Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168481.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_8, whole genome shotgun sequence
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: 25818110
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 67000 characters in sequence are not A, C, G, or T
File 97 of 127
Found at i:18322959 original size:22 final size:23
Alignment explanation
Indices: 18322934--18322979 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
18322924 GTAATCAAAT
18322934 TAAATAT-AATCATATCATGCAA
1 TAAATATAAATCATATCATGCAA
18322956 TAAATATAAAATCATATCATGCAA
1 TAAATAT-AAATCATATCATGCAA
18322980 ATAATAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 7 0.32
24 15 0.68
ACGTcount: A:0.52, C:0.13, G:0.04, T:0.30
Consensus pattern (23 bp):
TAAATATAAATCATATCATGCAA
Found at i:18322985 original size:24 final size:23
Alignment explanation
Indices: 18322941--18322990 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 23
18322931 AATTAAATAT
18322941 AATCATATCATGCAATAAATATAA
1 AATCATATCATGCAATAAATA-AA
18322965 AATCATATCATGCAA-ATAATAAA
1 AATCATATCATGCAATA-AATAAA
18322988 AAT
1 AAT
18322991 TATGCAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.56, C:0.12, G:0.04, T:0.28
Consensus pattern (23 bp):
AATCATATCATGCAATAAATAAA
Found at i:18324286 original size:12 final size:12
Alignment explanation
Indices: 18324271--18324344 Score: 64
Period size: 12 Copynumber: 6.3 Consensus size: 12
18324261 AAATAAATCA
18324271 CAAAATTAAAAT
1 CAAAATTAAAAT
*
18324283 CAAAACTAAAA-
1 CAAAATTAAAAT
*
18324294 -AGAATCT-AAAT
1 CAAAAT-TAAAAT
*
18324305 TAAAATTAAAAT
1 CAAAATTAAAAT
* *
18324317 CAAAATCAATAT
1 CAAAATTAAAAT
*
18324329 TAAAATTAAAAT
1 CAAAATTAAAAT
18324341 CAAA
1 CAAA
18324345 TTACAATTAA
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
10 6 0.13
11 2 0.04
12 39 0.83
ACGTcount: A:0.65, C:0.09, G:0.01, T:0.24
Consensus pattern (12 bp):
CAAAATTAAAAT
Found at i:18324293 original size:18 final size:17
Alignment explanation
Indices: 18324272--18324347 Score: 66
Period size: 18 Copynumber: 4.4 Consensus size: 17
18324262 AATAAATCAC
18324272 AAAATTAAAATCAAAACT
1 AAAATTAAAATCAAAA-T
* *
18324290 AAAA--AGAATCTAAATT
1 AAAATTAAAATC-AAAAT
18324306 AAAATTAAAATCAAAAT
1 AAAATTAAAATCAAAAT
* *
18324323 CAATATTAAAATTAAAAT
1 -AAAATTAAAATCAAAAT
*
18324341 CAAATTA
1 AAAATTA
18324348 CAATTAAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
16 10 0.22
17 12 0.26
18 24 0.52
ACGTcount: A:0.64, C:0.08, G:0.01, T:0.26
Consensus pattern (17 bp):
AAAATTAAAATCAAAAT
Found at i:18324358 original size:18 final size:18
Alignment explanation
Indices: 18324309--18324356 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
18324299 CTAAATTAAA
*
18324309 ATTAAAATCAAAATCAAT
1 ATTAAAATTAAAATCAAT
18324327 ATTAAAATTAAAATCAA-
1 ATTAAAATTAAAATCAAT
*
18324344 ATTACAATTAAAA
1 ATTAAAATTAAAA
18324357 ATTTTAGGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.29
Consensus pattern (18 bp):
ATTAAAATTAAAATCAAT
Found at i:18324359 original size:24 final size:22
Alignment explanation
Indices: 18324302--18324356 Score: 74
Period size: 24 Copynumber: 2.4 Consensus size: 22
18324292 AAAGAATCTA
18324302 AATTAAAATTAAAATCAAAATC
1 AATTAAAATTAAAATCAAAATC
*
18324324 AATATTAAAATTAAAATCAAATTAC
1 -A-ATTAAAATTAAAATCAAAAT-C
18324349 AATTAAAA
1 AATTAAAA
18324357 ATTTTAGGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 8 0.28
24 20 0.69
25 1 0.03
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (22 bp):
AATTAAAATTAAAATCAAAATC
Found at i:18324829 original size:65 final size:65
Alignment explanation
Indices: 18324759--18324988 Score: 229
Period size: 65 Copynumber: 3.5 Consensus size: 65
18324749 TGAGATTAGT
18324759 AAGAATTTTATATTTAT-AAGAA-TTTTCAGGTTTGCAAGAATAGGATATTTGAATTTCAGATTT
1 AAGAATTTTA-ATTTATCAAGAACTTTT-AGGTTTGCAAGAATAGGATATTTGAATTTCAGATTT
18324822 GC
64 GC
* * *** * * *
18324824 AAGAATTTCAATTTTTCAAGAACTTTTAGGTTCATAAGAATGAAAGAT-TCGTAAGAACTT-AGA
1 AAGAATTTTAATTTATCAAGAACTTTTAGGTTTGCAAGAAT--AGGATAT--T-TGAATTTCAGA
* *
18324887 TTAGT
61 TTTGC
*
18324892 AAGAATTTTATATTCAT-AAGAA-TTTTCAGGTTTGCAAGAATAGGATATTTGAATTTCAGATTT
1 AAGAATTTTA-ATTTATCAAGAACTTTT-AGGTTTGCAAGAATAGGATATTTGAATTTCAGATTT
18324955 GC
64 GC
*
18324957 AAGAATTTTAATTTTTCAAGAACTTTTAGGTT
1 AAGAATTTTAATTTATCAAGAACTTTTAGGTT
18324989 CATAAGAATG
Statistics
Matches: 129, Mismatches: 23, Indels: 26
0.72 0.13 0.15
Matches are distributed among these distances:
64 14 0.11
65 52 0.40
66 13 0.10
67 9 0.07
68 32 0.25
69 9 0.07
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (65 bp):
AAGAATTTTAATTTATCAAGAACTTTTAGGTTTGCAAGAATAGGATATTTGAATTTCAGATTTGC
Found at i:18325029 original size:133 final size:133
Alignment explanation
Indices: 18324743--18325032 Score: 519
Period size: 133 Copynumber: 2.2 Consensus size: 133
18324733 TCAGATTTAG
* * *
18324743 AAGAACTGAGATTAGTAAGAATTTTATATTTATAAGAATTTTCAGGTTTGCAAGAATAGGATATT
1 AAGAACTTAGATTAGCAAGAATTTTATATTCATAAGAATTTTCAGGTTTGCAAGAATAGGATATT
18324808 TGAATTTCAGATTTGCAAGAATTTCAATTTTTCAAGAACTTTTAGGTTCATAAGAATGAAAGATT
66 TGAATTTCAGATTTGCAAGAATTTCAATTTTTCAAGAACTTTTAGGTTCATAAGAATGAAAGATT
18324873 CGT
131 CGT
*
18324876 AAGAACTTAGATTAGTAAGAATTTTATATTCATAAGAATTTTCAGGTTTGCAAGAATAGGATATT
1 AAGAACTTAGATTAGCAAGAATTTTATATTCATAAGAATTTTCAGGTTTGCAAGAATAGGATATT
*
18324941 TGAATTTCAGATTTGCAAGAATTTTAATTTTTCAAGAACTTTTAGGTTCATAAGAATGAAAGATT
66 TGAATTTCAGATTTGCAAGAATTTCAATTTTTCAAGAACTTTTAGGTTCATAAGAATGAAAGATT
18325006 CGT
131 CGT
18325009 AAGAACTTAGATTCA-CAAGAATTT
1 AAGAACTTAGATT-AGCAAGAATTT
18325033 CAGGTTCGCA
Statistics
Matches: 152, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
133 151 0.99
134 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (133 bp):
AAGAACTTAGATTAGCAAGAATTTTATATTCATAAGAATTTTCAGGTTTGCAAGAATAGGATATT
TGAATTTCAGATTTGCAAGAATTTCAATTTTTCAAGAACTTTTAGGTTCATAAGAATGAAAGATT
CGT
Found at i:18325046 original size:17 final size:17
Alignment explanation
Indices: 18325001--18325118 Score: 87
Period size: 17 Copynumber: 6.9 Consensus size: 17
18324991 TAAGAATGAA
* *
18325001 AGATTCGTAAGAACTT-
1 AGATTCGCAAGAATTTC
*
18325017 AGATTCACAAGAATTTC
1 AGATTCGCAAGAATTTC
*
18325034 AGGTTCGCAAGAATATTC
1 AGATTCGCAAGAAT-TTC
* *
18325052 AGACTCGCAAGAAATTC
1 AGATTCGCAAGAATTTC
** *
18325069 A-ATTTCATAAGAATTTT
1 AGA-TTCGCAAGAATTTC
*
18325086 AGATTTGCAAGAATTTC
1 AGATTCGCAAGAATTTC
* **
18325103 AGTTTCATAAGAATTT
1 AGATTCGCAAGAATTT
18325119 TCAAATTTGC
Statistics
Matches: 77, Mismatches: 21, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
16 14 0.18
17 48 0.62
18 15 0.19
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (17 bp):
AGATTCGCAAGAATTTC
Found at i:18325059 original size:18 final size:18
Alignment explanation
Indices: 18325024--18325069 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
18325014 CTTAGATTCA
**
18325024 CAAGAAT-TTCAGGTTCG
1 CAAGAATATTCAGACTCG
18325041 CAAGAATATTCAGACTCG
1 CAAGAATATTCAGACTCG
18325059 CAAGAA-ATTCA
1 CAAGAATATTCA
18325070 ATTTCATAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (18 bp):
CAAGAATATTCAGACTCG
Found at i:18325459 original size:32 final size:31
Alignment explanation
Indices: 18325423--18325494 Score: 99
Period size: 32 Copynumber: 2.3 Consensus size: 31
18325413 TTTCACATCC
18325423 AAAATTTCAAAGGTTCTCATTCAAAAACTTCT
1 AAAATTTCAAAGGTTCTCATTCAAAAACTT-T
* **
18325455 AAAATTTCTAAGGTTCTTGTTCAAAAACTTT
1 AAAATTTCAAAGGTTCTCATTCAAAAACTTT
*
18325486 ATAATTTCA
1 AAAATTTCA
18325495 TATCCAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 8 0.23
32 27 0.77
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (31 bp):
AAAATTTCAAAGGTTCTCATTCAAAAACTTT
Found at i:18325462 original size:46 final size:46
Alignment explanation
Indices: 18325349--18325462 Score: 115
Period size: 46 Copynumber: 2.5 Consensus size: 46
18325339 AAAGATTTTT
* * *
18325349 ATTTCAAAAAACTTAAAGA-TTAACATCCAAAATTTTAAAGATTCAC
1 ATTTCAAAAAATTTAAA-ATTTCACATCCAAAATTTCAAAGATTCAC
* ** * *
18325395 ATTTGAAAAAATTTAGCATTTCACATCCAAAATTTCAAAGGTTCTC
1 ATTTCAAAAAATTTAAAATTTCACATCCAAAATTTCAAAGATTCAC
*
18325441 A-TTCAAAAACTTCTAAAATTTC
1 ATTTCAAAAAATT-TAAAATTTC
18325463 TAAGGTTCTT
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
45 10 0.19
46 44 0.81
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (46 bp):
ATTTCAAAAAATTTAAAATTTCACATCCAAAATTTCAAAGATTCAC
Found at i:18325502 original size:23 final size:23
Alignment explanation
Indices: 18325476--18325549 Score: 73
Period size: 23 Copynumber: 3.2 Consensus size: 23
18325466 GGTTCTTGTT
18325476 CAAAAACTTTATA-ATTTCATATC
1 CAAAAACTTTA-AGATTTCATATC
*
18325499 C-AAAATTTTAAAGATTCTCAT-TC
1 CAAAAACTTT-AAGATT-TCATATC
* *
18325522 GAAAAACTTTAAGATTTCACATC
1 CAAAAACTTTAAGATTTCATATC
18325545 CAAAA
1 CAAAA
18325550 TTCAATGATT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
22 11 0.27
23 19 0.46
24 11 0.27
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.34
Consensus pattern (23 bp):
CAAAAACTTTAAGATTTCATATC
Found at i:18325529 original size:46 final size:45
Alignment explanation
Indices: 18325455--18325697 Score: 197
Period size: 46 Copynumber: 5.3 Consensus size: 45
18325445 AAAAACTTCT
* * ** *
18325455 AAAATTTCTAAGGTTCTTGTTC-AAAAACTTTATAATTTCATATCC
1 AAAATTTCAAAGATTCTCATTCAAAAAACTTTA-AATTTCACATCC
* *
18325500 AAAATTTTAAAGATTCTCATTCGAAAAACTTTAAGATTTCACATCC
1 AAAATTTCAAAGATTCTCATTCAAAAAACTTTAA-ATTTCACATCC
* * * *
18325546 AAAA-TTCAATGATTATCATTTAAAAAATTTTAAAGTTTCACATCC
1 AAAATTTCAAAGATTCTCATTCAAAAAACTTTAAA-TTTCACATCC
* * * **
18325591 AAAGTTTCAAAGATTCTTATTCAAAAAAATTTAGGGTTTCACATCC
1 AAAATTTCAAAGATTCTCATTCAAAAAACTTTA-AATTTCACATCC
* * ** *
18325637 AAAATTTCAAA-ATTTCTCCTTTAAATAAA-TTTAGGTTTTCACATTC
1 AAAATTTCAAAGA-TTCTCATTCAAA-AAACTTTA-AATTTCACATCC
*
18325683 AAAATTTTAAAGATT
1 AAAATTTCAAAGATT
18325698 TTTGTTCAAA
Statistics
Matches: 163, Mismatches: 27, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
44 1 0.01
45 55 0.34
46 103 0.63
47 4 0.02
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (45 bp):
AAAATTTCAAAGATTCTCATTCAAAAAACTTTAAATTTCACATCC
Found at i:18325618 original size:91 final size:91
Alignment explanation
Indices: 18325477--18325642 Score: 235
Period size: 91 Copynumber: 1.8 Consensus size: 91
18325467 GTTCTTGTTC
* * * *
18325477 AAAAACTTTATAATTTCATATCCAAAATTTTAAAGATTCTCATTCGAAAAACTTTAAGATTTCAC
1 AAAAACTTTATAATTTCACATCCAAAATTTCAAAGATTCTCATTCAAAAAAATTTAAGATTTCAC
18325542 ATCCAAAATTCAATGATTATCATTTA
66 ATCCAAAATTCAATGATTATCATTTA
* * * * *
18325568 AAAAATTTTA-AAGTTTCACATCCAAAGTTTCAAAGATTCTTATTCAAAAAAATTTAGGGTTTCA
1 AAAAACTTTATAA-TTTCACATCCAAAATTTCAAAGATTCTCATTCAAAAAAATTTAAGATTTCA
18325632 CATCCAAAATT
65 CATCCAAAATT
18325643 TCAAAATTTC
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
90 2 0.03
91 63 0.97
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (91 bp):
AAAAACTTTATAATTTCACATCCAAAATTTCAAAGATTCTCATTCAAAAAAATTTAAGATTTCAC
ATCCAAAATTCAATGATTATCATTTA
Found at i:18326011 original size:25 final size:25
Alignment explanation
Indices: 18325983--18326038 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
18325973 TAAATGATGG
18325983 AAATGCATGTCTTAAACAATAATGC
1 AAATGCATGTCTTAAACAATAATGC
18326008 AAATGCATGTCTTAAACAATAATGC
1 AAATGCATGTCTTAAACAATAATGC
18326033 AAATGC
1 AAATGC
18326039 CATATTATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (25 bp):
AAATGCATGTCTTAAACAATAATGC
Found at i:18326110 original size:24 final size:24
Alignment explanation
Indices: 18326064--18326110 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
18326054 ATATTCTCTA
*
18326064 CATGATGCAAATGCATTCTTCAAC
1 CATGATGCAAATGCATTCATCAAC
18326088 CATGATGCAAATGCAATT-ATCAA
1 CATGATGCAAATGC-ATTCATCAA
18326111 GGATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (24 bp):
CATGATGCAAATGCATTCATCAAC
Found at i:18326884 original size:18 final size:17
Alignment explanation
Indices: 18326845--18326887 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
18326835 TAAGTATTCC
18326845 TTTTTTTCTCATTTTTTT
1 TTTTTTTCT-ATTTTTTT
18326863 TTTTTTTCT-TTTTCTTT
1 TTTTTTTCTATTTT-TTT
18326880 ATTTTTTT
1 -TTTTTTT
18326888 TACAACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.17
17 3 0.13
18 16 0.70
ACGTcount: A:0.05, C:0.09, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTTTTCTATTTTTTT
Found at i:18326928 original size:145 final size:143
Alignment explanation
Indices: 18326746--18327005 Score: 339
Period size: 145 Copynumber: 1.8 Consensus size: 143
18326736 CTTTGAACCA
*
18326746 AACAAAATCCATATCTCAAGGATCTTCTAAATGAAACTATTTTTCCAAGTCTCCT-TTTTAACTT
1 AACAAAATCCATATCTCAAGGATCTTCAAAATGAAACTATTTTTCCAAGTCT-CTATTTTAACTT
***
18326810 AAATCACCCTTTC-TTGTTTTCAATTTAAGTATTCCTTTTTTTCTCATTTTTTTTTTTTTTCTTT
65 AAATCACCCTTTCAAAATTTT-AATTTAAGTATTCC-TTTTTTCTC-TTTTTTTTTTTTTTCTTT
18326874 TTCTTTATTTTTTTTAC
127 TTCTTTATTTTTTTTAC
* * * *
18326891 AACAAAATCCATATC-CTAGGGATCATT-AAAATGAAACTATTTTTCTAAGTCTCTATTTTTATT
1 AACAAAATCCATATCTC-AAGGATC-TTCAAAATGAAACTATTTTTCCAAGTCTCTATTTTAACT
** *
18326954 TAAATTGCCCTTTCAAAATTTTAATTTAAGTATTTCTTTTTTCTCTTTTTTT
64 TAAATCACCCTTTCAAAATTTTAATTTAAGTATTCCTTTTTTCTCTTTTTTT
18327006 ACCCTTTTTT
Statistics
Matches: 100, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
143 7 0.07
144 12 0.12
145 75 0.75
146 6 0.06
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.52
Consensus pattern (143 bp):
AACAAAATCCATATCTCAAGGATCTTCAAAATGAAACTATTTTTCCAAGTCTCTATTTTAACTTA
AATCACCCTTTCAAAATTTTAATTTAAGTATTCCTTTTTTCTCTTTTTTTTTTTTTTCTTTTTCT
TTATTTTTTTTAC
Found at i:18330284 original size:21 final size:21
Alignment explanation
Indices: 18330258--18330305 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
18330248 ATTAGTATAC
*
18330258 ACATAATATATACAAAGAATA
1 ACATAATATATACAAAGAACA
18330279 ACATAATATATACAAAGAACA
1 ACATAATATATACAAAGAACA
18330300 ACATAA
1 ACATAA
18330306 AGGGTTAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.62, C:0.12, G:0.04, T:0.21
Consensus pattern (21 bp):
ACATAATATATACAAAGAACA
Found at i:18331682 original size:20 final size:19
Alignment explanation
Indices: 18331637--18331690 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
18331627 TAAACAAAAT
18331637 TATCATGCAAATAATATAAA
1 TATCATGC-AATAATATAAA
*
18331657 TGTCATGCAATAATATAATA
1 TATCATGCAATAATATAA-A
*
18331677 TATCATGTAATAAT
1 TATCATGCAATAAT
18331691 CATGCAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 10 0.33
20 20 0.67
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.35
Consensus pattern (19 bp):
TATCATGCAATAATATAAA
Found at i:18331767 original size:18 final size:19
Alignment explanation
Indices: 18331729--18331770 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
18331719 AAATCATACA
18331729 ATAAAATATCAAGCAAAAT
1 ATAAAATATCAAGCAAAAT
18331748 ATAAAATATCATA-C-AAAT
1 ATAAAATATCA-AGCAAAAT
18331766 ATAAA
1 ATAAA
18331771 TCACACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.41
19 12 0.55
20 1 0.05
ACGTcount: A:0.64, C:0.10, G:0.02, T:0.24
Consensus pattern (19 bp):
ATAAAATATCAAGCAAAAT
Found at i:18331890 original size:24 final size:24
Alignment explanation
Indices: 18331850--18331911 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
18331840 ATAATCAAAT
*
18331850 TAAA-ATATAATCATATCATGCAA
1 TAAATATAAAATCATATCATGCAA
*
18331873 TAAATATAAAATCTTATCATGCAA
1 TAAATATAAAATCATATCATGCAA
18331897 -ATAATATAAAATCAT
1 TA-AATATAAAATCAT
18331912 GATAAATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 5 0.15
24 29 0.85
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.32
Consensus pattern (24 bp):
TAAATATAAAATCATATCATGCAA
Found at i:18332045 original size:36 final size:36
Alignment explanation
Indices: 18332005--18332073 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
18331995 AATAAACAAT
18332005 AAAATAAAATAAAACAGAAAAACCAAAA-AAAATTAG
1 AAAATAAAATAAAA-AGAAAAACCAAAATAAAATTAG
* *
18332041 AAAATAAAATAAAAATAAAAACTAAAATAAAAT
1 AAAATAAAATAAAAAGAAAAACCAAAATAAAAT
18332074 GAAAAGGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 11 0.37
36 19 0.63
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.14
Consensus pattern (36 bp):
AAAATAAAATAAAAAGAAAAACCAAAATAAAATTAG
Found at i:18332061 original size:12 final size:11
Alignment explanation
Indices: 18331981--18332078 Score: 53
Period size: 11 Copynumber: 8.9 Consensus size: 11
18331971 CAACTACAAT
*
18331981 TAAAATAAATA
1 TAAAATAAAAA
*
18331992 TATAATAAACAA
1 TAAAATAAA-AA
18332004 TAAAAT-AAAA
1 TAAAATAAAAA
* *
18332014 TAAAA-CAGAA
1 TAAAATAAAAA
**
18332024 -AAACCAAAAA
1 TAAAATAAAAA
*
18332034 -AAATTAGAAAA
1 TAAAATA-AAAA
18332045 TAAAATAAAAA
1 TAAAATAAAAA
18332056 TAAAA-ACTAAAA
1 TAAAATA--AAAA
18332068 TAAAATGAAAA
1 TAAAAT-AAAA
18332079 GGAAAAAGAA
Statistics
Matches: 68, Mismatches: 10, Indels: 17
0.72 0.11 0.18
Matches are distributed among these distances:
9 3 0.04
10 18 0.26
11 23 0.34
12 23 0.34
14 1 0.01
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.17
Consensus pattern (11 bp):
TAAAATAAAAA
Found at i:18332066 original size:7 final size:6
Alignment explanation
Indices: 18331982--18332072 Score: 50
Period size: 6 Copynumber: 15.5 Consensus size: 6
18331972 AACTACAATT
* * * **
18331982 AAAATA AATAT- ATAATA AACAAT- AAAAT- AAAATA AAACAGA AAAACC
1 AAAATA AAAATA AAAATA AA-AATA AAAATA AAAATA AAA-ATA AAAATA
*
18332029 AAAA-A AAATTA GAAAAT- AAAATA AAAATA AAAACT- AAAATA AAA
1 AAAATA AAAATA -AAAATA AAAATA AAAATA AAAA-TA AAAATA AAA
18332073 TGAAAAGGAA
Statistics
Matches: 66, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
5 20 0.30
6 33 0.50
7 13 0.20
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:18332078 original size:18 final size:17
Alignment explanation
Indices: 18332005--18332078 Score: 62
Period size: 18 Copynumber: 4.2 Consensus size: 17
18331995 AATAAACAAT
*
18332005 AAAATAAAATAAAACAGA
1 AAAATAAAATAAAA-TGA
* *
18332023 AAAACCAAAA-AAAATTA
1 AAAA-TAAAATAAAATGA
18332040 GAAAATAAAATAAAAAT-A
1 -AAAATAAAAT-AAAATGA
18332058 AAAACTAAAATAAAATGA
1 AAAA-TAAAATAAAATGA
18332076 AAA
1 AAA
18332079 GGAAAAAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
17 14 0.30
18 23 0.50
19 9 0.20
ACGTcount: A:0.77, C:0.05, G:0.04, T:0.14
Consensus pattern (17 bp):
AAAATAAAATAAAATGA
Found at i:18332084 original size:23 final size:23
Alignment explanation
Indices: 18332041--18332085 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
18332031 AAAAAATTAG
*
18332041 AAAATAAAATAAAAATAAAAACT
1 AAAATAAAATAAAAAGAAAAACT
*
18332064 AAAATAAAATGAAAAGGAAAAA
1 AAAATAAAAT-AAAAAGAAAAA
18332086 GAAAAGCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.13
Consensus pattern (23 bp):
AAAATAAAATAAAAAGAAAAACT
Found at i:18332266 original size:15 final size:16
Alignment explanation
Indices: 18332241--18332270 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18332231 TCTAGTTTTT
18332241 TTTTCTCTCTCTACAC
1 TTTTCTCTCTCTACAC
18332257 TTTT-TCTCTCTACA
1 TTTTCTCTCTCTACA
18332271 TTCTCTCTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.13, C:0.33, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTCTCTCTCTACAC
Found at i:18332825 original size:23 final size:24
Alignment explanation
Indices: 18332785--18332836 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
18332775 AAAGCCCATG
* * *
18332785 TTTTTATTTTTGGATTTTTTTAAT
1 TTTTTATTTTTAGATTTTCTTAAC
18332809 TTTTTATTTTTAG-TTTTCTTAAC
1 TTTTTATTTTTAGATTTTCTTAAC
18332832 TTTTT
1 TTTTT
18332837 GACTTTGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.75
Consensus pattern (24 bp):
TTTTTATTTTTAGATTTTCTTAAC
Found at i:18341700 original size:5 final size:4
Alignment explanation
Indices: 18341614--18341700 Score: 54
Period size: 4 Copynumber: 21.8 Consensus size: 4
18341604 TGTTTTTATA
** * * *
18341614 AAAT AAAT AAAT AAAT AAAT CCAT AAAT CAAT AAGT AGCA- AAAT -AAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT
* * *
18341661 AAAT -AAT ATAT AAAA AAATT AAAT AAAC AAAT AAACT AAA
1 AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAA-T AAA
18341701 AAGGAAGGAA
Statistics
Matches: 61, Mismatches: 16, Indels: 11
0.69 0.18 0.12
Matches are distributed among these distances:
3 7 0.11
4 47 0.77
5 7 0.11
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:18343723 original size:15 final size:16
Alignment explanation
Indices: 18343703--18343735 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18343693 GATAAAACAA
18343703 AACTCC-AAAAATTAC
1 AACTCCTAAAAATTAC
*
18343718 AACTCCTGAAAATTAC
1 AACTCCTAAAAATTAC
18343734 AA
1 AA
18343736 AGCTATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.52, C:0.24, G:0.03, T:0.21
Consensus pattern (16 bp):
AACTCCTAAAAATTAC
Found at i:18352395 original size:16 final size:16
Alignment explanation
Indices: 18352369--18352413 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
18352359 CCAAATCTAA
*
18352369 TAAAATAAAAAGGGTCC
1 TAAAATTAAAAGGG-CC
18352386 -AAAATTAAAAGGGCC
1 TAAAATTAAAAGGGCC
*
18352401 TAAAATTAGAAGG
1 TAAAATTAAAAGG
18352414 AGATCACAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.53, C:0.09, G:0.20, T:0.18
Consensus pattern (16 bp):
TAAAATTAAAAGGGCC
Found at i:18355491 original size:11 final size:11
Alignment explanation
Indices: 18355475--18355515 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
18355465 TAATTGAAAA
18355475 ATAAAAAATAT
1 ATAAAAAATAT
*
18355486 ATAAAAAATTT
1 ATAAAAAATAT
*
18355497 TTAAAAAATA-
1 ATAAAAAATAT
18355507 ATAAAAAAT
1 ATAAAAAAT
18355516 GAAGAAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
ATAAAAAATAT
Found at i:18362209 original size:25 final size:25
Alignment explanation
Indices: 18362177--18362225 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
18362167 GTAAATTAAA
*
18362177 AAAGAAAAAAGAA-AGAAGAAAAAC
1 AAAGAAAAAAGAACAAAAGAAAAAC
*
18362201 AAAGCAAAAATGAACAAAAGAAAAA
1 AAAG-AAAAAAGAACAAAAGAAAAA
18362226 AAATTAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 8 0.38
26 9 0.43
ACGTcount: A:0.78, C:0.06, G:0.14, T:0.02
Consensus pattern (25 bp):
AAAGAAAAAAGAACAAAAGAAAAAC
Found at i:18369179 original size:13 final size:13
Alignment explanation
Indices: 18369164--18369204 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
18369154 GCATTTTCTT
18369164 TTTTTATTTT-TA
1 TTTTTATTTTATA
18369176 TTTTCGTATTTTATA
1 TTTT--TATTTTATA
18369191 TTTTTATTTTATA
1 TTTTTATTTTATA
18369204 T
1 T
18369205 ATATATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 4 0.15
13 10 0.38
14 6 0.23
15 6 0.23
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTTATTTTATA
Found at i:18369192 original size:21 final size:19
Alignment explanation
Indices: 18369156--18369214 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
18369146 GGGTAAGCGC
*
18369156 ATTTTCTTTTTTTATTTTT
1 ATTTTCTTTTTATATTTTT
18369175 ATTTTCGTATTTTATATTTTT
1 ATTTTC-T-TTTTATATTTTT
* * *
18369196 ATTTTATATATATATTTTT
1 ATTTTCTTTTTATATTTTT
18369215 TCTCTCTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 16 0.47
20 2 0.06
21 16 0.47
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (19 bp):
ATTTTCTTTTTATATTTTT
Found at i:18369233 original size:4 final size:4
Alignment explanation
Indices: 18369226--18369298 Score: 53
Period size: 4 Copynumber: 18.8 Consensus size: 4
18369216 CTCTCTTTCT
* * *
18369226 TTTA TTTA TTTA TTTA TTTA TTTA TCT- TTTA TATA TTT- GTTA -TTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * *
18369271 TTTA TACTA TTAA TTTA TCTA TTAA TTT
1 TTTA T-TTA TTTA TTTA TTTA TTTA TTT
18369299 TTTGGTTTAT
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
3 7 0.13
4 42 0.81
5 3 0.06
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:18369262 original size:19 final size:20
Alignment explanation
Indices: 18369226--18369293 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 20
18369216 CTCTCTTTCT
* *
18369226 TTTATTTATTTATTTATTTA
1 TTTATCTATTTATATATTTA
18369246 TTTATCT-TTTATATATTT-
1 TTTATCTATTTATATATTTA
* *
18369264 GTTAT-TATTTATACTATTAA
1 TTTATCTATTTATA-TATTTA
18369284 TTTATCTATT
1 TTTATCTATT
18369294 AATTTTTTGG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 1 0.03
18 10 0.26
19 14 0.36
20 10 0.26
21 4 0.10
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.68
Consensus pattern (20 bp):
TTTATCTATTTATATATTTA
Found at i:18370195 original size:9 final size:9
Alignment explanation
Indices: 18370181--18370205 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
18370171 TTCCCAGGTT
18370181 TTTTATTAG
1 TTTTATTAG
18370190 TTTTATTAG
1 TTTTATTAG
18370199 TTTTATT
1 TTTTATT
18370206 TTATTTATTT
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:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (9 bp):
TTTTATTAG
Found at i:18370381 original size:60 final size:60
Alignment explanation
Indices: 18370308--18370647 Score: 384
Period size: 59 Copynumber: 5.6 Consensus size: 60
18370298 AAATAAAATA
* *
18370308 TTTTT-AGGAAAAAGTTGAAAGTATCAATTTTCCTTAAGAATGAATTTTCAAAAAAAGGTT
1 TTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGGTT
* * * *
18370368 TTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTTAAGAATAAATTTTCAAAAAAATG-T
1 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGGTT
* * ** * * *
18370427 TTTTAGAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCCAAAAAAA--TA
1 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTTCAAAAAAAGGTT
* * *
18370486 TTTTTG-GGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAGTTTCAAAAAAAAAAGTT
1 TTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC--AAAAAAAGGTT
*
18370548 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAAAAGTTTT
1 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC---AAAAAAAG-GTT
* *
18370612 TTTTTAAGGAAAAGTTAAAAGTATCAATTTTTCCTT
1 TTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCCTT
18370648 GTACAAAAGT
Statistics
Matches: 243, Mismatches: 25, Indels: 19
0.85 0.09 0.07
Matches are distributed among these distances:
58 5 0.02
59 76 0.31
60 69 0.28
61 2 0.01
62 45 0.19
63 11 0.05
64 27 0.11
65 8 0.03
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (60 bp):
TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGGTT
Found at i:18370399 original size:29 final size:29
Alignment explanation
Indices: 18370366--18370458 Score: 68
Period size: 29 Copynumber: 3.2 Consensus size: 29
18370356 CAAAAAAAGG
18370366 TTTTTTTGAAGAAAAGTTGAAAGTATCAA
1 TTTTTTTGAAGAAAAGTTGAAAGTATCAA
* * *
18370395 TTTTTCTT-AAGAATAAATTTTCAAA--A-AAA
1 TTTTT-TTGAAG-A-AAA-GTTGAAAGTATCAA
* *
18370424 TGTTTTTAGAGGAAAAGTTGAAAGTATCAA
1 T-TTTTTTGAAGAAAAGTTGAAAGTATCAA
18370454 TTTTT
1 TTTTT
18370459 CTCGAAATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 18
0.64 0.11 0.25
Matches are distributed among these distances:
27 5 0.11
28 3 0.06
29 18 0.38
30 13 0.28
31 3 0.06
32 5 0.11
ACGTcount: A:0.41, C:0.04, G:0.14, T:0.41
Consensus pattern (29 bp):
TTTTTTTGAAGAAAAGTTGAAAGTATCAA
Found at i:18374645 original size:42 final size:43
Alignment explanation
Indices: 18374574--18374665 Score: 116
Period size: 42 Copynumber: 2.1 Consensus size: 43
18374564 ACAACGGATG
* * *
18374574 AAAAATGAGAAAAAAAAAAGATGATGAAAGAA-AAAAAATAGA
1 AAAAATGAGAAAAAAAAAAGAAGAAGAAAGAAGAAAAAATAAA
*
18374616 AAAAAT-AGAAAAAAAAAAGAAAGAAGAAAGAATGAGAAAATAAA
1 AAAAATGAGAAAAAAAAAAG-AAGAAGAAAGAA-GAAAAAATAAA
18374660 AAAAAT
1 AAAAAT
18374666 TTAAATTGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 13 0.30
42 16 0.37
44 14 0.33
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (43 bp):
AAAAATGAGAAAAAAAAAAGAAGAAGAAAGAAGAAAAAATAAA
Found at i:18374656 original size:35 final size:34
Alignment explanation
Indices: 18374599--18374664 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
18374589 AAAAGATGAT
18374599 GAAAGAAAAAAAATAGAAAAAATAGAAAAAAAAAA
1 GAAAGAAAAAAAATAGAAAAAATA-AAAAAAAAAA
* *
18374634 GAAAGAAGAAAGAAT-GAGAAAATAAAAAAAA
1 GAAAGAA-AAAAAATAGAAAAAATAAAAAAAA
18374665 TTTAAATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 7 0.25
35 15 0.54
36 6 0.21
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (34 bp):
GAAAGAAAAAAAATAGAAAAAATAAAAAAAAAAA
Found at i:18375893 original size:22 final size:22
Alignment explanation
Indices: 18375868--18375926 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
18375858 GAATATTTTG
*
18375868 ATGAGAATTTTTGAGAACTC-AA
1 ATGAGAATCTTTGAG-ACTCAAA
**
18375890 ATGAGAATCTTTGAGTTTCAAA
1 ATGAGAATCTTTGAGACTCAAA
18375912 ATGAGAATCTTTGAG
1 ATGAGAATCTTTGAG
18375927 GAGTGAAACC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 2 0.06
22 31 0.94
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.34
Consensus pattern (22 bp):
ATGAGAATCTTTGAGACTCAAA
Found at i:18376497 original size:42 final size:41
Alignment explanation
Indices: 18376447--18376653 Score: 174
Period size: 42 Copynumber: 5.0 Consensus size: 41
18376437 TAAGGAGTAG
18376447 TTTA-TTTTCCAAAGTTCCGTT-GCCTCTGTTTAGAGGAGCAA
1 TTTACTTTTCCAAAG-T-CGTTAGCCTCTGTTTAGAGGAGCAA
* *
18376488 TTTACTTTT-CAAAGTCGTGGTTGCCTTTGTTTAGAGGAGCAA
1 TTTACTTTTCCAAAGTCGT--TAGCCTCTGTTTAGAGGAGCAA
* * **
18376530 TTTAC-TTTCCAAAGTCGTTGAGCCTCTGATTACAGGAGCTTTG
1 TTTACTTTTCCAAAGTCGTT-AGCCTCTGTTTAGAGGAGC--AA
* * * * *
18376573 TTTA-TTTTTCAAAGTTGTTGAGCTTCTGATTAGAGGAGCCA
1 TTTACTTTTCCAAAGTCGTT-AGCCTCTGTTTAGAGGAGCAA
*
18376614 TTTACTTTTTCAAAGTCGTTGAGCCTCT-TATTAGAGGAGC
1 TTTACTTTTCCAAAGTCGTT-AGCCTCTGT-TTAGAGGAGC
18376654 TTTGTTCATC
Statistics
Matches: 139, Mismatches: 16, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
39 3 0.02
40 2 0.01
41 32 0.23
42 68 0.49
43 34 0.24
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (41 bp):
TTTACTTTTCCAAAGTCGTTAGCCTCTGTTTAGAGGAGCAA
Found at i:18376632 original size:85 final size:84
Alignment explanation
Indices: 18376488--18376788 Score: 338
Period size: 84 Copynumber: 3.5 Consensus size: 84
18376478 AGAGGAGCAA
* * * * * * *
18376488 TTTACTTTTCAAAGTCGTGGTTGCCTTTGTTTAGAGGAGCAATTTAC-TTTCCAAAGTCGTTGAG
1 TTTATTTTTCAAAGTCGTTG-AGCCTCTGATTAGAAGAGC-ATTTACTTTTTCAAAGTCGTTGAG
* *
18376552 CCTCTGATTACAGGAGCTTTG
64 CCTCTAATTAGAGGAGCTTTG
* * *
18376573 TTTATTTTTCAAAGTTGTTGAGCTTCTGATTAGAGGAGCCATTTACTTTTTCAAAGTCGTTGAGC
1 TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAAGAG-CATTTACTTTTTCAAAGTCGTTGAGC
*
18376638 CTCTTATTAGAGGAGCTTTG
65 CTCTAATTAGAGGAGCTTTG
* * * * *
18376658 TTCA-TCTTCAAAGTCGTTGAGCGTCTGATTAGAAGAGC-TTTATTTATCTTCAAAGTCGTTGAA
1 TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAAGAGCATTTACTT-T-TTCAAAGTCGTTGAG
18376721 CCTCTAATTAGAGGAGCATTTG
64 CCTCTAATTAGAGGAGC-TTTG
18376743 TTTATTCTTCTTCAAAGTCGTTGAGCCTCTGATTAGAAGAGCATTT
1 TTTA-T-TT-TTCAAAGTCGTTGAGCCTCTGATTAGAAGAGCATTT
18376789 GTTTATGATT
Statistics
Matches: 185, Mismatches: 21, Indels: 15
0.84 0.10 0.07
Matches are distributed among these distances:
82 6 0.03
83 2 0.01
84 79 0.43
85 63 0.34
88 1 0.01
89 31 0.17
90 3 0.02
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (84 bp):
TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAAGAGCATTTACTTTTTCAAAGTCGTTGAGCC
TCTAATTAGAGGAGCTTTG
Found at i:18376731 original size:126 final size:127
Alignment explanation
Indices: 18376476--18376818 Score: 322
Period size: 126 Copynumber: 2.6 Consensus size: 127
18376466 TTGCCTCTGT
* * * * **
18376476 TTAGAGGAGCAATTTAC-TTTTCAAAGTCGTGGTTGCCT-TTGTTTAGAGGAGCAAT-TTACTTT
1 TTAGAGGAGCCATTTACTTTTTCAAAGTCGTTG-AGCCTCTT-ATTAGAGGAGCTTTGTTACTTT
* * * * * * *
18376538 CCAAAGTCGTTGAGCCTCTGATTACAGGAGCTTTGTTTATTTTTCAAAGTTGTTGAGCTTCTGA
64 CCAAAGTCGTTGAGCCTCTGATTACAAGAGCTTTATTTATTCTTCAAAGTCGTTGAACCTCTAA
18376602 TTAGAGGAGCCATTTACTTTTTCAAAGTCGTTGAGCCTCTTATTAGAGGAGCTTTGTT-CATCTT
1 TTAGAGGAGCCATTTACTTTTTCAAAGTCGTTGAGCCTCTTATTAGAGGAGCTTTGTTAC-T-TT
* *
18376666 -CAAAGTCGTTGAGCGTCTGATTAGAAGAGCTTTATTTA-TCTTCAAAGTCGTTGAACCTCTAA
64 CCAAAGTCGTTGAGCCTCTGATTACAAGAGCTTTATTTATTCTTCAAAGTCGTTGAACCTCTAA
* * *
18376728 TTAGAGGAG-CATTTGTTTATTCTTCTTCAAAGTCGTTGAGCCTCTGATTAGAAGAGCATTTGTT
1 TTAGAGGAGCCA----TTTA--CTTTTTCAAAGTCGTTGAGCCTCTTATTAGAGGAGC-TTTG-T
* **
18376792 TATGATTTTTAAAGTCGTTGAGCCTCT
58 TA--CTTTCCAAAGTCGTTGAGCCTCT
18376819 CCTTATAAGA
Statistics
Matches: 179, Mismatches: 21, Indels: 25
0.80 0.09 0.11
Matches are distributed among these distances:
125 2 0.01
126 60 0.34
127 53 0.30
128 2 0.01
129 4 0.02
131 33 0.18
132 4 0.02
133 2 0.01
134 2 0.01
135 17 0.09
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (127 bp):
TTAGAGGAGCCATTTACTTTTTCAAAGTCGTTGAGCCTCTTATTAGAGGAGCTTTGTTACTTTCC
AAAGTCGTTGAGCCTCTGATTACAAGAGCTTTATTTATTCTTCAAAGTCGTTGAACCTCTAA
Found at i:18376765 original size:47 final size:45
Alignment explanation
Indices: 18376539--18376818 Score: 296
Period size: 42 Copynumber: 6.4 Consensus size: 45
18376529 ATTTACTTTC
*
18376539 CAAAGTCGTTGAGCCTCTGATTACAGGAGCTTTGTTTAT-TT-TT
1 CAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTGTTTATCTTCTT
* * ** *
18376582 CAAAGTTGTTGAGCTTCTGATTAGAGGAGC--CATTTA-CTTTTT
1 CAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTGTTTATCTTCTT
* *
18376624 CAAAGTCGTTGAGCCTCTTATTAGAGGAGCTTTG--T-TCATCTT
1 CAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTGTTTATCTTCTT
* * *
18376666 CAAAGTCGTTGAGCGTCTGATTAGAAGAGCTTTATTTA---TCTT
1 CAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTGTTTATCTTCTT
* *
18376708 CAAAGTCGTTGAACCTCTAATTAGAGGAGCATTTGTTTATTCTTCTT
1 CAAAGTCGTTGAGCCTCTGATTAGAGGAGC-TTTGTTTA-TCTTCTT
* *
18376755 CAAAGTCGTTGAGCCTCTGATTAGAAGAGCATTTGTTTATGATT-TT
1 CAAAGTCGTTGAGCCTCTGATTAGAGGAGC-TTTGTTTAT-CTTCTT
*
18376801 TAAAGTCGTTGAGCCTCT
1 CAAAGTCGTTGAGCCTCT
18376819 CCTTATAAGA
Statistics
Matches: 197, Mismatches: 26, Indels: 25
0.79 0.10 0.10
Matches are distributed among these distances:
41 6 0.03
42 94 0.48
43 34 0.17
44 1 0.01
46 20 0.10
47 42 0.21
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (45 bp):
CAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTGTTTATCTTCTT
Found at i:18377052 original size:21 final size:20
Alignment explanation
Indices: 18377026--18377067 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 20
18377016 AACCCATTTT
18377026 TTTTTTATTTTTATTTTCATA
1 TTTTTTATTTTTATTTT-ATA
18377047 TTTTTTATTTTTATTTTATA
1 TTTTTTATTTTTATTTTATA
18377067 T
1 T
18377068 ATATATTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTATTTTTATTTTATA
Found at i:18377073 original size:26 final size:26
Alignment explanation
Indices: 18377022--18377076 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
18377012 AGTAAACCCA
*
18377022 TTTTTTTTTTATTTTTATTTTCATAT
1 TTTTTTTTTTATTTTTATTATCATAT
18377048 TTTTTATTTTTA-TTTTATATAT-ATAT
1 TTTTT-TTTTTATTTTTAT-TATCATAT
18377074 TTT
1 TTT
18377077 CTCTCTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTTTTTTTATTTTTATTATCATAT
Found at i:18377090 original size:4 final size:4
Alignment explanation
Indices: 18377083--18377133 Score: 54
Period size: 4 Copynumber: 13.5 Consensus size: 4
18377073 TTTTCTCTCT
* *
18377083 TTTA TTTA TTTA TTTA TTTA TCT- TTTA TATA TTTA -TTA -TTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
*
18377128 TCTA TT
1 TTTA TT
18377134 ATTATTGTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 8 0.21
4 31 0.79
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:18377133 original size:14 final size:14
Alignment explanation
Indices: 18377083--18377139 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
18377073 TTTTCTCTCT
18377083 TTTATTTA-T-TTA
1 TTTATTTATTATTA
*
18377095 TTTATTTATCTTTTA
1 TTTATTTAT-TATTA
*
18377110 TATATTTATTATTA
1 TTTATTTATTATTA
*
18377124 TTTATCTATTATTA
1 TTTATTTATTATTA
18377138 TT
1 TT
18377140 GTTAATTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.21
14 19 0.50
15 11 0.29
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTATTTATTATTA
Found at i:18377149 original size:25 final size:24
Alignment explanation
Indices: 18377084--18377149 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 24
18377074 TTTCTCTCTT
* *
18377084 TTATTTATTT-ATTTATTTATCTT
1 TTATATATTTAATTTATTTATCTA
*
18377107 TTATATATTTATTATTATTTATCTA
1 TTATATATTTAAT-TTATTTATCTA
18377132 TTAT-TATTGTTAATTTAT
1 TTATATA-T-TTAATTTAT
18377150 CTGTTAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 9 0.26
24 3 0.09
25 19 0.54
26 4 0.11
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (24 bp):
TTATATATTTAATTTATTTATCTA
Found at i:18377212 original size:8 final size:8
Alignment explanation
Indices: 18377201--18377230 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
18377191 TATATTAATA
18377201 TTTTTTAT
1 TTTTTTAT
18377209 TTTTTTAT
1 TTTTTTAT
18377217 TTTTTTAAT
1 TTTTTT-AT
18377226 TTTTT
1 TTTTT
18377231 CGATTGAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 14 0.67
9 7 0.33
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTAT
Found at i:18378070 original size:9 final size:9
Alignment explanation
Indices: 18378043--18378127 Score: 50
Period size: 9 Copynumber: 8.9 Consensus size: 9
18378033 CCCAGGTTTT
18378043 TTTTA-TTA
1 TTTTATTTA
18378051 GTTTTATTTTA
1 -TTTTA-TTTA
18378062 TTTTATTTA
1 TTTTATTTA
18378071 TTATTATATTA
1 TT-TTAT-TTA
** *
18378082 GGATTGTTTAA
1 -TTTTATTT-A
18378093 TTTT-TTTA
1 TTTTATTTA
18378101 -TTTATTTTCA
1 TTTTA-TTT-A
18378111 TTTTATTTA
1 TTTTATTTA
18378120 TTTTATTT
1 TTTTATTT
18378128 TCTTTAAATA
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
7 3 0.05
8 1 0.02
9 26 0.43
10 17 0.28
11 14 0.23
ACGTcount: A:0.22, C:0.01, G:0.05, T:0.72
Consensus pattern (9 bp):
TTTTATTTA
Found at i:18378209 original size:62 final size:62
Alignment explanation
Indices: 18378138--18378256 Score: 186
Period size: 62 Copynumber: 1.9 Consensus size: 62
18378128 TCTTTAAATA
18378138 AAATTAAAAA-AAAATAAAAAAATAGATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTCG
1 AAATTAAAAATAAAA-AAAAAAATAGATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTCG
*** *
18378200 AAATTAAAAATTTCAAAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTT
1 AAATTAAAAATAAAAAAAAAAATAGATTTTTAGGGAAAAGTTGAAAGTATCAATTTT
18378257 CTTTAAAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
62 51 0.98
63 1 0.02
ACGTcount: A:0.51, C:0.04, G:0.12, T:0.33
Consensus pattern (62 bp):
AAATTAAAAATAAAAAAAAAAATAGATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTCG
Found at i:18378277 original size:61 final size:61
Alignment explanation
Indices: 18378153--18378319 Score: 196
Period size: 62 Copynumber: 2.7 Consensus size: 61
18378143 AAAAAAAAAT
*
18378153 AAAAAAATAGATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAAATTTC-A
1 AAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAA-TTTTCTCGAAA-TAAAAATTTCAA
**
18378215 AAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCTTTAAA-AATAAATTTTCAA
1 AAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCTCGAAATAA-AAA-TTTCAA
* * * *
18378277 AAAAAAAAAGTTTTTTTTGAGTAAAAGTTGAAAGTA-CAATTTT
1 AAAAAAATA-TATTTTTAG-GGAAAAGTTGAAAGTATCAATTTT
18378320 TCCTTGTACA
Statistics
Matches: 93, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
59 2 0.02
60 3 0.03
61 13 0.14
62 46 0.49
63 14 0.15
64 15 0.16
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.36
Consensus pattern (61 bp):
AAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCTCGAAATAAAAATTTCAA
Found at i:18382250 original size:26 final size:27
Alignment explanation
Indices: 18382195--18382250 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
18382185 ATAAGCTTTG
* **
18382195 GTTTGAAAAAAATAAATTTAAACATTA
1 GTTTGAAAAAAATAAATATAAACAAAA
18382222 GTTTG-AAAAAATAAAGTATAAA-AAAA
1 GTTTGAAAAAAATAAA-TATAAACAAAA
18382248 GTT
1 GTT
18382251 AAAATAACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.57, C:0.02, G:0.11, T:0.30
Consensus pattern (27 bp):
GTTTGAAAAAAATAAATATAAACAAAA
Found at i:18391079 original size:17 final size:19
Alignment explanation
Indices: 18391045--18391085 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
18391035 GTGTAGAACA
*
18391045 ACAAATCTATTATCTAACT
1 ACAACTCTATTATCTAACT
18391064 -CAACTCTATT-TCTAACT
1 ACAACTCTATTATCTAACT
18391081 ACAAC
1 ACAAC
18391086 ATTTTCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.34
Consensus pattern (19 bp):
ACAACTCTATTATCTAACT
Found at i:18392989 original size:14 final size:15
Alignment explanation
Indices: 18392970--18392998 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
18392960 ATTTTCTGTA
18392970 CATAAAAA-AATTTT
1 CATAAAAATAATTTT
18392984 CATAAAAATAATTTT
1 CATAAAAATAATTTT
18392999 TTTATAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
CATAAAAATAATTTT
Found at i:18393187 original size:28 final size:28
Alignment explanation
Indices: 18393154--18393215 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
18393144 AATATAAAAA
* *
18393154 TTAATATATCTAGTTTTATTATTCACTT
1 TTAATACATCTAGTTTTATCATTCACTT
*
18393182 TTAATACATCTAGTTTTATCATTTACTT
1 TTAATACATCTAGTTTTATCATTCACTT
*
18393210 TAAATA
1 TTAATA
18393216 AGCAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.53
Consensus pattern (28 bp):
TTAATACATCTAGTTTTATCATTCACTT
Found at i:18395990 original size:25 final size:25
Alignment explanation
Indices: 18395962--18396018 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
18395952 GCATTGATTA
** *
18395962 CAAAAACTTAAAATTTCTCAACA-AG
1 CAAAAACACAAAATCTC-CAACAGAG
18395987 CAAATAACACAAAATCTCCAACAGAG
1 CAAA-AACACAAAATCTCCAACAGAG
18396013 CAAAAA
1 CAAAAA
18396019 AGAATTAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 11 0.41
26 16 0.59
ACGTcount: A:0.56, C:0.23, G:0.05, T:0.16
Consensus pattern (25 bp):
CAAAAACACAAAATCTCCAACAGAG
Found at i:18396386 original size:45 final size:45
Alignment explanation
Indices: 18396329--18396420 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
18396319 ACCAAAATAA
18396329 AACTCTAGAAGAAATAAAAATAAGGTGTAAAAATAATGCAAAAAT
1 AACTCTAGAAGAAATAAAAATAAGGTGTAAAAATAATGCAAAAAT
18396374 AACTCTAGAAGAAATAAAAATAAGGTGTAAAAATAATGCAAAAAT
1 AACTCTAGAAGAAATAAAAATAAGGTGTAAAAATAATGCAAAAAT
18396419 AA
1 AA
18396421 AATAGATGTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.61, C:0.07, G:0.13, T:0.20
Consensus pattern (45 bp):
AACTCTAGAAGAAATAAAAATAAGGTGTAAAAATAATGCAAAAAT
Found at i:18397124 original size:21 final size:22
Alignment explanation
Indices: 18397099--18397139 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
18397089 AATTAGAGAC
18397099 AATTATAAAAAAAAT-TAATAA
1 AATTATAAAAAAAATATAATAA
* *
18397120 AATTATTATAAAAATATAAT
1 AATTATAAAAAAAATATAAT
18397140 TTAAGGATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
AATTATAAAAAAAATATAATAA
Found at i:18398044 original size:28 final size:29
Alignment explanation
Indices: 18397989--18398062 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
18397979 CATGTTTTTA
*
18397989 AAATAAATTTTTATGTTTTTATTATATTC
1 AAATAAATTTTTATTTTTTTATTATATTC
*
18398018 AAATAAATCTTTATTTTTTTATT-TATTC
1 AAATAAATTTTTATTTTTTTATTATATTC
*
18398046 CAATAAATTTTTATTTT
1 AAATAAATTTTTATTTT
18398063 AAATAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 20 0.49
29 21 0.51
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.59
Consensus pattern (29 bp):
AAATAAATTTTTATTTTTTTATTATATTC
Found at i:18398139 original size:31 final size:31
Alignment explanation
Indices: 18398099--18398185 Score: 74
Period size: 31 Copynumber: 2.8 Consensus size: 31
18398089 TTATACAATA
*
18398099 CAAATTAAAAAAGTTAAGACTTATTTGGATAT
1 CAAACTAAAAAAGTTAAGACTTATTTGGAT-T
* *
18398131 -AAACT--AAAAGTTAAAACTTTATTTGTATT
1 CAAACTAAAAAAGTTAAGAC-TTATTTGGATT
* *
18398160 CAAATTAAAATA-TTAAGAACTTATTT
1 CAAACTAAAAAAGTTAAG-ACTTATTT
18398186 TAGTATAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
29 12 0.27
30 13 0.30
31 14 0.32
32 5 0.11
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.38
Consensus pattern (31 bp):
CAAACTAAAAAAGTTAAGACTTATTTGGATT
Found at i:18406770 original size:3 final size:3
Alignment explanation
Indices: 18406748--18406811 Score: 73
Period size: 3 Copynumber: 22.3 Consensus size: 3
18406738 TTGTATTTTA
* *
18406748 TAT T-T TAT T-T TAT T-T TAT TAT TAT TATT TAT CAA TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
18406790 TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
18406812 TATCTAATTA
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
2 8 0.15
3 42 0.79
4 3 0.06
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:18406802 original size:36 final size:34
Alignment explanation
Indices: 18406747--18406815 Score: 111
Period size: 36 Copynumber: 2.0 Consensus size: 34
18406737 TTTGTATTTT
*
18406747 ATATTTTATTTTATTTTATTATTATTATTTATCA
1 ATATATTATTTTATTTTATTATTATTATTTATCA
18406781 ATATATTATTATTATTATTATTATTATTATTTATC
1 ATATATTATT-TTATT-TTATTATTATTATTTATC
18406816 TAATTAATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 9 0.28
35 5 0.16
36 18 0.56
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (34 bp):
ATATATTATTTTATTTTATTATTATTATTTATCA
Found at i:18406867 original size:26 final size:26
Alignment explanation
Indices: 18406804--18406888 Score: 113
Period size: 26 Copynumber: 3.3 Consensus size: 26
18406794 ATTATTATTA
* *
18406804 TTATTATTTATCTAATT-A-ATGTATG
1 TTATTATTTATCT-ATTAATATATATT
18406829 TT-TTATTTATCTATTAATATATATT
1 TTATTATTTATCTATTAATATATATT
18406854 TTATTATTTATCTATTAATATATATT
1 TTATTATTTATCTATTAATATATATT
*
18406880 TTTTTATTT
1 TTATTATTT
18406889 TATTTTTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
23 3 0.06
24 11 0.20
25 9 0.17
26 31 0.57
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.64
Consensus pattern (26 bp):
TTATTATTTATCTATTAATATATATT
Found at i:18407164 original size:11 final size:11
Alignment explanation
Indices: 18407150--18407175 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
18407140 TGAAGTTTTT
18407150 TTTTTGAAAAA
1 TTTTTGAAAAA
18407161 TTTTTGAAAAA
1 TTTTTGAAAAA
18407172 TTTT
1 TTTT
18407176 CAGAATTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (11 bp):
TTTTTGAAAAA
Found at i:18407611 original size:3 final size:3
Alignment explanation
Indices: 18407603--18407646 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
18407593 TTCCAAAGGT
*
18407603 TTA TTA TTA TTA TTA TTA TTA TT- TCTT TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TT
18407647 TATTGATTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
2 1 0.03
3 36 0.95
4 1 0.03
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:18407791 original size:58 final size:57
Alignment explanation
Indices: 18407710--18408050 Score: 447
Period size: 58 Copynumber: 5.9 Consensus size: 57
18407700 TTATTTTATG
**
18407710 ATTTTT-TT-AAAATAAAATTCTAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCA
1 ATTTTTCTTGAAAATAATTTTCTAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCA
* * * * *
18407765 ATTTTCCTTGAAAATAAGTTTCCTAAAAAATATTTTCGAGGAAAAGTTGAAAGTATTA
1 ATTTTTCTTGAAAATAA-TTTTCTAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCA
* *
18407823 ATTTTTCTTGAAAATAAGTTTTCTAAAAAATATTTTTGAGGAAAAGTTAAAAGTATCA
1 ATTTTTCTTGAAAATAA-TTTTCTAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCA
* * *
18407881 ATTTTTCTTAAAAATAATTTTCTAAAAAAATATTTTTGAGGAAAAGTTAAAAGTATCA
1 ATTTTTCTTGAAAATAATTTTCT-AAAAAATATTTTTGAAGAAAAGTTGAAAGTATCA
* *
18407939 ATTTTTCTTGAAAATAAAATTTTTTAAAAAATATTTTTTAAAGAAAAGTTGAAAGTATCA
1 ATTTTTCTTGAAAAT--AATTTTCTAAAAAATA-TTTTTGAAGAAAAGTTGAAAGTATCA
*
18407999 ATTTTTCTTAAAAATAATTTT-TAAAAAAATATTTTTG-AGAAAAAGTTGAAAG
1 ATTTTTCTTGAAAATAATTTTCT-AAAAAATATTTTTGAAG-AAAAGTTGAAAG
18408051 CATCTCGAAA
Statistics
Matches: 257, Mismatches: 20, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
55 5 0.02
56 4 0.02
57 31 0.12
58 165 0.64
59 8 0.03
60 44 0.17
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (57 bp):
ATTTTTCTTGAAAATAATTTTCTAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCA
Found at i:18407849 original size:116 final size:116
Alignment explanation
Indices: 18407710--18408050 Score: 496
Period size: 116 Copynumber: 3.0 Consensus size: 116
18407700 TTATTTTATG
*
18407710 ATTTTT-TT-AAAATAAAA--TTCTAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTC
1 ATTTTTCTTGAAAATAAAATTTTCTAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTT
* * *
18407771 CTTGAAAATAAGTTTCCT-AAAAAATATTTTCGAGGAAAAGTTGAAAGTATTA
66 CTTAAAAATAA-TTT-CTAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCA
* * *
18407823 ATTTTTCTTGAAAAT-AAGTTTTCTAAAAAATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTT
1 ATTTTTCTTGAAAATAAAATTTTCTAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTT
*
18407887 CTTAAAAATAATTTTCTAAAAAAATATTTTTGAGGAAAAGTTAAAAGTATCA
66 CTTAAAAATAA-TTTCTAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCA
* *
18407939 ATTTTTCTTGAAAATAAAATTTTTTAAAAAATATTTTTTAAAGAAAAGTTGAAAGTATCAATTTT
1 ATTTTTCTTGAAAATAAAATTTTCTAAAAAATA-TTTTTGAAGAAAAGTTGAAAGTATCAATTTT
* *
18408004 TCTTAAAAATAATTTTTAAAAAAATATTTTTGAGAAAAAGTTGAAAG
65 TCTTAAAAATAATTTCTAAAAAAATATTTTTGAGGAAAAGTTGAAAG
18408051 CATCTCGAAA
Statistics
Matches: 204, Mismatches: 17, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
113 6 0.03
114 4 0.02
115 7 0.03
116 100 0.49
117 47 0.23
118 40 0.20
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (116 bp):
ATTTTTCTTGAAAATAAAATTTTCTAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTT
CTTAAAAATAATTTCTAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCA
Found at i:18418654 original size:1 final size:1
Alignment explanation
Indices: 18418648--18418751 Score: 64
Period size: 1 Copynumber: 104.0 Consensus size: 1
18418638 ACTATACTTT
* * * * * * ** *
18418648 AAAAAAATAAAAAAATAAAAAAATAAAAAATAAAAAAATAAAAAATAAAAAAATGAAAAATAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** ** ** *
18418713 AAATGAAAAAATGAAAAAATGAAAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
18418752 GATGAAGACT
Statistics
Matches: 75, Mismatches: 28, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 75 1.00
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.11
Consensus pattern (1 bp):
A
Found at i:18418660 original size:8 final size:8
Alignment explanation
Indices: 18418647--18418740 Score: 131
Period size: 8 Copynumber: 12.0 Consensus size: 8
18418637 TACTATACTT
18418647 TAAAAAAA
1 TAAAAAAA
18418655 TAAAAAAA
1 TAAAAAAA
18418663 TAAAAAAA
1 TAAAAAAA
18418671 T-AAAAAA
1 TAAAAAAA
18418678 TAAAAAAA
1 TAAAAAAA
18418686 T-AAAAAA
1 TAAAAAAA
18418693 TAAAAAAA
1 TAAAAAAA
*
18418701 T-GAAAAA
1 TAAAAAAA
18418708 TAAAAAAA
1 TAAAAAAA
*
18418716 TGAAAAAA
1 TAAAAAAA
*
18418724 TGAAAAAA
1 TAAAAAAA
18418732 TGAAAAAAA
1 T-AAAAAAA
18418741 AAGAAAAAAA
Statistics
Matches: 78, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
7 20 0.26
8 52 0.67
9 6 0.08
ACGTcount: A:0.83, C:0.00, G:0.04, T:0.13
Consensus pattern (8 bp):
TAAAAAAA
Found at i:18418669 original size:15 final size:15
Alignment explanation
Indices: 18418647--18418751 Score: 142
Period size: 15 Copynumber: 6.9 Consensus size: 15
18418637 TACTATACTT
18418647 TAAAAAAATAAAAAAA
1 TAAAAAAAT-AAAAAA
18418663 TAAAAAAATAAAAAA
1 TAAAAAAATAAAAAA
18418678 TAAAAAAATAAAAAA
1 TAAAAAAATAAAAAA
*
18418693 TAAAAAAATGAAAAA
1 TAAAAAAATAAAAAA
18418708 TAAAAAAATGAAAAAA
1 TAAAAAAAT-AAAAAA
*
18418724 TGAAAAAATGAAAAAA
1 TAAAAAAAT-AAAAAA
18418740 -AAAGAAAA-AAAA
1 TAAA-AAAATAAAA
18418752 GATGAAGACT
Statistics
Matches: 83, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
14 4 0.05
15 46 0.55
16 33 0.40
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (15 bp):
TAAAAAAATAAAAAA
Found at i:18418678 original size:23 final size:23
Alignment explanation
Indices: 18418649--18418740 Score: 125
Period size: 23 Copynumber: 4.0 Consensus size: 23
18418639 CTATACTTTA
18418649 AAAAAATAAAAAAATAAAAAAAT
1 AAAAAATAAAAAAATAAAAAAAT
18418672 AAAAAATAAAAAAAT-AAAAAAT
1 AAAAAATAAAAAAATAAAAAAAT
*
18418694 AAAAAA-ATGAAAAATAAAAAAAT
1 AAAAAATA-AAAAAATAAAAAAAT
*
18418717 GAAAAAATGAAAAAATGAAAAAAA
1 -AAAAAATAAAAAAAT-AAAAAAA
18418741 AAGAAAAAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
21 1 0.02
22 19 0.31
23 22 0.36
24 12 0.20
25 7 0.11
ACGTcount: A:0.84, C:0.00, G:0.04, T:0.12
Consensus pattern (23 bp):
AAAAAATAAAAAAATAAAAAAAT
Found at i:18419887 original size:41 final size:42
Alignment explanation
Indices: 18419770--18419950 Score: 212
Period size: 41 Copynumber: 4.4 Consensus size: 42
18419760 CAATGAGTAT
*
18419770 TTTATTTTTCAAAGTTCTGTTGCCTC-TATTTAGAGGAGTCA
1 TTTATTTTTCAAAGTTCTGTTACCTCTTATTTAGAGGAGTCA
* * *
18419811 TTTATTTTCTTAAAAGTTCTGTTGCCT-TTATTTAGAGGAGCCA
1 TTTA-TTT-TTCAAAGTTCTGTTACCTCTTATTTAGAGGAGTCA
* *
18419854 TTTATTTTTCAAAGTTCTGTTACCTCTGA-TTAGAGGAGTTA
1 TTTATTTTTCAAAGTTCTGTTACCTCTTATTTAGAGGAGTCA
* *
18419895 TTTATTTTTCAAAG-TC-GTTAAGCCTTTTA-TTAGAGGAGTTA
1 TTTATTTTTCAAAGTTCTGTT-A-CCTCTTATTTAGAGGAGTCA
18419936 TTTATTTTTCAAAGT
1 TTTATTTTTCAAAGT
18419951 CATTGAGCCT
Statistics
Matches: 124, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
39 3 0.02
40 3 0.02
41 75 0.60
42 8 0.06
43 35 0.28
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (42 bp):
TTTATTTTTCAAAGTTCTGTTACCTCTTATTTAGAGGAGTCA
Found at i:18419962 original size:82 final size:84
Alignment explanation
Indices: 18419770--18419973 Score: 212
Period size: 82 Copynumber: 2.5 Consensus size: 84
18419760 CAATGAGTAT
*
18419770 TTTATTTTTCAAAGT-TCTGTTGCCTCT-ATTTAGAGGAGTCATTTATTTTCTTAAAAGTTCTGT
1 TTTATTTTTCAAAGTCTCTG-AGCCTCTGA-TTAGAGGAGTCATTTATTTTCTTAAAAGTTCTGT
18419833 TGCCTTTATTTAGAGGAGCCA
64 TGCCTTTATTTAGAGGAGCCA
* *
18419854 TTTATTTTTCAAAGT-TCTGTTA-CCTCTGATTAGAGGAGTTATTTA-TTT-TTCAAAG-TC-GT
1 TTTATTTTTCAAAGTCTCTG--AGCCTCTGATTAGAGGAGTCATTTATTTTCTTAAAAGTTCTGT
**
18419913 TAAGCCTTT-TATTAGAGGAGTTA
64 T--GCCTTTAT-TTAGAGGAGCCA
*
18419936 TTTATTTTTCAAAGTCAT-TGAGCCTCTGCTTAGAGGAG
1 TTTATTTTTCAAAGTC-TCTGAGCCTCTGATTAGAGGAG
18419974 CTTAATCAAA
Statistics
Matches: 106, Mismatches: 6, Indels: 18
0.82 0.05 0.14
Matches are distributed among these distances:
80 3 0.03
81 4 0.04
82 52 0.49
83 5 0.05
84 40 0.38
85 2 0.02
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (84 bp):
TTTATTTTTCAAAGTCTCTGAGCCTCTGATTAGAGGAGTCATTTATTTTCTTAAAAGTTCTGTTG
CCTTTATTTAGAGGAGCCA
Found at i:18419969 original size:41 final size:40
Alignment explanation
Indices: 18419842--18419973 Score: 158
Period size: 41 Copynumber: 3.2 Consensus size: 40
18419832 TTGCCTTTAT
** *
18419842 TTAGAGGAGCCATTTATTTTTCAAAGTTCTGTTA-CCTCTGA
1 TTAGAGGAGTTATTTATTTTTCAAAG-TCT-TAAGCCTCTGA
* *
18419883 TTAGAGGAGTTATTTATTTTTCAAAGTCGTTAAGCCTTTTA
1 TTAGAGGAGTTATTTATTTTTCAAAGTC-TTAAGCCTCTGA
* *
18419924 TTAGAGGAGTTATTTATTTTTCAAAGTCATTGAGCCTCTGC
1 TTAGAGGAGTTATTTATTTTTCAAAGTC-TTAAGCCTCTGA
18419965 TTAGAGGAG
1 TTAGAGGAG
18419974 CTTAATCAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
40 4 0.05
41 75 0.95
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.42
Consensus pattern (40 bp):
TTAGAGGAGTTATTTATTTTTCAAAGTCTTAAGCCTCTGA
Found at i:18420162 original size:6 final size:6
Alignment explanation
Indices: 18420151--18420193 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
18420141 GTAAGCCCAT
* *
18420151 TTTGTA TTTGTA TTTTTA TTTGTG TTT-TA TTT-TA TTTGTA TTT
1 TTTGTA TTTGTA TTTGTA TTTGTA TTTGTA TTTGTA TTTGTA TTT
18420194 TTATCATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 9 0.28
6 23 0.72
ACGTcount: A:0.14, C:0.00, G:0.12, T:0.74
Consensus pattern (6 bp):
TTTGTA
Found at i:18420185 original size:16 final size:16
Alignment explanation
Indices: 18420151--18420194 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 16
18420141 GTAAGCCCAT
18420151 TTTGTATTTGTATTTTTA
1 TTTGTATTT-TA-TTTTA
*
18420169 TTTGTGTTTTATTTTA
1 TTTGTATTTTATTTTA
18420185 TTTGTATTTT
1 TTTGTATTTT
18420195 TATCATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.58
17 2 0.08
18 8 0.33
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.75
Consensus pattern (16 bp):
TTTGTATTTTATTTTA
Found at i:18420252 original size:21 final size:22
Alignment explanation
Indices: 18420228--18420281 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
18420218 ATTTTTATTA
18420228 TTATTTATCTATTAAT-GTTTT
1 TTATTTATCTATTAATAGTTTT
*
18420249 TTATTTATCTATTAATATTTTT
1 TTATTTATCTATTAATAGTTTT
18420271 TTATTTTATCT
1 TTA-TTTATCT
18420282 TTTTCTTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 16 0.53
22 7 0.23
23 7 0.23
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.69
Consensus pattern (22 bp):
TTATTTATCTATTAATAGTTTT
Found at i:18420583 original size:22 final size:23
Alignment explanation
Indices: 18420540--18420586 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
18420530 GAAATTTTTT
* *
18420540 AAAATTTTTGAAGTTTTTTTTAG
1 AAAATTTCTGAAGATTTTTTTAG
18420563 AAAATTTCTGAA-ATTTTTTTAG
1 AAAATTTCTGAAGATTTTTTTAG
18420585 AA
1 AA
18420587 TCTGACGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (23 bp):
AAAATTTCTGAAGATTTTTTTAG
Found at i:18421157 original size:59 final size:58
Alignment explanation
Indices: 18421017--18421240 Score: 305
Period size: 58 Copynumber: 3.9 Consensus size: 58
18421007 TATTTTATGA
* * *
18421017 TTTTCTTAAAATAAAA-TTCTAAAAAAAT-TTTTTGAGGAAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAATAAAATTTTTTAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAAT
* * * *
18421073 TTTCCTTAAAA-ATAAGTTTTCTAAAAAATATTTTCGAAGAAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAATA-AAATTTTTTAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAAT
18421131 TTTTCTTGAAAATAAAATTTTTTAAAAAATATTTTT-AAGAAAAAGTTGAAAGTATCAAT
1 TTTTCTT-AAAATAAAATTTTTTAAAAAATATTTTTGAAG-AAAAGTTGAAAGTATCAAT
*
18421190 TTTTCTTAAAA-ATAATTTTTTAAAAAAATATTTTTGAAGAAAAGTTGAAAG
1 TTTTCTTAAAATAAAATTTTTT-AAAAAATATTTTTGAAGAAAAGTTGAAAG
18421241 CATCTCGAAA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
55 1 0.01
56 12 0.08
57 18 0.12
58 64 0.43
59 52 0.35
60 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (58 bp):
TTTTCTTAAAATAAAATTTTTTAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAAT
Found at i:18421190 original size:117 final size:114
Alignment explanation
Indices: 18421017--18421240 Score: 342
Period size: 117 Copynumber: 1.9 Consensus size: 114
18421007 TATTTTATGA
* *
18421017 TTTTCTTAAAATAAAATTCTAAAAAAATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
1 TTTTCTTAAAATAAAATTCTAAAAAAATTTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTTAA
18421082 AAATAAGTTTTCT-AAAAAATATTTTCGAAGAAAAGTTGAAAGTATCAAT
66 AAATAA-TTTTCTAAAAAAATATTTTCGAAGAAAAGTTGAAAGTATCAAT
* * *
18421131 TTTTCTTGAAAATAAAATTTTTTAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCT
1 TTTTCTT-AAAATAAAA-TTCTAAAAAAAT-TTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCT
* *
18421196 TAAAAATAATTTTTTAAAAAAATATTTTTGAAGAAAAGTTGAAAG
63 TAAAAATAATTTTCTAAAAAAATATTTTCGAAGAAAAGTTGAAAG
18421241 CATCTCGAAA
Statistics
Matches: 99, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
114 7 0.07
115 9 0.09
116 15 0.15
117 68 0.69
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (114 bp):
TTTTCTTAAAATAAAATTCTAAAAAAATTTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTTAA
AAATAATTTTCTAAAAAAATATTTTCGAAGAAAAGTTGAAAGTATCAAT
Found at i:18421352 original size:45 final size:47
Alignment explanation
Indices: 18421263--18421359 Score: 137
Period size: 46 Copynumber: 2.1 Consensus size: 47
18421253 AAAGTTTCAG
*
18421263 AAAAACATTTTGAGAAAAAGTTGAAAATATCAAATTTTCTTTAAAA-
1 AAAAACATTTTAAGAAAAAGTTGAAAATATCAAATTTTCTTTAAAAT
* *
18421309 AAAAACATTTTAAGGAAAAGTT-AAAAGTATCAATTTTTC-TTAAAAT
1 AAAAACATTTTAAGAAAAAGTTGAAAA-TATCAAATTTTCTTTAAAAT
18421355 AAAAA
1 AAAAA
18421360 TTCCCTAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
45 10 0.22
46 36 0.78
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.32
Consensus pattern (47 bp):
AAAAACATTTTAAGAAAAAGTTGAAAATATCAAATTTTCTTTAAAAT
Found at i:18422498 original size:28 final size:28
Alignment explanation
Indices: 18422465--18422520 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
18422455 TGTGTATCAA
* *
18422465 ATTTTTGTATTCTTTTTAATATGT-AAGT
1 ATTTTTGTA-TATTATTAATATGTCAAGT
*
18422493 ATTTTTTTATATTATTAATATGTCAAGT
1 ATTTTTGTATATTATTAATATGTCAAGT
18422521 TTATTAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.29, C:0.04, G:0.09, T:0.59
Consensus pattern (28 bp):
ATTTTTGTATATTATTAATATGTCAAGT
Found at i:18424958 original size:20 final size:19
Alignment explanation
Indices: 18424933--18424984 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
18424923 TGGTATTTTT
**
18424933 AAATATTTATATTTTTTAAA
1 AAATATTT-TATTTTAAAAA
18424953 AAATATTTTATATTTAAAAA
1 AAATATTTTAT-TTTAAAAA
18424973 AAATATTTTATT
1 AAATATTTTATT
18424985 AATTTTGGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AAATATTTTATTTTAAAAA
Found at i:18425823 original size:3 final size:3
Alignment explanation
Indices: 18425815--18425854 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
18425805 GCACGAAGAA
18425815 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
18425855 ATTATTAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:18428622 original size:2 final size:2
Alignment explanation
Indices: 18428615--18428651 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
18428605 GCTTTTGCTT
18428615 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18428652 TGCTTGGGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18430553 original size:21 final size:20
Alignment explanation
Indices: 18430527--18430588 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 20
18430517 TTTTCATCTC
18430527 AATTCATATTATCTCTCTAAA
1 AATTCATATT-TCTCTCTAAA
*
18430548 AATTCATATTCTCTCTTTAAA
1 AATTCATATT-TCTCTCTAAA
*
18430569 AATTCAT-TTTCTTTCTAAA
1 AATTCATATTTCTCTCTAAA
18430588 A
1 A
18430589 TCAAACCAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.24
20 2 0.05
21 26 0.70
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTCATATTTCTCTCTAAA
Found at i:18434267 original size:19 final size:21
Alignment explanation
Indices: 18434228--18434270 Score: 72
Period size: 19 Copynumber: 2.1 Consensus size: 21
18434218 AATAAAATTT
18434228 AATTATTATATTTTATTAAAA
1 AATTATTATATTTTATTAAAA
18434249 AATTATT-TATTTT-TTAAAA
1 AATTATTATATTTTATTAAAA
18434268 AAT
1 AAT
18434271 AAAAATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 9 0.41
20 6 0.27
21 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AATTATTATATTTTATTAAAA
Found at i:18435346 original size:26 final size:26
Alignment explanation
Indices: 18435290--18435346 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
18435280 TAACCTTTAT
*
18435290 ATTTT-CTATCAAATTGGTACTTAAA
1 ATTTTACTATCAAATTGGTACCTAAA
* *
18435315 ACTTTACTATCACATTGGTACCTAAA
1 ATTTTACTATCAAATTGGTACCTAAA
*
18435341 TTTTTA
1 ATTTTA
18435347 AATCCGTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (26 bp):
ATTTTACTATCAAATTGGTACCTAAA
Found at i:18435543 original size:8 final size:9
Alignment explanation
Indices: 18435483--18435898 Score: 80
Period size: 9 Copynumber: 42.7 Consensus size: 9
18435473 AATATTTTCA
18435483 AAAAATTTT
1 AAAAATTTT
*
18435492 AAAAATTCT
1 AAAAATTTT
*
18435501 AAAATTTTT
1 AAAAATTTT
* *
18435510 CCAAAATTATA
1 -AAAAATT-TT
**
18435521 AAAAATTCAA
1 AAAAATT-TT
18435531 AAAAATTTT
1 AAAAATTTT
**
18435540 AAAAAGTTCAA
1 AAAAA-TT-TT
* *
18435551 AAAAATCTA
1 AAAAATTTT
18435560 AAAAATTTCT
1 AAAAATTT-T
*
18435570 AAAAATTCT
1 AAAAATTTT
*
18435579 AAAATTTCTT
1 AAAAATT-TT
*
18435589 TAAAATTTT
1 AAAAATTTT
*
18435598 AAAAATTCT
1 AAAAATTTT
*
18435607 AAAATAATTT
1 AAAA-ATTTT
*
18435617 AAATAAATTT
1 AAA-AATTTT
**
18435627 AGAAAATTCAA
1 A-AAAATT-TT
*
18435638 AAAAAATTT
1 AAAAATTTT
**
18435647 AAAAATTCAAA
1 AAAAATT--TT
18435658 ACAAAATTTT
1 A-AAAATTTT
**
18435668 AAAAATTCCAA
1 AAAAATT--TT
18435679 AAAAATTTT
1 AAAAATTTT
18435688 ACAAAATTTT
1 A-AAAATTTT
* *
18435698 -CAAATTAT
1 AAAAATTTT
* *
18435706 AAAAAATTC
1 AAAAATTTT
* *
18435715 AAAATAATCT
1 AAAA-ATTTT
18435725 AAAAACTTTTT
1 AAAAA--TTTT
*
18435736 AAAAATTCT
1 AAAAATTTT
*
18435745 AACAATTTTT
1 AA-AAATTTT
* *
18435755 AAAAAAATTC
1 -AAAAATTTT
18435765 AAAAATGATTT
1 AAAAAT--TTT
18435776 CAAAAAATTTT
1 --AAAAATTTT
***
18435787 AGAAAATGCAAAA
1 A-AAAAT---TTT
*
18435800 AAAAATTCTG
1 AAAAATT-TT
18435810 AAAAATTTT
1 AAAAATTTT
*
18435819 AAAAATTCT
1 AAAAATTTT
* *
18435828 AATACTTTT
1 AAAAATTTT
* *
18435837 GAAAGTTTT
1 AAAAATTTT
*
18435846 CAAAAATTCTA
1 -AAAAATT-TT
**
18435857 AAAAAAATT
1 AAAAATTTT
**
18435866 AAAAAAATT
1 AAAAATTTT
18435875 -AAAATTTT
1 AAAAATTTT
*
18435883 CAAAAAATTT
1 -AAAAATTTT
18435893 AAAAAT
1 AAAAAT
18435899 AAAAATCTTT
Statistics
Matches: 289, Mismatches: 83, Indels: 70
0.65 0.19 0.16
Matches are distributed among these distances:
8 12 0.04
9 117 0.40
10 109 0.38
11 33 0.11
12 11 0.04
13 7 0.02
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (9 bp):
AAAAATTTT
Found at i:18435543 original size:11 final size:10
Alignment explanation
Indices: 18435520--18435566 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
18435510 CCAAAATTAT
18435520 AAAAAATTCA
1 AAAAAATTCA
**
18435530 AAAAAATTTT
1 AAAAAATTCA
*
18435540 AAAAAGTTCA
1 AAAAAATTCA
*
18435550 AAAAAA-TCT
1 AAAAAATTCA
18435559 AAAAAATT
1 AAAAAATT
18435567 TCTAAAAATT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
9 8 0.28
10 21 0.72
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (10 bp):
AAAAAATTCA
Found at i:18435573 original size:20 final size:20
Alignment explanation
Indices: 18435482--18435626 Score: 77
Period size: 20 Copynumber: 7.5 Consensus size: 20
18435472 GAATATTTTC
*
18435482 AAAAAATTT-TAAAAATTCT
1 AAAAAATTTCTAAAAAATCT
** * * *
18435501 AAAATTTTTC-CAAAATTAT
1 AAAAAATTTCTAAAAAATCT
* *
18435520 AAAAAA-TTCAAAAAAATTT
1 AAAAAATTTCTAAAAAATCT
* * *
18435539 TAAAAAGTTCAAAAAAATCT
1 AAAAAATTTCTAAAAAATCT
*
18435559 AAAAAATTTCTAAAAATTCT
1 AAAAAATTTCTAAAAAATCT
** *
18435579 --AAAATTTCTTTAAAATTT
1 AAAAAATTTCTAAAAAATCT
* *
18435597 TAAAAA-TTCTAAAATAATTT
1 AAAAAATTTCTAAAA-AATCT
18435617 AAATAAATTT
1 AAA-AAATTT
18435627 AGAAAATTCA
Statistics
Matches: 96, Mismatches: 22, Indels: 13
0.73 0.17 0.10
Matches are distributed among these distances:
18 17 0.18
19 35 0.36
20 39 0.41
21 3 0.03
22 2 0.02
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.37
Consensus pattern (20 bp):
AAAAAATTTCTAAAAAATCT
Found at i:18435646 original size:20 final size:19
Alignment explanation
Indices: 18435621--18435686 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 19
18435611 TAATTTAAAT
18435621 AAATTTAGAAAATTCAAAAA
1 AAATTTA-AAAATTCAAAAA
18435641 AAATTTAAAAATTCAAAACA
1 AAATTTAAAAATTCAAAA-A
*
18435661 AAATTTTAAAAATTCCAAAA
1 AAA-TTTAAAAATTCAAAAA
18435681 AAATTT
1 AAATTT
18435687 TACAAAATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
19 14 0.33
20 15 0.35
21 14 0.33
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.29
Consensus pattern (19 bp):
AAATTTAAAAATTCAAAAA
Found at i:18435668 original size:21 final size:21
Alignment explanation
Indices: 18435624--18435695 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
18435614 TTTAAATAAA
*
18435624 TTTAGAAAATTCAAAAAAAA-
1 TTTACAAAATTCAAAAAAAAT
18435644 TTTA-AAAATTCAAAACAAAAT
1 TTTACAAAATTCAAAA-AAAAT
*
18435665 TTTA-AAAATTCCAAAAAAAT
1 TTTACAAAATTCAAAAAAAAT
18435685 TTTACAAAATT
1 TTTACAAAATT
18435696 TTCAAATTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
19 11 0.23
20 17 0.35
21 20 0.42
ACGTcount: A:0.60, C:0.08, G:0.01, T:0.31
Consensus pattern (21 bp):
TTTACAAAATTCAAAAAAAAT
Found at i:18435745 original size:20 final size:19
Alignment explanation
Indices: 18435722--18435759 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
18435712 TTCAAAATAA
18435722 TCTAAAAACTTTTTAAAAAT
1 TCTAAAAA-TTTTTAAAAAT
*
18435742 TCTAACAATTTTTAAAAA
1 TCTAAAAATTTTTAAAAA
18435760 AATTCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (19 bp):
TCTAAAAATTTTTAAAAAT
Found at i:18435787 original size:32 final size:33
Alignment explanation
Indices: 18435736--18435823 Score: 90
Period size: 32 Copynumber: 2.7 Consensus size: 33
18435726 AAAACTTTTT
* * *
18435736 AAAAATTCTAACAATTTTTAAAAAAATTCAAAA
1 AAAAATTCTAAAAAATTTTAAAAAAATGCAAAA
** * *
18435769 ATGATTTC-AAAAAATTTT-AGAAAATGCAAAA
1 AAAAATTCTAAAAAATTTTAAAAAAATGCAAAA
*
18435800 AAAAATTCTGAAAAATTTTAAAAA
1 AAAAATTCTAAAAAATTTTAAAAA
18435824 TTCTAATACT
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
31 16 0.39
32 17 0.41
33 8 0.20
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.30
Consensus pattern (33 bp):
AAAAATTCTAAAAAATTTTAAAAAAATGCAAAA
Found at i:18435909 original size:27 final size:24
Alignment explanation
Indices: 18435858--18435928 Score: 61
Period size: 27 Copynumber: 2.8 Consensus size: 24
18435848 AAAATTCTAA
* *
18435858 AAAAAATTAAAAAAATTAAAATTTT
1 AAAAAATT-TAAAAATAAAAATTTT
18435883 CAAAAAATTTAAAAATAAAAATCTTTT
1 -AAAAAATTTAAAAATAAAAA--TTTT
**
18435910 AAAATTTTTTAAAAATAAA
1 AAAA-AATTTAAAAATAAA
18435929 TCTAAAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
25 10 0.26
26 12 0.32
27 16 0.42
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (24 bp):
AAAAAATTTAAAAATAAAAATTTT
Found at i:18435913 original size:26 final size:25
Alignment explanation
Indices: 18435858--18435928 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
18435848 AAAATTCTAA
* *
18435858 AAAAAATTAAAAAAATTAAAATTTTC
1 AAAAAATT-TAAAAATAAAAATTTTC
*
18435884 AAAAAATTTAAAAATAAAAATCTTTT
1 AAAAAATTTAAAAATAAAAAT-TTTC
**
18435910 AAAATTTTTTAAAAATAAA
1 AAAA-AATTTAAAAATAAA
18435929 TCTAAAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
25 11 0.29
26 15 0.39
27 12 0.32
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (25 bp):
AAAAAATTTAAAAATAAAAATTTTC
Found at i:18436035 original size:14 final size:15
Alignment explanation
Indices: 18436010--18436042 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
18436000 CAAATTTTAA
18436010 AAAAAATCAAAAAAT
1 AAAAAATCAAAAAAT
*
18436025 AAAAAAT-AAAAACT
1 AAAAAATCAAAAAAT
18436039 AAAA
1 AAAA
18436043 TGATGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAAAATCAAAAAAT
Found at i:18436089 original size:10 final size:10
Alignment explanation
Indices: 18436074--18436107 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
18436064 AAATTCCAAT
18436074 AAAATTAAAA
1 AAAATTAAAA
18436084 AAAATTAATAA
1 AAAATTAA-AA
*
18436095 AAACTTAAAA
1 AAAATTAAAA
18436105 AAA
1 AAA
18436108 TAAAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAATTAAAA
Found at i:18436127 original size:20 final size:21
Alignment explanation
Indices: 18436104--18436149 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
18436094 AAAACTTAAA
*
18436104 AAAATAAAATA-AATTTTTTT
1 AAAATAAAATATAATTATTTT
*
18436124 AAAA-AATATATAATTATTTT
1 AAAATAAAATATAATTATTTT
18436144 ATAAAT
1 A-AAAT
18436150 TTTTTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
19 5 0.24
20 13 0.62
21 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAATAAAATATAATTATTTT
Found at i:18436182 original size:30 final size:30
Alignment explanation
Indices: 18436118--18436186 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
18436108 TAAAATAAAT
18436118 TTTTTTAAAAAATATATAATTATTTTATAAA
1 TTTTTTAAAAAATATATAATTATTTTAT-AA
* *
18436149 TTTTTTAAAAAAT-TCTAAATTGTTTTCAT-A
1 TTTTTTAAAAAATATAT-AATTATTTT-ATAA
18436179 TTTTTTAA
1 TTTTTTAA
18436187 TCTTACAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 11 0.32
31 21 0.62
32 2 0.06
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (30 bp):
TTTTTTAAAAAATATATAATTATTTTATAA
Found at i:18436584 original size:12 final size:11
Alignment explanation
Indices: 18436556--18436580 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18436546 TAGATTTTTT
18436556 AAATTTTTGAA
1 AAATTTTTGAA
18436567 AAATTTTTGAA
1 AAATTTTTGAA
18436578 AAA
1 AAA
18436581 ATTTAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATTTTTGAA
Found at i:18436605 original size:9 final size:9
Alignment explanation
Indices: 18436484--18436606 Score: 50
Period size: 9 Copynumber: 12.8 Consensus size: 9
18436474 TTTTTATAAA
18436484 TTTAAAATT
1 TTTAAAATT
*
18436493 TTTAGTAATTT
1 TTTA--AAATT
*
18436504 TTTGAAAGTT
1 TTT-AAAATT
**
18436514 TTTAGCATT
1 TTTAAAATT
18436523 ATTTAAAAATGT
1 -TTT-AAAAT-T
*
18436535 TTT-GAATT
1 TTTAAAATT
* *
18436543 TTTTAGATT
1 TTTAAAATT
*
18436552 TTTTAAATT
1 TTTAAAATT
18436561 TTTGAAAAATT
1 TTT--AAAATT
**
18436572 TTTGAAAAAA
1 TTT-AAAATT
*
18436582 TTTAATATT
1 TTTAAAATT
*
18436591 TATAAAATT
1 TTTAAAATT
18436600 TTTAAAA
1 TTTAAAA
18436607 AAATTTAAGA
Statistics
Matches: 84, Mismatches: 21, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
8 4 0.05
9 40 0.48
10 17 0.20
11 21 0.25
12 2 0.02
ACGTcount: A:0.39, C:0.01, G:0.07, T:0.53
Consensus pattern (9 bp):
TTTAAAATT
Found at i:18436620 original size:29 final size:28
Alignment explanation
Indices: 18436565--18436626 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
18436555 TAAATTTTTG
* *
18436565 AAAAATTTTTGAAAAAATTTAATATTTA
1 AAAAATTTTTAAAAAAATTTAAAATTTA
*
18436593 TAAAATTTTTAAAAAAATTTAAGAATTTA
1 AAAAATTTTTAAAAAAATTTAA-AATTTA
18436622 AAAAA
1 AAAAA
18436627 AATTATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (28 bp):
AAAAATTTTTAAAAAAATTTAAAATTTA
Found at i:18436659 original size:19 final size:19
Alignment explanation
Indices: 18436625--18436672 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
18436615 GAATTTAAAA
18436625 AAAATTATTT-TTTAAA-TT
1 AAAATT-TTTATTTAAATTT
18436643 AAAATTTTTATTGTAAATTT
1 AAAATTTTTATT-TAAATTT
*
18436663 TAAATTTTTA
1 AAAATTTTTA
18436673 AAATTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 8 0.31
19 4 0.15
20 11 0.42
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
AAAATTTTTATTTAAATTT
Found at i:18436750 original size:20 final size:19
Alignment explanation
Indices: 18436727--18436791 Score: 85
Period size: 20 Copynumber: 3.3 Consensus size: 19
18436717 AATTGTGTTG
18436727 AATTTTTTAAAGTTTTTGAA
1 AATTTTTTAAAGTTTTT-AA
* *
18436747 AATTTTTTTACGTTTTTAA
1 AATTTTTTAAAGTTTTTAA
*
18436766 AATTTTTTATAAATTTTTAA
1 AATTTTTTA-AAGTTTTTAA
18436786 AATTTT
1 AATTTT
18436792 AAAAAATTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 10 0.26
20 29 0.74
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.60
Consensus pattern (19 bp):
AATTTTTTAAAGTTTTTAA
Found at i:18436784 original size:10 final size:9
Alignment explanation
Indices: 18436730--18436795 Score: 53
Period size: 10 Copynumber: 7.0 Consensus size: 9
18436720 TGTGTTGAAT
*
18436730 TTTTTAAAG
1 TTTTTAAAA
18436739 TTTTTGAAAA
1 TTTTT-AAAA
* **
18436749 TTTTTTTACG
1 -TTTTTAAAA
18436759 TTTTTAAAA
1 TTTTTAAAA
18436768 TTTTTTATAAA
1 -TTTTTA-AAA
18436779 TTTTTAAAA
1 TTTTTAAAA
18436788 -TTTTAAAA
1 TTTTTAAAA
18436796 AATTAAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
8 8 0.17
9 14 0.30
10 16 0.35
11 8 0.17
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.58
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:18436839 original size:18 final size:18
Alignment explanation
Indices: 18436816--18436866 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
18436806 ATAGAATTTC
*
18436816 ATTTTTAAAATTTTCAAT
1 ATTTTTAAAATTTTCAAA
*
18436834 ATTTTTAAAACTTTTGAAA
1 ATTTTTAAAA-TTTTCAAA
*
18436853 ATTTTAAAAATTTT
1 ATTTTTAAAATTTT
18436867 TTAAGAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (18 bp):
ATTTTTAAAATTTTCAAA
Found at i:18436848 original size:10 final size:9
Alignment explanation
Indices: 18436816--18436878 Score: 63
Period size: 9 Copynumber: 6.7 Consensus size: 9
18436806 ATAGAATTTC
18436816 ATTTTTAAA
1 ATTTTTAAA
* *
18436825 ATTTTCAAT
1 ATTTTTAAA
18436834 ATTTTTAAA
1 ATTTTTAAA
*
18436843 ACTTTTGAAA
1 A-TTTTTAAA
*
18436853 ATTTTAAAA
1 ATTTTTAAA
18436862 ATTTTTTAAGA
1 A-TTTTTAA-A
18436873 ATTTTT
1 ATTTTT
18436879 TAGGCTGACG
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
9 23 0.52
10 19 0.43
11 2 0.05
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:18437255 original size:27 final size:27
Alignment explanation
Indices: 18437202--18437257 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
18437192 TGTCTAAACA
* *
18437202 TATTAAATTAATGAAATTTAATTATTT
1 TATTAAATTAATAAAAATTAATTATTT
*
18437229 TATTAAATTAA-AAAAATTATTTAATTT
1 TATTAAATTAATAAAAATTAATT-ATTT
18437256 TA
1 TA
18437258 AAAATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
TATTAAATTAATAAAAATTAATTATTT
Found at i:18437650 original size:21 final size:21
Alignment explanation
Indices: 18437590--18437640 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
18437580 GTAATGACAG
*
18437590 TAAAATTAATTATTATAATAA
1 TAAAATTAAGTATTATAATAA
*
18437611 TAAGATTAAGTATTATAATAA
1 TAAAATTAAGTATTATAATAA
18437632 TAAAATTAA
1 TAAAATTAA
18437641 AATTAATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (21 bp):
TAAAATTAAGTATTATAATAA
Found at i:18437764 original size:24 final size:25
Alignment explanation
Indices: 18437737--18437796 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 25
18437727 TTAGATTAAA
18437737 AATTATATA-TAATAAAAAAATTTT
1 AATTATATATTAATAAAAAAATTTT
*
18437761 AATTATTTAATATTTATAAAAAAATTTT
1 AATTA--T-ATATTAATAAAAAAATTTT
18437789 -ATTATATA
1 AATTATATA
18437797 AAATTTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
24 8 0.26
25 1 0.03
26 1 0.03
27 7 0.23
28 14 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AATTATATATTAATAAAAAAATTTT
Found at i:18437779 original size:31 final size:30
Alignment explanation
Indices: 18437744--18437842 Score: 100
Period size: 28 Copynumber: 3.3 Consensus size: 30
18437734 AAAAATTATA
*
18437744 TATAATAAAAAAATTTTAATTATTTAATA-T
1 TATAATAAAAAAATTTT-ATTATATAATATT
*
18437774 T-T-ATAAAAAAATTTTATTATATAAAATT
1 TATAATAAAAAAATTTTATTATATAATATT
*
18437802 TATTAATAAATAAATATTTATTA-AT-ATATT
1 TA-TAATAAAAAAAT-TTTATTATATAATATT
18437832 ATATAATAAAA
1 -TATAATAAAA
18437843 TTTATTTATT
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
27 9 0.16
28 15 0.26
29 1 0.02
30 13 0.22
31 13 0.22
32 7 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TATAATAAAAAAATTTTATTATATAATATT
Done.