAC
1 TTTTCAA-TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* ** *
39255326 ATGCCAATGTA
65 ACGCTGAGGTA
* * **
39255337 TTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGTGTCGTA
1 TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA
39255402 CGCTGAGGTA
66 CGCTGAGGTA
** *
39255412 TTTT-AAGTTTCCATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGGCTCGGGTCAC
1 TTTTCAA-TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* *
39255476 ATGCCGAGGTA
65 ACGCTGAGGTA
* * * *
39255487 TTTCTTTTAAATTCTTGTTTTT-AAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTCGGGT
1 --T-TTTCAATTTC-TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
* *
39255551 CACATGCCGAGGTA
62 CACACGCTGAGGTA
* * *
39255565 TTTCTTTTAAATTT-T-TATTTTCAAAAATCAATTCATATTGTGAGAGGTGAGTTGAGCCTCGGG
1 ----TTTTCAATTTCTGT-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
* * *
39255628 TCACATGCCGATGTA
61 TCACACGCTGAGGTA
*
39255643 TTTCTTTTAAGTTTCTGTCTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
1 --T-TTTCAA-TTTCTG--TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
39255708 GTCACACGCTGAGGTA
60 GTCACACGCTGAGGTA
* * *
39255724 TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCGGGTCGCA
1 TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA
*
39255789 CACTGAGGTA
66 CGCTGAGGTA
* * * * *
39255799 TTTTTAAATTTCTATTTTTCAAAAATCAATTCATATTGCGAAAGGTGAGTTGAGCCTCGGGTCGC
1 -TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
39255864 ACGCTGAGGTA
65 ACGCTGAGGTA
* *
39255875 TTTCTTTTAAATTTCTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCGGGT
1 ----TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
*
39255939 CGCACGCTGAGGTA
62 CACACGCTGAGGTA
* *
39255953 TTTCTTTTAAATTTCTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGT
1 ----TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
39256017 --CACG-TCGAGGTA
62 CACACGCT-GAGGTA
* ** * * *
39256029 TTTTTCAATTTTTGGTTTTAAAAAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGAGT
1 -TTTTCAATTTCT-GTTTT--TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
39256094 --CACGCTGAGGTA
62 CACACGCTGAGGTA
* * **
39256106 TTTTCAATTTCTGTTTTTTAAAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTC-GAAC
1 TTTTCAATTTCTG-TTTTT--CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
* *
39256170 -CATGCCGAGGTA
63 ACACGCTGAGGTA
* ** * * *
39256182 -TATCTTTTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGTCTCGAGTCA
1 TTTTCAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
39256246 TA--CTGAGGTA
64 CACGCTGAGGTA
* * *
39256256 TTATCAATTTCTGTTTTTCAAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCT
1 TTTTCAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
39256314 TGGGCTGCAC
Statistics
Matches: 983, Mismatches: 106, Indels: 77
0.84 0.09 0.07
Matches are distributed among these distances:
73 10 0.01
74 52 0.05
75 355 0.36
76 171 0.17
77 67 0.07
78 241 0.25
79 28 0.03
80 2 0.00
81 56 0.06
82 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (75 bp):
TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA
CGCTGAGGTA
Found at i:39256578 original size:5 final size:5
Alignment explanation
Indices: 39256568--39256600 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
39256558 CCATTCTTCG
39256568 TATTT TATTT TA-TT TATTT TATTT TATTT TATT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATT
39256601 ATATATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:39256585 original size:9 final size:9
Alignment explanation
Indices: 39256571--39256600 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
39256561 TTCTTCGTAT
39256571 TTTATTTTA
1 TTTATTTTA
39256580 TTTATTTTA
1 TTTATTTTA
39256589 TTTTATTTTA
1 -TTTATTTTA
39256599 TT
1 TT
39256601 ATATATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTATTTTA
Found at i:39256587 original size:14 final size:14
Alignment explanation
Indices: 39256568--39256596 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39256558 CCATTCTTCG
39256568 TATTTTATTTTATT
1 TATTTTATTTTATT
39256582 TATTTTATTTTATT
1 TATTTTATTTTATT
39256596 T
1 T
39256597 TATTATATAT
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:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TATTTTATTTTATT
Found at i:39256609 original size:19 final size:19
Alignment explanation
Indices: 39256568--39256610 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
39256558 CCATTCTTCG
*
39256568 TATTTTATTTTATTTATTT
1 TATTTTATTTTATTTATTA
39256587 TATTTTATTTTA-TTATATA
1 TATTTTATTTTATTTAT-TA
39256606 TATTT
1 TATTT
39256611 AAAAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTTATTTTATTTATTA
Found at i:39263015 original size:52 final size:48
Alignment explanation
Indices: 39262996--39263198 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
39262986 TGACAAGTGG
* *
39262996 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
39263042 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
39263094 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
39263140 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
39263186 AAAGTGATAAGTG
1 AAAGTGATAAGTG
39263199 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:39263050 original size:98 final size:98
Alignment explanation
Indices: 39262930--39263198 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
39262920 TTTGAGTACT
*
39262930 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
39262995 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
39263028 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
39263093 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
39263126 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
39263191 GATAAGTG
65 GAAAAGTG
39263199 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:39263206 original size:37 final size:37
Alignment explanation
Indices: 39263162--39263270 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
39263152 GATAGCTTTA
39263162 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
39263199 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
39263236 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
39263271 ATCATACGTA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:39264998 original size:19 final size:19
Alignment explanation
Indices: 39264974--39265019 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
39264964 AATTAAACTT
39264974 GAAAATTGGATCTGAGATC
1 GAAAATTGGATCTGAGATC
*
39264993 GAAAATTGGATCTGAGATT
1 GAAAATTGGATCTGAGATC
39265012 GAAAATTG
1 GAAAATTG
39265020 AGCCCAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.39, C:0.07, G:0.26, T:0.28
Consensus pattern (19 bp):
GAAAATTGGATCTGAGATC
Found at i:39265515 original size:58 final size:58
Alignment explanation
Indices: 39265378--39265522 Score: 161
Period size: 58 Copynumber: 2.4 Consensus size: 58
39265368 TTAATAGCAT
* * * *
39265378 TTTATTAATTTAATATTAAATTTAATTAAATATTTATCTTATATATAAATATTCTATTAT
1 TTTAATAATTAAATATTAAATTTAATTAAATATTTA--TTATATATAAATATTATATTAA
*
39265438 TTTAATAAATTTAATATTAAATTTAATTAAATATTTA-TAT-TGATAAATATTATATTAA
1 TTTAAT-AATTAAATATTAAATTTAATTAAATATTTATTATAT-ATAAATATTATATTAA
*
39265496 TTTAAT-ATTAAAGTGATTAAGTTTAAT
1 TTTAATAATTAAA-T-ATTAAATTTAAT
39265523 CATAATTGAA
Statistics
Matches: 76, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
56 5 0.07
57 2 0.03
58 34 0.45
60 5 0.07
61 30 0.39
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (58 bp):
TTTAATAATTAAATATTAAATTTAATTAAATATTTATTATATATAAATATTATATTAA
Found at i:39266840 original size:16 final size:16
Alignment explanation
Indices: 39266819--39266850 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39266809 ATATAGCCAC
*
39266819 AAACCATGGATGCAAT
1 AAACCATGGATACAAT
39266835 AAACCATGGATACAAT
1 AAACCATGGATACAAT
39266851 GCAAATGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.19
Consensus pattern (16 bp):
AAACCATGGATACAAT
Found at i:39273846 original size:17 final size:17
Alignment explanation
Indices: 39273824--39273856 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
39273814 ATAGAAAGTC
39273824 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
39273841 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
39273857 AAATCTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.27, T:0.24
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:39274601 original size:20 final size:21
Alignment explanation
Indices: 39274568--39274616 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
39274558 ATTTTTAATT
*
39274568 ATTTTATTAATTTAATATTAA
1 ATTTAATTAATTTAATATTAA
* *
39274589 A-TTAATTATTTTACTATTAA
1 ATTTAATTAATTTAATATTAA
39274609 ATTTAATT
1 ATTTAATT
39274617 TAATACCCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTAATTAATTTAATATTAA
Found at i:39285023 original size:41 final size:41
Alignment explanation
Indices: 39284966--39285075 Score: 132
Period size: 41 Copynumber: 2.7 Consensus size: 41
39284956 ACCTTTTAGG
* *
39284966 GCTTTAGCGGCATTTTTGAAAAAGCGTCACTAATGCTCAGA
1 GCTTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGCTCAGA
** *
39285007 GCTTTAGCGGCGTTTTT-AAAGAAGCGCCACTAATGCTTGGG
1 GCTTTAGCGGCGTTTTTGAAA-AAGCGCCACTAATGCTCAGA
* * *
39285048 GATTAAGCGGCGTTTGTGAAAAAGCGCC
1 GCTTTAGCGGCGTTTTTGAAAAAGCGCC
39285076 GCAAAAACAT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
40 3 0.05
41 53 0.90
42 3 0.05
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (41 bp):
GCTTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGCTCAGA
Found at i:39285593 original size:6 final size:7
Alignment explanation
Indices: 39285567--39285599 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
39285557 TAAATAAGGT
39285567 TTAGGGG
1 TTAGGGG
*
39285574 TTAAGGG
1 TTAGGGG
39285581 TTAGGGG
1 TTAGGGG
39285588 TT-GGGG
1 TTAGGGG
39285594 TTAGGG
1 TTAGGG
39285600 ATTTGGGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.15, C:0.00, G:0.55, T:0.30
Consensus pattern (7 bp):
TTAGGGG
Found at i:39285596 original size:13 final size:14
Alignment explanation
Indices: 39285561--39285599 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
39285551 ATATATTAAA
*
39285561 TAAGGTTTAGGGGT
1 TAAGGGTTAGGGGT
39285575 TAAGGGTTAGGGGT
1 TAAGGGTTAGGGGT
*
39285589 T-GGGGTTAGGG
1 TAAGGGTTAGGG
39285600 ATTTGGGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.18, C:0.00, G:0.51, T:0.31
Consensus pattern (14 bp):
TAAGGGTTAGGGGT
Found at i:39285611 original size:20 final size:20
Alignment explanation
Indices: 39285570--39285624 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
39285560 ATAAGGTTTA
*
39285570 GGGGTTAAGGGTTAGGGGTT
1 GGGGTTAAGGGTTAGGGATT
*
39285590 GGGGTT-AGGGATTTGGGATT
1 GGGGTTAAGGG-TTAGGGATT
*
39285610 -GGATT-AGGGTTAGGG
1 GGGGTTAAGGGTTAGGG
39285625 TTAGGGTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 5 0.17
19 12 0.40
20 13 0.43
ACGTcount: A:0.16, C:0.00, G:0.53, T:0.31
Consensus pattern (20 bp):
GGGGTTAAGGGTTAGGGATT
Found at i:39285622 original size:6 final size:6
Alignment explanation
Indices: 39285571--39285632 Score: 54
Period size: 6 Copynumber: 9.8 Consensus size: 6
39285561 TAAGGTTTAG
* * *
39285571 GGGTTAA GGGTTA GGGGTTG GGGTTA GGGATTT GGGATT- GGATTA GGGTTA
1 GGGTT-A GGGTTA -GGGTTA GGGTTA GGG-TTA GGG-TTA GGGTTA GGGTTA
39285622 GGGTTA GGGTT
1 GGGTTA GGGTT
39285633 TAGATTAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
5 2 0.04
6 27 0.57
7 18 0.38
ACGTcount: A:0.16, C:0.00, G:0.50, T:0.34
Consensus pattern (6 bp):
GGGTTA
Found at i:39285802 original size:101 final size:101
Alignment explanation
Indices: 39285489--39285803 Score: 409
Period size: 107 Copynumber: 3.1 Consensus size: 101
39285479 ATATGGTTAA
* * * *
39285489 GGGTTAGGGATTTGGGGTCGAGTTATGGTTTAGGGTTTAGATTAATTAGTGTTTTTTAATTTATA
1 GGGTTAGGGATTCGAGGTTGGGTTATGGTTTAGGGTTTAGATTAATTAGTGTTTTTTAATTTATA
*
39285554 TATTAAATAAGGTTTAGGGGTTAAGGGTTAGGGGTT
66 TATTAAATAAGGTTTAGGGGTTAGGGGTTAGGGGTT
* *
39285590 GGGGTTAGGGATTTGGGATTGGATTAGGGTTA-GGGTTAGGGTTTAGATTAATTAGTGTTTTTTA
1 -GGGTTAGGGA-TT-CGA--GG-TT-GGGTTATGGTTTAGGGTTTAGATTAATTAGTGTTTTTTA
* * * * *
39285654 ATTTATATACTAAATAAGGTTTAAGGGTTAGGGGTTAAGGATC
59 ATTTATATATTAAATAAGGTTTAGGGGTTAGGGGTTAGGGGTT
* *
39285697 GGGTTAGGGATTCGAGGTTGGGTTATGGTTTAAGGTTTAGACTAATTAGTGTTTTTTAATTTATA
1 GGGTTAGGGATTCGAGGTTGGGTTATGGTTTAGGGTTTAGATTAATTAGTGTTTTTTAATTTATA
*
39285762 TATTAAATAAAGTTTAGGGGTTAGGGGGTT-GGGGTT
66 TATTAAATAAGGTTTAGGGGTTA-GGGGTTAGGGGTT
39285798 GGGTTA
1 GGGTTA
39285804 TGGTTTAGGG
Statistics
Matches: 184, Mismatches: 21, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
100 6 0.03
101 67 0.36
102 18 0.10
103 2 0.01
104 3 0.02
105 2 0.01
106 12 0.07
107 69 0.38
108 5 0.03
ACGTcount: A:0.24, C:0.02, G:0.33, T:0.41
Consensus pattern (101 bp):
GGGTTAGGGATTCGAGGTTGGGTTATGGTTTAGGGTTTAGATTAATTAGTGTTTTTTAATTTATA
TATTAAATAAGGTTTAGGGGTTAGGGGTTAGGGGTT
Found at i:39285834 original size:82 final size:82
Alignment explanation
Indices: 39285712--39285867 Score: 285
Period size: 82 Copynumber: 1.9 Consensus size: 82
39285702 AGGGATTCGA
39285712 GGTTGGGTTATGGTTTAAGGTTTAGACTAATTAGTGTTTTTTAATTTATATATTAAATAAAGTTT
1 GGTTGGGTTATGGTTTAAGGTTTAGACTAATTAGTGTTTTTTAATTTATATATTAAATAAAGTTT
39285777 AGGGGTTAGGGGGTTGG
66 AGGGGTTAGGGGGTTGG
* * *
39285794 GGTTGGGTTATGGTTTAGGGTTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAAGGTTT
1 GGTTGGGTTATGGTTTAAGGTTTAGACTAATTAGTGTTTTTTAATTTATATATTAAATAAAGTTT
39285859 AGGGGTTAG
66 AGGGGTTAG
39285868 AGATTAGGGT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 71 1.00
ACGTcount: A:0.26, C:0.01, G:0.28, T:0.46
Consensus pattern (82 bp):
GGTTGGGTTATGGTTTAAGGTTTAGACTAATTAGTGTTTTTTAATTTATATATTAAATAAAGTTT
AGGGGTTAGGGGGTTGG
Found at i:39285876 original size:14 final size:14
Alignment explanation
Indices: 39285857--39285915 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
39285847 TAAATAAGGT
*
39285857 TTAGGGGTTAGAGA
1 TTAGGGGTTAGAGG
39285871 TTA-GGGTTA-AGGG
1 TTAGGGGTTAGA-GG
* *
39285884 TTAGAGGTTAGGGG
1 TTAGGGGTTAGAGG
39285898 TTAGGGGTT-GA-G
1 TTAGGGGTTAGAGG
39285910 TTAGGG
1 TTAGGG
39285916 ATTCAGGGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
12 8 0.22
13 11 0.30
14 18 0.49
ACGTcount: A:0.22, C:0.00, G:0.47, T:0.31
Consensus pattern (14 bp):
TTAGGGGTTAGAGG
Found at i:39285886 original size:20 final size:19
Alignment explanation
Indices: 39285861--39285925 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
39285851 TAAGGTTTAG
39285861 GGGTTAGAGATTAGGGTTAA
1 GGGTTAGAG-TTAGGGTTAA
*
39285881 GGGTTAGAGGTTAGGGGTTAG
1 GGGTTAGA-GTTA-GGGTTAA
*
39285902 GGGTT-GAGTTAGGGATTCA
1 GGGTTAGAGTTAGGG-TTAA
39285921 GGGTT
1 GGGTT
39285926 GGGTTATGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 3 0.08
19 11 0.28
20 13 0.33
21 12 0.31
ACGTcount: A:0.22, C:0.02, G:0.46, T:0.31
Consensus pattern (19 bp):
GGGTTAGAGTTAGGGTTAA
Found at i:39286451 original size:84 final size:83
Alignment explanation
Indices: 39286319--39286524 Score: 198
Period size: 84 Copynumber: 2.4 Consensus size: 83
39286309 TTAGGAGTTT
* ** ** * *
39286319 AATTTTTTTAGTGACGTTTTTACGGAAAACGCCGTTATTATGTTTTAAAATTTGTCAAAACGGCG
1 AATTTTTTT-GTGGCGTTTTTA-GGAAAACGCCGCAAGGATGTTTTAAAATTTGGCAAAACGGCA
*
39286384 CCATTTATCTAGAGAAATGA
64 CCATTTATCTAGAGAAATAA
*
39286404 AATTTTTTTGTGGCGTTTTTAGTGAAAACGCCGCAAGGAT-TTATTAAAATTTGGCAAAGCGGCA
1 AATTTTTTTGTGGCGTTTTTAG-GAAAACGCCGCAAGGATGTT-TTAAAATTTGGCAAAACGGCA
* * * *
39286468 CCGTTTCTCTAGTGGAATAA
64 CCATTTATCTAGAGAAATAA
* * * * *
39286488 AATCTTATAGTGGCGTTTTTTAAGAAAACGCCACAAG
1 AATTTTTTTGTGGCG-TTTTTAGGAAAACGCCGCAAG
39286525 AGTGAATTAA
Statistics
Matches: 100, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
83 3 0.03
84 82 0.82
85 15 0.15
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (83 bp):
AATTTTTTTGTGGCGTTTTTAGGAAAACGCCGCAAGGATGTTTTAAAATTTGGCAAAACGGCACC
ATTTATCTAGAGAAATAA
Found at i:39286534 original size:84 final size:84
Alignment explanation
Indices: 39286453--39286676 Score: 358
Period size: 84 Copynumber: 2.7 Consensus size: 84
39286443 TTTATTAAAA
* * * * *
39286453 TTTGGCAAAGCGGCACCGTTTCTCTAGTGGAATAAAATCTTATAGTGGCGTTTTTTAAGAAAACG
1 TTTGCCAATGCGGCGCCGTTTCTCTACTGGAATAAAATCTTATAGTGGTGTTTTTTAAGAAAACG
39286518 CCACAAGAGTGAATTAATG
66 CCACAAGAGTGAATTAATG
* *
39286537 TTTGCCAATTCGGCGCCGTTTCTCTACTGGAATAAAATCTTATAGTGGTGTTTTTTAATAAAACG
1 TTTGCCAATGCGGCGCCGTTTCTCTACTGGAATAAAATCTTATAGTGGTGTTTTTTAAGAAAACG
*
39286602 CCGCAAGAGTGAATTAATG
66 CCACAAGAGTGAATTAATG
* *
39286621 TTTGCCAATGTGGCGTCGTTTCTCTACTGGAATAAAATCTTATAGTGGTGTTTTTT
1 TTTGCCAATGCGGCGCCGTTTCTCTACTGGAATAAAATCTTATAGTGGTGTTTTTT
39286677 GGTAACCATT
Statistics
Matches: 129, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 129 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (84 bp):
TTTGCCAATGCGGCGCCGTTTCTCTACTGGAATAAAATCTTATAGTGGTGTTTTTTAAGAAAACG
CCACAAGAGTGAATTAATG
Found at i:39289044 original size:42 final size:43
Alignment explanation
Indices: 39288926--39289052 Score: 161
Period size: 43 Copynumber: 3.0 Consensus size: 43
39288916 CACCAAACAA
** *
39288926 TAGCGGCGTTTGTGGGTAAAGTGTCGCTAAAGAACATGACTTT
1 TAGCGGCGTTTGTGGAAAAAGTGTCGCTAAAGAACATGACCTT
* *
39288969 TAGTGGCGTTTGTGGAAAAAGCGTCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGGAAAAAGTGTCGCTAAAGAACATGACCTT
*
39289012 TAGCGGCGTTT-T-TATAAAAGTG-CTGCTAAAGAACATGACCT
1 TAGCGGCGTTTGTGGA-AAAAGTGTC-GCTAAAGAACATGACCT
39289053 AACGCCACAA
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
41 2 0.03
42 24 0.32
43 48 0.65
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGAAAAAGTGTCGCTAAAGAACATGACCTT
Found at i:39293307 original size:4 final size:4
Alignment explanation
Indices: 39293291--39293346 Score: 94
Period size: 4 Copynumber: 14.0 Consensus size: 4
39293281 GAATATGACA
* *
39293291 TATG TATG CATG TATG TATG TATG TATG TGTG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
39293339 TATG TATG
1 TATG TATG
39293347 CTTAGAGAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.23, C:0.02, G:0.27, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:39311123 original size:14 final size:14
Alignment explanation
Indices: 39311109--39311164 Score: 62
Period size: 14 Copynumber: 4.0 Consensus size: 14
39311099 TATCCCCAAT
*
39311109 TATTATTTATTAAT
1 TATTATTTATTAAA
39311123 TATT-TTTATTTAAA
1 TATTATTTA-TTAAA
*
39311137 T-TTAATTATTATAA
1 TATTATTTATTA-AA
39311151 TATTATTTATTAAA
1 TATTATTTATTAAA
39311165 CTAATAATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
13 9 0.26
14 17 0.49
15 9 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTATTTATTAAA
Found at i:39319771 original size:16 final size:16
Alignment explanation
Indices: 39319750--39319818 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
39319740 TTTGGTTCGC
39319750 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
39319766 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
39319782 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
39319799 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
39319815 TGTA
1 TGTA
39319819 ATAGCTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:39319796 original size:33 final size:32
Alignment explanation
Indices: 39319750--39319818 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
39319740 TTTGGTTCGC
39319750 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
39319782 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
39319815 TGTA
1 TGTA
39319819 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:39319883 original size:44 final size:45
Alignment explanation
Indices: 39319799--39319889 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
39319789 GGATTAGAGG
* * *
39319799 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
39319844 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
39319888 TG
1 TG
39319890 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:39320075 original size:18 final size:17
Alignment explanation
Indices: 39320054--39320088 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39320044 TTATTATTAA
*
39320054 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
39320072 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
39320089 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:39320195 original size:18 final size:17
Alignment explanation
Indices: 39320174--39320208 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39320164 TTATTATTAA
*
39320174 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
39320192 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
39320209 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:39320250 original size:120 final size:121
Alignment explanation
Indices: 39320037--39320547 Score: 868
Period size: 120 Copynumber: 4.3 Consensus size: 121
39320027 ATCATATTTA
39320037 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* * *
39320102 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT-
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
39320157 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
39320222 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
* *
39320278 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* * *
39320342 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT-
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
* *
39320397 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
39320462 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
*
39320518 AA-ATAATTAATATTAAATATATTTTAATTA
1 AACATAATTATTATTAAATATATTTTAATTA
39320548 NCAATTACGG
Statistics
Matches: 366, Mismatches: 22, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
119 2 0.01
120 360 0.98
121 4 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
Found at i:39320463 original size:240 final size:240
Alignment explanation
Indices: 39320040--39320547 Score: 971
Period size: 240 Copynumber: 2.1 Consensus size: 240
39320030 ATATTTAAAC
*
39320040 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
1 ATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
39320105 TCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTATTA
66 TCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTATTA
*
39320170 TTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGA
131 TTAAATAAATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGA
39320235 ATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTGAA
196 ATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTGAA
*
39320280 ATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAATAT
1 ATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
39320345 TCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTATTA
66 TCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTATTA
* *
39320410 TTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATTA
131 TTAAATAAATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGA
39320475 ATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTGAA
196 ATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTGAA
39320520 ATAATTAATATTAAATATATTTTAATTA
1 ATAATTAATATTAAATATATTTTAATTA
39320548 NCAATTACGG
Statistics
Matches: 263, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
240 263 1.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (240 bp):
ATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
TCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTATTA
TTAAATAAATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGA
ATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTGAA
Found at i:39329341 original size:54 final size:54
Alignment explanation
Indices: 39329257--39329460 Score: 228
Period size: 54 Copynumber: 3.8 Consensus size: 54
39329247 TGTTCTCTTT
* * * ** *
39329257 AACATTAGTTGTTAGTGTAGCATTGTCTTTTACGACTGCCAAGTTTGAAGGAGA
1 AACATTAGCTGCTAGTGTAACATTGTCTTTTGTGACAGCCAAGTTTGAAGGAGA
* *
39329311 AGCATTAGCTGCTAGTGTAACATTGTCTTTTGTGTCAGCCAAGTTTGAAGGAGA
1 AACATTAGCTGCTAGTGTAACATTGTCTTTTGTGACAGCCAAGTTTGAAGGAGA
* * * ** * * *
39329365 AACATTAGCTGTTCGTATAACATCATCTTTTGTGACAGACAAGTTCGAAGGACA
1 AACATTAGCTGCTAGTGTAACATTGTCTTTTGTGACAGCCAAGTTTGAAGGAGA
** **
39329419 AACATTAGCTGCTAGTGTAACATCATCTTTTGCAACAGCCAA
1 AACATTAGCTGCTAGTGTAACATTGTCTTTTGTGACAGCCAA
39329461 ATTCAAAGGA
Statistics
Matches: 126, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 126 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (54 bp):
AACATTAGCTGCTAGTGTAACATTGTCTTTTGTGACAGCCAAGTTTGAAGGAGA
Found at i:39333696 original size:206 final size:206
Alignment explanation
Indices: 39333342--39333752 Score: 804
Period size: 206 Copynumber: 2.0 Consensus size: 206
39333332 ATGGTGTAAG
39333342 CAATGGAATTGTAAATCATGAGATATAATAGGTTTTGTGAGACAATGTCAGAATGAATTCTGGTT
1 CAATGGAATTGTAAATCATGAGATATAATAGGTTTTGTGAGACAATGTCAGAATGAATTCTGGTT
39333407 CCCCTGTTCTGACTTTGGAAAAATCATTAAAAATTGTACAAAAATTATTATGAGTTATACTTTAT
66 CCCCTGTTCTGACTTTGGAAAAATCATTAAAAATTGTACAAAAATTATTATGAGTTATACTTTAT
*
39333472 ATGGTTAGAATCCTTGATGAGTCTATTTTCATAATAAATAAACGGAAACATCATCCGAATTCTGT
131 ATGGTTAGAATCCTTGATGAGTATATTTTCATAATAAATAAACGGAAACATCATCCGAATTCTGT
39333537 ACAATGAGATT
196 ACAATGAGATT
39333548 CAATGGAATTGTAAATCATGAGATATAATAGGTTTTGTGAGACAATGTCAGAATGAATTCTGGTT
1 CAATGGAATTGTAAATCATGAGATATAATAGGTTTTGTGAGACAATGTCAGAATGAATTCTGGTT
*
39333613 CCCCTGTTCTGACTTTGGAAAAATTATTAAAAATTGTACAAAAATTATTATGAGTTATACTTTAT
66 CCCCTGTTCTGACTTTGGAAAAATCATTAAAAATTGTACAAAAATTATTATGAGTTATACTTTAT
39333678 ATGGTTAGAATCCTTGATGAGTATATTTTCATAATAAATAAACGGAAACATCATCCGAATTCTGT
131 ATGGTTAGAATCCTTGATGAGTATATTTTCATAATAAATAAACGGAAACATCATCCGAATTCTGT
39333743 ACAATGAGAT
196 ACAATGAGAT
39333753 AATTAATTTT
Statistics
Matches: 203, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
206 203 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (206 bp):
CAATGGAATTGTAAATCATGAGATATAATAGGTTTTGTGAGACAATGTCAGAATGAATTCTGGTT
CCCCTGTTCTGACTTTGGAAAAATCATTAAAAATTGTACAAAAATTATTATGAGTTATACTTTAT
ATGGTTAGAATCCTTGATGAGTATATTTTCATAATAAATAAACGGAAACATCATCCGAATTCTGT
ACAATGAGATT
Found at i:39334618 original size:44 final size:44
Alignment explanation
Indices: 39334553--39334679 Score: 148
Period size: 44 Copynumber: 2.8 Consensus size: 44
39334543 AAATTAGTTA
* *
39334553 AAAAAAAAAAAACAAAAAGCGCAAAAAAAAGTTGAGAAAAATCT
1 AAAAAAAAAAAGCAAACAGCGCAAAAAAAAGTTGAGAAAAATCT
39334597 AAAAAAAAAAAGCAAACAGCGCAAAAAAAAAAAGAGTTGAGAAAAATCT
1 AAAAAAAAAAAGCAAACAGCGC----AAAAAAA-AGTTGAGAAAAATCT
** *
39334646 -TTAAAAAAAAGCAAACAGCGTAAAAAAAAAGTTG
1 AAAAAAAAAAAGCAAACAGCG-CAAAAAAAAGTTG
39334680 CCTACCTCTC
Statistics
Matches: 72, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
44 25 0.35
45 7 0.10
48 25 0.35
49 15 0.21
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.10
Consensus pattern (44 bp):
AAAAAAAAAAAGCAAACAGCGCAAAAAAAAGTTGAGAAAAATCT
Found at i:39334627 original size:48 final size:48
Alignment explanation
Indices: 39334575--39334675 Score: 159
Period size: 48 Copynumber: 2.1 Consensus size: 48
39334565 CAAAAAGCGC
39334575 AAAAAAA-AGTTGAGAAAAATCTAAAAAAAAAAAGCAAACAGCGCAAAA
1 AAAAAAAGAGTTGAGAAAAATCT-AAAAAAAAAAGCAAACAGCGCAAAA
** *
39334623 AAAAAAAGAGTTGAGAAAAATCTTTAAAAAAAAGCAAACAGCGTAAAA
1 AAAAAAAGAGTTGAGAAAAATCTAAAAAAAAAAGCAAACAGCGCAAAA
39334671 AAAAA
1 AAAAA
39334676 GTTGCCTACC
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
48 34 0.69
49 15 0.31
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (48 bp):
AAAAAAAGAGTTGAGAAAAATCTAAAAAAAAAAGCAAACAGCGCAAAA
Found at i:39340239 original size:29 final size:27
Alignment explanation
Indices: 39340190--39340248 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 27
39340180 NATCTATCCT
39340190 TTTTATTTATTTATTTATTATTTAACTAA
1 TTTTATTTATTTATTTATTATTT--CTAA
39340219 TTTTATTTATTCTCA-TT-TTATTTCTAA
1 TTTTATTTATT-T-ATTTATTATTTCTAA
39340246 TTT
1 TTT
39340249 GTGTTTCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
27 7 0.25
29 17 0.61
30 3 0.11
31 1 0.04
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTTATTTATTTATTTATTATTTCTAA
Found at i:39343578 original size:12 final size:12
Alignment explanation
Indices: 39343561--39343593 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39343551 CATAAAAAAT
39343561 AATAATTTCT-TA
1 AATAATTT-TATA
39343573 AATAATTTTATA
1 AATAATTTTATA
39343585 AATAATTTT
1 AATAATTTT
39343594 TTTGGGCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 1 0.05
12 19 0.95
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (12 bp):
AATAATTTTATA
Found at i:39358418 original size:14 final size:14
Alignment explanation
Indices: 39358383--39358439 Score: 59
Period size: 13 Copynumber: 4.3 Consensus size: 14
39358373 TATACAACGC
*
39358383 ATTAATTAAA-AAT
1 ATTATTTAAATAAT
39358396 ATT-TTTAAATAAT
1 ATTATTTAAATAAT
39358409 -TTAATTTAAA-AAT
1 ATT-ATTTAAATAAT
*
39358422 ATTATTTTAATAAT
1 ATTATTTAAATAAT
39358436 ATTA
1 ATTA
39358440 CAAATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
12 7 0.19
13 15 0.41
14 15 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTATTTAAATAAT
Found at i:39358423 original size:26 final size:26
Alignment explanation
Indices: 39358384--39358435 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
39358374 ATACAACGCA
39358384 TTAATTAAAAATATT-TTTAAATAAT
1 TTAATTAAAAATATTATTTAAATAAT
*
39358409 TTAATTTAAAAATATTATTTTAATAAT
1 TTAA-TTAAAAATATTATTTAAATAAT
39358436 ATTACAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 4 0.17
26 11 0.46
27 9 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TTAATTAAAAATATTATTTAAATAAT
Found at i:39362074 original size:26 final size:26
Alignment explanation
Indices: 39362045--39362097 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
39362035 AGTTTAGAAA
39362045 TAATAA-AATATATTATAAATTATATT
1 TAATAATAAT-TATTATAAATTATATT
*
39362071 TAATAATAATTATTTTAAATTATATT
1 TAATAATAATTATTATAAATTATATT
39362097 T
1 T
39362098 TATAGTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TAATAATAATTATTATAAATTATATT
Found at i:39362098 original size:12 final size:12
Alignment explanation
Indices: 39362048--39362099 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
39362038 TTAGAAATAA
* *
39362048 TAAAATATATTA
1 TAAATTATATTT
39362060 TAAATTATATTT
1 TAAATTATATTT
* *
39362072 AATAATAATTATTT
1 TA-AATTA-TATTT
39362086 TAAATTATATTT
1 TAAATTATATTT
39362098 TA
1 TA
39362100 TAGTTTTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 18 0.56
13 8 0.25
14 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAATTATATTT
Found at i:39362170 original size:61 final size:61
Alignment explanation
Indices: 39362105--39362294 Score: 203
Period size: 61 Copynumber: 3.1 Consensus size: 61
39362095 TTTTATAGTT
39362105 TTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATACTAAGAATTTTATTAAA
1 TTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATACTAAGAATTTTATTAAA
* ** * * * * * * **
39362166 TTATATATTTTTG-TTAAATTATATTTA-ATAATAATTATTTTAA-A-TTA-TATTTTA-TAGTT
1 TTATATA-TTATGATTTTAGTAAATTCATATAAGAA-TA-TTTAATACTAAGAATTTTATTA-AA
39362225 TTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATACTAAGAATTTTATTAAA
1 TTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATACTAAGAATTTTATTAAA
39362286 TTATATATT
1 TTATATATT
39362295 TTTGTTAAAT
Statistics
Matches: 97, Mismatches: 22, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
58 11 0.11
59 25 0.26
60 16 0.16
61 34 0.35
62 11 0.11
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (61 bp):
TTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATACTAAGAATTTTATTAAA
Found at i:39362191 original size:120 final size:120
Alignment explanation
Indices: 39362060--39362329 Score: 531
Period size: 120 Copynumber: 2.2 Consensus size: 120
39362050 AAATATATTA
39362060 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTTTTATATATTATGATTTTAGT
1 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTTTTATATATTATGATTTTAGT
39362125 AAATTCATATAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGT
66 AAATTCATATAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGT
39362180 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTTTTATATATTATGATTTTAGT
1 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTTTTATATATTATGATTTTAGT
39362245 AAATTCATATAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGT
66 AAATTCATATAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGT
*
39362300 TAAATTATATTTAATAATAATTATGTTAAA
1 TAAATTATATTTAATAATAATTATTTTAAA
39362330 ATATGATTAA
Statistics
Matches: 149, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 149 1.00
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (120 bp):
TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTTTTATATATTATGATTTTAGT
AAATTCATATAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGT
Found at i:39363495 original size:12 final size:12
Alignment explanation
Indices: 39363478--39363502 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39363468 TCAATGCTAA
39363478 CCCAACAAAATT
1 CCCAACAAAATT
39363490 CCCAACAAAATT
1 CCCAACAAAATT
39363502 C
1 C
39363503 GATTCTCGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (12 bp):
CCCAACAAAATT
Found at i:39368926 original size:19 final size:18
Alignment explanation
Indices: 39368902--39368946 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
39368892 GTAGACAAAA
*
39368902 TTAAAAAAATAAAATTATT
1 TTAAAAAAAT-AAATTAAT
*
39368921 TTAAAAATATAAATTAAT
1 TTAAAAAAATAAATTAAT
39368939 TTAAAAAA
1 TTAAAAAA
39368947 TATATATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TTAAAAAAATAAATTAAT
Found at i:39368958 original size:17 final size:18
Alignment explanation
Indices: 39368905--39368965 Score: 72
Period size: 19 Copynumber: 3.4 Consensus size: 18
39368895 GACAAAATTA
39368905 AAAAAATA-AAATTATTT
1 AAAAAATATAAATTATTT
*
39368922 TAAAAATATAAATTAATTT
1 AAAAAATATAAATT-ATTT
*
39368941 AAAAAATATATATT-TTT
1 AAAAAATATAAATTATTT
39368958 AAACAAAT
1 AAA-AAAT
39368966 CCATATACCA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
17 13 0.34
18 9 0.24
19 16 0.42
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAAATATAAATTATTT
Found at i:39371719 original size:30 final size:30
Alignment explanation
Indices: 39371685--39371751 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
39371675 ACGGGCTATC
* *
39371685 ACACGGCCGTATGACACACACGGTCGGACT
1 ACACGGCCATATGACACACACGGTCGAACT
* * * *
39371715 ACACGACTATGTGACACACACGGTCTAACT
1 ACACGGCCATATGACACACACGGTCGAACT
39371745 ACACGGC
1 ACACGGC
39371752 TGTGTGTCAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.33, G:0.22, T:0.15
Consensus pattern (30 bp):
ACACGGCCATATGACACACACGGTCGAACT
Found at i:39371899 original size:54 final size:54
Alignment explanation
Indices: 39371785--39371919 Score: 128
Period size: 54 Copynumber: 2.5 Consensus size: 54
39371775 GGTGCAAGTT
* * **
39371785 AGACACGGCCTGCAACACGGCCGTGTGACCTAAGTCAGTGAATTACTTGATCTG
1 AGACACGGCCTGCAACACGGCCGTGTGACATAAGTCAGTGAACTACACGATCTG
* ** * * *
39371839 -GCACACGGCCTGCAACATGGTTGTGTGACATAAGTTAGTGAGCTACACGATTTG
1 AG-ACACGGCCTGCAACACGGCCGTGTGACATAAGTCAGTGAACTACACGATCTG
* ** *
39371893 AGACACGGGCTGGGACACGACCGTGTG
1 AGACACGGCCTGCAACACGGCCGTGTG
39371920 TCCTATTGTT
Statistics
Matches: 62, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
53 1 0.02
54 60 0.97
55 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.30, T:0.21
Consensus pattern (54 bp):
AGACACGGCCTGCAACACGGCCGTGTGACATAAGTCAGTGAACTACACGATCTG
Found at i:39374892 original size:21 final size:21
Alignment explanation
Indices: 39374861--39374900 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
39374851 ACCAAAAATT
39374861 TATTTTAAAAATAATAAAAAAG
1 TATTTTAAAAATAA-AAAAAAG
39374883 TATTTT-AAAATAAAAAAA
1 TATTTTAAAAATAAAAAAA
39374901 TAAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (21 bp):
TATTTTAAAAATAAAAAAAAG
Found at i:39375809 original size:19 final size:21
Alignment explanation
Indices: 39375787--39375832 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 21
39375777 AAACATTATG
39375787 AATTAATTA-AAAATC-ATAA
1 AATTAATTATAAAATCTATAA
39375806 AATT--TTATAAAATCTATAA
1 AATTAATTATAAAATCTATAA
*
39375825 AAATAATT
1 AATTAATT
39375833 TATTATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
17 3 0.14
18 6 0.27
19 11 0.50
21 2 0.09
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (21 bp):
AATTAATTATAAAATCTATAA
Found at i:39376097 original size:20 final size:19
Alignment explanation
Indices: 39376072--39376115 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
39376062 TACAAATGAT
39376072 TTTTTAATAAATTTTTATCG
1 TTTTTAAT-AATTTTTATCG
* *
39376092 TTTTTAGTAATTTTTATTG
1 TTTTTAATAATTTTTATCG
39376111 TTTTT
1 TTTTT
39376116 TTTTATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.68
Consensus pattern (19 bp):
TTTTTAATAATTTTTATCG
Found at i:39376116 original size:20 final size:19
Alignment explanation
Indices: 39376071--39376141 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 19
39376061 TTACAAATGA
*
39376071 TTTTTTAATAAATTTTTATCG
1 TTTTTT-AT-AATTTTTATTG
39376092 -TTTTTAGTAATTTTTATTG
1 TTTTTTA-TAATTTTTATTG
39376111 TTTTTTTTTATAATTTTTATATG
1 ---TTTTTTATAATTTTTAT-TG
39376134 TTTTTTAT
1 TTTTTTAT
39376142 GATTCTAGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
19 11 0.26
20 14 0.33
22 10 0.23
23 8 0.19
ACGTcount: A:0.23, C:0.01, G:0.06, T:0.70
Consensus pattern (19 bp):
TTTTTTATAATTTTTATTG
Found at i:39376118 original size:23 final size:23
Alignment explanation
Indices: 39376092--39376139 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
39376082 ATTTTTATCG
39376092 TTTTTAGTAATTTTTAT-TGTTTT
1 TTTTTA-TAATTTTTATATGTTTT
39376115 TTTTTATAATTTTTATATGTTTT
1 TTTTTATAATTTTTATATGTTTT
39376138 TT
1 TT
39376140 ATGATTCTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (23 bp):
TTTTTATAATTTTTATATGTTTT
Found at i:39376738 original size:23 final size:23
Alignment explanation
Indices: 39376712--39376759 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
39376702 ATTTTTTAAA
39376712 AATA-TTTATATGATTTTTAATTT
1 AATATTTTATAT-ATTTTTAATTT
*
39376735 AATATTTTTATATATTTTTCATTT
1 AATA-TTTTATATATTTTTAATTT
39376759 A
1 A
39376760 TTAAAATTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 4 0.18
24 11 0.50
25 7 0.32
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
AATATTTTATATATTTTTAATTT
Found at i:39397932 original size:18 final size:16
Alignment explanation
Indices: 39397908--39397955 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
39397898 ATTAAAAATA
39397908 TTTATTTTATATTATTT
1 TTTATTTTATATT-TTT
*
39397925 TATTATTTAATATTTTT
1 T-TTATTTTATATTTTT
*
39397942 TTTATTTTTTATTT
1 TTTATTTTATATTT
39397956 ATTGTAACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 11 0.41
17 5 0.19
18 11 0.41
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTATTTTATATTTTT
Found at i:39398557 original size:26 final size:26
Alignment explanation
Indices: 39398503--39398557 Score: 60
Period size: 25 Copynumber: 2.1 Consensus size: 26
39398493 TGTTTAGTTT
**
39398503 AATAAATAAATCATTAAAAAATATTA
1 AATAAATAAATCATTAAAAAATAAGA
39398529 AATAAA-AAAT-ATTAGAAAAATAGAGA
1 AATAAATAAATCATTA-AAAAATA-AGA
39398555 AAT
1 AAT
39398558 TTGATTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 4 0.16
25 11 0.44
26 10 0.40
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.25
Consensus pattern (26 bp):
AATAAATAAATCATTAAAAAATAAGA
Found at i:39416648 original size:31 final size:31
Alignment explanation
Indices: 39416612--39416672 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
39416602 ATTTACCGAA
39416612 GCCAAGTTCAAGTACC-AATTCGAACCAAAAG
1 GCCAAGTTCAAGTACCTAATT-GAACCAAAAG
* *
39416643 GCCAAGTTCAGGTACCTAATTGGACCAAAA
1 GCCAAGTTCAAGTACCTAATTGAACCAAAA
39416673 TAAACTTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (31 bp):
GCCAAGTTCAAGTACCTAATTGAACCAAAAG
Done.