Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 204 of 230
Found at i:60970933 original size:18 final size:18
Alignment explanation
Indices: 60970912--60970960 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
60970902 CTATTATAAC
60970912 TATTTATATATATCATCT
1 TATTTATATATATCATCT
*
60970930 TATTATATATTTAT-ATCT
1 TATT-TATATATATCATCT
60970948 TA-TTATATATATC
1 TATTTATATATATC
60970961 TATATATCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.30
17 1 0.04
18 10 0.37
19 8 0.30
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTATATATATCATCT
Found at i:60977271 original size:23 final size:22
Alignment explanation
Indices: 60977228--60977272 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
60977218 CAATTTAATC
* *
60977228 TATATTTTTCATTTTAATATTA
1 TATATTTTTAATATTAATATTA
*
60977250 TATATATTTTAATATTATTATTA
1 TATAT-TTTTAATATTAATATTA
60977273 ATTAATTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TATATTTTTAATATTAATATTA
Found at i:60981257 original size:14 final size:14
Alignment explanation
Indices: 60981238--60981266 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
60981228 AATATAGAAA
60981238 AGCAAGTAAATTGT
1 AGCAAGTAAATTGT
60981252 AGCAAGTAAATTGT
1 AGCAAGTAAATTGT
60981266 A
1 A
60981267 CCTAAGTCAA
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:0.45, C:0.07, G:0.21, T:0.28
Consensus pattern (14 bp):
AGCAAGTAAATTGT
Found at i:60985784 original size:6 final size:6
Alignment explanation
Indices: 60985727--60985764 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
60985717 GGTTATTGGA
60985727 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TT
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TT
60985765 TTGGTGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.16, C:0.00, G:0.47, T:0.37
Consensus pattern (6 bp):
TTAGGG
Found at i:60986108 original size:90 final size:89
Alignment explanation
Indices: 60985889--60986109 Score: 243
Period size: 94 Copynumber: 2.4 Consensus size: 89
60985879 GTTTATTATT
* * *
60985889 TTTTAAGAAAAAATCAATTAAATTAGGGTTTATGGTTTCTTGAGTAATTCAATTAAAAAATTTTA
1 TTTTAAG-AAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTCAATTAAAAAATTTTA
60985954 AAAATCAGATTAGGGTTTAAAGTTAAGAG
65 AAAATCAGATTAGGGTTT-AAG---AGAG
* * * *
60985983 TTTTATGGAAAAATCAAATAAATTAGGGTTCAGGGTTACTTGAGTAAATT-AATTATAAATTTTT
1 TTTTA-AGAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGT-AATTCAATTAAAAAATTTT
*
60986047 AAAAAAATTAGATTAGGGTTT-AG-G-G
64 --AAAAATCAGATTAGGGTTTAAGAGAG
60986072 TTTTAAGTAAAAACTCAAATAAATTAGGGTTTAGGGTT
1 TTTTAAG-AAAAA-TCAAATAAATTAGGGTTTAGGGTT
60986110 TAGGGTTACT
Statistics
Matches: 111, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
88 1 0.01
89 11 0.10
90 24 0.22
94 52 0.47
95 5 0.05
96 18 0.16
ACGTcount: A:0.41, C:0.04, G:0.18, T:0.37
Consensus pattern (89 bp):
TTTTAAGAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTCAATTAAAAAATTTTAA
AAATCAGATTAGGGTTTAAGAGAG
Found at i:60986373 original size:126 final size:126
Alignment explanation
Indices: 60986142--60986559 Score: 640
Period size: 126 Copynumber: 3.3 Consensus size: 126
60986132 CTATTAATTT
* * *
60986142 AAAGAATCTCTCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAAATAATTTCGAGTAGA
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTG-AAAAAATAATTTCGAGTTGA
*
60986207 CGTTTCTAAGCAAATAGTGTCAAAAACACTTTAAGTAGGATGCTTTGTCAGCAATAGTACTG
65 CGTTTCTAAGCAAATAGTGTCAAAAACGCTTTAAGTAGGATGCTTTGTCAGCAATAGTACTG
* * *
60986269 AAAGAAGCTCCCACCTGGACGCGCTTTTGCTATAGTAGCTCCTGAAAAAATAATTTTGAGTTGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTTGAC
* * * * *
60986334 GTTTCTGAGCAAATATTGTCAAAAACGCTTTAAGCAGGATACTTTGTCAGCAATAGTACTA
66 GTTTCTAAGCAAATAGTGTCAAAAACGCTTTAAGTAGGATGCTTTGTCAGCAATAGTACTG
* *
60986395 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAATAGCTCTTGAAAAAATAATTTCGAGTTGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTTGAC
* *
60986460 GTTTCTAAGCAAATAGTGTCAAAAACGCTTCAAGTAGGATGCTTTGTCAGCAGA-AGTATTG
66 GTTTCTAAGCAAATAGTGTCAAAAACGCTTTAAGTAGGATGCTTTGTCAGCA-ATAGTACTG
* * *
60986521 AAAGAAGCTCCCACGTGGATGTGCTTTTGCTACAATAGC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGC
60986560 GCATGTTTGG
Statistics
Matches: 264, Mismatches: 26, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
126 223 0.84
127 41 0.16
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (126 bp):
AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTTGAC
GTTTCTAAGCAAATAGTGTCAAAAACGCTTTAAGTAGGATGCTTTGTCAGCAATAGTACTG
Found at i:60999821 original size:53 final size:55
Alignment explanation
Indices: 60999706--60999924 Score: 253
Period size: 55 Copynumber: 4.0 Consensus size: 55
60999696 AATTAAAATT
* * * * * **
60999706 ACAATTAATTTAAATATATAAACAATCAATTTAAAATAAGTAGTATTCTAACACA
1 ACAATTGATTTAAACATATAAACAATCAATTTAAAAGAAATAGTATTCCAACATG
* *
60999761 ACAATTGATTTAAACATGTAAACAATCTA-TTAAAA-AAATAGTATTCCAACATG
1 ACAATTGATTTAAACATATAAACAATCAATTTAAAAGAAATAGTATTCCAACATG
* *
60999814 ACAATTGATTTAAACATATAAACAATCAATTTAAAAGAAACAGTATTCTAACATG
1 ACAATTGATTTAAACATATAAACAATCAATTTAAAAGAAATAGTATTCCAACATG
* * * * * * * *
60999869 ACAATCGGTTTAAACATAAAAACAATCGATTCAAAAGAAATAATATTTCAGCATG
1 ACAATTGATTTAAACATATAAACAATCAATTTAAAAGAAATAGTATTCCAACATG
60999924 A
1 A
60999925 TAATCAATTA
Statistics
Matches: 140, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
53 41 0.29
54 12 0.09
55 87 0.62
ACGTcount: A:0.51, C:0.13, G:0.07, T:0.29
Consensus pattern (55 bp):
ACAATTGATTTAAACATATAAACAATCAATTTAAAAGAAATAGTATTCCAACATG
Found at i:60999895 original size:108 final size:110
Alignment explanation
Indices: 60999706--60999933 Score: 289
Period size: 108 Copynumber: 2.1 Consensus size: 110
60999696 AATTAAAATT
* * ** *
60999706 ACAATTAATTTAAATATATAAACAATCAATTTAAAATAAGTAGTATTCTAACACAACAATTGATT
1 ACAATTAATTTAAACATATAAACAATCAATTTAAAAGAAACAGTATTCTAACACAACAATCGATT
** * *
60999771 TAAACATGTAAACAATCTATT-AAAA-AAATAGTATTCCAACATG
66 TAAACATAAAAACAATCGATTCAAAAGAAATAATATTCCAACATG
* ** *
60999814 ACAATTGATTTAAACATATAAACAATCAATTTAAAAGAAACAGTATTCTAACATGACAATCGGTT
1 ACAATTAATTTAAACATATAAACAATCAATTTAAAAGAAACAGTATTCTAACACAACAATCGATT
* *
60999879 TAAACATAAAAACAATCGATTCAAAAGAAATAATATTTCAGCATG
66 TAAACATAAAAACAATCGATTCAAAAGAAATAATATTCCAACATG
* *
60999924 ATAATCAATT
1 ACAATTAATT
60999934 AAGTGCAACC
Statistics
Matches: 100, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
108 74 0.74
109 4 0.04
110 22 0.22
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (110 bp):
ACAATTAATTTAAACATATAAACAATCAATTTAAAAGAAACAGTATTCTAACACAACAATCGATT
TAAACATAAAAACAATCGATTCAAAAGAAATAATATTCCAACATG
Found at i:61016889 original size:12 final size:11
Alignment explanation
Indices: 61016865--61016899 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 11
61016855 TTTCAACAAG
61016865 TTTTCC-TTCA
1 TTTTCCTTTCA
61016875 TTTTCCTTGTCA
1 TTTTCCTT-TCA
61016887 TTTTCCTTTCA
1 TTTTCCTTTCA
61016898 TT
1 TT
61016900 GTCTGCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.26
11 6 0.26
12 11 0.48
ACGTcount: A:0.09, C:0.26, G:0.03, T:0.63
Consensus pattern (11 bp):
TTTTCCTTTCA
Found at i:61031411 original size:15 final size:15
Alignment explanation
Indices: 61031372--61031423 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
61031362 AACATGCATG
61031372 AATAATAATGCAAGTAAC
1 AATAATAAT--AA-TAAC
61031390 AAT-ATAATAATAAC
1 AATAATAATAATAAC
*
61031404 AATAATAACAATAAC
1 AATAATAATAATAAC
*
61031419 GATAA
1 AATAA
61031424 AGATAATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 7 0.23
15 16 0.52
17 5 0.16
18 3 0.10
ACGTcount: A:0.62, C:0.10, G:0.06, T:0.23
Consensus pattern (15 bp):
AATAATAATAATAAC
Found at i:61036553 original size:15 final size:15
Alignment explanation
Indices: 61036533--61036574 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
61036523 TGTAGGTATA
*
61036533 ATAATAATATATAA-T
1 ATAATAATA-AAAATT
61036548 ATAATAATAAAAATT
1 ATAATAATAAAAATT
*
61036563 ATAATAACAAAA
1 ATAATAATAAAA
61036575 TTAATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 3 0.12
15 21 0.88
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAATAATAAAAATT
Found at i:61036569 original size:18 final size:18
Alignment explanation
Indices: 61036529--61036569 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
61036519 TATATGTAGG
*
61036529 TATAATAATAATATATAA
1 TATAATAATAATAAATAA
61036547 TATAATAATAA-AAAT--
1 TATAATAATAATAAATAA
61036562 TATAATAA
1 TATAATAA
61036570 CAAAATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 8 0.36
17 3 0.14
18 11 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TATAATAATAATAAATAA
Found at i:61036830 original size:20 final size:22
Alignment explanation
Indices: 61036791--61036831 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
61036781 CCCTTTTTAA
*
61036791 AATCGTAAATAAGTAAAAAAAT
1 AATCGTAAATAAGAAAAAAAAT
61036813 AATCG-AAA-AAGAAAAAAAA
1 AATCGTAAATAAGAAAAAAAA
61036832 ACAGTAAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 3 0.17
22 5 0.28
ACGTcount: A:0.71, C:0.05, G:0.10, T:0.15
Consensus pattern (22 bp):
AATCGTAAATAAGAAAAAAAAT
Found at i:61037050 original size:21 final size:21
Alignment explanation
Indices: 61037024--61037099 Score: 129
Period size: 21 Copynumber: 3.7 Consensus size: 21
61037014 AATCATATCT
61037024 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
61037045 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
61037066 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
*
61037085 TCTAAGATTGTATAT
1 TCTAAGATTGCATAT
61037100 CTTCGAAAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
19 18 0.35
21 34 0.65
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:61037356 original size:44 final size:44
Alignment explanation
Indices: 61037303--61037387 Score: 136
Period size: 44 Copynumber: 1.9 Consensus size: 44
61037293 AGGAATTCGT
61037303 GCTTCAATCTACTCCACTGCAACTTCAGG-GAGATAAGACTTATA
1 GCTTCAATCTACTCCACTGCAACTTCAGGAG-GATAAGACTTATA
* *
61037347 GCTTTAATCTGCTCCACTGCAACTTCAGGAGGATAAGACTT
1 GCTTCAATCTACTCCACTGCAACTTCAGGAGGATAAGACTT
61037388 GCTGGCTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 37 0.97
45 1 0.03
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (44 bp):
GCTTCAATCTACTCCACTGCAACTTCAGGAGGATAAGACTTATA
Found at i:61037530 original size:132 final size:132
Alignment explanation
Indices: 61037385--61038311 Score: 1557
Period size: 132 Copynumber: 7.0 Consensus size: 132
61037375 GAGGATAAGA
* *
61037385 CTTGCTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTACTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
* *
61037450 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGCCTACTCCACTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
61037515 GG
131 GG
* * *
61037517 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTTGATTTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
*
61037582 CACTACTTCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
61037647 GG
131 GG
* *
61037649 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCATCTTCGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
* * *
61037714 CACTACTGCTTAGGGAGATAAGATTTACAATCTTCAGCCTACTCCGCTACTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
61037779 GG
131 GG
* * * *
61037781 CTTGGTGGCTTAAATTTGCTTCCCAGTATCTTGGAAAGATAAGATTTGCCATCTTCGATCTTCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
* * * *
61037846 TACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGCCTACTCCACAGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
61037911 GG
131 GG
* *
61037913 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
*
61037978 CACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
61038043 GG
131 GG
* *
61038045 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCAATCTTCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
* *
61038110 CACTACTGCTTAGAGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCTGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
61038175 GG
131 GG
* *
61038177 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCCTCGATCTACTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
* * *
61038242 CACTACTGCTTAGGGAGATAAGATCTACGATCCTCAACCTACTCCGCTGTTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
61038307 GG
131 GG
61038309 CTT
1 CTT
61038312 AGTGTTTCAC
Statistics
Matches: 747, Mismatches: 48, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 747 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (132 bp):
CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
GG
Found at i:61045402 original size:21 final size:21
Alignment explanation
Indices: 61045376--61045430 Score: 87
Period size: 19 Copynumber: 2.7 Consensus size: 21
61045366 AATCATATCT
61045376 TCTAAGATTGTATATATCATA
1 TCTAAGATTGTATATATCATA
*
61045397 TCTAAGATTG--CATATCATA
1 TCTAAGATTGTATATATCATA
61045416 TCTAAGATTGTATAT
1 TCTAAGATTGTATAT
61045431 CCTCGAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 18 0.60
21 12 0.40
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (21 bp):
TCTAAGATTGTATATATCATA
Found at i:61045416 original size:24 final size:20
Alignment explanation
Indices: 61045367--61045418 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
61045357 ATATTACAAA
61045367 ATCATATCTTCTAAGATTGT
1 ATCATATCTTCTAAGATTGT
61045387 AT-ATATCATATCTAAGATTGCAT
1 ATCATATC-T-TCTAAGATTG--T
61045410 ATCATATCT
1 ATCATATCT
61045419 AAGATTGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 5 0.19
20 3 0.11
21 10 0.37
23 4 0.15
24 5 0.19
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (20 bp):
ATCATATCTTCTAAGATTGT
Found at i:61045510 original size:20 final size:21
Alignment explanation
Indices: 61045485--61045528 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
61045475 GTATTACATT
61045485 AAAAATAATGTTTTTG-TAAA
1 AAAAATAATGTTTTTGTTAAA
*
61045505 AAAAATAATTTTTTTGTTAAA
1 AAAAATAATGTTTTTGTTAAA
61045526 AAA
1 AAA
61045529 TAAAATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (21 bp):
AAAAATAATGTTTTTGTTAAA
Found at i:61058233 original size:13 final size:13
Alignment explanation
Indices: 61058212--61058244 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
61058202 TACATAAATT
*
61058212 ACAATAAAAAAAA
1 ACAAAAAAAAAAA
61058225 ACAAAAAAAAAAA
1 ACAAAAAAAAAAA
61058238 A-AAAAAA
1 ACAAAAAA
61058245 CTTTTTCGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.91, C:0.06, G:0.00, T:0.03
Consensus pattern (13 bp):
ACAAAAAAAAAAA
Found at i:61061824 original size:29 final size:29
Alignment explanation
Indices: 61061771--61061829 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
61061761 TCCGAGCCTT
* *
61061771 GGGGAAAAAATGTAATTATGTAAAATTTA
1 GGGGAAAAAATGTAATTATGAAAAAGTTA
* * *
61061800 GGGGCAAAATTGTAATTTTGAAAAAGTTA
1 GGGGAAAAAATGTAATTATGAAAAAGTTA
61061829 G
1 G
61061830 AGTCGAGGGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.44, C:0.02, G:0.24, T:0.31
Consensus pattern (29 bp):
GGGGAAAAAATGTAATTATGAAAAAGTTA
Found at i:61062057 original size:13 final size:13
Alignment explanation
Indices: 61062039--61062070 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
61062029 TTTCCAGCAA
61062039 TTATGAATTTATT
1 TTATGAATTTATT
61062052 TTATGAATTTATT
1 TTATGAATTTATT
*
61062065 TGATGA
1 TTATGA
61062071 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:61062278 original size:50 final size:50
Alignment explanation
Indices: 61062165--61062406 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
61062155 ATTTGGGTAA
* * *
61062165 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
61062221 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
61062271 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
61062321 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
61062371 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
61062407 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:61062354 original size:100 final size:103
Alignment explanation
Indices: 61062165--61062414 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
61062155 ATTTGGGTAA
61062165 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
61062230 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
61062271 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
61062333 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
61062371 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
61062415 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:61065068 original size:15 final size:15
Alignment explanation
Indices: 61065048--61065077 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
61065038 CATTTTGTAA
*
61065048 TTTTAAAATATTATT
1 TTTTAAAATAATATT
61065063 TTTTAAAATAATATT
1 TTTTAAAATAATATT
61065078 AATATTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTTAAAATAATATT
Found at i:61065118 original size:12 final size:12
Alignment explanation
Indices: 61065073--61065100 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
61065063 TTTTAAAATA
61065073 ATATTAATATTT
1 ATATTAATATTT
61065085 ATATTAATATTT
1 ATATTAATATTT
61065097 ATAT
1 ATAT
61065101 ATTTTATTAT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
ATATTAATATTT
Found at i:61066731 original size:21 final size:21
Alignment explanation
Indices: 61066707--61066752 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
61066697 TACAAGTGAA
*
61066707 AAATAT-TATGCATAAAATAAT
1 AAATATATATACATAAAA-AAT
61066728 AAAT-TATATACATAAAAAAT
1 AAATATATATACATAAAAAAT
61066748 AAATA
1 AAATA
61066753 ATTGATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (21 bp):
AAATATATATACATAAAAAAT
Found at i:61066770 original size:17 final size:18
Alignment explanation
Indices: 61066739--61066778 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
61066729 AATTATATAC
61066739 ATAAAAAATAAATAATTG
1 ATAAAAAATAAATAATTG
*
61066757 ATAAAAAA-AGATAATTG
1 ATAAAAAATAAATAATTG
61066774 -TAAAA
1 ATAAAA
61066779 TTTATATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.24
17 8 0.38
18 8 0.38
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (18 bp):
ATAAAAAATAAATAATTG
Found at i:61071550 original size:17 final size:16
Alignment explanation
Indices: 61071520--61071558 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
61071510 TTTAAAAATT
61071520 ATAA-TAAAAATATAA
1 ATAATTAAAAATATAA
*
61071535 ATCATTAAAAACTATAA
1 ATAATTAAAAA-TATAA
61071552 ATAATTA
1 ATAATTA
61071559 TTTAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 3 0.15
16 6 0.30
17 11 0.55
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAATTAAAAATATAA
Found at i:61071624 original size:16 final size:16
Alignment explanation
Indices: 61071575--61071624 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
61071565 AATTCTAAAA
*
61071575 AAATAAAAAAAATATT
1 AAATAATAAAAATATT
61071591 -AATAATAGAAAA-ATT
1 AAATAATA-AAAATATT
*
61071606 AAATTATAAAAATATT
1 AAATAATAAAAATATT
61071622 AAA
1 AAA
61071625 AAGTATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 13 0.45
16 16 0.55
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
AAATAATAAAAATATT
Found at i:61071841 original size:26 final size:25
Alignment explanation
Indices: 61071807--61071856 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
61071797 AATTTTAATA
* * *
61071807 AATTTTATATTTTTATAATTATTTG
1 AATTTTATAATTTTAAAAATATTTG
61071832 AATTTCTATAATTTTAAAAATATTT
1 AATTT-TATAATTTTAAAAATATTT
61071857 TATGATTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (25 bp):
AATTTTATAATTTTAAAAATATTTG
Found at i:61075724 original size:19 final size:20
Alignment explanation
Indices: 61075696--61075733 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
61075686 TAGTAAGAGG
61075696 ATTGTC-AAAAAAAATTCTA
1 ATTGTCAAAAAAAAATTCTA
*
61075715 ATTGTTAAAAAAAAATTCT
1 ATTGTCAAAAAAAAATTCT
61075734 TTAAAAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (20 bp):
ATTGTCAAAAAAAAATTCTA
Found at i:61076320 original size:31 final size:31
Alignment explanation
Indices: 61076280--61076383 Score: 104
Period size: 31 Copynumber: 3.3 Consensus size: 31
61076270 TTAAAACAGG
*
61076280 TGAGTTAATAATATTTTCATCATTATCTAAT
1 TGAGTTAATAATATTTTCATCATTATCCAAT
* ** * * *
61076311 TAAGTTAAT-ATCCGTTTAACTCATGA-CACAAG
1 TGAGTTAATAAT-ATTTTCA-TCATTATC-CAAT
61076343 TGAGTTAATAATATTTTCATCATTATCCAAT
1 TGAGTTAATAATATTTTCATCATTATCCAAT
61076374 TGAGTTAATA
1 TGAGTTAATA
61076384 TCCGTTTAAC
Statistics
Matches: 55, Mismatches: 13, Indels: 10
0.71 0.17 0.13
Matches are distributed among these distances:
30 2 0.04
31 31 0.56
32 20 0.36
33 2 0.04
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (31 bp):
TGAGTTAATAATATTTTCATCATTATCCAAT
Found at i:61076351 original size:32 final size:32
Alignment explanation
Indices: 61076313--61076408 Score: 90
Period size: 31 Copynumber: 3.0 Consensus size: 32
61076303 TATCTAATTA
*
61076313 AGTTAATATCCGTTTAACTCATGACACAAGTG
1 AGTTAATATCCGTTTAACTCATCACACAAGTG
** * * *
61076345 AGTTAATAAT-ATTTTCA-TCATTATC-CAATTG
1 AGTTAAT-ATCCGTTTAACTCATCA-CACAAGTG
*
61076376 AGTTAATATCCGTTTAACTCATCACACAGGTG
1 AGTTAATATCCGTTTAACTCATCACACAAGTG
61076408 A
1 A
61076409 TTATCTCCCA
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
30 2 0.04
31 22 0.46
32 22 0.46
33 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (32 bp):
AGTTAATATCCGTTTAACTCATCACACAAGTG
Found at i:61076353 original size:63 final size:63
Alignment explanation
Indices: 61076279--61076408 Score: 224
Period size: 63 Copynumber: 2.1 Consensus size: 63
61076269 CTTAAAACAG
* *
61076279 GTGAGTTAATAATATTTTCATCATTATCTAATTAAGTTAATATCCGTTTAACTCATGACACAA
1 GTGAGTTAATAATATTTTCATCATTATCCAATTAAGTTAATATCCGTTTAACTCATCACACAA
* *
61076342 GTGAGTTAATAATATTTTCATCATTATCCAATTGAGTTAATATCCGTTTAACTCATCACACAG
1 GTGAGTTAATAATATTTTCATCATTATCCAATTAAGTTAATATCCGTTTAACTCATCACACAA
61076405 GTGA
1 GTGA
61076409 TTATCTCCCA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (63 bp):
GTGAGTTAATAATATTTTCATCATTATCCAATTAAGTTAATATCCGTTTAACTCATCACACAA
Found at i:61079068 original size:28 final size:27
Alignment explanation
Indices: 61079002--61079069 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 27
61078992 TTATAGCATG
*
61079002 TTTATT-TTTATTTTAAAAATAGGAATT
1 TTTATTATTT-TTTTAAAAATAGGAACT
*
61079029 TTTATAGTATTTTTTTAAACATAGGAAACT
1 TTTAT--TATTTTTTTAAAAATAGG-AACT
61079059 TTTATTATTTT
1 TTTATTATTTT
61079070 AATTTGAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
27 5 0.14
28 6 0.17
29 13 0.37
30 11 0.31
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (27 bp):
TTTATTATTTTTTTAAAAATAGGAACT
Found at i:61079371 original size:15 final size:15
Alignment explanation
Indices: 61079353--61079387 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
61079343 TTAGTCACTG
61079353 AATTTACAGTGAATT
1 AATTTACAGTGAATT
61079368 AATTTACAGTGAATT
1 AATTTACAGTGAATT
61079383 AATTT
1 AATTT
61079388 GGAAGCAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (15 bp):
AATTTACAGTGAATT
Found at i:61082967 original size:26 final size:28
Alignment explanation
Indices: 61082913--61082976 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
61082903 TAAGAATAAG
* * *
61082913 AATTTTATTAAATTATATATTATTATTA
1 AATTATATTTAATAATATATTATTATTA
61082941 AATTATATTTAATAATA-ATTATT-TTA
1 AATTATATTTAATAATATATTATTATTA
61082967 AATTATATTT
1 AATTATATTT
61082977 TAGTATTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 13 0.39
27 6 0.18
28 14 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
AATTATATTTAATAATATATTATTATTA
Found at i:61083052 original size:17 final size:17
Alignment explanation
Indices: 61083032--61083065 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
61083022 TTTATTAACA
61083032 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
61083049 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
61083066 TCTATAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:61083257 original size:39 final size:41
Alignment explanation
Indices: 61083212--61083317 Score: 135
Period size: 44 Copynumber: 2.5 Consensus size: 41
61083202 TTTCCTTATG
* *
61083212 CTATTACACCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
61083252 C-ATTACGCCTCTATTCCATTACATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTCTATT-C----CATTCAACCAAACAAAAGAATTAC
61083297 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
61083318 ACGCTTCTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
39 13 0.23
40 2 0.04
41 4 0.07
44 19 0.33
45 5 0.09
46 14 0.25
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:61083292 original size:44 final size:46
Alignment explanation
Indices: 61083229--61083319 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
61083219 ACCTCTATTC
*
61083229 CATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
61083273 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
61083319 C
1 C
61083320 GCTTCTATTC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 19 0.43
45 4 0.09
46 21 0.48
ACGTcount: A:0.38, C:0.31, G:0.04, T:0.26
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
Found at i:61083320 original size:16 final size:16
Alignment explanation
Indices: 61083299--61083335 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
61083289 AGAATTACCT
61083299 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
* *
61083315 ATTACGCTTCTATTCT
1 ATTACGCCTCTATTCC
61083331 ATTAC
1 ATTAC
61083336 AGCGAACCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.22, C:0.30, G:0.05, T:0.43
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:61089548 original size:17 final size:16
Alignment explanation
Indices: 61089528--61089568 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
61089518 ATTAATGTTC
61089528 TTATTATTATAATTACA
1 TTATTATTATAATTA-A
* *
61089545 TTATTATTATATTTAT
1 TTATTATTATAATTAA
61089561 TTATTATT
1 TTATTATT
61089569 TATCATTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATTATTATAATTAA
Found at i:61090245 original size:42 final size:42
Alignment explanation
Indices: 61090198--61090444 Score: 280
Period size: 42 Copynumber: 5.8 Consensus size: 42
61090188 CAACCAAAAA
*
61090198 CGCCGCTAAAGAACATGATCTTTAACGGCGTTTTTTTATAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTATAAG
*
61090240 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCTATAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTATAAG
* * *
61090282 CGCCACTAAAGAACATGATTTTTAGTGGCG-TTTTTTATTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTA-TAAG
* * * * * * *
61090324 CGCAGCTAAAGAACATGTTCTTTAACGGCGCTTTGTATAAAAA
1 CGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTTTATAAG
* * * * *
61090367 TGCCGCTAAAGAACATGTTCTTCAGCGGCGCTTTTTTTACAAA
1 CGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTTTATAAG
* * *
61090410 CACCGCTAAAGAACATGTTCTTTAGCGGCGCTTTT
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
61090445 GTACAAAAAC
Statistics
Matches: 175, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
41 6 0.03
42 99 0.57
43 65 0.37
44 5 0.03
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTATAAG
Found at i:61090346 original size:84 final size:84
Alignment explanation
Indices: 61090193--61090457 Score: 309
Period size: 84 Copynumber: 3.1 Consensus size: 84
61090183 GTTTACAACC
* * *
61090193 AAAAACGCCGCTAAAGAACATGATCTTTAACGGCGTTTTTTTATAAGCGCCGCTAAAGAACATGA
1 AAAAACGCCGCTAAAGAACATGATTTTTAGCGGCGTTTTTTTATAAGCGCCGCTAAAGAACATGT
*
61090258 TCTTTAGCGGCGTTTTTCT
66 TCTTTAGCGGCGTTTTTAT
* * * * *
61090277 ATAAGCGCCACTAAAGAACATGATTTTTAGTGGCG-TTTTTTATTAAGCGCAGCTAAAGAACATG
1 AAAAACGCCGCTAAAGAACATGATTTTTAGCGGCGTTTTTTTA-TAAGCGCCGCTAAAGAACATG
* *
61090341 TTCTTTAACGGCGCTTTGTAT
65 TTCTTTAGCGGCG-TTTTTAT
* * * * *
61090362 AAAAATGCCGCTAAAGAACATG-TTCTTCAGCGGCGCTTTTTTTACAAACACCGCTAAAGAACAT
1 AAAAACGCCGCTAAAGAACATGATT-TTTAGCGGCG-TTTTTTTATAAGCGCCGCTAAAGAACAT
*
61090426 GTTCTTTAGCGGCGCTTTTGTAC
64 GTTCTTTAGCGGCG-TTTT-TAT
61090449 AAAAACGCC
1 AAAAACGCC
61090458 ACTATTTTGG
Statistics
Matches: 150, Mismatches: 25, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
83 7 0.05
84 62 0.41
85 31 0.21
86 33 0.22
87 17 0.11
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (84 bp):
AAAAACGCCGCTAAAGAACATGATTTTTAGCGGCGTTTTTTTATAAGCGCCGCTAAAGAACATGT
TCTTTAGCGGCGTTTTTAT
Found at i:61090852 original size:21 final size:21
Alignment explanation
Indices: 61090828--61090878 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
61090818 TTCTTTTGAA
*
61090828 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
*
61090849 CCTCTGCTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
*
61090870 CGTCTGCTT
1 CCTCTGCTT
61090879 TAAGTTGTAG
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:0.02, C:0.45, G:0.20, T:0.33
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:61102750 original size:27 final size:27
Alignment explanation
Indices: 61102719--61102801 Score: 148
Period size: 27 Copynumber: 3.1 Consensus size: 27
61102709 GTATTATGTA
*
61102719 ATGTAAGTTATGTAATTTATTTAATTT
1 ATGTAAGTTATGTAAGTTATTTAATTT
*
61102746 ATGTAAGTTATGTAAGTTGTTTAATTT
1 ATGTAAGTTATGTAAGTTATTTAATTT
61102773 ATGTAAGTTATGTAAGTTATTTAATTT
1 ATGTAAGTTATGTAAGTTATTTAATTT
61102800 AT
1 AT
61102802 TGAAATGCAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (27 bp):
ATGTAAGTTATGTAAGTTATTTAATTT
Found at i:61102802 original size:9 final size:9
Alignment explanation
Indices: 61102719--61102792 Score: 94
Period size: 9 Copynumber: 8.2 Consensus size: 9
61102709 GTATTATGTA
61102719 ATGTAAGTT
1 ATGTAAGTT
*
61102728 ATGTAATTT
1 ATGTAAGTT
* *
61102737 ATTTAATTT
1 ATGTAAGTT
61102746 ATGTAAGTT
1 ATGTAAGTT
61102755 ATGTAAGTT
1 ATGTAAGTT
* * *
61102764 GTTTAATTT
1 ATGTAAGTT
61102773 ATGTAAGTT
1 ATGTAAGTT
61102782 ATGTAAGTT
1 ATGTAAGTT
61102791 AT
1 AT
61102793 TTAATTTATT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 55 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.51
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:61103022 original size:16 final size:15
Alignment explanation
Indices: 61103009--61103321 Score: 85
Period size: 16 Copynumber: 19.7 Consensus size: 15
61102999 TCGTATTATG
61103009 TAAGTTATGTATTAA
1 TAAGTTATGTATTAA
*
61103024 AAATGTTATGTATTAA
1 TAA-GTTATGTATTAA
61103040 TAAGTTATGTAAGTT-A
1 TAAGTTATGT-A-TTAA
* **
61103056 T--GTATCATTTATCCA
1 TAAGT-T-ATGTATTAA
*
61103071 TAA---ATATATTAA
1 TAAGTTATGTATTAA
*
61103083 TAAGTTATGTCGTATTATG
1 TAAGTTA--T-GTATTA-A
61103102 TAAGTTATGTATTATA
1 TAAGTTATGTATTA-A
61103118 TAAGTTATGTATTAA
1 TAAGTTATGTATTAA
61103133 TAAGTTATGTAAGTTATGTA
1 TAAGTTATGT-A-TTA---A
* * ** *
61103153 TCA-TTTTAAAATATA
1 TAAGTTATGTATTA-A
*
61103168 TAAGTTATGTCGTATTATG
1 TAAGTTA--T-GTATTA-A
*
61103187 TAAGTTATCTATTAA
1 TAAGTTATGTATTAA
*
61103202 AAATGTTATGTATTAA
1 TAA-GTTATGTATTAA
61103218 TAAGTTATGTAAGTT-A
1 TAAGTTATGT-A-TTAA
* **
61103234 T--GTATCATTTATCCA
1 TAAGT-T-ATGTATTAA
*
61103249 TAA---ATATATTAA
1 TAAGTTATGTATTAA
*
61103261 TAAGTTATGTCGTATTATG
1 TAAGTTA--T-GTATTA-A
*
61103280 TAAGTTATATATTATA
1 TAAGTTATGTATTA-A
61103296 TAAGTTATGTATTAA
1 TAAGTTATGTATTAA
61103311 TAAGTTATGTA
1 TAAGTTATGTA
61103322 AGTTATGTAT
Statistics
Matches: 223, Mismatches: 36, Indels: 78
0.66 0.11 0.23
Matches are distributed among these distances:
12 18 0.08
14 6 0.03
15 55 0.25
16 87 0.39
17 14 0.06
18 12 0.05
19 28 0.13
20 3 0.01
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.46
Consensus pattern (15 bp):
TAAGTTATGTATTAA
Found at i:61103097 original size:93 final size:92
Alignment explanation
Indices: 61102994--61103400 Score: 625
Period size: 93 Copynumber: 4.5 Consensus size: 92
61102984 ATTTATGTTA
61102994 TTATGTCGTATTATGTAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGT
1 TTATGTCGTATTATGTAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGT
61103059 ATCATTTATCCATAAATATATTAATAAG
66 ATCATTT-TCCATAAATATATTAATAAG
*
61103087 TTATGTCGTATTATGTAAGTTATGTATTATATAA-GTTATGTATTAATAAGTTATGTAAGTTATG
1 TTATGTCGTATTATGTAAGTTATGTATTA-AAAATGTTATGTATTAATAAGTTATGTAAGTTATG
61103151 TATCA-TTT---TAAA-ATA-T-ATAAG
65 TATCATTTTCCATAAATATATTAATAAG
*
61103172 TTATGTCGTATTATGTAAGTTATCTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGT
1 TTATGTCGTATTATGTAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGT
61103237 ATCATTTATCCATAAATATATTAATAAG
66 ATCATTT-TCCATAAATATATTAATAAG
* *
61103265 TTATGTCGTATTATGTAAGTTATATATTATATAA-GTTATGTATTAATAAGTTATGTAAGTTATG
1 TTATGTCGTATTATGTAAGTTATGTATTA-AAAATGTTATGTATTAATAAGTTATGTAAGTTATG
** *
61103329 TATCATTTTAAAATATATATATTAATAAG
65 TATCATTTT-CCATAAATATATTAATAAG
* *
61103358 TTATGTCGTATTATATAAGTTATGTATTAAAAATGATATGTAT
1 TTATGTCGTATTATGTAAGTTATGTATTAAAAATGTTATGTAT
61103401 AAGTTATGTC
Statistics
Matches: 289, Mismatches: 12, Indels: 26
0.88 0.04 0.08
Matches are distributed among these distances:
84 3 0.01
85 68 0.24
86 3 0.01
87 4 0.01
88 4 0.01
90 4 0.01
91 4 0.01
92 7 0.02
93 186 0.64
94 6 0.02
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (92 bp):
TTATGTCGTATTATGTAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGT
ATCATTTTCCATAAATATATTAATAAG
Found at i:61103111 original size:9 final size:9
Alignment explanation
Indices: 61103097--61103152 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 9
61103087 TTATGTCGTA
61103097 TTATGTAAG
1 TTATGTAAG
61103106 TTATGT-A-
1 TTATGTAAG
*
61103113 TTATATAAG
1 TTATGTAAG
61103122 TTATGT-A-
1 TTATGTAAG
*
61103129 TTA-ATAAG
1 TTATGTAAG
61103137 TTATGTAAG
1 TTATGTAAG
61103146 TTATGTA
1 TTATGTA
61103153 TCATTTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
6 1 0.03
7 9 0.24
8 6 0.16
9 22 0.58
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:61103143 original size:40 final size:40
Alignment explanation
Indices: 61103097--61103238 Score: 128
Period size: 40 Copynumber: 3.4 Consensus size: 40
61103087 TTATGTCGTA
61103097 TTATGTAAGTTATGTATTATATAAGTTATGTATTAATAAG
1 TTATGTAAGTTATGTATTATATAAGTTATGTATTAATAAG
* * * **
61103137 TTATGTAAGTTATGTATCATTTTAAAATATATAAGTTATGTCGT-A-
1 TTATGTAAGTTATGTATTA-TAT-AAGT-TAT--G-TAT-TAATAAG
* *
61103182 TTATGTAAGTTATCTATTA-AAAATGTTATGTATTAATAAG
1 TTATGTAAGTTATGTATTATATAA-GTTATGTATTAATAAG
61103222 TTATGTAAGTTATGTAT
1 TTATGTAAGTTATGTAT
61103239 CATTTATCCA
Statistics
Matches: 79, Mismatches: 13, Indels: 20
0.71 0.12 0.18
Matches are distributed among these distances:
38 2 0.03
39 4 0.05
40 35 0.44
41 2 0.03
42 8 0.10
43 4 0.05
45 18 0.23
46 4 0.05
47 2 0.03
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (40 bp):
TTATGTAAGTTATGTATTATATAAGTTATGTATTAATAAG
Found at i:61103221 original size:50 final size:50
Alignment explanation
Indices: 61103167--61103400 Score: 187
Period size: 43 Copynumber: 5.0 Consensus size: 50
61103157 TTTAAAATAT
*
61103167 ATAAGTTATGTCGTATTATGTAAGTTATCTATTAAAAATGTTATGTATTA
1 ATAAGTTATGTCGTATTATGTAAGTTATCTATTAAAAATGATATGTATTA
* * * ** *
61103217 ATAAGTTATGT--AAGTTATGT-A-TCATTTATCCATAA--ATA--TATTA
1 ATAAGTTATGTCGTA-TTATGTAAGTTATCTATTAAAAATGATATGTATTA
* * *
61103260 ATAAGTTATGTCGTATTATGTAAGTTATATATTATATAA-GTTATGTATTA
1 ATAAGTTATGTCGTATTATGTAAGTTATCTATTA-AAAATGATATGTATTA
* * *
61103310 ATAAGTTATGT--AAGTTATGT-A-TCAT-T-TT-AAAAT-ATATATATTA
1 ATAAGTTATGTCGTA-TTATGTAAGTTATCTATTAAAAATGATATGTATTA
* *
61103353 ATAAGTTATGTCGTATTATATAAGTTATGTATTAAAAATGATATGTAT
1 ATAAGTTATGTCGTATTATGTAAGTTATCTATTAAAAATGATATGTAT
61103401 AAGTTATGTC
Statistics
Matches: 143, Mismatches: 22, Indels: 38
0.70 0.11 0.19
Matches are distributed among these distances:
43 38 0.27
44 11 0.08
45 8 0.06
46 10 0.07
47 17 0.12
48 8 0.06
49 17 0.12
50 34 0.24
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.46
Consensus pattern (50 bp):
ATAAGTTATGTCGTATTATGTAAGTTATCTATTAAAAATGATATGTATTA
Found at i:61103236 original size:24 final size:24
Alignment explanation
Indices: 61103206--61103331 Score: 74
Period size: 24 Copynumber: 5.4 Consensus size: 24
61103196 TATTAAAAAT
61103206 GTTATGTATTAATAAGTTATGTAA
1 GTTATGTATTAATAAGTTATGTAA
* *
61103230 GTTATGTA-TCAT---TTATCCATAA
1 GTTATGTATTAATAAGTTAT--GTAA
* *
61103252 ---ATATATTAATAAGTTATGT-C
1 GTTATGTATTAATAAGTTATGTAA
*
61103272 GTATTATGTAAGTT-ATATA-TTATATAA
1 G--TTATGT-A-TTAATA-AGTTATGTAA
61103299 GTTATGTATTAATAAGTTATGTAA
1 GTTATGTATTAATAAGTTATGTAA
61103323 GTTATGTAT
1 GTTATGTAT
61103332 CATTTTAAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 34
0.63 0.08 0.29
Matches are distributed among these distances:
19 4 0.05
20 7 0.09
21 1 0.01
22 3 0.04
23 10 0.13
24 28 0.37
25 9 0.12
26 9 0.12
27 4 0.05
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (24 bp):
GTTATGTATTAATAAGTTATGTAA
Found at i:61103254 original size:178 final size:184
Alignment explanation
Indices: 61102994--61103400 Score: 718
Period size: 178 Copynumber: 2.2 Consensus size: 184
61102984 ATTTATGTTA
61102994 TTATGTCGTATTATGTAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGT
1 TTATGTCGTATTATGTAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGT
*
61103059 ATCATTTATCCATAAATATATTAATAAGTTATGTCGTATTATGTAAGTTATGTATTATATAAGTT
66 ATCATTTATCCATAAATATATTAATAAGTTATGTCGTATTATGTAAGTTATATATTATATAAGTT
61103124 ATGTATTAATAAGTTATGTAAGTTATGTATCATTTT-A-A-A-ATA-T-ATAAG
131 ATGTATTAATAAGTTATGTAAGTTATGTATCATTTTAATATATATATTAATAAG
*
61103172 TTATGTCGTATTATGTAAGTTATCTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGT
1 TTATGTCGTATTATGTAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGT
61103237 ATCATTTATCCATAAATATATTAATAAGTTATGTCGTATTATGTAAGTTATATATTATATAAGTT
66 ATCATTTATCCATAAATATATTAATAAGTTATGTCGTATTATGTAAGTTATATATTATATAAGTT
61103302 ATGTATTAATAAGTTATGTAAGTTATGTATCATTTTAAAATATATATATTAATAAG
131 ATGTATTAATAAGTTATGTAAGTTATGTATCATTTT--AATATATATATTAATAAG
* *
61103358 TTATGTCGTATTATATAAGTTATGTATTAAAAATGATATGTAT
1 TTATGTCGTATTATGTAAGTTATGTATTAAAAATGTTATGTAT
61103401 AAGTTATGTC
Statistics
Matches: 216, Mismatches: 5, Indels: 8
0.94 0.02 0.03
Matches are distributed among these distances:
178 164 0.76
181 1 0.00
182 1 0.00
183 1 0.00
184 3 0.01
185 1 0.00
186 45 0.21
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (184 bp):
TTATGTCGTATTATGTAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGT
ATCATTTATCCATAAATATATTAATAAGTTATGTCGTATTATGTAAGTTATATATTATATAAGTT
ATGTATTAATAAGTTATGTAAGTTATGTATCATTTTAATATATATATTAATAAG
Found at i:61103281 original size:53 final size:51
Alignment explanation
Indices: 61103222--61103384 Score: 143
Period size: 53 Copynumber: 3.3 Consensus size: 51
61103212 TATTAATAAG
61103222 TTATGTAAGTTATGTATCATTTATCCATAAATATATTAATAAGTTATGTCGTA
1 TTATGTAAGTTATGTATCATTTAT--ATAAATATATTAATAAGTTATGTCGTA
* * *
61103275 TTATGTAAGTTA--TAT-A-TTATATAAGT-TATGTATTAA--TA---AG--
1 TTATGTAAGTTATGTATCATTTATATAAATATAT-TAATAAGTTATGTCGTA
* *
61103315 TTATGTAAGTTATGTATCATTTTAAAATATATATATTAATAAGTTATGTCGTA
1 TTATGTAAGTTATGTATCA-TTT-ATATAAATATATTAATAAGTTATGTCGTA
*
61103368 TTATATAAGTTATGTAT
1 TTATGTAAGTTATGTAT
61103385 TAAAAATGAT
Statistics
Matches: 86, Mismatches: 9, Indels: 30
0.69 0.07 0.24
Matches are distributed among these distances:
40 12 0.14
42 4 0.05
43 1 0.01
45 4 0.05
46 13 0.15
47 13 0.15
48 2 0.02
49 4 0.05
50 1 0.01
51 4 0.05
53 28 0.33
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.47
Consensus pattern (51 bp):
TTATGTAAGTTATGTATCATTTATATAAATATATTAATAAGTTATGTCGTA
Found at i:61103328 original size:9 final size:9
Alignment explanation
Indices: 61103275--61103330 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
61103265 TTATGTCGTA
61103275 TTATGTAAG
1 TTATGTAAG
*
61103284 TTATAT-A-
1 TTATGTAAG
*
61103291 TTATATAAG
1 TTATGTAAG
61103300 TTATGT-A-
1 TTATGTAAG
*
61103307 TTA-ATAAG
1 TTATGTAAG
61103315 TTATGTAAG
1 TTATGTAAG
61103324 TTATGTA
1 TTATGTA
61103331 TCATTTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
6 1 0.03
7 10 0.26
8 6 0.16
9 21 0.55
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:61105312 original size:15 final size:15
Alignment explanation
Indices: 61105294--61105327 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
61105284 ATAAAACTCA
61105294 TAAACCACAAAACAC
1 TAAACCACAAAACAC
* *
61105309 TAAACCACCAAACCC
1 TAAACCACAAAACAC
61105324 TAAA
1 TAAA
61105328 ATCCAAGTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.35, G:0.00, T:0.09
Consensus pattern (15 bp):
TAAACCACAAAACAC
Found at i:61106474 original size:206 final size:205
Alignment explanation
Indices: 61106114--61106489 Score: 540
Period size: 206 Copynumber: 1.8 Consensus size: 205
61106104 TTTTTTAGGC
* ** * *
61106114 AAAGCGCCGCTAAATGCCACTATACCTCACGGCCAAACGATGCATTTTGGTTAACTTTTTGCGGC
1 AAAGCGCCGCTAAATGCCACCATAAATCAAGGCCAAACGATGCATTTTGGTTAACTTTCTGCGGC
* *
61106179 GTTTACTAGTTAAGCGTCGTTAATACCGATCTTTAGCGGCGTTTTTCAATTAGCGCCGCGAAATC
66 GTTTACTAGTTAAGCGCCGTTAATACCGATATTTAGCGGCGTTTTTCAATTAGCGCCGCGAAATC
* *
61106244 CAGAATTGATCAAAACCGAACGCTGCGTTTAGTTTTAACATATTTTACGGCGTTTTTCTTTAGTG
131 CA-AATTGATCAAAACCAAACGCTGCATTTAGTTTTAACATATTTTACGGCGTTTTTCTTTAGTG
61106309 GCGTTTGGTTT
195 GCGTTTGGTTT
*
61106320 AAAGCGCCGCTAAATGCCACCATAAATCAAGGCCAAACGATGCGTTTTGGTTAACTTTCTGCGGC
1 AAAGCGCCGCTAAATGCCACCATAAATCAAGGCCAAACGATGCATTTTGGTTAACTTTCTGCGGC
* * * * * * *
61106385 GTTTATTCGTTAAGCGCCGTTAATTCTGATATTTCGCGGCGATTTTT-TATTAGCGCCGCTGGAA
66 GTTTACTAGTTAAGCGCCGTTAATACCGATATTTAGCGGCG-TTTTTCAATTAGCGCCGC-GAAA
*
61106449 TCGC-AATTGATTAAAACCAAACGCTGCATTTAGTTTTAACA
129 TC-CAAATTGATCAAAACCAAACGCTGCATTTAGTTTTAACA
61106490 GACTCGGCGG
Statistics
Matches: 149, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
206 138 0.93
207 10 0.07
208 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (205 bp):
AAAGCGCCGCTAAATGCCACCATAAATCAAGGCCAAACGATGCATTTTGGTTAACTTTCTGCGGC
GTTTACTAGTTAAGCGCCGTTAATACCGATATTTAGCGGCGTTTTTCAATTAGCGCCGCGAAATC
CAAATTGATCAAAACCAAACGCTGCATTTAGTTTTAACATATTTTACGGCGTTTTTCTTTAGTGG
CGTTTGGTTT
Found at i:61106756 original size:230 final size:226
Alignment explanation
Indices: 61106300--61106937 Score: 703
Period size: 230 Copynumber: 2.8 Consensus size: 226
61106290 ACGGCGTTTT
* *
61106300 TCTTTAGTGGCGTTTGGTTTAAAGCGCCGCTAAATGCCACCATAAATCAAGGCCAAACGATGCGT
1 TCTTTAGTGGCG-TTGGTTAAAAGCGCCGCTAAATGCCACCATACATCAAGGCCAAACGATGCGT
* *
61106365 TTTGGTTAACTTTCTGCGGCGTTTATTCGTTAAGCGCCGTTAAT-TCTGATATTTCGCGGCGATT
65 TTTGGTTAACTTTCTGCGGCGTTTA-TCGATAAGCGCCGTTAATATC-GATATTTAGCGGCG-TT
* * * * * * *
61106429 TTT-TATTAGCGCCGCTGGAATCGCAATTGATTAAAACCAAACGCTGCATTTAGTTTTAACAGAC
127 TTTATGTTAGCGCCGCT-AAACCACAATTGATCAACACCGAACGCTGCATTTAGTTTTAACAGAC
* * *
61106493 TCGGCGGCGTTTTAACAAAAACGCCGTTAATGAAGA
191 TCGGCGGCGCTATAACAAAAACGCCGCTAATGAAGA
*
61106529 TCTTTAGTGGCGTTCAGGTTAAAAGCGCCGCTAAATGCCACCATACATCAAGGCCAAATGATGCG
1 TCTTTAGTGGCGTT--GGTTAAAAGCGCCGCTAAATGCCACCATACATCAAGGCCAAACGATGCG
* * * *
61106594 TTTTGGTTAGCTTTCTGCGGCGTTTATCCGGTAAGCGCTGTTAATATCGATTTTTAGCGGCGTTT
64 TTTTGGTTAACTTTCTGCGGCGTTTAT-CGATAAGCGCCGTTAATATCGATATTTAGCGGCGTTT
* * * *
61106659 TTATGTTTGCGCCGCTAAAGCCACAATTGATGAACACCGAACGCTGCGTTTAGTTTTAACA-TCT
128 TTATGTTAGCGCCGCTAAA-CCACAATTGATCAACACCGAACGCTGCATTTAGTTTTAACAGAC-
** **** *
61106723 TTTGCGGCGCTATGGTGAAATCGCCGCTAATGAAGA
191 TCGGCGGCGCTATAACAAAAACGCCGCTAATGAAGA
* * * * *
61106759 TCTTTAGTGGCGTT-GTAACTAAAGCGCCGCTAAATGCCACTATACCTCGAGGCCAAACGATGCA
1 TCTTTAGTGGCGTTGGTTA--AAAGCGCCGCTAAATGCCACCATACATCAAGGCCAAACGATGCG
* ** * * *
61106823 TTTTGGTTAACTTTCTGTGGCGTTTAGTATATAAGCGCCGTTAATACCGATCTTTGGCGGCGTTT
64 TTTTGGTTAACTTTCTGCGGCGTTTA-TCGATAAGCGCCGTTAATATCGATATTTAGCGGCGTTT
* * *
61106888 CTA-GATTAGCGCCGCTAAACCAACAATTGATCAACACTGAACCCTG-ATTT
128 TTATG-TTAGCGCCGCTAAACC-ACAATTGATCAACACCGAACGCTGCATTT
61106938 TCCTTTAATA
Statistics
Matches: 348, Mismatches: 49, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
227 3 0.01
228 8 0.02
229 150 0.43
230 185 0.53
231 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (226 bp):
TCTTTAGTGGCGTTGGTTAAAAGCGCCGCTAAATGCCACCATACATCAAGGCCAAACGATGCGTT
TTGGTTAACTTTCTGCGGCGTTTATCGATAAGCGCCGTTAATATCGATATTTAGCGGCGTTTTTA
TGTTAGCGCCGCTAAACCACAATTGATCAACACCGAACGCTGCATTTAGTTTTAACAGACTCGGC
GGCGCTATAACAAAAACGCCGCTAATGAAGA
Found at i:61113234 original size:164 final size:164
Alignment explanation
Indices: 61112861--61113292 Score: 482
Period size: 164 Copynumber: 2.6 Consensus size: 164
61112851 TATCACATCC
* * * * * *
61112861 TTCTTCAGTTTCCCCTATCACGAATGGCAGCTT-TGACGTCGATTTCGCCTCCTTTTT-CTTCCC
1 TTCTTCAGGTTCCCCTATCACAAATGGCA-ATTGCGACGTCGATTCCGTCT-CTTTTTCCTTCCC
* * * * *
61112924 TACAATCCCACAACCAAAACCCCCCCAAGAAAACAGCCTTATATATGCTTGTCAAACCCTAAAAC
64 TACAATCCCATAACCAAAACCCCACCAAG-AAA-A--C--A-ATGT-C-AGTCAAACTCTAAAA-
* * * *
61112989 AAA---GT-AAAAAACGGTAACCGAGTTAAGAACTGAGTCACCTGT
119 AAATTTATAAAAAAACGATAACCGAGTTAAGAACGGACTCACCTGT
* * * *
61113031 TTCTTCAGGTTCCCCTCTCGCAAATGGCAGTTTCGACGTCGATTCCGTCTCTTCTTT-CTTCCCT
1 TTCTTCAGGTTCCCCTATCACAAATGGCAATTGCGACGTCGATTCCGTCTCTT-TTTCCTTCCCT
*
61113095 ATAATCCCATAACCAAAACCCCACCAAGAAAACAATGTCAGTCAAACTCTAAAAAAATTTATAAA
65 ACAATCCCATAACCAAAACCCCACCAAGAAAACAATGTCAGTCAAACTCTAAAAAAATTTATAAA
*
61113160 AAAACGATGACCGAGTTAAGAACGGACTCACCTGT
130 AAAACGATAACCGAGTTAAGAACGGACTCACCTGT
* **
61113195 TTCTTCAGGTTCCCCTATTACAAATGGCAATTGCGACGTCGATTTTGTCTCTTTTTCCTTCCCTA
1 TTCTTCAGGTTCCCCTATCACAAATGGCAATTGCGACGTCGATTCCGTCTCTTTTTCCTTCCCTA
61113260 CAATCCCATAACCAAAACCCCACCAAGAAAACA
66 CAATCCCATAACCAAAACCCCACCAAGAAAACA
61113293 GCATTATATA
Statistics
Matches: 228, Mismatches: 27, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
160 3 0.01
161 13 0.06
162 1 0.00
163 7 0.03
164 120 0.53
166 1 0.00
168 1 0.00
169 8 0.04
170 74 0.32
ACGTcount: A:0.31, C:0.30, G:0.12, T:0.27
Consensus pattern (164 bp):
TTCTTCAGGTTCCCCTATCACAAATGGCAATTGCGACGTCGATTCCGTCTCTTTTTCCTTCCCTA
CAATCCCATAACCAAAACCCCACCAAGAAAACAATGTCAGTCAAACTCTAAAAAAATTTATAAAA
AAACGATAACCGAGTTAAGAACGGACTCACCTGT
Found at i:61114530 original size:18 final size:20
Alignment explanation
Indices: 61114495--61114551 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 20
61114485 TATATTTTTC
61114495 TGAAAATA-TAT-ATAAAATA
1 TGAAAATATTATAAT-AAATA
*
61114514 T-AAAATGTT-TAATAAATA
1 TGAAAATATTATAATAAATA
*
61114532 TGCAAATATTATAATAAATA
1 TGAAAATATTATAATAAATA
61114552 CCAGTCATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 12 0.39
19 10 0.32
20 9 0.29
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (20 bp):
TGAAAATATTATAATAAATA
Found at i:61117171 original size:13 final size:13
Alignment explanation
Indices: 61117153--61117186 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
61117143 TTGACAATGT
61117153 TTTTGAAAAGTAC
1 TTTTGAAAAGTAC
*
61117166 TTTTGAGAAGTAC
1 TTTTGAAAAGTAC
61117179 TTTT-AAAA
1 TTTTGAAAA
61117187 ATTTTGAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 3 0.16
13 16 0.84
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (13 bp):
TTTTGAAAAGTAC
Found at i:61118065 original size:27 final size:26
Alignment explanation
Indices: 61118035--61118090 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
61118025 TATTTTTGCT
*
61118035 TTTAATAAT-TAATGAATTATTTTTAAA
1 TTTAATAATAT-ATGAAATA-TTTTAAA
*
61118062 TTTAATGATATATGAAATATTTTAAA
1 TTTAATAATATATGAAATATTTTAAA
61118088 TTT
1 TTT
61118091 TTAGATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 10 0.38
27 15 0.58
28 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (26 bp):
TTTAATAATATATGAAATATTTTAAA
Found at i:61122739 original size:47 final size:47
Alignment explanation
Indices: 61122683--61122964 Score: 231
Period size: 47 Copynumber: 5.7 Consensus size: 47
61122673 TTTATTTCAA
*
61122683 TGCATAACAAATATATATACATTCGGCCATAGTTTAATTCATTTCTC
1 TGCATAACAAATATATATACATTCGGCCATAGATTAATTCATTTCTC
* * * * **
61122730 TGCATAACAATTACATATACATTCAGCTATAGATTAATTCATTTCAA
1 TGCATAACAAATATATATACATTCGGCCATAGATTAATTCATTTCTC
* * *
61122777 TGTATAACAAATATATATATACATTCGGCCATAACCTATGTAATTTCAAATAATTTATTTC
1 TGCATAAC-AA-ATATATATACATTCGGCCAT-A--GAT-TAA-TTC-----A-TT-TCTC
* * *
61122838 AATGCATAACAAATATATATACGTTCGGCCATAGCTTAATTCATATCTC
1 --TGCATAACAAATATATATACATTCGGCCATAGATTAATTCATTTCTC
* * ** * **
61122887 TGCATAACAATTACATATACATTCAACTATAGATTAATTCATTTCAA
1 TGCATAACAAATATATATACATTCGGCCATAGATTAATTCATTTCTC
*
61122934 TGTATAACAAATATATATACATTCGGCCATA
1 TGCATAACAAATATATATACATTCGGCCATA
61122965 ACCTATGTAA
Statistics
Matches: 181, Mismatches: 38, Indels: 32
0.72 0.15 0.13
Matches are distributed among these distances:
47 109 0.60
48 2 0.01
49 19 0.10
50 2 0.01
51 1 0.01
52 2 0.01
53 3 0.02
54 3 0.02
56 3 0.02
57 3 0.02
58 1 0.01
59 1 0.01
60 3 0.02
61 20 0.11
62 2 0.01
63 7 0.04
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.36
Consensus pattern (47 bp):
TGCATAACAAATATATATACATTCGGCCATAGATTAATTCATTTCTC
Found at i:61122925 original size:157 final size:155
Alignment explanation
Indices: 61122634--61123019 Score: 666
Period size: 157 Copynumber: 2.5 Consensus size: 155
61122624 AACAATTCAC
* * *
61122634 TATAT-TACATTCGGCCATAGCTTATGTAACTTCAAATAATTTATTTCAATGCATAACAAATATA
1 TATATATACATTCGGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGCATAACAAATATA
* * *
61122698 TATACATTCGGCCATAGTTTAATTCATTTCTCTGCATAACAATTACATATACATTCAGCTATAGA
66 TATACATTCGGCCATAGCTTAATTCATATCTCTGCATAACAATTACATATACATTCAACTATAGA
61122763 TTAATTCATTTCAATGTATAACAAATA
131 TTAATTCATTTCAATGTATAAC-AA-A
61122790 TATATATACATTCGGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGCATAACAAATATA
1 TATATATACATTCGGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGCATAACAAATATA
*
61122855 TATACGTTCGGCCATAGCTTAATTCATATCTCTGCATAACAATTACATATACATTCAACTATAGA
66 TATACATTCGGCCATAGCTTAATTCATATCTCTGCATAACAATTACATATACATTCAACTATAGA
61122920 TTAATTCATTTCAATGTATAACAAA
131 TTAATTCATTTCAATGTATAACAAA
* *
61122945 TATATATACATTCGGCCATAACCTATGTAATTTCAAATAAATTATTTTAATGCATAACAAATATA
1 TATATATACATTCGGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGCATAACAAATATA
61123010 TATACATTCG
66 TATACATTCG
61123020 TAGTTAATTT
Statistics
Matches: 219, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
155 73 0.33
156 7 0.03
157 139 0.63
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (155 bp):
TATATATACATTCGGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGCATAACAAATATA
TATACATTCGGCCATAGCTTAATTCATATCTCTGCATAACAATTACATATACATTCAACTATAGA
TTAATTCATTTCAATGTATAACAAA
Found at i:61139960 original size:41 final size:43
Alignment explanation
Indices: 61139856--61139960 Score: 124
Period size: 43 Copynumber: 2.5 Consensus size: 43
61139846 GGAGCAACGT
* *
61139856 TAGCGGCGTTTTTCCCATAAATGCCGCAAAAGGTTAAATACGA
1 TAGCGGCGTTTTTCCCATAAACGCCGCAAAAGGTTAAATACAA
* ** * *
61139899 TAGCGGCATTTTTCTTATAAACGCCGCTAAAGG-TAAA-GCAA
1 TAGCGGCGTTTTTCCCATAAACGCCGCAAAAGGTTAAATACAA
*
61139940 TAGCGGCGTTTTGCCCATAAA
1 TAGCGGCGTTTTTCCCATAAA
61139961 TGCTATGAAT
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
41 19 0.37
42 4 0.08
43 28 0.55
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (43 bp):
TAGCGGCGTTTTTCCCATAAACGCCGCAAAAGGTTAAATACAA
Found at i:61146110 original size:20 final size:20
Alignment explanation
Indices: 61146087--61146124 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
61146077 ATTAAATATA
61146087 TTAAGTAAA-ACTATGTGACT
1 TTAA-TAAATACTATGTGACT
*
61146107 TTAATAAATATTATGTGA
1 TTAATAAATACTATGTGA
61146125 AAATAGTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.39
Consensus pattern (20 bp):
TTAATAAATACTATGTGACT
Found at i:61148571 original size:30 final size:31
Alignment explanation
Indices: 61148536--61148593 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
61148526 ATGGTCACCA
61148536 AACTATTC-AAAGTTTTCATTTAAGTCATTG
1 AACTATTCGAAAGTTTTCATTTAAGTCATTG
*
61148566 AACTATTCGAAAGTTTTTATTTAAGTCA
1 AACTATTCGAAAGTTTTCATTTAAGTCA
61148594 CTGGCTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.43
Consensus pattern (31 bp):
AACTATTCGAAAGTTTTCATTTAAGTCATTG
Found at i:61154829 original size:16 final size:16
Alignment explanation
Indices: 61154808--61154838 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61154798 GGGTTGGATG
*
61154808 AATAGAATAGGATTGA
1 AATAGAATAGAATTGA
61154824 AATAGAATAGAATTG
1 AATAGAATAGAATTG
61154839 TAATCTGTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.23, T:0.26
Consensus pattern (16 bp):
AATAGAATAGAATTGA
Found at i:61157987 original size:21 final size:19
Alignment explanation
Indices: 61157931--61157998 Score: 75
Period size: 19 Copynumber: 3.4 Consensus size: 19
61157921 TAATTATTTA
61157931 TTAAATT-TAATTAGAATAT
1 TTAAATTATAATTA-AATAT
* *
61157950 ATAAATTATATTTAAATAT
1 TTAAATTATAATTAAATAT
61157969 TTAAATATAATAATTAAATAT
1 TTAAAT-T-ATAATTAAATAT
61157990 TTATAATTA
1 TTA-AATTA
61157999 GATATTGACA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
19 16 0.39
20 7 0.17
21 15 0.37
22 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (19 bp):
TTAAATTATAATTAAATAT
Found at i:61168515 original size:23 final size:22
Alignment explanation
Indices: 61168477--61168525 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
61168467 AAAAACCTAT
61168477 AATATA-TAT-AAATTTATAAA
1 AATATATTATAAAATTTATAAA
*
61168497 AATATATTATAAAATTT-TATA
1 AATATATTATAAAATTTATAAA
61168518 AATATATT
1 AATATATT
61168526 TGTATAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 6 0.23
21 14 0.54
22 6 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATATATTATAAAATTTATAAA
Found at i:61168523 original size:37 final size:37
Alignment explanation
Indices: 61168443--61168540 Score: 94
Period size: 37 Copynumber: 2.6 Consensus size: 37
61168433 AAAATATATA
*
61168443 AAATATAAACTTATAAAAATAT-TTAAAAACCTATAAT
1 AAATATAAATTTATAAAAATATATTAAAAA-CTATAAT
* * *
61168480 ATATATAAATTTATAAAAATATATTATAAAA-TTTTAT
1 AAATATAAATTTATAAAAATATATTA-AAAACTATAAT
*
61168517 AAATAT-ATTTGTATAAAAAATATA
1 AAATATAAATT-TAT-AAAAATATA
61168541 AACATATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
36 3 0.06
37 32 0.63
38 12 0.24
39 4 0.08
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (37 bp):
AAATATAAATTTATAAAAATATATTAAAAACTATAAT
Found at i:61174440 original size:21 final size:20
Alignment explanation
Indices: 61174406--61174455 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
61174396 TTATATTGAG
*
61174406 ATTTTCAAAAATATATGAAA
1 ATTTTTAAAAATATATGAAA
*
61174426 ATTTTTAAAATATATATTAAA
1 ATTTTTAAAA-ATATATGAAA
*
61174447 ATATTTAAA
1 ATTTTTAAA
61174456 TTTTATTCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
ATTTTTAAAAATATATGAAA
Found at i:61175262 original size:16 final size:16
Alignment explanation
Indices: 61175241--61175272 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
61175231 ATCTCTCGTT
61175241 AGAAAAAAAAAAGAAA
1 AGAAAAAAAAAAGAAA
*
61175257 AGAAAAGAAAAAGAAA
1 AGAAAAAAAAAAGAAA
61175273 TGTGCAAAAC
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAAAAGAAA
Found at i:61177978 original size:15 final size:16
Alignment explanation
Indices: 61177960--61177993 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
61177950 ATAAAACTCT
61177960 TTAAAA-TTAAAAAAA
1 TTAAAATTTAAAAAAA
*
61177975 TTAAAATTTCAAAAAA
1 TTAAAATTTAAAAAAA
61177991 TTA
1 TTA
61177994 TAAAAAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
TTAAAATTTAAAAAAA
Found at i:61178450 original size:20 final size:20
Alignment explanation
Indices: 61178413--61178450 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
61178403 AAGAGGTATG
*
61178413 ATTAAATTATTATTTTTATT
1 ATTAAATTATTATATTTATT
61178433 ATTAAATATATTA-ATTTA
1 ATTAAAT-TATTATATTTA
61178451 ATCTGTACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTAAATTATTATATTTATT
Found at i:61184048 original size:266 final size:266
Alignment explanation
Indices: 61183574--61184105 Score: 1028
Period size: 266 Copynumber: 2.0 Consensus size: 266
61183564 CGTGATAAGA
61183574 GAAGGATGATAGTTTAATGGAGGACCACACAACCATTGCTCCGTGGCCCGAGAATTTAATGTGAC
1 GAAGGATGATAGTTTAATGGAGGACCACACAACCATTGCTCCGTGGCCCGAGAATTTAATGTGAC
*
61183639 AAGGATTATTTGAGAGCCGCTGAACTTTCTTAAAAGAGAAGCCAACGAGCACCATGAGGTTTAGT
66 AAGGATTATTCGAGAGCCGCTGAACTTTCTTAAAAGAGAAGCCAACGAGCACCATGAGGTTTAGT
*
61183704 GAGCAACGAGTCACGGCCCGGATTGAGTAAAAAGGAGATATAAGATACGTCCCTTTTGAAGAGTT
131 GAGCAACGAGTCACGGCCCGGATTGAGTAAAAAAGAGATATAAGATACGTCCCTTTTGAAGAGTT
* *
61183769 CGTGAGACTTATCTTAACGCTCGAATGAAGAAAATGATCGAATGTCTCCGCATATGAGGGCAAAG
196 CGTAAGACTTATCTTAACGCTCGAACGAAGAAAATGATCGAATGTCTCCGCATATGAGGGCAAAG
61183834 CCGTAT
261 CCGTAT
61183840 GAAGGATGATAGTTTAATGGAGGACCACACAACCATTGCTCCGTGGCCCGAGAATTTAATGTGAC
1 GAAGGATGATAGTTTAATGGAGGACCACACAACCATTGCTCCGTGGCCCGAGAATTTAATGTGAC
61183905 AAGGATTATTCGAGAGCCGCTGAACTTTCTTAAAAGAGAAGCCAACGAGCACCATGAGGTTTAGT
66 AAGGATTATTCGAGAGCCGCTGAACTTTCTTAAAAGAGAAGCCAACGAGCACCATGAGGTTTAGT
61183970 GAGCAACGAGTCACGGCCCGGATTGAGTAAAAAAGAGATATAAGATACGTCCCTTTTGAAGAGTT
131 GAGCAACGAGTCACGGCCCGGATTGAGTAAAAAAGAGATATAAGATACGTCCCTTTTGAAGAGTT
61184035 CGTAAGACTTATCTTAACGCTCGAACGAAGAAAATGATCGAATGTCTCCGCATATGAGGGCAAAG
196 CGTAAGACTTATCTTAACGCTCGAACGAAGAAAATGATCGAATGTCTCCGCATATGAGGGCAAAG
61184100 CCGTAT
261 CCGTAT
61184106 ATGTATCCGC
Statistics
Matches: 262, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
266 262 1.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (266 bp):
GAAGGATGATAGTTTAATGGAGGACCACACAACCATTGCTCCGTGGCCCGAGAATTTAATGTGAC
AAGGATTATTCGAGAGCCGCTGAACTTTCTTAAAAGAGAAGCCAACGAGCACCATGAGGTTTAGT
GAGCAACGAGTCACGGCCCGGATTGAGTAAAAAAGAGATATAAGATACGTCCCTTTTGAAGAGTT
CGTAAGACTTATCTTAACGCTCGAACGAAGAAAATGATCGAATGTCTCCGCATATGAGGGCAAAG
CCGTAT
Found at i:61189132 original size:44 final size:44
Alignment explanation
Indices: 61189065--61189990 Score: 827
Period size: 44 Copynumber: 21.2 Consensus size: 44
61189055 AAGTCATTAA
** * * *
61189065 AGCAGATCTTGTCTTTATGTATTGG-CGTGAAGTAGATCGAAGGT
1 AGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGAT
* * * * *
61189109 AGCAGATCCTATCTTCCTATATTGATAGGAAGTGGATCCAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAT
* * * *
61189153 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAA
1 AGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGAT
* * * *
61189197 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCG-AGAAT
1 AGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAG-AT
* * * *
61189241 AGCAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAT
* * * *
61189285 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAA
1 AGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGAT
* * *
61189329 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGAT
* * *
61189373 AGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAT
* * * *
61189417 -GCAGATCTTGTCTTCCCATAATGGT--G--GT-GA-AGTAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAT
* * * *
61189454 --CAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGGT
1 AGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGAT
*** *
61189496 AGCAGATCCCATCTTCCTATATTGGTAGGAAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAT
* * *
61189540 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGAT
** * * *
61189584 AGCAGATCTTGTCTTAATGTATTGG-CGTGAAGTAGATCAAATG-T
1 AGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAA-GAT
*** *
61189628 AGCAGATCCCATCTTCCTATATTGGTAGGAAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAT
* * *
61189672 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGAT
* * *
61189716 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAATG-T
1 AGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAA-GAT
* * *
61189760 AGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAT
* * * *
61189804 AGCTGATCTTGTCTTCCCATATTGGT-GGCAAAGTAGATCGCAGAA
1 AGCAGATCTTGTCTTCCTATATTGGTAGG--AAGTAGATCGAAGAT
* * * *
61189849 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGGT
1 AGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGAT
* * *
61189893 AGCAGATCCTATCTTCCTATATTGGTAGGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAT
* * * *
61189937 AGCTGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGAT
61189982 AGCAGATCT
1 AGCAGATCT
61189991 ATCTCCTTGT
Statistics
Matches: 700, Mismatches: 148, Indels: 67
0.77 0.16 0.07
Matches are distributed among these distances:
36 19 0.03
37 5 0.01
38 3 0.00
39 2 0.00
40 2 0.00
41 3 0.00
42 4 0.01
43 115 0.16
44 397 0.57
45 149 0.21
46 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (44 bp):
AGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAT
Found at i:61189300 original size:132 final size:132
Alignment explanation
Indices: 61189063--61189990 Score: 1552
Period size: 132 Copynumber: 7.1 Consensus size: 132
61189053 TGAAGTCATT
*
61189063 AAAGCAGATCTTGTCTTTATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTA
* * *
61189128 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
61189193 AG
131 AG
* * *
61189195 AAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCG-AGAATAGCAGGTCCTATCTTCCT
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG-GTAGCAGATCCTATCTTCCT
*
61189259 ATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCA
65 ATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
61189324 AAG
130 AAG
*
61189327 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTA
* *
61189392 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATAATGGTGGTGAAGTAGAT---
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
61189454 --
131 AG
*
61189454 ----CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCCATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTA
61189515 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
61189580 AG
131 AG
* * * *
61189582 AAAGCAGATCTTGTCTTAATGTATTGGCGTGAAGTAGATCAAATGTAGCAGATCCCATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTA
61189647 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
61189712 AG
131 AG
*
61189714 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAATGTAGCAGATCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTA
* *
61189779 TATTGGTAGGAAGTGGATCGAAGATAGCTGATCTTGTCTTCCCATATTGGTGGCAAAGTAGATCG
66 TATTGGTAGGAAGTGGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
*
61189844 CAG
130 AAG
61189847 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTA
* * *
61189912 TATTGGTAGGAAGTAGATCAAAGATAGCTGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
66 TATTGGTAGGAAGTGGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
61189977 AAG
130 AAG
61189980 AAAGCAGATCT
1 AAAGCAGATCT
61189991 ATCTCCTTGT
Statistics
Matches: 754, Mismatches: 30, Indels: 23
0.93 0.04 0.03
Matches are distributed among these distances:
123 119 0.16
131 2 0.00
132 453 0.60
133 180 0.24
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (132 bp):
AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTA
TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
AG
Found at i:61189781 original size:387 final size:389
Alignment explanation
Indices: 61189067--61189990 Score: 1552
Period size: 387 Copynumber: 2.4 Consensus size: 389
61189057 GTCATTAAAG
*
61189067 CAGATCTTGTCTTTATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTATATT
1 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTATATT
* * *
61189132 GATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAA
66 GGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
* * *
61189197 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAGAATAGCAGGTCCTATCTTCCTATA
131 AGCAGATCTTGTCTTAATGTATTGGCATGAAGTAGATCGAGAATAGCAGATCCCATCTTCCTATA
61189262 TTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAG
196 TTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAG
61189327 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTA
261 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTA
**
61189392 TATTGGTAGGAAGTGGATCGAAGAT-GCAGATCTTGTCTTCCCATAATGGTGGTGAAGTAGAT-
326 TATTGGTAGGAAGTGGATCGAAGATAGCAGATCTTGTCTTCCCATAATGGTGGCAAAGTAGATA
*
61189454 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCCATCTTCCTATATT
1 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTATATT
*
61189519 GGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
66 GGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
*
61189584 AGCAGATCTTGTCTTAATGTATTGGCGTGAAGTAGATC-A-AATGTAGCAGATCCCATCTTCCTA
131 AGCAGATCTTGTCTTAATGTATTGGCATGAAGTAGATCGAGAA--TAGCAGATCCCATCTTCCTA
*
61189647 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
194 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAA
61189712 AGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAATG-TAGCAGATCCTATCTTC
259 AGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAA-GATAGCAGATCCTATCTTC
* *
61189776 CTATATTGGTAGGAAGTGGATCGAAGATAGCTGATCTTGTCTTCCCATATTGGTGGCAAAGTAGA
323 CTATATTGGTAGGAAGTGGATCGAAGATAGCAGATCTTGTCTTCCCATAATGGTGGCAAAGTAGA
61189841 TCGCAGAAA
388 T-------A
61189850 GCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTATAT
1 -CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTATAT
* *
61189915 TGGTAGGAAGTAGATCAAAGATAGCTGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAG
65 TGGTAGGAAGTGGATCAAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAG
61189980 AAAGCAGATCT
129 AAAGCAGATCT
61189991 ATCTCCTTGT
Statistics
Matches: 505, Mismatches: 18, Indels: 17
0.94 0.03 0.03
Matches are distributed among these distances:
385 2 0.00
386 1 0.00
387 333 0.66
388 34 0.07
397 83 0.16
398 52 0.10
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (389 bp):
CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTATATT
GGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
AGCAGATCTTGTCTTAATGTATTGGCATGAAGTAGATCGAGAATAGCAGATCCCATCTTCCTATA
TTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAG
AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTA
TATTGGTAGGAAGTGGATCGAAGATAGCAGATCTTGTCTTCCCATAATGGTGGCAAAGTAGATA
Found at i:61190315 original size:50 final size:50
Alignment explanation
Indices: 61190148--61190420 Score: 187
Period size: 50 Copynumber: 5.5 Consensus size: 50
61190138 GCAGTGGAAT
* * ** * *
61190148 AGATTGAAGCTACAACGGCAAATCTTG-TTCCCCGACATTGCAATTAAAG
1 AGATTGAAGCCACAACGGCGAATCTTGCTTCCTTGACATTGCAATTTAAC
** * * * * ** **
61190197 AGATTGAAGCCACAACGGCGAATCTCACTT-CTCTGGCAGTACAGTGCAGT
1 AGATTGAAGCCACAACGGCGAATCTTGCTTCCT-TGACATTGCAATTTAAC
* * * * *
61190247 AGATTAAAGCTACGACGGCGAATCTTGCTTCCTTGATATTGCAATTTAAA
1 AGATTGAAGCCACAACGGCGAATCTTGCTTCCTTGACATTGCAATTTAAC
* * * * * * ** *
61190297 AGATTGAAGCCGCAACGGCGAATTTTACTTTCTTGGCGA-TGCAGTGGATC
1 AGATTGAAGCCACAACGGCGAATCTTGCTTCCTTGAC-ATTGCAATTTAAC
* **
61190347 AGATTGAAGCTACAACGGCGAATCTTG-TTCCCCGACATTGCAA-TTAATC
1 AGATTGAAGCCACAACGGCGAATCTTGCTTCCTTGACATTGCAATTTAA-C
61190396 AGATTGAAGCCACAACGGCGAATCT
1 AGATTGAAGCCACAACGGCGAATCT
61190421 CACTTCTCTA
Statistics
Matches: 163, Mismatches: 55, Indels: 12
0.71 0.24 0.05
Matches are distributed among these distances:
48 2 0.01
49 58 0.36
50 100 0.61
51 3 0.02
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGCGAATCTTGCTTCCTTGACATTGCAATTTAAC
Found at i:61190318 original size:100 final size:97
Alignment explanation
Indices: 61190146--61190438 Score: 376
Period size: 100 Copynumber: 3.0 Consensus size: 97
61190136 CAGCAGTGGA
*
61190146 ATAGATTGAAGCTACAACGGCAAATCTTGTTCCCCGACATTGCAATTAAAGAGATTGAAGCCACA
1 ATAGATTGAAGCTACAACGGCGAATCTTGTTCCCCGACATTGCAATTAAA-AGATTGAAGCCACA
61190211 ACGGCGAATCTCACTTCTCTGGCAGTACAGTGC
65 ACGGCGAATCTCACTTCTCTGGCAGTACAGTGC
* * ** * *
61190244 AGTAGATTAAAGCTACGACGGCGAATCTTGCTTCCTTGATATTGCAATTTAAAAGATTGAAGCCG
1 A-TAGATTGAAGCTACAACGGCGAATCTTG-TTCCCCGACATTGCAA-TTAAAAGATTGAAGCCA
* * * *
61190309 CAACGGCGAATTTTACTT-TCTTGGC-GATGCAGTGG
63 CAACGGCGAATCTCACTTCTC-TGGCAG-TACAGTGC
*
61190344 ATCAGATTGAAGCTACAACGGCGAATCTTGTTCCCCGACATTGCAATTAATCAGATTGAAGCCAC
1 AT-AGATTGAAGCTACAACGGCGAATCTTGTTCCCCGACATTGCAATTAA-AAGATTGAAGCCAC
*
61190409 AACGGCGAATCTCACTTCTCTAGCAG-ACAG
64 AACGGCGAATCTCACTTCTCTGGCAGTACAG
61190439 AAACCAGATC
Statistics
Matches: 164, Mismatches: 22, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
98 8 0.05
99 72 0.44
100 79 0.48
101 5 0.03
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (97 bp):
ATAGATTGAAGCTACAACGGCGAATCTTGTTCCCCGACATTGCAATTAAAAGATTGAAGCCACAA
CGGCGAATCTCACTTCTCTGGCAGTACAGTGC
Found at i:61190492 original size:40 final size:40
Alignment explanation
Indices: 61190447--61190762 Score: 361
Period size: 40 Copynumber: 7.8 Consensus size: 40
61190437 AGAAACCAGA
61190447 TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAG
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAG
* *
61190487 TCTTATCTCCCTAAGCAATAGTGGAGCAGA-CAGAACCACAG
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGATC-GCATCA-AG
* * * *
61190528 ATTTTATCTCCCAAAGCAGTAGTGGAGCAGATCGCATCAAA
1 -TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAG
* * *
61190569 TCTTACCTCCCTAAGCAATAGTGGAGCAGA-CAGAACCACAG
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGATC-GCATCA-AG
*
61190610 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
1 -TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAG
* *
61190651 TCTTATCTCCCTAAGCAATAGTGGAGCAGA-CAGAACCACAG
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGATC-GCATCA-AG
* * * *
61190692 ATCTTAT-TCCCCTAAGCAGTAGTGGAGTAGATCACATCCAG
1 -TCTTATCT-CCCTAAGCAATAGTGGAGCAGATCGCATCAAG
*
61190733 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGA
61190763 CTAAAAACAC
Statistics
Matches: 233, Mismatches: 29, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
39 3 0.01
40 124 0.53
41 12 0.05
42 91 0.39
43 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (40 bp):
TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAG
Found at i:61190785 original size:82 final size:82
Alignment explanation
Indices: 61190430--61190763 Score: 555
Period size: 82 Copynumber: 4.1 Consensus size: 82
61190420 TCACTTCTCT
* *
61190430 AGCAGACAGAAAC-CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATC
1 AGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATC
61190494 TCCCTAAGCAATAGTGG
66 TCCCTAAGCAATAGTGG
* * * *
61190511 AGCAGACAGAACCACAGATTTTATCTCCCAAAGCAGTAGTGGAGCAGATCGCATCAAATCTTACC
1 AGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATC
61190576 TCCCTAAGCAATAGTGG
66 TCCCTAAGCAATAGTGG
61190593 AGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATC
1 AGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATC
61190658 TCCCTAAGCAATAGTGG
66 TCCCTAAGCAATAGTGG
* * *
61190675 AGCAGACAGAACCACAGATCTTAT-TCCCCTAAGCAGTAGTGGAGTAGATCACATCCAGTCTTAT
1 AGCAGACAGAACCACAGATCTTATCT-CCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTAT
*
61190739 CTCCCTAAGCAGTAGTGG
65 CTCCCTAAGCAATAGTGG
61190757 AGCAGAC
1 AGCAGAC
61190764 TAAAAACACA
Statistics
Matches: 237, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
81 13 0.05
82 224 0.95
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (82 bp):
AGCAGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATC
TCCCTAAGCAATAGTGG
Found at i:61198770 original size:22 final size:24
Alignment explanation
Indices: 61198744--61198787 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
61198734 GAAAAATATT
61198744 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
61198766 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
61198788 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:61198917 original size:59 final size:59
Alignment explanation
Indices: 61198854--61199023 Score: 322
Period size: 59 Copynumber: 2.9 Consensus size: 59
61198844 TCAAGTTTGT
*
61198854 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
61198913 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
*
61198972 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATT
61199024 AATAATTTGA
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 109 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:61199055 original size:16 final size:16
Alignment explanation
Indices: 61199034--61199075 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
61199024 AATAATTTGA
*
61199034 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
61199050 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
61199066 TAGTTTTAAT
1 TAATTTTAAT
61199076 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:61199133 original size:15 final size:16
Alignment explanation
Indices: 61199113--61199142 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
61199103 AATTAAAAAC
61199113 GGGCCGGGC-CGGGCT
1 GGGCCGGGCTCGGGCT
61199128 GGGCCGGGCTCGGGC
1 GGGCCGGGCTCGGGC
61199143 CCCATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.00, C:0.33, G:0.60, T:0.07
Consensus pattern (16 bp):
GGGCCGGGCTCGGGCT
Found at i:61200203 original size:16 final size:15
Alignment explanation
Indices: 61200184--61200218 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
61200174 TTTTTGGTTC
61200184 AAATAAGTTTTTTGTA
1 AAATAA-TTTTTTGTA
*
61200200 AAATTATTTTTTGTA
1 AAATAATTTTTTGTA
61200215 AAAT
1 AAAT
61200219 TATTCCAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (15 bp):
AAATAATTTTTTGTA
Found at i:61200211 original size:15 final size:15
Alignment explanation
Indices: 61200191--61200222 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
61200181 TTCAAATAAG
61200191 TTTTTTGTAAAATTA
1 TTTTTTGTAAAATTA
61200206 TTTTTTGTAAAATTA
1 TTTTTTGTAAAATTA
61200221 TT
1 TT
61200223 CCAACTAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (15 bp):
TTTTTTGTAAAATTA
Found at i:61201861 original size:106 final size:106
Alignment explanation
Indices: 61201676--61201871 Score: 268
Period size: 106 Copynumber: 1.8 Consensus size: 106
61201666 TGACTTAAGT
* * * * *
61201676 TGGATTTTAGTAATTGATAATGGGTTAATCAAATGGGGTTATTGTTGATGGTTAAACCATGTAGG
1 TGGATTTTAGTAATTGATAATGGATTAATCAAATGGGGTTATTGTTGATGGCTAAACAATGAAGA
* *
61201741 AATTTGGTGGGTTTATAGCTTAAAAAATTGGTGGTTTCAGC
66 AATTTGATGGGTTTACAGCTTAAAAAATTGGTGGTTTCAGC
* * * * *
61201782 TGGATTTTAGTAATTGCTAGTGGATTTATGAAATGGGGTTATTGTTGATTGCTAAACAATTGAAG
1 TGGATTTTAGTAATTGATAATGGATTAATCAAATGGGGTTATTGTTGATGGCTAAACAA-TGAAG
61201847 AAATTT-ATGGGTTTACAGCTTAAAA
65 AAATTTGATGGGTTTACAGCTTAAAA
61201872 TTGGCGGATT
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
106 68 0.88
107 9 0.12
ACGTcount: A:0.30, C:0.06, G:0.26, T:0.39
Consensus pattern (106 bp):
TGGATTTTAGTAATTGATAATGGATTAATCAAATGGGGTTATTGTTGATGGCTAAACAATGAAGA
AATTTGATGGGTTTACAGCTTAAAAAATTGGTGGTTTCAGC
Found at i:61202734 original size:29 final size:30
Alignment explanation
Indices: 61202687--61202743 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
61202677 GTTAGCTATT
61202687 TTAAAATTTAGAACTTAGG-TAAGTAATCC
1 TTAAAATTTAGAACTTAGGTTAAGTAATCC
*
61202716 TTAAAATTTAGGA-TCTAGGTTAAGTAAT
1 TTAAAATTTAGAACT-TAGGTTAAGTAAT
61202744 GTTGGTCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 1 0.04
29 16 0.64
30 8 0.32
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (30 bp):
TTAAAATTTAGAACTTAGGTTAAGTAATCC
Found at i:61204282 original size:24 final size:22
Alignment explanation
Indices: 61204247--61204506 Score: 122
Period size: 24 Copynumber: 11.3 Consensus size: 22
61204237 GCATATACAT
*
61204247 ACCAAATTTAACAGCACTTTTAC
1 ACCAAATTTAACAGCA-TTATAC
*
61204270 ACCAAAATTTAACAACATATATAC
1 ACC-AAATTTAACAGCAT-TATAC
* *
61204294 AGCAAA--TAGGCAGCA-TATAC
1 ACCAAATTTA-ACAGCATTATAC
*
61204314 ATACCAAATTTAACAGCATTTTTAC
1 --ACCAAATTTAACAGCA-TTATAC
61204339 ACCAAAATTTAACAGCATATATAC
1 ACC-AAATTTAACAGCAT-TATAC
* ***
61204363 AACAAA-TGGGCAGCA-TATAC
1 ACCAAATTTAACAGCATTATAC
* * *
61204383 ATACCAAA-TGAGCAGCATTTTTAC
1 --ACCAAATTTAACAGCA-TTATAC
*
61204407 ACCAAAATTTATCAGCATATATAC
1 ACC-AAATTTAACAGCAT-TATAC
* ***
61204431 AACAAA-TGGGCAGCA-TATAC
1 ACCAAATTTAACAGCATTATAC
*
61204451 GTACCAAATTTAACAGCACTTTTAC
1 --ACCAAATTTAACAGCA-TTATAC
61204476 ACCAAAATTTAACAGCATATATAC
1 ACC-AAATTTAACAGCAT-TATAC
*
61204500 AGCAAAT
1 ACCAAAT
61204507 AGGCTTAAAT
Statistics
Matches: 182, Mismatches: 30, Indels: 50
0.69 0.11 0.19
Matches are distributed among these distances:
20 15 0.08
21 2 0.01
22 42 0.23
23 40 0.22
24 75 0.41
25 8 0.04
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.25
Consensus pattern (22 bp):
ACCAAATTTAACAGCATTATAC
Found at i:61204300 original size:69 final size:69
Alignment explanation
Indices: 61204218--61204506 Score: 481
Period size: 69 Copynumber: 4.2 Consensus size: 69
61204208 GGATAGCTCT
61204218 TATATACAACAAATGGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
1 TATATACAACAAATGGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
*
61204283 AACA
66 AGCA
* * *
61204287 TATATACAGCAAATAGGCAGCATATACATACCAAATTTAACAGCATTTTTACACCAAAATTTAAC
1 TATATACAACAAATGGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
61204352 AGCA
66 AGCA
* * * *
61204356 TATATACAACAAATGGGCAGCATATACATACCAAA-TGAGCAGCATTTTTACACCAAAATTTATC
1 TATATACAACAAATGGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
61204420 AGCA
66 AGCA
*
61204424 TATATACAACAAATGGGCAGCATATACGTACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
1 TATATACAACAAATGGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
61204489 AGCA
66 AGCA
*
61204493 TATATACAGCAAAT
1 TATATACAACAAAT
61204507 AGGCTTAAAT
Statistics
Matches: 204, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
68 64 0.31
69 140 0.69
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.25
Consensus pattern (69 bp):
TATATACAACAAATGGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
AGCA
Found at i:61204379 original size:22 final size:22
Alignment explanation
Indices: 61204351--61204449 Score: 90
Period size: 22 Copynumber: 4.4 Consensus size: 22
61204341 CAAAATTTAA
*
61204351 CAGCATATATACAACAAATGGG
1 CAGCATATATACAACAAATGAG
* * *
61204373 CAGCATATACATACCAAATGAG
1 CAGCATATATACAACAAATGAG
* * * * *
61204395 CAGCATTTTTACACCAAAATTTAT
1 CAGCATATATACAAC-AAA-TGAG
*
61204419 CAGCATATATACAACAAATGGG
1 CAGCATATATACAACAAATGAG
61204441 CAGCATATA
1 CAGCATATA
61204450 CGTACCAAAT
Statistics
Matches: 59, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
22 39 0.66
23 6 0.10
24 14 0.24
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.23
Consensus pattern (22 bp):
CAGCATATATACAACAAATGAG
Found at i:61204465 original size:137 final size:138
Alignment explanation
Indices: 61204218--61204506 Score: 481
Period size: 137 Copynumber: 2.1 Consensus size: 138
61204208 GGATAGCTCT
*
61204218 TATATACAACAAATGGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
1 TATATACAACAAATGGGCAGCATATACATACCAAATTGAACAGCACTTTTACACCAAAATTTAAC
* *
61204283 AACATATATACAGCAAATAGGCAGCATATACATACCAAATTTAACAGCATTTTTACACCAAAATT
66 AACATATATACAACAAATAGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATT
61204348 TAACAGCA
131 TAACAGCA
* * *
61204356 TATATACAACAAATGGGCAGCATATACATACCAAA-TGAGCAGCATTTTTACACCAAAATTTATC
1 TATATACAACAAATGGGCAGCATATACATACCAAATTGAACAGCACTTTTACACCAAAATTTAAC
* * *
61204420 AGCATATATACAACAAATGGGCAGCATATACGTACCAAATTTAACAGCACTTTTACACCAAAATT
66 AACATATATACAACAAATAGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATT
61204485 TAACAGCA
131 TAACAGCA
*
61204493 TATATACAGCAAAT
1 TATATACAACAAAT
61204507 AGGCTTAAAT
Statistics
Matches: 141, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
137 106 0.75
138 35 0.25
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.25
Consensus pattern (138 bp):
TATATACAACAAATGGGCAGCATATACATACCAAATTGAACAGCACTTTTACACCAAAATTTAAC
AACATATATACAACAAATAGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATT
TAACAGCA
Found at i:61205325 original size:41 final size:41
Alignment explanation
Indices: 61205275--61205427 Score: 198
Period size: 41 Copynumber: 3.7 Consensus size: 41
61205265 ATAAAACATT
* * * * * * *
61205275 GGCATAAAGCCTGCTAGGCACAGAGCCCGAGACATTTCACC
1 GGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
* *
61205316 GGCACAAAGCCTGCTAGACATAAAGTCTGATATAATTCACC
1 GGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
* *
61205357 GGCACAGAGCCTGCTAGGCATAAAGCCTAATATAATTCACC
1 GGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
*
61205398 GGCATAAAGCCTGCTAGGCATAAAGCCTGA
1 GGCACAAAGCCTGCTAGGCATAAAGCCTGA
61205428 ACTTACAAAA
Statistics
Matches: 96, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 96 1.00
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (41 bp):
GGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
Found at i:61207950 original size:27 final size:27
Alignment explanation
Indices: 61207917--61207989 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 27
61207907 TATGTCGAAT
61207917 TTGTTAGATATTGATTATGTTTTAAGC
1 TTGTTAGATATTGATTATGTTTTAAGC
*
61207944 TTGTTAGATATTGAATTTATTATGTTTTAATC
1 TTGTTAGATATTG-----ATTATGTTTTAAGC
*
61207976 TTGTTGGATATTGA
1 TTGTTAGATATTGA
61207990 AATGATTGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
27 14 0.36
32 25 0.64
ACGTcount: A:0.26, C:0.03, G:0.18, T:0.53
Consensus pattern (27 bp):
TTGTTAGATATTGATTATGTTTTAAGC
Found at i:61207969 original size:32 final size:32
Alignment explanation
Indices: 61207930--61207990 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
61207920 TTAGATATTG
61207930 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
* *
61207962 ATTATGTTTTAATCTTGTTGGATATTGAA
1 ATTATGTTTTAAGCTTGTTAGATATTGAA
61207991 ATGATTGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.03, G:0.16, T:0.52
Consensus pattern (32 bp):
ATTATGTTTTAAGCTTGTTAGATATTGAATTT
Found at i:61209251 original size:20 final size:20
Alignment explanation
Indices: 61209222--61209259 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
61209212 AAAATTTAAA
*
61209222 ATATATATTTATTAATATGT
1 ATATAAATTTATTAATATGT
61209242 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
61209260 ATGTAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
ATATAAATTTATTAATATGT
Found at i:61209387 original size:20 final size:19
Alignment explanation
Indices: 61209342--61209379 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
61209332 CATCCAAACA
61209342 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
61209361 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
61209380 TCTAGAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (19 bp):
CCAGAAAAGTAAATCATTT
Found at i:61210845 original size:19 final size:18
Alignment explanation
Indices: 61210821--61210866 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
61210811 GACTGAATAT
61210821 ATCAATTATTGAGATGTTA
1 ATCAATTATTGAGAT-TTA
* **
61210840 ATCAATCATTGTTATTTA
1 ATCAATTATTGAGATTTA
61210858 ATCAATTAT
1 ATCAATTAT
61210867 CTTTTAACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (18 bp):
ATCAATTATTGAGATTTA
Found at i:61212943 original size:11 final size:12
Alignment explanation
Indices: 61212927--61212963 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
61212917 TTGAAAGATG
61212927 AATTAAAAATA-
1 AATTAAAAATAT
61212938 AATTAAAAATATT
1 AATTAAAAATA-T
61212951 AATTAAAAA-AT
1 AATTAAAAATAT
61212962 AA
1 AA
61212964 CATGGAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 14 0.58
12 1 0.04
13 9 0.38
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AATTAAAAATAT
Found at i:61213153 original size:133 final size:135
Alignment explanation
Indices: 61213011--61213259 Score: 333
Period size: 133 Copynumber: 1.8 Consensus size: 135
61213001 AATGGAACCT
* * * *
61213011 GAGATTTAAGGATGTAATCGTAATTATTTAACCATCTAACAAAAAGAGCTAATATGTT-AAAAAT
1 GAGATTTAAGGATGTAATCGTAACTATCTAACCATCTAAC-AAAAGAACCAATATGTTAAAAAAT
* *
61213075 -ATT-AATTAAAAAAACTTGAAGTAACACGAAATAAAAAATATAAATGTGAATATGAAGTGAATC
65 AATTAAATTAAAAAAACTTGAAGCAACACGAAATAAAAAATAAAAATGTGAATATGAAGTGAATC
61213138 AAACTC
130 AAACTC
* * * *
61213144 GAGATTTAAGGATGTAATTGTAACTATCTAACCATTTAACAAAGGAACCAGTATGTTAAAAAATA
1 GAGATTTAAGGATGTAATCGTAACTATCTAACCATCTAACAAAAGAACCAATATGTTAAAAAATA
* * *
61213209 ATTAAAAATTTAAAAAGCTTGAAGCAACATGAAATAAAAAATAAAAATGTG
66 ATT--AAATTAAAAAAACTTGAAGCAACACGAAATAAAAAATAAAAATGTG
61213260 TGTAGGAGAA
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
132 13 0.13
133 42 0.43
134 3 0.03
137 40 0.41
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.27
Consensus pattern (135 bp):
GAGATTTAAGGATGTAATCGTAACTATCTAACCATCTAACAAAAGAACCAATATGTTAAAAAATA
ATTAAATTAAAAAAACTTGAAGCAACACGAAATAAAAAATAAAAATGTGAATATGAAGTGAATCA
AACTC
Found at i:61215704 original size:12 final size:12
Alignment explanation
Indices: 61215687--61215736 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
61215677 CCGATCTTCC
*
61215687 TCTCCGACTGCA
1 TCTCCGACTCCA
*
61215699 TCTCCGTCTCCA
1 TCTCCGACTCCA
61215711 TCTCC-ATCTCCA
1 TCTCCGA-CTCCA
61215723 TCTCC-ATCTCCA
1 TCTCCGA-CTCCA
61215735 TC
1 TC
61215737 AATCCCAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.14, C:0.48, G:0.06, T:0.32
Consensus pattern (12 bp):
TCTCCGACTCCA
Found at i:61215714 original size:6 final size:6
Alignment explanation
Indices: 61215697--61215736 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
61215687 TCTCCGACTG
*
61215697 CATCTC CGTCTC CATCTC CATCTC CATCTC CATCTC CATC
1 CATCTC CATCTC CATCTC CATCTC CATCTC CATCTC CATC
61215737 AATCCCAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.15, C:0.50, G:0.03, T:0.33
Consensus pattern (6 bp):
CATCTC
Found at i:61217430 original size:4 final size:4
Alignment explanation
Indices: 61217421--61217467 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
61217411 TATGTTGTAT
* *
61217421 ATAC ATAC ATAC ACAC ACT-G ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC A-TAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
61217468 TATATACACT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
3 1 0.03
4 36 0.97
ACGTcount: A:0.49, C:0.26, G:0.02, T:0.23
Consensus pattern (4 bp):
ATAC
Found at i:61219491 original size:45 final size:44
Alignment explanation
Indices: 61219425--61219578 Score: 150
Period size: 45 Copynumber: 3.5 Consensus size: 44
61219415 GATAAGATAA
* * *
61219425 CCAACACCAATACATAGTACCTCCTATATTTATATGGCATGAAAG
1 CCAACACCAATACATAATACCT-CTGTATGTATATGGCATGAAAG
** *
61219470 CCAACACCGGTACATAATACCTACTGTATGTATATGACATGAAAG
1 CCAACACCAATACATAATACCT-CTGTATGTATATGGCATGAAAG
*** * *
61219515 TTGACACCGATACATAATA-CT-TGTATGTATATGGCATGATAG
1 CCAACACCAATACATAATACCTCTGTATGTATATGGCATGAAAG
* * *
61219557 CCAACACTAGTACATAGTACCT
1 CCAACACCAATACATAATACCT
61219579 ATTATATATA
Statistics
Matches: 88, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
42 31 0.35
43 2 0.02
44 2 0.02
45 53 0.60
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.27
Consensus pattern (44 bp):
CCAACACCAATACATAATACCTCTGTATGTATATGGCATGAAAG
Found at i:61220630 original size:14 final size:15
Alignment explanation
Indices: 61220611--61220644 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
61220601 ATCCTTAATC
*
61220611 TTTTTTTCTTTC-TT
1 TTTTTTTCATTCATT
61220625 TTTTTTTCATTCATT
1 TTTTTTTCATTCATT
61220640 TTTTT
1 TTTTT
61220645 CTATTCTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTTCATTCATT
Found at i:61220650 original size:14 final size:13
Alignment explanation
Indices: 61220609--61220651 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
61220599 TCATCCTTAA
61220609 TCTTTTTTTCT-T
1 TCTTTTTTTCTAT
*
61220621 TCTTTTTTTTTCAT
1 TCTTTTTTTCT-AT
61220635 TCATTTTTTTCTAT
1 TC-TTTTTTTCTAT
61220649 TCT
1 TCT
61220652 CTTTCTCGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 10 0.38
13 1 0.04
14 7 0.27
15 8 0.31
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (13 bp):
TCTTTTTTTCTAT
Found at i:61229408 original size:27 final size:28
Alignment explanation
Indices: 61229356--61229430 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 28
61229346 AAAAATTAAA
61229356 AAATATTAAAAGAATATATAAATGAT-T
1 AAATATTAAAAGAATATATAAATGATAT
*
61229383 AAATATTAAAA-ACTATGA-AAATTGATAT
1 AAATATTAAAAGAATAT-ATAAA-TGATAT
*
61229411 AAATATT-ATA-AATATATAAA
1 AAATATTAAAAGAATATATAAA
61229431 ATAATCTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
26 8 0.20
27 25 0.61
28 8 0.20
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.33
Consensus pattern (28 bp):
AAATATTAAAAGAATATATAAATGATAT
Found at i:61229510 original size:9 final size:9
Alignment explanation
Indices: 61229389--61229550 Score: 67
Period size: 9 Copynumber: 16.7 Consensus size: 9
61229379 GATTAAATAT
*
61229389 TAAAAACTA
1 TAAAAATTA
*
61229398 TGAAAATTGA
1 TAAAAATT-A
61229408 TATAAATATTA
1 TA-AAA-ATTA
*
61229419 TAAATA-TA
1 TAAAAATTA
* *
61229427 TAAAATAATC
1 TAAAA-ATTA
61229437 TAATAAATTA
1 TAA-AAATTA
61229447 T-AAAATTAA
1 TAAAAATT-A
*
61229456 TAAAACATATT
1 TAAAA-AT-TA
*
61229467 TAAAATTTTA
1 TAAAA-ATTA
**
61229477 TAACAACGTA
1 TAA-AAATTA
*
61229487 TTAAAATTCTA
1 -TAAAAAT-TA
61229498 TAAAAATTA
1 TAAAAATTA
*
61229507 TAAAAAGTA
1 TAAAAATTA
*
61229516 TTAAAATTAA
1 TAAAAATT-A
*
61229526 TATAAACTTA
1 TA-AAAATTA
61229536 TAAAAATTA
1 TAAAAATTA
61229545 TAAAAA
1 TAAAAA
61229551 CTTGAATTGG
Statistics
Matches: 115, Mismatches: 23, Indels: 30
0.68 0.14 0.18
Matches are distributed among these distances:
8 11 0.10
9 39 0.34
10 33 0.29
11 28 0.24
12 4 0.03
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (9 bp):
TAAAAATTA
Found at i:61229523 original size:29 final size:29
Alignment explanation
Indices: 61229389--61229550 Score: 84
Period size: 29 Copynumber: 5.5 Consensus size: 29
61229379 GATTAAATAT
* * *
61229389 TAAAAACTATGAAAATTGATATAAATATTA
1 TAAAAAGTATTAAAATTAATATAAA-ATTA
* *
61229419 TAAATA-TA-TAAAA-TAATCTAATAAATTA
1 TAAAAAGTATTAAAATTAATAT-A-AAATTA
* * * *
61229447 T-AAAATTAATAAAA-CATATTTAAAATTTTA
1 TAAAAAGTATTAAAATTA-ATATAAAA--TTA
* *
61229477 TAACAACGTATTAAAATT-CTATAAAAATTA
1 TAA-AAAGTATTAAAATTAATAT-AAAATTA
*
61229507 TAAAAAGTATTAAAATTAATATAAACTTA
1 TAAAAAGTATTAAAATTAATATAAAATTA
* *
61229536 TAAAAATTATAAAAA
1 TAAAAAGTATTAAAA
61229551 CTTGAATTGG
Statistics
Matches: 102, Mismatches: 18, Indels: 25
0.70 0.12 0.17
Matches are distributed among these distances:
27 7 0.07
28 15 0.15
29 43 0.42
30 21 0.21
31 3 0.03
32 13 0.13
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (29 bp):
TAAAAAGTATTAAAATTAATATAAAATTA
Found at i:61229551 original size:19 final size:19
Alignment explanation
Indices: 61229496--61229553 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
61229486 ATTAAAATTC
*
61229496 TATAAAAATTATAAAAA-G
1 TATAAAAATTATAAAAACT
* *
61229514 TATTAAAATTAATATAAACT
1 TATAAAAATT-ATAAAAACT
61229534 TATAAAAATTATAAAAACT
1 TATAAAAATTATAAAAACT
61229553 T
1 T
61229554 GAATTGGACC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
18 9 0.27
19 15 0.45
20 9 0.27
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (19 bp):
TATAAAAATTATAAAAACT
Found at i:61238952 original size:46 final size:46
Alignment explanation
Indices: 61238899--61238991 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
61238889 TACATAGGCT
* *
61238899 CTTCCACTCGTACCAATGTATCCCTTTCCCTATTTTGGAGTTTCTC
1 CTTCCACTCGCACCAATGTATCCCTTTCCCCATTTTGGAGTTTCTC
* *
61238945 CTTCCACTCGCACCAATGTATTCCTTTCCCCGTTTTGGAGTTTCTC
1 CTTCCACTCGCACCAATGTATCCCTTTCCCCATTTTGGAGTTTCTC
61238991 C
1 C
61238992 ACAAAAACTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.14, C:0.34, G:0.12, T:0.40
Consensus pattern (46 bp):
CTTCCACTCGCACCAATGTATCCCTTTCCCCATTTTGGAGTTTCTC
Found at i:61242600 original size:17 final size:19
Alignment explanation
Indices: 61242566--61242612 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
61242556 TATGCATGGT
*
61242566 AAATAATAAAAGTCAACAA
1 AAATAATAAAAGTAAACAA
61242585 AAATAA-AAAA-TAAACAA
1 AAATAATAAAAGTAAACAA
*
61242602 ACAAGAATAAA
1 A-AATAATAAA
61242613 GACATTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 7 0.29
18 8 0.33
19 9 0.38
ACGTcount: A:0.74, C:0.09, G:0.04, T:0.13
Consensus pattern (19 bp):
AAATAATAAAAGTAAACAA
Found at i:61243099 original size:14 final size:14
Alignment explanation
Indices: 61243062--61243095 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
61243052 GCACATATAT
61243062 ATATGAATAATAATA
1 ATAT-AATAATAATA
61243077 ATATAATAATAATA
1 ATATAATAATAATA
61243091 A-ATAA
1 ATATAA
61243096 ATAAATGAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.21
14 11 0.58
15 4 0.21
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (14 bp):
ATATAATAATAATA
Found at i:61245610 original size:17 final size:19
Alignment explanation
Indices: 61245588--61245622 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
61245578 TATTAATCAT
61245588 AAAATTAA-AT-TTATAAA
1 AAAATTAATATATTATAAA
61245605 AAAATTAATATATTATAA
1 AAAATTAATATATTATAA
61245623 TGGATGCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATTAATATATTATAAA
Found at i:61247094 original size:18 final size:18
Alignment explanation
Indices: 61247067--61247102 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
61247057 ATGGGAGAGT
*
61247067 TTGGGTAAAAATATAGGC
1 TTGGGCAAAAATATAGGC
*
61247085 TTGGGCAAAAATTTAGGC
1 TTGGGCAAAAATATAGGC
61247103 CCGTTTAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.08, G:0.28, T:0.28
Consensus pattern (18 bp):
TTGGGCAAAAATATAGGC
Done.