Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_pilon, whole genome shotgun sequence
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: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 91
Found at i:5311491 original size:21 final size:21
Alignment explanation
Indices: 5311458--5311497 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
5311448 TTTGAGTAGA
*
5311458 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
5311480 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
5311498 AGATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:5313781 original size:22 final size:22
Alignment explanation
Indices: 5313755--5313801 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
5313745 GTTTAGTTTG
5313755 AAAAATTCAATTTCTTAATAAA
1 AAAAATTCAATTTCTTAATAAA
*
5313777 AAAAATTCAATTTCTTAATGAA
1 AAAAATTCAATTTCTTAATAAA
5313799 AAA
1 AAA
5313802 GGGGGAGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAAATTCAATTTCTTAATAAA
Found at i:5314058 original size:31 final size:31
Alignment explanation
Indices: 5313960--5314050 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
5313950 CAATTTAAGG
5313960 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
5313991 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
5314022 CAAAATGG-TTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
5314051 TTCAAAATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 10 0.17
31 39 0.65
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.42
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:5314257 original size:21 final size:21
Alignment explanation
Indices: 5314231--5314272 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5314221 TATTGAATAT
*
5314231 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
5314252 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
5314273 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:5314333 original size:21 final size:21
Alignment explanation
Indices: 5314300--5314339 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
5314290 TTTGAGTAGA
*
5314300 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
5314322 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
5314340 AGATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:5316610 original size:22 final size:22
Alignment explanation
Indices: 5316584--5316630 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
5316574 GTTTAGTTTG
5316584 AAAAATTCAATTTCTTAATAAA
1 AAAAATTCAATTTCTTAATAAA
*
5316606 AAAAATTCAATTTCTTAATGAA
1 AAAAATTCAATTTCTTAATAAA
5316628 AAA
1 AAA
5316631 GGGGGAGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAAATTCAATTTCTTAATAAA
Found at i:5316878 original size:31 final size:30
Alignment explanation
Indices: 5316781--5316870 Score: 164
Period size: 31 Copynumber: 3.0 Consensus size: 30
5316771 CAATTTAAGG
5316781 CAAAATGGTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTGGACTTGAATTGAATTTA
5316811 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGG-TTTTGGACTTGAATTGAATTTA
5316842 CAAAATGGTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTGGACTTGAATTGAATTTA
5316871 TTCAAAATTT
Statistics
Matches: 59, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
29 11 0.19
30 18 0.31
31 30 0.51
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.41
Consensus pattern (30 bp):
CAAAATGGTTTTGGACTTGAATTGAATTTA
Found at i:5317079 original size:21 final size:21
Alignment explanation
Indices: 5317053--5317094 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5317043 TATTGAATAT
*
5317053 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
5317074 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
5317095 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:5317155 original size:21 final size:21
Alignment explanation
Indices: 5317122--5317161 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
5317112 TTTTGAGTAG
*
5317122 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
5317144 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
5317162 AGATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:5317437 original size:33 final size:33
Alignment explanation
Indices: 5317370--5317439 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
5317360 TTTTGTAAAG
** *
5317370 GGGAAAGGTTCTAGCTTAGCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCGTAAAAAAACTA
*
5317403 GGGAAAGGTTCTAGTTTAGCCCG-AAAAAAACTA
1 GGGAAAGGTTCTAGCTTAG-CCGTAAAAAAACTA
5317436 GGGA
1 GGGA
5317440 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 29 0.91
34 3 0.09
ACGTcount: A:0.34, C:0.14, G:0.30, T:0.21
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTTAGCCGTAAAAAAACTA
Found at i:5319400 original size:23 final size:22
Alignment explanation
Indices: 5319372--5319419 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
5319362 GTTTAGTTTG
5319372 AAAAAATTCAATTTCTTAATAAA
1 AAAAAATTCAA-TTCTTAATAAA
*
5319395 AAAAAATTCAATTCTTAATGAA
1 AAAAAATTCAATTCTTAATAAA
5319417 AAA
1 AAA
5319420 GGGGGAGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAAAATTCAATTCTTAATAAA
Found at i:5319610 original size:31 final size:31
Alignment explanation
Indices: 5319575--5319671 Score: 164
Period size: 31 Copynumber: 3.2 Consensus size: 31
5319565 TAAATTAAGG
5319575 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
5319606 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
5319637 CAAAATGG--TTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
5319665 TCAAAAT
1 -CAAAAT
5319672 TTACAAAAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
28 11 0.17
29 15 0.23
31 39 0.60
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:5319877 original size:20 final size:21
Alignment explanation
Indices: 5319847--5319887 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
5319837 ATTTGAATAT
*
5319847 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
5319868 TATG-AGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
5319888 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:5319949 original size:21 final size:21
Alignment explanation
Indices: 5319916--5319955 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
5319906 TTTGAGTAGA
*
5319916 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
5319938 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
5319956 AGATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:5323045 original size:15 final size:15
Alignment explanation
Indices: 5323027--5323144 Score: 68
Period size: 15 Copynumber: 7.9 Consensus size: 15
5323017 GGCTAATGTC
5323027 AAAAAAGAAAAAAAT
1 AAAAAAGAAAAAAAT
*
5323042 AAAAAATAAAAAAAT
1 AAAAAAGAAAAAAAT
*
5323057 AAAACAA-AACAAAAT
1 AAAA-AAGAAAAAAAT
* *
5323072 --AAAA-TAAAAGAT
1 AAAAAAGAAAAAAAT
5323084 AAAAAAGAAAAAGAA-
1 AAAAAAGAAAAA-AAT
* *
5323099 AAAGAA-AACAAAAT
1 AAAAAAGAAAAAAAT
*
5323113 AAAATAATGGAAAATAAT
1 AAAA-AA--GAAAAAAAT
*
5323131 AAATAAGATAAAAA
1 AAAAAAGA-AAAAA
5323145 CAGAAATAGA
Statistics
Matches: 78, Mismatches: 14, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
12 7 0.09
13 4 0.05
14 11 0.14
15 38 0.49
16 7 0.09
17 2 0.03
18 9 0.12
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.11
Consensus pattern (15 bp):
AAAAAAGAAAAAAAT
Found at i:5323095 original size:41 final size:42
Alignment explanation
Indices: 5323036--5323119 Score: 118
Period size: 41 Copynumber: 2.0 Consensus size: 42
5323026 CAAAAAAGAA
5323036 AAAAATAAAAAATAAAAAA-ATAAAACAAAACAAAATAAAATA
1 AAAAATAAAAAATAAAAAAGA-AAAACAAAACAAAATAAAATA
* * *
5323078 AAAGATAAAAAA-GAAAAAGAAAAAGAAAACAAAATAAAATA
1 AAAAATAAAAAATAAAAAAGAAAAACAAAACAAAATAAAATA
5323119 A
1 A
5323120 TGGAAAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 26 0.68
42 12 0.32
ACGTcount: A:0.82, C:0.04, G:0.05, T:0.10
Consensus pattern (42 bp):
AAAAATAAAAAATAAAAAAGAAAAACAAAACAAAATAAAATA
Found at i:5323112 original size:56 final size:55
Alignment explanation
Indices: 5323027--5323168 Score: 151
Period size: 57 Copynumber: 2.5 Consensus size: 55
5323017 GGCTAATGTC
* *
5323027 AAAAAAGAAAAAAATAAAAAATAAAAAAATAAAACAAAACAAAATAA-AATAAAAGAT
1 AAAAAAGAAAAAGA-AAAAAA-AACAAAATAAAACAAAACAAAATAATAA-AAAAGAT
* *** *
5323084 AAAAAAGAAAAAGAAAAAGAAAACAAAATAAAATAATGGAAAATAATAAATAAGAT
1 AAAAAAGAAAAAGAAAAA-AAAACAAAATAAAACAAAACAAAATAATAAAAAAGAT
*
5323140 AAAAACAGAAATAGAAACAAAAAACAAAA
1 AAAAA-AGAAAAAGAAA-AAAAAACAAAA
5323169 AGCAAAACAA
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
56 35 0.48
57 36 0.49
58 2 0.03
ACGTcount: A:0.79, C:0.04, G:0.07, T:0.10
Consensus pattern (55 bp):
AAAAAAGAAAAAGAAAAAAAAACAAAATAAAACAAAACAAAATAATAAAAAAGAT
Found at i:5323164 original size:19 final size:18
Alignment explanation
Indices: 5323140--5323182 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
5323130 TAAATAAGAT
5323140 AAAAACAGAAATAG-AAACA
1 AAAAACA-AAA-AGAAAACA
5323159 AAAAACAAAAAGCAAAACA
1 AAAAACAAAAAG-AAAACA
5323178 AAAAA
1 AAAAA
5323183 TATATAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.09
18 3 0.14
19 17 0.77
ACGTcount: A:0.79, C:0.12, G:0.07, T:0.02
Consensus pattern (18 bp):
AAAAACAAAAAGAAAACA
Found at i:5323183 original size:56 final size:52
Alignment explanation
Indices: 5323028--5323191 Score: 142
Period size: 57 Copynumber: 3.1 Consensus size: 52
5323018 GCTAATGTCA
* * *
5323028 AAAAAGA-AAAAAATAAAAA-ATAAAAAAA-TAAAACAAAACAAAATAA-AAT
1 AAAAAGATAAAAAAGAAAAAGAAAAAAAAACAAAAACAAAACAAAA-AATAAT
* *
5323077 -AAAAGATAAAAAAGAAAAAGAAAAAGAAAAC-AAAATAAAATAATGGAAAATAAT
1 AAAAAGATAAAAAAGAAAAAGAAAAA-AAAACAAAAACAAAACAA---AAAATAAT
*
5323131 AAATAAGATAAAAACAGAAATAGAAACAAAAAACAAAAAGCAAAACAAAAAATATAT
1 AAA-AAGATAAAAA-AGAAAAAGAAA-AAAAAACAAAAA-CAAAACAAAAAATA-AT
5323188 AAAA
1 AAAA
5323192 GAAATGTTAG
Statistics
Matches: 93, Mismatches: 7, Indels: 23
0.76 0.06 0.19
Matches are distributed among these distances:
48 6 0.06
49 11 0.12
50 4 0.04
51 14 0.15
53 2 0.02
54 5 0.05
55 2 0.02
56 17 0.18
57 20 0.22
58 6 0.06
59 6 0.06
ACGTcount: A:0.78, C:0.05, G:0.07, T:0.10
Consensus pattern (52 bp):
AAAAAGATAAAAAAGAAAAAGAAAAAAAAACAAAAACAAAACAAAAAATAAT
Found at i:5324190 original size:12 final size:12
Alignment explanation
Indices: 5324173--5324207 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
5324163 CCTTAATCAA
5324173 AAAAAAGAAAAG
1 AAAAAAGAAAAG
5324185 AAAAAAGAAAAG
1 AAAAAAGAAAAG
5324197 AAAAAAGAAAA
1 AAAAAAGAAAA
5324208 AAATATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:5324221 original size:14 final size:15
Alignment explanation
Indices: 5324204--5324256 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
5324194 AAGAAAAAAG
5324204 AAAAAAAT-ATTAAT
1 AAAAAAATAATTAAT
* *
5324218 AAAATAATAAATAAT
1 AAAAAAATAATTAAT
*
5324233 AAATAAATAATATAAT
1 AAAAAAATAAT-TAAT
*
5324249 ATAAAAAT
1 AAAAAAAT
5324257 CATTTTTAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
14 7 0.23
15 13 0.43
16 10 0.33
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAAAAATAATTAAT
Found at i:5324237 original size:11 final size:12
Alignment explanation
Indices: 5324215--5324249 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
5324205 AAAAAATATT
*
5324215 AATAAAATAATA
1 AATAATATAATA
5324227 AATAATA-AATA
1 AATAATATAATA
5324238 AATAATATAATA
1 AATAATATAATA
5324250 TAAAAATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AATAATATAATA
Found at i:5324240 original size:18 final size:18
Alignment explanation
Indices: 5324209--5324253 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
5324199 AAAAGAAAAA
*
5324209 AATATTAATAAAATAATA-
1 AATATAAAT-AAATAATAT
5324227 AATAATAAATAAATAATAT
1 AAT-ATAAATAAATAATAT
5324246 AATATAAA
1 AATATAAA
5324254 AATCATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AATATAAATAAATAATAT
Found at i:5324713 original size:2 final size:2
Alignment explanation
Indices: 5324706--5324781 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
5324696 GATATTTAAG
5324706 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5324748 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5324782 CATGCTTAGG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5325023 original size:24 final size:25
Alignment explanation
Indices: 5324989--5325054 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 25
5324979 AAGGCTAATG
*
5324989 TCAAAAAAAAATTAAAAAAAT-AAAA
1 TCAAAAGAAAA-TAAAAAAATGAAAA
*
5325014 -CAAAAGAAAAT-AAAAGATGAAAA
1 TCAAAAGAAAATAAAAAAATGAAAA
*
5325037 TAAAAAGAAAATAAAAAA
1 TCAAAAGAAAATAAAAAA
5325055 TAATGGAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 6 0.18
23 5 0.15
24 19 0.56
25 4 0.12
ACGTcount: A:0.79, C:0.03, G:0.06, T:0.12
Consensus pattern (25 bp):
TCAAAAGAAAATAAAAAAATGAAAA
Found at i:5325054 original size:18 final size:17
Alignment explanation
Indices: 5325033--5325071 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
5325023 ATAAAAGATG
5325033 AAAATAAAAAGAAAATAA
1 AAAAT-AAAAGAAAATAA
**
5325051 AAAATAATGGAAAATAA
1 AAAATAAAAGAAAATAA
5325068 AAAA
1 AAAA
5325072 AGAAAAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (17 bp):
AAAATAAAAGAAAATAA
Found at i:5325091 original size:28 final size:26
Alignment explanation
Indices: 5325005--5325091 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 26
5324995 AAAAATTAAA
* *
5325005 AAAATAAAACAAAAGAAAATAAAAGATG
1 AAAAT-AAA-AAAAGAAAAAAAAAAATG
*
5325033 AAAATAAAAAGAA-AATAAAAAATAATGG
1 AAAATAAAAA-AAGAA-AAAAAAAAAT-G
5325061 AAAATAAAAAAAGAAAAAACAAAAATAG
1 AAAATAAAAAAAGAAAAAA-AAAAAT-G
5325089 AAA
1 AAA
5325092 CAAAAAACAA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
26 4 0.08
27 18 0.37
28 27 0.55
ACGTcount: A:0.78, C:0.02, G:0.09, T:0.10
Consensus pattern (26 bp):
AAAATAAAAAAAGAAAAAAAAAAATG
Found at i:5326540 original size:33 final size:34
Alignment explanation
Indices: 5326492--5326561 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 34
5326482 GCTTTCAAAT
5326492 AAATTATTTTCAAAACCATATAAAATATAATTTC
1 AAATTATTTTCAAAACCATATAAAATATAATTTC
* * * * *
5326526 AAATT-TTTTTAAAACTATTTAATATATATTTTC
1 AAATTATTTTCAAAACCATATAAAATATAATTTC
5326559 AAA
1 AAA
5326562 AATTTTCCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (34 bp):
AAATTATTTTCAAAACCATATAAAATATAATTTC
Found at i:5326731 original size:72 final size:74
Alignment explanation
Indices: 5326636--5326773 Score: 199
Period size: 72 Copynumber: 1.9 Consensus size: 74
5326626 ATATTTTTTC
* * *
5326636 AAAAATGTTTTCAAAATTATATAATATA-TGTCTTC-AAAATATTTTCAAAACCATATAATATAT
1 AAAAATGTTTACAAAACTATATAATATACTATCTTCAAAAATATTTTCAAAACCATATAATATAT
5326699 TTTCAAAAA
66 TTTCAAAAA
* **
5326708 AAAAATGTTTACAAAACTATATAATATATCTATTTTCAAAAATATTTTCAAAATTATATAATATA
1 AAAAATGTTTACAAAACTATATAATATA-CTATCTTCAAAAATATTTTCAAAACCATATAATATA
5326773 T
65 T
5326774 ATTCTCGAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
72 26 0.46
74 5 0.09
75 26 0.46
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (74 bp):
AAAAATGTTTACAAAACTATATAATATACTATCTTCAAAAATATTTTCAAAACCATATAATATAT
TTTCAAAAA
Found at i:5326802 original size:36 final size:35
Alignment explanation
Indices: 5326625--5326811 Score: 144
Period size: 36 Copynumber: 5.2 Consensus size: 35
5326615 ATATATTATG
* * ** *
5326625 TATATTTTTTCAAAAATGTTTTCAAAATTATATAA
1 TATATATTCTCAAAAACATTTTCAAAACTATATAA
* * *
5326660 TATAT-GTCTTC-AAAATATTTTCAAAACCATATAA
1 TATATATTC-TCAAAAACATTTTCAAAACTATATAA
* ** *
5326694 TATATTTTCAAAAAAAAAATGTTTACAAAACTATATAA
1 TATATATTC-TCAAAAACAT-TTT-CAAAACTATATAA
* * *
5326732 TATATCTATTTTCAAAAATATTTTCAAAATTATATAA
1 TATA--TATTCTCAAAAACATTTTCAAAACTATATAA
* *
5326769 TATATATTCTCGAAAACCATTTTCAAAGCTATATAA
1 TATATATTCTC-AAAAACATTTTCAAAACTATATAA
5326805 TATATAT
1 TATATAT
5326812 ATTTTTGAAA
Statistics
Matches: 122, Mismatches: 22, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
34 26 0.21
35 15 0.12
36 33 0.27
37 19 0.16
38 19 0.16
39 7 0.06
40 3 0.02
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (35 bp):
TATATATTCTCAAAAACATTTTCAAAACTATATAA
Found at i:5326810 original size:75 final size:74
Alignment explanation
Indices: 5326636--5326826 Score: 192
Period size: 75 Copynumber: 2.6 Consensus size: 74
5326626 ATATTTTTTC
* * * *
5326636 AAAAATGTTTTCAAAATTATATAATATAT-GTCTTC-AAAATATTTTCAAAACCATATAATATAT
1 AAAAATGTTTACAAAACTATATAATATATATTTTTCAAAAATATTTTCAAAACCATATAATATAT
*
5326699 TTTCAAAAA
66 ATTCAAAAA
* **
5326708 AAAAATGTTTACAAAACTATATAATATATCTATTTTCAAAAATATTTTCAAAATTATATAATATA
1 AAAAATGTTTACAAAACTATATAATATATAT-TTTTCAAAAATATTTTCAAAACCATATAATATA
***
5326773 TATTCTCGAA
65 TATTCAAAAA
** * *
5326783 AACCAT-TTT-CAAAGCTATATAATATATATATTTTTGAAAAATAT
1 AAAAATGTTTACAAAACTATAT-A-ATATATATTTTTCAAAAATAT
5326827 ATATTATATG
Statistics
Matches: 99, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
72 27 0.27
73 10 0.10
74 20 0.20
75 42 0.42
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.40
Consensus pattern (74 bp):
AAAAATGTTTACAAAACTATATAATATATATTTTTCAAAAATATTTTCAAAACCATATAATATAT
ATTCAAAAA
Found at i:5326827 original size:24 final size:23
Alignment explanation
Indices: 5326804--5326846 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5326794 AAGCTATATA
*
5326804 ATATA-TATAT-TTTTGAAAAAT
1 ATATATTATATGTTTTCAAAAAT
5326825 ATATATTATATGTTTTCAAAAA
1 ATATATTATATGTTTTCAAAAA
5326847 ACCGTTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 5 0.26
23 9 0.47
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (23 bp):
ATATATTATATGTTTTCAAAAAT
Found at i:5326847 original size:24 final size:21
Alignment explanation
Indices: 5326804--5326847 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5326794 AAGCTATATA
*
5326804 ATATATATATTTTTGAAAAAT
1 ATATATATATTTTTAAAAAAT
5326825 ATATATTATATGTTTTCAAAAAA
1 ATATA-TATAT-TTTT-AAAAAA
5326848 CCGTTTTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 5 0.26
23 4 0.21
24 5 0.26
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (21 bp):
ATATATATATTTTTAAAAAAT
Found at i:5329240 original size:42 final size:42
Alignment explanation
Indices: 5329173--5329253 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
5329163 TCAAAATGAT
*
5329173 TTTTTATAGCTTATGCAACATGTATTGAA-TTTGGAGGATCAC
1 TTTTTATAGCTTATGCAACAAGTATTGAAGTTT-GAGGATCAC
* *
5329215 TTTTTATAGCTTATGTAATAAGTATTGAAGTTTGAGGAT
1 TTTTTATAGCTTATGCAACAAGTATTGAAGTTTGAGGAT
5329254 GATTTATGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 32 0.91
43 3 0.09
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (42 bp):
TTTTTATAGCTTATGCAACAAGTATTGAAGTTTGAGGATCAC
Found at i:5330918 original size:54 final size:54
Alignment explanation
Indices: 5330853--5331310 Score: 607
Period size: 54 Copynumber: 8.5 Consensus size: 54
5330843 CAATACGATC
* * * * ** * * *
5330853 ATTCATAAACATATTATGAAATCCGTGGTTTGCACACACAGTGTCAAAATGGTT
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCGAAACGGTT
* * *
5330907 ATTCATCAACATATGATGAATTCCGT-ACATTGCACACTTAGTGTCGAAATGGTT
1 ATTCATCAACATATGATGAATTCCGTGA-TTTGCACACTTAGTGCCGAAACGGTT
* * *
5330961 ATTCATCAACATATGATGAATTCTGTGATTTGCATACTTAGTGCCAAAACGGTT
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCGAAACGGTT
* *
5331015 ATTCATCAACATATGATGAATTCCAT-ACTTTGCACACTTAGTGCCGAAATGGTT
1 ATTCATCAACATATGATGAATTCCGTGA-TTTGCACACTTAGTGCCGAAACGGTT
*
5331069 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCGAAACAGTT
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCGAAACGGTT
*
5331123 ATTCATCAACACATGATGAATTCCGTGATTTGCACACTTAGTGCCGAAACGGTT
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCGAAACGGTT
* * * *
5331177 ATTCATCAACATATGATGAATTACGT-ACTTTGCACACTTAATACCGAAACAGTT
1 ATTCATCAACATATGATGAATTCCGTGA-TTTGCACACTTAGTGCCGAAACGGTT
* ** * * *
5331231 ATTCATCAACATATGATTAATTTTGTGATTTGCACACTTAGTGTCAAAACGATT
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCGAAACGGTT
5331285 ATTCATCAACATATGATGAATTCCGT
1 ATTCATCAACATATGATGAATTCCGT
5331311 TAGTGCCTAT
Statistics
Matches: 357, Mismatches: 41, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
53 2 0.01
54 352 0.99
55 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (54 bp):
ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCGAAACGGTT
Found at i:5339550 original size:54 final size:54
Alignment explanation
Indices: 5339468--5339855 Score: 512
Period size: 54 Copynumber: 7.2 Consensus size: 54
5339458 TGATCTATAT
* *
5339468 ACTTAGTGCCGAAACAGTTATTCATCAACATATAATGAATTTCGT-ACTTTGCAC
1 ACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGA-TTTGCAC
* * * *
5339522 ACTTAGTGCCAAAACGATTATTCATCAACATGTGATGAA-TTCTGTGATTTCCAC
1 ACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTC-GTGATTTGCAC
* ** * *
5339576 ACTTAGTGTCGAAATAGTTATGCATCAACATATGACGAATTTCGTGATTTGCAC
1 ACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGATTTGCAC
** * *
5339630 ACTTAGTGTTGAAACGGTTATTCATCAACATATGTTGAATTCCGT-ACTTTGCAC
1 ACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGA-TTTGCAC
*
5339684 ACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAACTTCGTGATTTGCAC
1 ACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGATTTGCAC
* *
5339738 ACTTAGTGCCGAAACGGTTTTTCATCAACATATGATGAACTTCGTGATTTGCAC
1 ACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGATTTGCAC
* * ** *
5339792 ACTTAGTGCTGAAACGGTTATTCATCAATATATGATGAATAACGTGAATTGCAC
1 ACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGATTTGCAC
*
5339846 ATTTAGTGCC
1 ACTTAGTGCC
5339856 TATTTGGTAA
Statistics
Matches: 292, Mismatches: 37, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
53 4 0.01
54 283 0.97
55 5 0.02
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (54 bp):
ACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGATTTGCAC
Found at i:5347517 original size:16 final size:16
Alignment explanation
Indices: 5347496--5347534 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
5347486 GAAAAAAAGG
5347496 AAAAAAATAGTAGTTCA
1 AAAAAAAT-GTAGTTCA
*
5347513 AAAAAAATGTTGTTCA
1 AAAAAAATGTAGTTCA
5347529 AAAAAA
1 AAAAAA
5347535 GAGAAAAGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (16 bp):
AAAAAAATGTAGTTCA
Found at i:5352584 original size:16 final size:16
Alignment explanation
Indices: 5352555--5352591 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
5352545 TGTTCTTTTG
*
5352555 TTGTGTTATGTTCATT
1 TTGTGATATGTTCATT
*
5352571 TTGTGATATTTTCATT
1 TTGTGATATGTTCATT
5352587 TTGTG
1 TTGTG
5352592 TTAATTAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.14, C:0.05, G:0.19, T:0.62
Consensus pattern (16 bp):
TTGTGATATGTTCATT
Found at i:5356357 original size:25 final size:25
Alignment explanation
Indices: 5356323--5356370 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5356313 CGGGCTGACG
*
5356323 GTCGGCGAGGGCTAGACGGCCGACA
1 GTCGGCGAGGGCCAGACGGCCGACA
* *
5356348 GTCGGTGAGGTCCAGACGGCCGA
1 GTCGGCGAGGGCCAGACGGCCGA
5356371 AGAGGGGCCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.19, C:0.27, G:0.44, T:0.10
Consensus pattern (25 bp):
GTCGGCGAGGGCCAGACGGCCGACA
Found at i:5358135 original size:53 final size:53
Alignment explanation
Indices: 5358071--5358179 Score: 164
Period size: 53 Copynumber: 2.1 Consensus size: 53
5358061 CTATGTGTAC
** *
5358071 TTTCGACACTATATGTGCATTCATGGTATTCATAATGAGTTTGTGAATTACCA
1 TTTCGACACTATATGTGCACCCATGATATTCATAATGAGTTTGTGAATTACCA
* * *
5358124 TTTCGGCACTATGTGTGCACCCATGATATTCATAATGAGTTTGTGAATTTCCA
1 TTTCGACACTATATGTGCACCCATGATATTCATAATGAGTTTGTGAATTACCA
5358177 TTT
1 TTT
5358180 TGTTACCTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (53 bp):
TTTCGACACTATATGTGCACCCATGATATTCATAATGAGTTTGTGAATTACCA
Found at i:5363492 original size:76 final size:76
Alignment explanation
Indices: 5363401--5363541 Score: 255
Period size: 76 Copynumber: 1.9 Consensus size: 76
5363391 ATACATAAAA
* *
5363401 ATTTGTCTCGCTTGAGACATTTTTTACTCGAAAGAAGACATTTCATTTCACTCAAGATTGTTTTT
1 ATTTGCCTCGCTTGAGACAGTTTTTACTCGAAAGAAGACATTTCATTTCACTCAAGATTGTTTTT
5363466 CTTAAAACTAG
66 CTTAAAACTAG
*
5363477 ATTTGCCTCGCTTGAGACAGTTTTTACTCGAAAGAAGACATTTCATTTCACTCAGGATTGTTTTT
1 ATTTGCCTCGCTTGAGACAGTTTTTACTCGAAAGAAGACATTTCATTTCACTCAAGATTGTTTTT
5363542 AAAACATGAT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 62 1.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (76 bp):
ATTTGCCTCGCTTGAGACAGTTTTTACTCGAAAGAAGACATTTCATTTCACTCAAGATTGTTTTT
CTTAAAACTAG
Found at i:5363594 original size:39 final size:39
Alignment explanation
Indices: 5363551--5363805 Score: 314
Period size: 39 Copynumber: 6.6 Consensus size: 39
5363541 TAAAACATGA
* * * *
5363551 TTTATCTTGCTTTACATAGTTTCACTCGAAACAAAAGAT
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGAT
* * *
5363590 TTTATCTCGCTTGAAATAGTTTTACTCGAAATAGAAGAT
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGAT
*
5363629 TTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGAT
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGAT
* * * *
5363668 TTTGTCTCGCTTGAGATAGTTTCACTAGAAAGAGAATAT
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGAT
* * ** * *
5363707 TTTATTTCACTCAAGATAGTTTCACTCGAAAGAAAAGAT
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGAT
*
5363746 TTTATCTCTCTTGAGATAGTTTCACTCGAAACAGAAGA-
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGAT
* *
5363784 TTTATCTCACTTGAGATTGTTT
1 TTTATCTCGCTTGAGATAGTTT
5363806 TTCTTAAAAC
Statistics
Matches: 185, Mismatches: 31, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
38 20 0.11
39 165 0.89
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (39 bp):
TTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGAT
Found at i:5363884 original size:59 final size:59
Alignment explanation
Indices: 5363821--5363935 Score: 180
Period size: 59 Copynumber: 1.9 Consensus size: 59
5363811 AAAACAAACT
* *
5363821 ACGCCTCACTAGA-GAGATTAATATTTCCTTTGCT-AGATTCACAACACTTCGAATCAGTA
1 ACGCCCCACTAGAGGAG-TTAACATTTCCTTTGCTCA-ATTCACAACACTTCGAATCAGTA
5363880 ACGCCCCACTAGAGGAGTTAACATTTCCTTTGCTCAATTCACAACACTTCGAATCA
1 ACGCCCCACTAGAGGAGTTAACATTTCCTTTGCTCAATTCACAACACTTCGAATCA
5363936 ACTTAAGTCC
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
59 48 0.92
60 4 0.08
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (59 bp):
ACGCCCCACTAGAGGAGTTAACATTTCCTTTGCTCAATTCACAACACTTCGAATCAGTA
Found at i:5370212 original size:39 final size:39
Alignment explanation
Indices: 5370169--5370399 Score: 304
Period size: 39 Copynumber: 6.0 Consensus size: 39
5370159 CATCAGGTGG
* * * **
5370169 TCTTCCCAAGGAGTTTTGACAATACTAGATGTTGTATTA
1 TCTTCCTAAGGAGTTTTGACAAGACTAGATATTGGGTTA
* * *
5370208 TCTTCCAAAGGAGTTTTAACAAGACTAGATATTGGGTTG
1 TCTTCCTAAGGAGTTTTGACAAGACTAGATATTGGGTTA
* * *
5370247 TCTTCTTAAGGAGTTTTGAGAAGATTAGATATTGGGTTA
1 TCTTCCTAAGGAGTTTTGACAAGACTAGATATTGGGTTA
*
5370286 TCTTCCTAAGGAGTTTTGACAAGACTAGATATTGGGTAA
1 TCTTCCTAAGGAGTTTTGACAAGACTAGATATTGGGTTA
**
5370325 TCTT-CTAAGGAGTTTTGACAAGACTAGATATTGGGCAA
1 TCTTCCTAAGGAGTTTTGACAAGACTAGATATTGGGTTA
* *
5370363 TCTT-CTAAGGAGTTTTGACAAGACTAGTTATTTGGTT
1 TCTTCCTAAGGAGTTTTGACAAGACTAGATATTGGGTT
5370400 GAAATGGCCT
Statistics
Matches: 170, Mismatches: 22, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
38 66 0.39
39 104 0.61
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.37
Consensus pattern (39 bp):
TCTTCCTAAGGAGTTTTGACAAGACTAGATATTGGGTTA
Found at i:5389075 original size:22 final size:24
Alignment explanation
Indices: 5389026--5389075 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5389016 TCCAATGTTA
*
5389026 AAATGTTTATTTTATATTACTATG
1 AAATGTTTATTTTATATTACCATG
*
5389050 AAATGTTTATTTTA-A-TCCCATG
1 AAATGTTTATTTTATATTACCATG
5389072 AAAT
1 AAAT
5389076 TTCTAAGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.38
23 1 0.04
24 14 0.58
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (24 bp):
AAATGTTTATTTTATATTACCATG
Found at i:5390119 original size:30 final size:32
Alignment explanation
Indices: 5390062--5390138 Score: 86
Period size: 30 Copynumber: 2.4 Consensus size: 32
5390052 GTCATCAAAC
* * *
5390062 TAATAGATGTTAATGGTACAGTGATCAAAATG
1 TAATAGTTGATAATGGTACAGTAATCAAAATG
*
5390094 TAATAGTTGATAAT-GTA-AGTAATCAAAATT
1 TAATAGTTGATAATGGTACAGTAATCAAAATG
*
5390124 TAATAAATTGATAAT
1 TAAT-AGTTGATAAT
5390139 ATTAATTATC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 15 0.38
31 12 0.31
32 12 0.31
ACGTcount: A:0.45, C:0.04, G:0.16, T:0.35
Consensus pattern (32 bp):
TAATAGTTGATAATGGTACAGTAATCAAAATG
Found at i:5391838 original size:29 final size:29
Alignment explanation
Indices: 5391797--5391854 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
5391787 GTAAAGTTAG
* * *
5391797 ATTAATTCGTTATTTTGTTTG-CTCCAAAC
1 ATTAAATCCTTATTTCGTTTGTC-CCAAAC
5391826 ATTAAATCCTTATTTCGTTTGTCCCAAAC
1 ATTAAATCCTTATTTCGTTTGTCCCAAAC
5391855 CGTTAATTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.45
Consensus pattern (29 bp):
ATTAAATCCTTATTTCGTTTGTCCCAAAC
Found at i:5392322 original size:20 final size:20
Alignment explanation
Indices: 5392297--5392334 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5392287 ATATATTTAT
5392297 ATCATGTATAAAATCAAACG
1 ATCATGTATAAAATCAAACG
5392317 ATCATGTATAAAATCAAA
1 ATCATGTATAAAATCAAA
5392335 TGATGCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.13, G:0.08, T:0.26
Consensus pattern (20 bp):
ATCATGTATAAAATCAAACG
Found at i:5393153 original size:2 final size:2
Alignment explanation
Indices: 5393146--5393177 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5393136 TGAATAAAGT
5393146 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5393178 ACTTTATTCA
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):
TA
Found at i:5395100 original size:25 final size:26
Alignment explanation
Indices: 5395054--5395102 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
5395044 GGATGGTCAT
*
5395054 TTATATTAAAAGATAAAACATATACA
1 TTATATTAAAAGACAAAACATATACA
* *
5395080 TTAT-TTAAAATACAAACCATATA
1 TTATATTAAAAGACAAAACATATA
5395103 TATTTTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (26 bp):
TTATATTAAAAGACAAAACATATACA
Found at i:5397330 original size:28 final size:29
Alignment explanation
Indices: 5397279--5397337 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
5397269 AAGATTTAAA
* *
5397279 TTTTAAAATAAATTTATTATTTTTATATT
1 TTTTAAAATAAATTCAGTATTTTTATATT
*
5397308 TTTTAAATTAAATTCAGTATTTTTATATT
1 TTTTAAAATAAATTCAGTATTTTTATATT
5397337 T
1 T
5397338 ATATTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTAAAATAAATTCAGTATTTTTATATT
Found at i:5397367 original size:20 final size:20
Alignment explanation
Indices: 5397342--5397381 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5397332 ATATTTATAT
5397342 TTATAAAAATAAATATAAAA
1 TTATAAAAATAAATATAAAA
* *
5397362 TTATAAACATAAGTATAAAA
1 TTATAAAAATAAATATAAAA
5397382 ATATTGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (20 bp):
TTATAAAAATAAATATAAAA
Found at i:5397499 original size:23 final size:24
Alignment explanation
Indices: 5397454--5397500 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
5397444 TAAATACGGT
*
5397454 TTATAATAAATATAATCTATTTAA
1 TTATAATAAATATAATATATTTAA
* *
5397478 TTATAA-AAATATTATATTTTTAA
1 TTATAATAAATATAATATATTTAA
5397501 CTAATTTAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
TTATAATAAATATAATATATTTAA
Found at i:5399150 original size:34 final size:34
Alignment explanation
Indices: 5399097--5399166 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
5399087 AAATAAAATT
*
5399097 TACAGTCAAAATTTTGATTCTTTGAGTATCAATC
1 TACAATCAAAATTTTGATTCTTTGAGTATCAATC
*
5399131 TACAATCAAGATTTTGATTCTTTGAGTATCAATC
1 TACAATCAAAATTTTGATTCTTTGAGTATCAATC
5399165 TA
1 TA
5399167 TTTATAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.41
Consensus pattern (34 bp):
TACAATCAAAATTTTGATTCTTTGAGTATCAATC
Found at i:5399799 original size:20 final size:22
Alignment explanation
Indices: 5399769--5399808 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
5399759 CATAAATTAA
5399769 AAATAGAAAAGGAA-AAAAATG
1 AAATAGAAAAGGAAGAAAAATG
5399790 AAAT-GAAAAGGAAGAAAAA
1 AAATAGAAAAGGAAGAAAAA
5399809 AAAAGTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.07
Consensus pattern (22 bp):
AAATAGAAAAGGAAGAAAAATG
Found at i:5400655 original size:18 final size:20
Alignment explanation
Indices: 5400609--5400657 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
5400599 AAAGTGGAAT
*
5400609 TAAATTACAAATATCAATAA
1 TAAATTAAAAATATCAATAA
*
5400629 AATAATTAAAAAT-TC-ATAA
1 TA-AATTAAAAATATCAATAA
5400648 TAAATTAAAA
1 TAAATTAAAA
5400658 TTCTTGTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 8 0.32
19 5 0.20
20 3 0.12
21 9 0.36
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAATTAAAAATATCAATAA
Found at i:5401038 original size:56 final size:56
Alignment explanation
Indices: 5400968--5401088 Score: 215
Period size: 56 Copynumber: 2.2 Consensus size: 56
5400958 CTAAATAATC
*
5400968 TTCTTTTCTAGAGATGGACTCTGAAAACAATCTTGTTCCTCTGATGCCAATCCATA
1 TTCTTTTCTAGAGATGGACTCTGAAAACAATCTTGTTCCTCTGATGCCAATCCACA
*
5401024 TTCTTTTCTGGAGATGGACTCTGAAAACAATCTTGTTCCTCTGATGCCAATCCACA
1 TTCTTTTCTAGAGATGGACTCTGAAAACAATCTTGTTCCTCTGATGCCAATCCACA
*
5401080 TTCATTTCT
1 TTCTTTTCT
5401089 TCACCCATAA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (56 bp):
TTCTTTTCTAGAGATGGACTCTGAAAACAATCTTGTTCCTCTGATGCCAATCCACA
Found at i:5401245 original size:85 final size:85
Alignment explanation
Indices: 5401133--5401291 Score: 221
Period size: 85 Copynumber: 1.9 Consensus size: 85
5401123 CCTTAGAATG
* * * *
5401133 AGGATGCCAAGTCATCATTAGTAGTTGATAC-GCTCCTTTCTCTAAAGGACGCCAAATTGAATAA
1 AGGATGCCAAGTCATAATCAGTAGTTGAT-CTACTCCTTTCTCTAAAGGACGCCAAATTGAAGAA
*
5401197 CTATCTTACTATTCTATCTAC
65 CAATCTTACTATTCTATCTAC
* * * *
5401218 AGGATGTCAAGTCATAATCATTGGTTGATCTACTCCTTTCTCTAAAGGATGCCAAATTGAAGAAC
1 AGGATGCCAAGTCATAATCAGTAGTTGATCTACTCCTTTCTCTAAAGGACGCCAAATTGAAGAAC
5401283 AATCTTACT
66 AATCTTACT
5401292 TTTTTCTTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
84 1 0.02
85 63 0.98
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (85 bp):
AGGATGCCAAGTCATAATCAGTAGTTGATCTACTCCTTTCTCTAAAGGACGCCAAATTGAAGAAC
AATCTTACTATTCTATCTAC
Found at i:5401314 original size:85 final size:85
Alignment explanation
Indices: 5401165--5401359 Score: 210
Period size: 85 Copynumber: 2.3 Consensus size: 85
5401155 AGTTGATACG
* * * * * ***
5401165 CTCCTTTCTCTAAAGGACGCCAAATTGAATAACTATCTTACTATTCTATCTACAGGATGTCAAGT
1 CTCCTTTCTCTAAAGGATGCCAAATTGAAGAACAATCTTACTATTCTATCTAAAGAACACCAAGT
* * *
5401230 CATAATCATTGGTTGATCTA
66 CATAATCAATGGTTAATATA
* * * *
5401250 CTCCTTTCTCTAAAGGATGCCAAATTGAAGAACAATCTTACTTTTTTCTTTAAAGAACACCAAGT
1 CTCCTTTCTCTAAAGGATGCCAAATTGAAGAACAATCTTACTATTCTATCTAAAGAACACCAAGT
* *
5401315 TATAATCAATGGTTAATATT
66 CATAATCAATGGTTAATATA
* * *
5401335 CTCCTTTCTCTGAAGGTTTCCAAAT
1 CTCCTTTCTCTAAAGGATGCCAAAT
5401360 CAGAGAATGA
Statistics
Matches: 90, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
85 90 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (85 bp):
CTCCTTTCTCTAAAGGATGCCAAATTGAAGAACAATCTTACTATTCTATCTAAAGAACACCAAGT
CATAATCAATGGTTAATATA
Found at i:5402158 original size:8 final size:8
Alignment explanation
Indices: 5402145--5402180 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
5402135 ATTAATTACA
5402145 AAAAATGG
1 AAAAATGG
5402153 AAAAATGG
1 AAAAATGG
5402161 AAAAATGG
1 AAAAATGG
5402169 AAAAATGG
1 AAAAATGG
5402177 AAAA
1 AAAA
5402181 GTAGAAGCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.11
Consensus pattern (8 bp):
AAAAATGG
Found at i:5405912 original size:20 final size:20
Alignment explanation
Indices: 5405883--5405944 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
5405873 GTCAACGCCT
*
5405883 TCGTTGCATTTGCATTTGCA
1 TCGTTACATTTGCATTTGCA
*
5405903 TCGTTACATTTACATTTGCA
1 TCGTTACATTTGCATTTGCA
** *
5405923 TTTTTACATCATGCATTTGCA
1 TCGTTACAT-TTGCATTTGCA
5405944 T
1 T
5405945 TTTTACATCA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
20 25 0.71
21 10 0.29
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.47
Consensus pattern (20 bp):
TCGTTACATTTGCATTTGCA
Found at i:5405941 original size:21 final size:21
Alignment explanation
Indices: 5405893--5405964 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 21
5405883 TCGTTGCATT
** *
5405893 TGCATTTGCATCGTTACAT-T
1 TGCATTTGCATTTTTACATCA
*
5405913 TACATTTGCATTTTTACATCA
1 TGCATTTGCATTTTTACATCA
5405934 TGCATTTGCATTTTTACATCA
1 TGCATTTGCATTTTTACATCA
*
5405955 TCCATTTGCA
1 TGCATTTGCA
5405965 CTTTGTTTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.46
Consensus pattern (21 bp):
TGCATTTGCATTTTTACATCA
Found at i:5408950 original size:10 final size:10
Alignment explanation
Indices: 5408932--5409072 Score: 60
Period size: 10 Copynumber: 13.7 Consensus size: 10
5408922 ACTACACTTG
5408932 AAAAA-AGAA
1 AAAAAGAGAA
5408941 AAAAAGAGAA
1 AAAAAGAGAA
*
5408951 AAAATGTATGAA
1 AAAAAG-A-GAA
*
5408963 AAAAGAAATGAA
1 AAAA-AGA-GAA
*
5408975 AAGGAAAAAGAA
1 AA--AAAGAGAA
* *
5408987 AAGAAAAACAA
1 AA-AAAGAGAA
5408998 AAAAA-A-AA
1 AAAAAGAGAA
* *
5409006 AAAAACAAAA
1 AAAAAGAGAA
5409016 AAAAAGAAGAA
1 AAAAAG-AGAA
5409027 AGAAAAGA-AA
1 A-AAAAGAGAA
*
5409037 AAATAGA-AA
1 AAAAAGAGAA
* *
5409046 AAATAGAAAA
1 AAAAAGAGAA
5409056 AAAAAGA-AA
1 AAAAAGAGAA
5409065 AAGAAAGA
1 AA-AAAGA
5409073 ATGAATGAAA
Statistics
Matches: 112, Mismatches: 8, Indels: 23
0.78 0.06 0.16
Matches are distributed among these distances:
8 7 0.06
9 25 0.22
10 35 0.31
11 16 0.14
12 24 0.21
13 3 0.03
14 2 0.02
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.04
Consensus pattern (10 bp):
AAAAAGAGAA
Found at i:5408987 original size:12 final size:11
Alignment explanation
Indices: 5408963--5409070 Score: 86
Period size: 11 Copynumber: 10.3 Consensus size: 11
5408953 AATGTATGAA
*
5408963 AAAAG-AAATG
1 AAAAGAAAAAG
5408973 AAAAGGAAAAAG
1 AAAA-GAAAAAG
*
5408985 AAAAGAAAAAC
1 AAAAGAAAAAG
* *
5408996 AAAAAAAAAAA
1 AAAAGAAAAAG
*
5409007 AAAACAAAAA-
1 AAAAGAAAAAG
5409017 AAAAGAAGAAAG
1 AAAAGAA-AAAG
5409029 AAAAG-AAAA-
1 AAAAGAAAAAG
*
5409038 AATAG-AAAA-
1 AAAAGAAAAAG
*
5409047 AATAGAAAAA-
1 AAAAGAAAAAG
5409057 AAAAGAAAAAG
1 AAAAGAAAAAG
5409068 AAA
1 AAA
5409071 GAATGAATGA
Statistics
Matches: 84, Mismatches: 8, Indels: 11
0.82 0.08 0.11
Matches are distributed among these distances:
9 13 0.15
10 26 0.31
11 32 0.38
12 13 0.15
ACGTcount: A:0.82, C:0.02, G:0.13, T:0.03
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:5408994 original size:18 final size:17
Alignment explanation
Indices: 5408962--5409113 Score: 104
Period size: 16 Copynumber: 8.9 Consensus size: 17
5408952 AAATGTATGA
* *
5408962 AAAAAGAAATGAAAAGG
1 AAAAAGAAAAGAAAAAG
*
5408979 AAAAAGAAAAGAAAAAC
1 AAAAAGAAAAGAAAAAG
* *
5408996 AAAAA-AAAAAAAAAAC
1 AAAAAGAAAAGAAAAAG
5409012 AAAAA-AAAAGAAGAAAG
1 AAAAAGAAAAGAA-AAAG
5409029 -AAAAGAAAA-AATAGAA-
1 AAAAAGAAAAGAA-A-AAG
5409045 AAAATAGAAAA-AAAAAG
1 AAAA-AGAAAAGAAAAAG
*
5409062 AAAAAG-AAAGAATGAATG
1 AAAAAGAAAAGAA--AAAG
* *
5409080 AAAAAG-AATGAAAAAT
1 AAAAAGAAAAGAAAAAG
5409096 AAAAAGAGATAAGAAAAA
1 AAAAAGA-A-AAGAAAAA
5409114 AAGGAGGGTT
Statistics
Matches: 111, Mismatches: 12, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
15 3 0.03
16 42 0.38
17 36 0.32
18 23 0.21
19 7 0.06
ACGTcount: A:0.79, C:0.01, G:0.14, T:0.05
Consensus pattern (17 bp):
AAAAAGAAAAGAAAAAG
Found at i:5409000 original size:34 final size:32
Alignment explanation
Indices: 5408961--5409102 Score: 94
Period size: 34 Copynumber: 4.2 Consensus size: 32
5408951 AAAATGTATG
5408961 AAAAAAGAAATGAAAAGGAAAAAGAAAAGAAAA
1 AAAAAAGAAA-GAAAAGGAAAAAGAAAAGAAAA
* * **
5408994 ACAAAAAAAAAAAAAAACAAAAA-AAAAGAAGAA
1 A-AAAAAGAAAGAAAAGGAAAAAGAAAAGAA-AA
* *
5409027 AGAAAAGAAA-AAATAGAAAAAATAGAAAA-AAAA
1 AAAAAAGAAAGAAA-AG-GAAAA-AGAAAAGAAAA
* *
5409060 AGAAAAAGAAAGAATGAATGAAAAAG-AATGAAAA
1 A-AAAAAGAAAGAA--AAGGAAAAAGAAAAGAAAA
5409094 ATAAAAAGA
1 A-AAAAAGA
5409103 GATAAGAAAA
Statistics
Matches: 85, Mismatches: 13, Indels: 21
0.71 0.11 0.18
Matches are distributed among these distances:
31 3 0.04
32 15 0.18
33 22 0.26
34 33 0.39
35 10 0.12
36 1 0.01
37 1 0.01
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.05
Consensus pattern (32 bp):
AAAAAAGAAAGAAAAGGAAAAAGAAAAGAAAA
Found at i:5409029 original size:39 final size:39
Alignment explanation
Indices: 5408979--5409070 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 39
5408969 AATGAAAAGG
5408979 AAAAAG-AAAAGAAAA-ACAAAAA-AAAAAAAAAACAAAA
1 AAAAAGAAAAAGAAAAGA-AAAAATAAAAAAAAAACAAAA
* * *
5409016 AAAAAGAAGAAAGAAAAGAAAAAATAGAAAAAATAGAAAA
1 AAAAAGAA-AAAGAAAAGAAAAAATAAAAAAAAAACAAAA
5409056 AAAAAGAAAAAGAAA
1 AAAAAGAAAAAGAAA
5409071 GAATGAATGA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
37 6 0.12
38 1 0.02
39 20 0.42
40 21 0.44
ACGTcount: A:0.85, C:0.02, G:0.11, T:0.02
Consensus pattern (39 bp):
AAAAAGAAAAAGAAAAGAAAAAATAAAAAAAAAACAAAA
Found at i:5409073 original size:10 final size:10
Alignment explanation
Indices: 5408962--5409094 Score: 73
Period size: 10 Copynumber: 13.5 Consensus size: 10
5408952 AAATGTATGA
5408962 AAAAAGAAATG
1 AAAAAGAAA-G
* *
5408973 AAAAGGAAAA
1 AAAAAGAAAG
5408983 AGAAAAGAAA-
1 A-AAAAGAAAG
5408993 AACAAA-AAA-
1 AA-AAAGAAAG
* *
5409002 AAAAAAAAAC
1 AAAAAGAAAG
*
5409012 AAAAAAAAAG
1 AAAAAGAAAG
5409022 AAGAAAGAAAAG
1 AA-AAAG-AAAG
*
5409034 AAAAA-ATAG
1 AAAAAGAAAG
*
5409043 AAAAA-ATAG
1 AAAAAGAAAG
*
5409052 AAAAAAAAAG
1 AAAAAGAAAG
5409062 AAAAAGAAAG
1 AAAAAGAAAG
* *
5409072 --AATGAATG
1 AAAAAGAAAG
*
5409080 AAAAAGAATG
1 AAAAAGAAAG
5409090 AAAAA
1 AAAAA
5409095 TAAAAAGAGA
Statistics
Matches: 102, Mismatches: 11, Indels: 19
0.77 0.08 0.14
Matches are distributed among these distances:
8 9 0.09
9 26 0.25
10 40 0.39
11 21 0.21
12 6 0.06
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.05
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:5409082 original size:28 final size:27
Alignment explanation
Indices: 5409002--5409094 Score: 70
Period size: 25 Copynumber: 3.6 Consensus size: 27
5408992 AAACAAAAAA
* *
5409002 AAAAAAAAACAAAAAAAAAGAA-GAA-
1 AAAAAAAAAGAAAAAGAAAGAATGAAG
* * *
5409027 AGAAAAGAAA-AAATAGAAAAAAT--AG
1 A-AAAAAAAAGAAAAAGAAAGAATGAAG
5409052 AAAAAAAAAGAAAAAGAAAGAATGAATG
1 AAAAAAAAAGAAAAAGAAAGAATGAA-G
* *
5409080 AAAAAGAATGAAAAA
1 AAAAAAAAAGAAAAA
5409095 TAAAAAGAGA
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
24 8 0.15
25 22 0.42
26 7 0.13
27 1 0.02
28 14 0.27
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.05
Consensus pattern (27 bp):
AAAAAAAAAGAAAAAGAAAGAATGAAG
Found at i:5409084 original size:1 final size:1
Alignment explanation
Indices: 5408979--5409066 Score: 59
Period size: 1 Copynumber: 88.0 Consensus size: 1
5408969 AATGAAAAGG
* * * * * * * * * *
5408979 AAAAAGAAAAGAAAAACAAAAAAAAAAAAAAACAAAAAAAAAGAAGAAAGAAAAGAAAAAATAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
5409044 AAAAATAGAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAA
5409067 GAAAGAATGA
Statistics
Matches: 61, Mismatches: 26, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.85, C:0.02, G:0.10, T:0.02
Consensus pattern (1 bp):
A
Found at i:5411241 original size:12 final size:12
Alignment explanation
Indices: 5411224--5411248 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5411214 TTGTTGTGCT
5411224 TGCTCCTCGGGC
1 TGCTCCTCGGGC
5411236 TGCTCCTCGGGC
1 TGCTCCTCGGGC
5411248 T
1 T
5411249 CATCTTTGGC
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:0.00, C:0.40, G:0.32, T:0.28
Consensus pattern (12 bp):
TGCTCCTCGGGC
Found at i:5429097 original size:13 final size:13
Alignment explanation
Indices: 5429079--5429111 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
5429069 AATTAAGAAA
5429079 GGAGAAGTTAGCT
1 GGAGAAGTTAGCT
5429092 GGAGAAGTTAGCT
1 GGAGAAGTTAGCT
5429105 GGAGAAG
1 GGAGAAG
5429112 ATCTCACATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.33, C:0.06, G:0.42, T:0.18
Consensus pattern (13 bp):
GGAGAAGTTAGCT
Found at i:5433938 original size:37 final size:37
Alignment explanation
Indices: 5433836--5433977 Score: 218
Period size: 37 Copynumber: 3.9 Consensus size: 37
5433826 TTCTCAAGCC
5433836 AATCAAGCCTTCAC-AAAAGAATAGTGAAGCAATGCA
1 AATCAAGCCTTCACAAAAAGAATAGTGAAGCAATGCA
* * *
5433872 AATCAAGCCTTCA-AAAAAGAGTAGCGAAGCAATGTA
1 AATCAAGCCTTCACAAAAAGAATAGTGAAGCAATGCA
*
5433908 AATCAAGCCTTCACAAAAAGAGTAGTGAAGCAATGCA
1 AATCAAGCCTTCACAAAAAGAATAGTGAAGCAATGCA
5433945 AATTC-AGCCTTCACAAAAAGAATAGTGAAGCAA
1 AA-TCAAGCCTTCACAAAAAGAATAGTGAAGCAA
5433978 GATCATATCA
Statistics
Matches: 97, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
36 45 0.46
37 50 0.52
38 2 0.02
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.17
Consensus pattern (37 bp):
AATCAAGCCTTCACAAAAAGAATAGTGAAGCAATGCA
Found at i:5433954 original size:73 final size:73
Alignment explanation
Indices: 5433836--5433977 Score: 225
Period size: 73 Copynumber: 1.9 Consensus size: 73
5433826 TTCTCAAGCC
*
5433836 AATCAAGCCTTCACAAAAGAATAGTGAAGCAATGCAAATCAAGCCTTCA-AAAAAGAGTAGCGAA
1 AATCAAGCCTTCACAAAAGAATAGTGAAGCAATGCAAATCAAGCCTTCACAAAAAGAATAGCGAA
5433900 GCAATGTA
66 GCAATGTA
* *
5433908 AATCAAGCCTTCACAAAAAGAGTAGTGAAGCAATGCAAATTC-AGCCTTCACAAAAAGAATAGTG
1 AATCAAGCCTTCAC-AAAAGAATAGTGAAGCAATGCAAA-TCAAGCCTTCACAAAAAGAATAGCG
5433972 AAGCAA
64 AAGCAA
5433978 GATCATATCA
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
72 14 0.22
73 31 0.48
74 19 0.30
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.17
Consensus pattern (73 bp):
AATCAAGCCTTCACAAAAGAATAGTGAAGCAATGCAAATCAAGCCTTCACAAAAAGAATAGCGAA
GCAATGTA
Found at i:5435383 original size:2 final size:2
Alignment explanation
Indices: 5435376--5435414 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5435366 CACTATTACG
5435376 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5435415 TAGGTTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5436380 original size:115 final size:116
Alignment explanation
Indices: 5436243--5436627 Score: 450
Period size: 115 Copynumber: 3.3 Consensus size: 116
5436233 AAAAGTTCAA
* * * * * *
5436243 AACTCGACACATCCATCACACAATGAGGTGGATCAATATTTCTGTGGAAGGGCTCATGATAAGAA
1 AACTCGACACATCCATCACACAAGGAGGTGGATCAACATTTCTGAGGAAGGGTTCATAATGAGAA
* *
5436308 GAACTCATCCGATGA-GAAGAAGAAGTTCATAATGAGGAGAACTTGTTTAG
66 GAACTCATCCGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAG
* * * * *
5436358 AACTCGACACATACATCGCACAAGAAGGTGTATCAACATTTCTGAGGAAGGGTTTATAATGAGAA
1 AACTCGACACATCCATCACACAAGGAGGTGGATCAACATTTCTGAGGAAGGGTTCATAATGAGAA
* * * * *
5436423 GAACTCATTCGACGATG-AGAAGAAGTTCAAAATGAGAAGAACTTGTTTAT
66 GAACTCATCCGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAG
* ** * * * ***
5436473 AATTTTACACATCCATCGCACAAGGAGGTGAATCAACATTTCTAAGGAAATATTCATAATGAGAA
1 AACTCGACACATCCATCACACAAGGAGGTGGATCAACATTTCTGAGGAAGGGTTCATAATGAGAA
* ** * *
5436538 GAACTCGTCTAAAGAGGGAAAAAGAAGTTCATAATGAGAAGAACATGTTTAG
66 GAACTCATCCGAAGA-GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAG
*
5436590 AACTCGGCACATCCATCACACAAGGAGGTGGATCAACA
1 AACTCGACACATCCATCACACAAGGAGGTGGATCAACA
5436628 AATAGTTCGT
Statistics
Matches: 224, Mismatches: 43, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
115 161 0.72
116 2 0.01
117 61 0.27
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (116 bp):
AACTCGACACATCCATCACACAAGGAGGTGGATCAACATTTCTGAGGAAGGGTTCATAATGAGAA
GAACTCATCCGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAG
Found at i:5436422 original size:207 final size:210
Alignment explanation
Indices: 5436065--5436454 Score: 547
Period size: 207 Copynumber: 1.9 Consensus size: 210
5436055 AGTCTCGACA
* * *
5436065 GGATCAATATTTCTTAGGAATGGTACATAATGAGAAGAACTCATCCGACAAGGAGAAGAAGTTCA
1 GGATCAATATTTCTTAGGAAGGGTACATAATAAGAAGAACTCATCCGACAAGAAGAAGAAGTTCA
* * *
5436130 TAATAAGAAAAACTTGTTTAGAACTCAACACATCCATTGCACAAGGAGGTGGATCAACATTTCTG
66 TAATAAGAAAAACTTGTTTAGAACTCAACACATACATCGCACAAGAAGGTGGATCAACATTTCTG
*
5436195 AAGAAGGGCTCATGATGAGAAGAACTCATCCAACGA-GA-AA-AAGTTCAAAACTCGACACATCC
131 AAGAAGGGCTCATAATGAGAAGAACTCATCCAACGATGAGAAGAAGTTCAAAACTCGACACATCC
5436257 ATCACACAATGAGGT
196 ATCACACAATGAGGT
* **
5436272 GGATCAATATTTCTGT-GGAAGGGCT-CATGATAAGAAGAACTCATCCGATGAGAAGAAGAAGTT
1 GGATCAATATTTCT-TAGGAAGGG-TACATAATAAGAAGAACTCATCCGACAAGAAGAAGAAGTT
* * * * *
5436335 CATAATGAGGAGAACTTGTTTAGAACTCGACACATACATCGCACAAGAAGGTGTATCAACATTTC
64 CATAATAAGAAAAACTTGTTTAGAACTCAACACATACATCGCACAAGAAGGTGGATCAACATTTC
* * * * *
5436400 TGAGGAAGGGTTTATAATGAGAAGAACTCATTCGACGATGAGAAGAAGTTCAAAA
129 TGAAGAAGGGCTCATAATGAGAAGAACTCATCCAACGATGAGAAGAAGTTCAAAA
5436455 TGAGAAGAAC
Statistics
Matches: 158, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
207 142 0.90
208 4 0.03
209 2 0.01
210 10 0.06
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.22
Consensus pattern (210 bp):
GGATCAATATTTCTTAGGAAGGGTACATAATAAGAAGAACTCATCCGACAAGAAGAAGAAGTTCA
TAATAAGAAAAACTTGTTTAGAACTCAACACATACATCGCACAAGAAGGTGGATCAACATTTCTG
AAGAAGGGCTCATAATGAGAAGAACTCATCCAACGATGAGAAGAAGTTCAAAACTCGACACATCC
ATCACACAATGAGGT
Found at i:5439225 original size:38 final size:40
Alignment explanation
Indices: 5439145--5439227 Score: 143
Period size: 41 Copynumber: 2.1 Consensus size: 40
5439135 AATGATCAAA
5439145 AGTATTGTCAGTAGTTTTTCTTTCTCCTTCTTAAAGTCGAT
1 AGTATTGTCAGTAGTTTTTCTTTCTCC-TCTTAAAGTCGAT
5439186 AGTATTGTCAGTAGTTTTTCTTTCT-C-CTTAAAGTCGAT
1 AGTATTGTCAGTAGTTTTTCTTTCTCCTCTTAAAGTCGAT
5439224 AGTA
1 AGTA
5439228 AATGGTTTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
38 16 0.38
40 1 0.02
41 25 0.60
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.47
Consensus pattern (40 bp):
AGTATTGTCAGTAGTTTTTCTTTCTCCTCTTAAAGTCGAT
Found at i:5439569 original size:39 final size:39
Alignment explanation
Indices: 5439519--5439642 Score: 189
Period size: 39 Copynumber: 3.2 Consensus size: 39
5439509 CTATTTAGAA
5439519 AAAT-AAA-AAGATAAAGTTATAGTTAATCTAAACTACT
1 AAATCAAATAAGATAAAGTTATAGTTAATCTAAACTACT
*
5439556 AAATCAAATAAGATAGAGTTATAGTTAATCTAAACTACT
1 AAATCAAATAAGATAAAGTTATAGTTAATCTAAACTACT
* * *
5439595 AAATCAAATAGGATATAGTTATAGTTAATCTAAATTACT
1 AAATCAAATAAGATAAAGTTATAGTTAATCTAAACTACT
*
5439634 AATTCAAAT
1 AAATCAAAT
5439643 TACTGATTCA
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
37 4 0.05
38 3 0.04
39 73 0.91
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (39 bp):
AAATCAAATAAGATAAAGTTATAGTTAATCTAAACTACT
Found at i:5445326 original size:24 final size:21
Alignment explanation
Indices: 5445237--5445315 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
5445227 TCCTTAAGTA
*
5445237 GTGGTCCTTCGAGACATAC-AT
1 GTGGTCCTTCGGGACAT-CTAT
*
5445258 GTGGTCCTTCGGGACATATAT
1 GTGGTCCTTCGGGACATCTAT
* *
5445279 GTGGTCTTTCAGGACATCTAT
1 GTGGTCCTTCGGGACATCTAT
5445300 GTGGTCCTTCGGGACA
1 GTGGTCCTTCGGGACA
5445316 AATTCTATGT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.32
Consensus pattern (21 bp):
GTGGTCCTTCGGGACATCTAT
Found at i:5457211 original size:76 final size:77
Alignment explanation
Indices: 5457052--5457260 Score: 282
Period size: 76 Copynumber: 2.8 Consensus size: 77
5457042 CAAAGCCAAA
* * * **
5457052 AATTACAGATTGCGCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTAAATGG
1 AATTCCAGAATGCTCAGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
5457116 TTTTGGCCCCGAG
65 TTTTGGCCCCGAG
*
5457129 ATTTCCAGAATGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
*
5457194 TTT-GCTCCGAG
66 TTTGGCCCCGAG
* * * *
5457205 AATTCCAGTATGCTCGGAGGGAACCGA-TCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
5457261 TGTACAACGG
Statistics
Matches: 119, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
74 19 0.16
75 8 0.07
76 53 0.45
77 39 0.33
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:5463070 original size:23 final size:21
Alignment explanation
Indices: 5463018--5463078 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 21
5463008 TTTTGGTGCA
*
5463018 GAGGGAATCGA-TCCCCCTCT
1 GAGGGAACCGATTCCCCCTCT
*
5463038 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCTCT
5463059 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
5463079 CCACAGGGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCTCT
Found at i:5465338 original size:30 final size:30
Alignment explanation
Indices: 5465304--5465375 Score: 126
Period size: 30 Copynumber: 2.3 Consensus size: 30
5465294 GGAGAAGAAT
5465304 AGGTGTTAAATGTTTTACATAATAAATTGA
1 AGGTGTTAAATGTTTTACATAATAAATTGA
5465334 AGGTGTTAAATGTTTTACATAATAAATTGA
1 AGGTGTTAAATGTTTTACATAATAAATTGA
5465364 AGAAGTGTTAAA
1 AG--GTGTTAAA
5465376 GTAAGGGGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 32 0.80
32 8 0.20
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.38
Consensus pattern (30 bp):
AGGTGTTAAATGTTTTACATAATAAATTGA
Found at i:5465837 original size:76 final size:77
Alignment explanation
Indices: 5465685--5465895 Score: 275
Period size: 76 Copynumber: 2.8 Consensus size: 77
5465675 CAAAGCCAAA
* * * * **
5465685 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCATAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
5465749 TTTTGGCCCCGAG
65 TTTTGGCCCCGAG
*
5465762 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
*
5465827 TTT-GCTCCGAG
66 TTTGGCCCCGAG
* * * *
5465838 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCCATAGGAGGAACCGATTCCCCCCT
5465896 TGTACAACGG
Statistics
Matches: 119, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
76 74 0.62
77 45 0.38
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:5469289 original size:16 final size:16
Alignment explanation
Indices: 5469255--5469289 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5469245 CTGAAACAAT
* *
5469255 AAAATAAAAGAACATA
1 AAAATAAAAGAAAAGA
5469271 AAAATAAAAGAAAAGA
1 AAAATAAAAGAAAAGA
5469287 AAA
1 AAA
5469290 GAATTGTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.80, C:0.03, G:0.09, T:0.09
Consensus pattern (16 bp):
AAAATAAAAGAAAAGA
Found at i:5469671 original size:13 final size:13
Alignment explanation
Indices: 5469653--5469677 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5469643 AATCTTAGAC
5469653 ACAACTTTGAGAG
1 ACAACTTTGAGAG
5469666 ACAACTTTGAGA
1 ACAACTTTGAGA
5469678 CACGATGCAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (13 bp):
ACAACTTTGAGAG
Found at i:5471469 original size:13 final size:13
Alignment explanation
Indices: 5471447--5471480 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
5471437 GCACAATCTT
5471447 AGACACAACTTTG
1 AGACACAACTTTG
*
5471460 AGAGACAACTTTG
1 AGACACAACTTTG
5471473 AGACACAA
1 AGACACAA
5471481 TTCACAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (13 bp):
AGACACAACTTTG
Found at i:5476908 original size:2 final size:2
Alignment explanation
Indices: 5476901--5476926 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5476891 CCTCTTCGCA
5476901 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
5476927 CCTGCCTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5483301 original size:3 final size:3
Alignment explanation
Indices: 5483293--5483318 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5483283 TTATATTAGT
5483293 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
5483319 TAAAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:5484377 original size:20 final size:19
Alignment explanation
Indices: 5484352--5484405 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
5484342 GCGAAATAAA
5484352 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
5484372 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
5484392 AATCGCAACGCGAT
1 AATCGCAACGCGAT
5484406 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:5484416 original size:21 final size:21
Alignment explanation
Indices: 5484392--5484524 Score: 91
Period size: 20 Copynumber: 6.5 Consensus size: 21
5484382 CAGTTCCCAG
5484392 AATCGCAACGCGATTATGA-A
1 AATCGCAACGCGATTATGACA
*
5484412 GAATCGCAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-ACA
** *
5484433 AATTCGCATTGCGATT-TTACA
1 AA-TCGCAACGCGATTATGACA
*
5484454 TAATCGCAACGCGAATATGA-A
1 -AATCGCAACGCGATTATGACA
** *
5484475 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGATTATGACA
*
5484495 AATCGCAACGCGATTCTGAC-
1 AATCGCAACGCGATTATGACA
*
5484515 TATCGCAACG
1 AATCGCAACG
5484525 AGTATCCGTA
Statistics
Matches: 90, Mismatches: 13, Indels: 19
0.74 0.11 0.16
Matches are distributed among these distances:
19 2 0.02
20 45 0.50
21 38 0.42
22 5 0.06
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTATGACA
Found at i:5484480 original size:20 final size:20
Alignment explanation
Indices: 5484455--5484746 Score: 252
Period size: 20 Copynumber: 14.5 Consensus size: 20
5484445 GATTTTACAT
* *
5484455 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* **
5484475 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
*
5484495 AATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * * *
5484514 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATACGT-A
* * *
5484536 AATCGCAACGCGTATCCTTA
1 AATCGCAACGCGAATACGTA
5484556 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* * *
5484577 AATCACAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
5484597 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
*
5484617 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
* *
5484637 AATCGCAATGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
5484657 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
5484677 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
*
5484697 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
*
5484717 AATCGCAATGCGAAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
5484737 AATCGCAACG
1 AATCGCAACG
5484747 AGATTCTGAC
Statistics
Matches: 228, Mismatches: 34, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
18 1 0.00
19 4 0.02
20 185 0.81
21 36 0.16
22 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:5485465 original size:12 final size:12
Alignment explanation
Indices: 5485444--5485477 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5485434 ACCACATTTC
*
5485444 CAATACCAAACA
1 CAATATCAAACA
5485456 CAATATCAAACA
1 CAATATCAAACA
*
5485468 CAATCTCAAA
1 CAATATCAAA
5485478 ACCTACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:5485630 original size:24 final size:24
Alignment explanation
Indices: 5485603--5485656 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
5485593 GTATTCAAAA
5485603 TTTGATCTAGGTCAATACCCGGAC
1 TTTGATCTAGGTCAATACCCGGAC
* * *
5485627 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTAGGTCAATACCCGGAC
5485651 TTTGAT
1 TTTGAT
5485657 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATCTAGGTCAATACCCGGAC
Found at i:5488077 original size:20 final size:20
Alignment explanation
Indices: 5488052--5488104 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
5488042 AGACATTCAT
5488052 TTGACTATCGCAATGCGGAA
1 TTGACTATCGCAATGCGGAA
5488072 TTGACTATCGCAATGCGGAA
1 TTGACTATCGCAATGCGGAA
*
5488092 ATGACTATCGCAA
1 TTGACTATCGCAA
5488105 CGAGAGAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (20 bp):
TTGACTATCGCAATGCGGAA
Found at i:5488135 original size:19 final size:20
Alignment explanation
Indices: 5488111--5488157 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
5488101 GCAACGAGAG
5488111 AATCGCAATGCG-AAATGAA
1 AATCGCAATGCGAAAATGAA
5488130 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
5488150 AATCGCAA
1 AATCGCAA
5488158 CGAGTGAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.49, C:0.17, G:0.19, T:0.15
Consensus pattern (20 bp):
AATCGCAATGCGAAAATGAA
Found at i:5488141 original size:53 final size:54
Alignment explanation
Indices: 5488058--5488173 Score: 162
Period size: 53 Copynumber: 2.2 Consensus size: 54
5488048 TCATTTGACT
* ** * **
5488058 ATCGCAATGCGGAATTGACTATCGCAATGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
*
5488112 ATCGCAATGC-GAAATGAAAATCGCAATGCGAAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
5488165 ATCGCAATG
1 ATCGCAATG
5488174 ACGATTTTCA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
53 45 0.82
54 10 0.18
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (54 bp):
ATCGCAATGCGGAAATGAAAATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:5488199 original size:19 final size:20
Alignment explanation
Indices: 5488175--5488217 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
5488165 ATCGCAATGA
5488175 CGATTTTCATTT-CGCATTG
1 CGATTTTCATTTCCGCATTG
*
5488194 CGATTTTCATTTCCGCGTTG
1 CGATTTTCATTTCCGCATTG
5488214 CGAT
1 CGAT
5488218 AGTCTGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (20 bp):
CGATTTTCATTTCCGCATTG
Found at i:5488338 original size:14 final size:14
Alignment explanation
Indices: 5488319--5488355 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5488309 CATCAATTAA
5488319 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
5488333 ACAAATCATCTTTT
1 ACAAATCAACATTT
5488347 ACAAATCAA
1 ACAAATCAA
5488356 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:5489768 original size:21 final size:21
Alignment explanation
Indices: 5489702--5489768 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
5489692 GTGAATCGGG
*
5489702 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
5489722 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
5489744 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
5489765 CTCT
1 CTCT
5489769 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:5489787 original size:42 final size:41
Alignment explanation
Indices: 5489702--5489824 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 41
5489692 GTGAATCGGG
* * * *
5489702 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
5489744 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * * *
5489786 CTCTTCAACGATAGGAGTGGACTCTTGAGGGGTGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
5489825 TGAGTCGGGC
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
41 4 0.06
42 56 0.85
43 6 0.09
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:5491859 original size:19 final size:19
Alignment explanation
Indices: 5491784--5491882 Score: 117
Period size: 19 Copynumber: 5.1 Consensus size: 19
5491774 TCTTTTGGTT
*
5491784 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
5491803 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
5491823 GGAAATGACTATTGCAACGC
1 -GAAATGAAAATCGCAACGC
*
5491843 GAAATGAAAATCACAACGC
1 GAAATGAAAATCGCAACGC
* *
5491862 GAAATTAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
5491881 GA
1 GA
5491883 TTTTGGTTTC
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
19 35 0.52
20 30 0.45
21 2 0.03
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:5491894 original size:19 final size:19
Alignment explanation
Indices: 5491878--5491930 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
5491868 AAAATCGCAA
*
5491878 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
5491897 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
5491916 TGCGATTTTCATTTC
1 TGCGATTTTGATTTC
5491931 TCTCGTTGCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.09, C:0.17, G:0.23, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:5491972 original size:20 final size:20
Alignment explanation
Indices: 5491889--5491985 Score: 90
Period size: 20 Copynumber: 4.8 Consensus size: 20
5491879 GCGATTTTGG
* *
5491889 TTTCGCGTTGCGATTTTTA-
1 TTTCGTGTTGCGATTTTCAT
*
5491908 TTTCGCGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
** *
5491928 TTCTC-TCGTTGCGATAGTCAA
1 TT-TCGT-GTTGCGATTTTCAT
5491949 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
* *
5491969 TTTCATGTAGCGATTTT
1 TTTCGTGTTGCGATTTT
5491986 AAGTTTAGAA
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
19 18 0.28
20 30 0.47
21 16 0.25
ACGTcount: A:0.13, C:0.18, G:0.20, T:0.49
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTCAT
Found at i:5492592 original size:20 final size:20
Alignment explanation
Indices: 5492548--5492741 Score: 176
Period size: 20 Copynumber: 9.6 Consensus size: 20
5492538 CTTTAAAAAT
*
5492548 CGCGTTGCGATTTTA-GGTATT
1 CGCGTTGCGA-TTTACGG-ATA
*
5492569 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
5492589 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* * *
5492609 CTCGTTGCAATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* * *
5492629 TGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
**
5492649 TTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5492669 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
5492689 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
5492710 CGCATTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
5492731 CTCGTTGCGAT
1 CGCGTTGCGAT
5492742 AGTCAGAATC
Statistics
Matches: 140, Mismatches: 28, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
20 94 0.67
21 46 0.33
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:5492696 original size:41 final size:41
Alignment explanation
Indices: 5492548--5492741 Score: 266
Period size: 40 Copynumber: 4.8 Consensus size: 41
5492538 CTTTAAAAAT
* * *
5492548 CGCGTTGCGATTTTAGGTATTCGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
* * *
5492589 CGCATTGCGA-TTTACGTATTCTCGTTGCAATTTACAGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
* *
5492629 TGCGTTGCGA-TTTACGTATTTTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
*
5492669 CGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
* * *
5492710 CGCATTGCGATTTTACGGATACTCGTTGCGAT
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGAT
5492742 AGTCAGAATC
Statistics
Matches: 135, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 69 0.51
41 66 0.49
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (41 bp):
CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
Found at i:5492759 original size:41 final size:41
Alignment explanation
Indices: 5492548--5492763 Score: 158
Period size: 41 Copynumber: 5.3 Consensus size: 41
5492538 CTTTAAAAAT
* * *
5492548 CGCGTTGCGATTTTA-GG-TATTCGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGGATACTCG--TTGCGATTCACGAATA
* * * * *
5492589 CGCATTGCGA-TTTACGTATTCTCGTTGCAATTTAC-AGATA
1 CGCGTTGCGATTTTACGGATACTCGTTGCGATTCACGA-ATA
* * ** * *
5492629 TGCGTTGCGA-TTTACGTATTTTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGGATACTCGTTGCGATTCACGAATA
* ** * *
5492669 CGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGGATACTCGTTGCGATTCACGAATA
*
5492710 CGCATTGCGATTTTACGGATACTCGTTGCGATAGTCA-GAAT-
1 CGCGTTGCGATTTTACGGATACTCGTTGCGAT--TCACGAATA
5492751 CGCGTTGCGATTT
1 CGCGTTGCGATTT
5492764 ATATGTTCGC
Statistics
Matches: 148, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
40 60 0.41
41 79 0.53
42 7 0.05
43 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
CGCGTTGCGATTTTACGGATACTCGTTGCGATTCACGAATA
Found at i:5492773 original size:20 final size:19
Alignment explanation
Indices: 5492750--5492820 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
5492740 ATAGTCAGAA
*
5492750 TCGCGTTGCGATTTATATGT
1 TCGCGTTGCGATTT-TATAT
5492770 TCGCGTTGCGATTTTTATAT
1 TCGCGTTGCGA-TTTTATAT
5492790 T--CGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTT-ATAT
*
5492808 CCGCGTTGCGATT
1 TCGCGTTGCGATT
5492821 ATGGAAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
17 4 0.09
18 12 0.27
20 26 0.58
21 3 0.07
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTATAT
Found at i:5496983 original size:21 final size:21
Alignment explanation
Indices: 5496932--5496991 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
5496922 GTCGAGCCCA
* *
5496932 CAGGGTTATATTCTGAGCTAG
1 CAGGGTTATATTCCGAGCAAG
* *
5496953 CAAGGCTATATTCCGAGCAAG
1 CAGGGTTATATTCCGAGCAAG
* *
5496974 CTGGGTTATATTTCGAGC
1 CAGGGTTATATTCCGAGC
5496992 CTCCCTAGAG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (21 bp):
CAGGGTTATATTCCGAGCAAG
Found at i:5499882 original size:167 final size:167
Alignment explanation
Indices: 5499574--5500433 Score: 732
Period size: 167 Copynumber: 5.1 Consensus size: 167
5499564 AATATATAGT
* * * * * * *
5499574 GAGTTATTGTGATGACTAGTTTCCCGAAGGGGAATATCATCTATACATAAAATGGATTGGAAAAT
1 GAGTTATTGTGATGAATAGTTTCCCAAAGGGGAACATCATATTTACATATAATTGATTGGAAAAT
* * * **
5499639 -TAAGAAAATCTTT-GAAAAAGGGAAGACGTTTTTCACAAGAAGCACTTTCACCTTTTGCAATGA
66 GT-AGAGAATCTTTAAAAAAAGGGAAGAC--TTTTCACAAGAAGCACTTTTACCTTTTGCAGGGA
5499702 ATCTCTGTCATGTCATAGTGTCTCATCCCATCAGACATAA
128 ATCTCTGTCATGTCATAGTGTCTCATCCCATCAGACATAA
* * * * *
5499742 GATTTATTATGATGAATAGTTTCCCAAAGGGGAACATCATATTTGCATATAATTGACTGAAAAAT
1 GAGTTATTGTGATGAATAGTTTCCCAAAGGGGAACATCATATTTACATATAATTGATTGGAAAAT
* * * *
5499807 GTAGAGAATCTTTAAAAAAAAGGAAGACTTTTCACAAGAAGCATTTTTATCTTTTACAGGGAATC
66 GTAGAGAATCTTTAAAAAAAGGGAAGACTTTTCACAAGAAGCACTTTTACCTTTTGCAGGGAATC
** * * * *
5499872 TCAATCATGTCATAGTGTCTCTTACCATTAGACATAT
131 TCTGTCATGTCATAGTGTCTCATCCCATCAGACATAA
* * * *
5499909 GAGTTATTGTGATGAATAGTTCCCCAAAGGGAAACATCATATTTACATATAATTGACTGGTAAAT
1 GAGTTATTGTGATGAATAGTTTCCCAAAGGGGAACATCATATTTACATATAATTGATTGGAAAAT
* * * * * * * **
5499974 GTAGATAA-CTTT-GAAAAA-TGAAGGCTCTTTTCATAAGAAGAACTTTTACATTTTATA-GGAA
66 GTAGAGAATCTTTAAAAAAAGGGAA-G-ACTTTTCACAAGAAGCACTTTTACCTTTTGCAGGGAA
* * * *
5500035 TCTATGCCATGTAATAGTGTTTCATCCCATCAGACATAA
129 TCTCTGTCATGTCATAGTGTCTCATCCCATCAGACATAA
* * * * ** *
5500074 GAGTTATTTTGATGAATA-ATTCTACGAAGCAGAACATCAT-TTTTCTATATAATTGATTGGAAA
1 GAGTTATTGTGATGAATAGTTTC-CCAAAGGGGAACATCATATTTAC-ATATAATTGATTGGAAA
* * ** *** *
5500137 ATGCAAAGAATCCCTAAAGAAAAGGGAAGGGTA-TTTTCACAAGAAGTGTTTTTACCTTTTGTAG
64 ATGTAGAGAATCTTTAAA-AAAAGGGAA--G-ACTTTTCACAAGAAGCACTTTTACCTTTTGCAG
* * * * *
5500201 GGAATCCCTGCCATGTCATATTATCTCATCCCATCAGACATGA
125 GGAATCTCTGTCATGTCATAGTGTCTCATCCCATCAGACATAA
* * * * * *
5500244 CAGTTATTGTGATGAATA-ATTCCCTAAAAGGGAACATCATCTGTGCATATAATTGATTGGAAAA
1 GAGTTATTGTGATGAATAGTTTCCC-AAAGGGGAACATCATATTTACATATAATTGATTGGAAAA
* ** * * * ** * **
5500308 TGTATAGAATCTTTGGAAAACGGGAATAATCTTTTCACAAGAGGTGCTTTAAGATTTTGCAGGGA
65 TGTAGAGAATCTTTAAAAAAAGGGAA-GA-CTTTTCACAAGAAGCACTTTTACCTTTTGCAGGGA
* * * * * *
5500373 ATTTCTGCCATGCCCTAGTGTCTCGTCCCATCAGACATGA
128 ATCTCTGTCATGTCATAGTGTCTCATCCCATCAGACATAA
*
5500413 GAGTTATTATGATGAATAGTT
1 GAGTTATTGTGATGAATAGTT
5500434 CCCTGAAGGA
Statistics
Matches: 554, Mismatches: 121, Indels: 32
0.78 0.17 0.05
Matches are distributed among these distances:
164 9 0.02
165 90 0.16
166 31 0.06
167 129 0.23
168 67 0.12
169 126 0.23
170 99 0.18
171 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (167 bp):
GAGTTATTGTGATGAATAGTTTCCCAAAGGGGAACATCATATTTACATATAATTGATTGGAAAAT
GTAGAGAATCTTTAAAAAAAGGGAAGACTTTTCACAAGAAGCACTTTTACCTTTTGCAGGGAATC
TCTGTCATGTCATAGTGTCTCATCCCATCAGACATAA
Found at i:5500253 original size:335 final size:333
Alignment explanation
Indices: 5499575--5500430 Score: 823
Period size: 335 Copynumber: 2.5 Consensus size: 333
5499565 ATATATAGTG
* * * * * *
5499575 AGTTATTGTGATGACTAGTTTCCCGAAGGGGAATATCATCTATACATAAAATGGATTGGAAAAT-
1 AGTTATTGTGATGAATAG-TTCCCCAAAGGGAACATCATCTATACATATAATTGATTGGAAAATG
* * *
5499639 TAAGAAAATCTTTGAAAAAGGGAAGACGTTTTTCACAAGAAGCACTTTCACCTTTTGCAATGAAT
65 T-AGAAAATCTTTGAAAAAGGGAAGACGTTTTTCACAAGAAGAACTTTCACATTTT-CAAGGAAT
* * * * * *
5499704 CTCTGTCATGTCATAGTGTCTCATCCCATCAGACATAAGATTTATTATGATGAATAGTTTCCCAA
128 CTATGCCATGTAATAGTGTCTCATCCCATCAGACATAAGAGTTATTATGATGAATAATTTCACAA
** * * **
5499769 AGGGGAACATCATATTTGCATATAATTGACTGAAAAATGTAGAGAATCTTTAAAAAAAAGGAAGA
193 AGCAGAACATCATATTTGCATATAATTGACTGAAAAATGCAAAGAATCCCTAAAAAAAAGGAAGA
* * * * *
5499834 CTTTTCACAAGAAGCATTTTTATCTTTTACAGGGAATCTCAATCATGTCATAGTGTCTCTTACCA
258 CTTTTCACAAGAAGCATTTTTACCTTTTACAGGGAATCCCAACCATGTCATAGTATCTCATACCA
* *
5499899 TTAGACATATG
323 TCAGACATATC
* * * *
5499910 AGTTATTGTGATGAATAGTTCCCCAAAGGGAAACATCATATTTACATATAATTGACTGGTAAATG
1 AGTTATTGTGATGAATAGTTCCCCAAAGGG-AACATCATCTATACATATAATTGATTGGAAAATG
* * * * *
5499975 TAGATAA-CTTTGAAAAA-TGAAGGC-TCTTTTCATAAGAAGAACTTTTACATTTT-ATAGGAAT
65 TAGAAAATCTTTGAAAAAGGGAAGACGT-TTTTCACAAGAAGAACTTTCACATTTTCA-AGGAAT
* * *
5500036 CTATGCCATGTAATAGTGTTTCATCCCATCAGACATAAGAGTTATTTTGATGAATAA-TTCTACG
128 CTATGCCATGTAATAGTGTCTCATCCCATCAGACATAAGAGTTATTATGATGAATAATTTC-ACA
* * * *
5500100 AAGCAGAACATCAT-TTTTCTATATAATTGATTGGAAAATGCAAAGAATCCCTAAAGAAAAGGGA
192 AAGCAGAACATCATATTTGC-ATATAATTGACTGAAAAATGCAAAGAATCCCTAAA-AAAAAGGA
** ** ** *
5500164 AGGGTA-TTTTCACAAGAAGTGTTTTTACCTTTTGTAGGGAATCCCTGCCATGTCATATTATCTC
255 A--G-ACTTTTCACAAGAAGCATTTTTACCTTTTACAGGGAATCCCAACCATGTCATAGTATCTC
*
5500228 ATCCCATCAGACATGA-C
317 ATACCATCAGACAT-ATC
* * * *
5500245 AGTTATTGTGATGAATAATTCCCTAAAAGGGAACATCATCTGTGCATATAATTGATTGGAAAATG
1 AGTTATTGTGATGAATAGTTCCC-CAAAGGGAACATCATCTATACATATAATTGATTGGAAAATG
* * * * * * ** * * *
5500310 TATAGAATCTTTGGAAAACGGGAATA-ATCTTTTCACAAGAGGTGCTTTAAGATTTTGCAGGGAA
65 TAGAAAATCTTT-GAAAAAGGGAAGACGT-TTTTCACAAGAAGAACTTTCACATTTT-CAAGGAA
* * *** * *
5500374 TTTCTGCCATGCCCTAGTGTCTCGTCCCATCAGACATGAGAGTTATTATGATGAATA
127 TCTATGCCATGTAATAGTGTCTCATCCCATCAGACATAAGAGTTATTATGATGAATA
5500431 GTTCCCTGAA
Statistics
Matches: 422, Mismatches: 81, Indels: 32
0.79 0.15 0.06
Matches are distributed among these distances:
331 8 0.02
332 98 0.23
333 36 0.09
334 20 0.05
335 163 0.39
336 13 0.03
337 5 0.01
338 26 0.06
339 52 0.12
340 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (333 bp):
AGTTATTGTGATGAATAGTTCCCCAAAGGGAACATCATCTATACATATAATTGATTGGAAAATGT
AGAAAATCTTTGAAAAAGGGAAGACGTTTTTCACAAGAAGAACTTTCACATTTTCAAGGAATCTA
TGCCATGTAATAGTGTCTCATCCCATCAGACATAAGAGTTATTATGATGAATAATTTCACAAAGC
AGAACATCATATTTGCATATAATTGACTGAAAAATGCAAAGAATCCCTAAAAAAAAGGAAGACTT
TTCACAAGAAGCATTTTTACCTTTTACAGGGAATCCCAACCATGTCATAGTATCTCATACCATCA
GACATATC
Found at i:5500454 original size:169 final size:167
Alignment explanation
Indices: 5499574--5500452 Score: 695
Period size: 169 Copynumber: 5.2 Consensus size: 167
5499564 AATATATAGT
* * * * * * * * * * *
5499574 GAGTTATTGTGATGACTAGTTTCCCGAAGGGGAATATCATCTATACATAAAATGGATTGGAAAAT
1 GAGTTATTATGATGAATAG-TTCCCAAAGGAGAACATCATATTTGCATATAATTGACTGGAAAAT
* * * * * **
5499639 -TAAGAAAATCTTT-GAAAAAGGGAA-GA-CGTTTTTCACAAGAAGCACTTTCACCTTTTGCAAT
65 GT-AGAGAATCTTTAGAAAAA-GGAAGGATC--TTTTCACAAGAAGTACTTTTACATTTTACAGG
*
5499700 GAATCTCTGTCATGTCATAGTGTCTCATCCCATCAGACATAA
126 GAATCTCTGCCATGTCATAGTGTCTCATCCCATCAGACATAA
* * *
5499742 GATTTATTATGATGAATAGTTTCCCAAAGGGGAACATCATATTTGCATATAATTGACTGAAAAAT
1 GAGTTATTATGATGAATAG-TTCCCAAAGGAGAACATCATATTTGCATATAATTGACTGGAAAAT
* * *
5499807 GTAGAGAATCTTTAAAAAAAAGGAA-GA-CTTTTCACAAGAAGCATTTTTATC-TTTTACAGGGA
65 GTAGAGAATCTTT-AGAAAAAGGAAGGATCTTTTCACAAGAAGTACTTTTA-CATTTTACAGGGA
*** * * * *
5499869 ATCTCAATCATGTCATAGTGTCTCTTACCATTAGACATAT
128 ATCTCTGCCATGTCATAGTGTCTCATCCCATCAGACATAA
* * *
5499909 GAGTTATTGTGATGAATAGTTCCCCAAAGG-GAAACATCATATTTACATATAATTGACTGGTAAA
1 GAGTTATTATGATGAATAGTT-CCCAAAGGAG-AACATCATATTTGCATATAATTGACTGGAAAA
* * * * * *
5499973 TGTAGATAA-CTTT-GAAAAATGAAGGCTCTTTTCATAAGAAGAACTTTTACATTTTATA-GGAA
64 TGTAGAGAATCTTTAGAAAAAGGAAGGATCTTTTCACAAGAAGTACTTTTACATTTTACAGGGAA
* * *
5500035 TCTATGCCATGTAATAGTGTTTCATCCCATCAGACATAA
129 TCTCTGCCATGTCATAGTGTCTCATCCCATCAGACATAA
* * * * * * *
5500074 GAGTTATTTTGATGAATAATTCTACGAAGCAGAACATCAT-TTTTCTATATAATTGATTGGAAAA
1 GAGTTATTATGATGAATAGTTC-CCAAAGGAGAACATCATATTTGC-ATATAATTGACTGGAAAA
* * ** * * * ** * **
5500138 TGCAAAGAATCCCTAAAGAAAAGGGAAGGGTATTTTCACAAGAAGTGTTTTTACCTTTTGTAGGG
64 TGTAGAGAAT--CTTTAGAAAAAGGAAGGATCTTTTCACAAGAAGTACTTTTACATTTTACAGGG
* * * *
5500203 AATCCCTGCCATGTCATATTATCTCATCCCATCAGACATGA
127 AATCTCTGCCATGTCATAGTGTCTCATCCCATCAGACATAA
* * * * * *
5500244 CAGTTATTGTGATGAATAATTCCCTAAAAGG-GAACATCATCTGTGCATATAATTGATTGGAAAA
1 GAGTTATTATGATGAATAGTTCCC--AAAGGAGAACATCATATTTGCATATAATTGACTGGAAAA
* * * ** * * * * *
5500308 TGTATAGAATCTTTGGAAAACGGGAATAATCTTTTCACAAGAGGTGCTTTAAGATTTTGCAGGGA
64 TGTAGAGAATCTTTAGAAAA-AGGAAGGATCTTTTCACAAGAAGTACTTTTACATTTTACAGGGA
* * * * *
5500373 ATTTCTGCCATGCCCTAGTGTCTCGTCCCATCAGACATGA
128 ATCTCTGCCATGTCATAGTGTCTCATCCCATCAGACATAA
* *
5500413 GAGTTATTATGATGAATAGTTCCCTGAAGGAAAACATCAT
1 GAGTTATTATGATGAATAGTTCCC-AAAGGAGAACATCAT
5500453 CTATACACAT
Statistics
Matches: 576, Mismatches: 113, Indels: 43
0.79 0.15 0.06
Matches are distributed among these distances:
164 13 0.02
165 88 0.15
166 33 0.06
167 123 0.21
168 77 0.13
169 140 0.24
170 96 0.17
171 6 0.01
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (167 bp):
GAGTTATTATGATGAATAGTTCCCAAAGGAGAACATCATATTTGCATATAATTGACTGGAAAATG
TAGAGAATCTTTAGAAAAAGGAAGGATCTTTTCACAAGAAGTACTTTTACATTTTACAGGGAATC
TCTGCCATGTCATAGTGTCTCATCCCATCAGACATAA
Found at i:5502713 original size:23 final size:24
Alignment explanation
Indices: 5502678--5502726 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
5502668 GCTACAAGAG
5502678 TTGCAAGCAAAAAATGACCAAAGT
1 TTGCAAGCAAAAAATGACCAAAGT
5502702 TTGCAAGCAAAAAATGACCAAAGT
1 TTGCAAGCAAAAAATGACCAAAGT
5502726 T
1 T
5502727 ACAATTAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.18
Consensus pattern (24 bp):
TTGCAAGCAAAAAATGACCAAAGT
Found at i:5503547 original size:15 final size:15
Alignment explanation
Indices: 5503480--5503549 Score: 50
Period size: 15 Copynumber: 4.7 Consensus size: 15
5503470 TAATTATATA
*
5503480 ATTGTATTTTGTGGT
1 ATTGTATTTTATGGT
* * *
5503495 ATTGAAATTTATGTT
1 ATTGTATTTTATGGT
* *
5503510 ATTTTAATTTATGGT
1 ATTGTATTTTATGGT
*** *
5503525 AAAATATTTTATGTT
1 ATTGTATTTTATGGT
5503540 ATTGTATTTT
1 ATTGTATTTT
5503550 CTAATCTTAT
Statistics
Matches: 40, Mismatches: 15, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (15 bp):
ATTGTATTTTATGGT
Found at i:5504359 original size:19 final size:19
Alignment explanation
Indices: 5504299--5504369 Score: 78
Period size: 19 Copynumber: 3.8 Consensus size: 19
5504289 TTGCAGCCAA
5504299 GGGGTATAGATACCCCTAGGG
1 GGGGTATAGATACCCCT--GG
* *
5504320 GGGGTATCGATA---CT-C
1 GGGGTATAGATACCCCTGG
5504335 GGGGTATAGATACCCCTGG
1 GGGGTATAGATACCCCTGG
5504354 GGGGTATAGATACCCC
1 GGGGTATAGATACCCC
5504370 CCGAGCAATC
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
15 11 0.26
18 4 0.10
19 16 0.38
21 11 0.26
ACGTcount: A:0.23, C:0.21, G:0.35, T:0.21
Consensus pattern (19 bp):
GGGGTATAGATACCCCTGG
Found at i:5504366 original size:34 final size:35
Alignment explanation
Indices: 5504299--5504366 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 35
5504289 TTGCAGCCAA
*
5504299 GGGGTATAGATACCCCTAGGGGGGGTATCGATACTC
1 GGGGTATAGATACCCCTA-GGGGGGTATAGATACTC
5504335 GGGGTATAGATACCCCT-GGGGGGTATAGATAC
1 GGGGTATAGATACCCCTAGGGGGGTATAGATAC
5504367 CCCCCGAGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 14 0.45
36 17 0.55
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.22
Consensus pattern (35 bp):
GGGGTATAGATACCCCTAGGGGGGTATAGATACTC
Found at i:5504554 original size:30 final size:30
Alignment explanation
Indices: 5504507--5504566 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
5504497 AAACTTTGAA
5504507 TAAATTAAATTAAGTCCAAAAA-CATTTTG
1 TAAATTAAATTAAGTCCAAAAACCATTTTG
*
5504536 TAAATTCAATTAAAGTCCAAAAACCATTTTG
1 TAAATTAAATT-AAGTCCAAAAACCATTTTG
5504567 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 11 0.39
31 7 0.25
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTAAATTAAGTCCAAAAACCATTTTG
Found at i:5504695 original size:23 final size:21
Alignment explanation
Indices: 5504669--5504720 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
5504659 CTTAATAAAA
5504669 TGTTTAATGAAAAAGATACAAAT
1 TGTTTAA--AAAAAGATACAAAT
* *
5504692 TG-TTAAAAAAGGATACTAAT
1 TGTTTAAAAAAAGATACAAAT
5504712 TG-TTAAAAA
1 TGTTTAAAAA
5504721 GATAACCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 21 0.78
22 4 0.15
23 2 0.07
ACGTcount: A:0.52, C:0.04, G:0.13, T:0.31
Consensus pattern (21 bp):
TGTTTAAAAAAAGATACAAAT
Found at i:5504706 original size:20 final size:19
Alignment explanation
Indices: 5504678--5504734 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
5504668 ATGTTTAATG
5504678 AAAAAGATACAAATTGTTA
1 AAAAAGATACAAATTGTTA
*
5504697 AAAAAGGATACTAATTGTT-
1 AAAAA-GATACAAATTGTTA
*
5504716 AAAAAGATAACCAATTGTT
1 AAAAAGAT-ACAAATTGTT
5504735 GGGAAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.09
19 19 0.56
20 12 0.35
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.28
Consensus pattern (19 bp):
AAAAAGATACAAATTGTTA
Found at i:5505081 original size:26 final size:27
Alignment explanation
Indices: 5505052--5505116 Score: 100
Period size: 26 Copynumber: 2.5 Consensus size: 27
5505042 TACTTTATGC
5505052 AATACCAAATT-TTGAAATTTGATATT
1 AATACCAAATTGTTGAAATTTGATATT
*
5505078 AATATC-AATTGTTGAAATTTGATATT
1 AATACCAAATTGTTGAAATTTGATATT
5505104 AATACC-AATTGTT
1 AATACCAAATTGTT
5505117 TAAAATTAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 4 0.11
26 32 0.89
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (27 bp):
AATACCAAATTGTTGAAATTTGATATT
Done.