Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 196 of 345
Found at i:55875442 original size:40 final size:40
Alignment explanation
Indices: 55875397--55875526 Score: 142
Period size: 40 Copynumber: 3.2 Consensus size: 40
55875387 CGGAATATAA
55875397 CCGGATATAAGCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAAGCATGTGCACAAATGCCTTCGGGTCTTAGC
* * *
55875437 CCGGATAGAATG-ACT-CGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA-GCA-TGTGCACAAATGCCTTCGGGTCTTAGC
* * *
55875477 CCGGATAT-AGC-CGCTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAAGCATG-T-GCACAAATGCCTTCGGGTCTTAGC
55875517 CCGGATATAA
1 CCGGATATAA
55875527 TTTCCAGCAT
Statistics
Matches: 74, Mismatches: 9, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 69 0.93
41 3 0.04
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.24
Consensus pattern (40 bp):
CCGGATATAAGCATGTGCACAAATGCCTTCGGGTCTTAGC
Found at i:55875541 original size:40 final size:40
Alignment explanation
Indices: 55875413--55875564 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
55875403 ATAAGCATGT
* * *
55875413 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCAC-CA
** * *
55875453 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAGCCGCTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCACCA
* **
55875493 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCACCA
* * *
55875533 GCATAATTGTCTTCGGGGCTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
55875565 CATTCAATTT
Statistics
Matches: 93, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
39 2 0.02
40 89 0.96
41 2 0.02
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCACCA
Found at i:55875547 original size:80 final size:80
Alignment explanation
Indices: 55875413--55875564 Score: 200
Period size: 80 Copynumber: 1.9 Consensus size: 80
55875403 ATAAGCATGT
* *
55875413 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
55875478 CGGATATAGCCGCTA
66 CGGATATAGCCGCTA
* * ** * *
55875493 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGGCTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGGCTTAG
55875556 CCCGGATAT
64 CCCGGATAT
55875565 CATTCAATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
79 3 0.05
80 59 0.95
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.26
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
CGGATATAGCCGCTA
Found at i:55877503 original size:48 final size:46
Alignment explanation
Indices: 55877387--55877507 Score: 138
Period size: 46 Copynumber: 2.6 Consensus size: 46
55877377 TGATATGTGT
* *
55877387 GCTAGTGTAAGACATGTCTGAGACATGCATCGCCTACATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGCCGACATTATGAGA
* * *
55877433 GCAAGTGTAAGACATGTTTGGGACATGCATCGGTCTCGAGATATAT-AG-
1 GCTAGTGTAAGACATGTCTGGGACATGCATC-G-C-CGACAT-TATGAGA
*
55877481 GCTAGTGTAAGACCTGTCTGGGACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
55877508 GCGTCAGCTT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
46 28 0.44
47 1 0.02
48 25 0.40
49 6 0.10
50 3 0.05
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.26
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGCCGACATTATGAGA
Found at i:55877645 original size:142 final size:138
Alignment explanation
Indices: 55877382--55877651 Score: 321
Period size: 142 Copynumber: 1.9 Consensus size: 138
55877372 TTGAGTGATA
* *
55877382 TGTGTGCTAGTGTAAGACATGTCTGAGACATGCATCGCCTACATTATGAGAGCAAGTGTAAGACA
1 TGTGTGCTAGTGTAAGACATGTCTGAGACATGCATCGCATACATGATGAGAGCAAGTGTAAGACA
* * * * * *
55877447 TGTTTGGGACATGCATCGGTCTCGAGATATATAGGCTAGTGTAAGACCTGTCTGGGACATGGCGT
66 TGTCTAGAACACGCATCGGCCTCGAGATATAAAGGCTAGTGTAAGACCTGTCTGGGACATGGCGT
55877512 CAGCTTGT
131 CAGCTTGT
* * *
55877520 TGTGTG-TCAGTGTAAGACCTGTCTGGGACATGGCATCGACAT-CAATAGATGAGAGCCAGTGTA
1 TGTGTGCT-AGTGTAAGACATGTCTGAGACAT-GCATCG-CATAC-AT-GATGAGAGCAAGTGTA
* * * *
55877583 AGACTTGTCTAGAACACGACATCGGCCTCGATATATAAAAG-TCAGTGTAAGACCTGTTTGGGAC
61 AGACATGTCTAGAACACG-CATCGGCCTCGAGATATAAAGGCT-AGTGTAAGACCTGTCTGGGAC
55877647 ATGGC
124 ATGGC
55877652 ATCGACTTTG
Statistics
Matches: 110, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
137 1 0.01
138 27 0.25
139 7 0.06
140 4 0.04
141 28 0.25
142 43 0.39
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (138 bp):
TGTGTGCTAGTGTAAGACATGTCTGAGACATGCATCGCATACATGATGAGAGCAAGTGTAAGACA
TGTCTAGAACACGCATCGGCCTCGAGATATAAAGGCTAGTGTAAGACCTGTCTGGGACATGGCGT
CAGCTTGT
Found at i:55877655 original size:49 final size:48
Alignment explanation
Indices: 55877390--55877655 Score: 183
Period size: 49 Copynumber: 5.6 Consensus size: 48
55877380 TATGTGTGCT
* *
55877390 AGTGTAAGACATGTCTGAGACAT-GCATC-GCCTAC-AT-TATGAGAG-C
1 AGTGTAAGACCTGTCTGGGACATGGCATCGGCCT-CGATATAT-AGAGTC
* * * * * *
55877435 AAGTGTAAGACATGTTTGGGACAT-GCATCGGTCTCGAGATATATAGGC
1 -AGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATATATAGAGTC
* * * * *
55877483 TAGTGTAAGACCTGTCTGGGACATGGCGTCAG-CTTG-T-TGT-GTGTC
1 -AGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATATATAGAGTC
* * * * *
55877528 AGTGTAAGACCTGTCTGGGACATGGCATCGACATCAATAGATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATATAT-AGAGTC
* * * * * *
55877577 AGTGTAAGACTTGTCTAGAACACGACATCGGCCTCGATATATAAAAGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATATAT-AGAGTC
*
55877626 AGTGTAAGACCTGTTTGGGACATGGCATCG
1 AGTGTAAGACCTGTCTGGGACATGGCATCG
55877656 ACTTTGATAT
Statistics
Matches: 166, Mismatches: 44, Indels: 17
0.73 0.19 0.07
Matches are distributed among these distances:
44 28 0.17
45 3 0.02
46 30 0.18
47 8 0.05
48 28 0.17
49 69 0.42
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (48 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATATATAGAGTC
Found at i:55883756 original size:11 final size:11
Alignment explanation
Indices: 55883720--55883759 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
55883710 CATTACAATT
55883720 TTATCATTCTC
1 TTATCATTCTC
*
55883731 TTAT-ATGCTC
1 TTATCATTCTC
55883741 GTTATCATTCTC
1 -TTATCATTCTC
55883753 TTATCAT
1 TTATCAT
55883760 ACTAAGTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 5 0.20
11 15 0.60
12 5 0.20
ACGTcount: A:0.20, C:0.23, G:0.05, T:0.53
Consensus pattern (11 bp):
TTATCATTCTC
Found at i:55885811 original size:32 final size:32
Alignment explanation
Indices: 55885775--55885841 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
55885765 AGTGCCTTAA
55885775 TATGTATTTTGGACTAATTTGAATAAAGAGAT
1 TATGTATTTTGGACTAATTTGAATAAAGAGAT
55885807 TATGTATTTTGGACTAATTTGAATAAAGAGAT
1 TATGTATTTTGGACTAATTTGAATAAAGAGAT
55885839 TAT
1 TAT
55885842 TAATAAGTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.42
Consensus pattern (32 bp):
TATGTATTTTGGACTAATTTGAATAAAGAGAT
Found at i:55889424 original size:27 final size:27
Alignment explanation
Indices: 55889394--55889446 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
55889384 GTCGATAAGG
* *
55889394 CATTCCTTTCAGAGTGTGCCACAAAGC
1 CATTCCTTTCAAAGTGTGCCAAAAAGC
*
55889421 CATTCCTTTCAAAGTGTTCCAAAAAG
1 CATTCCTTTCAAAGTGTGCCAAAAAG
55889447 GTTAATAGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (27 bp):
CATTCCTTTCAAAGTGTGCCAAAAAGC
Found at i:55893702 original size:28 final size:27
Alignment explanation
Indices: 55893639--55893708 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
55893629 ATAGTGAGTC
55893639 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
55893666 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
55893694 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
55893709 GTACAAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:55896860 original size:17 final size:16
Alignment explanation
Indices: 55896811--55896905 Score: 50
Period size: 17 Copynumber: 5.8 Consensus size: 16
55896801 TCGTGGATGA
55896811 AAGTACATGTATCTTCC
1 AAGTACATGTATCTT-C
* *
55896828 TA-TGCGATGTATCTTC
1 AAGTAC-ATGTATCTTC
55896844 AAGTACATGTATCCTTC
1 AAGTACATGTAT-CTTC
* * * *
55896861 GAGTTCATGAATCCTC
1 AAGTACATGTATCTTC
* * *
55896877 -CGATGCAATGTATCTTT
1 AAG-TAC-ATGTATCTTC
55896894 AAGTACATGTAT
1 AAGTACATGTAT
55896906 GATCATTAAT
Statistics
Matches: 57, Mismatches: 15, Indels: 13
0.67 0.18 0.15
Matches are distributed among these distances:
15 1 0.02
16 21 0.37
17 34 0.60
18 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (16 bp):
AAGTACATGTATCTTC
Found at i:55899873 original size:46 final size:45
Alignment explanation
Indices: 55899779--55899873 Score: 104
Period size: 46 Copynumber: 2.1 Consensus size: 45
55899769 GGTTTAGTAA
* *** *
55899779 CAGAAGCAATTTCAGTTCATATTTAGAACAGATCAATTGCATATG
1 CAGAAGCAATTTCAGTTCAGAAACAGAACAGATCAATTGCAGATG
55899824 CAGAAGCAATTTCAGTTTCAGAAACAGAACATGA-CAGATT-CAGATG
1 CAGAAGCAATTTCAG-TTCAGAAACAGAACA-GATCA-ATTGCAGATG
55899870 CAGA
1 CAGA
55899874 TATTCCTACC
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
45 15 0.36
46 22 0.52
47 5 0.12
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (45 bp):
CAGAAGCAATTTCAGTTCAGAAACAGAACAGATCAATTGCAGATG
Found at i:55912137 original size:19 final size:21
Alignment explanation
Indices: 55912102--55912140 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
55912092 ATTTTTTTCC
55912102 TCCTTCGTCCGTTCTTCATCT
1 TCCTTCGTCCGTTCTTCATCT
55912123 TCCTTC-TCC-TTCTTCATC
1 TCCTTCGTCCGTTCTTCATC
55912141 CAGGTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 3 0.17
21 6 0.33
ACGTcount: A:0.05, C:0.41, G:0.05, T:0.49
Consensus pattern (21 bp):
TCCTTCGTCCGTTCTTCATCT
Found at i:55914360 original size:40 final size:39
Alignment explanation
Indices: 55914238--55914366 Score: 154
Period size: 40 Copynumber: 3.3 Consensus size: 39
55914228 CGGAATATAA
55914238 CCGGATATAACCA-TGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACT-TGCAC-AATGCCTTCGGGTCTTAGC
* ** *
55914278 CC-GATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTTGCAC-AATGCCTTCGGGTCTTAGC
* *
55914317 CCGGATATAGCCACTTGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTTGCACAA-TGCCTTCGGGTCTTAGC
55914357 CCGGATATAA
1 CCGGATATAA
55914367 TTTCCAGCAT
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
39 34 0.46
40 40 0.54
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCACTTGCACAATGCCTTCGGGTCTTAGC
Found at i:55914381 original size:40 final size:40
Alignment explanation
Indices: 55914238--55914403 Score: 142
Period size: 40 Copynumber: 4.2 Consensus size: 40
55914228 CGGAATATAA
*** *
55914238 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAGC
* **
55914278 CC-GATAGAATGACTC-GCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-CAGCAC-AATTGCCTTCGGGTCTTAGC
* ** *
55914317 CCGGATATAGCCACTTGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAGC
*** * *
55914357 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAGC
55914396 CCGGATAT
1 CCGGATAT
55914404 CATTCAATTT
Statistics
Matches: 101, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
39 45 0.45
40 56 0.55
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.27
Consensus pattern (40 bp):
CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAGC
Found at i:55925479 original size:27 final size:28
Alignment explanation
Indices: 55925423--55925492 Score: 133
Period size: 27 Copynumber: 2.5 Consensus size: 28
55925413 AAATTTGTAC
55925423 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
55925451 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
55925478 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
55925493 GACTCACTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 25 0.60
28 17 0.40
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:55933389 original size:27 final size:28
Alignment explanation
Indices: 55933342--55933410 Score: 124
Period size: 27 Copynumber: 2.5 Consensus size: 28
55933332 AAATTTGTAC
55933342 AGCACTAAGT-TGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
55933369 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
55933396 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
55933411 GACTCACTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 35 0.85
28 6 0.15
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:55933421 original size:27 final size:27
Alignment explanation
Indices: 55933342--55933422 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
55933332 AAATTTGTAC
* * *
55933342 AGCACTAAGT-TGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
* * *
55933369 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
55933396 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
55933423 GCTTTTGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
26 1 0.02
27 42 0.86
28 6 0.12
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:55935207 original size:15 final size:14
Alignment explanation
Indices: 55935173--55935207 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
55935163 ACTGACTTAG
55935173 GTTATTATCCCCCT
1 GTTATTATCCCCCT
55935187 GATTATTATCCCCCT
1 G-TTATTATCCCCCT
55935202 AGTTAT
1 -GTTAT
55935208 CATTCCAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.05
15 17 0.89
16 1 0.05
ACGTcount: A:0.20, C:0.29, G:0.09, T:0.43
Consensus pattern (14 bp):
GTTATTATCCCCCT
Found at i:55939071 original size:41 final size:41
Alignment explanation
Indices: 55939026--55939165 Score: 201
Period size: 41 Copynumber: 3.4 Consensus size: 41
55939016 GGCATTTTTG
** * * *
55939026 GTAAAACGCCGCTAAAAAATAGAGCAATGGCGGTGCTTTCT
1 GTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCT
* *
55939067 GTAAAATGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCG
1 GTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCT
55939108 GTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTT-T
1 GTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCT
55939148 GATAAAACGCCGCTAAAA
1 G-TAAAACGCCGCTAAAA
55939166 TTCATATAAC
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 1 0.01
41 88 0.99
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (41 bp):
GTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCT
Found at i:55939201 original size:18 final size:18
Alignment explanation
Indices: 55939180--55939214 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55939170 TATAACCCCT
* *
55939180 AAAATCCTAAACCCTAAA
1 AAAATCATAAACACTAAA
55939198 AAAATCATAAACACTAA
1 AAAATCATAAACACTAA
55939215 TCTATAACCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.23, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAATCATAAACACTAAA
Found at i:55939257 original size:17 final size:16
Alignment explanation
Indices: 55939239--55939299 Score: 65
Period size: 16 Copynumber: 4.0 Consensus size: 16
55939229 AATACTAAAC
*
55939239 CCCTAAACCTTAAAAA
1 CCCTAAACCCTAAAAA
55939255 CCCTAAACCCT--AAA
1 CCCTAAACCCTAAAAA
** *
55939269 CTATAACCCCT-AAAA
1 CCCTAAACCCTAAAAA
55939284 CCCTAAACCCTAAAAA
1 CCCTAAACCCTAAAAA
55939300 ATATCATATG
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
14 11 0.31
15 11 0.31
16 14 0.39
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (16 bp):
CCCTAAACCCTAAAAA
Found at i:55939262 original size:7 final size:7
Alignment explanation
Indices: 55939233--55939297 Score: 58
Period size: 7 Copynumber: 8.7 Consensus size: 7
55939223 CCCTAAAATA
55939233 CTAAACCC
1 CTAAA-CC
55939241 CTAAACC
1 CTAAACC
*
55939248 TTAAAAACC
1 CT--AAACC
55939257 CTAAACC
1 CTAAACC
*
55939264 CTAAACT
1 CTAAACC
* *
55939271 ATAACCC
1 CTAAACC
55939278 CTAAAACC
1 CT-AAACC
55939286 CTAAACC
1 CTAAACC
55939293 CTAAA
1 CTAAA
55939298 AAATATCATA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
7 29 0.63
8 11 0.24
9 6 0.13
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.17
Consensus pattern (7 bp):
CTAAACC
Found at i:55939299 original size:16 final size:15
Alignment explanation
Indices: 55939233--55939298 Score: 71
Period size: 15 Copynumber: 4.4 Consensus size: 15
55939223 CCCTAAAATA
*
55939233 CTAAACCCCTAAACC
1 CTAAAACCCTAAACC
*
55939248 TTAAAAACCCTAAACC
1 CT-AAAACCCTAAACC
** *
55939264 CT-AAACTATAACCC
1 CTAAAACCCTAAACC
55939278 CTAAAACCCTAAACC
1 CTAAAACCCTAAACC
55939293 CTAAAA
1 CTAAAA
55939299 AATATCATAT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
14 11 0.28
15 16 0.40
16 13 0.32
ACGTcount: A:0.47, C:0.36, G:0.00, T:0.17
Consensus pattern (15 bp):
CTAAAACCCTAAACC
Found at i:55940406 original size:7 final size:7
Alignment explanation
Indices: 55940394--55940425 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
55940384 TTTCTTTAAA
55940394 CCCTAAC
1 CCCTAAC
55940401 CCCTAAC
1 CCCTAAC
*
55940408 CCCTAAT
1 CCCTAAC
55940415 CCCTAAC
1 CCCTAAC
55940422 CCCT
1 CCCT
55940426 TAAATCAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.25, C:0.56, G:0.00, T:0.19
Consensus pattern (7 bp):
CCCTAAC
Found at i:55940509 original size:66 final size:66
Alignment explanation
Indices: 55940428--55940557 Score: 161
Period size: 66 Copynumber: 2.0 Consensus size: 66
55940418 TAACCCCTTA
* * * *
55940428 AATCAACAACCCTTTAAACCCCAAACCTTAAATCTCTAATCATAAACCCCTAAAACTATAAACAC
1 AATCAACAACCCTTTAAACACCAAACCCTAAATATCAAATCATAAACCCCTAAAACTATAAACAC
55940493 T
66 T
* * * * * * *
55940494 AATCAATAACTCTTTAAATATCAGACCCTAAATATCAAATCATAAACCCTTAAAACTCTAAACA
1 AATCAACAACCCTTTAAACACCAAACCCTAAATATCAAATCATAAACCCCTAAAACTATAAACA
55940558 ACAAACCTTA
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.47, C:0.28, G:0.01, T:0.25
Consensus pattern (66 bp):
AATCAACAACCCTTTAAACACCAAACCCTAAATATCAAATCATAAACCCCTAAAACTATAAACAC
T
Found at i:55940612 original size:22 final size:22
Alignment explanation
Indices: 55940518--55940612 Score: 56
Period size: 22 Copynumber: 4.4 Consensus size: 22
55940508 TAAATATCAG
*
55940518 ACCC-TAAATATCAAATCATAA
1 ACCCTTAAATCTCAAATCATAA
*
55940539 ACCCTTAAAACTCTAAA-CA-ACA
1 ACCCTTAAATCTC-AAATCATA-A
* * * * *
55940561 AACCTT-AATCCCAACACCCTGA
1 ACCCTTAAATCTCAA-ATCATAA
*
55940583 ACTC-TAAATCTCAAATCATAA
1 ACCCTTAAATCTCAAATCATAA
55940604 ACCCTTAAA
1 ACCCTTAAA
55940613 ACTCCAACCC
Statistics
Matches: 52, Mismatches: 14, Indels: 15
0.64 0.17 0.19
Matches are distributed among these distances:
20 2 0.04
21 18 0.35
22 29 0.56
23 3 0.06
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.22
Consensus pattern (22 bp):
ACCCTTAAATCTCAAATCATAA
Found at i:55940973 original size:8 final size:7
Alignment explanation
Indices: 55940940--55940972 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
55940930 AAATAAACTC
55940940 AAAAATT
1 AAAAATT
55940947 AAAAATT
1 AAAAATT
55940954 AAAAATT
1 AAAAATT
55940961 AAAAATT
1 AAAAATT
55940968 AAAAA
1 AAAAA
55940973 ACTAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAAATT
Found at i:55940979 original size:14 final size:14
Alignment explanation
Indices: 55940940--55940980 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
55940930 AAATAAACTC
*
55940940 AAAAATTAAAAATT
1 AAAAACTAAAAATT
*
55940954 AAAAATTAAAAATT
1 AAAAACTAAAAATT
55940968 AAAAAACTAAAAA
1 -AAAAACTAAAAA
55940981 ATTTAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAAACTAAAAATT
Found at i:55940979 original size:21 final size:20
Alignment explanation
Indices: 55940926--55940979 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
55940916 TAAACCGAAA
*
55940926 TAAAAAATAAACTCAAAAAT
1 TAAAAAATAAAATCAAAAAT
* *
55940946 TAAAAATTAAAAATTAAAAAT
1 TAAAAAAT-AAAATCAAAAAT
55940967 TAAAAAACTAAAA
1 TAAAAAA-TAAAA
55940980 AATTTAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 7 0.25
21 20 0.71
22 1 0.04
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (20 bp):
TAAAAAATAAAATCAAAAAT
Found at i:55940995 original size:14 final size:15
Alignment explanation
Indices: 55940978--55941007 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
55940968 AAAAAACTAA
55940978 AAAATTTAA-ATTTT
1 AAAATTTAATATTTT
55940992 AAAATTTAATATTTT
1 AAAATTTAATATTTT
55941007 A
1 A
55941008 GTCCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAAATTTAATATTTT
Found at i:55945323 original size:39 final size:39
Alignment explanation
Indices: 55945242--55945404 Score: 254
Period size: 39 Copynumber: 4.2 Consensus size: 39
55945232 TATGGTAACC
** *
55945242 CGCACAAACGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
55945282 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
55945321 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
55945360 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
55945399 CGCACA
1 CGCACA
55945405 TTCATTCACA
Statistics
Matches: 115, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 99 0.86
40 16 0.14
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:55953238 original size:40 final size:39
Alignment explanation
Indices: 55953194--55953386 Score: 251
Period size: 39 Copynumber: 4.9 Consensus size: 39
55953184 GTTCAAAACA
* * ** * *
55953194 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
55953234 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
55953274 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
55953313 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
55953352 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACA
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACA
55953387 TTCATTCACA
Statistics
Matches: 139, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 99 0.71
40 40 0.29
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:55953305 original size:39 final size:39
Alignment explanation
Indices: 55953224--55953386 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
55953214 TATGGTAACC
* *
55953224 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
55953264 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
55953303 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
55953342 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
55953381 CGCACA
1 CGCACA
55953387 TTCATTCACA
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 99 0.85
40 17 0.15
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:55956821 original size:43 final size:43
Alignment explanation
Indices: 55956760--55956864 Score: 158
Period size: 43 Copynumber: 2.4 Consensus size: 43
55956750 TTTAAAATTT
* **
55956760 CATGACCTTTAGCGGCGTTTGTGG-GAGAAGCGCTGCTAAAGGC
1 CATGACCTTTAGCGGCGTTTGTGGAGA-AAACGCCACTAAAGGC
*
55956803 CATGATCTTTAGCGGCGTTTGTGGAGAAAACGCCACTAAAGGC
1 CATGACCTTTAGCGGCGTTTGTGGAGAAAACGCCACTAAAGGC
55956846 CATGACCTTTAGCGGCGTT
1 CATGACCTTTAGCGGCGTT
55956865 ATCTATAATG
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
43 54 0.96
44 2 0.04
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (43 bp):
CATGACCTTTAGCGGCGTTTGTGGAGAAAACGCCACTAAAGGC
Found at i:55971527 original size:27 final size:27
Alignment explanation
Indices: 55971482--55971542 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
55971472 AATTTTTATT
*
55971482 GTAATATAAAAGTATGTTTAAAAATAA
1 GTAATATAAAAGCATGTTTAAAAATAA
* *
55971509 GTAATA-AAAAGCATGGTTTGAAACTAA
1 GTAATATAAAAGCAT-GTTTAAAAATAA
*
55971536 TTAATAT
1 GTAATAT
55971543 TAACACATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.51, C:0.03, G:0.13, T:0.33
Consensus pattern (27 bp):
GTAATATAAAAGCATGTTTAAAAATAA
Found at i:55974001 original size:50 final size:50
Alignment explanation
Indices: 55973933--55974249 Score: 284
Period size: 50 Copynumber: 6.6 Consensus size: 50
55973923 TCAAAGTCGG
*
55973933 TGCCATGTCCCAGACATGGTCTTACATTGACTCTCATATATCGAGGCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATCGAGGCCGA
* * * * *
55973983 TGCCATGTCCCA-ATCATGGTCTTACACTGGCTTTCATCTGTCGATGCCGA
1 TGCCATGTCCCAGA-CATGGTCTTACACTGACTCTCATATATCGAGGCCGA
* * ** *
55974033 TGCCATGTCCTAGACATGGTCTTACATTGA----CACGTATC-AAGCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATCGAGGCCGA
* *
55974078 TGCCATGTCCCAGACATGGTCTTACACT-AGCTTTCATATCTCGAGGCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTGA-CTCTCATATATCGAGGCCGA
* ** * * * * *
55974128 TGCCATATCTTAGACATGGTCTTACA-TTAGCTCTCGTCT-T-AATGCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTGA-CTCTCATATATCGAGGCCGA
* * * *
55974176 TGCCATGTCCCAGACAGGGTCTTACACTGGCTCTCATA-AT-GTGGTCGA
1 TGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATCGAGGCCGA
55974224 TG-CATGTCCCAGACAT-GTCTTACACT
1 TGCCATGTCCCAGACATGGTCTTACACT
55974250 AGCACACATG
Statistics
Matches: 216, Mismatches: 40, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
44 1 0.00
45 32 0.15
46 15 0.07
47 13 0.06
48 41 0.19
49 9 0.04
50 104 0.48
51 1 0.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (50 bp):
TGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATCGAGGCCGA
Found at i:55974104 original size:95 final size:95
Alignment explanation
Indices: 55973933--55974247 Score: 334
Period size: 95 Copynumber: 3.3 Consensus size: 95
55973923 TCAAAGTCGG
* ** *
55973933 TGCCATGTCCCAGACATGGTCTTACATTGACTCTCATATATCGAGGCCGATGCCATGTCCCA-AT
1 TGCCATGTCCTAGACATGGTCTTACATTGA----CACGTATC-AAGCCGATGCCATGTCCCAGA-
* * *
55973997 CATGGTCTTACACTGGCTTTCATCTGTCGATGCCGA
60 CATGGTCTTACACTGGCTTTCATATCTCGAGGCCGA
55974033 TGCCATGTCCTAGACATGGTCTTACATTGACACGTATCAAGCCGATGCCATGTCCCAGACATGGT
1 TGCCATGTCCTAGACATGGTCTTACATTGACACGTATCAAGCCGATGCCATGTCCCAGACATGGT
*
55974098 CTTACACTAGCTTTCATATCTCGAGGCCGA
66 CTTACACTGGCTTTCATATCTCGAGGCCGA
* * * * * * *
55974128 TGCCATATCTTAGACATGGTCTTACATTAGCTCTCGTCTTAATGCCGATGCCATGTCCCAGACAG
1 TGCCATGTCCTAGACATGGTCTTACATT-G-ACACGTATCAA-GCCGATGCCATGTCCCAGACAT
* * * *
55974193 GGTCTTACACTGGCTCTCATA-AT-GTGGTCGA
63 GGTCTTACACTGGCTTTCATATCTCGAGGCCGA
*
55974224 TG-CATGTCCCAGACAT-GTCTTACA
1 TGCCATGTCCTAGACATGGTCTTACA
55974248 CTAGCACACA
Statistics
Matches: 188, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
94 8 0.04
95 87 0.46
96 16 0.09
97 8 0.04
98 40 0.21
100 29 0.15
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.30
Consensus pattern (95 bp):
TGCCATGTCCTAGACATGGTCTTACATTGACACGTATCAAGCCGATGCCATGTCCCAGACATGGT
CTTACACTGGCTTTCATATCTCGAGGCCGA
Found at i:55974146 original size:145 final size:146
Alignment explanation
Indices: 55973877--55974206 Score: 391
Period size: 145 Copynumber: 2.3 Consensus size: 146
55973867 CATAGGGTAA
* * * * * *
55973877 GATGCCGACGCCATGTTCTGGACATGGTCTTACACTGGCTCACACATCAAAGTCGGTGCCATGTC
1 GATGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCACACACATCAAAGCCGATGCCATGTC
* *
55973942 CCAGACATGGTCTTACATTGACTCTCATATATCGAGGCCGATGCCATGTCCCAATCATGGTCTTA
66 CCAGACATGGTCTTACATAGACTCTCATATATCGAGGCCGATGCCATATCCCAATCATGGTCTTA
* *
55974007 CACTGGCTTTCATCTGT
131 CACTAGCTCTCATCT-T
* **
55974024 CGATGCCGATGCCATGTCCTAGACATGGTCTTACA-TTG-ACACGTATC-AAGCCGATGCCATGT
1 -GATGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCACACACATCAAAGCCGATGCCATGT
* * **
55974086 CCCAGACATGGTCTTACACTAG-CTTTCATATCTCGAGGCCGATGCCATATCTTAGA-CATGGTC
65 CCCAGACATGGTCTTACA-TAGACTCTCATATATCGAGGCCGATGCCATATCCCA-ATCATGGTC
* *
55974149 TTACATTAGCTCTCGTCTT
128 TTACACTAGCTCTCATCTT
* * *
55974168 AATGCCGATGCCATGTCCCAGACAGGGTCTTACACTGGC
1 GATGCCGATGCCATGTCCTAGACATGGTCTTACACTGGC
55974207 TCTCATAATG
Statistics
Matches: 155, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
143 31 0.20
144 3 0.02
145 79 0.51
146 9 0.06
147 2 0.01
148 31 0.20
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.28
Consensus pattern (146 bp):
GATGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCACACACATCAAAGCCGATGCCATGTC
CCAGACATGGTCTTACATAGACTCTCATATATCGAGGCCGATGCCATATCCCAATCATGGTCTTA
CACTAGCTCTCATCTT
Found at i:55975319 original size:40 final size:40
Alignment explanation
Indices: 55975275--55975356 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
55975265 GAAAAAGATT
55975275 ACAACTTTTTCTTTATTTTATTTTATTACCAAAACAAGTC
1 ACAACTTTTTCTTTATTTTATTTTATTACCAAAACAAGTC
55975315 ACAACTTTTTCTTTATTTTATTTTATTACCAAAACAAGTC
1 ACAACTTTTTCTTTATTTTATTTTATTACCAAAACAAGTC
55975355 AC
1 AC
55975357 CTAATGCCAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.33, C:0.18, G:0.02, T:0.46
Consensus pattern (40 bp):
ACAACTTTTTCTTTATTTTATTTTATTACCAAAACAAGTC
Found at i:55977540 original size:49 final size:49
Alignment explanation
Indices: 55977468--55977565 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
55977458 GCTCTCTATT
55977468 CTCTTATTCACAAAGAATAATGAAACAATGAATGGAGTGAGTACAAATG
1 CTCTTATTCACAAAGAATAATGAAACAATGAATGGAGTGAGTACAAATG
55977517 CTCTTATTCACAAAGAATAATGAAACAATGAATGGAGTGAGTACAAATG
1 CTCTTATTCACAAAGAATAATGAAACAATGAATGGAGTGAGTACAAATG
55977566 AGGGGGAGGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.24
Consensus pattern (49 bp):
CTCTTATTCACAAAGAATAATGAAACAATGAATGGAGTGAGTACAAATG
Found at i:55977764 original size:51 final size:51
Alignment explanation
Indices: 55977665--55977797 Score: 140
Period size: 51 Copynumber: 2.6 Consensus size: 51
55977655 CCATCAAATC
* * * *
55977665 TCTAAGAATATAATATCATATCTTCTAAAATTACATATCTTAGATAAGATA
1 TCTAAGATTATAATATCATATCTTATAAGATTACATATCATAGATAAGATA
* ** * * * ** *
55977716 TGTAATCTTATAAAATAATATCTTATAAGATTCCATATCATATCTAAGATC
1 TCTAAGATTATAATATCATATCTTATAAGATTACATATCATAGATAAGATA
*
55977767 TCTAAGATTATAATATCATATCTTTTAAGAT
1 TCTAAGATTATAATATCATATCTTATAAGAT
55977798 CATGTTTCCA
Statistics
Matches: 63, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40
Consensus pattern (51 bp):
TCTAAGATTATAATATCATATCTTATAAGATTACATATCATAGATAAGATA
Found at i:55978598 original size:2 final size:2
Alignment explanation
Indices: 55978591--55978626 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
55978581 ACTTACATAC
55978591 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55978627 AACAACGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55978927 original size:24 final size:25
Alignment explanation
Indices: 55978891--55978938 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
55978881 TAGTAAACAG
* *
55978891 GTTATAAGGAGATGAAATGTGAAAA
1 GTTATAAGAAGATGAAAGGTGAAAA
55978916 GTTA-AAGAAGATGAAAGGTGAAA
1 GTTATAAGAAGATGAAAGGTGAAA
55978939 GGTGAAAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (25 bp):
GTTATAAGAAGATGAAAGGTGAAAA
Found at i:55978946 original size:24 final size:24
Alignment explanation
Indices: 55978900--55978946 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
55978890 GGTTATAAGG
* *
55978900 AGATGAAATGTGAAAAGTTAAAGA
1 AGATGAAAGGTGAAAAGTGAAAGA
*
55978924 AGATGAAAGGTGAAAGGTGAAAG
1 AGATGAAAGGTGAAAAGTGAAAG
55978947 GTTGATTACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.32, T:0.17
Consensus pattern (24 bp):
AGATGAAAGGTGAAAAGTGAAAGA
Found at i:55981504 original size:21 final size:20
Alignment explanation
Indices: 55981475--55981513 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
55981465 CAAAACTTGT
55981475 ATAATTATCATCAAACATTC
1 ATAATTATCATCAAACATTC
55981495 ATAATCTATCATCAAACAT
1 ATAAT-TATCATCAAACAT
55981514 CAAAATACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAATTATCATCAAACATTC
Found at i:55987766 original size:27 final size:28
Alignment explanation
Indices: 55987709--55987778 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
55987699 AAATTTGTAC
**
55987709 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
*
55987737 AGCACTATGTGTGCG-AGCTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
55987764 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
55987779 GACTTATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 24 0.63
28 14 0.37
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:55987787 original size:27 final size:27
Alignment explanation
Indices: 55987709--55987790 Score: 103
Period size: 27 Copynumber: 3.0 Consensus size: 27
55987699 AAATTTGTAC
* *
55987709 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGGACTT-ATTATAT
* *
55987737 AGCACTATGTGTGC-GAGCTGATTATAT
1 AGCACTAAGTGTGCGGA-CTTATTATAT
55987764 AGCACTAAGTGTGCGGACTTATTATAT
1 AGCACTAAGTGTGCGGACTTATTATAT
55987791 GCTTTTGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
27 30 0.65
28 16 0.35
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.34
Consensus pattern (27 bp):
AGCACTAAGTGTGCGGACTTATTATAT
Found at i:55995700 original size:27 final size:28
Alignment explanation
Indices: 55995643--55995712 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
55995633 AAATTTGTAC
**
55995643 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
*
55995671 AGCACTATGTGTGCG-AGCTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
55995698 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
55995713 GACTTATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 24 0.63
28 14 0.37
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:55995721 original size:27 final size:27
Alignment explanation
Indices: 55995643--55995724 Score: 103
Period size: 27 Copynumber: 3.0 Consensus size: 27
55995633 AAATTTGTAC
* *
55995643 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGGACTT-ATTATAT
* *
55995671 AGCACTATGTGTGC-GAGCTGATTATAT
1 AGCACTAAGTGTGCGGA-CTTATTATAT
55995698 AGCACTAAGTGTGCGGACTTATTATAT
1 AGCACTAAGTGTGCGGACTTATTATAT
55995725 GCTTTTGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
27 30 0.65
28 16 0.35
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.34
Consensus pattern (27 bp):
AGCACTAAGTGTGCGGACTTATTATAT
Found at i:56000260 original size:21 final size:20
Alignment explanation
Indices: 56000232--56000270 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
56000222 CAAAACTTGT
56000232 ATAACTATCATCAAACATTC
1 ATAACTATCATCAAACATTC
56000252 ATAATCTATCATCAAACAT
1 ATAA-CTATCATCAAACAT
56000271 CAAAATACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:56008209 original size:29 final size:29
Alignment explanation
Indices: 56008169--56008271 Score: 152
Period size: 29 Copynumber: 3.6 Consensus size: 29
56008159 GTTGAGAGAT
*
56008169 TGGCACTGAGTGTGCGAGCTTGAAGTGCA
1 TGGCACTAAGTGTGCGAGCTTGAAGTGCA
*
56008198 TGGCACTAAGTGTGCGAGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAGCTTGAAGTGCA
* * **
56008227 TGGCACTAAGTGTGCGAGTTTAAAGTATA
1 TGGCACTAAGTGTGCGAGCTTGAAGTGCA
56008256 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
56008272 CGGCTGATTA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.25, C:0.16, G:0.33, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAGTGCA
Found at i:56012683 original size:29 final size:29
Alignment explanation
Indices: 56012579--56012729 Score: 128
Period size: 29 Copynumber: 5.2 Consensus size: 29
56012569 CCCGGTGGTG
* * * *
56012579 ATCTCTGTTATAAGAAAGTCTTTATGG-T
1 ATCTCTGTTATAAGGATGCCTTTGTGGCT
** * * *
56012607 AATCTCTGTTATAAAAAAGTCTTTATGG-T
1 -ATCTCTGTTATAAGGATGCCTTTGTGGCT
*
56012636 GATCTCT-TCTATAAAGATGCCTTTGTGGCT
1 -ATCTCTGT-TATAAGGATGCCTTTGTGGCT
* **
56012666 ATCTTTGTTATAAGGATGAATTTGTGGCT
1 ATCTCTGTTATAAGGATGCCTTTGTGGCT
56012695 ATCTCTGTTATAAGGATGCCTTTGTGGCT
1 ATCTCTGTTATAAGGATGCCTTTGTGGCT
*
56012724 ACCTCT
1 ATCTCT
56012730 ATTAAAAGAA
Statistics
Matches: 105, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
28 1 0.01
29 102 0.97
30 2 0.02
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.42
Consensus pattern (29 bp):
ATCTCTGTTATAAGGATGCCTTTGTGGCT
Found at i:56017400 original size:2 final size:2
Alignment explanation
Indices: 56017393--56017420 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
56017383 ATAGCCGAAC
56017393 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56017421 TAATTATGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56018050 original size:3 final size:3
Alignment explanation
Indices: 56018042--56018095 Score: 85
Period size: 3 Copynumber: 18.3 Consensus size: 3
56018032 TCATATCATT
56018042 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
56018087 TTA TT- TTA T
1 TTA TTA TTA T
56018096 ACTTTTCAAC
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.08
3 41 0.85
4 3 0.06
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:56018425 original size:28 final size:28
Alignment explanation
Indices: 56018369--56018438 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
56018359 ATATTTTCCT
* *
56018369 TCGCACACTTAGTGCTCGATAATCGAAC
1 TCGCACACTTAGTGCTCGATAACCAAAC
56018397 TCGCACACTTAGTGCTC-ATTAACCAAAC
1 TCGCACACTTAGTGCTCGA-TAACCAAAC
**
56018425 TCGCATGCTTAGTG
1 TCGCACACTTAGTG
56018439 AAATTTTCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 1 0.03
28 36 0.97
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (28 bp):
TCGCACACTTAGTGCTCGATAACCAAAC
Found at i:56021383 original size:57 final size:58
Alignment explanation
Indices: 56021312--56021444 Score: 223
Period size: 58 Copynumber: 2.3 Consensus size: 58
56021302 GTGCCCACTG
*
56021312 ACCGATCTCGCACACATAGTGCTCGGTTGAA-GAACTCGCACACACAGTGCCTCAATT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAACTCGCACACACAGTGCCTCAATT
* * *
56021369 ACCGATCTCTCACACATAGTGCTCGGTTAAAGGAATTTGCACACACAGTGCCTCAATT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAACTCGCACACACAGTGCCTCAATT
56021427 ACCGATCTCGCACACATA
1 ACCGATCTCGCACACATA
56021445 ATGCCCATAT
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
57 29 0.41
58 41 0.59
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (58 bp):
ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAACTCGCACACACAGTGCCTCAATT
Found at i:56021449 original size:29 final size:30
Alignment explanation
Indices: 56021312--56021449 Score: 101
Period size: 29 Copynumber: 4.8 Consensus size: 30
56021302 GTGCCCACTG
**
56021312 ACCGATCTCGCACACATAGTG-CTCGGTTGA
1 ACCGATCTCGCACACATAGTGCCTCAATT-A
* *
56021342 A--GAACTCGCACACACAGTGCCTCAATT-
1 ACCGATCTCGCACACATAGTGCCTCAATTA
* **
56021369 ACCGATCTCTCACACATAGTG-CTCGGTTA
1 ACCGATCTCGCACACATAGTGCCTCAATTA
** * *
56021398 AAGGAAT-TTGCACACACAGTGCCTCAATT-
1 ACCG-ATCTCGCACACATAGTGCCTCAATTA
*
56021427 ACCGATCTCGCACACATAATGCC
1 ACCGATCTCGCACACATAGTGCC
56021450 CATATTCATT
Statistics
Matches: 80, Mismatches: 21, Indels: 15
0.69 0.18 0.13
Matches are distributed among these distances:
27 1 0.01
28 23 0.29
29 48 0.60
30 8 0.10
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.22
Consensus pattern (30 bp):
ACCGATCTCGCACACATAGTGCCTCAATTA
Found at i:56021641 original size:43 final size:43
Alignment explanation
Indices: 56021580--56021756 Score: 309
Period size: 43 Copynumber: 4.1 Consensus size: 43
56021570 CCTTGCTCGA
** *
56021580 ATCACCGGCATTAAGCCTGCTAGGCACGAAGACCCTAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGACCCGAATACAC
56021623 ATCACCGGCACGAAGCCTGCTAGGCACGAAGACCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGACCCGAATACAC
*
56021666 ATCACCGGCACGAAGCCTGCTAGGCACGAAAACCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGACCCGAATACAC
*
56021709 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGACCCGAATACAC
56021752 ATCAC
1 ATCAC
56021757 TGAGTTTCAT
Statistics
Matches: 128, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 128 1.00
ACGTcount: A:0.33, C:0.34, G:0.21, T:0.11
Consensus pattern (43 bp):
ATCACCGGCACGAAGCCTGCTAGGCACGAAGACCCGAATACAC
Found at i:56023685 original size:3 final size:3
Alignment explanation
Indices: 56023677--56023723 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
56023667 TCATATCATT
56023677 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
56023723 T
1 T
56023724 ACTTTTCAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:56024028 original size:28 final size:28
Alignment explanation
Indices: 56023997--56024066 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
56023987 ATATTTTCCT
*
56023997 TCGCACACTTAGTGCTCGA-TAATCAAAC
1 TCGCACACTTAGTGCTC-ATTAACCAAAC
56024025 TCGCACACTTAGTGCTCATTAACCAAAC
1 TCGCACACTTAGTGCTCATTAACCAAAC
**
56024053 TCGCATGCTTAGTG
1 TCGCACACTTAGTG
56024067 AAATTTTCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 1 0.03
28 37 0.97
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (28 bp):
TCGCACACTTAGTGCTCATTAACCAAAC
Found at i:56032241 original size:19 final size:20
Alignment explanation
Indices: 56032208--56032245 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
56032198 TACCCAAATG
56032208 GTACAACTTGAAAAGGTTAT
1 GTACAACTTGAAAAGGTTAT
*
56032228 GTAC-ACTTGGAAAGGTTA
1 GTACAACTTGAAAAGGTTA
56032246 GATATACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.29
Consensus pattern (20 bp):
GTACAACTTGAAAAGGTTAT
Found at i:56040023 original size:30 final size:30
Alignment explanation
Indices: 56039989--56040049 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
56039979 TCCTTAACTC
56039989 AAACTTTTGCAAAATTACAATTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
* * * *
56040019 AAACTTTTTCATATTTACACTTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
56040049 A
1 A
56040050 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.41
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCCCT
Found at i:56045202 original size:40 final size:40
Alignment explanation
Indices: 56045117--56045267 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
56045107 AATTGAATGA
* * *
56045117 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
56045157 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
56045198 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
56045237 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
56045268 ACATGGTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:56045281 original size:40 final size:40
Alignment explanation
Indices: 56045154--56045283 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
56045144 ATGCTGGAAA
* * * *
56045154 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
56045194 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
*
56045234 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
56045274 TTATATCCGG
1 TTATATCCGG
56045284 TTATATTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:56048223 original size:50 final size:48
Alignment explanation
Indices: 56048106--56048429 Score: 274
Period size: 50 Copynumber: 6.7 Consensus size: 48
56048096 TGATATGTGT
* ** *
56048106 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATTATGAGG
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAAGATGAGA
* *
56048152 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAAGACCTGAAA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAAGA--TGAGA
* * **
56048202 GCTAGTGTAAGACCATATCTGGGACATGGCATCGG-CT--TGAT-ATTT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAAGATGA-GA
* * * *
56048247 GTTAGTGTAAAACCATGTCTAGGATATGGCATCGGCAC-CGACAGATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTC-A-AGATGAGA
* * *
56048297 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGTCTCGATATATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC-A-AGATGAGA
*
56048347 G-TCAGTGTAAGACCATGTCTGGGACATGGCATCGAG-TTC--GATGTATGA
1 GCT-AGTGTAAGACCATGTCTGGGACATGGCATCG-GCCTCAAGATG-A-GA
* * *
56048395 GCCAGTGTAAGACCATGTCTGGGATATGGCGTCGG
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGG
56048430 TATCTTACCC
Statistics
Matches: 227, Mismatches: 33, Indels: 35
0.77 0.11 0.12
Matches are distributed among these distances:
44 1 0.00
45 31 0.14
46 14 0.06
47 19 0.08
48 44 0.19
49 3 0.01
50 113 0.50
51 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (48 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAAGATGAGA
Found at i:56048263 original size:95 final size:98
Alignment explanation
Indices: 56048109--56048430 Score: 294
Period size: 95 Copynumber: 3.3 Consensus size: 98
56048099 TATGTGTGCT
* * * *
56048109 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCAC-AT-TATGAGGGCCAGTGTAAGACCATGT
1 AGTGTAAGACCATATCTGGGACATGGCATCGGTCTCGATATATGA--GTCAGTGTAAGACCATGT
*
56048170 CTGGGACATGGCATCGGC-CTC-A-AGACCTGAAAGCT
64 CTGGGACATGGCATCGGCAC-CGACAGA--TGAAAGCC
* * * *
56048205 AGTGTAAGACCATATCTGGGACATGGCATCGG-CTTGATAT-T-TGTTAGTGTAAAACCATGTCT
1 AGTGTAAGACCATATCTGGGACATGGCATCGGTCTCGATATATGAGTCAGTGTAAGACCATGTCT
* * *
56048267 AGGATATGGCATCGGCACCGACAGATGAGAGCC
66 GGGACATGGCATCGGCACCGACAGATGAAAGCC
*
56048300 AGTGTAAGACCATGTCTGGGACATGGCATCGGTCTCGATATATGAGAGTCAGTGTAAGACCATGT
1 AGTGTAAGACCATATCTGGGACATGGCATCGGTCTCGATATAT--GAGTCAGTGTAAGACCATGT
** *
56048365 CTGGGACATGGCATCGAG-TTCGA-TGTATG--AGCC
64 CTGGGACATGGCATCG-GCACCGACAG-ATGAAAGCC
* * *
56048398 AGTGTAAGACCATGTCTGGGATATGGCGTCGGT
1 AGTGTAAGACCATATCTGGGACATGGCATCGGT
56048431 ATCTTACCCT
Statistics
Matches: 189, Mismatches: 23, Indels: 26
0.79 0.10 0.11
Matches are distributed among these distances:
95 69 0.37
96 18 0.10
97 18 0.10
98 45 0.24
99 2 0.01
100 36 0.19
101 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (98 bp):
AGTGTAAGACCATATCTGGGACATGGCATCGGTCTCGATATATGAGTCAGTGTAAGACCATGTCT
GGGACATGGCATCGGCACCGACAGATGAAAGCC
Found at i:56053284 original size:21 final size:21
Alignment explanation
Indices: 56053251--56053291 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
56053241 TGGGGAAATT
*
56053251 CAAAATAAATAAT-AATAAAA
1 CAAAAAAAATAATAAATAAAA
56053271 CAAAAAAAAGTAATAAATAAA
1 CAAAAAAAA-TAATAAATAAA
56053292 TAAATCAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 4 0.22
22 6 0.33
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.17
Consensus pattern (21 bp):
CAAAAAAAATAATAAATAAAA
Found at i:56054996 original size:177 final size:178
Alignment explanation
Indices: 56054573--56055018 Score: 635
Period size: 177 Copynumber: 2.5 Consensus size: 178
56054563 CTTCTAGCTT
56054573 AAATCTGCTCCATTACCGATACATGGAGATAAGATTCACCGTCTTCGATTTGCTCCACTACTGCT
1 AAATCTGCTCCATTACCGATACATGGAGATAAGATTCACCGTCTTCGATTTGCTCCACTACTGCT
* * *
56054638 TAGGGAGATAAGATCTGTAACTTTCAGTCTACTCCCTTGCTACCTCAGGAAAGATAAGACTTGTA
66 TAGGGAGATAAGATCTGTAATTTTCAGTCTACTCCCTTACTACCTCAAGAAAGATAAGACTTGTA
* *
56054703 TCTTCAACCTGCTCTCCTGCTACCTCAGAGAGATAAGGCTAGTGGCTA
131 TCTTCAACCTGCTCTCCTGCAACCTCAGAGAGACAAGGCTAGTGGCTA
* * *
56054751 AAATTTGCTCCATTGCCGATACATGGAGATAAGATTCACCGTTTTCGATTTGCTCCACTACTGCT
1 AAATCTGCTCCATTACCGATACATGGAGATAAGATTCACCGTCTTCGATTTGCTCCACTACTGCT
* *
56054816 TAGGGAGATAAGATCTGCAATTTTCAGTCTACTTCCTTACTACCTCAAG-AAGATAAGACTTGTA
66 TAGGGAGATAAGATCTGTAATTTTCAGTCTACTCCCTTACTACCTCAAGAAAGATAAGACTTGTA
* * * * * *
56054880 TCTTGAACCTGCTC-CACTGCAACTTCAGGGAGACGAGGTTGGTGGCTA
131 TCTTCAACCTGCTCTC-CTGCAACCTCAGAGAGACAAGGCTAGTGGCTA
* ** * * * * * *
56054928 AAATCTACTCCATTTTCGATACATGGGGATAAGATTCGCCGTCTTCGATCTACTCCCCTACAGCT
1 AAATCTGCTCCATTACCGATACATGGAGATAAGATTCACCGTCTTCGATTTGCTCCACTACTGCT
*
56054993 TAGGGAGATAAGATCTGTGATTTTCA
66 TAGGGAGATAAGATCTGTAATTTTCA
56055019 CTGATGTCGC
Statistics
Matches: 238, Mismatches: 29, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
176 1 0.00
177 131 0.55
178 106 0.45
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (178 bp):
AAATCTGCTCCATTACCGATACATGGAGATAAGATTCACCGTCTTCGATTTGCTCCACTACTGCT
TAGGGAGATAAGATCTGTAATTTTCAGTCTACTCCCTTACTACCTCAAGAAAGATAAGACTTGTA
TCTTCAACCTGCTCTCCTGCAACCTCAGAGAGACAAGGCTAGTGGCTA
Found at i:56055109 original size:12 final size:12
Alignment explanation
Indices: 56055092--56055116 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56055082 TTATTCCAAA
56055092 TGATTAGGATGC
1 TGATTAGGATGC
56055104 TGATTAGGATGC
1 TGATTAGGATGC
56055116 T
1 T
56055117 ATGATCAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.32, T:0.36
Consensus pattern (12 bp):
TGATTAGGATGC
Found at i:56061723 original size:42 final size:42
Alignment explanation
Indices: 56061673--56061973 Score: 234
Period size: 49 Copynumber: 6.7 Consensus size: 42
56061663 CTTCATTTTC
** *
56061673 TCGATGCCATAGTTCAGCTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
*
56061716 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
56061757 TCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC---AT---AT-TCACATA
*
56061806 TCGATGCCATAGCCCAGCTATGGTTTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC---AT---AT-TCACATA
*
56061855 TCGATGCCATAGCCTAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
* *
56061896 TCTCACTGATGCCATATCCCAGATATGGTCTTACAGTAGCATATATCAC--A
1 --T--C-GATGCCATAGCCCAGCTATGGTCTTAC---A-CATAT-TCACATA
* * *
56061946 CCGATGCCATATCCCAGATATGGTCTTA
1 TCGATGCCATAGCCCAGCTATGGTCTTA
56061974 TACGGAAATC
Statistics
Matches: 225, Mismatches: 13, Indels: 38
0.82 0.05 0.14
Matches are distributed among these distances:
41 9 0.04
42 64 0.28
43 3 0.01
45 29 0.13
46 25 0.11
47 1 0.00
48 2 0.01
49 85 0.38
50 3 0.01
52 4 0.02
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:56061816 original size:49 final size:49
Alignment explanation
Indices: 56061743--56061973 Score: 296
Period size: 49 Copynumber: 4.8 Consensus size: 49
56061733 TATGGTCTTA
*
56061743 CACATATTCATATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAAT
1 CACATA-TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAAT
*
56061793 CACATATCACATATCGATGCCATAGCCCAGCTATGGTTTTACACGTAAT
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAAT
*
56061842 CACATATCACATATCGATGCCATAGCCTAGCTATGGTCTTACACG-AAT
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAAT
* * * * *
56061890 CACATATCTCA-CT-GATGCCATATCCCAGATATGGTCTTACA-GT-AG
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAAT
* * * *
56061935 CATATATCAC--ACCGATGCCATATCCCAGATATGGTCTTA
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTA
56061974 TACGGAAATC
Statistics
Matches: 165, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
45 36 0.22
46 25 0.15
47 1 0.01
48 13 0.08
49 84 0.51
50 6 0.04
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (49 bp):
CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAAT
Found at i:56061822 original size:91 final size:92
Alignment explanation
Indices: 56061708--56061973 Score: 299
Period size: 91 Copynumber: 2.9 Consensus size: 92
56061698 TTACACATCT
*
56061708 TCACATAATGATGCCATAGCCCAGCTATGGTCTTACAC-AT-AT-TCATATATCGATGCCATAGC
1 TCACAT-ATGATGCCATAGCCCAGCTATGGTCTTACACAATCATATCACATATCGATGCCATAGC
56061770 CCAGCTATGGTCTTACACGTAATCACATA
65 CCAGCTATGGTCTTACACG-AATCACATA
*
56061799 TCACATATCGATGCCATAGCCCAGCTATGGTTTTACACGTAATCACATATCACATATCGATGCCA
1 TCACATAT-GATGCCATAGCCCAGCTATGGTCTTACAC--AAT--CATATCACATATCGATGCCA
*
56061864 TAGCCTAGCTATGGTCTTACACGAATCACATA
61 TAGCCCAGCTATGGTCTTACACGAATCACATA
* * * * ** * * * *
56061896 TCTCA-CTGATGCCATATCCCAGATATGGTCTTACAGTAGCATAT-ATCACACCGATGCCATATC
1 TCACATATGATGCCATAGCCCAGCTATGGTCTTACACAATCATATCA-CATATCGATGCCATAGC
*
56061959 CCAGATATGGTCTTA
65 CCAGCTATGGTCTTA
56061974 TACGGAAATC
Statistics
Matches: 150, Mismatches: 16, Indels: 18
0.82 0.09 0.10
Matches are distributed among these distances:
90 3 0.02
91 66 0.44
93 1 0.01
94 2 0.01
95 25 0.17
96 1 0.01
97 15 0.10
98 37 0.25
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.29
Consensus pattern (92 bp):
TCACATATGATGCCATAGCCCAGCTATGGTCTTACACAATCATATCACATATCGATGCCATAGCC
CAGCTATGGTCTTACACGAATCACATA
Found at i:56061939 original size:140 final size:139
Alignment explanation
Indices: 56061708--56061969 Score: 320
Period size: 140 Copynumber: 1.9 Consensus size: 139
56061698 TTACACATCT
*
56061708 TCACATAATGATGCCATAGCCCAGCTATGGTCTTACACATATTCATATATCGATGCCATAGCCCA
1 TCACATAATGATGCCATAGCCCAGCTATGGTCTTACACATATACATATATCGATGCCATAGCCCA
* * * *
56061773 GCTATGGTCTTACACGTAATCACATATCA-CATATCGATGCCATAGCCCAGCTATGGTTTTACAC
66 GATATGGTCTTACACGTAA-CACATAT-ATCACACCGATGCCATAGCCCAGATATGGTTTTACAC
56061837 GTAATCACATA
129 GTAATCACATA
* *
56061848 TCACAT-ATCGATGCCATAGCCTAGCTATGGTCTTACACGA-ATCACATATCTCACTGATGCCAT
1 TCACATAAT-GATGCCATAGCCCAGCTATGGTCTTACAC-ATAT-ACATATAT--C-GATGCCAT
* * *
56061911 ATCCCAGATATGGTCTTACA-GT-A-GCATATATCACACCGATGCCATATCCCAGATATGGT
60 AGCCCAGATATGGTCTTACACGTAACACATATATCACACCGATGCCATAGCCCAGATATGGT
56061970 CTTATACGGA
Statistics
Matches: 105, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
139 3 0.03
140 65 0.62
141 7 0.07
142 1 0.01
143 3 0.03
144 26 0.25
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (139 bp):
TCACATAATGATGCCATAGCCCAGCTATGGTCTTACACATATACATATATCGATGCCATAGCCCA
GATATGGTCTTACACGTAACACATATATCACACCGATGCCATAGCCCAGATATGGTTTTACACGT
AATCACATA
Found at i:56062030 original size:31 final size:31
Alignment explanation
Indices: 56061995--56062112 Score: 191
Period size: 31 Copynumber: 3.8 Consensus size: 31
56061985 CTTGTCACAT
* *
56061995 GTAGCTGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
56062026 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
56062057 GTAGCCGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
56062088 GTAGCAGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
56062113 TGTCATTTGT
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 80 1.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:56062187 original size:50 final size:50
Alignment explanation
Indices: 56062088--56062264 Score: 248
Period size: 50 Copynumber: 3.5 Consensus size: 50
56062078 CACTGATCAG
* ** *
56062088 GTAGCAGAAGCTACCACTTTTCACTTGTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTTTCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGT
* * *
56062139 GTAGTCGAAGCTTTCACTTATCACTTTCAGTTGTCCTTGATCAAATAAGT
1 GTAGCCGAAGCTTTCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
*
56062189 GTAGCCGAAGCTATT-ACTTATCACTTTCATTTTTCCTTGATCAGATAAGT
1 GTAGCCGAAGCT-TTCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
*
56062239 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTTTCACTTATCACTT
56062265 GTTGCCATGG
Statistics
Matches: 112, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
49 1 0.01
50 88 0.79
51 23 0.21
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (50 bp):
GTAGCCGAAGCTTTCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:56072641 original size:18 final size:18
Alignment explanation
Indices: 56072615--56072662 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
56072605 TAAATATTTA
* *
56072615 AAATGAATAAAAAACCAT
1 AAATAAATAAAAAACAAT
56072633 AAATAAATAATAAAACAAT
1 AAATAAATAA-AAAACAAT
56072652 -AATAAA-AAAAA
1 AAATAAATAAAAA
56072663 TTTTGAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 3 0.11
17 2 0.07
18 15 0.56
19 7 0.26
ACGTcount: A:0.75, C:0.06, G:0.02, T:0.17
Consensus pattern (18 bp):
AAATAAATAAAAAACAAT
Found at i:56075677 original size:5 final size:5
Alignment explanation
Indices: 56075667--56075741 Score: 102
Period size: 5 Copynumber: 15.2 Consensus size: 5
56075657 ACTGAATGCA
56075667 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC -AAA- AAAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
*
56075715 AAAA- AAAAGA AAAAC AAAAAC AAAAC A
1 AAAAC AAAA-C AAAAC -AAAAC AAAAC A
56075742 TCATTGAAGA
Statistics
Matches: 64, Mismatches: 1, Indels: 10
0.85 0.01 0.13
Matches are distributed among these distances:
4 10 0.16
5 45 0.70
6 9 0.14
ACGTcount: A:0.83, C:0.16, G:0.01, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:56083864 original size:20 final size:20
Alignment explanation
Indices: 56083820--56083891 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 20
56083810 ATTAAAAGAT
*
56083820 ATATACGTAATATATA-AAA
1 ATATACATAATATATAGAAA
*
56083839 TGTATACATAATATATAGAAA
1 -ATATACATAATATATAGAAA
* * *
56083860 ATATA-ATATTTAAAAAGAATA
1 ATATACATA-ATATATAGAA-A
56083881 ATATACATAAT
1 ATATACATAAT
56083892 GCAAGAATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
19 3 0.07
20 25 0.61
21 10 0.24
22 3 0.07
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (20 bp):
ATATACATAATATATAGAAA
Found at i:56086291 original size:13 final size:13
Alignment explanation
Indices: 56086275--56086299 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56086265 GAAATTAAAG
56086275 ACAGAATTTGAAC
1 ACAGAATTTGAAC
56086288 ACAGAATTTGAA
1 ACAGAATTTGAA
56086300 AATACCTCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (13 bp):
ACAGAATTTGAAC
Found at i:56086460 original size:75 final size:74
Alignment explanation
Indices: 56086298--56086665 Score: 246
Period size: 75 Copynumber: 4.7 Consensus size: 74
56086288 ACAGAATTTG
*
56086298 AAAATACCTCAGCATGTGACCTGAGGCCCCAACTCACTTCTCGCAATATGAGTTGA-TTTTTTGA
1 AAAATACCTCAG--TGT-ACCTGAGG-CTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGA
*
56086362 AAAGTAAAAATTA
62 AAAGCAAAAATTA
* *
56086375 AAAATACCTCAACGTGT-CTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA
1 AAAATACCTC-A-GTGTACCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAA
* *
56086439 AGCAGAAATTG
64 AGCAAAAATTA
* * * * * * *
56086450 AATATTCCTCAGTGTACCCTGAGGTTCAACTCATTTCTTGCAATATGAGTTCATTTTTTTTTAAA
1 AAAATACCTCAGTGTA-CCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGA--TTTTTTT-GA
*
56086515 AGAATTTGCAAAACAAACTTTG
62 A-AA---GC--AA-AAA--TTA
* * * * *
56086537 AAAATAACTCGGCATGTGGCCTGAGGCTCAACTCACCTCTCACAATATGAGTTGA--TTTTTG-A
1 AAAATACCTCAG--TGT-ACCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAA
* *
56086599 AA-CATAAATTG
63 AAGCAAAAATTA
* * * *
56086610 AAAATACCTTAACGTGT-CATGAGGCTCATCTCACCTCTCGCAATATGAGTTGATTT
1 AAAATACC-TCA-GTGTACCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTT
56086666 CTGAAACTTA
Statistics
Matches: 232, Mismatches: 35, Indels: 52
0.73 0.11 0.16
Matches are distributed among these distances:
71 33 0.14
73 18 0.08
74 29 0.12
75 66 0.28
76 1 0.00
77 20 0.09
78 4 0.02
79 3 0.01
82 4 0.02
83 1 0.00
84 1 0.00
85 8 0.03
87 11 0.05
89 33 0.14
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (74 bp):
AAAATACCTCAGTGTACCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAAAG
CAAAAATTA
Found at i:56086692 original size:14 final size:14
Alignment explanation
Indices: 56086675--56086706 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
56086665 TCTGAAACTT
*
56086675 AAAAGCAGAAATTG
1 AAAAGAAGAAATTG
56086689 AAAAGAAGAAATTG
1 AAAAGAAGAAATTG
56086703 AAAA
1 AAAA
56086707 TACCTCAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.66, C:0.03, G:0.19, T:0.12
Consensus pattern (14 bp):
AAAAGAAGAAATTG
Found at i:56097944 original size:8 final size:9
Alignment explanation
Indices: 56097914--56097942 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
56097904 TTAAAAAACT
56097914 AAACTAAAA
1 AAACTAAAA
56097923 AAACTAAAA
1 AAACTAAAA
56097932 AAACTAAAA
1 AAACTAAAA
56097941 AA
1 AA
56097943 CTTAGAGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.10
Consensus pattern (9 bp):
AAACTAAAA
Found at i:56099846 original size:16 final size:16
Alignment explanation
Indices: 56099825--56099864 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
56099815 AAATGTATAC
56099825 ATAATATATAGAAAA-A
1 ATAATATATA-AAAAGA
*
56099841 ATAATATTTAAAAAGA
1 ATAATATATAAAAAGA
56099857 ATAATATA
1 ATAATATA
56099865 CATAATGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (16 bp):
ATAATATATAAAAAGA
Found at i:56100772 original size:19 final size:20
Alignment explanation
Indices: 56100737--56100775 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
56100727 AAGAAAACAA
56100737 AAGAGAGAAGAAGGGAGAGG
1 AAGAGAGAAGAAGGGAGAGG
*
56100757 AAGAGAG-AGGAGGGAGAGG
1 AAGAGAGAAGAAGGGAGAGG
56100776 GGAAAGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (20 bp):
AAGAGAGAAGAAGGGAGAGG
Found at i:56102701 original size:5 final size:4
Alignment explanation
Indices: 56102648--56102699 Score: 70
Period size: 4 Copynumber: 12.8 Consensus size: 4
56102638 ATAGAAAGCG
*
56102648 AAAT AAAT AAAT AAAT AAAT AAAG AAAT GAAAT -AAT AAAT AAAT CAAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT -AAAT
56102697 AAA
1 AAA
56102700 ATGTAATAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
3 3 0.07
4 32 0.74
5 8 0.19
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:56105173 original size:2 final size:2
Alignment explanation
Indices: 56105166--56105195 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
56105156 GTATTCCTTA
56105166 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56105196 TAACTTTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56106405 original size:32 final size:31
Alignment explanation
Indices: 56106361--56106424 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
56106351 GCAAATTTCT
* * *
56106361 TTAATTAGTATGAGTTATCAAATTAAATTAA
1 TTAATTAGTATGAATAATCAAATTAAAGTAA
* *
56106392 TTAATTTATTATGAATAATTAAATTAAAGTAA
1 TTAA-TTAGTATGAATAATCAAATTAAAGTAA
56106424 T
1 T
56106425 CACTTATAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 4 0.15
32 23 0.85
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.44
Consensus pattern (31 bp):
TTAATTAGTATGAATAATCAAATTAAAGTAA
Found at i:56108117 original size:22 final size:24
Alignment explanation
Indices: 56108055--56108117 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 24
56108045 GTGCAACTAT
*
56108055 ATGCATGAGTAAACAGAGAGCACCG
1 ATGCATG-CTAAACAGAGAGCACCG
56108080 ATG--TGCTAATAC-GAGAGCA-C-
1 ATGCATGCTAA-ACAGAGAGCACCG
56108100 ATGCATGCTAAACAGAGA
1 ATGCATGCTAAACAGAGA
56108118 ACACTTACGT
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
20 3 0.09
21 3 0.09
22 20 0.61
23 4 0.12
25 3 0.09
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.16
Consensus pattern (24 bp):
ATGCATGCTAAACAGAGAGCACCG
Found at i:56111622 original size:16 final size:16
Alignment explanation
Indices: 56111601--56111632 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
56111591 TTTGCAACGC
56111601 CCCAAAAATCTCGAAA
1 CCCAAAAATCTCGAAA
*
56111617 CCCAAAAATCTTGAAA
1 CCCAAAAATCTCGAAA
56111633 TCCTGAACTT
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:0.50, C:0.28, G:0.06, T:0.16
Consensus pattern (16 bp):
CCCAAAAATCTCGAAA
Found at i:56112888 original size:8 final size:8
Alignment explanation
Indices: 56112865--56112931 Score: 98
Period size: 8 Copynumber: 8.4 Consensus size: 8
56112855 ATGAATTGAC
*
56112865 AAAAGCTG
1 AAAAGCCG
*
56112873 AAATGCCG
1 AAAAGCCG
56112881 AAAAGCCG
1 AAAAGCCG
56112889 AAAAGCCG
1 AAAAGCCG
56112897 AAAAGCCG
1 AAAAGCCG
56112905 AAAAGCCG
1 AAAAGCCG
* *
56112913 AAATGTCG
1 AAAAGCCG
56112921 AAAAGCCG
1 AAAAGCCG
56112929 AAA
1 AAA
56112932 GTTGGGCTAC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 52 1.00
ACGTcount: A:0.49, C:0.21, G:0.24, T:0.06
Consensus pattern (8 bp):
AAAAGCCG
Found at i:56113192 original size:29 final size:29
Alignment explanation
Indices: 56113142--56113249 Score: 96
Period size: 29 Copynumber: 3.8 Consensus size: 29
56113132 TGTGAGCATG
* *
56113142 AATAT-AATATGATTTGGACCTAATGGGC
1 AATATGAATATGAATTGGGCCTAATGGGC
* *
56113170 AATATGAATGTGAATTGGGCCTAGTGGGC
1 AATATGAATATGAATTGGGCCTAATGGGC
* * *
56113199 CATAAGAATATGAACTGGGCC-AGATGGGC
1 AATATGAATATGAATTGGGCCTA-ATGGGC
* * *
56113228 CATTTGAATAAG-ATTGGGCCTA
1 AATATGAATATGAATTGGGCCTA
56113250 GTAGGCCATA
Statistics
Matches: 64, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
28 13 0.20
29 51 0.80
ACGTcount: A:0.32, C:0.13, G:0.28, T:0.27
Consensus pattern (29 bp):
AATATGAATATGAATTGGGCCTAATGGGC
Found at i:56113210 original size:58 final size:57
Alignment explanation
Indices: 56113147--56113259 Score: 129
Period size: 58 Copynumber: 2.0 Consensus size: 57
56113137 GCATGAATAT
** ** *
56113147 AATATGATTTGGACCTA-ATGGGCAATATGAATGTGAATTGGGCCTAGTGGGCCATAAG
1 AATATGAACTGGACC-AGATGGGCAATATGAATAAG-ATTGGGCCTAGTAGGCCATAAG
* * *
56113205 AATATGAACTGGGCCAGATGGGCCATTTGAATAAGATTGGGCCTAGTAGGCCATA
1 AATATGAACTGGACCAGATGGGCAATATGAATAAGATTGGGCCTAGTAGGCCATA
56113260 TGCATGTATG
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
57 20 0.43
58 26 0.57
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (57 bp):
AATATGAACTGGACCAGATGGGCAATATGAATAAGATTGGGCCTAGTAGGCCATAAG
Found at i:56117690 original size:29 final size:29
Alignment explanation
Indices: 56117657--56117736 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
56117647 ATATGATTTG
* *
56117657 GGCCTAATGGGCCATATGAATGTGAATTA
1 GGCCTAATGGGCCATATGAATATGAACTA
* * *
56117686 GGCCTAGTGGGCCATAAGAATATGAACTG
1 GGCCTAATGGGCCATATGAATATGAACTA
*
56117715 GGCC-AGATGGGCCATTTGAATA
1 GGCCTA-ATGGGCCATATGAATA
56117737 AGATTGGGCC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 1 0.02
29 41 0.98
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (29 bp):
GGCCTAATGGGCCATATGAATATGAACTA
Found at i:56117709 original size:58 final size:57
Alignment explanation
Indices: 56117646--56117758 Score: 138
Period size: 58 Copynumber: 2.0 Consensus size: 57
56117636 GCATGAATAT
** ** *
56117646 AATATGATTTGGGCCTA-ATGGGCCATATGAATGTGAATTAGGCCTAGTGGGCCATAAG
1 AATATGAACTGGGCC-AGATGGGCCATATGAATAAG-ATTAGGCCTAGTAGGCCATAAG
* *
56117704 AATATGAACTGGGCCAGATGGGCCATTTGAATAAGATTGGGCCTAGTAGGCCATA
1 AATATGAACTGGGCCAGATGGGCCATATGAATAAGATTAGGCCTAGTAGGCCATA
56117759 TGCATGTATG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
57 19 0.40
58 28 0.60
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (57 bp):
AATATGAACTGGGCCAGATGGGCCATATGAATAAGATTAGGCCTAGTAGGCCATAAG
Found at i:56122096 original size:12 final size:12
Alignment explanation
Indices: 56122079--56122103 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56122069 GTTTGGCACA
56122079 ACCTAGCACACG
1 ACCTAGCACACG
56122091 ACCTAGCACACG
1 ACCTAGCACACG
56122103 A
1 A
56122104 GCGTGTGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.40, G:0.16, T:0.08
Consensus pattern (12 bp):
ACCTAGCACACG
Found at i:56127010 original size:30 final size:30
Alignment explanation
Indices: 56126976--56127093 Score: 218
Period size: 30 Copynumber: 3.9 Consensus size: 30
56126966 CACGGACTGG
*
56126976 CATATGGGCTTGTGGCCAGCCCGTGTGGCT
1 CATATGGGCTTGCGGCCAGCCCGTGTGGCT
*
56127006 CATATGGGCTTGCGGCCAGCCTGTGTGGCT
1 CATATGGGCTTGCGGCCAGCCCGTGTGGCT
56127036 CATATGGGCTTGCGGCCAGCCCGTGTGGCT
1 CATATGGGCTTGCGGCCAGCCCGTGTGGCT
56127066 CATATGGGCTTGCGGCCAGCCCGTGTGG
1 CATATGGGCTTGCGGCCAGCCCGTGTGG
56127094 AAATGCCCAG
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 85 1.00
ACGTcount: A:0.10, C:0.28, G:0.37, T:0.25
Consensus pattern (30 bp):
CATATGGGCTTGCGGCCAGCCCGTGTGGCT
Found at i:56128969 original size:12 final size:12
Alignment explanation
Indices: 56128917--56128971 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
56128907 ATAAACATAA
56128917 AAAGA-AAATAT
1 AAAGATAAATAT
*
56128928 AAATATAAATAT
1 AAAGATAAATAT
*
56128940 AAATATAAATAT
1 AAAGATAAATAT
*
56128952 -AA-ATAAACAT
1 AAAGATAAATAT
56128962 AAAGATAAAT
1 AAAGATAAAT
56128972 GGACTCAATG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
10 7 0.18
11 8 0.21
12 23 0.61
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (12 bp):
AAAGATAAATAT
Found at i:56128970 original size:6 final size:6
Alignment explanation
Indices: 56128922--56128956 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
56128912 CATAAAAAGA
56128922 AAATAT AAATAT AAATAT AAATAT AAATAT AAATA
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATA
56128957 AACATAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATAT
Found at i:56130583 original size:12 final size:12
Alignment explanation
Indices: 56130566--56130592 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
56130556 TAGAAAACAA
56130566 AAATAAAGAAAT
1 AAATAAAGAAAT
56130578 AAATAAAGAAAT
1 AAATAAAGAAAT
56130590 AAA
1 AAA
56130593 GAATAATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (12 bp):
AAATAAAGAAAT
Found at i:56136212 original size:42 final size:43
Alignment explanation
Indices: 56136133--56136234 Score: 118
Period size: 42 Copynumber: 2.4 Consensus size: 43
56136123 TCCCGGACGT
* ** *
56136133 GGTCTTACATGTAATTCAATATCGATGCCTCTGTCCCAGGCAA
1 GGTCTTACATGTAAATCAATATCGATGCCGATGTCCCAGACAA
*
56136176 GGTCTTACATG-AAATCAGATA-CGATGCCGATGTCCCAGACAT
1 GGTCTTACATGTAAATCA-ATATCGATGCCGATGTCCCAGACAA
* *
56136218 GGTCTTATACGTAAATC
1 GGTCTTACATGTAAATC
56136235 TCAACCGAGG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 31 0.62
43 19 0.38
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (43 bp):
GGTCTTACATGTAAATCAATATCGATGCCGATGTCCCAGACAA
Found at i:56138942 original size:6 final size:6
Alignment explanation
Indices: 56138931--56138956 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
56138921 TTAGTAAACA
56138931 AAAATT AAAATT AAAATT AAAATT AA
1 AAAATT AAAATT AAAATT AAAATT AA
56138957 TTGTAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:56141853 original size:46 final size:46
Alignment explanation
Indices: 56141803--56141978 Score: 183
Period size: 46 Copynumber: 3.8 Consensus size: 46
56141793 TGTTTGGGCA
*
56141803 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*** * * ** *
56141849 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGC-AAACG
* * * *
56141896 TCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
56141942 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
56141979 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 24, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
46 69 0.67
47 34 0.33
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:56141958 original size:93 final size:93
Alignment explanation
Indices: 56141799--56141971 Score: 283
Period size: 93 Copynumber: 1.9 Consensus size: 93
56141789 AGGATGTTTG
* * *
56141799 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAG
56141864 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * * *
56141892 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTCATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAG
56141957 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
56141972 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:56148180 original size:23 final size:23
Alignment explanation
Indices: 56148098--56148185 Score: 60
Period size: 23 Copynumber: 4.0 Consensus size: 23
56148088 TAAAATTTTA
*
56148098 AAAATTATGAT-TATT--TATTT
1 AAAATTATTATATATTAATATTT
**
56148118 -AAATTATTATACCTTAATATTT
1 AAAATTATTATATATTAATATTT
** * *
56148140 ATTACTATCATA-ACTTAATATTT
1 AAAATTATTATATA-TTAATATTT
*
56148163 AAAATTATTATATATTAAAATTT
1 AAAATTATTATATATTAATATTT
56148186 TAGGATTGCT
Statistics
Matches: 49, Mismatches: 13, Indels: 9
0.69 0.18 0.13
Matches are distributed among these distances:
19 9 0.18
20 2 0.04
22 5 0.10
23 32 0.65
24 1 0.02
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (23 bp):
AAAATTATTATATATTAATATTT
Found at i:56148727 original size:15 final size:15
Alignment explanation
Indices: 56148709--56148786 Score: 63
Period size: 14 Copynumber: 5.1 Consensus size: 15
56148699 ATACTACAAA
56148709 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
56148724 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
56148741 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
*
56148758 ATA-TTAATATTAA-
1 ATATTTATTATTAAT
*
56148771 ATATTT-TTAATAAT
1 ATATTTATTATTAAT
56148785 AT
1 AT
56148787 GTGAAAAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
13 8 0.16
14 13 0.25
15 12 0.24
16 1 0.02
17 7 0.14
18 1 0.02
19 9 0.18
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:56148847 original size:16 final size:15
Alignment explanation
Indices: 56148795--56148846 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
56148785 ATGTGAAAAA
56148795 TATTATTTAA-AATT
1 TATTATTTAATAATT
* *
56148809 TATTATTAAAATAATA
1 TATTATT-TAATAATT
*
56148825 AATTATATTAATAATT
1 TATTAT-TTAATAATT
56148841 TATTAT
1 TATTAT
56148847 AATAATTAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 7 0.24
15 2 0.07
16 19 0.66
17 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTATTTAATAATT
Found at i:56148852 original size:16 final size:16
Alignment explanation
Indices: 56148805--56148852 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
56148795 TATTATTTAA
56148805 AATTTATTATTAA-AAT
1 AATTTATTA-TAATAAT
** *
56148821 AATAAATTATATTAAT
1 AATTTATTATAATAAT
56148837 AATTTATTATAATAAT
1 AATTTATTATAATAAT
56148853 TAAATATGTA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTTATTATAATAAT
Found at i:56163165 original size:23 final size:23
Alignment explanation
Indices: 56163125--56163169 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
56163115 TTCAGCCGCA
56163125 ATTTCTCACATTTTCAATTCAATC
1 ATTTCTCACATTTTCAA-TCAATC
*
56163149 ATTTTTCAC-TTTTCAATCAAT
1 ATTTCTCACATTTTCAATCAAT
56163170 TTTCAATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 7 0.35
24 8 0.40
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTCTCACATTTTCAATCAATC
Found at i:56163463 original size:15 final size:15
Alignment explanation
Indices: 56163421--56163463 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
56163411 TACTTACTAT
* *
56163421 AAAATAAATAAATTT
1 AAAATAAATAACTTA
*
56163436 AAAATTAAT-ACTTA
1 AAAATAAATAACTTA
56163450 AAAATAAATAACTT
1 AAAATAAATAACTT
56163464 GAATTATAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATAAATAACTTA
Found at i:56166272 original size:34 final size:35
Alignment explanation
Indices: 56166225--56166298 Score: 107
Period size: 34 Copynumber: 2.1 Consensus size: 35
56166215 AGATTTTTCA
56166225 GGTTTAGGGTTTTGCTAAAATA-ATTTA-GGTTTAG
1 GGTTTAGGGTTTTGCTAAAATACA-TTAGGGTTTAG
* *
56166259 GGTTTAGGTTTTTGTTAAAATACATTAGGGTTTAG
1 GGTTTAGGGTTTTGCTAAAATACATTAGGGTTTAG
56166294 GGTTT
1 GGTTT
56166299 TAGTGAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
34 23 0.64
35 13 0.36
ACGTcount: A:0.24, C:0.03, G:0.27, T:0.46
Consensus pattern (35 bp):
GGTTTAGGGTTTTGCTAAAATACATTAGGGTTTAG
Found at i:56166848 original size:126 final size:126
Alignment explanation
Indices: 56166476--56166849 Score: 559
Period size: 126 Copynumber: 3.0 Consensus size: 126
56166466 TTTTCCTTAC
* *
56166476 AAAAATAATTTTGAGAAGACGTTTCTAAACAAATAGTGTCAAAAACGCTTTAAGCAGGATGCACT
1 AAAAATAATTTTGAGAAGACGTTTCTAAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCAAT
** * * * * *
56166541 GTGTGCAAAATTACTGAAAAAAGCTCCAATGTGGACGCTTTTTTTTTACAGTATTTCCTGA
66 GTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTCCTGA
* * *
56166602 AAAAATAATTTTGAGAAGACGTTTCTTAACAAATAGTGTCAAAAATGCTTCAAGCAGAATGCAAT
1 AAAAATAATTTTGAGAAGACGTTTCTAAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCAAT
* *
56166667 GTCAACAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAATAGTTCCTGA
66 GTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTCCTGA
* * * *
56166728 AAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAAAAACACTTCAATCAGGATGCAAT
1 AAAAATAATTTTGAGAAGACGTTTCTAAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCAAT
* * *
56166793 ATCAGCAAAATTTCTGAAAAAAACTCCCACGTGGACGCTCTTTTTCTACAGTAGTTC
66 GTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTC
56166850 ATGTTTGGCC
Statistics
Matches: 223, Mismatches: 25, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
126 223 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (126 bp):
AAAAATAATTTTGAGAAGACGTTTCTAAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCAAT
GTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTCCTGA
Found at i:56170997 original size:14 final size:14
Alignment explanation
Indices: 56170974--56171004 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
56170964 TATTAGTTAT
*
56170974 ATACATAATACTAA
1 ATACAAAATACTAA
56170988 ATACAAAATACTAA
1 ATACAAAATACTAA
56171002 ATA
1 ATA
56171005 TGAAACAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (14 bp):
ATACAAAATACTAA
Found at i:56171963 original size:26 final size:25
Alignment explanation
Indices: 56171934--56172023 Score: 74
Period size: 25 Copynumber: 3.4 Consensus size: 25
56171924 ATAAAAAATT
56171934 ATAAATTACAAATTAATTAAAATTAC
1 ATAAATTA-AAATTAATTAAAATTAC
* * *
56171960 ATAAATGAAAA-AATATTAAATAATATTC
1 ATAAATTAAAATTA-ATT-AA-AAT-TAC
* *
56171988 AAAAATTAAAATTAATTAGAATTAC
1 ATAAATTAAAATTAATTAAAATTAC
*
56172013 ATAAATGAAAA
1 ATAAATTAAAA
56172024 AATATTAAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
24 1 0.02
25 17 0.35
26 12 0.24
27 4 0.08
28 14 0.29
29 1 0.02
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.31
Consensus pattern (25 bp):
ATAAATTAAAATTAATTAAAATTAC
Found at i:56171991 original size:19 final size:18
Alignment explanation
Indices: 56171969--56172050 Score: 55
Period size: 18 Copynumber: 4.6 Consensus size: 18
56171959 CATAAATGAA
56171969 AAAATATTAAATAATATTC
1 AAAA-ATTAAATAATATTC
*
56171988 AAAAATTAAA-ATTAATT-
1 AAAAATTAAATAAT-ATTC
* * **
56172005 -AGAATTACATAA-ATGAA
1 AAAAATTAAATAATAT-TC
56172022 AAAATATTAAATAATATTC
1 AAAA-ATTAAATAATATTC
56172041 AAAAATTAAA
1 AAAAATTAAA
56172051 ATTAACCTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 15
0.66 0.13 0.21
Matches are distributed among these distances:
15 2 0.04
16 7 0.15
17 3 0.06
18 17 0.36
19 16 0.34
20 2 0.04
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAAATTAAATAATATTC
Found at i:56172000 original size:53 final size:53
Alignment explanation
Indices: 56171936--56172055 Score: 222
Period size: 53 Copynumber: 2.2 Consensus size: 53
56171926 AAAAAATTAT
56171936 AAATTACAAATTAATTAAAATTACATAAATGAAAAAATATTAAATAATATTCAA
1 AAATTA-AAATTAATTAAAATTACATAAATGAAAAAATATTAAATAATATTCAA
*
56171990 AAATTAAAATTAATTAGAATTACATAAATGAAAAAATATTAAATAATATTCAA
1 AAATTAAAATTAATTAAAATTACATAAATGAAAAAATATTAAATAATATTCAA
56172043 AAATTAAAATTAA
1 AAATTAAAATTAA
56172056 CCTTTACCAT
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
53 59 0.91
54 6 0.09
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.32
Consensus pattern (53 bp):
AAATTAAAATTAATTAAAATTACATAAATGAAAAAATATTAAATAATATTCAA
Found at i:56172024 original size:26 final size:25
Alignment explanation
Indices: 56171934--56172033 Score: 71
Period size: 26 Copynumber: 3.9 Consensus size: 25
56171924 ATAAAAAATT
* *
56171934 ATAAATTACAAATTAATTAAAATTAC
1 ATAAATGAAAAATTAATT-AAATTAC
*
56171960 ATAAATGAAAAAAT-ATTAAATAATATTC
1 ATAAATGAAAAATTAATTAAAT--TA--C
* *
56171988 AAAAAT-TAAAATTAATTAGAATTAC
1 ATAAATGAAAAATTAATTA-AATTAC
*
56172013 ATAAATGAAAAAAT-ATTAAAT
1 ATAAATGAAAAATTAATTAAAT
56172034 AATATTCAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
24 7 0.12
25 13 0.22
26 18 0.31
27 7 0.12
28 10 0.17
29 3 0.05
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (25 bp):
ATAAATGAAAAATTAATTAAATTAC
Found at i:56172259 original size:21 final size:21
Alignment explanation
Indices: 56172210--56172259 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
56172200 TAAAGAAAGC
** *
56172210 TTTGAGAAATTTAATGAGAAA
1 TTTGAGAGCTTTAAGGAGAAA
56172231 TTTGAGAGCTTTAAGGAGAAA
1 TTTGAGAGCTTTAAGGAGAAA
*
56172252 TTTTAGAG
1 TTTGAGAG
56172260 TTTTTTTTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (21 bp):
TTTGAGAGCTTTAAGGAGAAA
Found at i:56177776 original size:23 final size:21
Alignment explanation
Indices: 56177731--56177778 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
56177721 AGTTTTAAAT
* *
56177731 TTTTATAATATTTATTCAATA
1 TTTTATAATATTCATGCAATA
56177752 TTTTATAATATATCATGCAATTA
1 TTTTATAATAT-TCATGCAA-TA
56177775 TTTT
1 TTTT
56177779 TTTATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 6 0.26
23 6 0.26
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTATAATATTCATGCAATA
Found at i:56181256 original size:2 final size:2
Alignment explanation
Indices: 56181249--56181273 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56181239 TTAAATATCA
56181249 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
56181274 GATTTTTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.