Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 47 of 82
Found at i:17368497 original size:24 final size:24
Alignment explanation
Indices: 17368469--17368521 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
17368459 ATGGTTAGCG
*
17368469 TGTGACACGTCATATACAAAAACC
1 TGTGACAAGTCATATACAAAAACC
* *
17368493 TGTGATAAGTCATGTACAAAAACC
1 TGTGACAAGTCATATACAAAAACC
17368517 TGTGA
1 TGTGA
17368522 AACTTTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.25
Consensus pattern (24 bp):
TGTGACAAGTCATATACAAAAACC
Found at i:17372014 original size:16 final size:16
Alignment explanation
Indices: 17371990--17372023 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17371980 ACTATGCAGG
17371990 TGATCTTGGTGGGGCA
1 TGATCTTGGTGGGGCA
* *
17372006 TGATTTTGGTGGTGCA
1 TGATCTTGGTGGGGCA
17372022 TG
1 TG
17372024 TGTATCCTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.41, T:0.38
Consensus pattern (16 bp):
TGATCTTGGTGGGGCA
Found at i:17372426 original size:6 final size:6
Alignment explanation
Indices: 17372415--17372443 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
17372405 GCTACTGCAA
17372415 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
17372444 GGATTATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:17388609 original size:27 final size:27
Alignment explanation
Indices: 17388557--17388610 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
17388547 TGTTTAGAGG
* *
17388557 TGTTCCAAGTATGAAAACGCCTAGGGA
1 TGTTCCAAGTATGAAAACACCCAGGGA
*
17388584 TGTTCCAAGTGT-AAAAGCACCCAGGGA
1 TGTTCCAAGTATGAAAA-CACCCAGGGA
17388611 CAATCCCAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.20
Consensus pattern (27 bp):
TGTTCCAAGTATGAAAACACCCAGGGA
Found at i:17393353 original size:20 final size:20
Alignment explanation
Indices: 17393328--17393367 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17393318 TTGAGGGCTC
*
17393328 GGGTTTGCGCTGGCAGGAGA
1 GGGTTTACGCTGGCAGGAGA
*
17393348 GGGTTTATGCTGGCAGGAGA
1 GGGTTTACGCTGGCAGGAGA
17393368 AGAGTGAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.12, G:0.47, T:0.23
Consensus pattern (20 bp):
GGGTTTACGCTGGCAGGAGA
Found at i:17393556 original size:111 final size:111
Alignment explanation
Indices: 17393362--17393592 Score: 365
Period size: 111 Copynumber: 2.1 Consensus size: 111
17393352 TTATGCTGGC
* * * *
17393362 AGGAGAAGAGTGAGAGAGAGGAAGCTCGATCGTCACTCCACTAGATCCGGCGCAAGGAAGAGAGG
1 AGGAGAAGAGTGAGAGAGAGGAAGCTCGACCGTCACGCCACCAGATCCAGCGCAAGGAAGAGAGG
* **
17393427 GGAGACACCCGATCGACGCCAAGGGGGTTGGAAGCCGGCAAAGTGT
66 GGAGACACCCGATCGACGCCAAGGGGGTTAGAAGCCGGCAAAACGT
* * *
17393473 AGGAGAAGAGTGAGAGAGAGGAAGCTCGACCGTCGCGCCACCAGATTCAGCGCAGGGAAGAGAGG
1 AGGAGAAGAGTGAGAGAGAGGAAGCTCGACCGTCACGCCACCAGATCCAGCGCAAGGAAGAGAGG
17393538 GGAGACACCCGATCGACGCCAAGGGGGTTAGAAGCCGGCAAAACGT
66 GGAGACACCCGATCGACGCCAAGGGGGTTAGAAGCCGGCAAAACGT
17393584 AGG-GAAGAG
1 AGGAGAAGAG
17393593 AGGGGAGACA
Statistics
Matches: 110, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
110 6 0.05
111 104 0.95
ACGTcount: A:0.32, C:0.21, G:0.39, T:0.09
Consensus pattern (111 bp):
AGGAGAAGAGTGAGAGAGAGGAAGCTCGACCGTCACGCCACCAGATCCAGCGCAAGGAAGAGAGG
GGAGACACCCGATCGACGCCAAGGGGGTTAGAAGCCGGCAAAACGT
Found at i:17394243 original size:16 final size:17
Alignment explanation
Indices: 17394219--17394251 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
17394209 AAATAAAAAA
17394219 AATAAAATAAAA-ATGT
1 AATAAAATAAAATATGT
*
17394235 AATAGAATAAAATATGT
1 AATAAAATAAAATATGT
17394252 GGATATCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (17 bp):
AATAAAATAAAATATGT
Found at i:17394540 original size:3 final size:3
Alignment explanation
Indices: 17394532--17394566 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
17394522 AAATCTTCAA
* *
17394532 AAT AAT AAT AAT AGT AAT AAT AAT AAA AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
17394567 ATAGACAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:17394567 original size:9 final size:9
Alignment explanation
Indices: 17394530--17394605 Score: 52
Period size: 9 Copynumber: 8.4 Consensus size: 9
17394520 CAAAATCTTC
17394530 AAAATAATA
1 AAAATAATA
* *
17394539 ATAATAGTA
1 AAAATAATA
*
17394548 ATAATAATA
1 AAAATAATA
17394557 AAAATAAT-
1 AAAATAATA
*
17394565 -AAATAGACA
1 AAAATA-ATA
17394574 AAAATAA-A
1 AAAATAATA
17394582 AAAAT-ATCA
1 AAAATAAT-A
17394591 AAGAATAAATA
1 AA-AAT-AATA
17394602 AAAA
1 AAAA
17394606 ATAAAATGAT
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
7 6 0.11
8 7 0.13
9 26 0.48
10 10 0.19
11 3 0.06
12 2 0.04
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.21
Consensus pattern (9 bp):
AAAATAATA
Found at i:17394904 original size:3 final size:3
Alignment explanation
Indices: 17394896--17394983 Score: 61
Period size: 3 Copynumber: 31.7 Consensus size: 3
17394886 ATTGCTTACA
17394896 AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT CAA- AAT -AT AA- AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
* *
17394937 AAT ATAT AAT AAAT AAT -AT AAA AAT AA- AA- AAT AGT AA- AA- AAT
1 AAT A-AT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17394979 AAT AA
1 AAT AA
17394984 ATTCTTGTTC
Statistics
Matches: 71, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
2 20 0.28
3 43 0.61
4 8 0.11
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:17394910 original size:9 final size:9
Alignment explanation
Indices: 17394896--17394983 Score: 61
Period size: 8 Copynumber: 10.6 Consensus size: 9
17394886 ATTGCTTACA
17394896 AATAATAAT
1 AATAATAAT
17394905 AATAATAAT
1 AATAATAAT
17394914 AAT-ATAAT
1 AATAATAAT
17394922 AATCAA-AAT
1 AAT-AATAAT
17394931 -ATAA-AA-
1 AATAATAAT
17394937 AATATATAAT
1 AATA-ATAAT
17394947 AAATAAT-AT
1 -AATAATAAT
*
17394956 AAAAATAA-
1 AATAATAAT
*
17394964 AA-AATAGT
1 AATAATAAT
17394972 AA-AA-AAT
1 AATAATAAT
17394979 AATAA
1 AATAA
17394984 ATTCTTGTTC
Statistics
Matches: 66, Mismatches: 3, Indels: 21
0.73 0.03 0.23
Matches are distributed among these distances:
7 15 0.23
8 24 0.36
9 20 0.30
10 3 0.05
11 4 0.06
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (9 bp):
AATAATAAT
Found at i:17394940 original size:29 final size:29
Alignment explanation
Indices: 17394895--17394982 Score: 92
Period size: 29 Copynumber: 2.9 Consensus size: 29
17394885 GATTGCTTAC
17394895 AAATAATAATAATA-ATAATAATATAATAATCAA
1 AAATAA-AA-AATATATAATAA-ATAAT-AT-AA
17394928 AATATAAAAAATATATAATAAATAATATAA
1 AA-ATAAAAAATATATAATAAATAATATAA
17394958 AAATAAAAAATAGTA-AA-AAATAATA
1 AAATAAAAAATA-TATAATAAATAATA
17394983 AATTCTTGTT
Statistics
Matches: 52, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
28 8 0.15
29 12 0.23
30 6 0.12
31 2 0.04
32 9 0.17
33 11 0.21
34 4 0.08
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (29 bp):
AAATAAAAAATATATAATAAATAATATAA
Found at i:17394943 original size:25 final size:23
Alignment explanation
Indices: 17394915--17394960 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
17394905 AATAATAATA
17394915 ATATAATAATCAAAATATAAAAAAT
1 ATATAATAA--AAAATATAAAAAAT
*
17394940 ATATAATAAATAATATAAAAA
1 ATATAATAAAAAATATAAAAA
17394961 TAAAAAATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
25 9 0.45
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (23 bp):
ATATAATAAAAAATATAAAAAAT
Found at i:17395108 original size:24 final size:24
Alignment explanation
Indices: 17395080--17395145 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 24
17395070 AATGTAAGGT
* *
17395080 ATAAAAAAAATAATTAGACATAAA
1 ATAAAAAAAATAATTAAAAATAAA
* * *
17395104 ATAAAAAACATGATAAAAAATAAA
1 ATAAAAAAAATAATTAAAAATAAA
* *
17395128 ATGAAAATAATAATTAAA
1 ATAAAAAAAATAATTAAA
17395146 TTATAAAAAA
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (24 bp):
ATAAAAAAAATAATTAAAAATAAA
Found at i:17396161 original size:14 final size:15
Alignment explanation
Indices: 17396133--17396162 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17396123 TTTTGTTTAG
17396133 TGCATTTGTTTATTT
1 TGCATTTGTTTATTT
17396148 TGCATTTG-TTATTT
1 TGCATTTGTTTATTT
17396162 T
1 T
17396163 ATTACTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (15 bp):
TGCATTTGTTTATTT
Found at i:17407195 original size:37 final size:37
Alignment explanation
Indices: 17407143--17407431 Score: 301
Period size: 37 Copynumber: 7.6 Consensus size: 37
17407133 GAAAAAAGGT
17407143 TTCGTTGCCTCAGTTTTGAGGAATTCATTTTTAAAGA
1 TTCGTTGCCTCAGTTTTGAGGAATTCATTTTTAAAGA
* * *
17407180 TACGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAAGTT
1 TTCGTTGCCTCAGTTTTGAGGAATTCATTTTT-AAAG-A
* *
17407219 TTTGTTGCCTCAGTTTTGAGGAATTCATTTTTAGAGA
1 TTCGTTGCCTCAGTTTTGAGGAATTCATTTTTAAAGA
* * * * *
17407256 TACCTTGCCTTAGTTTTGAGGAGTTCATTTTTAAAAGC
1 TTCGTTGCCTCAGTTTTGAGGAATTCATTTTT-AAAGA
* * * * *
17407294 TTTGATTGCCTCAGTTTTGAAGAGTTCATTTTGAAAGT
1 TTCG-TTGCCTCAGTTTTGAGGAATTCATTTTTAAAGA
* * *
17407332 TTTGTTGCCTCAGCTTTGAGGAGTTCATTTTTAAA-A
1 TTCGTTGCCTCAGTTTTGAGGAATTCATTTTTAAAGA
* *
17407368 GTCACGTTGCCTCAGTTTTGAGGAATTCATTTTTAAAAGT
1 -T-TCGTTGCCTCAGTTTTGAGGAATTCATTTTT-AAAGA
* * *
17407408 TTTGTTGCCTAAGCTTTGAGGAAT
1 TTCGTTGCCTCAGTTTTGAGGAAT
17407432 CTCAAAAAAA
Statistics
Matches: 209, Mismatches: 35, Indels: 15
0.81 0.14 0.06
Matches are distributed among these distances:
37 86 0.41
38 65 0.31
39 58 0.28
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.43
Consensus pattern (37 bp):
TTCGTTGCCTCAGTTTTGAGGAATTCATTTTTAAAGA
Found at i:17407264 original size:76 final size:75
Alignment explanation
Indices: 17407136--17407404 Score: 378
Period size: 76 Copynumber: 3.5 Consensus size: 75
17407126 AAAAAAGGAA
17407136 AAAAGGTTTCGTTGCCTCAGTTTTGAGGAATTCATTTTTAAAGATACGTTGCCTCAGTTTTGAGG
1 AAAA-GTTTCGTTGCCTCAGTTTTGAGGAATTCATTTTTAAAGATACGTTGCCTCAGTTTTGAGG
17407201 AGTTCATTTTT
65 AGTTCATTTTT
* * * *
17407212 AAAAGTTTTTGTTGCCTCAGTTTTGAGGAATTCATTTTTAGAGATACCTTGCCTTAGTTTTGAGG
1 AAAAG-TTTCGTTGCCTCAGTTTTGAGGAATTCATTTTTAAAGATACGTTGCCTCAGTTTTGAGG
17407277 AGTTCATTTTT
65 AGTTCATTTTT
* * * * ** *
17407288 AAAAGCTTT-GATTGCCTCAGTTTTGAAGAGTTCATTTTGAAAGTTTTGTTGCCTCAGCTTTGAG
1 AAAAG-TTTCG-TTGCCTCAGTTTTGAGGAATTCATTTTTAAAGATACGTTGCCTCAGTTTTGAG
17407352 GAGTTCATTTTT
64 GAGTTCATTTTT
**
17407364 AAAAGTCACGTTGCCTCAGTTTTGAGGAATTCATTTTTAAA
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAATTCATTTTTAAA
17407405 AGTTTTGTTG
Statistics
Matches: 170, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
75 31 0.18
76 139 0.82
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (75 bp):
AAAAGTTTCGTTGCCTCAGTTTTGAGGAATTCATTTTTAAAGATACGTTGCCTCAGTTTTGAGGA
GTTCATTTTT
Found at i:17407350 original size:113 final size:115
Alignment explanation
Indices: 17407147--17407426 Score: 381
Period size: 113 Copynumber: 2.5 Consensus size: 115
17407137 AAAGGTTTCG
** *
17407147 TTGCCTCAGTTTTGAGGAATTCATTTTT-AAAGATACGTTGCCTCAGTTTTGAGGAGTTCATTTT
1 TTGCCTCAGTTTTGAGGAATTCATTTTTAAAAGATTTGTTGCCTCAGTTTTGAAGAGTTCATTTT
* *
17407211 TAAAAGTTTTTGTTGCCTCAGTTTTGAGGAATTCATTTTT-AGAGAT-ACC
66 TAAAAGTTTTTGTTGCCTCAGCTTTGAGGAATTCATTTTTAAAAG-TCACC
* * *
17407260 TTGCCTTAGTTTTGAGGAGTTCATTTTTAAAAGCTTTGATTGCCTCAGTTTTGAAGAGTTCA-TT
1 TTGCCTCAGTTTTGAGGAATTCATTTTTAAAAGATTTG-TTGCCTCAGTTTTGAAGAGTTCATTT
* * *
17407324 TTGAAAG-TTTTGTTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAGTCACG
65 TTAAAAGTTTTTGTTGCCTCAGCTTTGAGGAATTCATTTTTAAAAGTCACC
* * *
17407374 TTGCCTCAGTTTTGAGGAATTCATTTTTAAAAGTTTTGTTGCCTAAGCTTTGA
1 TTGCCTCAGTTTTGAGGAATTCATTTTTAAAAGATTTGTTGCCTCAGTTTTGA
17407427 GGAATCTCAA
Statistics
Matches: 147, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
113 71 0.48
114 54 0.37
115 22 0.15
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.44
Consensus pattern (115 bp):
TTGCCTCAGTTTTGAGGAATTCATTTTTAAAAGATTTGTTGCCTCAGTTTTGAAGAGTTCATTTT
TAAAAGTTTTTGTTGCCTCAGCTTTGAGGAATTCATTTTTAAAAGTCACC
Found at i:17408235 original size:111 final size:111
Alignment explanation
Indices: 17408041--17408267 Score: 339
Period size: 111 Copynumber: 2.0 Consensus size: 111
17408031 GTTTATGCTG
* *
17408041 GCAGGAGAAGAGTGAAAGAGAGGAAGCTCGACCGTTACACCACCAGATCCGGCGTAGGGAAGAGA
1 GCAGGAGAAGAGTGAAAGAGAGGAAGCCCGACCGTCACACCACCAGATCCGGCGTAGGGAAGAGA
* *
17408106 GGGGAGACATCTGATCGGCGCCAAGGGGGTTAGAAGCCGGCAAAGT
66 GGGGAGACATCTGATCGGCGCCAAGGGGGTTAGAAGCCGACAAAGC
* * * * *
17408152 GCAGGAGAAGAGTGAGAGAGAGGAAGCCCGACTGTCGCGCCTCCAGATCCGGCGTAGGGAAGAGA
1 GCAGGAGAAGAGTGAAAGAGAGGAAGCCCGACCGTCACACCACCAGATCCGGCGTAGGGAAGAGA
* *
17408217 GGGGAGACA-CTCGATCGGCGCCAATGGGGTTGGAAGCCGACAAAGC
66 GGGGAGACATCT-GATCGGCGCCAAGGGGGTTAGAAGCCGACAAAGC
17408263 GCAGG
1 GCAGG
17408268 GAAAAGAGGG
Statistics
Matches: 104, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
110 2 0.02
111 102 0.98
ACGTcount: A:0.30, C:0.21, G:0.39, T:0.10
Consensus pattern (111 bp):
GCAGGAGAAGAGTGAAAGAGAGGAAGCCCGACCGTCACACCACCAGATCCGGCGTAGGGAAGAGA
GGGGAGACATCTGATCGGCGCCAAGGGGGTTAGAAGCCGACAAAGC
Found at i:17408297 original size:58 final size:58
Alignment explanation
Indices: 17408207--17408320 Score: 192
Period size: 58 Copynumber: 2.0 Consensus size: 58
17408197 GATCCGGCGT
* * *
17408207 AGGGAAGAGAGGGGAGACACTCGATCGGCGCCAATGGGGTTGGAAGCCGACAAAGCGC
1 AGGGAAAAGAGGGGAGACACCCGATCGGCGCCAAGGGGGTTGGAAGCCGACAAAGCGC
*
17408265 AGGGAAAAGAGGGGAGACACCCGATCGGCGCCAAGGGGGTTGGAAGCCGGCAAAGC
1 AGGGAAAAGAGGGGAGACACCCGATCGGCGCCAAGGGGGTTGGAAGCCGACAAAGC
17408321 ATAGCAAAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.30, C:0.21, G:0.42, T:0.07
Consensus pattern (58 bp):
AGGGAAAAGAGGGGAGACACCCGATCGGCGCCAAGGGGGTTGGAAGCCGACAAAGCGC
Found at i:17408334 original size:58 final size:59
Alignment explanation
Indices: 17408211--17408339 Score: 181
Period size: 58 Copynumber: 2.2 Consensus size: 59
17408201 CGGCGTAGGG
* * * *
17408211 AAGAGAGGGGAGACACTCGATCGGCGCCAATGGGGTTGGAAGCCGACAAAGCGCAGGGA
1 AAGAGAGGGGAGACACCCGATCGGCGCCAAGGGGGTTGGAAGCCGACAAAGCACAGGCA
* *
17408270 AA-AGAGGGGAGACACCCGATCGGCGCCAAGGGGGTTGGAAGCCGGCAAAGCATA-GCA
1 AAGAGAGGGGAGACACCCGATCGGCGCCAAGGGGGTTGGAAGCCGACAAAGCACAGGCA
*
17408327 AAGAGAGGAGAGA
1 AAGAGAGGGGAGA
17408340 GGTTGGCCGG
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
57 4 0.06
58 56 0.90
59 2 0.03
ACGTcount: A:0.33, C:0.19, G:0.40, T:0.07
Consensus pattern (59 bp):
AAGAGAGGGGAGACACCCGATCGGCGCCAAGGGGGTTGGAAGCCGACAAAGCACAGGCA
Found at i:17408923 original size:16 final size:17
Alignment explanation
Indices: 17408899--17408931 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
17408889 AAATAAAAAA
17408899 AATAAAATAAAA-ATGT
1 AATAAAATAAAATATGT
*
17408915 AATAGAATAAAATATGT
1 AATAAAATAAAATATGT
17408932 GGATATCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (17 bp):
AATAAAATAAAATATGT
Found at i:17409223 original size:3 final size:3
Alignment explanation
Indices: 17409215--17409249 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
17409205 AAATCCTCAA
* *
17409215 AAT AAT AAT AAT AGT AAT AAT AAT AAA AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
17409250 ATAGACAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:17409601 original size:14 final size:14
Alignment explanation
Indices: 17409582--17409642 Score: 53
Period size: 14 Copynumber: 4.7 Consensus size: 14
17409572 CTTACAAATA
17409582 ATAATAATAATAAT
1 ATAATAATAATAAT
17409596 ATAATAATCAA-AAT
1 ATAATAAT-AATAAT
*
17409610 TTAA-AA-AAT-AT
1 ATAATAATAATAAT
17409621 ATAAT-A-AATAAT
1 ATAATAATAATAAT
*
17409633 ATAAAAATAA
1 ATAATAATAA
17409643 AAAATAGTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
11 11 0.29
12 6 0.16
13 3 0.08
14 16 0.42
15 2 0.05
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:17409621 original size:23 final size:23
Alignment explanation
Indices: 17409577--17409639 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 23
17409567 GATTGCTTAC
17409577 AAATAATAATAATAATAATATAATAAT
1 AAATAAT-ATAA-AA-AATAT-ATAAT
* *
17409604 CAA-AATTTAAAAAATATATAAT
1 AAATAATATAAAAAATATATAAT
17409626 AAATAATATAAAAA
1 AAATAATATAAAAA
17409640 TAAAAAATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
22 7 0.23
23 14 0.45
24 2 0.06
25 3 0.10
26 3 0.10
27 2 0.06
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
AAATAATATAAAAAATATATAAT
Found at i:17409636 original size:37 final size:37
Alignment explanation
Indices: 17409581--17409662 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 37
17409571 GCTTACAAAT
* * *
17409581 AATAATAATAATAATATAATAAT-CAAAAT-TTAAAA
1 AATAATAATAATAATATAAAAATAAAAAATAGTAAAA
17409616 AATATATAATAAATAATATAAAAATAAAAAATAGTAAAA
1 AATA-ATAAT-AATAATATAAAAATAAAAAATAGTAAAA
17409655 AATAATAA
1 AATAATAA
17409663 AATTCTTGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
35 4 0.10
36 5 0.12
37 13 0.32
38 9 0.22
39 9 0.22
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (37 bp):
AATAATAATAATAATATAAAAATAAAAAATAGTAAAA
Found at i:17409647 original size:18 final size:17
Alignment explanation
Indices: 17409621--17409665 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
17409611 TAAAAAATAT
*
17409621 ATAATAAATAATATAAAA
1 ATAAAAAATAATA-AAAA
*
17409639 ATAAAAAATAGTAAAAA
1 ATAAAAAATAATAAAAA
17409656 ATAATAAAAT
1 ATAA-AAAAT
17409666 TCTTGTTCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
ATAAAAAATAATAAAAA
Found at i:17409655 original size:10 final size:9
Alignment explanation
Indices: 17409605--17409664 Score: 50
Period size: 10 Copynumber: 6.2 Consensus size: 9
17409595 TATAATAATC
*
17409605 AAAATTTAA
1 AAAATATAA
17409614 AAAATATATA
1 AAAATATA-A
*
17409624 ATAAATAATAT
1 A-AAAT-ATAA
17409635 AAAA-ATAA
1 AAAATATAA
17409643 AAAATAGTAA
1 AAAATA-TAA
17409653 AAAATAATAA
1 AAAAT-ATAA
17409663 AA
1 AA
17409665 TTCTTGTTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
8 7 0.17
9 8 0.19
10 18 0.43
11 6 0.14
12 3 0.07
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (9 bp):
AAAATATAA
Found at i:17409832 original size:25 final size:26
Alignment explanation
Indices: 17409764--17409835 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 26
17409754 AAGGTATAAA
* *
17409764 AAAATAATAATT-AGTCATAAAATAG
1 AAAATAATAATTAAATAATAAAATAG
* * * *
17409789 AAAA-CATGATAAAAAAATAAAAT-G
1 AAAATAATAATTAAATAATAAAATAG
17409813 AAAATAATAATTAAATAATAAAA
1 AAAATAATAATTAAATAATAAAA
17409836 AATGACAAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
24 9 0.26
25 26 0.74
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.24
Consensus pattern (26 bp):
AAAATAATAATTAAATAATAAAATAG
Found at i:17413331 original size:45 final size:45
Alignment explanation
Indices: 17413275--17413366 Score: 159
Period size: 45 Copynumber: 2.0 Consensus size: 45
17413265 TTATATATTA
*
17413275 AAAGTATATATATAATAGTAATTATATT-CTTTATAATATGATAT
1 AAAGTACATATATAATAGTAATTATATTCCTTTATAATATGATAT
17413319 NAAAGTACATATATAATAGTAATTATATTCCTTTATAATATGATAT
1 -AAAGTACATATATAATAGTAATTATATTCCTTTATAATATGATAT
17413365 AA
1 AA
17413367 TATTCAAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 29 0.64
46 16 0.36
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.42
Consensus pattern (45 bp):
AAAGTACATATATAATAGTAATTATATTCCTTTATAATATGATAT
Found at i:17418519 original size:2 final size:2
Alignment explanation
Indices: 17418514--17418550 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
17418504 GTGTGTTTCT
17418514 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
17418551 GGTAAGCATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17433318 original size:7 final size:7
Alignment explanation
Indices: 17433308--17433340 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
17433298 AAAAACAAAT
*
17433308 AAGATGA
1 AAGAAGA
17433315 AAGAAGA
1 AAGAAGA
17433322 AAGAAGA
1 AAGAAGA
17433329 AAGAAGA
1 AAGAAGA
17433336 AAGAA
1 AAGAA
17433341 ACCAAACCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (7 bp):
AAGAAGA
Found at i:17436126 original size:15 final size:15
Alignment explanation
Indices: 17436103--17436132 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17436093 TATTTTCATT
*
17436103 TTATTATATTTTTTA
1 TTATCATATTTTTTA
17436118 TTATCATATTTTTTA
1 TTATCATATTTTTTA
17436133 CTTTATTTTT
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:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATCATATTTTTTA
Found at i:17436412 original size:17 final size:18
Alignment explanation
Indices: 17436376--17436413 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
17436366 TTTTATCATC
*
17436376 ATTTTTTTATCTATTGTT
1 ATTTATTTATCTATTGTT
*
17436394 ATTTATTTAT-TATTTTT
1 ATTTATTTATCTATTGTT
17436411 ATT
1 ATT
17436414 GAGTAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (18 bp):
ATTTATTTATCTATTGTT
Found at i:17436680 original size:3 final size:3
Alignment explanation
Indices: 17436672--17436724 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
17436662 TATAAAGCTA
* * *
17436672 TAT TAT TAT TAT TCT T-T TAT TTT TCAT TAT TAT TTT TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TA-T TAT TAT
17436718 TAT TAT T
1 TAT TAT T
17436725 TTTTAAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.83
4 5 0.12
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (3 bp):
TAT
Found at i:17436723 original size:13 final size:13
Alignment explanation
Indices: 17436672--17436725 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
17436662 TATAAAGCTA
17436672 TATTATTATTATT
1 TATTATTATTATT
* *
17436685 CTTTTATTTTTCA-T
1 -TATTATTATT-ATT
*
17436699 TATTATTTTTATT
1 TATTATTATTATT
17436712 TATTATTATTATT
1 TATTATTATTATT
17436725 T
1 T
17436726 TTTAAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
12 1 0.03
13 23 0.68
14 9 0.26
15 1 0.03
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:17438019 original size:21 final size:21
Alignment explanation
Indices: 17437971--17438023 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
17437961 AAATTTACGT
* *
17437971 CTGGCAAGGTGAGGGTGGTTA
1 CTGGCAGGGTGAGGGTGGTGA
* *
17437992 CTAGCAGGGTGAGGGTGGTGG
1 CTGGCAGGGTGAGGGTGGTGA
*
17438013 TTGGCAGGGTG
1 CTGGCAGGGTG
17438024 TGGACGCACC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.15, C:0.09, G:0.53, T:0.23
Consensus pattern (21 bp):
CTGGCAGGGTGAGGGTGGTGA
Found at i:17439877 original size:18 final size:15
Alignment explanation
Indices: 17439854--17439906 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 15
17439844 TTTTCCTCAC
17439854 TTTTCTTTCTTTTTCT
1 TTTTCTTT-TTTTTCT
17439870 AATTTTCTTTTTTTTCCT
1 --TTTTCTTTTTTTT-CT
17439888 TTTTCTTTTTTTTCT
1 TTTTCTTTTTTTTCT
17439903 TTTT
1 TTTT
17439907 TCCATTAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.18
16 13 0.38
17 5 0.15
18 10 0.29
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTCTTTTTTTTCT
Found at i:17439884 original size:9 final size:9
Alignment explanation
Indices: 17439854--17439907 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
17439844 TTTTCCTCAC
17439854 TTTTCTTTCT
1 TTTTCTTT-T
**
17439864 TTTTC-TAA
1 TTTTCTTTT
17439872 TTTTCTTTT
1 TTTTCTTTT
*
17439881 TTTTC--CT
1 TTTTCTTTT
17439888 TTTTCTTTT
1 TTTTCTTTT
17439897 TTTTCTTTT
1 TTTTCTTTT
17439906 TT
1 TT
17439908 CCATTAATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
7 6 0.17
8 5 0.14
9 19 0.54
10 5 0.14
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:17439889 original size:24 final size:24
Alignment explanation
Indices: 17439853--17439907 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
17439843 TTTTTCCTCA
*
17439853 CTTTTCTTTCTTTTTC-TAATTTT
1 CTTTTTTTTCTTTTTCTTAATTTT
**
17439876 CTTTTTTTTCCTTTTTCTTTTTTTT
1 CTTTTTTTT-CTTTTTCTTAATTTT
17439901 CTTTTTT
1 CTTTTTT
17439908 CCATTAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 8 0.30
24 7 0.26
25 12 0.44
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (24 bp):
CTTTTTTTTCTTTTTCTTAATTTT
Found at i:17439908 original size:23 final size:24
Alignment explanation
Indices: 17439853--17439909 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
17439843 TTTTTCCTCA
*
17439853 CTTTTCTTTCTTTTTCTAATTTTCTT
1 CTTTT-TTCCTTTTTCT-ATTTTCTT
*
17439879 -TTTTTTCCTTTTTCT-TTTTTTT
1 CTTTTTTCCTTTTTCTATTTTCTT
17439901 CTTTTTTCC
1 CTTTTTTCC
17439910 ATTAATTACC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 6 0.21
23 8 0.29
24 10 0.36
25 4 0.14
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (24 bp):
CTTTTTTCCTTTTTCTATTTTCTT
Found at i:17443563 original size:3 final size:3
Alignment explanation
Indices: 17443555--17443581 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
17443545 AGTTTAGCTT
17443555 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
17443582 CAAAGAGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:17447247 original size:36 final size:37
Alignment explanation
Indices: 17447207--17447284 Score: 140
Period size: 37 Copynumber: 2.1 Consensus size: 37
17447197 TTTACTCAAA
17447207 TTTTT-AAATTTTTAAAGTTCTCCACCCATTTTTCTT
1 TTTTTAAAATTTTTAAAGTTCTCCACCCATTTTTCTT
*
17447243 TTTTTAAAATTTTTAAAGTTCTCCACCTATTTTTCTT
1 TTTTTAAAATTTTTAAAGTTCTCCACCCATTTTTCTT
17447280 TTTTT
1 TTTTT
17447285 TTCTTTTCTG
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
36 5 0.12
37 35 0.88
ACGTcount: A:0.22, C:0.17, G:0.03, T:0.59
Consensus pattern (37 bp):
TTTTTAAAATTTTTAAAGTTCTCCACCCATTTTTCTT
Found at i:17447366 original size:18 final size:17
Alignment explanation
Indices: 17447345--17447384 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
17447335 TAATTTTTTC
17447345 TATTTATA-TTACTATTAT
1 TATTTATATTTA-T-TTAT
17447363 TATTTATATTTATTTAT
1 TATTTATATTTATTTAT
17447380 TATTT
1 TATTT
17447385 TCAATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.43
18 9 0.43
19 3 0.14
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTTATATTTATTTAT
Found at i:17450108 original size:16 final size:17
Alignment explanation
Indices: 17450078--17450115 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
17450068 ATCATAAACA
*
17450078 AAAAATGAATTAAAAAT
1 AAAAATGAATAAAAAAT
*
17450095 AAAAAT-AATAAAAATT
1 AAAAATGAATAAAAAAT
17450111 AAAAA
1 AAAAA
17450116 ATAAAGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAAATGAATAAAAAAT
Found at i:17450116 original size:17 final size:17
Alignment explanation
Indices: 17450077--17450119 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
17450067 AATCATAAAC
17450077 AAAAAATGAATTAAAAAT
1 AAAAAAT-AATTAAAAAT
17450095 -AAAAATAA-TAAAAATT
1 AAAAAATAATTAAAAA-T
17450111 AAAAAATAA
1 AAAAAATAA
17450120 AGAAAGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 6 0.26
16 3 0.13
17 14 0.61
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (17 bp):
AAAAAATAATTAAAAAT
Found at i:17450441 original size:11 final size:10
Alignment explanation
Indices: 17450425--17450467 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 10
17450415 AAATTTATCA
17450425 ATAGAAAAAAT
1 ATAG-AAAAAT
17450436 ATAGAAAAAT
1 ATAGAAAAAT
*
17450446 CAAAGAAAAAT
1 -ATAGAAAAAT
17450457 AT-GAAAAAT
1 ATAGAAAAAT
17450466 AT
1 AT
17450468 GCAATGGGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 9 0.31
10 7 0.24
11 13 0.45
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (10 bp):
ATAGAAAAAT
Found at i:17451120 original size:275 final size:275
Alignment explanation
Indices: 17450623--17451135 Score: 875
Period size: 275 Copynumber: 1.9 Consensus size: 275
17450613 GAAAACACCC
17450623 GATCGAGCTGAGGGTTCGTTGCCGGCTAAGAGAAAAAAGGGCTTGGAGTTTACCACCGGTTGGGA
1 GATCGAGCTGAGGGTTCGTTGCCGGCTAAGAGAAAAAAGGGCTTGGAGTTTACCACCGGTTGGGA
*
17450688 GGTAAGCTAGAGAGAGAGAGGTTCGACGCCTAAGGGAGAGAAAGGAAAGGTCCCATTTTGGGTGG
66 GGTAAGCTAGAGAGAGAGAGGTTCGACGCCTAAAGGAGAGAAAGGAAAGGTCCCATTTTGGGTGG
* * * * *
17450753 CCGGCGATTGGAAGGCTAGAGAGGAAAAAGGAACGGTGGTGAGAGAGAGAGAAAGGAGTCGCCGG
131 CCGACGACTGAAAGGCTAGAAAGGAAAAAGGAACGATGGTGAGAGAGAGAGAAAGGAGTCGCCGG
17450818 TGTATGGGTGAGAGAGAAAGGTGAGAAGAGAAGTTGGGGGGGTTAGAGAGAAGTGAGAGAGTCCG
196 TGTATGGGTGAGAGAGAAAGGTGAGAAGAGAAGTTGGGGGGGTTAGAGAGAAGTGAGAGAGTCCG
17450883 GCTAGAGAAAGGATT
261 GCTAGAGAAAGGATT
* * * *
17450898 GATCGGGCTGAGGGTTCGTTGCCTGCTAGGAGAAAAAAGGGCTTGGAGTTTACCTCCGGTTGGGA
1 GATCGAGCTGAGGGTTCGTTGCCGGCTAAGAGAAAAAAGGGCTTGGAGTTTACCACCGGTTGGGA
**
17450963 GGTAAGCTAGAGAGAGAGAGGTTCGGTGCCTAAAGGAGAGAAAGGAAAGGTCCCATTTTGGGTGG
66 GGTAAGCTAGAGAGAGAGAGGTTCGACGCCTAAAGGAGAGAAAGGAAAGGTCCCATTTTGGGTGG
* * *
17451028 CTGACGACTGAAAGGCTAGAAAGGAAGAAA-GAACGATGGTGAGAGAGAGCGAAAGGAGTCGTCG
131 CCGACGACTGAAAGGCTAGAAAGGAA-AAAGGAACGATGGTGAGAGAGAGAGAAAGGAGTCGCCG
17451092 GTGTATGGGTGAGAGAGAAAGGTGAGAAGAGAAGTTGGGGGGGT
195 GTGTATGGGTGAGAGAGAAAGGTGAGAAGAGAAGTTGGGGGGGT
17451136 NNNNNNNNNN
Statistics
Matches: 222, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
275 219 0.99
276 3 0.01
ACGTcount: A:0.30, C:0.11, G:0.42, T:0.17
Consensus pattern (275 bp):
GATCGAGCTGAGGGTTCGTTGCCGGCTAAGAGAAAAAAGGGCTTGGAGTTTACCACCGGTTGGGA
GGTAAGCTAGAGAGAGAGAGGTTCGACGCCTAAAGGAGAGAAAGGAAAGGTCCCATTTTGGGTGG
CCGACGACTGAAAGGCTAGAAAGGAAAAAGGAACGATGGTGAGAGAGAGAGAAAGGAGTCGCCGG
TGTATGGGTGAGAGAGAAAGGTGAGAAGAGAAGTTGGGGGGGTTAGAGAGAAGTGAGAGAGTCCG
GCTAGAGAAAGGATT
Found at i:17452117 original size:7 final size:7
Alignment explanation
Indices: 17452105--17452146 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
17452095 TACACACGAC
17452105 AAAAAAT
1 AAAAAAT
17452112 AAAAAAT
1 AAAAAAT
*
17452119 AAAAAAC
1 AAAAAAT
17452126 AAAAAAT
1 AAAAAAT
*
17452133 AAATAAT
1 AAAAAAT
17452140 AATAAAA
1 AA-AAAA
17452147 AATCTAAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
7 27 0.90
8 3 0.10
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAAAT
Found at i:17452127 original size:21 final size:22
Alignment explanation
Indices: 17452103--17452146 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
17452093 AATACACACG
17452103 ACAAAAAATAAAAAATAA-AAA
1 ACAAAAAATAAAAAATAATAAA
*
17452124 ACAAAAAATAAATAATAATAAA
1 ACAAAAAATAAAAAATAATAAA
17452146 A
1 A
17452147 AATCTAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.14
Consensus pattern (22 bp):
ACAAAAAATAAAAAATAATAAA
Found at i:17452310 original size:20 final size:20
Alignment explanation
Indices: 17452285--17452351 Score: 64
Period size: 23 Copynumber: 3.1 Consensus size: 20
17452275 AATGAAATAG
17452285 AAAATAATAAAAAATATAAT
1 AAAATAATAAAAAATATAAT
*
17452305 AAAATAAAAATAAGAAT-TAATT
1 AAAATAATAA-AA-AATATAA-T
17452327 AATAATAACTAAAAAATATAGAT
1 AA-AATAA-TAAAAAATATA-AT
17452350 AA
1 AA
17452352 TTGCATTAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
20 9 0.24
21 5 0.13
22 9 0.24
23 12 0.32
24 3 0.08
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.25
Consensus pattern (20 bp):
AAAATAATAAAAAATATAAT
Found at i:17464714 original size:38 final size:37
Alignment explanation
Indices: 17464444--17464770 Score: 415
Period size: 37 Copynumber: 8.8 Consensus size: 37
17464434 GAAAAAGGTT
* *
17464444 TCGTTGCCTCAATTTTGAGGAATTCATTTTTAAAGGT-
1 TCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAA-GTC
* ** *
17464481 ACGTTGCCTCAACTTTGAGGAGCTCATTTTTAAAAGTTC
1 TCGTTGCCTCAGTTTTGAGGAGTTCATTTTT-AAAG-TC
* * * *
17464520 TCGTTGTCTTAGTTTTGAGGAGTTTACTTTTAAAGTC
1 TCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAGTC
* * *
17464557 TTGATGCCTCAGCTTTGAGGAGTTCATTTTTAAAGTC
1 TCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAGTC
17464594 TCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAGTC
1 TCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAGTC
17464631 TCGTTGCCTCAGTTTTGAGGAGTTCA-TTTTAAAGTC
1 TCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAGTC
* *
17464667 TCGGTGCCTCAGTTTTGAGGAATTCATTTTTAAAAGTC
1 TCGTTGCCTCAGTTTTGAGGAGTTCATTTTT-AAAGTC
*
17464705 TCGTGGCCTCAGTTTTGAGGAGTTCATTTTTAAAAGTC
1 TCGTTGCCTCAGTTTTGAGGAGTTCATTTTT-AAAGTC
* * * *
17464743 GCATTGTCTCAGTTTTGAGGATTTCATT
1 TCGTTGCCTCAGTTTTGAGGAGTTCATT
17464771 AAAAAAAAAA
Statistics
Matches: 253, Mismatches: 32, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
36 34 0.13
37 124 0.49
38 72 0.28
39 23 0.09
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (37 bp):
TCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAGTC
Found at i:17464924 original size:16 final size:17
Alignment explanation
Indices: 17464894--17464931 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
17464884 ATCATAAACA
*
17464894 AAAAATGAATGAAAAAT
1 AAAAATGAATAAAAAAT
*
17464911 AAAAAT-AATAAAAATT
1 AAAAATGAATAAAAAAT
17464927 AAAAA
1 AAAAA
17464932 ATAAAGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (17 bp):
AAAAATGAATAAAAAAT
Found at i:17464932 original size:17 final size:17
Alignment explanation
Indices: 17464893--17464950 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
17464883 AATCATAAAC
17464893 AAAAAATGAATGAAAAAT
1 AAAAAAT-AATGAAAAAT
17464911 -AAAAATAAT-AAAAATT
1 AAAAAATAATGAAAAA-T
*
17464927 AAAAAATAAAGAAAGAAT
1 AAAAAATAATGAAA-AAT
17464945 GAAAAA
1 -AAAAA
17464951 GGGTGGAGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
15 5 0.15
16 4 0.12
17 14 0.41
18 4 0.12
19 7 0.21
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.16
Consensus pattern (17 bp):
AAAAAATAATGAAAAAT
Found at i:17465934 original size:277 final size:276
Alignment explanation
Indices: 17465436--17465977 Score: 870
Period size: 277 Copynumber: 2.0 Consensus size: 276
17465426 ACGGAAGCAC
* * * *
17465436 CTGATTGGGCTGAGGGTTCGTTGCCGGCTAGGAGGAAAAGGGGCTTGGAGTTTACCGCTAGTTGG
1 CTGATCGGGCTGAGGGTTCGTTGCCGGCTAGGAGAAAAAAGGGCTTGGAGTTTACCGCTAGTTAG
* *
17465501 GAGGTAAGCTAGAGAGAGAGAGGTTCGGCGCCTAAGAGAGAGAAAAGAAAGGTCTCATTTTGGGT
66 GAGGTAAGCTAGAGAGAGAGAGGTTCGACGCCTAAGAGAGAGAAAAGAAAGGTCCCATTTTGGGT
* * * *
17465566 GGTCGGCGACTAGAAGGCTAGAGAGGAAGAAGGAACGGTGGTGAGAGAGAGCGAAAGGAGTCGTC
131 GGCCGGCGACTAGAAGGCTAGAAAGGAAAAAGGAACGATGGTGAGAGAGAGCGAAAGGAGTCGTC
* *
17465631 GGTGTATGGGTGAGAAAGAAAGGTGAGAAAAGAAGTT-GGGGGGGTTAGAGAGAAGTGAGAGAGT
196 GGTGTATGGGTGAGAAAGAAAGGTGAGAAAAGAAGTTGGGGGGGGTTAGAGAGAAATGAAAGAGT
17465695 CCGGCCAGAGAGAGGA
261 CCGGCCAGAGAGAGGA
* *
17465711 CTGATCGGGCTGAGGGTTCGTTGCCGGCTAGGAGAAAAAAGGGCTTGGAGTTTACCGTTGGTTAG
1 CTGATCGGGCTGAGGGTTCGTTGCCGGCTAGGAGAAAAAAGGGCTTGGAGTTTACCGCTAGTTAG
*
17465776 GAGGTAAGCTAGAGAGAGAGAGAGGTTCGACGCCTAAGGGAGAGAAAAGAAAGGTCCCATTTTGG
66 GAGGTAAGCT--AGAGAGAGAGAGGTTCGACGCCTAAGAGAGAGAAAAGAAAGGTCCCATTTTGG
* *
17465841 GTGGCCGGCGATTGGAAGGCTAGAAAGGAAAAAGGAACGATGGTGAGAGAGAGCGAAAGGAGTCG
129 GTGGCCGGCGACTAGAAGGCTAGAAAGGAAAAAGGAACGATGGTGAGAGAGAGCGAAAGGAGTCG
* *
17465906 TCGGTGTATGGGTGAGAGAGAAAGGTGAGAAGAGAAGTTGGGGGGGGGGTTAGAGAGAAATGAAA
194 TCGGTGTATGGGTGAGAAAGAAAGGTGAGAAAAGAAGTT--GGGGGGGGTTAGAGAGAAATGAAA
17465971 GAGTCCG
257 GAGTCCG
17465978 ACCGGTAGAG
Statistics
Matches: 243, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
275 69 0.28
277 146 0.60
280 28 0.12
ACGTcount: A:0.30, C:0.11, G:0.42, T:0.17
Consensus pattern (276 bp):
CTGATCGGGCTGAGGGTTCGTTGCCGGCTAGGAGAAAAAAGGGCTTGGAGTTTACCGCTAGTTAG
GAGGTAAGCTAGAGAGAGAGAGGTTCGACGCCTAAGAGAGAGAAAAGAAAGGTCCCATTTTGGGT
GGCCGGCGACTAGAAGGCTAGAAAGGAAAAAGGAACGATGGTGAGAGAGAGCGAAAGGAGTCGTC
GGTGTATGGGTGAGAAAGAAAGGTGAGAAAAGAAGTTGGGGGGGGTTAGAGAGAAATGAAAGAGT
CCGGCCAGAGAGAGGA
Found at i:17467070 original size:7 final size:7
Alignment explanation
Indices: 17467058--17467099 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
17467048 TACACACGAC
17467058 AAAAAAT
1 AAAAAAT
17467065 AAAAAAT
1 AAAAAAT
*
17467072 AAAAAAC
1 AAAAAAT
17467079 AAAAAAT
1 AAAAAAT
*
17467086 AAATAAT
1 AAAAAAT
17467093 AATAAAA
1 AA-AAAA
17467100 AATCTAAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
7 27 0.90
8 3 0.10
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAAAT
Found at i:17467080 original size:21 final size:22
Alignment explanation
Indices: 17467056--17467099 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
17467046 AATACACACG
17467056 ACAAAAAATAAAAAATAA-AAA
1 ACAAAAAATAAAAAATAATAAA
*
17467077 ACAAAAAATAAATAATAATAAA
1 ACAAAAAATAAAAAATAATAAA
17467099 A
1 A
17467100 AATCTAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.14
Consensus pattern (22 bp):
ACAAAAAATAAAAAATAATAAA
Found at i:17467263 original size:20 final size:20
Alignment explanation
Indices: 17467238--17467304 Score: 64
Period size: 23 Copynumber: 3.1 Consensus size: 20
17467228 AATGAAATAG
17467238 AAAATAATAAAAAATATAAT
1 AAAATAATAAAAAATATAAT
*
17467258 AAAATAA-AAATAATAATTAATT
1 AAAATAATAAAAAAT-A-TAA-T
17467280 AATAATAACTAAAAAATATAGAT
1 AA-AATAA-TAAAAAATATA-AT
17467303 AA
1 AA
17467305 TTGCATTAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
19 6 0.16
20 8 0.21
21 3 0.08
22 3 0.08
23 10 0.26
24 2 0.05
25 6 0.16
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (20 bp):
AAAATAATAAAAAATATAAT
Found at i:17467273 original size:17 final size:17
Alignment explanation
Indices: 17467247--17467297 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
17467237 GAAAATAATA
17467247 AAAAAT-ATAATAAAAT
1 AAAAATAATAATAAAAT
* *
17467263 AAAAATAATAATTAATT
1 AAAAATAATAATAAAAT
*
17467280 AATAATAACTAA-AAAAT
1 AAAAATAA-TAATAAAAT
17467297 A
1 A
17467298 TAGATAATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 6 0.21
17 19 0.68
18 3 0.11
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAATAATAATAAAAT
Found at i:17467297 original size:14 final size:13
Alignment explanation
Indices: 17467211--17467297 Score: 52
Period size: 14 Copynumber: 6.6 Consensus size: 13
17467201 GTAAGGTGTA
*
17467211 AAAAAATAGTAAT
1 AAAAAATAATAAT
* * *
17467224 TAGAAATGA-AAT
1 AAAAAATAATAAT
*
17467236 AGAAAATAATAA-
1 AAAAAATAATAAT
* *
17467248 AAAATATAATAAA
1 AAAAAATAATAAT
17467261 ATAAAAATAATAATT
1 A-AAAAATAATAA-T
**
17467276 AATTAATAATAACT
1 AAAAAATAATAA-T
17467290 AAAAAATA
1 AAAAAATA
17467298 TAGATAATTG
Statistics
Matches: 53, Mismatches: 17, Indels: 7
0.69 0.22 0.09
Matches are distributed among these distances:
12 18 0.34
13 8 0.15
14 26 0.49
15 1 0.02
ACGTcount: A:0.69, C:0.01, G:0.05, T:0.25
Consensus pattern (13 bp):
AAAAAATAATAAT
Found at i:17469303 original size:30 final size:32
Alignment explanation
Indices: 17469267--17469326 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 32
17469257 GTCTTTTGAT
* *
17469267 TTTATGTTAATTTT-TTC-TTATTTTTTCAAA
1 TTTATGTCAATTTTCTTCATTATTTCTTCAAA
17469297 TTTATGTCAATTTTCTTCATTATTTCTTCA
1 TTTATGTCAATTTTCTTCATTATTTCTTCA
17469327 CCAAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 13 0.50
31 3 0.12
32 10 0.38
ACGTcount: A:0.22, C:0.12, G:0.03, T:0.63
Consensus pattern (32 bp):
TTTATGTCAATTTTCTTCATTATTTCTTCAAA
Found at i:17469743 original size:14 final size:14
Alignment explanation
Indices: 17469724--17469766 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
17469714 GTTTATATCA
17469724 TGTAGAGAATACCC
1 TGTAGAGAATACCC
*
17469738 TGTAGATGATATTCCC
1 TGTAGA-GA-ATACCC
*
17469754 TGAAGAGAATACC
1 TGTAGAGAATACC
17469767 TTAGTTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 10 0.42
15 4 0.17
16 10 0.42
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Consensus pattern (14 bp):
TGTAGAGAATACCC
Found at i:17473995 original size:39 final size:39
Alignment explanation
Indices: 17473938--17474264 Score: 440
Period size: 39 Copynumber: 8.4 Consensus size: 39
17473928 TATCATTGGA
*
17473938 ATTGTTCTCTGCTGGATCCCTATCATGGTTTTTTGATGT
1 ATTGTTCTCTGCTGGATCCCTATCATGGTTTTCTGATGT
* *
17473977 GTTGTTCTCTGCTAGATCCCTATCAT-GTTTCTCTGATGT
1 ATTGTTCTCTGCTGGATCCCTATCATGGTTT-TCTGATGT
* * * * *
17474016 GTTGTTCTCTACTGGGTCCTTATCATGGTTTTATGATGT
1 ATTGTTCTCTGCTGGATCCCTATCATGGTTTTCTGATGT
* *
17474055 ATTGTTCTCTGCTGGATCCCTATCATGGTATTCTAATGT
1 ATTGTTCTCTGCTGGATCCCTATCATGGTTTTCTGATGT
* ** * *
17474094 ATTGTACTCTATTGGATCCCCATCATGGTTTTCTGATAT
1 ATTGTTCTCTGCTGGATCCCTATCATGGTTTTCTGATGT
* * *
17474133 ATTGTTCTTTGCTGGATCCTTATCATGGTTTTTTGATGT
1 ATTGTTCTCTGCTGGATCCCTATCATGGTTTTCTGATGT
* * *
17474172 ATTGTTCTCTGTTGGATCCCTATCATGTTTTTATGATGT
1 ATTGTTCTCTGCTGGATCCCTATCATGGTTTTCTGATGT
*
17474211 ATTGTTCTTTGCTGGATCCCTATCATGGTTTTCTGATGT
1 ATTGTTCTCTGCTGGATCCCTATCATGGTTTTCTGATGT
17474250 ATTGTTCTCTGCTGG
1 ATTGTTCTCTGCTGG
17474265 GAGCTTCTTT
Statistics
Matches: 246, Mismatches: 40, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
38 4 0.02
39 238 0.97
40 4 0.02
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.48
Consensus pattern (39 bp):
ATTGTTCTCTGCTGGATCCCTATCATGGTTTTCTGATGT
Found at i:17474857 original size:16 final size:16
Alignment explanation
Indices: 17474836--17474867 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17474826 CCTTTGAAAA
17474836 TGATTTTTAAAGCATT
1 TGATTTTTAAAGCATT
*
17474852 TGATTTTTAAGGCATT
1 TGATTTTTAAAGCATT
17474868 AGTTCTACAA
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:0.28, C:0.06, G:0.16, T:0.50
Consensus pattern (16 bp):
TGATTTTTAAAGCATT
Found at i:17481367 original size:40 final size:40
Alignment explanation
Indices: 17481303--17481381 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
17481293 TTGGCTATTT
* *
17481303 TTCACCTTAGTAGGGTTTTTAACCTTACCAAGATTGGTGA
1 TTCACCTTAGTAGGGTTTTCAACCTCACCAAGATTGGTGA
* * * *
17481343 TTCATCTTAGTGGGGTTTTCAACCTCACTACGATTGGTG
1 TTCACCTTAGTAGGGTTTTCAACCTCACCAAGATTGGTG
17481382 TCTTTCATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (40 bp):
TTCACCTTAGTAGGGTTTTCAACCTCACCAAGATTGGTGA
Found at i:17485786 original size:31 final size:31
Alignment explanation
Indices: 17485739--17485878 Score: 217
Period size: 31 Copynumber: 4.5 Consensus size: 31
17485729 GTGTCAGCGT
* * *
17485739 TGGCATGTTACAACATTTTACGTTATATGCA
1 TGGCGTGTTACCACATTCTACGTTATATGCA
* *
17485770 TGGTGTGTTACCACATTTTACGTTATATGCA
1 TGGCGTGTTACCACATTCTACGTTATATGCA
*
17485801 TGGCGTGTTACCACATTCTACGCTATATGCA
1 TGGCGTGTTACCACATTCTACGTTATATGCA
17485832 TGGCGTGTTACCACATTCTACGTTATATGCA
1 TGGCGTGTTACCACATTCTACGTTATATGCA
*
17485863 TGGCGTGTTACAACAT
1 TGGCGTGTTACCACAT
17485879 GACTGACAAA
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 101 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.36
Consensus pattern (31 bp):
TGGCGTGTTACCACATTCTACGTTATATGCA
Found at i:17489606 original size:118 final size:117
Alignment explanation
Indices: 17489403--17489853 Score: 584
Period size: 118 Copynumber: 3.8 Consensus size: 117
17489393 GCTGACACGC
* * * *
17489403 TGAGTGCATGCAGATTTTTATGGTGACACACTGACTTCTTGCAGTATTGTTGGGTGACATGGCAC
1 TGAGTGCATGCAGATTTCTATGATGACACACTGACTTCTTGCAGTATTGTGGGGTGACACGGCAC
*
17489468 GCCCCATCTTGTGGTAACACGCTGAGTGGAACTAGATTGTTGGTGTGACATGT
66 GCCCCATCTTGTGGTGACACGCTGAGTGGAACTAGATT-TTGGTGTGACATGT
* * *
17489521 TGAAG-GCATGCAGATTTCTGTGGTGACAC-GTCGACTTCTTGCAGTATTGTGGGGTGACACGGC
1 TG-AGTGCATGCAGATTTCTATGATGACACACT-GACTTCTTGCAGTATTGTGGGGTGACACGGC
* *
17489584 ACGCCCCATCTTGTGGTGACACGCTGACTGGAACTAGATATTTGGTGTGACATGC
64 ACGCCCCATCTTGTGGTGACACGCTGAGTGGAACTAGAT-TTTGGTGTGACATGT
* * *
17489639 TGAGTGCATGCACATTTCTATGATGACACACTGACTTCTTGCTGTATTCTGGGGTGACACGGCAC
1 TGAGTGCATGCAGATTTCTATGATGACACACTGACTTCTTGCAGTATTGTGGGGTGACACGGCAC
* * **
17489704 GCCCCATCTTGTGGTGACACGCTGAGTGGAACCAGATACTTGGCATGACATGT
66 GCCCCATCTTGTGGTGACACGCTGAGTGGAACTAGAT-TTTGGTGTGACATGT
* * * * * *
17489757 TGAGTGCATGTAGATTTCTATGATGACCCTCTGACTTCTTGCTGTATTGTGGGGTGACTCGGCAT
1 TGAGTGCATGCAGATTTCTATGATGACACACTGACTTCTTGCAGTATTGTGGGGTGACACGGCAC
* * * * *
17489822 GCCCTA-ATTGTAGTGACACGCTAAATGGAACT
66 GCCCCATCTTGTGGTGACACGCTGAGTGGAACT
17489854 GGATACTTGG
Statistics
Matches: 295, Mismatches: 33, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
117 24 0.08
118 267 0.91
119 4 0.01
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (117 bp):
TGAGTGCATGCAGATTTCTATGATGACACACTGACTTCTTGCAGTATTGTGGGGTGACACGGCAC
GCCCCATCTTGTGGTGACACGCTGAGTGGAACTAGATTTTGGTGTGACATGT
Found at i:17489814 original size:236 final size:235
Alignment explanation
Indices: 17489395--17489876 Score: 662
Period size: 236 Copynumber: 2.0 Consensus size: 235
17489385 TATACTAAGC
* * * * *
17489395 TGACACGCTGAGTGCATGCAGATTTTTATGGTGACACACTGACTTCTTGCAGTATTGTTGGGTGA
1 TGACACGCTGAGTGCATGCACATTTCTATGATGACACACTGACTTCTTGCAGTATTCTGGGGTGA
* * ** **
17489460 CATGGCACGCCCCATCTTGTGGTAACACGCTGAGTGGAACTAGATTGTTGGTGTGACATGTTGAA
66 CACGGCACGCCCCATCTTGTGGTAACACGCTGAGTGGAACCAGATACTTGGCATGACATGTTGAA
* * *
17489525 GGCATGCAGATTTCTGTGGTGACACGTCGACTTCTTGCAGTATTGTGGGGTGACACGGCACGCCC
131 GGCATGCAGATTTCTATGATGACACCTCGACTTCTTGCAGTATTGTGGGGTGACACGGCACGCCC
* * * * * *
17489590 CATCTTGTGGTGACACGCTGACTGGAACTAGATATTTGGTG
196 CA-ATTGTAGTGACACGCTAAATGGAACTAGATACTTGGAG
* *
17489631 TGACATGCTGAGTGCATGCACATTTCTATGATGACACACTGACTTCTTGCTGTATTCTGGGGTGA
1 TGACACGCTGAGTGCATGCACATTTCTATGATGACACACTGACTTCTTGCAGTATTCTGGGGTGA
*
17489696 CACGGCACGCCCCATCTTGTGGTGACACGCTGAGTGGAACCAGATACTTGGCATGACATGTTG-A
66 CACGGCACGCCCCATCTTGTGGTAACACGCTGAGTGGAACCAGATACTTGGCATGACATGTTGAA
* * * *
17489760 GTGCATGTAGATTTCTATGATGAC-CCTCTGACTTCTTGCTGTATTGTGGGGTGACTCGGCATGC
131 G-GCATGCAGATTTCTATGATGACACCTC-GACTTCTTGCAGTATTGTGGGGTGACACGGCACGC
* *
17489824 CCTAATTGTAGTGACACGCTAAATGGAACTGGATACTTGGAG
194 CCCAATTGTAGTGACACGCTAAATGGAACTAGATACTTGGAG
17489866 TGACACGCTGA
1 TGACACGCTGA
17489877 CTTGTTCCAG
Statistics
Matches: 214, Mismatches: 30, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
235 46 0.21
236 168 0.79
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (235 bp):
TGACACGCTGAGTGCATGCACATTTCTATGATGACACACTGACTTCTTGCAGTATTCTGGGGTGA
CACGGCACGCCCCATCTTGTGGTAACACGCTGAGTGGAACCAGATACTTGGCATGACATGTTGAA
GGCATGCAGATTTCTATGATGACACCTCGACTTCTTGCAGTATTGTGGGGTGACACGGCACGCCC
CAATTGTAGTGACACGCTAAATGGAACTAGATACTTGGAG
Found at i:17503774 original size:31 final size:30
Alignment explanation
Indices: 17503736--17503938 Score: 289
Period size: 31 Copynumber: 6.6 Consensus size: 30
17503726 GTTAACTCAT
*
17503736 AATGTGGTAACACACCATGCATATAACGTA
1 AATGTGGTAACACGCCATGCATATAACGTA
*
17503766 GAATGTGGTAACACACCATGCATATAACGTA
1 -AATGTGGTAACACGCCATGCATATAACGTA
17503797 GAATGTGGTAACACGCCATGCATATAACGTA
1 -AATGTGGTAACACGCCATGCATATAACGTA
* * *
17503828 ACTTGTGCTAACACGCTATGCATATAACGTA
1 A-ATGTGGTAACACGCCATGCATATAACGTA
17503859 AATTGTGGTAACACGCCATGCATATAACGTAA
1 AA-TGTGGTAACACGCCATGCATATAACGT-A
*
17503891 AATGTGGTAACATGCCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGT-A
*
17503922 AATGTAGTAACACGCCA
1 AATGTGGTAACACGCCA
17503939 ACGCTGACAT
Statistics
Matches: 159, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
30 1 0.01
31 155 0.97
32 3 0.02
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (30 bp):
AATGTGGTAACACGCCATGCATATAACGTA
Found at i:17504315 original size:27 final size:27
Alignment explanation
Indices: 17504277--17504330 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
17504267 ATTTTCAGAT
*
17504277 TGACTGACCTCTTCACTGATAACTGAC
1 TGACTCACCTCTTCACTGATAACTGAC
17504304 TGACTCACCTCTTCACTGATAACTGAC
1 TGACTCACCTCTTCACTGATAACTGAC
17504331 ATTGTTGCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.30
Consensus pattern (27 bp):
TGACTCACCTCTTCACTGATAACTGAC
Found at i:17504768 original size:71 final size:71
Alignment explanation
Indices: 17504687--17504826 Score: 163
Period size: 71 Copynumber: 2.0 Consensus size: 71
17504677 GCATGTCAAG
* * * **
17504687 ACTCTAAACACTAACGTCTCACAAATTCCCTCCATGGCATGTCACCAACTCTGAACGTTGGTGTG
1 ACTCTAAACACTAACGTCTCACAAATTCCCTCCACGACATATCACCAACTCTGAACGTTGACGTG
17504752 TCACCA
66 TCACCA
* * * * * * * *
17504758 ACTCTGAACACTGACGTGTCATAGATTCCCTTCACGACGTATCAGCAACTCTGAACGTTGACGTG
1 ACTCTAAACACTAACGTCTCACAAATTCCCTCCACGACATATCACCAACTCTGAACGTTGACGTG
17504823 TCAC
66 TCAC
17504827 AGATTCCCTC
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
71 56 1.00
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (71 bp):
ACTCTAAACACTAACGTCTCACAAATTCCCTCCACGACATATCACCAACTCTGAACGTTGACGTG
TCACCA
Found at i:17504776 original size:24 final size:24
Alignment explanation
Indices: 17504726--17504778 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
17504716 CTCCATGGCA
** **
17504726 TGTCACCAACTCTGAACGTTGGTG
1 TGTCACCAACTCTGAACACTGACG
17504750 TGTCACCAACTCTGAACACTGACG
1 TGTCACCAACTCTGAACACTGACG
17504774 TGTCA
1 TGTCA
17504779 TAGATTCCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (24 bp):
TGTCACCAACTCTGAACACTGACG
Found at i:17504810 original size:47 final size:47
Alignment explanation
Indices: 17504752--17504920 Score: 187
Period size: 47 Copynumber: 3.6 Consensus size: 47
17504742 CGTTGGTGTG
* * *
17504752 TCACCAACTCTGAACACTGACGTGTCATAGATTCCCTTCACGACGTA
1 TCACCAACTCTGAACGCTGACGTGTCACAGATTCCCTCCACGACGTA
* * * *
17504799 TCAGCAACTCTGAACGTTGACGTGTCACAGATTCCCTCCACGGCGTG
1 TCACCAACTCTGAACGCTGACGTGTCACAGATTCCCTCCACGACGTA
** * * * *
17504846 TCACCAACTCTGAACGCTGGTGTGTCACAGATTCCCTCAATGGCGTG
1 TCACCAACTCTGAACGCTGACGTGTCACAGATTCCCTCCACGACGTA
* *
17504893 TCACCAACTTTGAACTCT-AGCGTGTCAC
1 TCACCAACTCTGAACGCTGA-CGTGTCAC
17504921 CAACTTTGAA
Statistics
Matches: 104, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
47 104 1.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (47 bp):
TCACCAACTCTGAACGCTGACGTGTCACAGATTCCCTCCACGACGTA
Found at i:17505034 original size:23 final size:24
Alignment explanation
Indices: 17505004--17505061 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 24
17504994 TTGTGTCACA
* *
17505004 GTCGTGTCACACACTC-CAACCAT
1 GTCGTGTCACAAACTCTAAACCAT
*
17505027 GTCGTGTCACAAACTCTAAACCTT
1 GTCGTGTCACAAACTCTAAACCAT
*
17505051 GCCGTGTCACA
1 GTCGTGTCACA
17505062 GCCCTGCCGC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 15 0.50
24 15 0.50
ACGTcount: A:0.26, C:0.34, G:0.16, T:0.24
Consensus pattern (24 bp):
GTCGTGTCACAAACTCTAAACCAT
Found at i:17505056 original size:24 final size:23
Alignment explanation
Indices: 17505006--17505061 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
17504996 GTGTCACAGT
* * *
17505006 CGTGTCACACACTCCAACCATGT
1 CGTGTCACAAACTCAAACCATGC
*
17505029 CGTGTCACAAACTCTAAACCTTGC
1 CGTGTCACAAACTC-AAACCATGC
17505053 CGTGTCACA
1 CGTGTCACA
17505062 GCCCTGCCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 13 0.46
24 15 0.54
ACGTcount: A:0.27, C:0.36, G:0.14, T:0.23
Consensus pattern (23 bp):
CGTGTCACAAACTCAAACCATGC
Found at i:17505086 original size:58 final size:58
Alignment explanation
Indices: 17504939--17505094 Score: 161
Period size: 58 Copynumber: 2.7 Consensus size: 58
17504929 AACGTTGACA
* * * **
17504939 TGTCACAGCCATGTCACACATTTCCACCACGGCGTGTCACAAAACCTAAACCCTGTTG
1 TGTCACAGCCATGTCACACATTCCCACCATGTCGTGTCACAAAACCTAAACCCTGCCG
* * * * *
17504997 TGTCACAGTCGTGTCACACACTCCAACCATGTCGTGTCAC-AAACTCTAAACCTTGCCG
1 TGTCACAGCCATGTCACACATTCCCACCATGTCGTGTCACAAAAC-CTAAACCCTGCCG
* * * * *
17505055 TGTCACAGCCCTGCCGCACATTCCCATCATGTCATGTCAC
1 TGTCACAGCCATGTCACACATTCCCACCATGTCGTGTCAC
17505095 TCATTCTCAA
Statistics
Matches: 79, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
57 4 0.05
58 75 0.95
ACGTcount: A:0.25, C:0.36, G:0.15, T:0.24
Consensus pattern (58 bp):
TGTCACAGCCATGTCACACATTCCCACCATGTCGTGTCACAAAACCTAAACCCTGCCG
Found at i:17509960 original size:15 final size:16
Alignment explanation
Indices: 17509940--17509977 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
17509930 TAAGTAAAAT
*
17509940 TTTTTTTTTAAA-TAA
1 TTTTTTTTAAAATTAA
17509955 TTTTTTTTAAAATTTAA
1 TTTTTTTTAAAA-TTAA
17509972 TTTTTT
1 TTTTTT
17509978 ATATCTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
17 9 0.45
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTTTTAAAATTAA
Found at i:17520743 original size:17 final size:16
Alignment explanation
Indices: 17520721--17520772 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 16
17520711 ATGATTAAAA
17520721 TATTTCATCTAAATAT
1 TATTTCATCTAAATAT
17520737 GTATTTCATAACATAAATAT
1 -TATTTCAT--C-TAAATAT
*
17520757 TCATTTCATTTAAATA
1 T-ATTTCATCTAAATA
17520773 GTCAACATGG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
17 14 0.47
19 2 0.07
20 14 0.47
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.46
Consensus pattern (16 bp):
TATTTCATCTAAATAT
Found at i:17529015 original size:23 final size:23
Alignment explanation
Indices: 17528932--17529002 Score: 115
Period size: 23 Copynumber: 3.1 Consensus size: 23
17528922 AATTGATTGA
*
17528932 TAGGTCATTGCGTGACTAGTTTC
1 TAGGTCATTGCGTGACTGGTTTC
* *
17528955 TAGGTCATTACGTGACTGGATTC
1 TAGGTCATTGCGTGACTGGTTTC
17528978 TAGGTCATTGCGTGACTGGTTTC
1 TAGGTCATTGCGTGACTGGTTTC
17529001 TA
1 TA
17529003 AGTTATTGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.38
Consensus pattern (23 bp):
TAGGTCATTGCGTGACTGGTTTC
Found at i:17529123 original size:22 final size:21
Alignment explanation
Indices: 17529097--17529158 Score: 52
Period size: 22 Copynumber: 2.8 Consensus size: 21
17529087 TGTATAAATC
*
17529097 ATTGCGTGATTTATTGTTAGTA
1 ATTGCGTGA-TTATTGTTAGGA
* * *
17529119 ATTGCATGACTAATTGATTAGGC
1 ATTGCGTGA-TTATTG-TTAGGA
*
17529142 ATTGCGTGACTATTGTT
1 ATTGCGTGATTATTGTT
17529159 GTAGGAAATT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
21 2 0.06
22 17 0.55
23 12 0.39
ACGTcount: A:0.24, C:0.10, G:0.23, T:0.44
Consensus pattern (21 bp):
ATTGCGTGATTATTGTTAGGA
Found at i:17531136 original size:24 final size:24
Alignment explanation
Indices: 17531039--17531152 Score: 110
Period size: 24 Copynumber: 4.9 Consensus size: 24
17531029 AGATGCAGAT
17531039 GCAGTCAATGCAGTTGGAGATCCA
1 GCAGTCAATGCAGTTGGAGATCCA
* *
17531063 GCAGGT-GATGCAGTTGGAGATCTA
1 GCA-GTCAATGCAGTTGGAGATCCA
* * * * ** *
17531087 GTAGGCAATGTAGATACAAAT---
1 GCAGTCAATGCAGTTGGAGATCCA
17531108 GCAGTCAATGCAGTTGGAGATCCA
1 GCAGTCAATGCAGTTGGAGATCCA
17531132 GCAGTCAATGCAGTTGGAGAT
1 GCAGTCAATGCAGTTGGAGAT
17531153 TCAATGGGCA
Statistics
Matches: 68, Mismatches: 17, Indels: 10
0.72 0.18 0.11
Matches are distributed among these distances:
21 14 0.21
23 1 0.01
24 51 0.75
25 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.23
Consensus pattern (24 bp):
GCAGTCAATGCAGTTGGAGATCCA
Found at i:17531164 original size:24 final size:24
Alignment explanation
Indices: 17531044--17531168 Score: 67
Period size: 24 Copynumber: 5.3 Consensus size: 24
17531034 CAGATGCAGT
*
17531044 CAATGCAGTTGGAGATCCAGCAGG
1 CAATGCAGTTGGAGATCCAACAGG
** * **
17531068 TGATGCAGTTGGAGATCTAGTAGG
1 CAATGCAGTTGGAGATCCAACAGG
* * ** * * *
17531092 CAATGTAGATACAAAT---GCAGT
1 CAATGCAGTTGGAGATCCAACAGG
* *
17531113 CAATGCAGTTGGAGATCCAGCAGT
1 CAATGCAGTTGGAGATCCAACAGG
* **
17531137 CAATGCAGTTGGAGATTCAATGGG
1 CAATGCAGTTGGAGATCCAACAGG
17531161 CAATGCAG
1 CAATGCAG
17531169 ATGTAGATGT
Statistics
Matches: 75, Mismatches: 23, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
21 14 0.19
24 61 0.81
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.22
Consensus pattern (24 bp):
CAATGCAGTTGGAGATCCAACAGG
Found at i:17531183 original size:69 final size:69
Alignment explanation
Indices: 17531026--17531183 Score: 212
Period size: 69 Copynumber: 2.3 Consensus size: 69
17531016 CTCTAGTCAT
* *
17531026 TGCAGATGCAGATGCAGTCAATGCAGTTGGAGATCCAGCAGGTGATGCAGTTGGAGATCTAGTAG
1 TGCAGATGCAGATGCAGTCAATGCAGTTGGAGATCCAGCAGGTAATGCAGTTGGAGATCTAATAG
17531091 GCAA
66 GCAA
* * *
17531095 TGTAGATACAAATGCAGTCAATGCAGTTGGAGATCCAGCA-GTCAATGCAGTTGGAGAT-TCAAT
1 TGCAGATGCAGATGCAGTCAATGCAGTTGGAGATCCAGCAGGT-AATGCAGTTGGAGATCT-AAT
*
17531158 GGGCAA
64 AGGCAA
* *
17531164 TGCAGATGTAGATGTAGTCA
1 TGCAGATGCAGATGCAGTCA
17531184 CTACATGAGC
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
68 3 0.04
69 73 0.96
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.23
Consensus pattern (69 bp):
TGCAGATGCAGATGCAGTCAATGCAGTTGGAGATCCAGCAGGTAATGCAGTTGGAGATCTAATAG
GCAA
Found at i:17532819 original size:26 final size:25
Alignment explanation
Indices: 17532790--17532846 Score: 80
Period size: 26 Copynumber: 2.3 Consensus size: 25
17532780 CATTATTCTG
*
17532790 TATCATTTTCATATTATTCTTTGTTA
1 TATCATTTACATATTATTCTTTG-TA
*
17532816 TATCATTTAGATATTATTCTTTGTA
1 TATCATTTACATATTATTCTTTGTA
17532841 T-TCATT
1 TATCATT
17532847 CATGTGATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 5 0.17
25 3 0.10
26 21 0.72
ACGTcount: A:0.25, C:0.11, G:0.05, T:0.60
Consensus pattern (25 bp):
TATCATTTACATATTATTCTTTGTA
Found at i:17533203 original size:92 final size:92
Alignment explanation
Indices: 17533079--17533266 Score: 279
Period size: 92 Copynumber: 2.0 Consensus size: 92
17533069 TAGAATCGCT
**
17533079 TCACCAGTTGATATTGATTCGAAGGAGTATTTGTTATGGAGTCACGTGAGTACTAAATGTTGAAT
1 TCACCAGTTGATATTGATTCGAAGGAGTATTTGTTATGGAGTCACGCAAGTACTAAATGTTGAAT
* *
17533144 GACGTTAGTAGTTAATATGGAATCACG
66 CACGTCAGTAGTTAATATGGAATCACG
* * *
17533171 TCACCAGTTGATATTGATTC-ACGAGAGTATTTGTTATGGAGTCACGCAAGTAGTAAATTTTGAA
1 TCACCAGTTGATATTGATTCGAAG-GAGTATTTGTTATGGAGTCACGCAAGTACTAAATGTTGAA
* *
17533235 TCACGTCGGTAGTTAATATGGAATCGCG
65 TCACGTCAGTAGTTAATATGGAATCACG
17533263 TCAC
1 TCAC
17533267 TAATCCACAT
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
91 2 0.02
92 84 0.98
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (92 bp):
TCACCAGTTGATATTGATTCGAAGGAGTATTTGTTATGGAGTCACGCAAGTACTAAATGTTGAAT
CACGTCAGTAGTTAATATGGAATCACG
Found at i:17533209 original size:46 final size:45
Alignment explanation
Indices: 17533079--17533216 Score: 114
Period size: 46 Copynumber: 3.0 Consensus size: 45
17533069 TAGAATCGCT
*
17533079 TCACCAGTTGATATTGATTCGAAGGAGTATTTGTTATGGAGTCACG
1 TCACCAGTTGATATTGATTC-ACGGAGTATTTGTTATGGAGTCACG
* ** * ** * * * * * ** *
17533125 TGAGTACTAAATGTTGAATGACGTTAGTAGTTAATATGGAATCACG
1 TCACCAGTTGATATTGATTCACG-GAGTATTTGTTATGGAGTCACG
17533171 TCACCAGTTGATATTGATTCACGAGAGTATTTGTTATGGAGTCACG
1 TCACCAGTTGATATTGATTCACG-GAGTATTTGTTATGGAGTCACG
17533217 CAAGTAGTAA
Statistics
Matches: 61, Mismatches: 30, Indels: 2
0.66 0.32 0.02
Matches are distributed among these distances:
45 2 0.03
46 59 0.97
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (45 bp):
TCACCAGTTGATATTGATTCACGGAGTATTTGTTATGGAGTCACG
Found at i:17533239 original size:46 final size:45
Alignment explanation
Indices: 17533103--17533239 Score: 103
Period size: 46 Copynumber: 3.0 Consensus size: 45
17533093 TGATTCGAAG
* * * * *
17533103 GAGTATTTGTTATGGAGTCACGTGAGTACTAAATGTTGAATGACGT
1 GAGTATTTGTTATGGAGTCACG-CAGTAGTAAATATTGAATCACGA
* * ** * ** ** *
17533149 TAGTAGTTAATATGGAATCACGTCACCAGTTGATATTGATTCACGA
1 GAGTATTTGTTATGGAGTCACG-CAGTAGTAAATATTGAATCACGA
*
17533195 GAGTATTTGTTATGGAGTCACGCAAGTAGTAAATTTTGAATCACG
1 GAGTATTTGTTATGGAGTCACGC-AGTAGTAAATATTGAATCACG
17533240 TCGGTAGTTA
Statistics
Matches: 64, Mismatches: 26, Indels: 2
0.70 0.28 0.02
Matches are distributed among these distances:
45 1 0.02
46 63 0.98
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.34
Consensus pattern (45 bp):
GAGTATTTGTTATGGAGTCACGCAGTAGTAAATATTGAATCACGA
Found at i:17538649 original size:19 final size:19
Alignment explanation
Indices: 17538625--17538668 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
17538615 TAAACTCAAA
17538625 ATGCTCTTTTAGTGCCAAC
1 ATGCTCTTTTAGTGCCAAC
17538644 ATGCTCTTTTAGTGCCAAC
1 ATGCTCTTTTAGTGCCAAC
17538663 ATGCTC
1 ATGCTC
17538669 AAAGCTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.36
Consensus pattern (19 bp):
ATGCTCTTTTAGTGCCAAC
Found at i:17540129 original size:117 final size:117
Alignment explanation
Indices: 17539954--17540315 Score: 486
Period size: 117 Copynumber: 3.1 Consensus size: 117
17539944 AACAAGAGGC
* * ** * * *
17539954 GAATTACACAAGTCACGCGCCACTGCTCTCGCAATATATAACAACAGGTCACGTAATATATAAAA
1 GAATTGCACAAGTCACACGCCACCACTTTCGCAA-ACATAACAACAAGTCACGTAATATATAAAA
*
17540019 ACCAATCACGCAAGCCTAAAAAACTACTAAACAAAAGCCTCAAAACAACATAT
65 ACCAGTCACGCAAGCCTAAAAAACTACTAAACAAAAGCCTCAAAACAACATAT
* * *
17540072 GAATTGCACAAGTCACATG-CACCACTTTCGCAAAACATAACAACATGTCACGCAATATATAAAA
1 GAATTGCACAAGTCACACGCCACCACTTTCGC-AAACATAACAACAAGTCACGTAATATATAAAA
* * * *
17540136 ACCAGTTACACAAGCCTAAAAAACTACTGAACAAAAGCCTCAAAAAAACATAT
65 ACCAGTCACGCAAGCCTAAAAAACTACTAAACAAAAGCCTCAAAACAACATAT
*
17540189 GAATTGCACAAGTCACACGCCACCACTTTCG----C-T-ACAACAAGTAACGTAATATATAAAAA
1 GAATTGCACAAGTCACACGCCACCACTTTCGCAAACATAACAACAAGTCACGTAATATATAAAAA
* *
17540248 CCAGTCACGCATTGCCTAAAAAACTACTAAACAAAAGCCTCAAAACAACAAAT
66 CCAGTCACGCA-AGCCTAAAAAACTACTAAACAAAAGCCTCAAAACAACATAT
17540301 GAATTGCACAAGTCA
1 GAATTGCACAAGTCA
17540316 GTCACGCACC
Statistics
Matches: 217, Mismatches: 24, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
111 32 0.15
112 53 0.24
113 1 0.00
117 102 0.47
118 29 0.13
ACGTcount: A:0.46, C:0.26, G:0.10, T:0.18
Consensus pattern (117 bp):
GAATTGCACAAGTCACACGCCACCACTTTCGCAAACATAACAACAAGTCACGTAATATATAAAAA
CCAGTCACGCAAGCCTAAAAAACTACTAAACAAAAGCCTCAAAACAACATAT
Found at i:17540435 original size:83 final size:85
Alignment explanation
Indices: 17540282--17540438 Score: 219
Period size: 83 Copynumber: 1.8 Consensus size: 85
17540272 TACTAAACAA
*
17540282 AAGCCTCAAAACAACAAATGAATTGCACAAGTCAGTCACGCACCGCTAGGCTCGCAACACCTAAG
1 AAGCCTCAAAACAACAAATGAATTGCACAA--CAGTCACGCACCACTAGGCTCGCAACACCTAAG
17540347 AATAAGTCACTCAATGAATAAT
64 AATAAGTCACTCAATGAATAAT
* ** * * *
17540369 AAGCCTCAAAACAAGAGGTGAATTGCAC-A-AGTCACGCACCACTAGTCTCGCAATACCTAATAA
1 AAGCCTCAAAACAACAAATGAATTGCACAACAGTCACGCACCACTAGGCTCGCAACACCTAAGAA
17540432 TAAGTCA
66 TAAGTCA
17540439 ATCGATTCTT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
83 37 0.59
86 1 0.02
87 25 0.40
ACGTcount: A:0.41, C:0.26, G:0.15, T:0.18
Consensus pattern (85 bp):
AAGCCTCAAAACAACAAATGAATTGCACAACAGTCACGCACCACTAGGCTCGCAACACCTAAGAA
TAAGTCACTCAATGAATAAT
Found at i:17541806 original size:15 final size:15
Alignment explanation
Indices: 17541786--17541819 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
17541776 ATGCTCAACA
*
17541786 AATATTCAGTCAGGT
1 AATATTCAGTCACGT
17541801 AATATTCAGTCACGT
1 AATATTCAGTCACGT
17541816 AATA
1 AATA
17541820 CTTGTCACGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (15 bp):
AATATTCAGTCACGT
Found at i:17541846 original size:103 final size:103
Alignment explanation
Indices: 17541697--17541894 Score: 315
Period size: 103 Copynumber: 1.9 Consensus size: 103
17541687 AATGCTCAAC
* * *
17541697 TAATATTCAGTCACGTAACGCCTGTCACATAACGATCAATAAATATTAAGTCACGTAATGCCTAT
1 TAATATTCAGTCACGTAACACCTGTCACACAACGATCAACAAATATTAAGTCACGTAATGCCTAT
17541762 AAAGAACTCACGCAATGCTCAACAAATATTCAGTCAGG
66 AAAGAACTCACGCAATGCTCAACAAATATTCAGTCAGG
* * * * * *
17541800 TAATATTCAGTCACGTAATACTTGTCACGCAACGCTCAACATATATTCAGTCACGTAATGCCTAT
1 TAATATTCAGTCACGTAACACCTGTCACACAACGATCAACAAATATTAAGTCACGTAATGCCTAT
17541865 AAAGAACTCACGCAATGCTCAACAAATATT
66 AAAGAACTCACGCAATGCTCAACAAATATT
17541895 TAGGCACCTA
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 86 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
TAATATTCAGTCACGTAACACCTGTCACACAACGATCAACAAATATTAAGTCACGTAATGCCTAT
AAAGAACTCACGCAATGCTCAACAAATATTCAGTCAGG
Found at i:17556933 original size:3 final size:3
Alignment explanation
Indices: 17556927--17556955 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
17556917 CATCATCATC
17556927 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
17556956 ATACAATGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:17557835 original size:30 final size:29
Alignment explanation
Indices: 17557797--17557857 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
17557787 GTTAATTATA
17557797 AAGACTTATTTAACTGAAAATAAAAATAT
1 AAGACTTATTTAACTGAAAATAAAAATAT
* *
17557826 AAGATCTTATTTAACTTAAAATAAAAGTAT
1 AAGA-CTTATTTAACTGAAAATAAAAATAT
17557856 AA
1 AA
17557858 AAGCTTGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.33
Consensus pattern (29 bp):
AAGACTTATTTAACTGAAAATAAAAATAT
Found at i:17563349 original size:11 final size:10
Alignment explanation
Indices: 17563335--17563359 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
17563325 TTTTTATCTG
17563335 TTTTTTTTTA
1 TTTTTTTTTA
17563345 TTTTTTTTTA
1 TTTTTTTTTA
17563355 TTTTT
1 TTTTT
17563360 CTATATCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:17584144 original size:6 final size:6
Alignment explanation
Indices: 17584133--17584159 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
17584123 GCTCATGATT
17584133 TATAAA TATAAA TATAAA TATAAA TAT
1 TATAAA TATAAA TATAAA TATAAA TAT
17584160 TTAATTGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
TATAAA
Found at i:17586763 original size:35 final size:35
Alignment explanation
Indices: 17586624--17586764 Score: 185
Period size: 35 Copynumber: 4.0 Consensus size: 35
17586614 AATAAGCCAA
*** *
17586624 TGTGCACTCCCTA-TACGCACAAGGCAATATCATCA
1 TGTGCACTCCCTACT-CGCACACTTCAATATCATCG
* *
17586659 TGTGCACTCCCTACTCGCACATTTCTATATCATCG
1 TGTGCACTCCCTACTCGCACACTTCAATATCATCG
**
17586694 TGTGCACTCCCTACTTTCACACTTCAATATCATCG
1 TGTGCACTCCCTACTCGCACACTTCAATATCATCG
*
17586729 TGTGCACTCCCTACTCGCACGCTTCAATATCATCG
1 TGTGCACTCCCTACTCGCACACTTCAATATCATCG
17586764 T
1 T
17586765 CCACACTTCC
Statistics
Matches: 93, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
35 92 0.99
36 1 0.01
ACGTcount: A:0.23, C:0.34, G:0.12, T:0.30
Consensus pattern (35 bp):
TGTGCACTCCCTACTCGCACACTTCAATATCATCG
Found at i:17586869 original size:2 final size:2
Alignment explanation
Indices: 17586862--17586923 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
17586852 CATACACAAC
*
17586862 AT AT AT AT AT AT AT AT AT AT AT AT AT AN AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17586904 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
17586924 TTATCCACAT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17587468 original size:20 final size:21
Alignment explanation
Indices: 17587445--17587488 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
17587435 AAGAAGAAGA
17587445 AGAAGAAGTTGCTAGAAA-TT
1 AGAAGAAGTTGCTAGAAACTT
17587465 AGAAGAAGTTGCTAGAAACTT
1 AGAAGAAGTTGCTAGAAACTT
17587486 AGA
1 AGA
17587489 TATTTATGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.45, C:0.07, G:0.25, T:0.23
Consensus pattern (21 bp):
AGAAGAAGTTGCTAGAAACTT
Found at i:17594854 original size:21 final size:20
Alignment explanation
Indices: 17594830--17594869 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
17594820 AAAAACTAAT
*
17594830 AAATAATAATCAAATTAAAAG
1 AAATAA-AATAAAATTAAAAG
*
17594851 AAATAACATAAAATTAAAA
1 AAATAAAATAAAATTAAAA
17594870 TAACTCACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.23
Consensus pattern (20 bp):
AAATAAAATAAAATTAAAAG
Found at i:17596182 original size:20 final size:20
Alignment explanation
Indices: 17596153--17596200 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
17596143 TATTTTTTTT
*
17596153 AAACACAAATAAAACATACA
1 AAACATAAATAAAACATACA
*
17596173 AAACATAAATAAAACATGCA
1 AAACATAAATAAAACATACA
*
17596193 AGACATAA
1 AAACATAA
17596201 CTTAAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.67, C:0.17, G:0.04, T:0.12
Consensus pattern (20 bp):
AAACATAAATAAAACATACA
Found at i:17599859 original size:19 final size:19
Alignment explanation
Indices: 17599832--17599883 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
17599822 AGGAGACAAG
*
17599832 ATAAAATTTTTAGAATAAA
1 ATAATATTTTTAGAATAAA
*
17599851 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTA-GAATAAA
*
17599870 ATATTATTATTTAG
1 ATAATATT-TTTAG
17599884 CCAGATGTCG
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 5 0.19
19 16 0.62
20 1 0.04
21 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (19 bp):
ATAATATTTTTAGAATAAA
Found at i:17600229 original size:6 final size:5
Alignment explanation
Indices: 17600216--17600301 Score: 59
Period size: 6 Copynumber: 15.6 Consensus size: 5
17600206 TAGTGAAATA
*
17600216 ATAAT ATAAGT ATAAA ATAAT AT-AT -TAAT ATATAT ATATAT ATATAT
1 ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT ATA-AT ATA-AT ATA-AT
17600263 ATATAT ATATAT ATAAT AATATAT ATATAT ATATAT ATA
1 ATA-AT ATA-AT ATAAT -ATA-AT ATA-AT ATA-AT ATA
17600302 TATTAGAAGA
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
3 1 0.01
4 4 0.05
5 14 0.19
6 52 0.71
7 2 0.03
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (5 bp):
ATAAT
Found at i:17600248 original size:2 final size:2
Alignment explanation
Indices: 17600235--17600304 Score: 112
Period size: 2 Copynumber: 37.0 Consensus size: 2
17600225 GTATAAAATA
17600235 AT AT AT -T A- AT 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 AT AT AT AT AT AT
17600275 AT A- AT A- 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 AT
17600305 TAGAAGACCA
Statistics
Matches: 64, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
1 4 0.06
2 60 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17600253 original size:24 final size:25
Alignment explanation
Indices: 17600226--17600301 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 25
17600216 ATAATATAAG
17600226 TATAAAATAATATATTA-ATATATA
1 TATAAAATAATATATTATATATATA
*
17600250 TAT-ATAT-ATATA-TATATATATA
1 TATAAAATAATATATTATATATATA
*
17600272 TATATAATAATATATATATATATATA
1 TATAAAATAATATAT-TATATATATA
17600298 TATA
1 TATA
17600302 TATTAGAAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
21 2 0.05
22 15 0.34
23 5 0.11
24 8 0.18
26 14 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAAAATAATATATTATATATATA
Found at i:17601001 original size:33 final size:34
Alignment explanation
Indices: 17600963--17601047 Score: 86
Period size: 36 Copynumber: 2.5 Consensus size: 34
17600953 TTTTGTTTTG
* *
17600963 GCTGCTAATTTTTGGAGGGAAA-AGTA-CAGCTTA
1 GCTGCTAATTTTTGAAGAGAAATAG-AGCAGCTTA
*
17600996 GCTGCTGATTTTTTTGAAGAGAAATAGAGCAGCTTA
1 GCTGCT-A-ATTTTTGAAGAGAAATAGAGCAGCTTA
*
17601032 GCTGCTGA-TTTTGAAG
1 GCTGCTAATTTTTGAAG
17601048 CCAATATGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
33 14 0.33
34 1 0.02
35 13 0.30
36 15 0.35
ACGTcount: A:0.28, C:0.12, G:0.27, T:0.33
Consensus pattern (34 bp):
GCTGCTAATTTTTGAAGAGAAATAGAGCAGCTTA
Found at i:17601059 original size:33 final size:34
Alignment explanation
Indices: 17600989--17601073 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 34
17600979 GGGAAAAGTA
*
17600989 CAGCTTAGCTGCTGATTTTTTTGAAGAGAAATAGAG
1 CAGCTTAGCTGCTGA--TTTTTGAAGACAAATAGAG
*
17601025 CAGCTTAGCTGCTGA-TTTTGAAG-CCAATATGAG
1 CAGCTTAGCTGCTGATTTTTGAAGACAAATA-GAG
*
17601058 CAACTTTAGCTGCTGA
1 CAGC-TTAGCTGCTGA
17601074 AAATTGAAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
32 4 0.09
33 14 0.32
34 11 0.25
36 15 0.34
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (34 bp):
CAGCTTAGCTGCTGATTTTTGAAGACAAATAGAG
Found at i:17601221 original size:5 final size:5
Alignment explanation
Indices: 17601203--17601253 Score: 63
Period size: 5 Copynumber: 10.6 Consensus size: 5
17601193 ACGGTGGAAG
*
17601203 AAAG- AAAG- AAAGA AAAGA AAAGA AAAGA AAAGA AAATA ACAAG- AAAGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA A-AAGA AAAGA
17601251 AAA
1 AAA
17601254 AATGGGCATG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
4 11 0.26
5 29 0.69
6 2 0.05
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:17601281 original size:27 final size:28
Alignment explanation
Indices: 17601240--17601296 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 28
17601230 AAAAGAAAAT
17601240 AACAAGAAAGAAAAAATGGGCATGACCC
1 AACAAGAAAGAAAAAATGGGCATGACCC
*
17601268 AACAAGAAAG-AAAAATGGGCATGGCCC
1 AACAAGAAAGAAAAAATGGGCATGACCC
17601295 AA
1 AA
17601297 TAGAAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 18 0.64
28 10 0.36
ACGTcount: A:0.53, C:0.18, G:0.23, T:0.07
Consensus pattern (28 bp):
AACAAGAAAGAAAAAATGGGCATGACCC
Found at i:17603482 original size:21 final size:21
Alignment explanation
Indices: 17603458--17603507 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
17603448 TAGTAAGCTT
17603458 TTAGTCGACTAACAATTCTTC
1 TTAGTCGACTAACAATTCTTC
*
17603479 TTAGTCGACTAATAATTCTTC
1 TTAGTCGACTAACAATTCTTC
17603500 TTAGTCGA
1 TTAGTCGA
17603508 TTAAGTTGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (21 bp):
TTAGTCGACTAACAATTCTTC
Found at i:17609881 original size:18 final size:17
Alignment explanation
Indices: 17609858--17609891 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17609848 TTTTTCTTCT
17609858 TCTTTTGCTTCTCTCTTG
1 TCTTTTGCTTC-CTCTTG
*
17609876 TCTTTTTCTTCCTCTT
1 TCTTTTGCTTCCTCTT
17609892 CCTTAAGTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.00, C:0.29, G:0.06, T:0.65
Consensus pattern (17 bp):
TCTTTTGCTTCCTCTTG
Found at i:17614536 original size:37 final size:37
Alignment explanation
Indices: 17614489--17614607 Score: 177
Period size: 37 Copynumber: 3.2 Consensus size: 37
17614479 AATGCAATAT
*
17614489 CATCATCATGTGTGCACTCCTTACTCACGCACTTCAA
1 CATCATCATGTGTGCACTCCTTACTCACACACTTCAA
* *
17614526 CATCATCATGTGTGCACT-CTCCACTCTCACACTTCAA
1 CATCATCATGTGTGCACTCCT-TACTCACACACTTCAA
* *
17614563 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCTTACTCACACACTTCAA
17614600 CATCATCA
1 CATCATCA
17614608 CACAACATTA
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
36 2 0.03
37 71 0.96
38 1 0.01
ACGTcount: A:0.25, C:0.37, G:0.09, T:0.29
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCTTACTCACACACTTCAA
Found at i:17615224 original size:2 final size:2
Alignment explanation
Indices: 17615217--17615247 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
17615207 TCATGGAAAG
*
17615217 TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
17615248 AAAATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:17615463 original size:19 final size:20
Alignment explanation
Indices: 17615439--17615477 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
17615429 ATGGGAGGAA
17615439 GAAAAA-CAAGAAGCTGCTG
1 GAAAAATCAAGAAGCTGCTG
* *
17615458 GAAAAATGAGGAAGCTGCTG
1 GAAAAATCAAGAAGCTGCTG
17615478 AAGATATGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.44, C:0.13, G:0.31, T:0.13
Consensus pattern (20 bp):
GAAAAATCAAGAAGCTGCTG
Found at i:17621617 original size:20 final size:21
Alignment explanation
Indices: 17621581--17621620 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
17621571 TAAAACTAAT
*
17621581 AAATAACAATCAAATTAAAAG
1 AAATAACAATAAAATTAAAAG
17621602 AAATAAC-ATAAAATTAAAA
1 AAATAACAATAAAATTAAAA
17621621 TAACTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (21 bp):
AAATAACAATAAAATTAAAAG
Found at i:17621633 original size:20 final size:19
Alignment explanation
Indices: 17621610--17621655 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
17621600 AGAAATAACA
*
17621610 TAAAATTAAAATAACTTATT
1 TAAAAATAAAATAA-TTATT
17621630 TAAAAATAAAATAATTA--
1 TAAAAATAAAATAATTATT
17621647 TAAAAATAA
1 TAAAAATAA
17621656 CTAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 9 0.36
19 3 0.12
20 13 0.52
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAAATAAAATAATTATT
Found at i:17621637 original size:15 final size:16
Alignment explanation
Indices: 17621617--17621659 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
17621607 ACATAAAATT
*
17621617 AAAATAACTTATT-TA
1 AAAATAACTAATTATA
*
17621632 AAAATAAAATAATTATA
1 AAAAT-AACTAATTATA
17621649 AAAATAACTAA
1 AAAATAACTAA
17621660 AAATAAGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 5 0.22
16 11 0.48
17 7 0.30
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATAACTAATTATA
Found at i:17625129 original size:10 final size:10
Alignment explanation
Indices: 17625098--17625149 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
17625088 TTTAGGGAGA
17625098 ATATTGTGACTG
1 ATATT-TGA-TG
17625110 A-ATTTGATG
1 ATATTTGATG
*
17625119 ATATTTCATG
1 ATATTTGATG
*
17625129 ATACTTTGGTG
1 ATA-TTTGATG
17625140 ATATTTGATG
1 ATATTTGATG
17625150 TTTGGTGAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 3 0.09
10 19 0.56
11 11 0.32
12 1 0.03
ACGTcount: A:0.27, C:0.06, G:0.21, T:0.46
Consensus pattern (10 bp):
ATATTTGATG
Found at i:17641930 original size:23 final size:23
Alignment explanation
Indices: 17641868--17641944 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 23
17641858 ACTGGTTTCT
*
17641868 TTGTAACCAAATCGACTAAATTA
1 TTGTAACCAAATCGACTAAAGTA
* *
17641891 TTG---CAAAATCGAGTAAAGTA
1 TTGTAACCAAATCGACTAAAGTA
*
17641911 TTGTAACCAAATAGACTAAAGTA
1 TTGTAACCAAATCGACTAAAGTA
17641934 TTGTAACCAAA
1 TTGTAACCAAA
17641945 AGAATGAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
20 17 0.38
23 28 0.62
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.27
Consensus pattern (23 bp):
TTGTAACCAAATCGACTAAAGTA
Found at i:17642426 original size:17 final size:17
Alignment explanation
Indices: 17642404--17642437 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
17642394 TTGAATGTCC
17642404 CATTTCCTTTCACTATT
1 CATTTCCTTTCACTATT
17642421 CATTTCCTTTCACTATT
1 CATTTCCTTTCACTATT
17642438 GTCCCAAAAG
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:0.18, C:0.29, G:0.00, T:0.53
Consensus pattern (17 bp):
CATTTCCTTTCACTATT
Done.