Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold176
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: 960511
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 25 characters in sequence are not A, C, G, or T
File 2 of 6
Found at i:153907 original size:24 final size:24
Alignment explanation
Indices: 153875--153926 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
153865 TAGATTCTTC
*
153875 TTTTTTTTTTCTTTTTG-TTCTTTG
1 TTTTGTTTTT-TTTTTGTTTCTTTG
*
153899 TTTTGTTTTTTTTTTGTTTTTTTG
1 TTTTGTTTTTTTTTTGTTTCTTTG
153923 TTTT
1 TTTT
153927 TTTGGTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.87
Consensus pattern (24 bp):
TTTTGTTTTTTTTTTGTTTCTTTG
Found at i:153913 original size:31 final size:29
Alignment explanation
Indices: 153875--153952 Score: 95
Period size: 31 Copynumber: 2.6 Consensus size: 29
153865 TAGATTCTTC
*
153875 TTTTTTTTTTCTTTTTGTTCTTTGTT-TTGT
1 TTTTTTTTTTTTTTTTGTT-TTT-TTGTTGT
153905 TTTTTTTTTGTTTTTTTGTTTTTTTGGTTGT
1 TTTTTTTTT-TTTTTTTGTTTTTTT-GTTGT
153936 TTTTTTCTTTTTTTTTT
1 TTTTTT-TTTTTTTTTT
153953 TAAAAAGAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
29 2 0.05
30 12 0.28
31 26 0.60
32 3 0.07
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.86
Consensus pattern (29 bp):
TTTTTTTTTTTTTTTTGTTTTTTTGTTGT
Found at i:153918 original size:28 final size:28
Alignment explanation
Indices: 153875--153953 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 28
153865 TAGATTCTTC
153875 TTTTTTTTTTCTTTTTGTTCTTTGTTTT-G
1 TTTTTTTTTTC-TTTTGTTCTTT-TTTTGG
* * *
153904 TTTTTTTTTTGTTTTTTTGTTTTTTTGG
1 TTTTTTTTTTCTTTTGTTCTTTTTTTGG
*
153932 TTGTTTTTTTCTTTT-TT-TTTTT
1 TTTTTTTTTTCTTTTGTTCTTTTT
153954 AAAAAGAATG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
26 5 0.11
27 6 0.14
28 23 0.52
29 10 0.23
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.86
Consensus pattern (28 bp):
TTTTTTTTTTCTTTTGTTCTTTTTTTGG
Found at i:166573 original size:51 final size:51
Alignment explanation
Indices: 166507--166625 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 51
166497 TGAAAATAAT
*
166507 GGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAGGCC
1 GGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAAGCC
* ** * *
166558 GGGGTTGAAGTATCCCTGATTGTGAGAAATCAATATTTTGGAAATAAAGCC
1 GGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAAGCC
*
166609 AGGGTTGGAGTATCCCC
1 GGGGTTGGAGTATCCCC
166626 TCGGAAATAA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (51 bp):
GGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAAGCC
Found at i:166603 original size:130 final size:128
Alignment explanation
Indices: 166328--166651 Score: 327
Period size: 130 Copynumber: 2.5 Consensus size: 128
166318 ACGAGAAATT
* *
166328 TAATATTTTGGAGATAATAACGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCC
1 TAATATTTTGGAAATAA-AAC-GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCC
* * ** * *
166393 CGATTGTGAAAAATTGATGATTTAGAAATAAGGCAAGGGTTGAAGTGTTGCCGATTATAGAGAAA
64 CAATTATGAAAAATCAATGATTTAGAAATAAGGCAAGGGTTGAAGTGATCCCGATTATAGAGAAA
* *** *
166458 -AGATGTTTCAAAAATAAAATCGGGATTTGG-GTATCCCCGT-GAAAATAATGGGGTTGGAGTAT
1 TA-ATATTTTGGAAATAAAA-CGGG--TTGGAGTATCCCC-TCGAAAATAACGGGGTTGGAGTAT
* ** *
166520 CCCCAATTATGAGAAATCAAT-ATTTTAGAAATAAGGCCGGGGTTGAAGT-ATCCCTGATTGT-G
61 CCCCAATTATGAAAAATCAATGA-TTTAGAAATAAGGCAAGGGTTGAAGTGATCCC-GATTATAG
166582 AGAAA
124 AGAAA
* *
166587 TCAATATTTTGGAAATAAAGCCAGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCC
1 T-AATATTTTGGAAATAAA-AC-GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCC
166652 TCGATGAAAT
Statistics
Matches: 157, Mismatches: 24, Indels: 26
0.76 0.12 0.13
Matches are distributed among these distances:
129 21 0.13
130 127 0.81
131 9 0.06
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.27
Consensus pattern (128 bp):
TAATATTTTGGAAATAAAACGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCA
ATTATGAAAAATCAATGATTTAGAAATAAGGCAAGGGTTGAAGTGATCCCGATTATAGAGAAA
Found at i:166680 original size:28 final size:28
Alignment explanation
Indices: 166610--166684 Score: 118
Period size: 28 Copynumber: 2.7 Consensus size: 28
166600 AATAAAGCCA
166610 GGGTTGGAGTATCCCCTCG--GAAATAACG
1 GGGTTGGAGTAT--CCTCGATGAAATAACG
166638 GGGTTGGAGTATCCTCGATGAAATAACG
1 GGGTTGGAGTATCCTCGATGAAATAACG
166666 GGGTTGGAGTATCCTCGAT
1 GGGTTGGAGTATCCTCGAT
166685 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
26 5 0.11
28 40 0.89
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.25
Consensus pattern (28 bp):
GGGTTGGAGTATCCTCGATGAAATAACG
Found at i:166736 original size:51 final size:51
Alignment explanation
Indices: 166668--166783 Score: 151
Period size: 51 Copynumber: 2.3 Consensus size: 51
166658 AAATAACGGG
* * *
166668 GTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCAGA
* * * * *
166719 GTTGGAATATCCCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAACCAGG
1 GTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCAGA
*
166770 GTTAGAGTATCCCC
1 GTTGGAGTATCCCC
166784 TCGGAAATAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCAGA
Found at i:166838 original size:79 final size:78
Alignment explanation
Indices: 166743--167017 Score: 356
Period size: 79 Copynumber: 3.5 Consensus size: 78
166733 GATTGTGGAG
* * * * **
166743 AATTGGTGTTTTAGAAATAAAACCAGGGTTAGAGTATCCCCTCGGAAATAACGGGGTTAAAGTAT
1 AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTAT
166808 CCCTAATTATGAAA
66 CCCT-ATTATGAAA
*
166822 AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATGACGGGGTTGGAGTAT
1 AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTAT
* *
166887 CCTCGATTATGAGA
66 CC-CTATTATGAAA
* * * * *
166901 AATTAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCTCCAAAATAACAGGGTTGGAGTAT
1 AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTAT
**
166966 CCC--CGATGAAA
66 CCCTATTATGAAA
* *
166977 ATTTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCC
1 AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
167018 GATTAAGAAA
Statistics
Matches: 172, Mismatches: 23, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
76 41 0.24
78 1 0.01
79 129 0.75
80 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (78 bp):
AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTAT
CCCTATTATGAAA
Found at i:166860 original size:288 final size:287
Alignment explanation
Indices: 166343--166861 Score: 636
Period size: 288 Copynumber: 1.8 Consensus size: 287
166333 TTTTGGAGAT
166343 AATAACGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATT
1 AATAACGGGGTTGGAGTAT-CCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATT
* * * **
166408 GATGATTTAGAAATAAGGCAAGGGTTGAAGTGTTGCCGATTATAGAGAAAAGATGTTTCAAAAAT
65 GATGATTTAGAAATAAAGCAAGAGTTGAAGTATCCCCGATTATAGAGAAAAGATGTTTCAAAAAT
* * * * ** *
166473 AAAATCGGGATTTGGGTATCCCCGTGAAAATAATGGGGTTGGAGTATCCCCAATTATGAGAAATC
130 AAAACCGGGATTAGAGTATCCCCGTGAAAATAACGGGGTTAAAGTATCCCCAATTATGAAAAATC
**
166538 AATATTTTAGAAATAAGGCCGGGGTTGAAGTATCCCTGATTGTGAGAAATCAATATTTTGGAAAT
195 AATATTTTAGAAATAAAACCGGGGTTGAAGTATCCCTGATTGTGAGAAATCAATATTTTGGAAAT
166603 AAAGCCAGGGTTGGAGTATCCCCTCGGA
260 AAAGCCAGGGTTGGAGTATCCCCTCGGA
* *
166631 AATAACGGGGTTGGAGTAT-CCTCGATGAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAAT
1 AATAACGGGGTTGGAGTATCCCTC-A-AAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAAT
* * * * * ** * * *
166695 T-AGTGTTTTGGAAATAAAATC-AGAGTTGGAA-TATCCCCGATTGTGGAGAATTGGTGTTTTAG
64 TGA-TGATTTAGAAAT-AAAGCAAGAGTT-GAAGTATCCCCGATTATAGAGAAAAGATGTTTCAA
* *
166757 AAATAAAACCAGGG-TTAGAGTATCCCC-TCGGAAATAACGGGGTTAAAGTATCCCTAATTATGA
126 AAATAAAACC-GGGATTAGAGTATCCCCGT-GAAAATAACGGGGTTAAAGTATCCCCAATTATGA
** * *
166820 AAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
189 AAAATCAATATTTTAGAAATAAAACCGGGGTTGAAGTATCCC
166862 CTCGAAAATG
Statistics
Matches: 192, Mismatches: 32, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
286 4 0.02
287 3 0.02
288 176 0.92
289 9 0.05
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.28
Consensus pattern (287 bp):
AATAACGGGGTTGGAGTATCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTG
ATGATTTAGAAATAAAGCAAGAGTTGAAGTATCCCCGATTATAGAGAAAAGATGTTTCAAAAATA
AAACCGGGATTAGAGTATCCCCGTGAAAATAACGGGGTTAAAGTATCCCCAATTATGAAAAATCA
ATATTTTAGAAATAAAACCGGGGTTGAAGTATCCCTGATTGTGAGAAATCAATATTTTGGAAATA
AAGCCAGGGTTGGAGTATCCCCTCGGA
Found at i:166881 original size:158 final size:155
Alignment explanation
Indices: 166719--167017 Score: 393
Period size: 158 Copynumber: 1.9 Consensus size: 155
166709 TAAAATCAGA
* ** *
166719 GTTGGAATATCCCCGATTGTG-GAGAATTGGTGTTTTAGAAATAAAACCAGGGTTAGAGTATCCC
1 GTTGGAATATCCCCGATTATGAGA-AATTAATATTTTAGAAATAAAACCAGGGTTAGAGTATCCC
** * **
166783 CTCGGAAATAACGGGGTTAAAGTATCCCTAATTATGAAAAATTGATGTTTTAGAAATAAAACCGG
65 CTCCAAAATAACAGGGTTAAAGTATCCC---CGATGAAAAATTGATGTTTTAGAAATAAAACCGG
166848 GGTTGGAGTATCCCCTCGAAAATGACGGG
127 GGTTGGAGTATCCCCTCGAAAATGACGGG
* * * * *
166877 GTTGGAGTATCCTCGATTATGAGAAATTAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCCCC
1 GTTGGAATATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAACCAGGGTTAGAGTATCCCC
** * *
166942 TCCAAAATAACAGGGTTGGAGTATCCCCGATGAAAATTTGATGTTTTAGAAATAAAATCGGGGTT
66 TCCAAAATAACAGGGTTAAAGTATCCCCGATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTT
167007 GGAGTATCCCC
131 GGAGTATCCCC
167018 GATTAAGAAA
Statistics
Matches: 122, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
155 45 0.37
158 75 0.61
159 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (155 bp):
GTTGGAATATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAACCAGGGTTAGAGTATCCCC
TCCAAAATAACAGGGTTAAAGTATCCCCGATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTT
GGAGTATCCCCTCGAAAATGACGGG
Found at i:167014 original size:48 final size:48
Alignment explanation
Indices: 166954--167079 Score: 135
Period size: 51 Copynumber: 2.5 Consensus size: 48
166944 CAAAATAACA
* * *
166954 GGGTTGGAGTATCCCCGATGAAAATTTGATGTTTTAGAAATAAAATCG
1 GGGTTGGAGTATCCCCGATGAAAATTTAACGTTTTAGAAATAAAACCG
* * *
167002 GGGTTGGAGTATCCCCGATTAAGAAAAATTAACGTTTTGGAAATAGAACCG
1 GGGTTGGAGTATCCCCGA-T--GAAAATTTAACGTTTTAGAAATAAAACCG
* *
167053 GGATTGGTGTATCCCCGAGATGAAAAT
1 GGGTTGGAGTATCCCC--GATGAAAAT
167080 CTAGAAATTT
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
48 18 0.28
49 1 0.02
50 5 0.08
51 37 0.58
52 1 0.02
53 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (48 bp):
GGGTTGGAGTATCCCCGATGAAAATTTAACGTTTTAGAAATAAAACCG
Found at i:168715 original size:20 final size:19
Alignment explanation
Indices: 168669--168763 Score: 91
Period size: 20 Copynumber: 4.8 Consensus size: 19
168659 AAAATGCCTG
* * *
168669 AATGTACCGATACATTGTAA
1 AATGTATCGATACAATG-AC
168689 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
* *
168709 AACGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AC
*
168729 AATGTATCGATATAATGAAC
1 AATGTATCGATACAATG-AC
*
168749 AATGTATCAATACAA
1 AATGTATCGATACAA
168764 ATTGTGAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
19 1 0.02
20 60 0.97
21 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (19 bp):
AATGTATCGATACAATGAC
Found at i:168731 original size:40 final size:40
Alignment explanation
Indices: 168676--168763 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
168666 CTGAATGTAC
* * *
168676 CGATACATTGTAAAATGTATCGATACAATGAGCAACGTAT
1 CGATACAATGCAAAATGTATCGATACAATGAACAACGTAT
* *
168716 CGATACAATGCAAAATGTATCGATATAATGAACAATGTAT
1 CGATACAATGCAAAATGTATCGATACAATGAACAACGTAT
*
168756 CAATACAA
1 CGATACAA
168764 ATTGTGAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (40 bp):
CGATACAATGCAAAATGTATCGATACAATGAACAACGTAT
Found at i:172789 original size:333 final size:330
Alignment explanation
Indices: 171844--172971 Score: 1383
Period size: 333 Copynumber: 3.4 Consensus size: 330
171834 AATAACATAA
* ** * * * *
171844 GATGAGTTTTAAAAATTTTAAACCAAGAAAAATCCCCTCGAAAAAA-TTACGGAGTAAAAAATAT
1 GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGAAGTAGAAAACAA
** * * *
171908 CGTATTTCA-AAAAAATATGAGTTTCAAG-----GA-AAAAAA-TCA--AAAATGAATGAATTTT
66 CGTATTTCAGAAAAAA-GGGAATTTCAAGAAAAAAATAAAAAACTCATGAAAAAGAATGAATTTT
* * *
171963 TGAAAATTGAATTAACATGAATCAAATAATGATGTTTTATGAATTTTAAAAATTGAAAACCAAGA
130 TAAAAACTGAATTAACATGAATCAAATAATGATGTTTCATGAATTTTAAAAATTGAAAACCAAGA
* * ** *
172028 AAAATCCCCTTGAAAAAATTTATGGAGTAGAAAACACTACAT-TTAGAAAAAAGAGAAATTTCAC
195 AAAAT-CCCTCGAAAAAATTTATGAAGTAGAAAACA--ACATATTTCAAAAAAGGGAAATTTCAC
** * * * * *
172092 -AAAAAAAGCTCTAAAACTCATGAACATGATTGAATTTTTGAAAAATGAATTAATATGAATTAAA
257 GAAAAAAA--TAAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAACATGAATCAAA
*
172156 TAATGATATTT
320 TAATGATGTTT
* * * *
172167 GATGAATTTTAAAAGTTGAAAATCAAGAAAAATCCCTTC-AAAAGAATTTAC-ATATTAGAAAAC
1 GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAA-AATTTACGA-AGTAGAAAAC
* * * *
172230 ACCATATTTCGAAAAAAAAGGGAATTTCAAGGCAAAAAATAAAAAACTCATGAAAATA-AATGAA
64 AACGTATTTC-AGAAAAAAGGGAATTTCAA-GAAAAAAATAAAAAACTCATGAAAA-AGAATGAA
** * * *
172294 TTTTTAAAAACTGAATTAATGTGAATCAAATAATGATATTTGATAAATTTTAAAAATTGAAAACC
126 TTTTTAAAAACTGAATTAACATGAATCAAATAATGATGTTTCATGAATTTTAAAAATTGAAAACC
* *
172359 AAGAAAAATACCCTCGGAAAAATTTATGAAGTAGAAAACAACATATTTCAGAAAAGGGAAATTTC
191 AAGAAAAAT-CCCTCGAAAAAATTTATGAAGTAGAAAACAACATATTTCAAAAAAGGGAAATTTC
* *
172424 AAGAAAAAAATAAAAAA-TGAATGAAAATGAATGAATTTTTGAAAACTGAATTAACATGAATCAA
255 ACGAAAAAAATAAAAAACT-CATGAAAATGAATGAATTTTTGAAAACTGAATTAACATGAATCAA
172488 ATAATGATGTTT
319 ATAATGATGTTT
* *
172500 GATGAATTTTAAAAATAGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGAAGTAGAAAATAA
1 GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGAAGTAGAAAACAA
* * *
172565 TGTATTTTAGAAAAAAGGGAATTTCTAGAAAAAAATAAAAAAACTCATGAAAAAGAATGAATTTT
66 CGTATTTCAGAAAAAAGGGAATTTCAAGAAAAAAAT-AAAAAACTCATGAAAAAGAATGAATTTT
* * *
172630 TGAAAACTAAATTAACATGAATCAAATAATGATGTTTCATGAATTTTAAAAATTGAAAAGCAAGA
130 TAAAAACTGAATTAACATGAATCAAATAATGATGTTTCATGAATTTTAAAAATTGAAAACCAAGA
** *
172695 AAAATCCCATCGAAAAAATTTACAAAGTAGAAAACAACATATTTCAAAAAGAGGGGAATTTCACG
195 AAAATCCC-TCGAAAAAATTTATGAAGTAGAAAACAACATATTTCAAAAA-AGGGAAATTTCACG
* *
172760 GAAAAAATAAAAAACTCATGAAAATGAATGAATTTTTGAAAACTAAATT-ACTATGAATCAAATA
258 AAAAAAATAAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAAC-ATGAATCAAATA
172824 ATGATGTTT
322 ATGATGTTT
* * * *
172833 GATGAATTTTAAAATTTGAAAACCAAGAAAAATCTCGTAGAAAAAATTTACGAAGTAGAAAACAA
1 GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGAAGTAGAAAACAA
* * * *
172898 CGTATTTCAGAAAAAACGAAATTTCAAGAAAAAAATAAAAAACTCATGAAAATGAATGACTTTTT
66 CGTATTTCAGAAAAAAGGGAATTTCAAGAAAAAAATAAAAAACTCATGAAAAAGAATGAATTTTT
172963 AAAAACTGA
131 AAAAACTGA
172972 GTTACTATTA
Statistics
Matches: 691, Mismatches: 87, Indels: 45
0.84 0.11 0.05
Matches are distributed among these distances:
322 4 0.01
323 35 0.05
324 19 0.03
325 9 0.01
326 7 0.01
331 13 0.02
332 185 0.27
333 285 0.41
334 23 0.03
335 111 0.16
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (330 bp):
GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGAAGTAGAAAACAA
CGTATTTCAGAAAAAAGGGAATTTCAAGAAAAAAATAAAAAACTCATGAAAAAGAATGAATTTTT
AAAAACTGAATTAACATGAATCAAATAATGATGTTTCATGAATTTTAAAAATTGAAAACCAAGAA
AAATCCCTCGAAAAAATTTATGAAGTAGAAAACAACATATTTCAAAAAAGGGAAATTTCACGAAA
AAAATAAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAACATGAATCAAATAATGA
TGTTT
Found at i:172792 original size:166 final size:166
Alignment explanation
Indices: 171844--172971 Score: 1351
Period size: 167 Copynumber: 6.8 Consensus size: 166
171834 AATAACATAA
* ** * * * *
171844 GATGAGTTTTAAAAATTTTAAACCAAGAAAAATCCCCTCGAAAAAA-TTACGGAGTAAAAAATAT
1 GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGAAGTAGAAAACAA
* * * * *
171908 CGTATTTCAAAAAAATATG-AGTTTCAAG-----GA-AAAAAA-TCA--AAAATGAATGAATTTT
66 CATATTTCAGAAAAA-AGGAAATTTCAAGAAAAAAATAAAAAACTCATGAAAATGAATGAATTTT
*
171963 TGAAAATTGAATTAACATGAATCAAATAATGATGTTT
130 TGAAAACTGAATTAACATGAATCAAATAATGATGTTT
* * * *
172000 TATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTTGAAAAAATTTATGGAGTAGAAAAC-A
1 GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGAAGTAGAAAACAA
* * ** * *
172064 CTACATTT-AGAAAAAAGAGAAATTTCACA-AAAAAAGCTCTAAAACTCATGAACATGATTGAAT
66 C-ATATTTCAGAAAAAAG-GAAATTTCA-AGAAAAAA-ATAAAAAACTCATGAAAATGAATGAAT
* * * *
172127 TTTTGAAAAATGAATTAATATGAATTAAATAATGATATTT
127 TTTTGAAAACTGAATTAACATGAATCAAATAATGATGTTT
* * * *
172167 GATGAATTTTAAAAGTTGAAAATCAAGAAAAATCCCTTC-AAAAGAATTTAC-ATATTAGAAAAC
1 GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAA-AATTTACGA-AGTAGAAAAC
* * * * *
172230 ACCATATTTCGAAAAAAAAGGGAATTTCAAGGCAAAAAATAAAAAACTCATGAAAATAAATGAAT
64 AACATATTTC-AGAAAAAAGGAAATTTCAA-GAAAAAAATAAAAAACTCATGAAAATGAATGAAT
* ** *
172295 TTTTAAAAACTGAATTAATGTGAATCAAATAATGATATTT
127 TTTTGAAAACTGAATTAACATGAATCAAATAATGATGTTT
* * * *
172335 GATAAATTTTAAAAATTGAAAACCAAGAAAAATACCCTCGGAAAAATTTATGAAGTAGAAAACAA
1 GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGAAGTAGAAAACAA
* *
172400 CATATTTCAG-AAAAGGGAAATTTCAAGAAAAAAATAAAAAA-TGAATGAAAATGAATGAATTTT
66 CATATTTCAGAAAAAAGGAAATTTCAAGAAAAAAATAAAAAACT-CATGAAAATGAATGAATTTT
172463 TGAAAACTGAATTAACATGAATCAAATAATGATGTTT
130 TGAAAACTGAATTAACATGAATCAAATAATGATGTTT
* *
172500 GATGAATTTTAAAAATAGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGAAGTAGAAAATAA
1 GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGAAGTAGAAAACAA
** * * * *
172565 TGTATTTTAGAAAAAAGGGAATTTCTAGAAAAAAATAAAAAAACTCATGAAAAAGAATGAATTTT
66 CATATTTCAGAAAAAAGGAAATTTCAAGAAAAAAAT-AAAAAACTCATGAAAATGAATGAATTTT
*
172630 TGAAAACTAAATTAACATGAATCAAATAATGATGTTT
130 TGAAAACTGAATTAACATGAATCAAATAATGATGTTT
* * * *
172667 CATGAATTTTAAAAATTGAAAAGCAAGAAAAATCCCATCGAAAAAATTTACAAAGTAGAAAACAA
1 GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGAAGTAGAAAACAA
* * * *
172732 CATATTTCA-AAAAGAGGGGAATTTCACGGAAAAAATAAAAAACTCATGAAAATGAATGAATTTT
66 CATATTTCAGAAAA-AAGGAAATTTCAAGAAAAAAATAAAAAACTCATGAAAATGAATGAATTTT
*
172796 TGAAAACTAAATT-ACTATGAATCAAATAATGATGTTT
130 TGAAAACTGAATTAAC-ATGAATCAAATAATGATGTTT
* * * *
172833 GATGAATTTTAAAATTTGAAAACCAAGAAAAATCTCGTAGAAAAAATTTACGAAGTAGAAAACAA
1 GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGAAGTAGAAAACAA
* * *
172898 CGTATTTCAGAAAAAACGAAATTTCAAGAAAAAAATAAAAAACTCATGAAAATGAATGACTTTTT
66 CATATTTCAGAAAAAAGGAAATTTCAAGAAAAAAATAAAAAACTCATGAAAATGAATGAATTTTT
*
172963 AAAAACTGA
131 GAAAACTGA
172972 GTTACTATTA
Statistics
Matches: 830, Mismatches: 111, Indels: 52
0.84 0.11 0.05
Matches are distributed among these distances:
155 1 0.00
156 49 0.06
157 23 0.03
158 1 0.00
164 5 0.01
165 136 0.16
166 223 0.27
167 250 0.30
168 125 0.15
169 17 0.02
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (166 bp):
GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGAAGTAGAAAACAA
CATATTTCAGAAAAAAGGAAATTTCAAGAAAAAAATAAAAAACTCATGAAAATGAATGAATTTTT
GAAAACTGAATTAACATGAATCAAATAATGATGTTT
Found at i:173804 original size:50 final size:50
Alignment explanation
Indices: 173729--173829 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
173719 CCAGGAGGTT
*
173729 ACCCATCTTAGTACTACTCTCGCCCAAGCACACTTAACTACGAAGTTCTA
1 ACCCATCCTAGTACTACTCTCGCCCAAGCACACTTAACTACGAAGTTCTA
173779 ACCCATCCTAGTACTACTCTCGCCCAAGCACACTTAACTACGAAGTTCTA
1 ACCCATCCTAGTACTACTCTCGCCCAAGCACACTTAACTACGAAGTTCTA
173829 A
1 A
173830 TGGGATCTGG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.31, C:0.35, G:0.10, T:0.25
Consensus pattern (50 bp):
ACCCATCCTAGTACTACTCTCGCCCAAGCACACTTAACTACGAAGTTCTA
Found at i:174177 original size:20 final size:19
Alignment explanation
Indices: 174135--174188 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
174125 TTTTACCTAG
*
174135 ATGTATCGATACATATATGA
1 ATGTATCGATACAT-TATCA
*
174155 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATT-ATCA
*
174175 ATGTACCGAT-CATT
1 ATGTATCGATACATT
174189 TTATTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.17
20 25 0.83
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (19 bp):
ATGTATCGATACATTATCA
Found at i:174230 original size:20 final size:20
Alignment explanation
Indices: 174205--174299 Score: 145
Period size: 20 Copynumber: 4.8 Consensus size: 20
174195 TTTTACCCAG
*
174205 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
****
174225 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTCTTCA
174245 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
174265 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
174285 ATGTATCGATACATT
1 ATGTATCGATACATT
174300 TTGTCTTTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:174248 original size:70 final size:71
Alignment explanation
Indices: 174124--174259 Score: 184
Period size: 70 Copynumber: 1.9 Consensus size: 71
174114 AAGAGTCACA
* * **
174124 TTTTTACCTAGATGTATCGATACATATATGAATGTATCGATACATTCTTCAATGTACCGAT-CAT
1 TTTTTACCCAGATGTATCGATACATATATCAATGTATCGATACATTCAACAATGTACCGATACAT
174188 TTTATT
66 TTTATT
* * * * *
174194 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTGAAGAATGTATCGATACAT
1 TTTTTACCCAGATGTATCGATACATATATCAATGTATCGATACATTCAACAATGTACCGATACAT
174259 T
66 T
174260 CTTCAATGTA
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
70 52 0.93
71 4 0.07
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (71 bp):
TTTTTACCCAGATGTATCGATACATATATCAATGTATCGATACATTCAACAATGTACCGATACAT
TTTATT
Found at i:179020 original size:168 final size:165
Alignment explanation
Indices: 178679--179305 Score: 691
Period size: 168 Copynumber: 3.8 Consensus size: 165
178669 AACAACATTA
* ** * * * * * * *
178679 GATGAGTTTTAAAAATTTTAAACCAA-AAAAAACCCCCCGAAAAAAATTACGGAGTAGAAAATAT
1 GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGGAATAAAAAACAC
** * * *
178743 CATATTT-TGAAAAAATGGGAGTTTCAAGGAACAAAATCAAAAA-TCAATGAAAATGAATGAATT
66 CATATTTCAAAAAAAATAGAAATTTCAAGGAA-AAAATCAAAAACTC-ATGAAAATG-ATGAATT
*
178806 TTTGAAAATTGAATTAACATGAATCAAATAATGATGTTT
128 TTTG-AAATTGAATTAATATGAATCAAATAATGATGTTT
* *
178845 TATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTTGAAAAAATTTACGGAATAAAAAAACA
1 GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGGAAT-AAAAAACA
* * *
178910 CCGTTTTTCAAAAAAAA-AGAGAATTTTAAGGAAAAAACTCAAAAACTCATGAAAATGATGGAAT
65 CCATATTTCAAAAAAAATAGA-AATTTCAAGGAAAAAA-TCAAAAACTCATGAAAATGAT-GAAT
*
178974 TTTTGAAATTGAATTAATATGAATTAAATAATGATGTTT
127 TTTTGAAATTGAATTAATATGAATCAAATAATGATGTTT
* * * *
179013 GATGAATTTTAAAAATTGAAAATCAAGAAAAATCCACTCGAAAAAATTTACGGAGTAGAAAACAC
1 GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGGAATAAAAAACAC
* * * * *
179078 TATATTTCAAAAAAAATAGAAATTTCAAGAAAAAAATAAAAAAACTCATGAAAGTAAATGAATTT
66 CATATTTCAAAAAAAATAGAAATTTCAAGGAAAAAAT-CAAAAACTCATGAAAAT-GATGAA-TT
* * *
179143 TTTAAAACTGAATTACTATGAATCAAATAATGATGTTT
128 TTTGAAATTGAATTAATATGAATCAAATAATGATGTTT
* ** * *
179181 GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCG-----ATTTAC-GAAGAGGAAATAA
1 GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGGAATAAAAAACAC
* *
179240 CATATTTCGAAAAAAAA-AGAAATTTCAAGAAAAAAATAAAAAACTCATGAAAATGAATGAATTT
66 CATATTTC-AAAAAAAATAGAAATTTCAAGGAAAAAATCAAAAACTCATGAAAATG-ATGAATTT
179304 TT
129 TT
179306 TAAAACTAAA
Statistics
Matches: 398, Mismatches: 50, Indels: 32
0.83 0.10 0.07
Matches are distributed among these distances:
160 5 0.01
161 21 0.05
162 35 0.09
163 14 0.04
166 23 0.06
167 77 0.19
168 180 0.45
169 41 0.10
170 2 0.01
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (165 bp):
GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGGAATAAAAAACAC
CATATTTCAAAAAAAATAGAAATTTCAAGGAAAAAATCAAAAACTCATGAAAATGATGAATTTTT
GAAATTGAATTAATATGAATCAAATAATGATGTTT
Found at i:180323 original size:42 final size:42
Alignment explanation
Indices: 180197--180860 Score: 336
Period size: 42 Copynumber: 15.9 Consensus size: 42
180187 AAATAATGAA
* * * *
180197 ATGAAGAAGTCTCCCTGATTTAAGTCGATGGGTAGACGAAAG
1 ATGAAGAAGTCTCCCAGGTCTAAGTCGACGGGTAGACGAAAG
* * * * *** * *
180239 GTGAAGAAATCT-CCTGAGTCTGAGGT-GTTAGGCAGACAAAAG
1 ATGAAGAAGTCTCCCAG-GTCT-AAGTCGACGGGTAGACGAAAG
* *
180281 ATGAAGAAGTCTCCCAGGACTAAGTCGATGGGTAGACGAAAG
1 ATGAAGAAGTCTCCCAGGTCTAAGTCGACGGGTAGACGAAAG
** * ** * * **
180323 AAAAAGAGGTCTCCTGGGTCTAAG-CTAATGGGTAGACGATTG
1 ATGAAGAAGTCTCCCAGGTCTAAGTC-GACGGGTAGACGAAAG
* ** **
180365 ATGAAGAAGTCTCCCTA-GTCTAAGTCGACGAGCGGACGATTG
1 ATGAAGAAGTCTCCC-AGGTCTAAGTCGACGGGTAGACGAAAG
* * * *
180407 ATGAAGAGGTCTCCCAAGTCTAAGTCGACGAGTAGATG-AAG
1 ATGAAGAAGTCTCCCAGGTCTAAGTCGACGGGTAGACGAAAG
* * * *
180448 AATGAAGAGGTCTCTCAGGTCTAAGCCGACGGGTAGATGAAAG
1 -ATGAAGAAGTCTCCCAGGTCTAAGTCGACGGGTAGACGAAAG
* * * * * **
180491 ATAAAG-AGTCTCTC-GAGTTTAAG-CTGATGGGCAGACGATTG
1 ATGAAGAAGTCTCCCAG-GTCTAAGTC-GACGGGTAGACGAAAG
* * *
180532 ATGAAGAAGTCT--CATGGTTCTGAGCCGACGGGCAGACGAAAG
1 ATGAAGAAGTCTCCCA-GG-TCTAAGTCGACGGGTAGACGAAAG
* * ** * * * *
180574 ATGAAGAGGTCT-CAAAATCTAAGCCAACGGGAAGAC-AATTG
1 ATGAAGAAGTCTCCCAGGTCTAAGTCGACGGGTAGACGAA-AG
* * * * *
180615 ATGAAGAAGTCTCCCAAGTCTGAGTCGACGTGCAGATGAAAG
1 ATGAAGAAGTCTCCCAGGTCTAAGTCGACGGGTAGACGAAAG
* * * *
180657 ATGAAGAGGTCTCCC-GAGTCTAAG-CCATTGGGTAAAC-AAATG
1 ATGAAGAAGTCTCCCAG-GTCTAAGTCGA-CGGGTAGACGAAA-G
* * * *
180699 ATGAA-AAGGTCTCTCGGGTCTAAGCCGACGGGTAGACAAAAG
1 ATGAAGAA-GTCTCCCAGGTCTAAGTCGACGGGTAGACGAAAG
* * * * * *
180741 ATGAAGAAGTCTCCTAGGTTTAAGCCAATGGGCAGACGAAAG
1 ATGAAGAAGTCTCCCAGGTCTAAGTCGACGGGTAGACGAAAG
* * * *
180783 ATGAAGCAGTCTCCCGGGTCTGAG-CTGACAGGTAGACGAAAG
1 ATGAAGAAGTCTCCCAGGTCTAAGTC-GACGGGTAGACGAAAG
* * * *
180825 ATGAATAGGTCTCCTAGGTCAAAGTCGACGGGTAGA
1 ATGAAGAAGTCTCCCAGGTCTAAGTCGACGGGTAGA
180861 TGATTGATGA
Statistics
Matches: 473, Mismatches: 118, Indels: 62
0.72 0.18 0.09
Matches are distributed among these distances:
40 5 0.01
41 75 0.16
42 370 0.78
43 23 0.05
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.20
Consensus pattern (42 bp):
ATGAAGAAGTCTCCCAGGTCTAAGTCGACGGGTAGACGAAAG
Found at i:180368 original size:84 final size:84
Alignment explanation
Indices: 180197--180872 Score: 427
Period size: 84 Copynumber: 8.1 Consensus size: 84
180187 AAATAATGAA
* * * * * * ** * *
180197 ATGAAGAAGTCTCCCTGATTTAAGTCGATGGGTAGACGAAAGGTGAAGAAATCTCCTGAGTCTGA
1 ATGAAGAAGTCTCCCAGGTCTAAGCCGACGGGTAGACGAAAGATGAAGAGGTCTCCTAAGTCTAA
* ** * * * **
180262 GGTGTTAGGCAGACAAAAG
66 GCTAATGGGTAGACGATTG
* * * ** **
180281 ATGAAGAAGTCTCCCAGGACTAAGTCGATGGGTAGACGAAAGAAAAAGAGGTCTCCTGGGTCTAA
1 ATGAAGAAGTCTCCCAGGTCTAAGCCGACGGGTAGACGAAAGATGAAGAGGTCTCCTAAGTCTAA
180346 GCTAATGGGTAGACGATTG
66 GCTAATGGGTAGACGATTG
* * ** ** *
180365 ATGAAGAAGTCTCCCTA-GTCTAAGTCGACGAGCGGACGATTGATGAAGAGGTCTCCCAAGTCTA
1 ATGAAGAAGTCTCCC-AGGTCTAAGCCGACGGGTAGACGAAAGATGAAGAGGTCTCCTAAGTCTA
* * * * *
180429 AG-TCGACGAGTAGATGA-AG
65 AGCT-AATGGGTAGACGATTG
* * * * * *
180448 AATGAAGAGGTCTCTCAGGTCTAAGCCGACGGGTAGATGAAAGATAAAGA-GTCT-CTCGAGTTT
1 -ATGAAGAAGTCTCCCAGGTCTAAGCCGACGGGTAGACGAAAGATGAAGAGGTCTCCT-AAGTCT
* *
180511 AAGCTGATGGGCAGACGATTG
64 AAGCTAATGGGTAGACGATTG
* * * *
180532 ATGAAGAAGTCT--CATGGTTCTGAGCCGACGGGCAGACGAAAGATGAAGAGGTCT-CAAAATCT
1 ATGAAGAAGTCTCCCA-GG-TCTAAGCCGACGGGTAGACGAAAGATGAAGAGGTCTCCTAAGTCT
* * * *
180594 AAGCCAACGGGAAGACAATTG
64 AAGCTAATGGGTAGACGATTG
* * * * * * **
180615 ATGAAGAAGTCTCCCAAGTCTGAGTCGACGTGCAGATGAAAGATGAAGAGGTCTCCCGAGTCTAA
1 ATGAAGAAGTCTCCCAGGTCTAAGCCGACGGGTAGACGAAAGATGAAGAGGTCTCCTAAGTCTAA
* * * * *
180680 GCCATTGGGTAAACAAATG
66 GCTAATGGGTAGACGATTG
* * * * * *
180699 ATGAA-AAGGTCTCTCGGGTCTAAGCCGACGGGTAGACAAAAGATGAAGAAGTCTCCTAGGTTTA
1 ATGAAGAA-GTCTCCCAGGTCTAAGCCGACGGGTAGACGAAAGATGAAGAGGTCTCCTAAGTCTA
* * **
180763 AGCCAATGGGCAGACGAAAG
65 AGCTAATGGGTAGACGATTG
* * * * * * * *
180783 ATGAAGCAGTCTCCCGGGTCTGAGCTGACAGGTAGACGAAAGATGAATAGGTCTCCTAGGTCAAA
1 ATGAAGAAGTCTCCCAGGTCTAAGCCGACGGGTAGACGAAAGATGAAGAGGTCTCCTAAGTCTAA
* * *
180848 G-TCGACGGGTAGATGATTG
66 GCT-AATGGGTAGACGATTG
180867 ATGAAG
1 ATGAAG
180873 TTTGGAAAGA
Statistics
Matches: 460, Mismatches: 116, Indels: 32
0.76 0.19 0.05
Matches are distributed among these distances:
81 2 0.00
82 3 0.01
83 127 0.28
84 324 0.70
85 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.20
Consensus pattern (84 bp):
ATGAAGAAGTCTCCCAGGTCTAAGCCGACGGGTAGACGAAAGATGAAGAGGTCTCCTAAGTCTAA
GCTAATGGGTAGACGATTG
Found at i:180579 original size:167 final size:168
Alignment explanation
Indices: 180281--180754 Score: 406
Period size: 167 Copynumber: 2.8 Consensus size: 168
180271 CAGACAAAAG
* * *
180281 ATGAAGAAGTCTCCCAGGACTAAGTCGATGGGTAGACGAAAGAAAAAGAGGTCTCCTGGGTCTAA
1 ATGAAGAAGTCTCCCAGGACTAAGCCGACGGGTAGACGAAAGAAAAAGAGGTCTCCTGAGTCTAA
* * * * **
180346 GCTAATGGGTAGACGATTGATGAAGAAGTCTCCCTAGTCTAAGTCGACGAGCGGACGATTGATGA
66 GCTAATGGGCAGACGATTGATGAAGAAGTCTCCATAGTCTAAGCCGACGAGCAGACGAAAGATGA
180411 AGAGGTCTCCCAAGTCTAAGTCGACGAGTAGATGAAGA
131 AGAGGTCTCCCAAGTCTAAGTCGACGAGTAGATGAAGA
* * * * * *
180449 ATGAAGAGGTCTCTCAGGTCTAAGCCGACGGGTAGATGAAAGATAAAGA-GTCT-CTCGAGTTTA
1 ATGAAGAAGTCTCCCAGGACTAAGCCGACGGGTAGACGAAAGAAAAAGAGGTCTCCT-GAGTCTA
* * * *
180512 AGCTGATGGGCAGACGATTGATGAAGAAGTCT-CATGGTTCTGAGCCGACGGGCAGACGAAAGAT
65 AGCTAATGGGCAGACGATTGATGAAGAAGTCTCCATAG-TCTAAGCCGACGAGCAGACGAAAGAT
* * * * * * *
180576 GAAGAGGTCT-CAAAATCTAAGCCAACGGGAAGA-CAATTG-
129 GAAGAGGTCTCCCAAGTCTAAGTCGACGAGTAGATGAA--GA
* * * * * * * ** *
180615 ATGAAGAAGTCTCCCAAGTCTGAGTCGACGTGCAGATGAAAGATGAAGAGGTCTCCCGAGTCTAA
1 ATGAAGAAGTCTCCCAGGACTAAGCCGACGGGTAGACGAAAGAAAAAGAGGTCTCCTGAGTCTAA
* * * * * * ** * * *
180680 GCCATTGGGTAAACAAATGATGAA-AAGGTCTCTC-GGGTCTAAGCCGACGGGTAGACAAAAGAT
66 GCTAATGGGCAGACGATTGATGAAGAA-GTCTC-CATAGTCTAAGCCGACGAGCAGACGAAAGAT
*
180743 GAAGAAGTCTCC
129 GAAGAGGTCTCC
180755 TAGGTTTAAG
Statistics
Matches: 248, Mismatches: 48, Indels: 20
0.78 0.15 0.06
Matches are distributed among these distances:
165 2 0.01
166 65 0.26
167 134 0.54
168 46 0.19
169 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.20
Consensus pattern (168 bp):
ATGAAGAAGTCTCCCAGGACTAAGCCGACGGGTAGACGAAAGAAAAAGAGGTCTCCTGAGTCTAA
GCTAATGGGCAGACGATTGATGAAGAAGTCTCCATAGTCTAAGCCGACGAGCAGACGAAAGATGA
AGAGGTCTCCCAAGTCTAAGTCGACGAGTAGATGAAGA
Found at i:180650 original size:125 final size:124
Alignment explanation
Indices: 180341--180669 Score: 290
Period size: 125 Copynumber: 2.6 Consensus size: 124
180331 GTCTCCTGGG
* * * * *
180341 TCTAAGCTAATGGGTAGACGATTGATGAAGAAGTCTCCCTAGTCTAAGTCGACGAGCGGACGATT
1 TCTAAGCCAACGGGTAGACAATTGATGAAGAAGTCTCCCAAGTCTAAGTCGACGAGCAGACGATT
* * * * **
180406 GATGAAGAGGTCTCCCAAGTCTAAGTCGACGAGTAGATGAAGAATGAAGAGGTCTCTCAGG
66 GATGAAGAGGTCT--CAAGTCTAAGCCGACGAGCAGACGAAGAATGAAGAGGTCTCTAAAA
* * * * * * * * *
180467 TCTAAGCCGACGGGTAGATGAA-AGATAAAG-AGTCTCTCGAGTTTAAG-CTGATGGGCAGACGA
1 TCTAAGCCAACGGGTAGA-CAATTGATGAAGAAGTCTCCCAAGTCTAAGTC-GACGAGCAGACGA
* * * *
180529 TTGATGAAGAAGTCTCATGGTTCTGAGCCGACGGGCAGACGAA-AGATGAAGAGGTCTC-AAAA
64 TTGATGAAGAGGTCTCA-AG-TCTAAGCCGACGAGCAGACGAAGA-ATGAAGAGGTCTCTAAAA
* * * * **
180591 TCTAAGCCAACGGGAAGACAATTGATGAAGAAGTCTCCCAAGTCTGAGTCGACGTGCAGATGAAA
1 TCTAAGCCAACGGGTAGACAATTGATGAAGAAGTCTCCCAAGTCTAAGTCGACGAGCAGACGATT
180656 GATGAAGAGGTCTC
66 GATGAAGAGGTCTC
180670 CCGAGTCTAA
Statistics
Matches: 157, Mismatches: 38, Indels: 17
0.74 0.18 0.08
Matches are distributed among these distances:
123 4 0.03
124 26 0.17
125 104 0.66
126 22 0.14
127 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (124 bp):
TCTAAGCCAACGGGTAGACAATTGATGAAGAAGTCTCCCAAGTCTAAGTCGACGAGCAGACGATT
GATGAAGAGGTCTCAAGTCTAAGCCGACGAGCAGACGAAGAATGAAGAGGTCTCTAAAA
Found at i:180870 original size:126 final size:124
Alignment explanation
Indices: 180269--180872 Score: 423
Period size: 126 Copynumber: 4.8 Consensus size: 124
180259 TGAGGTGTTA
* * * * **
180269 GGCAGACAAAAGATGAAGAAGTCTCCCAGGACTAAG-TCGATGGGTAGACGAAAGAAAAAGAGGT
1 GGCAGACGAAAGATGAAG-AGTCTCCCGGGTCTAAGCT-GACGGGTAGACGAAAGATGAAGAGGT
* ** * *
180333 CTCCTGGGTCTAAGCTAATGGGTAGACGATTGATGAAGAAGTCTCCCTA-GTCTAAGTCGACG
64 CT-CTAGGTCTAAGCCGACGGGTAGACGATTGATGAAGAAGTCT-CCTAGGTCTAAGCCGACG
* * ** ** * *
180395 AGCGGACGATTGATGAAGAGGTCTCCCAAGTCTAAG-TCGACGAGTAGATG-AAGAATGAAGAGG
1 GGCAGACGAAAGATGAAGA-GTCTCCCGGGTCTAAGCT-GACGGGTAGACGAAAG-ATGAAGAGG
* ** * * * * *
180458 TCTCTCAGGTCTAAGCCGACGGGTAGATGAAAGATAAAG-AGTCT-CTCGAGTTTAAGCTGATG
63 TCTCT-AGGTCTAAGCCGACGGGTAGACGATTGATGAAGAAGTCTCCTAG-GTCTAAGCCGACG
** ** * * * *
180520 GGCAGACGATTGATGAAGAAGTCTCATGGTTCTGAGCCGACGGGCAGACGAAAGATGAAGAGGTC
1 GGCAGACGAAAGATGAAG-AGTCTCCCGGGTCTAAGCTGACGGGTAGACGAAAGATGAAGAGGTC
* ** * * * * * * *
180585 TCAAAATCTAAGCCAACGGGAAGACAATTGATGAAGAAGTCTCCCAAGTCTGAGTCGACG
65 TCTAGGTCTAAGCCGACGGGTAGACGATTGATGAAGAAGTCTCCTAGGTCTAAGCCGACG
* * * * * * *
180645 TGCAGATGAAAGATGAAGAGGTCTCCCGAGTCTAAGC-CATTGGGTAAAC-AAATGATGAAAAGG
1 GGCAGACGAAAGATGAAGA-GTCTCCCGGGTCTAAGCTGA-CGGGTAGACGAAA-GATGAAGAGG
* * ** * * *
180708 TCTCTCGGGTCTAAGCCGACGGGTAGACAAAAGATGAAGAAGTCTCCTAGGTTTAAGCCAATG
63 TCTCT-AGGTCTAAGCCGACGGGTAGACGATTGATGAAGAAGTCTCCTAGGTCTAAGCCGACG
* * *
180771 GGCAGACGAAAGATGAAGCAGTCTCCCGGGTCTGAGCTGACAGGTAGACGAAAGATGAATAGGTC
1 GGCAGACGAAAGATGAAG-AGTCTCCCGGGTCTAAGCTGACGGGTAGACGAAAGATGAAGAGGTC
* * *
180836 TCCTAGGTCAAAGTCGACGGGTAGATGATTGATGAAG
65 T-CTAGGTCTAAGCCGACGGGTAGACGATTGATGAAG
180873 TTTGGAAAGA
Statistics
Matches: 360, Mismatches: 100, Indels: 36
0.73 0.20 0.07
Matches are distributed among these distances:
123 2 0.01
124 29 0.08
125 126 0.35
126 196 0.54
127 7 0.02
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.20
Consensus pattern (124 bp):
GGCAGACGAAAGATGAAGAGTCTCCCGGGTCTAAGCTGACGGGTAGACGAAAGATGAAGAGGTCT
CTAGGTCTAAGCCGACGGGTAGACGATTGATGAAGAAGTCTCCTAGGTCTAAGCCGACG
Found at i:181491 original size:78 final size:78
Alignment explanation
Indices: 181357--181554 Score: 189
Period size: 78 Copynumber: 2.5 Consensus size: 78
181347 GCCCCTTATG
** * * * * *
181357 GCCATGTGATGCATTAATACCATTTAGTGTTTGGGAAAGAGGGATACGACTAGGAATGTATGGGA
1 GCCATGTGATGCACCAATATCATCTAGTATTTGGGAAAGAAGGATACGACTAGGAATATATGGGA
* **
181422 AACGTCATTTTTA
66 AACGCCACCTTTA
* * * * *
181435 GCCATGTAATGCACCAATATCATCTAGTATTTGGGAAAGAAGGATATGATTGGGAATATGTGGGA
1 GCCATGTGATGCACCAATATCATCTAGTATTTGGGAAAGAAGGATACGACTAGGAATATATGGGA
** * *
181500 AGTGCCCCCTTTG
66 AACGCCACCTTTA
* * * *
181513 GCCTTGTGATGGACCAATATCATCTAGCATCTGGGAAAGAAG
1 GCCATGTGATGCACCAATATCATCTAGTATTTGGGAAAGAAG
181555 AGAATGACTG
Statistics
Matches: 96, Mismatches: 24, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
78 96 1.00
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (78 bp):
GCCATGTGATGCACCAATATCATCTAGTATTTGGGAAAGAAGGATACGACTAGGAATATATGGGA
AACGCCACCTTTA
Found at i:184435 original size:79 final size:78
Alignment explanation
Indices: 184213--184443 Score: 232
Period size: 79 Copynumber: 2.9 Consensus size: 78
184203 TCCAAAATAG
* * * *
184213 TTTTTCACAATCGGGGATACTCCAA-CCTCATTATTTTT-GAGGGCATACTCTAACCTCGATTTT
1 TTTTCCACAATCGGGGATACTCCAACCCT-ATTATTTTTAAAGGG-ATACTCCAACCTAG-TTTT
** * *
184276 ATTTTTAAAATATCAA
63 ATTTCCAAAACACCAA
** * * *
184292 TTTTCCACAATCGGGGATACTCCAACCCTATTATTTCCAAAGGGATACTTCAACCCCAATTTTAT
1 TTTTCCACAATCGGGGATACTCCAACCCTATTATTTTTAAAGGGATACTCCAA-CCTAGTTTTAT
* *
184357 TTCCAGAACACCGA
65 TTCCAAAACACCAA
* * *
184371 TTTTCCACAATCGGGGATACTCCAACCCTGTTATTTTTAAAAGGATACTCCAACCTTGTCTTTAT
1 TTTTCCACAATCGGGGATACTCCAACCCTATTATTTTTAAAGGGATACTCCAACCTAGT-TTTAT
*
184436 CTCCAAAA
65 TTCCAAAA
184444 TATTAAATTT
Statistics
Matches: 123, Mismatches: 25, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
78 3 0.02
79 111 0.90
80 9 0.07
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.34
Consensus pattern (78 bp):
TTTTCCACAATCGGGGATACTCCAACCCTATTATTTTTAAAGGGATACTCCAACCTAGTTTTATT
TCCAAAACACCAA
Found at i:196784 original size:10 final size:9
Alignment explanation
Indices: 196771--196808 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
196761 AAAAAACAAC
196771 AAAAAAAGA
1 AAAAAAAGA
*
196780 GAAAAAAGA
1 AAAAAAAGA
196789 AAAAAAAGA
1 AAAAAAAGA
196798 AAAGAAAAGA
1 AAA-AAAAGA
196808 A
1 A
196809 CCTGCTTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:197881 original size:61 final size:62
Alignment explanation
Indices: 197751--197892 Score: 234
Period size: 61 Copynumber: 2.3 Consensus size: 62
197741 AACCTTTTAT
* * *
197751 CCTTTCAGTCCTCAAAGAGCAGGATACCATTTCCTTTTCATAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACACCATTTCCTTATCAAAGCCCACACAAGTTGGTGGCA
197813 CCTTTCAGTCCTCAAAGAGCAGGACACC-TTCTCCTTAT-AAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACACCATT-TCCTTATCAAAGCCCACACAAGTTGGTGGCA
197874 CCTTTCAGTCCTCAAAGAG
1 CCTTTCAGTCCTCAAAGAG
197893 TAAGCACCTT
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
61 43 0.57
62 33 0.43
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (62 bp):
CCTTTCAGTCCTCAAAGAGCAGGACACCATTTCCTTATCAAAGCCCACACAAGTTGGTGGCA
Found at i:197905 original size:25 final size:25
Alignment explanation
Indices: 197871--197919 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
197861 CAAGTTGGTG
197871 GCACCTTTCAGTCCTCAAAGAGTAA
1 GCACCTTTCAGTCCTCAAAGAGTAA
197896 GCACCTTTCAGTCCTCAAAGAGTA
1 GCACCTTTCAGTCCTCAAAGAGTA
197920 GGACGCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (25 bp):
GCACCTTTCAGTCCTCAAAGAGTAA
Found at i:197955 original size:86 final size:86
Alignment explanation
Indices: 197810--197980 Score: 272
Period size: 86 Copynumber: 2.0 Consensus size: 86
197800 CAAGTTGGTG
197810 GCACCTTTCAGTCCTCAAAGAGCAGGACACCTTCTCCTTATAAAGCCCACACAAGTTGGTGGCAC
1 GCACCTTTCAGTCCTCAAAGAGCAGGACACCTTCTCCTTATAAAGCCCACACAAGTTGGTGGCA-
197875 CTT-TCAGTCCTCAAAGAGTAA
65 CTTGTCAGTCCTCAAAGAGTAA
* * * * *
197896 GCACCTTTCAGTCCTCAAAGAGTAGGACGCCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCAC
1 GCACCTTTCAGTCCTCAAAGAGCAGGACACCTTCTCCTTATAAAGCCCACACAAGTTGGTGGCAC
*
197961 TTGTCAGTCCTTAAAGAGTA
66 TTGTCAGTCCTCAAAGAGTA
197981 GGACGCCTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
85 3 0.04
86 75 0.96
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.26
Consensus pattern (86 bp):
GCACCTTTCAGTCCTCAAAGAGCAGGACACCTTCTCCTTATAAAGCCCACACAAGTTGGTGGCAC
TTGTCAGTCCTCAAAGAGTAA
Found at i:198080 original size:59 final size:59
Alignment explanation
Indices: 197896--198337 Score: 633
Period size: 59 Copynumber: 7.5 Consensus size: 59
197886 CAAAGAGTAA
* * *
197896 GCACCTTTCAGTCCTCAAAGAGTAGGACGCCTTTTCTTTTTAAAGCCCACACAAGTTGGTG
1 GCACCTTCCAGTCCTCAAAGAGTAGGACG--TTTTCCTTTCAAAGCCCACACAAGTTGGTG
* *
197957 GCA-CTTGTCAGTCCTTAAAGAGTAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTG
1 GCACCTT-CCAGTCCTCAAAGAGTAGGACG--TTTTCCTTTCAAAGCCCACACAAGTTGGTG
198018 GCACCTTCCAGTCCTCAAAGAGTAGGACGTTTTCCTTTCAAAGCCCACACAAGTTGGTG
1 GCACCTTCCAGTCCTCAAAGAGTAGGACGTTTTCCTTTCAAAGCCCACACAAGTTGGTG
** *
198077 GCACCTTTTAGTCCTCAAAGAGCAGGACGTTTTCCTTTCAAAGCCCACACAAGTTGGTG
1 GCACCTTCCAGTCCTCAAAGAGTAGGACGTTTTCCTTTCAAAGCCCACACAAGTTGGTG
*
198136 GCACCTCCCAGTCCTCAAAGAGTAGGACGTTTTCCTTTCAAAGCCCACACAAGTTGGTG
1 GCACCTTCCAGTCCTCAAAGAGTAGGACGTTTTCCTTTCAAAGCCCACACAAGTTGGTG
*
198195 GCACCTTCCAGTCCTCAAAGAGTAGGATAG-TTTCCTTTCAAAGCCCACACAAGTTGGTG
1 GCACCTTCCAGTCCTCAAAGAGTAGGA-CGTTTTCCTTTCAAAGCCCACACAAGTTGGTG
* * * * * *
198254 GCACCTTCTAGTCCTCAAAGAGTAGTATGCTTTCCTTTC-AA-CCCACACAAGTTGCTA
1 GCACCTTCCAGTCCTCAAAGAGTAGGACGTTTTCCTTTCAAAGCCCACACAAGTTGGTG
*
198311 GCACCTTCTAGTTCC-CAAAGAGTAGGA
1 GCACCTTCCAG-TCCTCAAAGAGTAGGA
198338 TGCGCTTTAA
Statistics
Matches: 356, Mismatches: 20, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
57 36 0.10
58 6 0.02
59 230 0.65
60 4 0.01
61 77 0.22
62 3 0.01
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.27
Consensus pattern (59 bp):
GCACCTTCCAGTCCTCAAAGAGTAGGACGTTTTCCTTTCAAAGCCCACACAAGTTGGTG
Found at i:198466 original size:35 final size:35
Alignment explanation
Indices: 198397--198493 Score: 86
Period size: 35 Copynumber: 2.6 Consensus size: 35
198387 TTTATTTCCT
***
198397 TTTTTCCTTTGTCCTCAAAGAGTAAGATGTATTTC
1 TTTTTCCTTTGTCCTCAAAGAGTAAGACCCATTTC
* * *
198432 TTTTTCCTTTGTCCTTAAGGAGTAGGACCCATTTC
1 TTTTTCCTTTGTCCTCAAAGAGTAAGACCCATTTC
*
198467 ATTCTAGTTTCATTTGTCCTCAAAGAG
1 --T-T--TTTCCTTTGTCCTCAAAGAG
198494 CAGGACGTAT
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
35 29 0.60
37 1 0.02
38 1 0.02
40 17 0.35
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (35 bp):
TTTTTCCTTTGTCCTCAAAGAGTAAGACCCATTTC
Found at i:198527 original size:42 final size:42
Alignment explanation
Indices: 198349--198534 Score: 165
Period size: 42 Copynumber: 4.6 Consensus size: 42
198339 GCGCTTTAAG
* * *
198349 TTCCTTCTTTTCCTTTGTCTTTAAAAAGCAGGACGCATTTTAT
1 TTCCTT-TTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTTAT
* *
198392 TTCCTTTTTTCCTTTGTCCTCAAAGAGTA--A-G-A-TGTAT
1 TTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTTAT
* * * * *
198429 TT-C-TTTTTCCTTTGTCCTTAAGGAGTAGGACCCATTTCA-
1 TTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTTAT
** * *
198468 TT-CTAGTTTCATTTGTCCTCAAAGAGCAGGACGTATTTTAT
1 TTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTTAT
*
198509 TTCCTTTTTTCCTTTGTCCTCGAAGA
1 TTCCTTTTTTCCTTTGTCCTCAAAGA
198535 ATAGGATGTA
Statistics
Matches: 112, Mismatches: 23, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
35 22 0.20
36 1 0.01
37 7 0.06
38 1 0.01
39 5 0.04
40 30 0.27
41 2 0.02
42 38 0.34
43 6 0.05
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (42 bp):
TTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTTAT
Found at i:198569 original size:117 final size:117
Alignment explanation
Indices: 198357--198616 Score: 335
Period size: 117 Copynumber: 2.2 Consensus size: 117
198347 AGTTCCTTCT
* * * *
198357 TTTCCTTTGTCTTTAAAAAGCAGGACGCATTTTATTTCCTTTTTTCCTTTGTCCTCAAAGAGTAA
1 TTTCATTTGTCCTCAAAAAGCAGGACGCATTTTATTTCCTTTTTTCCTTTGTCCTCAAAGAATAA
* * *
198422 GATGTATTTCTTTTTCCTTTGTCCTTAAGGAGTAGGACCCATTTCATTCTAG
66 GATGTATCTCTTTTTCCTTTGTCCTCAAGGAGCAGGACCCATTTCATTCTAG
* * * *
198474 TTTCATTTGTCCTCAAAGAGCAGGACGTATTTTATTTCCTTTTTTCCTTTGTCCTCGAAGAATAG
1 TTTCATTTGTCCTCAAAAAGCAGGACGCATTTTATTTCCTTTTTTCCTTTGTCCTCAAAGAATAA
* *
198539 GATGTA-CTCTTTTTTCCTTTGTTCTCAAGGAGCAGGACCTATTTCATTCTCA-
66 GATGTATCTC-TTTTTCCTTTGTCCTCAAGGAGCAGGACCCATTTCATTCT-AG
* * * *
198591 TTTCTTTTGTTCTAAAAAAGTAGGAC
1 TTTCATTTGTCCTCAAAAAGCAGGAC
198617 ATTTTCCTTT
Statistics
Matches: 123, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
116 2 0.02
117 120 0.98
118 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (117 bp):
TTTCATTTGTCCTCAAAAAGCAGGACGCATTTTATTTCCTTTTTTCCTTTGTCCTCAAAGAATAA
GATGTATCTCTTTTTCCTTTGTCCTCAAGGAGCAGGACCCATTTCATTCTAG
Found at i:198685 original size:59 final size:58
Alignment explanation
Indices: 198612--198821 Score: 306
Period size: 59 Copynumber: 3.7 Consensus size: 58
198602 CTAAAAAAGT
* * *
198612 AGGACATTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACTGTTCAGTCCTCAAAGAGT
1 AGGACGTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACT-TCCAGTCCTCAAAGAGC
198671 AGGACGTTTTCCTTTCAAAGCCCACACAAG-T--TGG---TTCCAGTCCTCAAAGAGC
1 AGGACGTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCAGTCCTCAAAGAGC
* *
198723 AGGATGTTTTCCTTTCAAAGCCCACATAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGC
1 AGGACGTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTCCAGTCCTCAAAGAGC
*
198782 AGAACGTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCAC
1 AGGACGTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCAC
198822 CTTCTAATCC
Statistics
Matches: 136, Mismatches: 8, Indels: 15
0.86 0.05 0.09
Matches are distributed among these distances:
52 43 0.32
53 2 0.01
55 3 0.02
56 3 0.02
58 2 0.01
59 83 0.61
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (58 bp):
AGGACGTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCAGTCCTCAAAGAGC
Found at i:198947 original size:35 final size:38
Alignment explanation
Indices: 198857--199002 Score: 109
Period size: 42 Copynumber: 3.7 Consensus size: 38
198847 CGCTTTAATT
*
198857 TCCTTCTTTTCCTTTGTCCTCGAAGAGCAGGATGCATTTTATT
1 TCCTT-TTTTCCTTTGTCCTCGAAGAGCAGGATG----TTATG
*
198900 TCCTTTTTTCCTTTGTCCTCGAAGAGCTGGATG-TA-G
1 TCCTTTTTTCCTTTGTCCTCGAAGAGCAGGATGTTATG
* * * * * *
198936 TCC-TTTTTCCTTCGTCCTCTAGGAGCAGGACCTATTTTA
1 TCCTTTTTTCCTTTGTCCTCGAAGAGCAGGA--TGTTATG
* * *
198975 TTCTTGTTTCCTTTATCCTCGAAGAGCA
1 TCCTTTTTTCCTTTGTCCTCGAAGAGCA
199003 AGACGTGCTC
Statistics
Matches: 83, Mismatches: 15, Indels: 13
0.75 0.14 0.12
Matches are distributed among these distances:
35 23 0.28
36 3 0.04
37 3 0.04
38 1 0.01
39 2 0.02
40 19 0.23
42 27 0.33
43 5 0.06
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.42
Consensus pattern (38 bp):
TCCTTTTTTCCTTTGTCCTCGAAGAGCAGGATGTTATG
Found at i:199685 original size:20 final size:20
Alignment explanation
Indices: 199652--199723 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
199642 TTTACCCAGA
*
199652 TGTATCGATGCATTATTCAT
1 TGTATCGATACATTATTCAT
* *
199672 TGTATTGATACATTATTCTT
1 TGTATCGATACATTATTCAT
*
199692 TGTATCGATACATT-TTCAA
1 TGTATCGATACATTATTCAT
199711 TGTATCGATACAT
1 TGTATCGATACAT
199724 CCAAGCATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 16 0.35
20 30 0.65
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (20 bp):
TGTATCGATACATTATTCAT
Found at i:202094 original size:28 final size:28
Alignment explanation
Indices: 202035--202099 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
202025 AATCGGGGAG
* ** * *
202035 ACTCTAACCCTGTTATTTTCGTGGGGAT
1 ACTCCAACCCTGTTATTTTCGAAGGAAA
*
202063 ACTCCAACCCTGTTATTTTTGAAGGAAA
1 ACTCCAACCCTGTTATTTTCGAAGGAAA
202091 ACTCCAACC
1 ACTCCAACC
202100 TCGATTTTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (28 bp):
ACTCCAACCCTGTTATTTTCGAAGGAAA
Found at i:202157 original size:79 final size:78
Alignment explanation
Indices: 202057--202625 Score: 518
Period size: 79 Copynumber: 7.2 Consensus size: 78
202047 TTATTTTCGT
* * * *
202057 GGGGATACTCCAACCCTGTTATTTTTGAAGGAAAACTCCAACCTCGATTTTATTTCCAAAACATC
1 GGGGATACTCCAACCC-ATTATTTTTGAAGGGATACTCCAACCCCGATTTTATTTCCAAAACATC
*
202122 AATTTTTCATAATC
65 AATTTTTCACAATC
* * * **
202136 GGGGTTACTCTAATCCCGTTA-TTTCCAAGGAGATACTCCAACCCCGATTTTATTTCCAAAACA-
1 GGGGATACTCCAA-CCCATTATTTTTGAAGG-GATACTCCAACCCCGATTTTATTTCCAAAACAT
*
202199 CTAATTTTTCATAATC
64 C-AATTTTTCACAATC
* * * * *
202215 GAGGATACTCCAACCTCATTATTTCTGATGGGATACTCCAACCCCGATTTTACTTT-CAAAATAC
1 GGGGATACTCCAACC-CATTATTTTTGAAGGGATACTCCAACCCCGATTTTA-TTTCCAAAACAT
202279 CAATTTTTCACAATC
64 CAATTTTTCACAATC
* *
202294 GGGGATACTCCAATCCCATTATTTTTGAGGGGATACTCCAACCCCGATTTTATTTCCAAAAGATC
1 GGGGATACTCCAA-CCCATTATTTTTGAAGGGATACTCCAACCCCGATTTTATTTCCAAAACATC
*
202359 AGTTTTTCACAATC
65 AATTTTTCACAATC
* * ** * * ** ** * *
202373 AGAGATACTCCAACCTTGTTATTTTCGAGGGGATACTTTAACCCTAATTTTATTTCTAAAATATC
1 GGGGATACTCCAACC-CATTATTTTTGAAGGGATACTCCAACCCCGATTTTATTTCCAAAACATC
202438 AATTTTTCACAATC
65 AATTTTTCACAATC
* * *** * * *
202452 GGGGATACTCTAATCCTATTATTTCCAAAGGGATACTCCAACCCTGATTTTATTTTCAAAACACC
1 GGGGATACTCCAA-CCCATTATTTTTGAAGGGATACTCCAACCCCGATTTTATTTCCAAAACATC
* *
202517 GATTTTCCACAATC
65 AATTTTTCACAATC
* * * ** * * *
202531 GGGGATACTCTAGCCCTATTATTTTTGAAAGGATACTAAAACCCTG-TCTTTATGTCCAAAATAT
1 GGGGATACTCCAACCC-ATTATTTTTGAAGGGATACTCCAACCCCGAT-TTTATTTCCAAAACA-
*
202595 TAAATTTTTCATCAA-C
63 TCAATTTTTCA-CAATC
* *
202611 GAGTATACTCCAACC
1 GGGGATACTCCAACC
202626 GCGTACCCTG
Statistics
Matches: 405, Mismatches: 70, Indels: 29
0.80 0.14 0.06
Matches are distributed among these distances:
78 18 0.04
79 349 0.86
80 35 0.09
81 3 0.01
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (78 bp):
GGGGATACTCCAACCCATTATTTTTGAAGGGATACTCCAACCCCGATTTTATTTCCAAAACATCA
ATTTTTCACAATC
Found at i:202475 original size:237 final size:237
Alignment explanation
Indices: 202057--202623 Score: 635
Period size: 237 Copynumber: 2.4 Consensus size: 237
202047 TTATTTTCGT
* * * *
202057 GGGGATACTCCAACCCTGTTATTTTTGAAGGAAAACTCCAACCTCGATTTTATTTCCAAAACATC
1 GGGGATACTCCAACCCTATTATTTTTGAAGGGATACTCCAACCCCGATTTTATTTCCAAAACATC
* * * * * *
202122 AATTTTTCATAATCGGGGTTACTCTAATCCCGTTATTTCCAAGGAGATACTCCAACCCCGATTTT
66 AATTTTTCACAATCAGAGATACTCCAATCCCGTTATTTCCAAGGAGATACTCCAACCCCAATTTT
* ** *
202187 ATTTCCAAAACACTAATTTTTCATAATCGAGGATACTCCAACCTCATTATTTCTGATGGGATACT
131 ATTTCCAAAACACTAATTTTTCACAATCGAGGATACTCCAACCTCATTATTTCCAAAGGGATACT
* *
202252 CCAACCCCGATTTTACTTTCAAAATACCAATTTTTCACAATC
196 CCAACCCCGATTTTACTTTCAAAACACCAATTTTCCACAATC
* *
202294 GGGGATACTCCAATCCC-ATTATTTTTGAGGGGATACTCCAACCCCGATTTTATTTCCAAAAGAT
1 GGGGATACTCCAA-CCCTATTATTTTTGAAGGGATACTCCAACCCCGATTTTATTTCCAAAACAT
* * * * * ** *
202358 CAGTTTTTCACAATCAGAGATACTCCAA-CCTTGTTATTTTCGAGGGGATACTTTAACCCTAATT
65 CAATTTTTCACAATCAGAGATACTCCAATCC-CGTTATTTCCAAGGAGATACTCCAACCCCAATT
* * * *
202422 TTATTTCTAAAATA-TCAATTTTTCACAATCGGGGATACTCTAATCCT-ATTATTTCCAAAGGGA
129 TTATTTCCAAAACACT-AATTTTTCACAATCGAGGATACTCCAA-CCTCATTATTTCCAAAGGGA
* * *
202485 TACTCCAACCCTGATTTTATTTTCAAAACACCGATTTTCCACAATC
192 TACTCCAACCCCGATTTTACTTTCAAAACACCAATTTTCCACAATC
* * * ** * * *
202531 GGGGATACTCTAGCCCTATTATTTTTGAAAGGATACTAAAACCCTG-TCTTTATGTCCAAAATAT
1 GGGGATACTCCAACCCTATTATTTTTGAAGGGATACTCCAACCCCGAT-TTTATTTCCAAAACA-
*
202595 TAAATTTTTCATCAA-C-GAGTATACTCCAA
64 TCAATTTTTCA-CAATCAGAG-ATACTCCAA
202624 CCGCGTACCC
Statistics
Matches: 277, Mismatches: 44, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
236 7 0.03
237 242 0.87
238 25 0.09
239 3 0.01
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (237 bp):
GGGGATACTCCAACCCTATTATTTTTGAAGGGATACTCCAACCCCGATTTTATTTCCAAAACATC
AATTTTTCACAATCAGAGATACTCCAATCCCGTTATTTCCAAGGAGATACTCCAACCCCAATTTT
ATTTCCAAAACACTAATTTTTCACAATCGAGGATACTCCAACCTCATTATTTCCAAAGGGATACT
CCAACCCCGATTTTACTTTCAAAACACCAATTTTCCACAATC
Found at i:209733 original size:6 final size:6
Alignment explanation
Indices: 209722--209748 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
209712 TACGGAAGGG
209722 TTGGTT TTGGTT TTGGTT TTGGTT TTG
1 TTGGTT TTGGTT TTGGTT TTGGTT TTG
209749 TGGATAGTTT
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:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (6 bp):
TTGGTT
Found at i:216230 original size:10 final size:10
Alignment explanation
Indices: 216215--216261 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
216205 ACTAGCTTGT
*
216215 TTTTTCACTA
1 TTTTTCTCTA
216225 TTTTTCTCT-
1 TTTTTCTCTA
216234 TTTTTCTCTA
1 TTTTTCTCTA
* *
216244 TTTTCTTTCTC
1 TTTT-TCTCTA
216255 TTTTTCT
1 TTTTTCT
216262 TCTCACTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 9 0.29
10 14 0.45
11 8 0.26
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTTCTCTA
Found at i:216247 original size:11 final size:10
Alignment explanation
Indices: 216214--216265 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 10
216204 AACTAGCTTG
*
216214 TTTTTTCACT
1 TTTTTTCTCT
*
216224 ATTTTTCTCT
1 TTTTTTCTCT
*
216234 TTTTTCTCTAT
1 TTTTT-TCTCT
216245 TTTCTTTCTCT
1 TTT-TTTCTCT
216256 TTTTCTTCTC
1 TTTT-TTCTC
216266 ACTTTGCTAG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
10 13 0.38
11 19 0.56
12 2 0.06
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTTTCTCT
Found at i:216831 original size:166 final size:166
Alignment explanation
Indices: 216654--217458 Score: 915
Period size: 166 Copynumber: 4.8 Consensus size: 166
216644 ACATCATTAA
* ** * * * *
216654 ATGAGTTTTAAAAATTTTAAACCAAGAAAAATCCCCCTAAAAAAATTTATGAAGTAAAAAATATC
1 ATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCCTGAAAAAATTTACGAAGTAGAAAATACC
* *
216719 GTATTTCAAAAAAAACGAGTTTCAAGGAAAAAAATAAAAAATGAATGAAAATGAATGAATTTTTG
66 GTATTTCAAAAAAAAGGAATTTCAAGGAAAAAAATAAAAAATGAATGAAAATGAATGAATTTTTG
** *
216784 AAAATTGAATTAACGTGAATCAAATAATGTTGTTTG
131 AAAATTGAATTAATATGAATCAAATAATGATGTTTG
* *
216820 ATGAATTTTAAAAATTGAAAACCAAGAAAAAT-CCCCTCGAAAAAATTTACGGAGTAAAAAATAC
1 ATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCCT-GAAAAAATTTACGAAGTAGAAAATAC
* * *
216884 CGTGTTTCGAAAAAAGAA-GAATTTTAAGG-AAAAAATTAAAAATGAATGAAAATGAATGAATTT
65 CGTATTTC-AAAAAA-AAGGAATTTCAAGGAAAAAAATAAAAAATGAATGAAAATGAATGAATTT
* * * * * * *
216947 TCGAAAACTGAATTATTATGATTTAAATAATGATATTTT
128 TTGAAAATTGAATTAATATGAATCAAATAATGATGTTTG
* * * * * *
216986 ATGAATTTTAAAAATTTAAGATCAAGAAAAATGCCCTCT-AAAAAATTTACGGAGTAGAAAACAC
1 ATGAATTTTAAAAATTGAAAACCAAGAAAAAT-CCCCCTGAAAAAATTTACGAAGTAGAAAATAC
* *
217050 CGTATTTCAGAAAAAAGGAAATTTCAAGG-AAAAAATAAAATATGAATGAAAATGAATGAATTTT
65 CGTATTTCAAAAAAAAGG-AATTTCAAGGAAAAAAATAAAAAATGAATGAAAATGAATGAATTTT
* * *
217114 TGAAAAATGAATTAATATTAATCAAATAATGAAGTTTG
129 TGAAAATTGAATTAATATGAATCAAATAATGATGTTTG
* * * * * *
217152 ATGAATTTTAAAAATTGAAAACCAAAAAACAATCTCCTTGAAAAAATTTACGAAATAGAAAACAA
1 ATGAATTTTAAAAATTGAAAACCAAGAAA-AATCCCCCTGAAAAAATTTACGAAGTAGAAAATAC
* * * * *
217217 CGTATTTTGGAAAAAAAAGGAATTTCAAGGAAAAAAATCAAAAACT-CATGAAAATAAATAAATT
65 CGTA-TTT-CAAAAAAAAGGAATTTCAAGGAAAAAAAT-AAAAAATGAATGAAAATGAATGAATT
* * * *
217281 TTTAAAAAATTGAATTAAAATTAATCAAATAATGATGTTTT
127 TTT-GAAAATTGAATTAATATGAATCAAATAATGATGTTTG
* *
217322 ATGAATTTTAAAAATTGAAAACCAAGAAAAAT-CCCTTCGAAAAAATTTACGAAGTAGAAAATAA
1 ATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCCT-GAAAAAATTTACGAAGTAGAAAATAC
* * * *
217386 TGTATTTCGAAAAAAAAGGGAATTTCATGGAAAAAAATAAAAAAACT-CATAAAAATGAATGAAT
65 CGTATTTC-AAAAAAAA-GGAATTTCAAGGAAAAAAAT-AAAAAA-TGAATGAAAATGAATGAAT
217450 TTTTGAAAA
126 TTTTGAAAA
217459 ATAAGCTAAT
Statistics
Matches: 545, Mismatches: 76, Indels: 33
0.83 0.12 0.05
Matches are distributed among these distances:
164 2 0.00
165 11 0.02
166 278 0.51
167 44 0.08
168 34 0.06
169 92 0.17
170 84 0.15
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (166 bp):
ATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCCTGAAAAAATTTACGAAGTAGAAAATACC
GTATTTCAAAAAAAAGGAATTTCAAGGAAAAAAATAAAAAATGAATGAAAATGAATGAATTTTTG
AAAATTGAATTAATATGAATCAAATAATGATGTTTG
Found at i:223514 original size:20 final size:21
Alignment explanation
Indices: 223485--223537 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
223475 CACATGGTCC
*
223485 TGTATTGATACA-TTCACTTA-
1 TGTATCGATACATTTC-CTTAT
223505 TGTATCGATACATTTCCTTAT
1 TGTATCGATACATTTCCTTAT
*
223526 TGTACCGATACA
1 TGTATCGATACA
223538 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTTCCTTAT
Found at i:223534 original size:21 final size:20
Alignment explanation
Indices: 223491--223537 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
223481 GTCCTGTATT
*
223491 GATACATTCACTTATGTATC
1 GATACATTCACTTATGTACC
223511 GATACATTTC-CTTATTGTACC
1 GATACA-TTCACTTA-TGTACC
223532 GATACA
1 GATACA
223538 AATTGTTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (20 bp):
GATACATTCACTTATGTACC
Found at i:226926 original size:20 final size:21
Alignment explanation
Indices: 226887--226928 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
226877 ATAGCCCCAA
226887 TCATGCATATTTTACTATGTT
1 TCATGCATATTTTACTATGTT
226908 TCATGCAT-TTTTAGC-ATGTT
1 TCATGCATATTTTA-CTATGTT
226928 T
1 T
226929 AATTCCTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.21, C:0.14, G:0.12, T:0.52
Consensus pattern (21 bp):
TCATGCATATTTTACTATGTT
Found at i:229623 original size:31 final size:32
Alignment explanation
Indices: 229588--229658 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 32
229578 CTAATGACAT
*
229588 TGGGCTTAGAA-GGAGATGCGACCGACTTGTG
1 TGGGCTTAGAAGGGAGATGCCACCGACTTGTG
* * *
229619 TGGGCTTTTGAAGGGGGTTGCCACCGACTTGTG
1 TGGGC-TTAGAAGGGAGATGCCACCGACTTGTG
229652 TGGGCTT
1 TGGGCTT
229659 TTGAAGGTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 5 0.15
32 7 0.21
33 22 0.65
ACGTcount: A:0.15, C:0.17, G:0.39, T:0.28
Consensus pattern (32 bp):
TGGGCTTAGAAGGGAGATGCCACCGACTTGTG
Found at i:229701 original size:27 final size:28
Alignment explanation
Indices: 229670--229723 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
229660 TGAAGGTTAA
* *
229670 GGTGCCATAAAGTTATGGAC-TTAAAAG
1 GGTGCCACAAAGTTATAGACTTTAAAAG
*
229697 GGTGCCACAGAGTTATAGACTTTAAAA
1 GGTGCCACAAAGTTATAGACTTTAAAA
229724 AGTTACTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (28 bp):
GGTGCCACAAAGTTATAGACTTTAAAAG
Found at i:230025 original size:52 final size:52
Alignment explanation
Indices: 229928--230027 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 52
229918 TGAATTGAAT
** *
229928 TTAAAGATGATGAAGGTACCAACATGCTAATTCAAGGCTAGCAACATTGGTC
1 TTAAAGATGACAAAGGTACCAACATGCTAATTCAAGGCTAACAACATTGGTC
* *
229980 TTAAAGATGACAAAGGTGCCAACGTGCTAA-TCTAAGG-TCAACAACATT
1 TTAAAGATGACAAAGGTACCAACATGCTAATTC-AAGGCT-AACAACATT
230028 AGAATAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
51 3 0.07
52 38 0.93
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (52 bp):
TTAAAGATGACAAAGGTACCAACATGCTAATTCAAGGCTAACAACATTGGTC
Found at i:231277 original size:6 final size:6
Alignment explanation
Indices: 231258--231314 Score: 59
Period size: 6 Copynumber: 9.8 Consensus size: 6
231248 TTTTGTCATT
*
231258 TTTTTG -TTTT- TTTTTG TTTTTG TTTTTG -TTTTG TTTTTT TTGTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TT-TTTG
231304 TTGTTT- TTTTT
1 TT-TTTG TTTTT
231315 ATACGAAGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
5 16 0.36
6 20 0.44
7 9 0.20
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:231277 original size:16 final size:16
Alignment explanation
Indices: 231258--231311 Score: 74
Period size: 16 Copynumber: 3.3 Consensus size: 16
231248 TTTTGTCATT
231258 TTTTTGTTTTTTTTTG
1 TTTTTGTTTTTTTTTG
231274 TTTTTGTTTTTGTTTTG
1 TTTTTGTTTTT-TTTTG
*
231291 TTTTT-TTTGTTTGTTG
1 TTTTTGTTT-TTTTTTG
231307 TTTTT
1 TTTTT
231312 TTTATACGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
16 23 0.66
17 12 0.34
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (16 bp):
TTTTTGTTTTTTTTTG
Found at i:231277 original size:27 final size:24
Alignment explanation
Indices: 231247--231314 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 24
231237 CCGAACCCTT
231247 TTTTTGTCATTTTTTTGTTTTTTTTTG
1 TTTTTGT--TTTTTTTG-TTTTTTTTG
231274 TTTTTGTTTTTGTTTTGTTTTTTTTG
1 TTTTTG-TTTT-TTTTGTTTTTTTTG
231300 TTTGTTGTTTTTTTT
1 TTT-TTGTTTTTTTT
231315 ATACGAAGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
25 4 0.11
26 19 0.50
27 14 0.37
28 1 0.03
ACGTcount: A:0.01, C:0.01, G:0.13, T:0.84
Consensus pattern (24 bp):
TTTTTGTTTTTTTTGTTTTTTTTG
Found at i:235835 original size:16 final size:16
Alignment explanation
Indices: 235805--235834 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
235795 GAATTTTGCA
235805 TTTTTGTTTGTTTTTG
1 TTTTTGTTTGTTTTTG
235821 TTTTTGTTT-TTTTT
1 TTTTTGTTTGTTTTT
235835 TTCTTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (16 bp):
TTTTTGTTTGTTTTTG
Found at i:236615 original size:22 final size:23
Alignment explanation
Indices: 236578--236620 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
236568 CTAGTCCCGT
236578 TGCTTTCTCTTTTACGTTGCTCA
1 TGCTTTCTCTTTTACGTTGCTCA
236601 TGCTTTCT-TTTTACGTTGCT
1 TGCTTTCTCTTTTACGTTGCT
236621 GCTATTTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.07, C:0.23, G:0.14, T:0.56
Consensus pattern (23 bp):
TGCTTTCTCTTTTACGTTGCTCA
Found at i:237489 original size:43 final size:41
Alignment explanation
Indices: 237411--237490 Score: 97
Period size: 43 Copynumber: 1.9 Consensus size: 41
237401 CTAATTTCCT
* * * * *
237411 GCATGAATGCATGCATTGCCACCTAATTGATTTAGGTGGTA
1 GCATGAATGCATGCAATGCCACCAAAGTCAATTAGGTGGTA
237452 GCATGCAATGCAATGCAATGCCACCAAAGTCAATTAGGT
1 GCATG-AATGC-ATGCAATGCCACCAAAGTCAATTAGGT
237491 AAAAATGGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 5 0.16
42 5 0.16
43 22 0.69
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (41 bp):
GCATGAATGCATGCAATGCCACCAAAGTCAATTAGGTGGTA
Found at i:237506 original size:125 final size:125
Alignment explanation
Indices: 237366--237615 Score: 464
Period size: 125 Copynumber: 2.0 Consensus size: 125
237356 ATGCATGAAA
*
237366 AAAAATGGAATGTTCCATGGTCGTTGGTTGCTTATCTAATTTCCTGCATGAATGCATGCATTGCC
1 AAAAATGGAATGTTCCATGGTCGTTGGTTGCTTATCTAATTTCATGCATGAATGCATGCATTGCC
*
237431 ACCTAATTGATTTAGGTGGTAGCATGCAATGCAATGCAATGCCACCAAAGTCAATTAGGT
66 ACCTAATTGATTTAGGTGGTAGCATGCAATGCAATGCAATACCACCAAAGTCAATTAGGT
*
237491 AAAAATGGAATGTTCCATGGTCGTTGGTTGCTTTTCTAATTTCATGCATGAATGCATGCATTGCC
1 AAAAATGGAATGTTCCATGGTCGTTGGTTGCTTATCTAATTTCATGCATGAATGCATGCATTGCC
*
237556 ACCTAATTGATTTAGGTGGTAGCATGCAATGCAATGCAATACCACCTAAGTCAATTAGGT
66 ACCTAATTGATTTAGGTGGTAGCATGCAATGCAATGCAATACCACCAAAGTCAATTAGGT
237616 GGCTACAAAT
Statistics
Matches: 121, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
125 121 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (125 bp):
AAAAATGGAATGTTCCATGGTCGTTGGTTGCTTATCTAATTTCATGCATGAATGCATGCATTGCC
ACCTAATTGATTTAGGTGGTAGCATGCAATGCAATGCAATACCACCAAAGTCAATTAGGT
Found at i:237614 original size:43 final size:41
Alignment explanation
Indices: 237536--237617 Score: 101
Period size: 43 Copynumber: 2.0 Consensus size: 41
237526 CTAATTTCAT
* * * * *
237536 GCATGAATGCATGCATTGCCACCTAATTGATTTAGGTGGTA
1 GCATGAATGCATGCAATACCACCTAAGTCAATTAGGTGGTA
237577 GCATGCAATGCAATGCAATACCACCTAAGTCAATTAGGTGG
1 GCATG-AATGC-ATGCAATACCACCTAAGTCAATTAGGTGG
237618 CTACAAATCC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 5 0.15
42 5 0.15
43 24 0.71
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (41 bp):
GCATGAATGCATGCAATACCACCTAAGTCAATTAGGTGGTA
Found at i:238248 original size:42 final size:42
Alignment explanation
Indices: 238191--238938 Score: 390
Period size: 42 Copynumber: 17.7 Consensus size: 42
238181 GGCAGACAAA
* * * ** *
238191 AAGGTGGAAGAGTCTCCAGGGTCAAAGTTGACAAGCAGACTG
1 AAGGTAGAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTG
* * * * *
238233 AAGGTAGAAAAGTCTCCAGGGTCAAAACTGATAGGCAGACTT
1 AAGGTAGAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTG
** * **
238275 TCGATAAGGCAA-TCTCCAAGGTCAAAGCCGACAGGCAGACT-
1 AAGGT-AGAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTG
* *
238316 AAGGGTAGGAAAGTCTCCAAGGTCAAAGCCGATAGGCAGACATTAG
1 AA-GGTAGAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGAC--T-G
*
238362 ATGAGGCTA-AAAAGTCTCCAAGGTCAAAGCCGATAGGCAGACTG
1 A--AGG-TAGAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTG
* * * * * * *
238406 AGGGTGAGAAAAGTCTCTAGGGTTAAAGCCGACGGGCATACTT
1 AAGGT-AGAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTG
** ** * * *
238449 AAAAT-GAGGCAGTCTCTAAGGACAAAGCTGACAGGCAGACT-
1 AAGGTAGA-AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTG
* * *
238490 AAGGGTAGGAAAGTCTCCAAGGTCAAAGCCAACATGG-AGACTT
1 AA-GGTAGAAAAGTCTCCAAGGTCAAAGCCGACA-GGCAGACTG
** ** * * *
238533 AAAATA-AGGCAGTCTCTAAGGTCAAAGTCGATAGGCAGACTG
1 AAGGTAGA-AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTG
* * * * *
238575 AGGGTAGAAAAATCTCCAAAGTCAAAGCTGACAGGCAGACTA
1 AAGGTAGAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTG
* * * ** *
238617 AAGGTGAGAAAAGTCTCTAGGGTCAAA-CTCGACAAGTGGACTT
1 AAGGT-AGAAAAGTCTCCAAGGTCAAAGC-CGACAGGCAGACTG
** ** * * *
238660 AAAAT-GAGGCAGTCTCCAGGGTCAAAGTCGATAGGCAGACTG
1 AAGGTAGA-AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTG
* * * * * *
238702 AAGGTA-AAAAGTCTCTAGGGTCAAAGCCAATAGGTAGACTT
1 AAGGTAGAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTG
** ** * **
238743 AAAATA-AGGTAGTTTCCAAGGTCAAAGCTAACAGGCAGACTG
1 AAGGTAGA-AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTG
* * * *
238785 AGGGT-GAAAAGTCTCCAAGGTTAAAGCCGAGAGGCAGACTT
1 AAGGTAGAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTG
** ** * * *
238826 AAAAT-GAGCCAGTCTCCAGGGTCAAAGCCGACAGACAGACTT
1 AAGGTAGA-AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTG
** ** * *
238868 AAAAT-GAGGCAGTCTCTAGGGTCAAAGCCGACAGGCAGACTG
1 AAGGTAGA-AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTG
* *
238910 AGGGTAGAAAAGTCTTCAAGGTCAAAGCC
1 AAGGTAGAAAAGTCTCCAAGGTCAAAGCC
238939 AATAGACAAA
Statistics
Matches: 532, Mismatches: 145, Indels: 58
0.72 0.20 0.08
Matches are distributed among these distances:
41 76 0.14
42 343 0.64
43 71 0.13
44 3 0.01
45 1 0.00
46 1 0.00
47 34 0.06
48 3 0.01
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.17
Consensus pattern (42 bp):
AAGGTAGAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTG
Found at i:238630 original size:127 final size:125
Alignment explanation
Indices: 238471--238716 Score: 343
Period size: 127 Copynumber: 2.0 Consensus size: 125
238461 TCTCTAAGGA
* * *
238471 CAAAGCTGACAGGCAGACTAAGGGTAGGAAAGTCTCCAAGGTCAAAGC-CAACATG-GAGACTTA
1 CAAAGCTGACAGGCAGACTAAAGGTAGAAAAGTCTCCAAGGTCAAA-CTCAACAAGTG-GACTTA
* *
238534 AAATAAGGCAGTCTCTAAGGTCAAAGTCGATAGGCAGACTGAGGGTAGAAAAATCTCCAAAGT
64 AAATAAGGCAGTCTCCAAGGTCAAAGTCGATAGGCAGACTGAAGGTA-AAAAATCTCCAAAGT
* * *
238597 CAAAGCTGACAGGCAGACTAAAGGTGAGAAAAGTCTCTAGGGTCAAACTCGACAAGTGGACTTAA
1 CAAAGCTGACAGGCAGACTAAAGGT-AGAAAAGTCTCCAAGGTCAAACTCAACAAGTGGACTTAA
* * *
238662 AATGAGGCAGTCTCCAGGGTCAAAGTCGATAGGCAGACTGAAGGTAAAAAGTCTC
65 AATAAGGCAGTCTCCAAGGTCAAAGTCGATAGGCAGACTGAAGGTAAAAAATCTC
238717 TAGGGTCAAA
Statistics
Matches: 106, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
126 33 0.31
127 72 0.68
128 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.17
Consensus pattern (125 bp):
CAAAGCTGACAGGCAGACTAAAGGTAGAAAAGTCTCCAAGGTCAAACTCAACAAGTGGACTTAAA
ATAAGGCAGTCTCCAAGGTCAAAGTCGATAGGCAGACTGAAGGTAAAAAATCTCCAAAGT
Found at i:238745 original size:83 final size:82
Alignment explanation
Indices: 238595--238908 Score: 306
Period size: 83 Copynumber: 3.7 Consensus size: 82
238585 AATCTCCAAA
* * *
238595 GTCAAAGCTGACAGGCAGACTAAAGGTGAGAAAAGTCTCTAGGGTCAAA-CTCGACAAGTGGACT
1 GTCAAAGC-GACAGGCAGACTGAAGGT-A-AAAAGTCTCTAGGGTCAAAGC-CGACAGGTAGACT
238659 TAAAATGAGGCAGTCTCCAGG
62 TAAAATGAGGCAGTCTCCAGG
* * *
238680 GTCAAAGTCGATAGGCAGACTGAAGGTAAAAAGTCTCTAGGGTCAAAGCCAATAGGTAGACTTAA
1 GTCAAAG-CGACAGGCAGACTGAAGGTAAAAAGTCTCTAGGGTCAAAGCCGACAGGTAGACTTAA
* * * *
238745 AATAAGGTAGTTTCCAAG
65 AATGAGGCAGTCTCCAGG
* * * * * * * *
238763 GTCAAAGCTAACAGGCAGACTGAGGGTGAAAAGTCTCCAAGGTTAAAGCCGAGAGGCAGACTTAA
1 GTCAAAGC-GACAGGCAGACTGAAGGTAAAAAGTCTCTAGGGTCAAAGCCGACAGGTAGACTTAA
*
238828 AATGAGCCAGTCTCCAGG
65 AATGAGGCAGTCTCCAGG
* * ** *** *
238846 GTCAAAGCCGACAGACAGACTTAAAATGAGGCAGTCTCTAGGGTCAAAGCCGACAGGCAGACT
1 GTCAAAG-CGACAGGCAGACTGAAGGT-AAAAAGTCTCTAGGGTCAAAGCCGACAGGTAGACT
238909 GAGGGTAGAA
Statistics
Matches: 185, Mismatches: 39, Indels: 11
0.79 0.17 0.05
Matches are distributed among these distances:
82 1 0.01
83 130 0.70
84 30 0.16
85 23 0.12
86 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.18
Consensus pattern (82 bp):
GTCAAAGCGACAGGCAGACTGAAGGTAAAAAGTCTCTAGGGTCAAAGCCGACAGGTAGACTTAAA
ATGAGGCAGTCTCCAGG
Found at i:238847 original size:125 final size:126
Alignment explanation
Indices: 238711--238990 Score: 337
Period size: 125 Copynumber: 2.2 Consensus size: 126
238701 GAAGGTAAAA
* * ** * * *
238711 AGTCTCTAGGGTCAAAGCCAATAGGTAGACTTAAAATAAGGTAGTTTCCAAGGTCAAAGCTAACA
1 AGTCTCCAGGGTCAAAGCCAACAGACAGACTTAAAATAAGGCAGTCTCCAAGGTCAAAGCCAACA
* * * *
238776 GGCAGACTGAGGGT-GAAAAGTCTCCAAGGTTAAAGCCGAGAGGCAGACTTAAAATGAGCC
66 GGCAGACTGAGGGTAGAAAAGTCTCCAAGGTCAAAGCCAAGAGACAAACTTAAAATGAGCC
* * * * *
238836 AGTCTCCAGGGTCAAAGCCGACAGACAGACTTAAAATGAGGCAGTCTCTAGGGTCAAAGCCGACA
1 AGTCTCCAGGGTCAAAGCCAACAGACAGACTTAAAATAAGGCAGTCTCCAAGGTCAAAGCCAACA
* * * * *
238901 GGCAGACTGAGGGTAGAAAAGTCTTCAAGGTCAAAGCCAATAGACAAACTTTAGATGAGGC
66 GGCAGACTGAGGGTAGAAAAGTCTCCAAGGTCAAAGCCAAGAGACAAACTTAAAATGAGCC
* * *
238962 AGTCTCCAGAGTCAAAGCCGACAGGCAGA
1 AGTCTCCAGGGTCAAAGCCAACAGACAGA
238991 GAAGATTCGG
Statistics
Matches: 131, Mismatches: 23, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
125 67 0.51
126 64 0.49
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.17
Consensus pattern (126 bp):
AGTCTCCAGGGTCAAAGCCAACAGACAGACTTAAAATAAGGCAGTCTCCAAGGTCAAAGCCAACA
GGCAGACTGAGGGTAGAAAAGTCTCCAAGGTCAAAGCCAAGAGACAAACTTAAAATGAGCC
Found at i:238979 original size:126 final size:125
Alignment explanation
Indices: 238737--238990 Score: 337
Period size: 126 Copynumber: 2.0 Consensus size: 125
238727 GCCAATAGGT
* * *
238737 AGACTTAAAATAAGGTAGTTTCCAAGGTCAAAGCTAACAGGCAGACTGAGGGTGAAAAGTCTCCA
1 AGACTTAAAATAAGGCAGTCTCCAAGGTCAAAGCCAACAGGCAGACTGAGGGTGAAAAGTCTCCA
* * * * *
238802 AGGTTAAAGCCGAGAGGCAGACTTAAAATGAGCCAGTCTCCAGGGTCAAAGCCGACAGAC
66 AGGTCAAAGCCAAGAGACAAACTTAAAATGAGCCAGTCTCCAGAGTCAAAGCCGACAGAC
* * * * *
238862 AGACTTAAAATGAGGCAGTCTCTAGGGTCAAAGCCGACAGGCAGACTGAGGGTAGAAAAGTCTTC
1 AGACTTAAAATAAGGCAGTCTCCAAGGTCAAAGCCAACAGGCAGACTGAGGGT-GAAAAGTCTCC
* * * * *
238927 AAGGTCAAAGCCAATAGACAAACTTTAGATGAGGCAGTCTCCAGAGTCAAAGCCGACAGGC
65 AAGGTCAAAGCCAAGAGACAAACTTAAAATGAGCCAGTCTCCAGAGTCAAAGCCGACAGAC
238988 AGA
1 AGA
238991 GAAGATTCGG
Statistics
Matches: 110, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
125 46 0.42
126 64 0.58
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.17
Consensus pattern (125 bp):
AGACTTAAAATAAGGCAGTCTCCAAGGTCAAAGCCAACAGGCAGACTGAGGGTGAAAAGTCTCCA
AGGTCAAAGCCAAGAGACAAACTTAAAATGAGCCAGTCTCCAGAGTCAAAGCCGACAGAC
Found at i:247205 original size:13 final size:13
Alignment explanation
Indices: 247187--247212 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
247177 CAATTTTTTG
247187 TGTATCGATACAT
1 TGTATCGATACAT
247200 TGTATCGATACAT
1 TGTATCGATACAT
247213 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:247973 original size:21 final size:21
Alignment explanation
Indices: 247910--247973 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 21
247900 CTCTCCGTTA
* *
247910 TCTCCCCCGTTTATTAA-TAAT
1 TCTCCCCC-TTAATCAAGTAAT
*
247931 TCTCCCCATTAATCAAGT-AT
1 TCTCCCCCTTAATCAAGTAAT
247951 TCTCCCCCTTAATCAAGTAAT
1 TCTCCCCCTTAATCAAGTAAT
247972 TC
1 TC
247974 ATATCAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 25 0.68
21 12 0.32
ACGTcount: A:0.27, C:0.31, G:0.05, T:0.38
Consensus pattern (21 bp):
TCTCCCCCTTAATCAAGTAAT
Found at i:252338 original size:14 final size:12
Alignment explanation
Indices: 252305--252343 Score: 60
Period size: 12 Copynumber: 3.1 Consensus size: 12
252295 TAATCACCCT
252305 GTATCGATACAA
1 GTATCGATACAA
252317 GTATCGATACAA
1 GTATCGATACAA
252329 TGTAATCGATACAA
1 -GT-ATCGATACAA
252343 G
1 G
252344 GAAAAATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.48
13 3 0.12
14 10 0.40
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (12 bp):
GTATCGATACAA
Found at i:254439 original size:15 final size:15
Alignment explanation
Indices: 254419--254449 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
254409 AATTCGTTTG
*
254419 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
254434 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
254449 G
1 G
254450 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:263815 original size:13 final size:13
Alignment explanation
Indices: 263797--263822 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
263787 CAATTTTTTG
263797 TGTATCGATACAT
1 TGTATCGATACAT
263810 TGTATCGATACAT
1 TGTATCGATACAT
263823 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:264579 original size:21 final size:21
Alignment explanation
Indices: 264516--264579 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 21
264506 CTCTCCGTTA
* *
264516 TCTCCCCCGTTTATTAA-TAAT
1 TCTCCCCC-TTAATCAAGTAAT
*
264537 TCTCCCCATTAATCAAGT-AT
1 TCTCCCCCTTAATCAAGTAAT
264557 TCTCCCCCTTAATCAAGTAAT
1 TCTCCCCCTTAATCAAGTAAT
264578 TC
1 TC
264580 ATATCAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 25 0.68
21 12 0.32
ACGTcount: A:0.27, C:0.31, G:0.05, T:0.38
Consensus pattern (21 bp):
TCTCCCCCTTAATCAAGTAAT
Found at i:266399 original size:13 final size:13
Alignment explanation
Indices: 266381--266419 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
266371 ATAATCACCC
266381 TGTATCGATACAA
1 TGTATCGATACAA
266394 TGTATCGATACAA
1 TGTATCGATACAA
266407 TGTATCGATACAA
1 TGTATCGATACAA
266420 GGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:268517 original size:15 final size:15
Alignment explanation
Indices: 268497--268527 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
268487 ATTTCGTTTG
*
268497 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
268512 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
268527 G
1 G
268528 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:270378 original size:21 final size:21
Alignment explanation
Indices: 270331--270375 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
270321 AAGTTTTCAT
270331 TTTTC-TTAGCTAACTCATTA
1 TTTTCATTAGCTAACTCATTA
*
270351 TTTTCATTAGCTAACTTCTTTA
1 TTTTCATTAGCTAAC-TCATTA
270373 TTT
1 TTT
270376 CATCTTGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTCATTAGCTAACTCATTA
Found at i:272609 original size:13 final size:13
Alignment explanation
Indices: 272591--272616 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
272581 CAATTTTTTG
272591 TGTATCGATACAT
1 TGTATCGATACAT
272604 TGTATCGATACAT
1 TGTATCGATACAT
272617 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:272628 original size:32 final size:33
Alignment explanation
Indices: 272571--272634 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
272561 TACAAGCCAA
** *
272571 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCAATACAT
272604 TGTATCGATAC-ATACTTTGTGTATCAATACA
1 TGTATCGATACAATACTTTGTGTATCAATACA
272635 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCAATACAT
Found at i:278702 original size:16 final size:16
Alignment explanation
Indices: 278672--278701 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
278662 GAATTTTGCA
278672 TTTTTGTTTATTTTTG
1 TTTTTGTTTATTTTTG
278688 TTTTTGTTT-TTTTT
1 TTTTTGTTTATTTTT
278702 TTCTTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.87
Consensus pattern (16 bp):
TTTTTGTTTATTTTTG
Found at i:279306 original size:22 final size:23
Alignment explanation
Indices: 279265--279307 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
279255 TTGGTCCTGT
*
279265 TGCTTTCTCTTTTACGTTGCTCG
1 TGCTTTCTCTTTTACATTGCTCG
279288 TGCTTTCT-TTTTACATTGCT
1 TGCTTTCTCTTTTACATTGCT
279308 ATTGTTTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.07, C:0.23, G:0.14, T:0.56
Consensus pattern (23 bp):
TGCTTTCTCTTTTACATTGCTCG
Found at i:280016 original size:19 final size:19
Alignment explanation
Indices: 279987--280029 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
279977 TTTCCATGTG
279987 AATGC-ATGAAATGAAAGC
1 AATGCAATGAAATGAAAGC
*
280005 AATGCAATGAAATGAATGC
1 AATGCAATGAAATGAAAGC
280024 AATGCA
1 AATGCA
280030 TCAAATGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.49, C:0.12, G:0.21, T:0.19
Consensus pattern (19 bp):
AATGCAATGAAATGAAAGC
Found at i:280188 original size:43 final size:41
Alignment explanation
Indices: 280123--280205 Score: 103
Period size: 43 Copynumber: 2.0 Consensus size: 41
280113 CCAATTTCAT
* * * *
280123 GCATGAATGCATGCATTACCACCTAATTGATTTAGGTGGCA
1 GCATGAATGCATGCAATACCACCTAAGTCAATTAGGTGGCA
*
280164 GCATGCAATGCAATGCAATGCCACCTAAGTCAATTAGGTGGC
1 GCATG-AATGC-ATGCAATACCACCTAAGTCAATTAGGTGGC
280206 TATAAATCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 5 0.14
42 5 0.14
43 25 0.71
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (41 bp):
GCATGAATGCATGCAATACCACCTAAGTCAATTAGGTGGCA
Found at i:283400 original size:33 final size:33
Alignment explanation
Indices: 283358--283420 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
283348 AAGGAAATTT
283358 ATCGATACATT-ATTCAATGTATCGATACATTAG
1 ATCGATACATTGA-TCAATGTATCGATACATTAG
**
283391 ATCGATACATTGATCTTTGTATCGATACAT
1 ATCGATACATTGATCAATGTATCGATACAT
283421 CTGAGAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (33 bp):
ATCGATACATTGATCAATGTATCGATACATTAG
Found at i:293459 original size:96 final size:97
Alignment explanation
Indices: 293233--293448 Score: 256
Period size: 96 Copynumber: 2.2 Consensus size: 97
293223 TTGGTTGAAA
* * * *
293233 AATAAGGTTGGAGTGTCCCCGATGATGAGAATTTAGGCAAAAATAAGATTTAAAACTTGAGGAGT
1 AATAGGGTTGGAGTGTCCCCGATGATGAAAATTTAAGCAAAAATAAGATTTAAAACTTGAGAAGT
*
293298 TAAAAAGTGGGGTTGGAGTATTCCCTCAGAAG
66 TAAAAAGTGGGGTTGGAGCATTCCCTCAGAAG
* * * ** * * * *
293330 AATAGGGTTGGAGTATCCTCGACGATGCTAATTTAAGCAAAAA-AATATTTGAATCTTGATAAGT
1 AATAGGGTTGGAGTGTCCCCGATGATGAAAATTTAAGCAAAAATAAGATTTAAAACTTGAGAAGT
* *
293394 TTAAAAGTGGGGTTGGAGCA-TCCCTTCAGAGG
66 TAAAAAGTGGGGTTGGAGCATTCCC-TCAGAAG
*
293426 AATAGGGTTGAAGTGTCCCCGAT
1 AATAGGGTTGGAGTGTCCCCGAT
293449 AAATAAAATT
Statistics
Matches: 99, Mismatches: 19, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
95 4 0.04
96 59 0.60
97 36 0.36
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (97 bp):
AATAGGGTTGGAGTGTCCCCGATGATGAAAATTTAAGCAAAAATAAGATTTAAAACTTGAGAAGT
TAAAAAGTGGGGTTGGAGCATTCCCTCAGAAG
Found at i:294878 original size:13 final size:13
Alignment explanation
Indices: 294860--294885 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
294850 AATGTTTTTG
294860 TGTATCGATACAT
1 TGTATCGATACAT
294873 TGTATCGATACAT
1 TGTATCGATACAT
294886 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:295646 original size:21 final size:21
Alignment explanation
Indices: 295605--295647 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
295595 CTCCCCTTTA
* *
295605 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
295626 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
295647 T
1 T
295648 TATATCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.26, C:0.30, G:0.05, T:0.40
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:297462 original size:13 final size:13
Alignment explanation
Indices: 297444--297482 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
297434 ATAATCCCCC
*
297444 TGTATCGATACAG
1 TGTATCGATACAA
297457 TGTATCGATACAA
1 TGTATCGATACAA
297470 TGTATCGATACAA
1 TGTATCGATACAA
297483 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:299580 original size:15 final size:15
Alignment explanation
Indices: 299560--299590 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
299550 ATTTCGTTTG
*
299560 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
299575 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
299590 G
1 G
299591 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:303686 original size:13 final size:13
Alignment explanation
Indices: 303668--303693 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
303658 AATGTTTTTG
303668 TGTATCGATACAT
1 TGTATCGATACAT
303681 TGTATCGATACAT
1 TGTATCGATACAT
303694 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:306892 original size:211 final size:206
Alignment explanation
Indices: 306435--307248 Score: 612
Period size: 211 Copynumber: 3.9 Consensus size: 206
306425 GCTAGATATT
* *
306435 CTGATTTAAGGCCAGCGCCATTGGACTTAAAGATGATAAGAATGCCAAA-----T-ATTCAAAGC
1 CTGATTCAAGGCCAGCGCCATTGGACTTAGAGATGATAAGAATGCCAAATGTGTTGATTCAAAGC
* * * * * * * *
306494 TAGTGACATTGGACTTAAAGATGATAAAACAATGCCAATATGCTGGTTCACGGCTAGCGATATTG
66 TAGAGACATTGGACTTAGAGATGATAAAAAAATGCCAATATGCTGATTCACGACCAACGATATTA
* * * * *
306559 GTCTTAAAGATGGTGATGGTACCAATGTGTTGATTCAAGGCCAACGACATTAGATTTAAAAAAAG
131 GTCTCAAAGATGATGAAGGTACCAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAAAAAG
*
306624 TGATGGATGTG
196 AGATGGATGTG
* * * * *
306635 CTGATTCAAGGCCAACCCCATTGGACTTAGAGATGAGAAAAATGCCAAATGTGTTGATTCAACGC
1 CTGATTCAAGGCCAGCGCCATTGGACTTAGAGATGATAAGAATGCCAAATGTGTTGATTCAAAGC
*
306700 TAAAGACATTGGACTTAGAGATGATAAAAAAATGCCAA-ATGCTGATTCACGACCAACGATATTA
66 TAGAGACATTGGACTTAGAGATGATAAAAAAATGCCAATATGCTGATTCACGACCAACGATATTA
* ** * *
306764 GTCTCAAAGATGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAGGATAA
131 GTCTCAAAGATGATGAAGGTACCAATGTGCTGATTCAAGGCCAACGACATTAGACTTAA--AAAA
306829 AGAGAATGTCGAATGTG
194 AGAG-ATG--G-ATGTG
* * *
306846 CTGATTCAAGGCCAGCGCCATTAGACTTAGAGATGATAAGAATGCCAAATGTGTTGATTTAAGGC
1 CTGATTCAAGGCCAGCGCCATTGGACTTAGAGATGATAAGAATGCCAAATGTGTTGATTCAAAGC
* * * * * * * * * ** *
306911 CAGCGCCATTGGACTTAGAGATGAT--AAGAATGCTAAATGTGCTAATTCAAGGCCAGTGACATT
66 TAGAGACATTGGACTTAGAGATGATAAAAAAATGC-CAATATGCTGATTCACGACCAACGATATT
* * * * ** * * * * * * * * *
306974 GGACTTAAAGATGATAAAAAATGCCAATATGCTGATTCACGGCCAATGATATTGGCCTTAAGAAT
130 AGTCTCAAAGATGAT-GAAGGTACCAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAAAA
* * *
307039 GGTGAAGGTACCAATGTG
194 AGAGATGG-----ATGTG
* ** * * * * ** **
307057 CTGATTCAAGGCTAGCAACATTGGACTCAAAGATG--AAGAAAGTG-CTAATATCCTGATTCAGG
1 CTGATTCAAGGCCAGCGCCATTGGACTTAGAGATGATAAG-AA-TGCCAAATGTGTTGATTCAAA
* ** * * *
307119 GCCAGCA-ACATTAAACTTTGAAAATGATAAAAAAAAATGCCAATATGCTGATTCACGACCAATG
64 GCTAG-AGACATTGGACTTAG-AGATGAT--AAAAAAATGCCAATATGCTGATTCACGACCAACG
* * * * *
307183 ATATTGGTCTTAAAGATGATG-AGAGTACCAATGTACTGATTTAAGGCCAGCGACATTAGACTTA
125 ATATTAGTCTCAAAGATGATGAAG-GTACCAATGTGCTGATTCAAGGCCAACGACATTAGACTTA
307247 AA
189 AA
307249 GATGAAGAAA
Statistics
Matches: 481, Mismatches: 105, Indels: 43
0.76 0.17 0.07
Matches are distributed among these distances:
200 43 0.09
205 72 0.15
206 42 0.09
207 7 0.01
208 3 0.01
209 12 0.02
210 34 0.07
211 157 0.33
212 38 0.08
213 30 0.06
214 36 0.07
215 7 0.01
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (206 bp):
CTGATTCAAGGCCAGCGCCATTGGACTTAGAGATGATAAGAATGCCAAATGTGTTGATTCAAAGC
TAGAGACATTGGACTTAGAGATGATAAAAAAATGCCAATATGCTGATTCACGACCAACGATATTA
GTCTCAAAGATGATGAAGGTACCAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAAAAAG
AGATGGATGTG
Found at i:307148 original size:264 final size:264
Alignment explanation
Indices: 306630--307148 Score: 650
Period size: 264 Copynumber: 2.0 Consensus size: 264
306620 AAAGTGATGG
* *
306630 ATGTGCTGATTCAAGGCCAACCCCATTGGACTTAGAGATGAGAAAAATGCCAAATGTGTTGATTC
1 ATGTGCTGATTCAAGGCCAACCCCATTGGACTTAGAGATGAGAAAAATGCCAAATGTGCTAATTC
* *
306695 AACGCTAAAGACATTGGACTTAGAGATGATAAAAAAATGCCAAATGCTGATTCACGACCAACGAT
66 AACGCCAAAGACATTGGACTTAAAGATGATAAAAAAATGCCAAATGCTGATTCACGACCAACGAT
* * ** * *
306760 ATTAGTCTCAAAGATGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAGG
131 ATTAGCCTCAAAGATGATGAAGGTACCAATGTGCTGATTCAAGGCCAGCAACATTGGACTCAAAG
* * ** * *
306825 ATAAAGAGAATGTCGAATGTGCTGATTCAAGGCCAGCGCCATTAGACTTAGAGATGATAAGAATG
196 ATAAAGAGAATGTCGAATATCCTGATTCAAGGCCAGCAACATTAAACTTAGAAATGATAAGAATG
306890 CCAA
261 CCAA
* * * * * * *
306894 ATGTGTTGATTTAAGGCCAGCGCCATTGGACTTAGAGATGATAAGAATGCTAAATGTGCTAATTC
1 ATGTGCTGATTCAAGGCCAACCCCATTGGACTTAGAGATGAGAAAAATGCCAAATGTGCTAATTC
* ** * *
306959 AAGGCCAGTGACATTGGACTTAAAGATGAT-AAAAAATGCCAATATGCTGATTCACGGCCAATGA
66 AACGCCAAAGACATTGGACTTAAAGATGATAAAAAAATGCCAA-ATGCTGATTCACGACCAACGA
* * * *
307023 TATTGGCCT-TAAGAATGGTGAAGGTACCAATGTGCTGATTCAAGGCTAGCAACATTGGACTCAA
130 TATTAGCCTCAAAG-ATGATGAAGGTACCAATGTGCTGATTCAAGGCCAGCAACATTGGACTCAA
* * * *
307087 AGATGAAGA-AA-GTGCTAATATCCTGATTCAGGGCCAGCAACATTAAACTTTGAAAATGATAA
194 AGATAAAGAGAATGT-CGAATATCCTGATTCAAGGCCAGCAACATTAAACTTAG-AAATGATAA
307149 AAAAAAATGC
Statistics
Matches: 215, Mismatches: 36, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
262 2 0.01
263 47 0.22
264 166 0.77
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (264 bp):
ATGTGCTGATTCAAGGCCAACCCCATTGGACTTAGAGATGAGAAAAATGCCAAATGTGCTAATTC
AACGCCAAAGACATTGGACTTAAAGATGATAAAAAAATGCCAAATGCTGATTCACGACCAACGAT
ATTAGCCTCAAAGATGATGAAGGTACCAATGTGCTGATTCAAGGCCAGCAACATTGGACTCAAAG
ATAAAGAGAATGTCGAATATCCTGATTCAAGGCCAGCAACATTAAACTTAGAAATGATAAGAATG
CCAA
Found at i:307214 original size:161 final size:161
Alignment explanation
Indices: 306989--307303 Score: 472
Period size: 161 Copynumber: 2.0 Consensus size: 161
306979 TAAAGATGAT
* *
306989 AAAAAATGCCAATATGCTGATTCACGGCCAATGATATTGGCCTTAAGAATGGTGAAGGTACCAAT
1 AAAAAATGCCAATATGCTGATTCACGACCAATGATATTGGCCTTAAGAATGATGAAGGTACCAAT
* * * *
307054 GTGCTGATTCAAGGCTAGCAACATTGGACTCAAAGATGAAGAAAGTGCTAATATCCTGATTCAGG
66 GTACTGATTCAAGGCCAGCAACATTAGACTCAAAGATGAAGAAAGTGCTAATATACTGATTCAGG
*
307119 GCCAGCAACATTAAACTTTGAAAATGATAAA
131 GCCAACAACATTAAACTTTGAAAATGATAAA
*
307150 AAAAAATGCCAATATGCTGATTCACGACCAATGATATTGGTCTTAA-AGATGATG-AGAGTACCA
1 AAAAAATGCCAATATGCTGATTCACGACCAATGATATTGGCCTTAAGA-ATGATGAAG-GTACCA
* * *
307213 ATGTACTGATTTAAGGCCAGCGACATTAGACTTAAAGATGAAGAAAGTGCTAATATACTGATTCA
64 ATGTACTGATTCAAGGCCAGCAACATTAGACTCAAAGATGAAGAAAGTGCTAATATACTGATTCA
* * *
307278 GGGCTAACGACATTAGACTTTGAAAA
129 GGGCCAACAACATTAAACTTTGAAAA
307304 GAAAGATTGT
Statistics
Matches: 138, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
160 3 0.02
161 135 0.98
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (161 bp):
AAAAAATGCCAATATGCTGATTCACGACCAATGATATTGGCCTTAAGAATGATGAAGGTACCAAT
GTACTGATTCAAGGCCAGCAACATTAGACTCAAAGATGAAGAAAGTGCTAATATACTGATTCAGG
GCCAACAACATTAAACTTTGAAAATGATAAA
Found at i:307247 original size:52 final size:52
Alignment explanation
Indices: 306362--307297 Score: 429
Period size: 53 Copynumber: 17.9 Consensus size: 52
306352 AAATTTGAAA
* ** * *
306362 ATGATAAAAGTGCCAATGTGCT-AGTTCAAGGCCAAAGACATCGGACTCAAAG
1 ATGATGAAAGTGCCAATGTGCTGA-TTCAAGGCCAGCGACATTGGACTTAAAG
* * * * * * *
306414 AT-AGTAAAAATGCTAGATATTCTGATTTAAGGCCAGCGCCATTGGACTTAAAG
1 ATGA-TGAAAGTGCCA-ATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* * * * *
306467 ATGAT-AAGAATGCCAA----AT-ATTCAAAGCTAGTGACATTGGACTTAAAG
1 ATGATGAA-AGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* * * * * * * *
306514 ATGATAAAACAATGCCAATATGCTGGTTCACGGCTAGCGATATTGGTCTTAAAG
1 ATGAT-GAA-AGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* ** * * * * *
306568 ATGGTGATGGTACCAATGTGTTGATTCAAGGCCAACGACATTAGA-TTTAA-
1 ATGATGAAAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
*** * ** *
306618 A--A--AAAGTGATGGATGTGCTGATTCAAGGCCAACCCCATTGGACTTAGAG
1 ATGATGAAAGTG-CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* * * * ** *
306667 ATGA-GAAAAATGCCAAATGTGTTGATTCAACGCTAAAGACATTGGACTTAGAG
1 ATGATG-AAAGTGCC-AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* * * * * * * * * *
306720 ATGATAAAAAAATGCCAA-ATGCTGATTCACGACCAACGATATTAGTCTCAAAG
1 ATGAT--GAAAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* * *
306773 ATGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAGG
1 ATGATGAAAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* * * * * *
306825 ATAAAGAGAA-TGTCGAATGTGCTGATTCAAGGCCAGCGCCATTAGACTTAGAG
1 ATGATGA-AAGTG-CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* * * * *
306878 ATGAT-AAGAATGCCAAATGTGTTGATTTAAGGCCAGCGCCATTGGACTTAGAG
1 ATGATGAA-AGTGCC-AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* * * *
306931 ATGAT-AAGAATGCTAAATGTGCTAATTCAAGGCCAGTGACATTGGACTTAAAG
1 ATGATGAA-AGTGC-CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* * * * ** * *
306984 ATGATAAAAAATGCCAATATGCTGATTCACGGCCAATGATATTGGCCTT-AAG
1 ATGAT-GAAAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* * * * * *
307036 AATGGTGAAGGTACCAATGTGCTGATTCAAGGCTAGCAACATTGGACTCAAAG
1 -ATGATGAAAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* * * * * * **
307089 ATGAAGAAAGTGCTAATATCCTGATTCAGGGCCAGCAACATTAAACTTTGAAA-
1 ATGATGAAAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC-TT-AAAG
* * * * * ** * *
307142 ATGATAAAAAAAAATGCCAATATGCTGATTCACGACCAATGATATTGGTCTTAAAG
1 ATGAT----GAAAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* * * * *
307198 ATGATGAGAGTACCAATGTACTGATTTAAGGCCAGCGACATTAGACTTAAAG
1 ATGATGAAAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* * * * * * * *
307250 ATGAAGAAAGTGCTAATATACTGATTCAGGGCTAACGACATTAGACTT
1 ATGATGAAAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
307298 TGAAAAGAAA
Statistics
Matches: 661, Mismatches: 182, Indels: 82
0.71 0.20 0.09
Matches are distributed among these distances:
46 3 0.00
47 55 0.08
48 4 0.01
49 11 0.02
50 1 0.00
51 15 0.02
52 214 0.32
53 271 0.41
54 39 0.06
55 13 0.02
56 7 0.01
57 28 0.04
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (52 bp):
ATGATGAAAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
Found at i:312619 original size:1 final size:1
Alignment explanation
Indices: 312613--312708 Score: 75
Period size: 1 Copynumber: 96.0 Consensus size: 1
312603 TTTCATACCC
* * ** * * * *
312613 AAAAAAACAAAAAAAAAACAAAAAAACCAAAAAAAAAACAAAAAAAAAAACACAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
312678 AAAACAAGAAAAAAACAACAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
312709 GGGGTCTAGA
Statistics
Matches: 71, Mismatches: 24, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.86, C:0.12, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:312629 original size:11 final size:11
Alignment explanation
Indices: 312613--312708 Score: 112
Period size: 11 Copynumber: 9.2 Consensus size: 11
312603 TTTCATACCC
312613 AAAAAAACAAA
1 AAAAAAACAAA
312624 AAAAAAAC--A
1 AAAAAAACAAA
*
312633 AAAAAACCAAA
1 AAAAAAACAAA
312644 AAAAAAAC-AA
1 AAAAAAACAAA
*
312654 AAAAAAA-AAC
1 AAAAAAACAAA
*
312664 ACAAAAACAAA
1 AAAAAAACAAA
*
312675 AAAAAAACAAG
1 AAAAAAACAAA
312686 AAAAAAAC-AA
1 AAAAAAACAAA
*
312696 CAAAAAACAAA
1 AAAAAAACAAA
312707 AA
1 AA
312709 GGGGTCTAGA
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
9 8 0.11
10 24 0.34
11 38 0.54
ACGTcount: A:0.86, C:0.12, G:0.01, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:312648 original size:31 final size:30
Alignment explanation
Indices: 312613--312708 Score: 138
Period size: 32 Copynumber: 3.1 Consensus size: 30
312603 TTTCATACCC
312613 AAAAAAACAAAAAAAAAACAAAAAAACCAAA
1 AAAAAAACAAAAAAAAAACAAAAAAA-CAAA
*
312644 AAAAAAACAAAAAAAAAAACACAAAAACAAA
1 AAAAAAAC-AAAAAAAAAACAAAAAAACAAA
*
312675 AAAAAAACAAGAAAAAAACAACAAAAAACAAA
1 AAAAAAACAAAAAAAAAAC-A-AAAAAACAAA
312707 AA
1 AA
312709 GGGGTCTAGA
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
30 10 0.17
31 21 0.36
32 28 0.47
ACGTcount: A:0.86, C:0.12, G:0.01, T:0.00
Consensus pattern (30 bp):
AAAAAAACAAAAAAAAAACAAAAAAACAAA
Found at i:312703 original size:32 final size:31
Alignment explanation
Indices: 312613--312708 Score: 142
Period size: 31 Copynumber: 3.1 Consensus size: 31
312603 TTTCATACCC
*
312613 AAAAAAACAAAAAAAAAACAA-AAAAACCAAA
1 AAAAAAAC-AAAAAAAAACAACAAAAAACAAA
312644 AAAAAAACAAAAAAAAA-AACACAAAAACAAA
1 AAAAAAACAAAAAAAAACAACA-AAAAACAAA
312675 AAAAAAACAAGAAAAAAACAACAAAAAACAAA
1 AAAAAAACAA-AAAAAAACAACAAAAAACAAA
312707 AA
1 AA
312709 GGGGTCTAGA
Statistics
Matches: 60, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
29 2 0.03
30 10 0.17
31 26 0.43
32 18 0.30
33 4 0.07
ACGTcount: A:0.86, C:0.12, G:0.01, T:0.00
Consensus pattern (31 bp):
AAAAAAACAAAAAAAAACAACAAAAAACAAA
Found at i:313942 original size:28 final size:28
Alignment explanation
Indices: 313911--314574 Score: 857
Period size: 28 Copynumber: 23.5 Consensus size: 28
313901 ACTTCATCTC
313911 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
313939 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
313967 TTCAAAGCCCACAAGTCAGTGGCA-CTCT
1 TTCAAAGCCCACAAGTCAGTGGCATC-CT
* *
313995 TTCAAAACCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
*
314024 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
314052 TTCAAGGTCCACAAGTCAGCGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
314080 TTCAAAGCCAACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
* *
314109 TTCAAAGCCAATAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
314137 TTCAAAGCCCATAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
314165 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
314193 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
314221 TTCAAAGCCCACGAGTCAGTGGCAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGC-A-TCCT
**
314251 TTCAAAGCCCATGAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
314279 TTCAAAGCCCACGAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
314307 TTCAAAGCCCACAAGTCAGTAGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
314335 TTCAAAGTCCACTAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
314363 TTTAAAGCCCACCAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
314391 TTCAAAGCCCACCAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
314419 TTCAAAGCCCAC-AGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
* * *
314447 TTCAAAGCCTACAAGTCAGTGACACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
314475 TTTAAAGCCCATAAGTCAGTGGCA-CTGT
1 TTCAAAGCCCACAAGTCAGTGGCATC-CT
*
314503 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * **
314531 TTCAAAGCCCACAAGTTAGTGGCGCTATT
1 TTCAAAGCCCACAAGTCAGTGGC-ATCCT
314560 TTCAAAGCCCACAAG
1 TTCAAAGCCCACAAG
314575 CTAATGGTAA
Statistics
Matches: 563, Mismatches: 62, Indels: 21
0.87 0.10 0.03
Matches are distributed among these distances:
27 13 0.02
28 447 0.79
29 77 0.14
30 26 0.05
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:313997 original size:56 final size:56
Alignment explanation
Indices: 313911--314652 Score: 843
Period size: 56 Copynumber: 13.0 Consensus size: 56
313901 ACTTCATCTC
*
313911 TTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCATCCT
* *
313967 TTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAACCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCA-TCCT
* * * *
314024 TTCAAAGCCCACAAGTTAGTGGCA-TCCTTTCAAGGTCCACAAGTCAGCGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
314080 TTCAAAGCCAACAAGTTAGTGGCACTCTTTTCAAAGCCAATAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
314137 TTCAAAGCCCATAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCATCCT
* *
314193 TTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACGAGTCAGTGGCAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGC-A-TCCT
** *
314251 TTCAAAGCCCATGAGTCAGTGGCA-TCCTTTCAAAGCCCACGAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCATCCT
* * * * *
314307 TTCAAAGCCCACAAGTCAGTAGCA-TCCTTTCAAAGTCCACTAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCATCCT
* * * * *
314363 TTTAAAGCCCACCAGTCAGTGGCACCCTTTCAAAGCCCACCAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
314419 TTCAAAGCCCAC-AGTCAGTGGCACTCTTTTCAAAGCCTACAAGTCAGTGACACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
314475 TTTAAAGCCCATAAGTCAGTGGCACTGTTTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCATCCT
* * * * * *
314531 TTCAAAGCCCACAAGTTAGTGGCGCTATTTTCAAAGCCCACAAG-CTAATGGTAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAGCCCACAAGTC-AGTGG-CA-TCCT
* * *
314590 TTCAAAGCCTATACGAGTCAGTGGCAACTCTTTTCAAAGCCCACACAAGTTAGTGGCA-CCT
1 TTCAAAGCC--CACAAGTCAGTGGC-ACTC-TTTCAAAG-CC-CACAAGTCAGTGGCATCCT
314651 TT
1 TT
314653 TTTTTTAAAA
Statistics
Matches: 594, Mismatches: 70, Indels: 39
0.84 0.10 0.06
Matches are distributed among these distances:
55 13 0.02
56 346 0.58
57 133 0.22
58 53 0.09
59 11 0.02
61 15 0.03
62 10 0.02
63 3 0.01
64 10 0.02
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (56 bp):
TTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:321594 original size:24 final size:24
Alignment explanation
Indices: 321536--321594 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
321526 ACCTAAAACG
*
321536 AAATGATATAAAAATTATTATTAA
1 AAATGATATAAAAATTAGTATTAA
*
321560 AAATGGT-TAAAAATATAGTA-TAA
1 AAATGATATAAAAAT-TAGTATTAA
*
321583 AAATAATATAAA
1 AAATGATATAAA
321595 TACGATACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 15 0.52
24 14 0.48
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (24 bp):
AAATGATATAAAAATTAGTATTAA
Found at i:321649 original size:32 final size:33
Alignment explanation
Indices: 321604--321665 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
321594 ATACGATACA
321604 AAATATATGAATATGT-TAAAATTTATATAATAT
1 AAATATATGAATATGTCT-AAATTTATATAATAT
*
321637 AAAT-TATTAATATGTCTAAATTTATATAA
1 AAATATATGAATATGTCTAAATTTATATAA
321666 AACCTTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 22 0.81
33 5 0.19
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (33 bp):
AAATATATGAATATGTCTAAATTTATATAATAT
Found at i:323540 original size:13 final size:13
Alignment explanation
Indices: 323522--323560 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
323512 AAATTAAACT
323522 TTTAAAAAATATA
1 TTTAAAAAATATA
323535 TTTAAAAAATA-A
1 TTTAAAAAATATA
*
323547 TATAAATAAATATA
1 TTTAAA-AAATATA
323561 AACAAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 6 0.26
13 16 0.70
14 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TTTAAAAAATATA
Found at i:323587 original size:31 final size:29
Alignment explanation
Indices: 323552--323617 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
323542 AATAATATAA
*
323552 ATAAATATAAACAAATTTATATTACATATTT
1 ATAAATATAAACAAATTTA-AATACAT-TTT
* *
323583 ATAAATATTAATAAATTTAAATACATTTT
1 ATAAATATAAACAAATTTAAATACATTTT
323612 A-AAATA
1 ATAAATA
323618 AATAATTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 5 0.16
29 4 0.12
30 6 0.19
31 17 0.53
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (29 bp):
ATAAATATAAACAAATTTAAATACATTTT
Found at i:326689 original size:12 final size:12
Alignment explanation
Indices: 326672--326696 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
326662 ATCTCATTGC
326672 TGCCACTGTCGA
1 TGCCACTGTCGA
326684 TGCCACTGTCGA
1 TGCCACTGTCGA
326696 T
1 T
326697 TTTACTGTTG
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:0.16, C:0.32, G:0.24, T:0.28
Consensus pattern (12 bp):
TGCCACTGTCGA
Found at i:326964 original size:37 final size:40
Alignment explanation
Indices: 326900--326977 Score: 126
Period size: 37 Copynumber: 2.0 Consensus size: 40
326890 TAGCTATGGG
*
326900 AACATTTTAGAAATTTGATAATGCTTA-T-ATATATATAT
1 AACATTATAGAAATTTGATAATGCTTATTAATATATATAT
326938 AACATTATAGAAA-TTGATAATGCTTATTAATATATATAT
1 AACATTATAGAAATTTGATAATGCTTATTAATATATATAT
326977 A
1 A
326978 TATTTATATG
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
37 13 0.35
38 13 0.35
39 11 0.30
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (40 bp):
AACATTATAGAAATTTGATAATGCTTATTAATATATATAT
Found at i:326998 original size:2 final size:2
Alignment explanation
Indices: 326993--327020 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
326983 ATATGCGCAC
326993 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
327021 GGTTCAAATG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:340367 original size:16 final size:16
Alignment explanation
Indices: 340348--340386 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
340338 GACTCAGGTT
340348 ATTTTAGATTCGAGTC
1 ATTTTAGATTCGAGTC
** *
340364 ATTTCGGATTTGAGTC
1 ATTTTAGATTCGAGTC
340380 ATTTTAG
1 ATTTTAG
340387 GTTTTGGTTA
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.21, T:0.46
Consensus pattern (16 bp):
ATTTTAGATTCGAGTC
Found at i:341796 original size:2 final size:2
Alignment explanation
Indices: 341789--341825 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
341779 TATTGGACTT
*
341789 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
341826 AAACATTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:344276 original size:13 final size:13
Alignment explanation
Indices: 344258--344294 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
344248 CTCTCAGATG
344258 TATCGATACATTA
1 TATCGATACATTA
*
344271 TATCGATACACTA
1 TATCGATACATTA
344284 TATCGATACAT
1 TATCGATACAT
344295 GTTCATTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:346051 original size:3 final size:3
Alignment explanation
Indices: 346037--346067 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
346027 AGATGGTGGG
*
346037 GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
346068 TTGACTTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:349320 original size:79 final size:79
Alignment explanation
Indices: 349183--349335 Score: 207
Period size: 79 Copynumber: 1.9 Consensus size: 79
349173 AGTACCCCTG
* * * ***
349183 ATTATGGAAAATCGATGTTCTGAAAATAAAATCGGGGTTGGAGTATCCCTTTGGAAATAACAGGG
1 ATTATAGAAAATCGATGTTCTGAAAATAAAATCAGGGTTGGAGTATCCCCTCAAAAATAACAGGG
349248 TTGGAGTATTCCTA
66 TTGGAGTATTCCTA
* * * **
349262 ATTATAGAAAATTGGTGTTTTGAAAATAAAATCAGGGTTGGAGTATCCCCTCAAAAATAATGGGG
1 ATTATAGAAAATCGATGTTCTGAAAATAAAATCAGGGTTGGAGTATCCCCTCAAAAATAACAGGG
349327 TTGGAGTAT
66 TTGGAGTAT
349336 CCCGGCGAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
79 63 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.31
Consensus pattern (79 bp):
ATTATAGAAAATCGATGTTCTGAAAATAAAATCAGGGTTGGAGTATCCCCTCAAAAATAACAGGG
TTGGAGTATTCCTA
Found at i:349330 original size:28 final size:28
Alignment explanation
Indices: 349296--349364 Score: 102
Period size: 28 Copynumber: 2.5 Consensus size: 28
349286 AATAAAATCA
* *
349296 GGGTTGGAGTATCCCCTCAAAAATAATG
1 GGGTTGGAGTATCCCCGCAAAAATAACG
* *
349324 GGGTTGGAGTATCCCGGCGAAAATAACG
1 GGGTTGGAGTATCCCCGCAAAAATAACG
349352 GGGTTGGAGTATC
1 GGGTTGGAGTATC
349365 TCCGATTGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.28, C:0.16, G:0.33, T:0.23
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGCAAAAATAACG
Found at i:349406 original size:79 final size:79
Alignment explanation
Indices: 349323--349765 Score: 710
Period size: 79 Copynumber: 5.6 Consensus size: 79
349313 CAAAAATAAT
** *
349323 GGGGTTGGAGTATCCCGGCGAAAATAACGGGGTTGGAGTATCTCCGATTGTGAGAAATCAATATT
1 GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATT
*
349388 TTAGGAATAAAATC
66 TTAGGAATAAAGTC
349402 GGGGTTGGAGTATCCCCTC-AGAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
1 GGGGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
*
349466 TTTAGGAATAAAGTT
65 TTTAGGAATAAAGTC
*
349481 GGGGTTGGAGTATCCCCTC-AGAAATAACGGGGTTGGAGTATCTCCGATTGTGAGAAATCAATAT
1 GGGGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
*
349545 TTTAGGAATAAAGCC
65 TTTAGGAATAAAGTC
* *
349560 GGGGTTGGAGTATCCCCTCGAAAATATCGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATT
1 GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATT
349625 TTAGGAATAAAGTC
66 TTAGGAATAAAGTC
* * * *
349639 GGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATAAGAAATTAATATT
1 GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATT
*
349704 TTAGGAATAAAGCC
66 TTAGGAATAAAGTC
* *
349718 GGGGTTGGAGTATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
349766 GATTAACGGG
Statistics
Matches: 344, Mismatches: 18, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
78 1 0.00
79 342 0.99
80 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (79 bp):
GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATT
TTAGGAATAAAGTC
Found at i:349780 original size:27 final size:28
Alignment explanation
Indices: 349717--349786 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 28
349707 GGAATAAAGC
**
349717 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
* * *
349745 CGAGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
349772 CGGGGTTGGAGTATC
1 CGGGGTTGGAGTATC
349787 ATCGATTGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 18 0.50
28 18 0.50
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:352261 original size:19 final size:21
Alignment explanation
Indices: 352237--352288 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
352227 AGCGATACAC
*
352237 TGTATCGATACA-TTACT-TA
1 TGTATCGATACATTTACTGAA
352256 TGTATCGATACATTTACTGAA
1 TGTATCGATACATTTACTGAA
352277 TGTATCGATACA
1 TGTATCGATACA
352289 AATTATTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.40
20 5 0.17
21 13 0.43
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTACTGAA
Found at i:353113 original size:119 final size:117
Alignment explanation
Indices: 352893--353114 Score: 283
Period size: 119 Copynumber: 1.9 Consensus size: 117
352883 TGGAAGGGGT
* * * * *
352893 GTCCCATTTTTTGAGGACAAAGGAAAAGAGAATGAAATAGGTCTTGCTCCTTGAGGACAAAGGAA
1 GTCCCATTTTTTGAGGACAAAGGAAAAGAGAACGAAATACGTCCTACTCCTTGAGGACAAAAGAA
352958 GAGAAGAAAAGGAAAGTGTCCTGCTTCTTAAGGACAAAGTGGAAAAGAGTAC
66 GAGAAGAAAAGGAAAGTGTCCTGCTTCTTAAGGACAAAGTGGAAAAGAGTAC
*
353010 GTCCCATTTTTTGAGGACAAAGGAAAAAGGGAAACGAAATACGTCCTACT-CTCTGAGGACAAAA
1 GTCCCATTTTTTGAGGACAAAGG-AAAAGAG-AACGAAATACGTCCTACTCCT-TGAGGACAAAA
*
353074 GAA-A-AAGGAAAA-TAAAGTGCATCCTGC-TCTTTAAGGACAAA
63 GAAGAGAA-GAAAAGGAAAGTG--TCCTGCTTC-TTAAGGACAAA
353115 AGAGAAAAGA
Statistics
Matches: 91, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
117 31 0.34
118 16 0.18
119 44 0.48
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (117 bp):
GTCCCATTTTTTGAGGACAAAGGAAAAGAGAACGAAATACGTCCTACTCCTTGAGGACAAAAGAA
GAGAAGAAAAGGAAAGTGTCCTGCTTCTTAAGGACAAAGTGGAAAAGAGTAC
Found at i:353359 original size:60 final size:61
Alignment explanation
Indices: 353147--353374 Score: 275
Period size: 61 Copynumber: 3.8 Consensus size: 61
353137 GTGTCCTACT
* * * * *
353147 CTTTGAGGATTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGTGTCCTGCC
1 CTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCGTCCTGCA
* * * * * *
353208 CTTTGAGGACTGAAAGGTGCCACTAACTTGTGTGGGCTTTGCAAAATGAAA-GCATCCTACT
1 CTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTG-AAAAGGAAAGGCGTCCTGCA
* *
353269 CTTTCAAGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAGAAGGCGTCCTGCA
1 CTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGGA-AAGGCGTCCTGCA
**
353330 CTTTGAGGACT-AAAAGTGCCACCGGCTTGTGTGGGCTTT-AAAAGG
1 CTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGG
353375 CATCCTGTTC
Statistics
Matches: 142, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
59 6 0.04
60 34 0.24
61 95 0.67
62 7 0.05
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (61 bp):
CTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCGTCCTGCA
Found at i:354119 original size:55 final size:55
Alignment explanation
Indices: 353413--354117 Score: 828
Period size: 55 Copynumber: 12.4 Consensus size: 55
353403 AAAGGAGAGA
* *
353413 GCGTCCTACTCTTTGAGGACTAGG-AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAG
1 GCGTCCTGCTCTTTGAGGACT-GGAAAATGCCACCAACTTGTGTGGGCTTT-----GA-AAG
353474 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAG
* * *
353534 GCGTCCCGCTCTTTGAGGATTGGAAAATGCCACCCACTTGTGTGGGCTTTGAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG
* *
353590 AAAAAGCATCCTGCTGTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
1 -----GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
* *
353650 GCATCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAG
** * *
353705 GCGTCCTGCTCTTTGAGGACTAAAAAATACCACTAACTTGTGTGGGCTTT-AACAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AG
* *
353760 GCGTCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTATGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
* *
353815 GCGTCCCGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAG
*
353870 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACTAACTTGTGTGGGCTTT-AAGAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AG
* * *
353925 GTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACCTATGTGGGCTTTAAAAAGAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-----G-AAAG
* * * * * *
353986 GTGTCTTGCTCTTTGAGGATTAGAAAATGCCACCAACTCGTGTGGGCTTTAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
* * *
354041 GAGTCCTGCTCTTTGAGGACT-GAAAGGTGCCCCCAACTTGTGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAG
*
354096 GCGTCATGCTCTTTGAGGACTG
1 GCGTCCTGCTCTTTGAGGACTG
354118 AAGGGTGAAA
Statistics
Matches: 569, Mismatches: 52, Indels: 51
0.85 0.08 0.08
Matches are distributed among these distances:
54 16 0.03
55 339 0.60
56 15 0.03
60 59 0.10
61 138 0.24
62 2 0.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (55 bp):
GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
Found at i:355204 original size:15 final size:14
Alignment explanation
Indices: 355185--355250 Score: 80
Period size: 15 Copynumber: 4.5 Consensus size: 14
355175 CTTTTCTCGC
*
355185 TTTTTTCTTTGTTT
1 TTTTTTTTTTGTTT
355199 TATTTTTTTTTGTTT
1 T-TTTTTTTTTGTTT
355214 TTGTTTTTTTTGTTT
1 TT-TTTTTTTTGTTT
355229 TTGTTTTTTTT-TTGT
1 TT-TTTTTTTTGTT-T
355244 TTTTTTT
1 TTTTTTT
355251 AGAAAGAATG
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
14 9 0.19
15 39 0.81
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.88
Consensus pattern (14 bp):
TTTTTTTTTTGTTT
Found at i:355205 original size:1 final size:1
Alignment explanation
Indices: 355185--355250 Score: 60
Period size: 1 Copynumber: 66.0 Consensus size: 1
355175 CTTTTCTCGC
* * * * * * * *
355185 TTTTTTCTTTGTTTTATTTTTTTTTGTTTTTGTTTTTTTTGTTTTTGTTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
355250 T
1 T
355251 AGAAAGAATG
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.88
Consensus pattern (1 bp):
T
Found at i:355209 original size:21 final size:20
Alignment explanation
Indices: 355192--355250 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 20
355182 CGCTTTTTTC
355192 TTTGTTTTATTTTTTTTTGTT
1 TTTGTTTT-TTTTTTTTTGTT
355213 TTTGTTTTTTTTGTTTTTGTT
1 TTTGTTTTTTTT-TTTTTGTT
355234 TTT-TTTTTGTTTTTTTT
1 TTTGTTTTT-TTTTTTTT
355251 AGAAAGAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
20 14 0.39
21 22 0.61
ACGTcount: A:0.02, C:0.00, G:0.10, T:0.88
Consensus pattern (20 bp):
TTTGTTTTTTTTTTTTTGTT
Found at i:355214 original size:26 final size:24
Alignment explanation
Indices: 355185--355249 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 24
355175 CTTTTCTCGC
* *
355185 TTTTTTCTTTGTTTTATTTTT-TT
1 TTTTTTTTTTTTTTTATTTTTGTT
*
355208 TTGTTTTTGTTTTTTTTGTTTTTGTT
1 TT-TTTTT-TTTTTTTTATTTTTGTT
355234 TTTTTTTTGTTTTTTT
1 TTTTTTTT-TTTTTTT
355250 TAGAAAGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
23 2 0.06
24 5 0.14
25 24 0.69
26 4 0.11
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.88
Consensus pattern (24 bp):
TTTTTTTTTTTTTTTATTTTTGTT
Found at i:367690 original size:15 final size:16
Alignment explanation
Indices: 367667--367697 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
367657 AAAGGCTTTC
367667 AAAA-TTTTTAATAGA
1 AAAAGTTTTTAATAGA
367682 AAAAGTTTTTAATAGA
1 AAAAGTTTTTAATAGA
367698 GGAAATGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.39
Consensus pattern (16 bp):
AAAAGTTTTTAATAGA
Done.