Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 148 of 182
Found at i:45550724 original size:50 final size:50
Alignment explanation
Indices: 45550619--45550715 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 50
45550609 GTATCTTGTG
* * *
45550619 TGGTACTGGATCCGCCGTTACGGTCTTAGATCTTTCCCTTCATGTCTTCA
1 TGGTACTGGATCCACCGTTACAGTCTTAAATCTTTCCCTTCATGTCTTCA
* *
45550669 TGGTACTGGATTCACCGTTACAGT-TTAAATCTTTCCCTTCTTGTCTT
1 TGGTACTGGATCCACCGTTACAGTCTTAAATCTTTCCCTTCATGTCTT
45550716 TTGAGGTACA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
49 21 0.50
50 21 0.50
ACGTcount: A:0.15, C:0.26, G:0.18, T:0.41
Consensus pattern (50 bp):
TGGTACTGGATCCACCGTTACAGTCTTAAATCTTTCCCTTCATGTCTTCA
Found at i:45552046 original size:6 final size:6
Alignment explanation
Indices: 45552037--45552233 Score: 146
Period size: 6 Copynumber: 32.5 Consensus size: 6
45552027 TGACCTCTCC
*
45552037 TTTTCT TTTTCT TTTT-T TCTTT-T TTTTTT TTTTC- TTTTCTT TTTTCTTT
1 TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTTCT TTTTC-T TTTTC--T
* * *
45552086 TTTTCT TTTTAT TTTTCT TCTTCT TCTTT-T TCTTCT TCTTTCT TTTCTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT T-TTTCT TTT-TCT
* *
45552136 TCTTT-T TTTTTT TTTTTT TTTTC- TTTTCT TTTTCTT TTTTCTT TTTTCT
1 T-TTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTC-T TTTTC-T TTTTCT
45552185 TTTTC- TTTTCTT TTCTTCT TTTT-T TTTT-T TTTT-T TTTT-T ATTTTCT
1 TTTTCT TTTTC-T TT-TTCT TTTTCT TTTTCT TTTTCT TTTTCT -TTTTCT
45552231 TTT
1 TTT
45552234 ATTCATTGAA
Statistics
Matches: 165, Mismatches: 8, Indels: 36
0.79 0.04 0.17
Matches are distributed among these distances:
5 41 0.25
6 76 0.46
7 36 0.22
8 12 0.07
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:45552052 original size:1 final size:1
Alignment explanation
Indices: 45552037--45552233 Score: 124
Period size: 1 Copynumber: 197.0 Consensus size: 1
45552027 TGACCTCTCC
* * * * * * * *
45552037 TTTTCTTTTTCTTTTTTTCTTTTTTTTTTTTTTCTTTTCTTTTTTCTTTTTTTCTTTTTATTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * * * * * *
45552102 CTTCTTCTTCTTTTTCTTCTTCTTTCTTTTCTCTTCTTTTTTTTTTTTTTTTTTTTCTTTTCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * *
45552167 TTCTTTTTTCTTTTTTCTTTTTCTTTTCTTTTCTTCTTTTTTTTTTTTTTTTTTTTTATTTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
45552232 TT
1 TT
45552234 ATTCATTGAA
Statistics
Matches: 136, Mismatches: 60, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 136 1.00
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.85
Consensus pattern (1 bp):
T
Found at i:45552079 original size:26 final size:25
Alignment explanation
Indices: 45552037--45552233 Score: 175
Period size: 26 Copynumber: 7.7 Consensus size: 25
45552027 TGACCTCTCC
* *
45552037 TTTTCTTTTTCTT-TTTTTCTTTTT
1 TTTTTTTTTTTTTCTTTTTCTTTTT
45552061 TTTTTTTTTCTTTTCTTTTTTCTTTTT
1 TTTTTTTTT-TTTTC-TTTTTCTTTTT
* * *
45552088 TTCTTTTTATTTTTCTTCTTCTTCTT
1 TT-TTTTTTTTTTTCTTTTTCTTTTT
* * * *
45552114 TTTCTTCTTCTTTCTTTTCTCTTCTT
1 TTTTTTTTTTTTTCTTTT-TCTTTTT
45552140 TTTTTTTTTTTTT-TTTTTC-TTTT
1 TTTTTTTTTTTTTCTTTTTCTTTTT
* *
45552163 CTTTTTCTTTTTTCTTTTTTCTTTTT
1 TTTTTTTTTTTTTC-TTTTTCTTTTT
* * * *
45552189 CTTTTCTTTTCTTCTTTTTTTTTTTT
1 TTTTTTTTTTTTTC-TTTTTCTTTTT
45552215 TTTTTTTTTATTTTCTTTT
1 TTTTTTTTT-TTTTCTTTT
45552234 ATTCATTGAA
Statistics
Matches: 141, Mismatches: 23, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
23 14 0.10
24 10 0.07
25 24 0.17
26 65 0.46
27 22 0.16
28 6 0.04
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.85
Consensus pattern (25 bp):
TTTTTTTTTTTTTCTTTTTCTTTTT
Found at i:45552088 original size:35 final size:34
Alignment explanation
Indices: 45552036--45552233 Score: 211
Period size: 35 Copynumber: 5.5 Consensus size: 34
45552026 TTGACCTCTC
*
45552036 CTTTTCTTTTTCTTTTTTTCTTTTTTTTTTTTTT
1 CTTTTTTTTTTCTTTTTTTCTTTTTTTTTTTTTT
45552070 CTTTTCTTTTTTCTTTTTTTCTTTTTATTTTTCTTCTT
1 CTTTT-TTTTTTCTTTTTTTCTTTTT-TTTTT-TT-TT
*
45552108 CTTCTTTTTCTTCTTCTTTCTTTTCTCTTCTTTTTTTTTT
1 C-T-TTTTT-TT-TTCTTT-TTTTCT-TTTTTTTTTTTTT
45552148 -TTTTTTTTTTCTTTTCTTT-TTCTTTTTTCTTTTTT
1 CTTTTTTTTTTCTTTT-TTTCTT-TTTTTT-TTTTTT
* *
45552183 CTTTTTCTTTTCTTTTCTTCTTTTTTTTTTTTTT
1 CTTTTTTTTTTCTTTTTTTCTTTTTTTTTTTTTT
*
45552217 TTTTTTTATTTTCTTTT
1 CTTTTTT-TTTTCTTTT
45552234 ATTCATTGAA
Statistics
Matches: 141, Mismatches: 7, Indels: 31
0.79 0.04 0.17
Matches are distributed among these distances:
33 1 0.01
34 23 0.16
35 51 0.36
36 23 0.16
37 7 0.05
38 4 0.03
39 3 0.02
40 7 0.05
41 8 0.06
42 11 0.08
43 3 0.02
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (34 bp):
CTTTTTTTTTTCTTTTTTTCTTTTTTTTTTTTTT
Found at i:45557761 original size:58 final size:59
Alignment explanation
Indices: 45557672--45557795 Score: 171
Period size: 58 Copynumber: 2.1 Consensus size: 59
45557662 TCAAAAATGG
* * *
45557672 AATTTTTGGAAGTTTCAAGGTCAAAAATGGAATTTTTGGAAATTTTGGGGAT-AATATCT
1 AATTTTTAGAAGTTTCAAGGTCAAAAATGGAATTTTTAGAAATTTTGAGG-TCAATATCT
** *
45557731 AATTTTTAGAAGTTT-TGGGTCAAAAATGGAATTTTTAGAAATTTTGAGGTCAATATGT
1 AATTTTTAGAAGTTTCAAGGTCAAAAATGGAATTTTTAGAAATTTTGAGGTCAATATCT
45557789 AATTTTT
1 AATTTTT
45557796 GGATAATTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
57 1 0.02
58 43 0.74
59 14 0.24
ACGTcount: A:0.34, C:0.04, G:0.20, T:0.42
Consensus pattern (59 bp):
AATTTTTAGAAGTTTCAAGGTCAAAAATGGAATTTTTAGAAATTTTGAGGTCAATATCT
Found at i:45557804 original size:30 final size:30
Alignment explanation
Indices: 45557642--45557804 Score: 145
Period size: 29 Copynumber: 5.5 Consensus size: 30
45557632 GTAAAATAGT
* * *
45557642 AATTTTTGGAAGTTTCGGGGTCAAAAATGG
1 AATTTTTGGAAATTTTGAGGTCAAAAATGG
* **
45557672 AATTTTTGGAAGTTTCAAGGTCAAAAATGG
1 AATTTTTGGAAATTTTGAGGTCAAAAATGG
* * **
45557702 AATTTTTGGAAATTTTG-GG-GATAATATCT
1 AATTTTTGGAAATTTTGAGGTCA-AAAATGG
* *
45557731 AATTTTTAGAAGTTTTG-GGTCAAAAATGG
1 AATTTTTGGAAATTTTGAGGTCAAAAATGG
* * *
45557760 AATTTTTAGAAATTTTGAGGTC-AATATGT
1 AATTTTTGGAAATTTTGAGGTCAAAAATGG
45557789 AATTTTTGGATAATTT
1 AATTTTTGGA-AATTT
45557805 AGGGACCTTT
Statistics
Matches: 110, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
28 1 0.01
29 57 0.52
30 52 0.47
ACGTcount: A:0.33, C:0.04, G:0.22, T:0.40
Consensus pattern (30 bp):
AATTTTTGGAAATTTTGAGGTCAAAAATGG
Found at i:45558211 original size:6 final size:6
Alignment explanation
Indices: 45558202--45558277 Score: 61
Period size: 6 Copynumber: 13.0 Consensus size: 6
45558192 TTAATATTAA
** *
45558202 TTAAAT TTAAAT TTAAA- GCAATT TTAAATT TTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T TTAAAT TTAAAT TTAAAT
* *
45558249 AT-AAT TTAAAT TTAACA- ATAAAT TTAAAT
1 TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT
45558278 CTATTCAAAC
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
4 2 0.04
5 5 0.09
6 40 0.74
7 7 0.13
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (6 bp):
TTAAAT
Found at i:45558237 original size:30 final size:29
Alignment explanation
Indices: 45558202--45558261 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 29
45558192 TTAATATTAA
*
45558202 TTAAATTTAAATTTAAAGCAATTTTAAATT
1 TTAAATTTAAATTTAAAACAA-TTTAAATT
*
45558232 TTAAATTTAAATTTAAAATAATTTAAATT
1 TTAAATTTAAATTTAAAACAATTTAAATT
45558261 T
1 T
45558262 AACAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (29 bp):
TTAAATTTAAATTTAAAACAATTTAAATT
Found at i:45558242 original size:13 final size:13
Alignment explanation
Indices: 45558204--45558276 Score: 51
Period size: 16 Copynumber: 5.2 Consensus size: 13
45558194 AATATTAATT
45558204 AAATTTAAATTTAA
1 AAATTTAAATTT-A
*
45558218 AGCAATTTTAAATTTT
1 A--AA-TTTAAATTTA
45558234 AAATTTAAATTTAAA
1 AAATTTAAATTT--A
45558249 ATAATTTAAATTTA
1 A-AATTTAAATTTA
45558263 ACAA--TAAATTTA
1 A-AATTTAAATTTA
45558275 AA
1 AA
45558277 TCTATTCAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
11 1 0.02
12 9 0.18
13 9 0.18
14 7 0.14
15 1 0.02
16 14 0.28
17 9 0.18
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (13 bp):
AAATTTAAATTTA
Found at i:45567189 original size:78 final size:79
Alignment explanation
Indices: 45567079--45567371 Score: 324
Period size: 81 Copynumber: 3.7 Consensus size: 79
45567069 CCTTCCGTTT
* * * * * * *
45567079 TGGTGAAGGTGTATCATTTCTCG--CCCTTCGTTTCCGAGGTGGTGATAGATCAG-CACCTGCTC
1 TGGTGAAGGTGTGTCA-TTCT-GAACCCTCCATTTCCGAGGAGGAGATAAATCAGACATCTGCTC
*
45567141 TGTTTGCTAAAGGTTC
64 TGTTTACTAAAGGTTC
* ** *
45567157 TGGTGAAGGTGTGTCATTCTGAACCCTCCGTTTCCTTGGAGGAGATAAATCAGTACTATCTGTTC
1 TGGTGAAGGTGTGTCATTCTGAACCCTCCATTTCCGAGGAGGAGATAAATCAG-AC-ATCTGCTC
*
45567222 GGTTTACTAAAGGTTC
64 TGTTTACTAAAGGTTC
* * *
45567238 TGGTGAAGGTGTGTCATTCCGAACCCTACATTTCCTAGGAGGAGATAAATCAGTACCATCTGCTC
1 TGGTGAAGGTGTGTCATTCTGAACCCTCCATTTCCGAGGAGGAGATAAATCAG-A-CATCTGCTC
45567303 TGTTTACTAAAGGTTC
64 TGTTTACTAAAGGTTC
* * *
45567319 TGGTGAGGGTGTGCCATTCCT-AACCCTCCACTTCCGAGGAGGAGATAAATCAG
1 TGGTGAAGGTGTGTCATT-CTGAACCCTCCATTTCCGAGGAGGAGATAAATCAG
45567372 TACCACCTCT
Statistics
Matches: 185, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
76 1 0.01
77 4 0.02
78 39 0.21
80 1 0.01
81 138 0.75
82 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.31
Consensus pattern (79 bp):
TGGTGAAGGTGTGTCATTCTGAACCCTCCATTTCCGAGGAGGAGATAAATCAGACATCTGCTCTG
TTTACTAAAGGTTC
Found at i:45567246 original size:81 final size:81
Alignment explanation
Indices: 45567135--45567376 Score: 351
Period size: 81 Copynumber: 3.0 Consensus size: 81
45567125 AGATCAGCAC
* * * *
45567135 CTGCTCTGTTTGCTAAAGGTTCTGGTGAAGGTGTGTCATTCTGAACCCTCCGTTTCCTTGGAGGA
1 CTGCTCGGTTTACTAAAGGTTCTGGTGAAGGTGTGTCATTCTGAACCCTCCATTTCCTAGGAGGA
*
45567200 GATAAATCAGTACTAT
66 GATAAATCAGTACCAT
* * *
45567216 CTGTTCGGTTTACTAAAGGTTCTGGTGAAGGTGTGTCATTCCGAACCCTACATTTCCTAGGAGGA
1 CTGCTCGGTTTACTAAAGGTTCTGGTGAAGGTGTGTCATTCTGAACCCTCCATTTCCTAGGAGGA
45567281 GATAAATCAGTACCAT
66 GATAAATCAGTACCAT
* * * * *
45567297 CTGCTCTGTTTACTAAAGGTTCTGGTGAGGGTGTGCCATTCCT-AACCCTCCACTTCCGAGGAGG
1 CTGCTCGGTTTACTAAAGGTTCTGGTGAAGGTGTGTCATT-CTGAACCCTCCATTTCCTAGGAGG
45567361 AGATAAATCAGTACCA
65 AGATAAATCAGTACCA
45567377 CCTCTAGAAG
Statistics
Matches: 144, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
81 143 0.99
82 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (81 bp):
CTGCTCGGTTTACTAAAGGTTCTGGTGAAGGTGTGTCATTCTGAACCCTCCATTTCCTAGGAGGA
GATAAATCAGTACCAT
Found at i:45575737 original size:17 final size:17
Alignment explanation
Indices: 45575707--45575750 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
45575697 GCTAAATGCT
45575707 TTCCCTTTCTCCTTCCC
1 TTCCCTTTCTCCTTCCC
45575724 TTCCTCTTTC-CCTTCCCC
1 TTCC-CTTTCTCCTT-CCC
*
45575742 TTTCCTTTC
1 TTCCCTTTC
45575751 ATTGCGTCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (17 bp):
TTCCCTTTCTCCTTCCC
Found at i:45586322 original size:23 final size:23
Alignment explanation
Indices: 45586295--45586341 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
45586285 GGGAGGTCGA
45586295 AATTAAATTTTCATTTTTACGAT
1 AATTAAATTTTCATTTTTACGAT
45586318 AATTAAATTTTCATTTTTACGAT
1 AATTAAATTTTCATTTTTACGAT
45586341 A
1 A
45586342 GTAAAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (23 bp):
AATTAAATTTTCATTTTTACGAT
Found at i:45586346 original size:22 final size:23
Alignment explanation
Indices: 45586298--45586346 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
45586288 AGGTCGAAAT
*
45586298 TAAATTTTCATTTTTACGATAAT
1 TAAATTTTCATTTTTACGATAAG
45586321 TAAATTTTCATTTTTACGAT-AG
1 TAAATTTTCATTTTTACGATAAG
45586343 TAAA
1 TAAA
45586347 AATATAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (23 bp):
TAAATTTTCATTTTTACGATAAG
Found at i:45590250 original size:88 final size:88
Alignment explanation
Indices: 45590098--45590273 Score: 325
Period size: 88 Copynumber: 2.0 Consensus size: 88
45590088 TGCTCGGGCT
*
45590098 CTCTATAGAATCAAGAGACAACCTCAATCGAGGTCAATAATGACACCTTCTAATGCATTCGTCAA
1 CTCTATAGAATCAAGAAACAACCTCAATCGAGGTCAATAATGACACCTTCTAATGCATTCGTCAA
*
45590163 CTAACTAAAAATTCGACAGAGGC
66 CTAACTAAAAATTAGACAGAGGC
*
45590186 CTCTATAGAATCAAGAAACAACCTCAATCGAGGTCAATAATGACACCTTCTAATGCATTTGTCAA
1 CTCTATAGAATCAAGAAACAACCTCAATCGAGGTCAATAATGACACCTTCTAATGCATTCGTCAA
45590251 CTAACTAAAAATTAGACAGAGGC
66 CTAACTAAAAATTAGACAGAGGC
45590274 AAGTGCATTT
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 85 1.00
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (88 bp):
CTCTATAGAATCAAGAAACAACCTCAATCGAGGTCAATAATGACACCTTCTAATGCATTCGTCAA
CTAACTAAAAATTAGACAGAGGC
Found at i:45593660 original size:6 final size:6
Alignment explanation
Indices: 45593649--45593713 Score: 114
Period size: 6 Copynumber: 11.0 Consensus size: 6
45593639 CGGACGGTCA
45593649 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG
1 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG
*
45593697 GGAGGG GGAG-G GGAGAG
1 GGAGAG GGAGAG GGAGAG
45593714 CTGTGGTGGG
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
5 5 0.09
6 52 0.91
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (6 bp):
GGAGAG
Found at i:45593811 original size:24 final size:23
Alignment explanation
Indices: 45593782--45593833 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
45593772 TTTTTTAATT
45593782 TTATTTATTGAATATTTAATATAA
1 TTATTTATTGAAT-TTTAATATAA
* *
45593806 TTATTTTATTTAATTTTAATATTA
1 TTA-TTTATTGAATTTTAATATAA
45593830 TTAT
1 TTAT
45593834 AAAAATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 1 0.04
24 15 0.60
25 9 0.36
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
TTATTTATTGAATTTTAATATAA
Found at i:45595931 original size:11 final size:11
Alignment explanation
Indices: 45595915--45595953 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
45595905 TTTATTGAAT
45595915 TTTATTTCATA
1 TTTATTTCATA
*
45595926 TTTATTTCGTA
1 TTTATTTCATA
45595937 TTTATTTCATA
1 TTTATTTCATA
45595948 TTTATT
1 TTTATT
45595954 GAGTTCTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.67
Consensus pattern (11 bp):
TTTATTTCATA
Found at i:45601869 original size:142 final size:142
Alignment explanation
Indices: 45601613--45601887 Score: 451
Period size: 142 Copynumber: 1.9 Consensus size: 142
45601603 TTTTCACCTA
* * * * *
45601613 ATTGGAAGTTAATCAACAATTGACAAGCAAATCAACACTTACAATTTGCATTAGAGCTGGACACC
1 ATTGGAAGTTAACCAACAATAGACAAGCAAATCAACACTTACAATTCGCATTAAAGCTAGACACC
* *
45601678 TAACACACTAAGTGAAGATCTTGTTGTTGAATTTCTTAGAGATGGAAGGAACCTCAAATTCAAGA
66 TAACACACTAAGTGAAGATCTTGTTGTTAAATTTCTTAGAGAAGGAAGGAACCTCAAATTCAAGA
45601743 CCTATAACCATT
131 CCTATAACCATT
* * *
45601755 ATTGGAAGTTAACCAACAATAGACAAGCAACTCAACACTTGCAATTCGCATTAAAGCTAGACACT
1 ATTGGAAGTTAACCAACAATAGACAAGCAAATCAACACTTACAATTCGCATTAAAGCTAGACACC
*
45601820 TAACACACTAAGTGAAGATCTTGTTGTTAAATTTGTTAGAGAAGGAAGGAACCTCAAATTCAAGA
66 TAACACACTAAGTGAAGATCTTGTTGTTAAATTTCTTAGAGAAGGAAGGAACCTCAAATTCAAGA
45601885 CCT
131 CCT
45601888 CTTATGCCTG
Statistics
Matches: 122, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
142 122 1.00
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (142 bp):
ATTGGAAGTTAACCAACAATAGACAAGCAAATCAACACTTACAATTCGCATTAAAGCTAGACACC
TAACACACTAAGTGAAGATCTTGTTGTTAAATTTCTTAGAGAAGGAAGGAACCTCAAATTCAAGA
CCTATAACCATT
Found at i:45608905 original size:11 final size:11
Alignment explanation
Indices: 45608889--45608913 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
45608879 AAACAATTGC
45608889 CCATACTACCA
1 CCATACTACCA
45608900 CCATACTACCA
1 CCATACTACCA
45608911 CCA
1 CCA
45608914 ATACAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.48, G:0.00, T:0.16
Consensus pattern (11 bp):
CCATACTACCA
Found at i:45613740 original size:59 final size:59
Alignment explanation
Indices: 45613608--45614060 Score: 540
Period size: 59 Copynumber: 7.7 Consensus size: 59
45613598 AAACCGGGCC
* * *
45613608 AAAAATGGAATTTTGGAAAGTTCGAGGGGGTAAAATGGTATTTTTTGGTAAAATCGAGGTT
1 AAAAATGGAATTTTGGAAAGTTC-A-GGGGTAAAATGGTAATTTTTGGTAAAACCGGGGTT
* * **
45613669 -AAAATGGAATTTTGGAAAGTTCGGGGGTAAAACGGTAATTTTTGGTAAAACCGGGGAC
1 AAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTAAAACCGGGGTT
* * **
45613727 AAAAATGGAATTTTGGAGAGTTTAGGGGTAAAATGGTAATTTTTGGTAAAA-TTGGGTT
1 AAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTAAAACCGGGGTT
* * * *
45613785 AAAAAAGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTAGTAAAACCGGAGTT
1 AAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTAAAACCGGGGTT
* * * ***
45613844 AAAAATGGAATTTTAGAAAGTTCGGGGGT-AAATGGTAATTTTTGGTAAAATCTAAGTT
1 AAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTAAAACCGGGGTT
* * * *
45613902 -AAAATGGAATTTT-GAGAGTTTAGGGGTAAAATGGTAA-TTTTGGTAAAACCGAGGTC
1 AAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTAAAACCGGGGTT
* * * * * *
45613958 AAAAATGGAATTTTTGGAGAGTTTAAGGGTAAAATGGTAATTTTTGATGAAATCGGGGTT
1 AAAAATGGAA-TTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTAAAACCGGGGTT
* *
45614018 AAAAATGGAATTTTGGAAAGTTTAGGGGCAAAATGGTAATTTT
1 AAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTT
45614061 CGGACAGTCT
Statistics
Matches: 340, Mismatches: 45, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
56 26 0.08
57 31 0.09
58 107 0.31
59 130 0.38
60 46 0.14
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (59 bp):
AAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTAAAACCGGGGTT
Found at i:45613805 original size:117 final size:117
Alignment explanation
Indices: 45613598--45614060 Score: 587
Period size: 117 Copynumber: 4.0 Consensus size: 117
45613588 AACTTAGGTG
* * *
45613598 AAACC-GGGCCAAAAATGGAATTTTGGAAAGTTCGAGGGGGTAAAATGGTATTTTTTGGTAAAAT
1 AAACCGGGGTCAAAAATGGAATTTTGGAAAGTT-TA-GGGGTAAAATGGTAATTTTTGGTAAAAT
* *
45613662 C-GAGGTTAAAATGGAATTTTGGAAAGTTCGGGGGTAAAACGGTAATTTTTGGTA
64 CTG-GGTTAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTA
* *
45613716 AAACCGGGGACAAAAATGGAATTTTGGAGAGTTTAGGGGTAAAATGGTAATTTTTGGTAAAAT-T
1 AAACCGGGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTAAAATCT
* * *
45613780 GGGTTAAAAAAGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTAGTA
66 GGGTT-AAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTA
* * * **
45613833 AAACCGGAGTTAAAAATGGAATTTTAGAAAGTTCGGGGGT-AAATGGTAATTTTTGGTAAAATCT
1 AAACCGGGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTAAAATCT
** * *
45613897 AAGTTAAAATGGAATTTT-GAGAGTTTAGGGGTAAAATGGTAA-TTTTGGTA
66 GGGTTAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTA
* * * * *
45613947 AAACCGAGGTCAAAAATGGAATTTTTGGAGAGTTTAAGGGTAAAATGGTAATTTTTGATGAAATC
1 AAACCGGGGTCAAAAATGGAA-TTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTAAAATC
* * *
45614012 GGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGCAAAATGGTAATTTT
65 TGGGTT-AAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTT
45614061 CGGACAGTCT
Statistics
Matches: 300, Mismatches: 36, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
114 25 0.08
115 35 0.12
116 62 0.21
117 122 0.41
118 28 0.09
119 28 0.09
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.31
Consensus pattern (117 bp):
AAACCGGGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTAAAATCT
GGGTTAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTA
Found at i:45614050 original size:29 final size:29
Alignment explanation
Indices: 45613727--45614060 Score: 97
Period size: 30 Copynumber: 11.5 Consensus size: 29
45613717 AACCGGGGAC
*
45613727 AAAAATGG-AATTTTGGAGAGTTTAGGGG
1 AAAAATGGTAATTTTGGAAAGTTTAGGGG
* * *
45613755 TAAAATGGTAATTTTTGGTAAA-ATT-GGGTT
1 AAAAATGGTAA-TTTTGG-AAAGTTTAGGG-G
* **
45613785 AAAAAAGG-AATTTTGGAAAGTTCGGGGG
1 AAAAATGGTAATTTTGGAAAGTTTAGGGG
* * *** *
45613813 TAAAATGGTAATTTTTAGTAAA--ACCGGAGTT
1 AAAAATGGTAA-TTTT-GGAAAGTTTAGG-G-G
* *
45613844 AAAAATGG-AATTTTAGAAAG-TTCGGGG
1 AAAAATGGTAATTTTGGAAAGTTTAGGGG
** * * * *
45613871 GTAAATGGTAATTTTTGGTAAAATCTA-AGT
1 AAAAATGGTAA-TTTTGG-AAAGTTTAGGGG
* *
45613901 TAAAATGG-AATTTT-GAGAGTTTAGGGG
1 AAAAATGGTAATTTTGGAAAGTTTAGGGG
* **** **
45613928 TAAAATGGTAATTTTGGTAAAACCGAGGTC
1 AAAAATGGTAATTTTGG-AAAGTTTAGGGG
* *
45613958 AAAAATGG-AATTTTTGGAGAGTTTAAGGG
1 AAAAATGGTAA-TTTTGGAAAGTTTAGGGG
* *
45613987 TAAAATGGTAATTTTTGATGAAA---TCGGGG
1 AAAAATGGTAA-TTTTG--GAAAGTTTAGGGG
45614016 TTAAAAATGG-AATTTTGGAAAGTTTAGGGG
1 --AAAAATGGTAATTTTGGAAAGTTTAGGGG
*
45614046 CAAAATGGTAATTTT
1 AAAAATGGTAATTTT
45614061 CGGACAGTCT
Statistics
Matches: 217, Mismatches: 59, Indels: 59
0.65 0.18 0.18
Matches are distributed among these distances:
26 5 0.02
27 23 0.11
28 43 0.20
29 58 0.27
30 64 0.29
31 21 0.10
32 3 0.01
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (29 bp):
AAAAATGGTAATTTTGGAAAGTTTAGGGG
Found at i:45614370 original size:162 final size:162
Alignment explanation
Indices: 45614135--45614634 Score: 892
Period size: 162 Copynumber: 3.1 Consensus size: 162
45614125 GGTACCCAGA
* *
45614135 AGTCAAAGGACTAATTTATAAATCTTGAAAAATTCTTGGGCCAATTTTGTAATTAAATAAAAGTT
1 AGTCAAAGGACTAATTTATAAATCTTGAAAAATTCTTGGGTCAATTGTGTAATTAAATAAAAGTT
*
45614200 GATTTAAGGATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACAGAAATAAGCCAAAAA
66 GATTTAAGGATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACATAAATAAGCCAAAAA
*
45614265 GTGACACGTGGCAGCCTCTGGTGCAGGCAAAC
131 GTGACACGTGGCAGCCTCTGGTGCAGTCAAAC
45614297 AGTCAAAGGACTAATTTATAAATCTTGAAAAATTCTTGGGTCAATTGTGTAATTAAATAAAAGTT
1 AGTCAAAGGACTAATTTATAAATCTTGAAAAATTCTTGGGTCAATTGTGTAATTAAATAAAAGTT
*
45614362 AATTTAAGGATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACATAAATAAGCCAAAAA
66 GATTTAAGGATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACATAAATAAGCCAAAAA
* * *
45614427 GTGACACATGGCAGCCTCTGGTGCAGTTAAAT
131 GTGACACGTGGCAGCCTCTGGTGCAGTCAAAC
*
45614459 AGTCAAAGGACTAATTTATAAATCTTAAAAAATTCTTGGGTCAATTGTGTAATTAAATAAAAGTT
1 AGTCAAAGGACTAATTTATAAATCTTGAAAAATTCTTGGGTCAATTGTGTAATTAAATAAAAGTT
* *
45614524 GATTTAAGGATTAAATTAAAACAAATTAAAAATGATAGGGACTAGATATATAAATAAGCCAAAAA
66 GATTTAAGGATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACATAAATAAGCCAAAAA
*
45614589 GTGACACGTGGCAGCCTCTGGTGCAGTCAAGC
131 GTGACACGTGGCAGCCTCTGGTGCAGTCAAAC
45614621 AGTCAAAGGACTAA
1 AGTCAAAGGACTAA
45614635 ATTGAAAACC
Statistics
Matches: 322, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
162 322 1.00
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.27
Consensus pattern (162 bp):
AGTCAAAGGACTAATTTATAAATCTTGAAAAATTCTTGGGTCAATTGTGTAATTAAATAAAAGTT
GATTTAAGGATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACATAAATAAGCCAAAAA
GTGACACGTGGCAGCCTCTGGTGCAGTCAAAC
Found at i:45615449 original size:19 final size:20
Alignment explanation
Indices: 45615418--45615456 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
45615408 TTCTCTTTTT
45615418 TTTTATAAAATA-TTATTAA
1 TTTTATAAAATATTTATTAA
45615437 TTTTA-AAATATATTTATTAA
1 TTTTATAAA-ATATTTATTAA
45615457 AACCATTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 8 0.44
20 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTATAAAATATTTATTAA
Found at i:45616232 original size:14 final size:14
Alignment explanation
Indices: 45616213--45616240 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
45616203 CCTAAATTTA
45616213 AAGTAAATTTAAAT
1 AAGTAAATTTAAAT
45616227 AAGTAAATTTAAAT
1 AAGTAAATTTAAAT
45616241 TTAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AAGTAAATTTAAAT
Found at i:45616536 original size:38 final size:36
Alignment explanation
Indices: 45616487--45616741 Score: 158
Period size: 38 Copynumber: 6.7 Consensus size: 36
45616477 ATATCCAGCT
45616487 TTACTTCAATTTCGAGAGGATAGGAAATGATCTTGCTC
1 TTACTTCAATTTC-AGAGGATAGGAAATGAT-TTGCTC
* ** * *
45616525 TTACTTCAATTTCAGA-GATAAAGACTTGATATCCATC
1 TTACTTCAATTTCAGAGGAT-AGGAAATGATTTGC-TC
45616562 TTTACTTCAATTTCAAGAGGATAGGAAATGATGTTGCTC
1 -TTACTTCAATTTC-AGAGGATAGGAAATGAT-TTGCTC
* * ** * * *
45616601 CTACTTCAATTTCAGA-GATAAAGACTTTATATCCATC
1 TTACTTCAATTTCAGAGGAT-AGGAAATGATTTGC-TC
*
45616638 TTTACTTCAATTTCAAGAGGATAGGAAATGATGTCGCTC
1 -TTACTTCAATTTC-AGAGGATAGGAAATGAT-TTGCTC
* * * ** *
45616677 ATACTTCCATTTCAGA-GATAAAGACTTGATATCCAGCT-
1 TTACTTCAATTTCAGAGGAT-AGGAAATGAT-T--TGCTC
45616715 TTACTTCAATTTCAAGAGGATAGGAAA
1 TTACTTCAATTTC-AGAGGATAGGAAA
45616742 ATAATTTTGG
Statistics
Matches: 163, Mismatches: 37, Indels: 33
0.70 0.16 0.14
Matches are distributed among these distances:
36 13 0.08
37 34 0.21
38 72 0.44
39 32 0.20
40 12 0.07
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (36 bp):
TTACTTCAATTTCAGAGGATAGGAAATGATTTGCTC
Found at i:45616566 original size:76 final size:76
Alignment explanation
Indices: 45616438--45616741 Score: 491
Period size: 76 Copynumber: 4.0 Consensus size: 76
45616428 GACCTGCTGC
* *
45616438 ATCTTGCTCTTACTTCAATTTTAGAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCGAG
1 ATCTTGCTCTTACTTCAA-TTT-CAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAG
45616503 AGGATAGGAAATG
64 AGGATAGGAAATG
*
45616516 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCATCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAG
45616581 GATAGGAAATG
66 GATAGGAAATG
* * * *
45616592 ATGTTGCTCCTACTTCAATTTCAGAGATAAAGACTTTATATCCATCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAG
45616657 GATAGGAAATG
66 GATAGGAAATG
* * * *
45616668 ATGTCGCTCATACTTCCATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAG
45616733 GATAGGAAA
66 GATAGGAAA
45616742 ATAATTTTGG
Statistics
Matches: 215, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
76 194 0.90
77 3 0.01
78 18 0.08
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (76 bp):
ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAG
GATAGGAAATG
Found at i:45616719 original size:152 final size:154
Alignment explanation
Indices: 45616441--45617097 Score: 510
Period size: 152 Copynumber: 4.0 Consensus size: 154
45616431 CTGCTGCATC
* * *
45616441 TTGCTCTTACTTCAATTTTAGAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCGAGAGG
1 TTGCTCCTACTTCAATTTTACAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGG
* * *
45616506 ATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCATCTTTACTTCA
66 ATAGGAAATGATCTCGCTCATACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCA
45616571 ATTTCAAGAGGATAGGAAATGATG
131 ATTTCAAGAGGATAGGAAATGATG
* *
45616595 TTGCTCCTACTTCAA-TTT-CAGAGATAAAGACTTTATATCCATCTTTACTTCAATTTCAAGAGG
1 TTGCTCCTACTTCAATTTTACAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGG
* *
45616658 ATAGGAAATGATGTCGCTCATACTTCCATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCA
66 ATAGGAAATGATCTCGCTCATACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCA
*
45616723 ATTTCAAGAGGATAGGAAAATAATTTTGG
131 ATTTCAAGAGGATAGG-AAATGA---T-G
* * * * ** * * * *
45616752 TCCTTCTTCTCACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCCGCTTTGCTTCAAT
1 ----T-TGCT--C-C-TACTTCAATTTTACAGAGATAAAGACTTGATATCCAGCTTTACTTCAAT
* * * **
45616817 TTCAAGAGGATAGGAAAATGATGTTGGTCCTTCTTTTCACTCTTACTTCAATTTCTGAGGGACGA
57 TTCAAGAGGATAGG-AAATGA----------TC---TCGCTCATACTTCAATTTC--AGAGATAA
* * *
45616882 AGGCTTGTTATCCCGCTTTACTTCAATTTCAAGAGGATAGGAAAATGATG
106 AGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGG-AAATGATG
* * ** * * *
45616932 TTGGTCCTTCTTTTCACTCCTACTTCAATTTCT-GAGGGACGAAGGCTTGTTATCCCGCTTTACT
1 TT-G------------CTCCTACTTCAATTT-TACAGAGATAAAGACTTGATATCCAGCTTTACT
* * * *
45616996 TCAATTTCAAGAGGATAGGAAATAATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTAT
52 TCAATTTCAAGAGGATAGGAAATGATCTCGCTCATACTTCAATTTCAGAGATAAAGACTTGATAT
* *
45617061 CCAACTCTACTTCAATTTCAAGAGGATAGGAAATGAT
117 CCAGCTTTACTTCAATTTCAAGAGGATAGGAAATGAT
45617098 CTGGTTTGAT
Statistics
Matches: 410, Mismatches: 47, Indels: 79
0.76 0.09 0.15
Matches are distributed among these distances:
152 117 0.29
153 8 0.02
154 14 0.03
156 1 0.00
157 1 0.00
161 1 0.00
162 3 0.01
164 1 0.00
165 1 0.00
166 8 0.02
167 9 0.02
168 82 0.20
169 6 0.01
170 17 0.04
173 2 0.00
175 1 0.00
176 1 0.00
179 1 0.00
180 1 0.00
181 1 0.00
182 16 0.04
183 5 0.01
184 109 0.27
185 1 0.00
186 1 0.00
188 2 0.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Consensus pattern (154 bp):
TTGCTCCTACTTCAATTTTACAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGG
ATAGGAAATGATCTCGCTCATACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCA
ATTTCAAGAGGATAGGAAATGATG
Found at i:45616824 original size:92 final size:92
Alignment explanation
Indices: 45616701--45617021 Score: 554
Period size: 92 Copynumber: 3.5 Consensus size: 92
45616691 GAGATAAAGA
* * * *
45616701 CTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAATAATTTTGGTCCTTCTTCTCACT
1 CTTGTTATCCCGCTTTACTTCAATTTCAAGAGGATAGGAAAATAATGTTGGTCCTTCTTTTCACT
*
45616766 CTTACTTCAATTTCAGAGGGACGAAGG
66 CTTACTTCAATTTCTGAGGGACGAAGG
* *
45616793 CTTGTTATCCCGCTTTGCTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTCCTTCTTTTCACT
1 CTTGTTATCCCGCTTTACTTCAATTTCAAGAGGATAGGAAAATAATGTTGGTCCTTCTTTTCACT
45616858 CTTACTTCAATTTCTGAGGGACGAAGG
66 CTTACTTCAATTTCTGAGGGACGAAGG
*
45616885 CTTGTTATCCCGCTTTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTCCTTCTTTTCACT
1 CTTGTTATCCCGCTTTACTTCAATTTCAAGAGGATAGGAAAATAATGTTGGTCCTTCTTTTCACT
*
45616950 CCTACTTCAATTTCTGAGGGACGAAGG
66 CTTACTTCAATTTCTGAGGGACGAAGG
45616977 CTTGTTATCCCGCTTTACTTCAATTTCAAGAGGATAGG-AAATAAT
1 CTTGTTATCCCGCTTTACTTCAATTTCAAGAGGATAGGAAAATAAT
45617022 CTTGCTCTTA
Statistics
Matches: 219, Mismatches: 10, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
91 6 0.03
92 213 0.97
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (92 bp):
CTTGTTATCCCGCTTTACTTCAATTTCAAGAGGATAGGAAAATAATGTTGGTCCTTCTTTTCACT
CTTACTTCAATTTCTGAGGGACGAAGG
Found at i:45628876 original size:27 final size:26
Alignment explanation
Indices: 45628846--45628901 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
45628836 AAACGGGACT
45628846 TTTGGATACCCGGGGGCAAAATGGTAA
1 TTTGGATACCCGGGGGC-AAATGGTAA
*** *
45628873 TTTGGATGTGCGGGGGCAAATGGTGA
1 TTTGGATACCCGGGGGCAAATGGTAA
45628899 TTT
1 TTT
45628902 TTAGTGAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.23, C:0.11, G:0.38, T:0.29
Consensus pattern (26 bp):
TTTGGATACCCGGGGGCAAATGGTAA
Found at i:45629753 original size:162 final size:162
Alignment explanation
Indices: 45629570--45630072 Score: 902
Period size: 162 Copynumber: 3.1 Consensus size: 162
45629560 CACAGGTACC
* *
45629570 CAAA-AGTCAAAGGACTAATTTATAAATCTTGAAAAATTCTTGGGCCAATTTTGTAATTAAATAA
1 CAAACAGTCAAAGGACTAATTTATAAATCTTGAAAAATTCTTGGGTCAATTGTGTAATTAAATAA
* *
45629634 AAGTTGATTTAAGTATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACAGAAATAAGCC
66 AAGTTGATTTAAGGATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACATAAATAAGCC
*
45629699 AAAAAGTGACACGTGGCAGCCTCTGGTGCATT
131 AAAAAGTGACACGTGGCAGCCTCTGGTGCAGT
*
45629731 CAAACAGTCAAAGGACTAATTTATAAATCTTGAAAAATTCTTAGGTCAATTGTGTAATTAAATAA
1 CAAACAGTCAAAGGACTAATTTATAAATCTTGAAAAATTCTTGGGTCAATTGTGTAATTAAATAA
45629796 AAGTTGATTTAAGGATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACATAAATAAGCC
66 AAGTTGATTTAAGGATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACATAAATAAGCC
*
45629861 AAAAAGTGACACGTGGCAGCCTTTGGTGCAGT
131 AAAAAGTGACACGTGGCAGCCTCTGGTGCAGT
*
45629893 CAAACAGTCAAAGGACTAATTTATAAATCTTAAAAAATTCTTGGGTCAATTGTGTAATTAAATAA
1 CAAACAGTCAAAGGACTAATTTATAAATCTTGAAAAATTCTTGGGTCAATTGTGTAATTAAATAA
*
45629958 AAGTTGATTTAAGGATTAAATTAAAACAAATTAAAAATGATAGGGACTAGATACATAAATAAG-C
66 AAGTTGATTTAAGGATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACATAAATAAGCC
45630022 AAAAAGTGACACGTGGCAGCCTCTGGTGCAGT
131 AAAAAGTGACACGTGGCAGCCTCTGGTGCAGT
*
45630054 CAAGCAGTCAAAGGACTAA
1 CAAACAGTCAAAGGACTAA
45630073 ATTGAAAACC
Statistics
Matches: 329, Mismatches: 12, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
161 54 0.16
162 275 0.84
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (162 bp):
CAAACAGTCAAAGGACTAATTTATAAATCTTGAAAAATTCTTGGGTCAATTGTGTAATTAAATAA
AAGTTGATTTAAGGATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACATAAATAAGCC
AAAAAGTGACACGTGGCAGCCTCTGGTGCAGT
Found at i:45630908 original size:19 final size:20
Alignment explanation
Indices: 45630877--45630915 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
45630867 CTTCTCTTTT
45630877 TTTTATAAAATA-TTATTAA
1 TTTTATAAAATATTTATTAA
45630896 TTTTA-AAAGATATTTATTAA
1 TTTTATAAA-ATATTTATTAA
45630916 AACCATTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 8 0.44
20 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
TTTTATAAAATATTTATTAA
Found at i:45636227 original size:23 final size:22
Alignment explanation
Indices: 45636192--45636234 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
45636182 TTTTTTAAAA
* *
45636192 TTTTAAGAGATTTAATGAGATTT
1 TTTTAAAAAATTTAAT-AGATTT
45636215 TTTTAAAAAATTTAATAGAT
1 TTTTAAAAAATTTAATAGAT
45636235 CAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (22 bp):
TTTTAAAAAATTTAATAGATTT
Found at i:45636246 original size:31 final size:30
Alignment explanation
Indices: 45636175--45636260 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 30
45636165 TGAGAGGCTT
* * **
45636175 AATTAAATTTTTTAAAATTTTAAGAGATTT
1 AATTAATTTTTTTAAAAATTTAAGAGATCA
* *
45636205 AATGAGATTTTTTTAAAAAATTTAATAGATCA
1 AATTA-ATTTTTTT-AAAAATTTAAGAGATCA
45636237 AATTAATTTTTTTGAAAAATTTAA
1 AATTAATTTTTTT-AAAAATTTAA
45636261 AATTTGAATG
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
30 4 0.09
31 25 0.54
32 17 0.37
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.47
Consensus pattern (30 bp):
AATTAATTTTTTTAAAAATTTAAGAGATCA
Found at i:45641247 original size:16 final size:16
Alignment explanation
Indices: 45641228--45641259 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
45641218 CTCATATTAA
*
45641228 TTTTTTTATATATAAT
1 TTTTTTTAAATATAAT
45641244 TTTTTTTAAATATAAT
1 TTTTTTTAAATATAAT
45641260 ACATAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTTTTAAATATAAT
Found at i:45641515 original size:22 final size:23
Alignment explanation
Indices: 45641467--45641515 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
45641457 AAATGATAGC
*
45641467 AAAATAGTGAAAAAAACAACAAG
1 AAAATAGTGAAAAAAACAACAAA
* *
45641490 AAAATAGT-AACAAAACAATAAA
1 AAAATAGTGAAAAAAACAACAAA
45641512 AAAA
1 AAAA
45641516 GCAAGAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.73, C:0.08, G:0.08, T:0.10
Consensus pattern (23 bp):
AAAATAGTGAAAAAAACAACAAA
Found at i:45645046 original size:18 final size:16
Alignment explanation
Indices: 45645014--45645056 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 16
45645004 ATGGAATGAG
45645014 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
45645030 AATAAATTTAATTAATTA
1 AATAAATTT--TTAATTA
45645048 AATAAATTT
1 AATAAATTT
45645057 GGAAATCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 9 0.36
18 16 0.64
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:45652640 original size:27 final size:25
Alignment explanation
Indices: 45652602--45652657 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
45652592 CAAGGGAAAA
45652602 AAAAAAACCTTTTCAAA-AAATATATG
1 AAAAAAACC-TTTCAAATAAATA-ATG
* *
45652628 AAAAAGACACTTTGAAATAAATAATG
1 AAAAAAAC-CTTTCAAATAAATAATG
45652654 AAAA
1 AAAA
45652658 TGATGGAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 20 0.77
27 6 0.23
ACGTcount: A:0.61, C:0.09, G:0.07, T:0.23
Consensus pattern (25 bp):
AAAAAAACCTTTCAAATAAATAATG
Found at i:45654178 original size:15 final size:17
Alignment explanation
Indices: 45654148--45654179 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
45654138 TTTACATTAG
45654148 AGTAGTATTATATATTT
1 AGTAGTATTATATATTT
45654165 AGTA-TATT-TATATTT
1 AGTAGTATTATATATTT
45654180 TAATGTGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (17 bp):
AGTAGTATTATATATTT
Found at i:45655137 original size:25 final size:25
Alignment explanation
Indices: 45655103--45655152 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
45655093 TGAACCATGA
*
45655103 ATCTCAAACCTCAATGTTTAGTGTT
1 ATCTCAAACCTCAAGGTTTAGTGTT
45655128 ATCTCAAACCTCAAGGTTTAGTGTT
1 ATCTCAAACCTCAAGGTTTAGTGTT
45655153 CAAGGTTTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (25 bp):
ATCTCAAACCTCAAGGTTTAGTGTT
Found at i:45673461 original size:16 final size:16
Alignment explanation
Indices: 45673440--45673471 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
45673430 TGATCATAAC
45673440 TCTATTCCATTACAGT
1 TCTATTCCATTACAGT
45673456 TCTATTCCATTACAGT
1 TCTATTCCATTACAGT
45673472 GAACCAAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44
Consensus pattern (16 bp):
TCTATTCCATTACAGT
Found at i:45679358 original size:75 final size:75
Alignment explanation
Indices: 45679235--45679375 Score: 210
Period size: 75 Copynumber: 1.9 Consensus size: 75
45679225 AGGATAAAAT
* * *
45679235 TTTGAAAATGTGTACAATTCTAAAGAAGACACTACTTAATTTATGTGATACGAGACTCACTTACT
1 TTTGAAAATGTGTACAACTATAAAGAAGACACTACTTAATTTATGTGATACGAGAATCACTTACT
45679300 ATTTGATGAC
66 ATTTGATGAC
* * * * *
45679310 TTTGAAAATGTGTACTACTATATAGAAGACATTACTTGATTTATGTGATACGAGAATGACTTACT
1 TTTGAAAATGTGTACAACTATAAAGAAGACACTACTTAATTTATGTGATACGAGAATCACTTACT
45679375 A
66 A
45679376 GGTGATCAGA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 58 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (75 bp):
TTTGAAAATGTGTACAACTATAAAGAAGACACTACTTAATTTATGTGATACGAGAATCACTTACT
ATTTGATGAC
Found at i:45686124 original size:28 final size:30
Alignment explanation
Indices: 45686091--45686146 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
45686081 TTTTTGAATA
45686091 CTCGA-GGGTAAAATGGTAA-TTTGGGACT
1 CTCGAGGGGTAAAATGGTAATTTTGGGACT
45686119 CTCGAGGGGTAAAATGGTAATTTTGGGA
1 CTCGAGGGGTAAAATGGTAATTTTGGGA
45686147 AAGTTTGGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 5 0.19
29 14 0.54
30 7 0.27
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.29
Consensus pattern (30 bp):
CTCGAGGGGTAAAATGGTAATTTTGGGACT
Found at i:45686156 original size:29 final size:28
Alignment explanation
Indices: 45686096--45686200 Score: 81
Period size: 29 Copynumber: 3.6 Consensus size: 28
45686086 GAATACTCGA
* * *
45686096 GGGTAAAATGGTAA-TTTGGGACTCTCGAG
1 GGGTAAAATGGTAATTTTGGAAAT-T-TAG
45686125 GGGTAAAATGGTAATTTTGGGAAAGTTT-G
1 GGGTAAAATGGTAATTTT-GGAAA-TTTAG
* *
45686154 GGGTTAAAAAT-GTCATTTTGGACATTTAG
1 GGG-T-AAAATGGTAATTTTGGAAATTTAG
*
45686183 GGGTAAAACGGTAATTTT
1 GGGTAAAATGGTAATTTT
45686201 TAGAAAATCA
Statistics
Matches: 62, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
27 4 0.06
28 11 0.18
29 26 0.42
30 11 0.18
31 9 0.15
32 1 0.02
ACGTcount: A:0.30, C:0.06, G:0.30, T:0.33
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTGGAAATTTAG
Found at i:45686201 original size:29 final size:30
Alignment explanation
Indices: 45686123--45686414 Score: 91
Period size: 29 Copynumber: 10.1 Consensus size: 30
45686113 GGGACTCTCG
* *
45686123 AGGGGTAAAATGGTAATTTTGGGAAAGTTT
1 AGGGGTAAAAAGGTAATTTTTGGAAAGTTT
* * *
45686153 -GGGGTTAAAAATGTCA-TTTTGGACA-TTT
1 AGGGG-TAAAAAGGTAATTTTTGGAAAGTTT
* * * *
45686181 AGGGGTAAAACGGTAATTTTTAGAAA-ATC
1 AGGGGTAAAAAGGTAATTTTTGGAAAGTTT
* * * * **
45686210 A-GGATCAAAAACGAAATTTTTGGATA-TCC
1 AGGGGT-AAAAAGGTAATTTTTGGAAAGTTT
* *
45686239 A-AGGTAAAATGGTAATTTTT-GAAAGTTT
1 AGGGGTAAAAAGGTAATTTTTGGAAAGTTT
* * *
45686267 -CGGGTCAAAATGG-AATTTTTAG-AAG-TT
1 AGGGGT-AAAAAGGTAATTTTTGGAAAGTTT
* * * *
45686294 CGGGAGTAAAAATGTAA-TTTTCG-TAGTCTT
1 AGGG-GTAAAAAGGTAATTTTTGGAAAGT-TT
* *
45686324 -GAGGGTAAAAATGAAATTTTTGG-AAGTTT
1 AG-GGGTAAAAAGGTAATTTTTGGAAAGTTT
* * *
45686353 GGGGGTAAAAATGTAA-TTTTAGAAAGTTT
1 AGGGGTAAAAAGGTAATTTTTGGAAAGTTT
* * * *
45686382 GGGGGTTAAATA--TAATTTTTAGACAGTTT
1 AGGGG-TAAAAAGGTAATTTTTGGAAAGTTT
45686411 AGGG
1 AGGG
45686415 ACTTTCAAGG
Statistics
Matches: 201, Mismatches: 42, Indels: 39
0.71 0.15 0.14
Matches are distributed among these distances:
27 5 0.02
28 62 0.31
29 108 0.54
30 26 0.13
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (30 bp):
AGGGGTAAAAAGGTAATTTTTGGAAAGTTT
Found at i:45686275 original size:57 final size:57
Alignment explanation
Indices: 45686126--45686276 Score: 128
Period size: 57 Copynumber: 2.6 Consensus size: 57
45686116 ACTCTCGAGG
* * * * ** ** *
45686126 GGTAAAATGGTAATTTTGGGAAAGTTTGGGGTTAAAAATGTCATTTTGGACATTTAGG
1 GGTAAAATGGTAATTTT-TGAAAGTTTCGGGTCAAAAACGAAATTTTGGACATCCAGA
* * * *
45686184 GGTAAAACGGTAATTTTTAGAAA--ATCAGGATCAAAAACGAAATTTTTGGATATCCA-A
1 GGTAAAATGGTAATTTTT-GAAAGTTTC-GGGTCAAAAACGAAA-TTTTGGACATCCAGA
45686241 GGTAAAATGGTAATTTTTGAAAGTTTCGGGTCAAAA
1 GGTAAAATGGTAATTTTTGAAAGTTTCGGGTCAAAA
45686277 TGGAATTTTT
Statistics
Matches: 72, Mismatches: 16, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
56 5 0.07
57 35 0.49
58 32 0.44
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (57 bp):
GGTAAAATGGTAATTTTTGAAAGTTTCGGGTCAAAAACGAAATTTTGGACATCCAGA
Found at i:45686392 original size:28 final size:29
Alignment explanation
Indices: 45686244--45686410 Score: 135
Period size: 29 Copynumber: 5.8 Consensus size: 29
45686234 TATCCAAGGT
* * *
45686244 AAAATGGTAATTTTTGAAAGTTT-CGGGTC
1 AAAAT-GTAATTTTAGAAAGTTTGGGGGTA
* * *
45686273 AAAATGGAATTTTTAG-AAGTTCGGGAGTA
1 AAAATGTAA-TTTTAGAAAGTTTGGGGGTA
* * *
45686302 AAAATGTAATTTTCG-TAGTCTTGAGGGTA
1 AAAATGTAATTTTAGAAAGT-TTGGGGGTA
* * *
45686331 AAAATGAAATTTTTGGAAGTTTGGGGGTA
1 AAAATGTAATTTTAGAAAGTTTGGGGGTA
45686360 AAAATGTAATTTTAGAAAGTTTGGGGGT-
1 AAAATGTAATTTTAGAAAGTTTGGGGGTA
* * *
45686388 TAAATATAATTTTTAGACAGTTT
1 AAAATGTAA-TTTTAGAAAGTTT
45686411 AGGGACTTTC
Statistics
Matches: 111, Mismatches: 22, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
28 23 0.21
29 85 0.77
30 3 0.03
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTAGAAAGTTTGGGGGTA
Found at i:45686410 original size:58 final size:57
Alignment explanation
Indices: 45686244--45686415 Score: 170
Period size: 58 Copynumber: 2.9 Consensus size: 57
45686234 TATCCAAGGT
* * * *
45686244 AAAATGGTAATTTTTGAAAGTTT-CGGGTCAAAATGGAATTTTTAGAAGTTCGGGAGTA
1 AAAAT-GTAATTTTAGAAAGTTTGAGGGTTAAAAT-GAATTTTTAGAAGTTTGGGAGTA
* * * * *
45686302 AAAATGTAATTTTCG-TAGTCTTGAGGGTAAAAATGAAATTTTTGGAAGTTTGGGGGTA
1 AAAATGTAATTTTAGAAAGT-TTGAGGGTTAAAATG-AATTTTTAGAAGTTTGGGAGTA
*
45686360 AAAATGTAATTTTAGAAAGTTTGGGGGTTAAATAT-AATTTTTAGACAGTTTAGGGA
1 AAAATGTAATTTTAGAAAGTTTGAGGGTTAAA-ATGAATTTTTAGA-AGTTT-GGGA
45686416 CTTTCAAGGC
Statistics
Matches: 94, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
56 3 0.03
57 21 0.22
58 62 0.66
59 8 0.09
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (57 bp):
AAAATGTAATTTTAGAAAGTTTGAGGGTTAAAATGAATTTTTAGAAGTTTGGGAGTA
Found at i:45688155 original size:25 final size:25
Alignment explanation
Indices: 45688127--45688178 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
45688117 TTGGTTTGTT
45688127 TTGGACCTTTT-GTGATTGGGTCCAA
1 TTGGACCTTTTGGT-ATTGGGTCCAA
* *
45688152 TTGGGCCTTTTGGTTTTGGGTCCAA
1 TTGGACCTTTTGGTATTGGGTCCAA
45688177 TT
1 TT
45688179 TAAGTTTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.12, C:0.15, G:0.29, T:0.44
Consensus pattern (25 bp):
TTGGACCTTTTGGTATTGGGTCCAA
Found at i:45688300 original size:36 final size:35
Alignment explanation
Indices: 45688258--45688326 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 35
45688248 TTAGTTAATT
*
45688258 TAAATTTAAAA-CAAATCTAAATTTAAATTTAAAAAA
1 TAAATTTAAAATC-AATCTAAACTT-AATTTAAAAAA
45688294 TAAATTTAAAATCAATCTAAACTTAATTTAAAA
1 TAAATTTAAAATCAATCTAAACTTAATTTAAAA
45688327 TTAAAATTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
35 9 0.29
36 21 0.68
37 1 0.03
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (35 bp):
TAAATTTAAAATCAATCTAAACTTAATTTAAAAAA
Found at i:45691975 original size:55 final size:55
Alignment explanation
Indices: 45691788--45692949 Score: 526
Period size: 55 Copynumber: 20.9 Consensus size: 55
45691778 AAAATTTTTG
* ** ** * *
45691788 GGTGATGGCCATGGTTTGGTAAGCAC-CCCAAAATATTTTTTCATCTGAAATAAG-
1 GGTGATGGCCATGGCTTGACAAGCACTCAAAAAATATTTTTTTATCT-AAAAAAGA
* * * * * *
45691842 GGTGATGGTCATGACTTGA-TAGCATTCAAAAAATA-TTTTTTATCT-GAAAAGG
1 GGTGATGGCCATGGCTTGACAAGCACTCAAAAAATATTTTTTTATCTAAAAAAGA
* *
45691894 GGTGATGGTCATGGCTT-AGCAAGCACTCAAAAAATATTTTGTTATCTAAAAAAGA
1 GGTGATGGCCATGGCTTGA-CAAGCACTCAAAAAATATTTTTTTATCTAAAAAAGA
* * * * * *
45691949 GGTAATGGCCATTGTTTGGCAAGCACTCAAAAAATATTTTTTTATTTGAAAAAGGA
1 GGTGATGGCCATGGCTTGACAAGCACTCAAAAAATATTTTTTTATCT-AAAAAAGA
* * * *
45692005 AGTGATGGTCATGGCTTGATAAGCA-TCAAAAAATATTTTTTTATCTAAAAAAAAGG
1 GGTGATGGCCATGGCTTGACAAGCACTCAAAAAATATTTTTTTATCT--AAAAAAGA
*** * *
45692061 GGTGATGGCCATAATTTGACAAACACCCAAAAAATATTTTTTTATCTAAAAAA-A
1 GGTGATGGCCATGGCTTGACAAGCACTCAAAAAATATTTTTTTATCTAAAAAAGA
* ** * * * * * * * * *
45692115 GGGTAATGATCATGACTTGACCATCACCCAAATAATATTAAATATTTTTATTTGACAAAGG
1 -GGTGATGGCCATGGCTTGACAAGCACTCAAA-AA-A-T--ATTTTTTTATCTAAAAAAGA
** * * * *
45692176 GGTG-TCGATCATGGCATGGACGA-CACTCAAAAAA-ATATTTTTATCTGAAAAAGA
1 GGTGAT-GGCCATGGC-TTGACAAGCACTCAAAAAATATTTTTTTATCTAAAAAAGA
* * *
45692230 GGTGATGGCCATGACTTGATAAGCACCCAAAAAATATTTTTTTATCTAAAAAAG-
1 GGTGATGGCCATGGCTTGACAAGCACTCAAAAAATATTTTTTTATCTAAAAAAGA
* * * * * * * * * *
45692284 GGTAATGACCA-GGACTTGGCCATCACCCAAAAAATATTAAATATTTTTATTTGACAAAGG
1 GGTGATGGCCATGG-CTTGACAAGCACTCAAAAAATA-T---T-TTTTTATCTAAAAAAGA
* * * * *
45692344 GGTG-TCGGTCATAG-TATGGACGA-CACTCAAAAAA-ATATTTTTATCTGAAAAAG-
1 GGTGAT-GGCCATGGCT-T-GACAAGCACTCAAAAAATATTTTTTTATCTAAAAAAGA
**
45692397 GAGTGATGATCATGGCTTGACAAGCACT-AAAAAATATTTTTTTATCTAAAAAA-A
1 G-GTGATGGCCATGGCTTGACAAGCACTCAAAAAATATTTTTTTATCTAAAAAAGA
* *
45692451 GGATGATGGTCATGGCTTGACAAGCACCTAAAAAAATATTTTTTTATCTGAAATAAA-A
1 GG-TGATGGCCATGGCTTGACAAGCA-CTCAAAAAATATTTTTTTATCT-AAA-AAAGA
* * * * * * * * * *
45692509 GATGATGGCCATGGCTTGGCCATCGCTCAAAAAAAAATTTATT-T-GATAAAAGA
1 GGTGATGGCCATGGCTTGACAAGCACTCAAAAAATATTTTTTTATCTAAAAAAGA
*** * ** * *
45692562 GGTGATGATTATGGCTTGACCATTACCCAAAAATATTTTTTTTTATCTAAAAAAGGGAGAAAAAA
1 GGTGATGGCCATGGCTTGACAAGCACTCAAAAA-ATATTTTTTTATCT-----------AAAAAA
45692627 GA
54 GA
* * *
45692629 GGGTGGTGGCCATGACTTGATAAGCAACT-AAAAAATA-TTTTTTATCTGAAAAATA-A
1 -GGTGATGGCCATGGCTTGACAAGC-ACTCAAAAAATATTTTTTTATCT-AAAAA-AGA
* * * * *
45692685 TAGCGATAGTCATGGCTTGACAAGCACCCAAAAAATATTTTTTTATCTAAAAAATGA
1 -GGTGATGGCCATGGCTTGACAAGCACTCAAAAAATATTTTTTTATCTAAAAAA-GA
* * * *
45692742 -GTGATGGCCATAGTTTGACAAGC-GTCCAAAAAATATTTTTTTTATCTGAAAAAGA
1 GGTGATGGCCATGGCTTGACAAGCACT-CAAAAAATA-TTTTTTTATCTAAAAAAGA
* * ** * * ** * * *
45692797 AGTAATGGTTATGGCTTGACCATCAC-CAAAAAA-A---AATTATCTGATAAAGGG
1 GGTGATGGCCATGGCTTGACAAGCACTCAAAAAATATTTTTTTATCT-AAAAAAGA
* * *
45692848 GGTGATGGCCA-GAGCTTGACCATCAC-CCAAAAAT-TTTTTGTTATCTGAAAAATA-A
1 GGTGATGGCCATG-GCTTGACAAGCACTCAAAAAATATTTTT-TTATCT-AAAAA-AGA
* ** * *
45692903 TGTGATGGCCATGATTTGGCAAGTACTCAAAAAATATTTTTTTATCT
1 GGTGATGGCCATGGCTTGACAAGCACTCAAAAAATATTTTTTTATCT
45692950 GAATGGCTTG
Statistics
Matches: 841, Mismatches: 186, Indels: 160
0.71 0.16 0.13
Matches are distributed among these distances:
50 7 0.01
51 35 0.04
52 19 0.02
53 72 0.09
54 169 0.20
55 186 0.22
56 167 0.20
57 59 0.07
58 9 0.01
59 19 0.02
60 49 0.06
61 9 0.01
66 10 0.01
67 9 0.01
68 20 0.02
69 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (55 bp):
GGTGATGGCCATGGCTTGACAAGCACTCAAAAAATATTTTTTTATCTAAAAAAGA
Found at i:45692330 original size:168 final size:168
Alignment explanation
Indices: 45691869--45692449 Score: 682
Period size: 168 Copynumber: 3.5 Consensus size: 168
45691859 GATAGCATTC
* * *
45691869 AAAAAATATTTTTTATCTG-AAAAGGGGTGATGGTCATGGCTT-AGCAAGCACTCAAAAAATATT
1 AAAAAATA-TTTTTATCTGAAAAAGGGGTGATGGCCATGACTTGA-CAAGCACCCAAAAAATATT
* * * * * *
45691932 TTGTTATCTAAAAAAGAGGTAATGGCCATTG-TTTGGCAAGCACTCAAAAAATA-T---T-TTTT
64 TTTTTATCTAAAAAAG-GGTAATGACCA-TGACTTGGCCATCACCCAAAAAATATTAAATATTTT
* * * **
45691991 TATTTGAAAAAGGAAGTGAT-GGTCATGGC-TTGATAAGCA-TCA
127 TATTTGACAAAGG-GGTG-TCGGTCATGGCATGGACGA-CACTCA
* * * * *
45692033 AAAAATATTTTTTTATCTAAAAAAAAGGGGTGATGGCCATAATTTGACAAACACCCAAAAAATAT
1 AAAAA-ATATTTTTATCT--GAAAAAGGGGTGATGGCCATGACTTGACAAGCACCCAAAAAATAT
* * *
45692098 TTTTTTATCTAAAAAAAGGGTAATGATCATGACTTGACCATCACCCAAATAATATTAAATATTTT
63 TTTTTTATCT-AAAAAAGGGTAATGACCATGACTTGGCCATCACCCAAAAAATATTAAATATTTT
*
45692163 TATTTGACAAAGGGGTGTCGATCATGGCATGGACGACACTCA
127 TATTTGACAAAGGGGTGTCGGTCATGGCATGGACGACACTCA
* *
45692205 AAAAAATATTTTTATCTGAAAAAGAGGTGATGGCCATGACTTGATAAGCACCCAAAAAATATTTT
1 AAAAAATATTTTTATCTGAAAAAGGGGTGATGGCCATGACTTGACAAGCACCCAAAAAATATTTT
*
45692270 TTTATCTAAAAAAGGGTAATGACCAGGACTTGGCCATCACCCAAAAAATATTAAATATTTTTATT
66 TTTATCTAAAAAAGGGTAATGACCATGACTTGGCCATCACCCAAAAAATATTAAATATTTTTATT
* *
45692335 TGACAAAGGGGTGTCGGTCATAGTATGGACGACACTCA
131 TGACAAAGGGGTGTCGGTCATGGCATGGACGACACTCA
* ** * *
45692373 AAAAAATATTTTTATCTGAAAAAGGAGTGATGATCATGGCTTGACAAGCA-CTAAAAAATATTTT
1 AAAAAATATTTTTATCTGAAAAAGGGGTGATGGCCATGACTTGACAAGCACCCAAAAAATATTTT
45692437 TTTATCTAAAAAA
66 TTTATCTAAAAAA
45692450 AGGATGATGG
Statistics
Matches: 358, Mismatches: 44, Indels: 27
0.83 0.10 0.06
Matches are distributed among these distances:
164 14 0.04
165 2 0.01
166 2 0.01
167 95 0.27
168 142 0.40
169 49 0.14
170 1 0.00
171 25 0.07
172 28 0.08
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (168 bp):
AAAAAATATTTTTATCTGAAAAAGGGGTGATGGCCATGACTTGACAAGCACCCAAAAAATATTTT
TTTATCTAAAAAAGGGTAATGACCATGACTTGGCCATCACCCAAAAAATATTAAATATTTTTATT
TGACAAAGGGGTGTCGGTCATGGCATGGACGACACTCA
Found at i:45692816 original size:56 final size:55
Alignment explanation
Indices: 45692639--45692952 Score: 173
Period size: 56 Copynumber: 5.7 Consensus size: 55
45692629 GGGTGGTGGC
* * * * * *
45692639 CATGACTTGATAAGCAACTAAAAAATA-TTTTTTATCTGAAAAATAA-TAGCGATAGT
1 CATGGCTTGACAAGCACCCAAAAAATATTTTTTTATCTGAAAAAGAAGTA---ATGGT
* * *
45692695 CATGGCTTGACAAGCACCCAAAAAATATTTTTTTATCTAAAAAATG-AGTGATGGC
1 CATGGCTTGACAAGCACCCAAAAAATATTTTTTTATCTGAAAAA-GAAGTAATGGT
* * **
45692750 CATAGTTTGACAAGCGTCCAAAAAATATTTTTTTTATCTGAAAAAGAAGTAATGGT
1 CATGGCTTGACAAGCACCCAAAAAATA-TTTTTTTATCTGAAAAAGAAGTAATGGT
* * * ** * ** * *
45692806 TATGGCTTGACCATCA-CCAAAAAA-A---AATTATCTGATAAAGGGGGTGATGGC
1 CATGGCTTGACAAGCACCCAAAAAATATTTTTTTATCTGA-AAAAGAAGTAATGGT
* * * * *
45692857 CA-GAGCTTGACCATCACCC-AAAAAT-TTTTTGTTATCTGAAAAATAATGTGATGGC
1 CATG-GCTTGACAAGCACCCAAAAAATATTTTT-TTATCTGAAAAAGAA-GTAATGGT
** * * *
45692912 CATGATTTGGCAAGTACTCAAAAAATATTTTTTTATCTGAA
1 CATGGCTTGACAAGCACCCAAAAAATATTTTTTTATCTGAA
45692953 TGGCTTGGCA
Statistics
Matches: 198, Mismatches: 43, Indels: 34
0.72 0.16 0.12
Matches are distributed among these distances:
50 9 0.05
51 28 0.14
52 2 0.01
54 4 0.02
55 61 0.31
56 72 0.36
57 21 0.11
58 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (55 bp):
CATGGCTTGACAAGCACCCAAAAAATATTTTTTTATCTGAAAAAGAAGTAATGGT
Found at i:45708314 original size:28 final size:30
Alignment explanation
Indices: 45708263--45708329 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
45708253 ATTTAGGTTG
* *
45708263 TTTTTAA-TACTTATTATTATTATT-TATA
1 TTTTTAATTACTTATTATTAATATTCCATA
*
45708291 TTTTTAATTACTTTTTA-TAATATTCCATA
1 TTTTTAATTACTTATTATTAATATTCCATA
45708320 TTTTATAATT
1 TTTT-TAATT
45708330 TCTAATATGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 13 0.39
29 15 0.45
30 5 0.15
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTTTAATTACTTATTATTAATATTCCATA
Found at i:45711984 original size:2 final size:2
Alignment explanation
Indices: 45711977--45712008 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
45711967 TTAAAATTTA
45711977 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45712009 TAAAAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45725291 original size:12 final size:12
Alignment explanation
Indices: 45725265--45725305 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
45725255 TAATTTTTGG
45725265 TAATTTTATAAA
1 TAATTTTATAAA
45725277 TAAGTTTTA-AAA
1 TAA-TTTTATAAA
*
45725289 TAATTTT-TCAA
1 TAATTTTATAAA
45725300 TAATTT
1 TAATTT
45725306 CACAATTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 12 0.46
12 9 0.35
13 5 0.19
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (12 bp):
TAATTTTATAAA
Found at i:45732742 original size:12 final size:12
Alignment explanation
Indices: 45732727--45732808 Score: 94
Period size: 12 Copynumber: 6.8 Consensus size: 12
45732717 TAGATGGAAG
*
45732727 TGATGATGATTT
1 TGATGATGAGTT
45732739 TGATGATGAGTT
1 TGATGATGAGTT
*
45732751 CGATGATGAGTT
1 TGATGATGAGTT
*
45732763 CGATGATGAGTT
1 TGATGATGAGTT
*
45732775 TGATGATGA-TGA
1 TGATGATGAGT-T
* *
45732787 AGATGATGATTT
1 TGATGATGAGTT
45732799 TGATGATGAG
1 TGATGATGAG
45732809 GAATTTGGTC
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
11 1 0.02
12 58 0.97
13 1 0.02
ACGTcount: A:0.28, C:0.02, G:0.32, T:0.38
Consensus pattern (12 bp):
TGATGATGAGTT
Found at i:45733458 original size:30 final size:30
Alignment explanation
Indices: 45733415--45733500 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 30
45733405 CGGTAAGAAT
* *
45733415 ATGGGGCAGATGGGCCAAATGGGTGGTCAG
1 ATGGGTCACATGGGCCAAATGGGTGGTCAG
45733445 ATGGGTCACATGGGTCC-AATGGGTGGTCAG
1 ATGGGTCACATGGG-CCAAATGGGTGGTCAG
*
45733475 ATGGGTTATAACATGGGCCAAATGGG
1 ATGGG---TCACATGGGCCAAATGGG
45733501 AAACCATCCA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
30 30 0.62
31 2 0.04
32 2 0.04
33 14 0.29
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.21
Consensus pattern (30 bp):
ATGGGTCACATGGGCCAAATGGGTGGTCAG
Found at i:45736313 original size:15 final size:15
Alignment explanation
Indices: 45736290--45736325 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
45736280 AAATTTAAAG
*
45736290 AAAAATGAATCTTGT
1 AAAAATGAATATTGT
*
45736305 AAAATTGAATATTGT
1 AAAAATGAATATTGT
45736320 AAAAAT
1 AAAAAT
45736326 CTTGGTTTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.33
Consensus pattern (15 bp):
AAAAATGAATATTGT
Found at i:45738360 original size:17 final size:18
Alignment explanation
Indices: 45738340--45738376 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
45738330 AATAAAATAT
45738340 AAATATAATTATAAT-TA
1 AAATATAATTATAATCTA
*
45738357 AAATATAATTTTAATCTA
1 AAATATAATTATAATCTA
45738375 AA
1 AA
45738377 TATTATGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATATAATTATAATCTA
Found at i:45738790 original size:16 final size:18
Alignment explanation
Indices: 45738751--45738784 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
45738741 TAAGTTTATA
45738751 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
45738768 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
45738785 AATTTACAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:45743880 original size:12 final size:12
Alignment explanation
Indices: 45743863--45743887 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45743853 TAATTCAAGT
45743863 TATTTGAGTTGA
1 TATTTGAGTTGA
45743875 TATTTGAGTTGA
1 TATTTGAGTTGA
45743887 T
1 T
45743888 TGAGTTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (12 bp):
TATTTGAGTTGA
Found at i:45752722 original size:27 final size:27
Alignment explanation
Indices: 45752685--45752752 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
45752675 GATATTGGAG
*
45752685 ATATT-TTTTATTAAT-TAATTAGTTAA
1 ATATTATTTTATTAATAT-ATTACTTAA
*
45752711 ATATTATTTTATTAATATTTTACTTAA
1 ATATTATTTTATTAATATATTACTTAA
45752738 ATATTTATTATTATT
1 ATA-TTATT-TTATT
45752753 TTATTTAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
26 5 0.14
27 20 0.56
28 6 0.17
29 5 0.14
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (27 bp):
ATATTATTTTATTAATATATTACTTAA
Found at i:45752742 original size:13 final size:11
Alignment explanation
Indices: 45752715--45752757 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
45752705 AGTTAAATAT
45752715 TATTTTATTAA
1 TATTTTATTAA
45752726 TATTTTACTTAA
1 TATTTTA-TTAA
*
45752738 -ATATTTATTAT
1 TAT-TTTATTAA
45752749 TATTTTATT
1 TATTTTATT
45752758 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:45757570 original size:59 final size:60
Alignment explanation
Indices: 45757507--45757673 Score: 250
Period size: 60 Copynumber: 2.8 Consensus size: 60
45757497 ATGGATACCT
* *
45757507 GGGGGCAAAATGGTAATTTTTGGTGTAATCGGGGTTAAAAATGGAATTTTAGAAA-ATTCG
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-GAAAGATTCG
* *
45757567 GGGGGTAAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTGAAAGATTC-
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAGATTCG
* *
45757626 GGGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTT-AAAATGGGATTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTT
45757674 AGGGAAGTTT
Statistics
Matches: 98, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
58 11 0.11
59 37 0.38
60 50 0.51
ACGTcount: A:0.34, C:0.04, G:0.31, T:0.31
Consensus pattern (60 bp):
GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAGATTCG
Found at i:45757658 original size:30 final size:29
Alignment explanation
Indices: 45757507--45757668 Score: 127
Period size: 30 Copynumber: 5.4 Consensus size: 29
45757497 ATGGATACCT
* *
45757507 GGGGGCAAAATGGTAATTTTTGGTGTAATC
1 GGGGGTAAAATGGTAA-TTTTGGTGAAATC
* * *
45757537 GGGGTTAAAAATGG-AATTTTAG-AAAATTC
1 GGGGGT-AAAATGGTAATTTTGGTGAAA-TC
45757566 GGGGGGTAAAATGGTAATTTTCGGTGAAATC
1 -GGGGGTAAAATGGTAATTTT-GGTGAAATC
* * *
45757597 AGGGTTAAAAATGG-AATTTT-G-AAAGATTC
1 GGGGGT-AAAATGGTAATTTTGGTGAA-A-TC
45757626 GGGGGTAAAATGGTAAATTTTGGTGAAATC
1 GGGGGTAAAATGGT-AATTTTGGTGAAATC
*
45757656 GGGGTTAAAATGG
1 GGGGGTAAAATGG
45757669 GATTTAGGGA
Statistics
Matches: 104, Mismatches: 15, Indels: 26
0.72 0.10 0.18
Matches are distributed among these distances:
27 2 0.02
28 11 0.11
29 20 0.19
30 47 0.45
31 19 0.18
32 5 0.05
ACGTcount: A:0.34, C:0.04, G:0.31, T:0.30
Consensus pattern (29 bp):
GGGGGTAAAATGGTAATTTTGGTGAAATC
Found at i:45757739 original size:30 final size:30
Alignment explanation
Indices: 45757685--45757886 Score: 318
Period size: 30 Copynumber: 6.7 Consensus size: 30
45757675 GGGAAGTTTA
* *
45757685 GGGTTAAAATGATAATTTTTG-AAAGTTTTG
1 GGGTCAAAATG-TAATTTTGGAAAAGTTTTG
45757715 GGGTCAAAATGTAATTTTAGG-AAAGTTTTG
1 GGGTCAAAATGTAATTTT-GGAAAAGTTTTG
45757745 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
* *
45757775 GGGTCAAAATATAATTTTGGAAAAGTTTTA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
*
45757805 GGGTCAAAATATAATTTTGGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
45757835 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
45757865 GGGTCAAAATGTAATTTCTGGA
1 GGGTCAAAATGTAATTT-TGGA
45757887 CAATTTAGGG
Statistics
Matches: 163, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
29 9 0.06
30 150 0.92
31 4 0.02
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTGGAAAAGTTTTG
Found at i:45759423 original size:18 final size:15
Alignment explanation
Indices: 45759387--45759418 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
45759377 CATGGTGGAT
45759387 AGAGCTGGTGGTGGC
1 AGAGCTGGTGGTGGC
45759402 AGAGCTGGTGGTGGC
1 AGAGCTGGTGGTGGC
45759417 AG
1 AG
45759419 CAGAGGCACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.16, C:0.12, G:0.53, T:0.19
Consensus pattern (15 bp):
AGAGCTGGTGGTGGC
Found at i:45759496 original size:14 final size:14
Alignment explanation
Indices: 45759477--45759547 Score: 105
Period size: 14 Copynumber: 5.3 Consensus size: 14
45759467 TTGGGCCTAT
45759477 TTGGGCCATTGTAA
1 TTGGGCCATTGTAA
45759491 TTGGG-CATT-TAA
1 TTGGGCCATTGTAA
45759503 TTTGGGCCATTGTAA
1 -TTGGGCCATTGTAA
45759518 TTGGGCC-TT-TAA
1 TTGGGCCATTGTAA
45759530 TTGGGCCATTGTAA
1 TTGGGCCATTGTAA
45759544 TTGG
1 TTGG
45759548 ACTTTGGACT
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
12 13 0.25
13 13 0.25
14 23 0.44
15 3 0.06
ACGTcount: A:0.20, C:0.13, G:0.28, T:0.39
Consensus pattern (14 bp):
TTGGGCCATTGTAA
Found at i:45759540 original size:26 final size:27
Alignment explanation
Indices: 45759475--45759547 Score: 130
Period size: 27 Copynumber: 2.7 Consensus size: 27
45759465 CATTGGGCCT
45759475 ATTTGGGCCATTGTAATTGGGCATTTA
1 ATTTGGGCCATTGTAATTGGGCATTTA
*
45759502 ATTTGGGCCATTGTAATTGGGCCTTTA
1 ATTTGGGCCATTGTAATTGGGCATTTA
45759529 A-TTGGGCCATTGTAATTGG
1 ATTTGGGCCATTGTAATTGG
45759548 ACTTTGGACT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
26 18 0.40
27 27 0.60
ACGTcount: A:0.21, C:0.12, G:0.27, T:0.40
Consensus pattern (27 bp):
ATTTGGGCCATTGTAATTGGGCATTTA
Found at i:45759619 original size:17 final size:17
Alignment explanation
Indices: 45759597--45759629 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
45759587 TCCAAATTTA
45759597 ACAAATTTAAATTTAAC
1 ACAAATTTAAATTTAAC
45759614 ACAAATTTAAATTTAA
1 ACAAATTTAAATTTAA
45759630 AAATTGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (17 bp):
ACAAATTTAAATTTAAC
Found at i:45759660 original size:18 final size:18
Alignment explanation
Indices: 45759639--45759684 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
45759629 AAAATTGATT
45759639 TAAATTTAAATTT-TAAGA
1 TAAATTTAAATTTGTAA-A
*
45759657 TAAATTCAAATTTGTAAA
1 TAAATTTAAATTTGTAAA
*
45759675 TGAATTTAAA
1 TAAATTTAAA
45759685 ATTAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (18 bp):
TAAATTTAAATTTGTAAA
Found at i:45759667 original size:24 final size:24
Alignment explanation
Indices: 45759615--45759669 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
45759605 AAATTTAACA
**
45759615 CAAATTTAAATTTAAAAATTGATT
1 CAAATTTAAATTTAAAAATAAATT
* * *
45759639 TAAATTTAAATTTTAAGATAAATT
1 CAAATTTAAATTTAAAAATAAATT
45759663 CAAATTT
1 CAAATTT
45759670 GTAAATGAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (24 bp):
CAAATTTAAATTTAAAAATAAATT
Found at i:45759682 original size:42 final size:41
Alignment explanation
Indices: 45759599--45759694 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 41
45759589 CAAATTTAAC
*
45759599 AAATTTAAATTTAACACAAATTTAAATTTAAAAATTGATTT
1 AAATTTAAATTTAACACAAATTCAAATTTAAAAATTGATTT
* * **
45759640 AAATTTAAATTTTAAGATAAATTCAAATTTGTAAA-TGAATTT
1 AAATTTAAA-TTTAACACAAATTCAAATTTAAAAATTG-ATTT
*
45759682 AAAATT-AATTTAA
1 AAATTTAAATTTAA
45759695 ACCAAATATA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
40 5 0.11
41 13 0.28
42 29 0.62
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (41 bp):
AAATTTAAATTTAACACAAATTCAAATTTAAAAATTGATTT
Found at i:45763794 original size:2 final size:2
Alignment explanation
Indices: 45763787--45763845 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
45763777 TTCACTCTGG
45763787 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
45763829 TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC T
45763846 ATGTATTCAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:45764273 original size:49 final size:49
Alignment explanation
Indices: 45764201--45764300 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 49
45764191 ATGATCATTG
*
45764201 GAACTGTTAAATTTATTACTGCTCTAGTTGATGAGCAAAGTTTCCCTGA
1 GAACTGTTAAATCTATTACTGCTCTAGTTGATGAGCAAAGTTTCCCTGA
*
45764250 GAACTGTTAACTCTATTACTGCTCTAGTTGATGAGCAAAGTTTCCCTGA
1 GAACTGTTAAATCTATTACTGCTCTAGTTGATGAGCAAAGTTTCCCTGA
45764299 GA
1 GA
45764301 CAAGGATTGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (49 bp):
GAACTGTTAAATCTATTACTGCTCTAGTTGATGAGCAAAGTTTCCCTGA
Found at i:45771175 original size:30 final size:30
Alignment explanation
Indices: 45771141--45771208 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
45771131 TGTGACGGAA
45771141 AAGGACTGTTTTGTCACATTTTCAAAGTTG
1 AAGGACTGTTTTGTCACATTTTCAAAGTTG
* *
45771171 AAGGATTGTTTTGTCATATTTTCAAAGTTG
1 AAGGACTGTTTTGTCACATTTTCAAAGTTG
*
45771201 AGGGACTG
1 AAGGACTG
45771209 AAATGTAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (30 bp):
AAGGACTGTTTTGTCACATTTTCAAAGTTG
Found at i:45771585 original size:35 final size:37
Alignment explanation
Indices: 45771536--45771609 Score: 116
Period size: 35 Copynumber: 2.1 Consensus size: 37
45771526 ACAACAGTAA
45771536 TTTTAACAGCTCAGTGATTTAAAT-AAAAAA-TTATT
1 TTTTAACAGCTCAGTGATTTAAATAAAAAAACTTATT
* *
45771571 TTTTAGCAGTTCAGTGATTTAAATAAAAAAACTTATT
1 TTTTAACAGCTCAGTGATTTAAATAAAAAAACTTATT
45771608 TT
1 TT
45771610 AATTATAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 22 0.63
36 6 0.17
37 7 0.20
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (37 bp):
TTTTAACAGCTCAGTGATTTAAATAAAAAAACTTATT
Found at i:45772109 original size:6 final size:6
Alignment explanation
Indices: 45772077--45772119 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
45772067 ATTATATTTC
* *
45772077 TAAAAT TAAATT T-ACTT TAAA-T TAAATT TAAATT TAAATT TAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAA
45772120 TGCCTCAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 9 0.28
6 23 0.72
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (6 bp):
TAAATT
Found at i:45773489 original size:59 final size:59
Alignment explanation
Indices: 45773426--45773675 Score: 344
Period size: 59 Copynumber: 4.2 Consensus size: 59
45773416 GGACTGTCCG
* * **
45773426 AAAATTACCATTTTACTCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATTA
1 AAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
* ***
45773485 AAAATTACCATTTTACCCTCGAACTTTTTGAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
* * * *
45773544 AAAATTACCATTTTACCC-CTAAACTTTCTAAAATTCTATTTTTAACCTCGATTTCATCA
1 AAAATTACCATTTTACCCTC-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
45773603 AAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCA-TTTTAACCCCTG-TTTCACCAA
1 AAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCC-GATTTCACC-A
45773662 AAAATTACCATTTT
1 AAAATTACCATTTT
45773676 GCCCCCCGAG
Statistics
Matches: 171, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
58 16 0.09
59 154 0.90
60 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (59 bp):
AAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
Found at i:45773499 original size:30 final size:30
Alignment explanation
Indices: 45773455--45773616 Score: 110
Period size: 30 Copynumber: 5.4 Consensus size: 30
45773445 CGAACTTTCC
45773455 AAAATTCCATTTTTAACCCCGATTTCATTA
1 AAAATTCCATTTTTAACCCCGATTTCATTA
45773485 AAAATTACCA-TTTT-ACCCTCGAACTTT--TT-
1 AAAATT-CCATTTTTAACCC-CG-A-TTTCATTA
* **
45773514 GAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTCCATTTTTAACCCCGATTTCATTA
*
45773544 AAAATTACCA-TTTT-ACCCCTAAACTTTC--T-
1 AAAATT-CCATTTTTAACCCC--GA-TTTCATTA
* * *
45773573 AAAATTCTATTTTTAACCTCGATTTCATCA
1 AAAATTCCATTTTTAACCCCGATTTCATTA
45773603 AAAATTACCATTTT
1 AAAATT-CCATTTT
45773617 ACCCTCAAAC
Statistics
Matches: 102, Mismatches: 11, Indels: 37
0.68 0.07 0.25
Matches are distributed among these distances:
27 7 0.07
28 7 0.07
29 30 0.29
30 37 0.36
31 14 0.14
32 7 0.07
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (30 bp):
AAAATTCCATTTTTAACCCCGATTTCATTA
Found at i:45773649 original size:29 final size:29
Alignment explanation
Indices: 45773426--45773649 Score: 114
Period size: 29 Copynumber: 7.7 Consensus size: 29
45773416 GGACTGTCCG
*
45773426 AAAATTACCATTTT-ACTCTCGAACTTTCC
1 AAAATTACCATTTTAACCCTC-AACTTTCC
* *
45773455 AAAATT-CCATTTTTAACCC-CGA-TTTCATTA
1 AAAATTACCA-TTTTAACCCTCAACTTTC---C
**
45773485 AAAATTACCATTTT-ACCCTCGAACTTTTT
1 AAAATTACCATTTTAACCCTC-AACTTTCC
* *
45773514 GAAATT-CCATTTTTAACCC-CGA-TTTCACC
1 AAAATTACCA-TTTTAACCCTCAACTTT--CC
* * *
45773543 AAAAATTACCATTTTACCCCTAAACTTTCT
1 -AAAATTACCATTTTAACCCTCAACTTTCC
* *
45773573 AAAATT-CTATTTTTAA-CCTCGA-TTTCATC
1 AAAATTACCA-TTTTAACCCTCAACTTTC--C
45773602 AAAAATTACCATTTT-ACCCTCAAACTTTCC
1 -AAAATTACCATTTTAACCCTC-AACTTTCC
45773632 AAAATT-CCATTTTAACCC
1 AAAATTACCATTTTAACCC
45773650 CTGTTTCACC
Statistics
Matches: 147, Mismatches: 22, Indels: 52
0.67 0.10 0.24
Matches are distributed among these distances:
27 11 0.07
28 21 0.14
29 47 0.32
30 47 0.32
31 11 0.07
32 10 0.07
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAATTACCATTTTAACCCTCAACTTTCC
Found at i:45773692 original size:59 final size:59
Alignment explanation
Indices: 45773426--45773717 Score: 327
Period size: 59 Copynumber: 4.9 Consensus size: 59
45773416 GGACTGTCCG
* * * **
45773426 AAAATTACCATTTTACTCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATTA
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
* * ***
45773485 AAAATTACCATTTTACCCTCGAACTTTTTGAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
* * * * *
45773544 AAAATTACCATTTTACCCCTAAACTTTCTAAAATTCTATTTTTAACCTCGATTTCATCA
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
*
45773603 AAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCA-TTTTAACCCCTG-TTTCACCAA
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCC-GATTTCACC-A
* ** * * ** *
45773662 AAAATTACCATTTTGCCCCCCGAGTATCCAAAAGCCCCATTTTCAACCCCGATTTC
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAA-TTCCATTTTTAACCCCGATTTC
45773718 GTCGTTTCTT
Statistics
Matches: 199, Mismatches: 29, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
58 15 0.08
59 167 0.84
60 4 0.02
61 13 0.07
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
Found at i:45776532 original size:3 final size:3
Alignment explanation
Indices: 45776517--45776548 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
45776507 AGACTAGTGT
*
45776517 TGA TGA TGT TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
45776549 GATGGGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (3 bp):
TGA
Found at i:45780713 original size:7 final size:7
Alignment explanation
Indices: 45780703--45780736 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
45780693 AATCCGATGT
*
45780703 GGTGCAA
1 GGTGCTA
*
45780710 GGTGTTA
1 GGTGCTA
45780717 GGTGCTA
1 GGTGCTA
45780724 GGTGCTA
1 GGTGCTA
45780731 GGTGCT
1 GGTGCT
45780737 TTAATTAAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.15, C:0.12, G:0.44, T:0.29
Consensus pattern (7 bp):
GGTGCTA
Found at i:45793142 original size:11 final size:11
Alignment explanation
Indices: 45793096--45793139 Score: 56
Period size: 10 Copynumber: 4.2 Consensus size: 11
45793086 TGTTTAATTT
45793096 ATAATATAAAA
1 ATAATATAAAA
*
45793107 ATAAAAT-AAA
1 ATAATATAAAA
45793117 ATAAT-TAAAA
1 ATAATATAAAA
*
45793127 ATTATATAAAA
1 ATAATATAAAA
45793138 AT
1 AT
45793140 TATTTTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
9 1 0.04
10 14 0.50
11 13 0.46
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:45797311 original size:11 final size:11
Alignment explanation
Indices: 45797295--45797380 Score: 51
Period size: 11 Copynumber: 8.2 Consensus size: 11
45797285 CAACCAAAGC
45797295 ATTTTAAATTT
1 ATTTTAAATTT
45797306 ATTTTAAA---
1 ATTTTAAATTT
*
45797314 A--TTAAATTA
1 ATTTTAAATTT
*
45797323 AATTTAAATTT
1 ATTTTAAATTT
*
45797334 AATTTAAATTT
1 ATTTTAAATTT
45797345 GGA-TTT-AATTT
1 --ATTTTAAATTT
*
45797356 AAATTTAAATTT
1 -ATTTTAAATTT
*
45797368 ATTATAAATTT
1 ATTTTAAATTT
45797379 AT
1 AT
45797381 AAATAAATGT
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
6 5 0.08
8 1 0.02
9 1 0.02
10 1 0.02
11 45 0.73
12 8 0.13
13 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (11 bp):
ATTTTAAATTT
Found at i:45797329 original size:28 final size:28
Alignment explanation
Indices: 45797297--45797368 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
45797287 ACCAAAGCAT
*
45797297 TTTAAATTTATTTTAAAATTAAATTAAA
1 TTTAAATTTAATTTAAAATTAAATTAAA
* ** *
45797325 TTTAAATTTAATTTAAATTTGGATTTAA
1 TTTAAATTTAATTTAAAATTAAATTAAA
45797353 TTTAAATTTAAATTTA
1 TTTAAATTT-AATTTA
45797369 TTATAAATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
28 32 0.84
29 6 0.16
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (28 bp):
TTTAAATTTAATTTAAAATTAAATTAAA
Found at i:45797343 original size:6 final size:6
Alignment explanation
Indices: 45797297--45797368 Score: 80
Period size: 6 Copynumber: 12.7 Consensus size: 6
45797287 ACCAAAGCAT
* *
45797297 TTTAAA TTT-AT TTTAAA ATTAAA -TTAAA TTTAAA TTT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
**
45797342 TTTGGA TTT-AA TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA
45797369 TTATAAATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
5 18 0.32
6 38 0.68
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:45797378 original size:17 final size:17
Alignment explanation
Indices: 45797308--45797379 Score: 92
Period size: 17 Copynumber: 4.2 Consensus size: 17
45797298 TTAAATTTAT
* *
45797308 TTTAAAATTAAATTAAA
1 TTTAAATTTAATTTAAA
45797325 TTTAAATTTAATTTAAA
1 TTTAAATTTAATTTAAA
**
45797342 TTTGGATTTAATTTAAA
1 TTTAAATTTAATTTAAA
45797359 TTTAAATTT-ATTATAAA
1 TTTAAATTTAATT-TAAA
45797376 TTTA
1 TTTA
45797380 TAAATAAATG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
16 3 0.06
17 45 0.94
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
TTTAAATTTAATTTAAA
Found at i:45798096 original size:22 final size:20
Alignment explanation
Indices: 45798070--45798110 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
45798060 TATATTAAAC
45798070 GTATTAACTAAAGTTTTAAATG
1 GTATTAA-TAAA-TTTTAAATG
*
45798092 GTATTAATTAATTTTAAAT
1 GTATTAATAAATTTTAAAT
45798111 AAAAGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 3 0.17
22 7 0.39
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.46
Consensus pattern (20 bp):
GTATTAATAAATTTTAAATG
Found at i:45799274 original size:29 final size:28
Alignment explanation
Indices: 45799225--45799480 Score: 168
Period size: 29 Copynumber: 8.8 Consensus size: 28
45799215 TTTAACCTCA
* *
45799225 AAATTTTCTAAAAATTACATTTTGACCCTT
1 AAATTTTC-CAAAATTCCATTTTGACCC-T
45799255 AAACTTTT-CAAAATTCCATTTTGACCCT
1 AAA-TTTTCCAAAATTCCATTTTGACCCT
45799283 -AATTTTACCAAAAATTACCATTTT-ACCCCT
1 AAATTTT-CC-AAAATT-CCATTTTGA-CCCT
*
45799313 AAATTTTCCAAAATTCCATTTTTAGCCC-
1 AAATTTTCCAAAATTCCATTTTGA-CCCT
** * * *
45799341 CGATTTCACCAAAAATTACCA-TTTCACCCCC
1 AAATTT-TCC-AAAATT-CCATTTTGA-CCCT
* *
45799372 GAACTTTCCAAAATTCCATTTTGACCCT
1 AAATTTTCCAAAATTCCATTTTGACCCT
*
45799400 -AATTTCACCAAAAATTACCATTTT-ACCCCT
1 AAATTT-TCC-AAAATT-CCATTTTGA-CCCT
45799430 AAATTTTCCAAAATTCCATTTTTGA-CCT
1 AAATTTTCCAAAATTCCA-TTTTGACCCT
**
45799458 TGATTTTACCAAAATTACCATTT
1 AAATTTT-CCAAAATT-CCATTT
45799481 CACCGTCGAA
Statistics
Matches: 185, Mismatches: 19, Indels: 45
0.74 0.08 0.18
Matches are distributed among these distances:
26 4 0.02
27 6 0.03
28 32 0.17
29 74 0.40
30 48 0.26
31 21 0.11
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.38
Consensus pattern (28 bp):
AAATTTTCCAAAATTCCATTTTGACCCT
Found at i:45799328 original size:58 final size:58
Alignment explanation
Indices: 45799226--45799544 Score: 337
Period size: 58 Copynumber: 5.5 Consensus size: 58
45799216 TTAACCTCAA
* *
45799226 AATTTT-CTAAAAATTA-CATTTTGACCCTTAAACTTTT-CAAAATTCCATTTTGACCCT
1 AATTTTACCAAAAATTACCATTTT-ACCCCTAAA-TTTTCCAAAATTCCATTTTGACCCT
* *
45799283 AATTTTACCAAAAATTACCATTTTACCCCTAAATTTTCCAAAATTCCATTTTTAGCCCC
1 AATTTTACCAAAAATTACCATTTTACCCCTAAATTTTCCAAAATTCCATTTTGA-CCCT
* * * ** *
45799342 GATTTCACCAAAAATTACCATTTCACCCCCGAACTTTCCAAAATTCCATTTTGACCCT
1 AATTTTACCAAAAATTACCATTTTACCCCTAAATTTTCCAAAATTCCATTTTGACCCT
* *
45799400 AATTTCACCAAAAATTACCATTTTACCCCTAAATTTTCCAAAATTCCATTTTTGACCTT
1 AATTTTACCAAAAATTACCATTTTACCCCTAAATTTTCCAAAATTCCA-TTTTGACCCT
* * * * * * *
45799459 GATTTTACC-AAAATTACCATTTCA-CCGTCGAACTTTCCAAAACTCCCGTTTTGACCC-
1 AATTTTACCAAAAATTACCATTTTACCCCT-AAATTTTCCAAAA-TTCCATTTTGACCCT
* *
45799516 AATTTTAAGC-AAAATTACAATTTTACCCC
1 AATTTT-ACCAAAAATTACCATTTTACCCC
45799545 CGGGTATCCA
Statistics
Matches: 221, Mismatches: 32, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
57 18 0.08
58 126 0.57
59 77 0.35
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (58 bp):
AATTTTACCAAAAATTACCATTTTACCCCTAAATTTTCCAAAATTCCATTTTGACCCT
Found at i:45799334 original size:117 final size:116
Alignment explanation
Indices: 45799255--45799544 Score: 352
Period size: 117 Copynumber: 2.5 Consensus size: 116
45799245 TTTGACCCTT
* *
45799255 AAACTTTTCAAAATTCCATTTTGACCCTAATTTTACCAAAAATTACCATTTTACCCCTAAATTTT
1 AAACTTTCCAAAATTCCATTTTGACCCTAATTTCACCAAAAATTACCATTTTACCCCTAAATTTT
* **
45799320 CCAAAATTCCATTTTTAGCCCCGATTTCACCAAAAATTACCATTTCACCCCC
66 CCAAAATTCCA-TTTTAACCCAAATTTCACCAAAAATTACCATTTCACCCCC
*
45799372 GAACTTTCCAAAATTCCATTTTGACCCTAATTTCACCAAAAATTACCATTTTACCCCTAAATTTT
1 AAACTTTCCAAAATTCCATTTTGACCCTAATTTCACCAAAAATTACCATTTTACCCCTAAATTTT
* *** * **
45799437 CCAAAATTCCATTTTTGACCTTGATTTTACC-AAAATTACCATTTCACCGTC
66 CCAAAATTCCA-TTTTAACCCAAATTTCACCAAAAATTACCATTTCACCCCC
* * * * * *
45799488 GAACTTTCCAAAACTCCCGTTTTGACCC-AATTTTAAGC-AAAATTACAATTTTACCCC
1 AAACTTTCCAAAA-TTCCATTTTGACCCTAA-TTTCACCAAAAATTACCATTTTACCCC
45799545 CGGGTATCCA
Statistics
Matches: 156, Mismatches: 15, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
116 51 0.33
117 105 0.67
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (116 bp):
AAACTTTCCAAAATTCCATTTTGACCCTAATTTCACCAAAAATTACCATTTTACCCCTAAATTTT
CCAAAATTCCATTTTAACCCAAATTTCACCAAAAATTACCATTTCACCCCC
Found at i:45811413 original size:92 final size:92
Alignment explanation
Indices: 45811252--45811984 Score: 1184
Period size: 92 Copynumber: 8.0 Consensus size: 92
45811242 AGATCAAAAT
* * * *
45811252 AACATCAATTCCTATCCTGTTAAAGTTGTAGTAAAGTTGAATAGCAAGTTTTTGTCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTGTCTCTCTGAAG
*
45811317 TTGTAGTAAGAGCAAGATGAAGCATCG
66 TTGTAGTAAGAGCAAGATGAAGCATCA
* *
45811344 AGCATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTGTCTCTCTGAAA
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTGTCTCTCTGAAG
45811409 TTGTAGTAAGAGCAAGATGAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
* * *
45811436 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAAGATGGATAGCAAGTATTTGTCTCTCTAAA
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGT-AAAGTTGGATAGCAAGTCTTTGTCTCTCTGAA
* *
45811501 ATTGTAGTAAGAGCAAGATGAAGAATCA
65 GTTGTAGTAAGAGCAAGATGAAGCATCA
*
45811529 AGCATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTGTCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTGTCTCTCTGAAG
* *
45811594 TTGTAATAAGAGTAAGATGAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
* *
45811621 AACATCAATTCCTATCCTCTTGAAGTTATAGTAAAGTTGGATAGCAAGTCTTTGTCTCTCTAAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTGTCTCTCTGAAG
45811686 TTGTAGTAAGAGCAAGATGAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
* * *
45811713 AACATCAATTCCTATCCTCTTAAAGTTCTAGTAAAGATGGATAGCAAGTCTTTGTCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTGTCTCTCTGAAG
*
45811778 TTGTAGTAAGAGCAAGATGAAACATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
45811805 AACATCAATAT-CTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTGTCTCTCTGAA
1 AACATCAAT-TCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTGTCTCTCTGAA
45811869 GTTGTAGTAAGAGCAAGATGAAGCATCA
65 GTTGTAGTAAGAGCAAGATGAAGCATCA
* * * *
45811897 AACGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAATG-AA-TCTTTATCTCTCTGA
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGAT-A-GCAAGTCTTTGTCTCTCTGA
45811960 AGTTGTAGTAAGAGCAAGATGAAGC
64 AGTTGTAGTAAGAGCAAGATGAAGC
45811985 CTAGATGTCA
Statistics
Matches: 598, Mismatches: 38, Indels: 10
0.93 0.06 0.02
Matches are distributed among these distances:
91 1 0.00
92 505 0.84
93 91 0.15
94 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (92 bp):
AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTGTCTCTCTGAAG
TTGTAGTAAGAGCAAGATGAAGCATCA
Found at i:45812262 original size:17 final size:16
Alignment explanation
Indices: 45812240--45812283 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
45812230 CCAAGCCATT
*
45812240 TTAAATTTATTTTAAAA
1 TTAAATTTAATTT-AAA
*
45812257 TTAAATTAAATTTAAA
1 TTAAATTTAATTTAAA
45812273 TTCAAATTTAA
1 TT-AAATTTAA
45812284 ATTATTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAATTTAATTTAAA
Found at i:45812281 original size:12 final size:11
Alignment explanation
Indices: 45812240--45812287 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
45812230 CCAAGCCATT
**
45812240 TTAAATTTATT
1 TTAAATTTAAA
*
45812251 TTAAAATTAAA
1 TTAAATTTAAA
45812262 TTAAATTTAAA
1 TTAAATTTAAA
45812273 TTCAAATTTAAA
1 TT-AAATTTAAA
45812285 TTA
1 TTA
45812288 TTATAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 21 0.66
12 11 0.34
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:45813034 original size:22 final size:20
Alignment explanation
Indices: 45813008--45813048 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
45812998 TATATTAAAC
45813008 GTATTAACTAAAGTTTTAAATG
1 GTATTAA-TAAA-TTTTAAATG
*
45813030 GTATTAATTAATTTTAAAT
1 GTATTAATAAATTTTAAAT
45813049 AAAAGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 3 0.17
22 7 0.39
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.46
Consensus pattern (20 bp):
GTATTAATAAATTTTAAATG
Found at i:45814227 original size:29 final size:30
Alignment explanation
Indices: 45814149--45814229 Score: 103
Period size: 29 Copynumber: 2.7 Consensus size: 30
45814139 TTGGATTGTC
45814149 CAAAAATTATATTTTGACCCC-AAAATTTT
1 CAAAAATTATATTTTGACCCCTAAAATTTT
* * * *
45814178 CTAAAAACTACATTTTAACCCCTAAACTTTT
1 C-AAAAATTATATTTTGACCCCTAAAATTTT
45814209 C-AAAATTATATTTTGACCCCT
1 CAAAAATTATATTTTGACCCCT
45814230 GATTTCACCA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 18 0.42
30 17 0.40
31 8 0.19
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.37
Consensus pattern (30 bp):
CAAAAATTATATTTTGACCCCTAAAATTTT
Found at i:45814340 original size:58 final size:59
Alignment explanation
Indices: 45814180--45814544 Score: 444
Period size: 58 Copynumber: 6.3 Consensus size: 59
45814170 AAAATTTTCT
* *
45814180 AAAAACTA-CATTTTAACCCCTAAACTTTTCAAAATT--ATATTTTGACCCCTGATTTCACC
1 AAAAATTACCATTTT-ACCCCTAAACTTTCCAAAATTCCAT-TTTTGACCCC-GATTTCACC
* *
45814239 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCCCGATTTTACC
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCCCGATTTCACC
* * * * *
45814298 AAAAATTACCA-TTTACCCCTAAATTTTCCAAAATTCCATTTTTGGCCCCAATTTGACT
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCCCGATTTCACC
* * * *
45814356 AAAAATTACCATTTCA-CCCTCGAACTTTCTAAAATTCCA-TTTTGACCTCGATTTCACC
1 AAAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTGACCCCGATTTCACC
*
45814414 AAAAATTACCATTTTACCCCTAAATTTTCCAAAATTCCATTTTTGACCCCGATTTCACC
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCCCGATTTCACC
* ** *
45814473 -AAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTCCCGTTTTGA-CCCAATTTCAACC
1 AAAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTGACCCCGATTTC-ACC
45814531 -AAAATTACCATTTT
1 AAAAATTACCATTTT
45814545 GCCTCCGAGT
Statistics
Matches: 268, Mismatches: 29, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
57 12 0.04
58 153 0.57
59 85 0.32
60 16 0.06
61 2 0.01
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCCCGATTTCACC
Found at i:45814360 original size:117 final size:115
Alignment explanation
Indices: 45814195--45814543 Score: 465
Period size: 117 Copynumber: 3.0 Consensus size: 115
45814185 CTACATTTTA
45814195 ACCCCTAAACTTTT-CAAAATT--ATATTTTGACCCCTGATTTCACCAAAAATTACCATTTTACC
1 ACCCCTAAA-TTTTCCAAAATTCCAT-TTTTGACCCC-GATTTCA-CAAAAATTACCATTTTACC
* * *
45814257 CCCAAACTTTCCAAAATTCCATTTTTGACCCCGATTTTACCAAAAATTACCATTT
62 CTCGAACTTTCCAAAATTCCA-TTTTGACCCCGATTTAACCAAAAATTACCATTT
* * * *
45814312 ACCCCTAAATTTTCCAAAATTCCATTTTTGGCCCCAATTTGACTAAAAATTACCATTTCACCCTC
1 ACCCCTAAATTTTCCAAAATTCCATTTTTGACCCCGATTTCAC-AAAAATTACCATTTTACCCTC
* * *
45814377 GAACTTTCTAAAATTCCATTTTGACCTCGATTTCACCAAAAATTACCATTTT
65 GAACTTTCCAAAATTCCATTTTGACCCCGATTTAACCAAAAATTACCA-TTT
*
45814429 ACCCCTAAATTTTCCAAAATTCCATTTTTGACCCCGATTTCACCAAAATTACCATTTTACCCTCG
1 ACCCCTAAATTTTCCAAAATTCCATTTTTGACCCCGATTTCACAAAAATTACCATTTTACCCTCG
* *
45814494 AACTTTCCAAAATTCCCGTTTTGA-CCCAATTTCAACC-AAAATTACCATTT
66 AACTTTCCAAAATT-CCATTTTGACCCCGATTT-AACCAAAAATTACCATTT
45814544 TGCCTCCGAG
Statistics
Matches: 206, Mismatches: 19, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
115 3 0.01
116 82 0.40
117 110 0.53
118 9 0.04
119 2 0.01
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (115 bp):
ACCCCTAAATTTTCCAAAATTCCATTTTTGACCCCGATTTCACAAAAATTACCATTTTACCCTCG
AACTTTCCAAAATTCCATTTTGACCCCGATTTAACCAAAAATTACCATTT
Found at i:45814515 original size:29 final size:29
Alignment explanation
Indices: 45814240--45814545 Score: 152
Period size: 29 Copynumber: 10.5 Consensus size: 29
45814230 GATTTCACCA
* *
45814240 AAAATTACCATTTT-ACCCCCAAACTTTCC
1 AAAATTACCATTTTGACCCTCGAA-TTTCC
*
45814269 AAAATT-CCATTTTTGACCC-CGATTTTACC
1 AAAATTACCA-TTTTGACCCTCGAATTT-CC
*
45814298 AAAAATTACCA-TTT-ACCC-CTAAATTTTCC
1 -AAAATTACCATTTTGACCCTC-GAA-TTTCC
* *
45814327 AAAATT-CCATTTTTGGCCC-C-AATTTGACTA
1 AAAATTACCA-TTTTGACCCTCGAATTT--C-C
* *
45814357 AAAATTACCA-TTTCACCCTCGAACTTTCT
1 AAAATTACCATTTTGACCCTCGAA-TTTCC
45814386 AAAATT-CCATTTTGA-CCTCG-ATTTCACC
1 AAAATTACCATTTTGACCCTCGAATTT--CC
*
45814414 AAAAATTACCATTTT-ACCC-CTAAATTTTCC
1 -AAAATTACCATTTTGACCCTC-GAA-TTTCC
45814444 AAAATT-CCATTTTTGACCC-CG-ATTTCACC
1 AAAATTACCA-TTTTGACCCTCGAATTT--CC
45814473 AAAATTACCATTTT-ACCCTCGAACTTTCC
1 AAAATTACCATTTTGACCCTCGAA-TTTCC
* *
45814502 AAAATTCCCGTTTTGA-CC-C-AATTTCAACC
1 AAAATTACCATTTTGACCCTCGAATTT---CC
45814531 AAAATTACCATTTTG
1 AAAATTACCATTTTG
45814546 CCTCCGAGTA
Statistics
Matches: 222, Mismatches: 17, Indels: 76
0.70 0.05 0.24
Matches are distributed among these distances:
26 6 0.03
27 12 0.05
28 37 0.17
29 103 0.46
30 46 0.21
31 12 0.05
32 6 0.03
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (29 bp):
AAAATTACCATTTTGACCCTCGAATTTCC
Found at i:45829012 original size:81 final size:81
Alignment explanation
Indices: 45828876--45829036 Score: 261
Period size: 81 Copynumber: 2.0 Consensus size: 81
45828866 ACTCATTGGT
* * *
45828876 CCATCACTTTTTTGCAAACCTTTTCTGCTCTTCAATGGTGACACCAATCTGTTAGCCAAAT-GGG
1 CCATCACTTCTTTGCAAACCTTTTCTGCTCTTCAATGGTGAAACCAATCTATTAGCC-AATCGGG
*
45828940 AAGGTGAAAATGATCTG
65 AAGGTGAAAACGATCTG
*
45828957 CCATCACTTCTTTGCAAACTTTTTCTGCTCTTCAATGGTGAAACCAATCTATTAGCCAATCGGGA
1 CCATCACTTCTTTGCAAACCTTTTCTGCTCTTCAATGGTGAAACCAATCTATTAGCCAATCGGGA
45829022 AGGTGAAAACGATCT
66 AGGTGAAAACGATCT
45829037 CCGTAGCTTC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
80 3 0.04
81 71 0.96
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (81 bp):
CCATCACTTCTTTGCAAACCTTTTCTGCTCTTCAATGGTGAAACCAATCTATTAGCCAATCGGGA
AGGTGAAAACGATCTG
Found at i:45830106 original size:8 final size:9
Alignment explanation
Indices: 45830094--45830122 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
45830084 CCAAAAAGCA
45830094 AAAAAAAAG
1 AAAAAAAAG
45830103 AAAAAAAAG
1 AAAAAAAAG
45830112 AAAAAAAAG
1 AAAAAAAAG
45830121 AA
1 AA
45830123 GTGACCAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:45830928 original size:14 final size:14
Alignment explanation
Indices: 45830909--45830938 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
45830899 AAAAATTAAG
45830909 ATGGAAGTAAAATA
1 ATGGAAGTAAAATA
45830923 ATGGAAGTAAAATA
1 ATGGAAGTAAAATA
45830937 AT
1 AT
45830939 ATGTTTCGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (14 bp):
ATGGAAGTAAAATA
Found at i:45831133 original size:20 final size:19
Alignment explanation
Indices: 45831067--45831142 Score: 71
Period size: 20 Copynumber: 3.9 Consensus size: 19
45831057 TTAAAAACTT
* *
45831067 TAATGTTATAAGAAATTAA
1 TAATTTTATAAGAATTTAA
* **
45831086 TAATTTTGTAAGAAATTTGG
1 TAATTTTATAAG-AATTTAA
*
45831106 TAAGTTTATAAGATATTTAA
1 TAATTTTATAAGA-ATTTAA
*
45831126 TAATTTTATAAAAATTT
1 TAATTTTATAAGAATTT
45831143 GAAGATTTTA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
19 15 0.34
20 29 0.66
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (19 bp):
TAATTTTATAAGAATTTAA
Found at i:45831693 original size:31 final size:31
Alignment explanation
Indices: 45831635--45831701 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 31
45831625 GGTTCAGGAT
45831635 AAAAATTACTAAAATTATGCATTAATAACATA
1 AAAAATTACTAAAATTATGCATTAATAA-ATA
*
45831667 AAAAATTACTAAAA-TAT-CATTAAATAATTA
1 AAAAATTACTAAAATTATGCATT-AATAAATA
45831697 AAAAA
1 AAAAA
45831702 ACCATAAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
30 11 0.33
31 8 0.24
32 14 0.42
ACGTcount: A:0.61, C:0.07, G:0.01, T:0.30
Consensus pattern (31 bp):
AAAAATTACTAAAATTATGCATTAATAAATA
Found at i:45841772 original size:159 final size:157
Alignment explanation
Indices: 45841485--45841802 Score: 519
Period size: 159 Copynumber: 2.0 Consensus size: 157
45841475 GCCAACCTAA
*
45841485 AAGGCGAGTATCAATCGCCACCTTCCGGCCAGATTCACACATGACAACCGCTCTGCAGCTCTACT
1 AAGGCGAGTATCAATCGCCACCTTCCGGCCAGATTCACACATGACAACCGCTCCGCAGCTCTACT
* *
45841550 TCTGGTTTCAACCATACCAGTACAATGGATAGACCGTCGTTGATGCAGAATCCGAGGAAGGCAAG
66 TCTGGTTTCAACCATACCAGTACAATCGATAGACCATCGTTGATGCAGAATCCGAGGAAGGCAAG
*
45841615 GTATTCAAGATTGTTTTCTCCATTGCC
131 GTATTCAAGATTGTTTTCTACATTGCC
* *
45841642 AAGGCGAGTATCAATCGCCACGTTCCGGCCAGATTCACAGATGACAACACCGCTCCGCAGCTCTA
1 AAGGCGAGTATCAATCGCCACCTTCCGGCCAGATTCACACATGAC-A-ACCGCTCCGCAGCTCTA
* * * **
45841707 CTTTTGGTTTCAACCATACCAGTACAATCGATAGACCATCGTTGATGCGGGATCCGTTGAAGGCA
64 CTTCTGGTTTCAACCATACCAGTACAATCGATAGACCATCGTTGATGCAGAATCCGAGGAAGGCA
45841772 AGGTATTCAAGATTGTTTTCTACATTGCC
129 AGGTATTCAAGATTGTTTTCTACATTGCC
45841801 AA
1 AA
45841803 AGCTACCTAA
Statistics
Matches: 148, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
157 43 0.29
158 1 0.01
159 104 0.70
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (157 bp):
AAGGCGAGTATCAATCGCCACCTTCCGGCCAGATTCACACATGACAACCGCTCCGCAGCTCTACT
TCTGGTTTCAACCATACCAGTACAATCGATAGACCATCGTTGATGCAGAATCCGAGGAAGGCAAG
GTATTCAAGATTGTTTTCTACATTGCC
Found at i:45843218 original size:11 final size:11
Alignment explanation
Indices: 45843188--45843235 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
45843178 CGGTTGAATC
45843188 GAATTTTTAAT
1 GAATTTTTAAT
*
45843199 --ATTTCTAAT
1 GAATTTTTAAT
45843208 GAATTTTTAAT
1 GAATTTTTAAT
45843219 GAATTATTTAATT
1 GAATT-TTTAA-T
45843232 GAAT
1 GAAT
45843236 CAAACGAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
9 8 0.26
11 13 0.42
12 5 0.16
13 5 0.16
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (11 bp):
GAATTTTTAAT
Found at i:45844545 original size:31 final size:31
Alignment explanation
Indices: 45844507--45844574 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
45844497 GTTTTGCTAA
45844507 ATATTTGGAGGATTTTGGAGATGGTATCTCC
1 ATATTTGGAGGATTTTGGAGATGGTATCTCC
45844538 ATATTTGGAGGATTTTGGAGATGGTATCTCC
1 ATATTTGGAGGATTTTGGAGATGGTATCTCC
45844569 ATATTT
1 ATATTT
45844575 ATGTGTTAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (31 bp):
ATATTTGGAGGATTTTGGAGATGGTATCTCC
Found at i:45856993 original size:25 final size:24
Alignment explanation
Indices: 45856954--45857000 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
45856944 TTTCATTTTT
* *
45856954 AAAAAAATATTTTTAAATACTAGA
1 AAAAAAATATATTTAAAAACTAGA
45856978 AAAAAAATATAATTTAAAAACTA
1 AAAAAAATAT-ATTTAAAAACTA
45857001 AATATAAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (24 bp):
AAAAAAATATATTTAAAAACTAGA
Found at i:45864667 original size:259 final size:260
Alignment explanation
Indices: 45864205--45864679 Score: 688
Period size: 261 Copynumber: 1.8 Consensus size: 260
45864195 CATGCAAACA
* * *
45864205 TGCAAAAATTAATTAAAGACTAGTTTAACAATGCAAAAATACTTTTGAGTAAAAGTTAAAAATTT
1 TGCAAAAATTAATTAAAGACTAGTTTAACAATGCAAAAACACTTTTAAGTAAAAATTAAAAATTT
* * *
45864270 TTTTGTTTTTGCTATTGATCAAAAAAGTGTTTTTTTCAAAATATTTTTAAAAAACTCAAAATTAT
66 TTTTGCTTCTGCTATTGATCAAAAAAGTG-TTTTTTCAAAATATTTTTAAAAAACTCAAAATCAT
*
45864335 CTTGTTTAATAATATTTTTATCTAAAAATATTTTTTGTCCCAAAAGTATTTTTGAAAAACCAAGC
130 CTTGTTTAACAATATTTTTATCTAAAAATATTTTTTGTCCCAAAAGTATTTTTGAAAAACCAAGC
45864400 CAAATTAGCTCTAATTTTTTTAAATATACTGGTGTAATTACATAGTAGTATCTGTTTATGTGAAC
195 CAAATTAGCTCTAATTTTTTTAAATATACTGGTGTAATTACATAGTAGTATCTGTTTATGTGAAC
45864465 G
260 G
* * * **
45864466 TGCAAAAATTAATTAAGGACTTGTTTAGCAATGCAAAAACACTTTTAAGTAAAAATTAAATTTTT
1 TGCAAAAATTAATTAAAGACTAGTTTAACAATGCAAAAACACTTTTAAGTAAAAATTAAAAATTT
* * *
45864531 TTTTGCTTCTGCTCTTGATCAAAAAAGTG-TTTTT-AAAGCAT-TTTTTGAAAAATTCAAAATCA
66 TTTTGCTTCTGCTATTGATCAAAAAAGTGTTTTTTCAAA--ATATTTTTAAAAAACTCAAAATCA
** * * *
45864593 TCTTGTTTAACAATATTTTTATCTAAAAATATTTTTTGTTTTCAAAAGTATTTTTGAGAAATCAT
129 TCTTGTTTAACAATATTTTTATCTAAAAATATTTTTTG-TCCCAAAAGTATTTTTGAAAAACCAA
**
45864658 G-GTAATTAGCTCTAATTTTTTT
193 GCCAAATTAGCTCTAATTTTTTT
45864680 TTTGAATATA
Statistics
Matches: 189, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
258 3 0.02
259 79 0.42
260 24 0.13
261 83 0.44
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (260 bp):
TGCAAAAATTAATTAAAGACTAGTTTAACAATGCAAAAACACTTTTAAGTAAAAATTAAAAATTT
TTTTGCTTCTGCTATTGATCAAAAAAGTGTTTTTTCAAAATATTTTTAAAAAACTCAAAATCATC
TTGTTTAACAATATTTTTATCTAAAAATATTTTTTGTCCCAAAAGTATTTTTGAAAAACCAAGCC
AAATTAGCTCTAATTTTTTTAAATATACTGGTGTAATTACATAGTAGTATCTGTTTATGTGAACG
Found at i:45864963 original size:14 final size:14
Alignment explanation
Indices: 45864946--45864979 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
45864936 AAAAAGTGTG
45864946 TTGAAAAAGGAATT
1 TTGAAAAAGGAATT
*
45864960 TTG-AAAAGTAATT
1 TTGAAAAAGGAATT
45864973 TTGAAAA
1 TTGAAAA
45864980 GTTTGGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (14 bp):
TTGAAAAAGGAATT
Found at i:45864981 original size:13 final size:13
Alignment explanation
Indices: 45864950--45864981 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
45864940 AGTGTGTTGA
*
45864950 AAAAGGAATTTTG
1 AAAAGTAATTTTG
45864963 AAAAGTAATTTTG
1 AAAAGTAATTTTG
45864976 AAAAGT
1 AAAAGT
45864982 TTGGTTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (13 bp):
AAAAGTAATTTTG
Found at i:45870055 original size:5 final size:5
Alignment explanation
Indices: 45870028--45870070 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
45870018 GAACATATAT
* *
45870028 TATCA TATCA GATCA TAACA TATCA TATCGA -ATCA TATCA TAT
1 TATCA TATCA TATCA TATCA TATCA TATC-A TATCA TATCA TAT
45870071 AATGTCCTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 1 0.03
5 30 0.94
6 1 0.03
ACGTcount: A:0.42, C:0.19, G:0.05, T:0.35
Consensus pattern (5 bp):
TATCA
Found at i:45870860 original size:36 final size:36
Alignment explanation
Indices: 45870778--45870866 Score: 115
Period size: 36 Copynumber: 2.5 Consensus size: 36
45870768 AACGATTATA
*
45870778 TGCCCCACACAAGCTACAAAATCACACACAGCCAAG
1 TGCCCCACACGAGCTACAAAATCACACACAGCCAAG
* * **
45870814 TGCCCCACACGGGCTACAAAATCACAGAGGGCCAAG
1 TGCCCCACACGAGCTACAAAATCACACACAGCCAAG
**
45870850 TGCCTTACACGAGCTAC
1 TGCCCCACACGAGCTAC
45870867 CCACATGGGC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.35, C:0.36, G:0.18, T:0.11
Consensus pattern (36 bp):
TGCCCCACACGAGCTACAAAATCACACACAGCCAAG
Found at i:45877942 original size:7 final size:7
Alignment explanation
Indices: 45877929--45877981 Score: 72
Period size: 7 Copynumber: 7.7 Consensus size: 7
45877919 AACGATCAAA
45877929 GTCAACG
1 GTCAACG
*
45877936 GTTAACG
1 GTCAACG
*
45877943 GTCAA-A
1 GTCAACG
45877949 GTCAACG
1 GTCAACG
45877956 GTCAACG
1 GTCAACG
45877963 GTCAACG
1 GTCAACG
*
45877970 GTCAACA
1 GTCAACG
45877977 GTCAA
1 GTCAA
45877982 TCAACACCGG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
6 5 0.12
7 35 0.88
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:45877947 original size:20 final size:20
Alignment explanation
Indices: 45877917--45877981 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
45877907 TTCGAAAAAA
*
45877917 TCAACGATCAAAGTCAACGG
1 TCAACGGTCAAAGTCAACGG
*
45877937 TTAACGGTCAAAGTCAACGG
1 TCAACGGTCAAAGTCAACGG
* *
45877957 TCAACGGTCAACGGTCAACAG
1 TCAACGGTCAA-AGTCAACGG
45877978 TCAA
1 TCAA
45877982 TCAACACCGG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 28 0.72
21 11 0.28
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.17
Consensus pattern (20 bp):
TCAACGGTCAAAGTCAACGG
Done.