Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
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 103 of 143
Found at i:31620737 original size:17 final size:17
Alignment explanation
Indices: 31620710--31620776 Score: 77
Period size: 17 Copynumber: 4.0 Consensus size: 17
31620700 ATAAATAAAT
31620710 TAAAGAAAGAAAAAAGAA
1 TAAA-AAAGAAAAAAGAA
31620728 TAAAAAAGAAAAAAG-A
1 TAAAAAAGAAAAAAGAA
31620744 -AAAAAAGAAAAAA-AA
1 TAAAAAAGAAAAAAGAA
* *
31620759 GAGAAAATGAAAAAAGAA
1 TA-AAAAAGAAAAAAGAA
31620777 AAAGGAAATA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
15 14 0.32
16 2 0.05
17 22 0.50
18 6 0.14
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (17 bp):
TAAAAAAGAAAAAAGAA
Found at i:31620742 original size:24 final size:23
Alignment explanation
Indices: 31620715--31620779 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 23
31620705 TAAATTAAAG
31620715 AAAGAAAAAAGAATAAAAAAGAAA
1 AAAGAAAAAAGAA-AAAAAAGAAA
31620739 AAAGAAAAAAAGAAAAAAAAGAGAA
1 AAAG-AAAAAAGAAAAAAAAGA-AA
*
31620764 AATGAAAAAAGAAAAA
1 AAAGAAAAAAGAAAAA
31620780 GGAAATAGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
24 24 0.63
25 14 0.37
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (23 bp):
AAAGAAAAAAGAAAAAAAAGAAA
Found at i:31620748 original size:26 final size:25
Alignment explanation
Indices: 31620719--31620800 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
31620709 TTAAAGAAAG
31620719 AAAAAAGAATAAAAAAGAAAAAAG-A
1 AAAAAAGAA-AAAAAAGAAAAAAGAA
*
31620744 AAAAAAGAAAAAAAAGAGAAAATGAA
1 AAAAAAGAAAAAAAAGA-AAAAAGAA
* *
31620770 AAAAGAA-AAAGGAAATAGAAAATAGAA
1 AAAA-AAGAAA--AAAAAGAAAAAAGAA
31620797 AAAA
1 AAAA
31620801 GGGGAAAAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
24 8 0.17
25 14 0.29
26 8 0.17
27 12 0.25
28 6 0.12
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (25 bp):
AAAAAAGAAAAAAAAGAAAAAAGAA
Found at i:31620797 original size:13 final size:13
Alignment explanation
Indices: 31620717--31620799 Score: 52
Period size: 13 Copynumber: 6.5 Consensus size: 13
31620707 AATTAAAGAA
*
31620717 AGAAAAA-AGAAT
1 AGAAAAAGAAAAT
*
31620729 A-AAAAAGAAAAA
1 AGAAAAAGAAAAT
31620741 AGAAAAAAAGAAAA-
1 AG--AAAAAGAAAAT
*
31620755 A-AAAGAGAAAAT
1 AGAAAAAGAAAAT
31620767 -GAAAAAAGAAAA-
1 AG-AAAAAGAAAAT
*
31620779 AGGAAATAGAAAAT
1 A-GAAAAAGAAAAT
31620793 AGAAAAA
1 AGAAAAA
31620800 AGGGGAAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 19
0.69 0.08 0.24
Matches are distributed among these distances:
11 14 0.25
12 5 0.09
13 23 0.42
14 3 0.05
15 10 0.18
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.05
Consensus pattern (13 bp):
AGAAAAAGAAAAT
Found at i:31621838 original size:50 final size:50
Alignment explanation
Indices: 31621750--31621884 Score: 171
Period size: 50 Copynumber: 2.7 Consensus size: 50
31621740 AGAAAAATAT
* ** *
31621750 GAAGATTTGAAGGGAAAGGTTGAAGTTGAAACGACAAACCTGGTACCTAA
1 GAAGATGTGAAGGGAAAGGTTGAAGCCGAAACGACAAACCCGGTACCTAA
* * *
31621800 GAAGATGTGATGGGAAAGGTTGAAGCCGCAACGTCAAACCCGGTACCTAA
1 GAAGATGTGAAGGGAAAGGTTGAAGCCGAAACGACAAACCCGGTACCTAA
* * * *
31621850 GAAGATGTGAAGCGAAAAGTTGAGGCCGTAACGAC
1 GAAGATGTGAAGGGAAAGGTTGAAGCCGAAACGAC
31621885 GAATCCAGTA
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 72 1.00
ACGTcount: A:0.37, C:0.16, G:0.30, T:0.17
Consensus pattern (50 bp):
GAAGATGTGAAGGGAAAGGTTGAAGCCGAAACGACAAACCCGGTACCTAA
Found at i:31621896 original size:50 final size:50
Alignment explanation
Indices: 31621750--31621905 Score: 143
Period size: 50 Copynumber: 3.1 Consensus size: 50
31621740 AGAAAAATAT
* * * ** * **
31621750 GAAGATTTGAAGGGAAAGGTTGAAGTTGAAACGACAAACCTGGTACCTAA
1 GAAGATGTGAAGCGAAAAGTTGAAGCCGCAACGACAAACCCAGTACCTAA
* * * * *
31621800 GAAGATGTGATGGGAAAGGTTGAAGCCGCAACGTCAAACCCGGTACCTAA
1 GAAGATGTGAAGCGAAAAGTTGAAGCCGCAACGACAAACCCAGTACCTAA
* * * *
31621850 GAAGATGTGAAGCGAAAAGTTGAGGCCGTAACGACGAATCCAGTACCTTAA
1 GAAGATGTGAAGCGAAAAGTTGAAGCCGCAACGACAAACCCAGTACC-TAA
31621901 -AAGAT
1 GAAGAT
31621906 ATTATGGGAA
Statistics
Matches: 89, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
50 86 0.97
51 3 0.03
ACGTcount: A:0.38, C:0.16, G:0.28, T:0.18
Consensus pattern (50 bp):
GAAGATGTGAAGCGAAAAGTTGAAGCCGCAACGACAAACCCAGTACCTAA
Found at i:31622272 original size:197 final size:197
Alignment explanation
Indices: 31621870--31622274 Score: 465
Period size: 197 Copynumber: 2.1 Consensus size: 197
31621860 AGCGAAAAGT
* * * *
31621870 TGAGGCCGTAACGACGAATCCAGTACCTTAAAAGATATTATGGGAAAGATTAAGGCCGCACCGGT
1 TGAGGCCGCAACGACGAACCCAGTACCTTAAAAGATATTATGGGAAAGATTAAGGCCGCAACGAT
* * * ** *
31621935 GAATCCGGTTCCATAGAGATGCAATAGAAAAGGTTGTGGTCGTAACGTCGAACCCGATACCTAAG
66 GAATCCGATTCCATAAAGATGCAATAGAAAAGGTTGTGGCCACAACGGCGAACCCGATACCTAAG
* ** *
31622000 AAGATGTGAAGAGAAAAGTTGAGGTTGCAACGGCAAACCTAGTACCACAAAATTTGAAGGGAATG
131 AAGATGTGAAGAGAAAAGTTGAGGCTGCAACGGCAAACCTAGTACCACAAAACATGAAGGGAAAG
**
31622065 GT
196 AA
* * *
31622067 TAAGGCCGCAACGACGAACCCAGTACCTTAAAAGATATTATGGGAAAGATTGA-GCCTTCAACGA
1 TGAGGCCGCAACGACGAACCCAGTACCTTAAAAGATATTATGGGAAAGATTAAGGCC-GCAACGA
* * * * *
31622131 TGAATCCGATTCCATAAAGATGCAATAGGAAAGGTTG-GGACCACAATGGCGAACCTGGTTCC-A
65 TGAATCCGATTCCATAAAGATGCAATAGAAAAGGTTGTGG-CCACAACGGCGAACCCGATACCTA
* * * * * * ** *
31622194 TGAAGATTTGAAGGGAAATGTTGAGGCTGCAACGGCAAGCCTGGTACCTTAAAACCATGACGGGA
129 AGAAGATGTGAAGAGAAAAGTTGAGGCTGCAACGGCAAACCTAGTACCACAAAA-CATGAAGGGA
31622259 AAGAA
193 AAGAA
31622264 TGAGGCCGCAA
1 TGAGGCCGCAA
31622275 TGGTGAGCCT
Statistics
Matches: 171, Mismatches: 34, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
196 51 0.30
197 120 0.70
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.20
Consensus pattern (197 bp):
TGAGGCCGCAACGACGAACCCAGTACCTTAAAAGATATTATGGGAAAGATTAAGGCCGCAACGAT
GAATCCGATTCCATAAAGATGCAATAGAAAAGGTTGTGGCCACAACGGCGAACCCGATACCTAAG
AAGATGTGAAGAGAAAAGTTGAGGCTGCAACGGCAAACCTAGTACCACAAAACATGAAGGGAAAG
AA
Found at i:31622657 original size:39 final size:39
Alignment explanation
Indices: 31622541--31622781 Score: 120
Period size: 39 Copynumber: 6.2 Consensus size: 39
31622531 TATGAGGTAA
*
31622541 ATTGCAGCCATCCAATCTTTTAGCCCGAGCTTAGGGCA-
1 ATTGCAGCCATCCAATCTTTTACCCCGAGCTTAGGGCAG
* * * *
31622579 AAT-CA-CCATCAGCTAATCTCTTACCCTGAGCCT-GAGGCAG
1 ATTGCAGCCATC--C-AATCTTTTACCCCGAGCTTAG-GGCAG
*
31622619 ATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCAG
1 ATTGCAGCCATCCAATCTTTTACCCCGAGCTTAGGGCAG
* * *** *
31622658 A-T-CA-CCATCAGCCAATCTCTTACCCTGA-AAAAGGGGAAG
1 ATTGCAGCCAT---CCAATCTTTTACCCCGAGCTTA-GGGCAG
* ** * * * * *
31622697 ATTACAATCATCCGATCTTCTACCCCGACCATGGGGCAG
1 ATTGCAGCCATCCAATCTTTTACCCCGAGCTTAGGGCAG
** * * * *
31622736 ATCACAGCCATCCAATCTCTTACCCCGATCATAGGGTAG
1 ATTGCAGCCATCCAATCTTTTACCCCGAGCTTAGGGCAG
31622775 ATTGCAG
1 ATTGCAG
31622782 TTATCCAAAA
Statistics
Matches: 150, Mismatches: 37, Indels: 31
0.69 0.17 0.14
Matches are distributed among these distances:
36 9 0.06
37 4 0.03
38 6 0.04
39 113 0.75
40 6 0.04
41 4 0.03
42 8 0.05
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (39 bp):
ATTGCAGCCATCCAATCTTTTACCCCGAGCTTAGGGCAG
Found at i:31622699 original size:78 final size:78
Alignment explanation
Indices: 31622541--31622760 Score: 253
Period size: 78 Copynumber: 2.8 Consensus size: 78
31622531 TATGAGGTAA
* * * *
31622541 ATTGCAGCCATCCAATCTTTTAGCCCGAGCTTAGGGCAAATCACCATCAGCTAATCTCTTACCCT
1 ATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCAGATCACCATCAGCCAATCTCTTACCCT
**** *
31622606 GAGCCTGAGGCAG
66 GAAAAAGAGGAAG
31622619 ATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCAGATCACCATCAGCCAATCTCTTACCCT
1 ATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCAGATCACCATCAGCCAATCTCTTACCCT
*
31622684 GAAAAAGGGGAAG
66 GAAAAAGAGGAAG
* ** * * * * * *
31622697 ATTACAATCATCCGATCTTCTACCCCGACCATGGGGCAGATCA-CAGCCATCCAATCTCTTACCC
1 ATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCAGATCACCA-TCAGCCAATCTCTTACCC
31622761 CGATCATAGG
Statistics
Matches: 122, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
77 2 0.02
78 120 0.98
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23
Consensus pattern (78 bp):
ATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCAGATCACCATCAGCCAATCTCTTACCCT
GAAAAAGAGGAAG
Found at i:31623172 original size:209 final size:209
Alignment explanation
Indices: 31622795--31623380 Score: 835
Period size: 209 Copynumber: 2.8 Consensus size: 209
31622785 TCCAAAATAG
* * ** *
31622795 GTGATGCGGTCATCTTCTTGATGAGATACAAAAAAGTATACTGAATCAATGAAACAAGGCTCAAT
1 GTGAGGCGGTCATCTTCTTGATGAGATACAAATAAGTATACCAAATCAATGAAACAAGACTCAAT
* * * ** * *
31622860 ATGAGCGAAACTTCGAATCCCAACTTTCTGATAAGATACTGAGAAGCAAGTCGAAGTAATAAAAT
66 ATGAGCGAAACTTCGAA-CCCAGCTTCCTGATGAGATGTTGAGAAGCAGGTCGAAGCAATAAAAT
* *
31622925 GGTCAGCTTCCTGATGAGATACAAAGAAGT-AGACCAAATTCGTCTTTCTAATGAGATACAGAGA
130 GGTCAGCTTCCTGATGAGATACAGAGAAGTGAGACCAAATTCGTCTTCCTAATGAGATACAGAGA
31622989 AGCAGATTGAAACAA
195 AGCAGATTGAAACAA
*
31623004 GTGAGGCGGTCATCTTCTTGATGAGATACAAATAAGTATACCAAATCAATGACACAAGACTCAAT
1 GTGAGGCGGTCATCTTCTTGATGAGATACAAATAAGTATACCAAATCAATGAAACAAGACTCAAT
31623069 ATGAGCGAAACTTCGAACCCTAGCTTCCTGATGAGATGTTGAGAAGCAGGTCGAAGCAATAAAAT
66 ATGAGCGAAACTTCGAACCC-AGCTTCCTGATGAGATGTTGAGAAGCAGGTCGAAGCAATAAAAT
*
31623134 GGTCAGCTTCCTGATGAGATACAGAGAAGTGA-ACCAAATTCGTCTTCCTGATGAGATACAGAGA
130 GGTCAGCTTCCTGATGAGATACAGAGAAGTGAGACCAAATTCGTCTTCCTAATGAGATACAGAGA
31623198 AGCAGATTGAAACAA
195 AGCAGATTGAAACAA
* * * * * *
31623213 GTGAGACGGTCATCTTCCTGATGAGATGCAGATAAGCATACCAAATCAATAAAACAA-AGCTCAA
1 GTGAGGCGGTCATCTTCTTGATGAGATACAAATAAGTATACCAAATCAATGAAACAAGA-CTCAA
* * *
31623277 TGTGAGCGAAACTTCGAACCCCAGCTTCCTGATGAG--GTACGAGAAGTAGGTCGAAGCAATAAA
65 TATGAGCGAAACTTCGAA-CCCAGCTTCCTGATGAGATGT-TGAGAAGCAGGTCGAAGCAATAAA
*
31623340 ATGGTC-GACTTCCTGATGAGATACAGAGAAGTG-GATCAAAT
128 ATGGTCAG-CTTCCTGATGAGATACAGAGAAGTGAGACCAAAT
31623381 CAATAAAATG
Statistics
Matches: 343, Mismatches: 27, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
207 3 0.01
208 63 0.18
209 273 0.80
210 4 0.01
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.23
Consensus pattern (209 bp):
GTGAGGCGGTCATCTTCTTGATGAGATACAAATAAGTATACCAAATCAATGAAACAAGACTCAAT
ATGAGCGAAACTTCGAACCCAGCTTCCTGATGAGATGTTGAGAAGCAGGTCGAAGCAATAAAATG
GTCAGCTTCCTGATGAGATACAGAGAAGTGAGACCAAATTCGTCTTCCTAATGAGATACAGAGAA
GCAGATTGAAACAA
Found at i:31623385 original size:48 final size:48
Alignment explanation
Indices: 31623301--31623438 Score: 181
Period size: 48 Copynumber: 2.9 Consensus size: 48
31623291 CGAACCCCAG
* * *
31623301 CTTCCTGATGAGGTAC-GAGAAGTAGG-TCGAAGCAATAAAATGGTCGA
1 CTTCCTGATGAGATACAGAGAAGT-GGATCAAATCAATAAAATGGTCGA
31623348 CTTCCTGATGAGATACAGAGAAGTGGATCAAATCAATAAAATGGTCGA
1 CTTCCTGATGAGATACAGAGAAGTGGATCAAATCAATAAAATGGTCGA
* **
31623396 CTTCCTGATGAGATATAGAGAAGTATATATCAAATCAATAAAA
1 CTTCCTGATGAGATACAGAGAAG--TGGATCAAATCAATAAAA
31623439 CAAAGCTCAA
Statistics
Matches: 81, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
47 17 0.21
48 48 0.59
50 16 0.20
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (48 bp):
CTTCCTGATGAGATACAGAGAAGTGGATCAAATCAATAAAATGGTCGA
Found at i:31623686 original size:37 final size:37
Alignment explanation
Indices: 31623645--31623715 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
31623635 TAAAATGGTC
* *
31623645 GTCTTCCTGATGAGATATAGAGAAGTGGACTAAATCT
1 GTCTTCCTGATGAGATACAGAGAAGCGGACTAAATCT
* *
31623682 GTCTTCTTGATGAGATACAGAGAAGCGGATTAAA
1 GTCTTCCTGATGAGATACAGAGAAGCGGACTAAA
31623716 ATAAGTGAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (37 bp):
GTCTTCCTGATGAGATACAGAGAAGCGGACTAAATCT
Found at i:31624171 original size:6 final size:6
Alignment explanation
Indices: 31624160--31624236 Score: 60
Period size: 6 Copynumber: 13.7 Consensus size: 6
31624150 GACCCAACAG
* *
31624160 AATTTA AATTT- ATTTTA AGTTTA AATTT- -ATTTGA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA AATTTA
*
31624205 -ATTGTA AATTTA ATTTTA AATTT- -ATTTA AATT
1 AATT-TA AATTTA AATTTA AATTTA AATTTA AATT
31624237 ATTAATGTCC
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
4 11 0.19
5 5 0.09
6 34 0.60
7 7 0.12
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (6 bp):
AATTTA
Found at i:31624184 original size:17 final size:17
Alignment explanation
Indices: 31624160--31624222 Score: 90
Period size: 17 Copynumber: 3.7 Consensus size: 17
31624150 GACCCAACAG
31624160 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
* *
31624177 AGTTTAAATTTATTTGA
1 AATTTAAATTTATTTTA
*
31624194 AATTTAAATTTATTGTA
1 AATTTAAATTTATTTTA
*
31624211 AATTTAATTTTA
1 AATTTAAATTTA
31624223 AATTTATTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:31624890 original size:20 final size:22
Alignment explanation
Indices: 31624865--31624908 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
31624855 ACATTTATTG
*
31624865 TATATTAAA-GA-ATTAATAAA
1 TATATTAAACGATATAAATAAA
31624885 TATATTAAACGATATAAATAAA
1 TATATTAAACGATATAAATAAA
31624907 TA
1 TA
31624909 AATAAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
21 2 0.10
22 10 0.48
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (22 bp):
TATATTAAACGATATAAATAAA
Found at i:31626113 original size:30 final size:30
Alignment explanation
Indices: 31626040--31626114 Score: 100
Period size: 29 Copynumber: 2.5 Consensus size: 30
31626030 GAGGTCTTTG
* *
31626040 AACTGTCCAAAAATCATGTTTTGACCCTCA
1 AACTTTCCAAAAATTATGTTTTGACCCTCA
*
31626070 AACTTT-TAAAAATTATGTTTTGACCCTCA
1 AACTTTCCAAAAATTATGTTTTGACCCTCA
31626099 AA-TATTCCAAAAATTA
1 AACT-TTCCAAAAATTA
31626115 CATTTTAACC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 25 0.64
30 13 0.33
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.35
Consensus pattern (30 bp):
AACTTTCCAAAAATTATGTTTTGACCCTCA
Found at i:31626226 original size:30 final size:27
Alignment explanation
Indices: 31626166--31626236 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 27
31626156 CTAAACTTTA
* * *
31626166 AAAAATTACATTTTACCCCAAACTTCC
1 AAAAAGTATATTTTACCCCAAACATCC
31626193 AAAAAGTATTATTTTACCCCCAAAACATCC
1 AAAAAGTA-TATTTTA-CCCC-AAACATCC
*
31626223 AAAAATTATATTTT
1 AAAAAGTATATTTT
31626237 TGCCTCGAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.19
28 6 0.16
29 10 0.27
30 14 0.38
ACGTcount: A:0.44, C:0.23, G:0.01, T:0.32
Consensus pattern (27 bp):
AAAAAGTATATTTTACCCCAAACATCC
Found at i:31626324 original size:58 final size:56
Alignment explanation
Indices: 31626137--31626391 Score: 174
Period size: 58 Copynumber: 4.4 Consensus size: 56
31626127 CGAGCTTATT
* ** *
31626137 AAAAATTACATTTTTACCACT-AAACTTTAAAAAATTACATTTTACCCCAAACTTCC
1 AAAAAATACATTTTTACC-CTCAAACTTCCAAAAATTACATTTTGCCCCAAACTTCC
* * * * * * * *
31626193 AAAAAGTA-TTATTTTACCCCCAAAACATCCAAAAATTATATTTTTGCCTCGAACTTCTT
1 AAAAAATACAT-TTTTACCCTC-AAACTTCCAAAAATTACA-TTTTGCCCCAAACTTC-C
* * *
31626252 AACAATTACTTTTTTACCCTCAAACTTCCAAAAATTACATCTTTGCCCCCAAACTTCC
1 AAAAAATACATTTTTACCCTCAAACTTCCAAAAATTACAT-TTTG-CCCCAAACTTCC
* * * * * * * *
31626310 AAAAAACACATTTTTGCCCTCGAACTTCTAAAAATCAAATTTTTACCCCAAATTTTCC
1 AAAAAATACATTTTTACCCTCAAACTTCCAAAAATTACA-TTTTGCCCCAAA-CTTCC
* *
31626368 -CAAAATGACATTTTTACCCCCAAA
1 AAAAAAT-ACATTTTTACCCTCAAA
31626392 AATTTTAAAA
Statistics
Matches: 153, Mismatches: 35, Indels: 20
0.74 0.17 0.10
Matches are distributed among these distances:
55 2 0.01
56 14 0.09
57 26 0.17
58 84 0.55
59 25 0.16
60 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (56 bp):
AAAAAATACATTTTTACCCTCAAACTTCCAAAAATTACATTTTGCCCCAAACTTCC
Found at i:31626325 original size:29 final size:29
Alignment explanation
Indices: 31626137--31626391 Score: 153
Period size: 29 Copynumber: 8.8 Consensus size: 29
31626127 CGAGCTTATT
* * * **
31626137 AAAAATTACATTTTTACCACTAAACTTTA
1 AAAAATCACATTTTTACCCCCAAACTTCC
*
31626166 AAAAATTACA-TTTTA-CCCCAAACTTCC
1 AAAAATCACATTTTTACCCCCAAACTTCC
* *
31626193 AAAAAGT-A-TTATTTTACCCCCAAAACATCC
1 AAAAA-TCACAT-TTTTACCCCC-AAACTTCC
* * * * * *
31626223 AAAAATTATATTTTT-GCCTCGAACTTCTT
1 AAAAATCACATTTTTACCCCCAAACTTC-C
* * * *
31626252 AACAATTACTTTTTTACCCTCAAACTTCC
1 AAAAATCACATTTTTACCCCCAAACTTCC
* * *
31626281 AAAAATTACATCTTTGCCCCCAAACTTCC
1 AAAAATCACATTTTTACCCCCAAACTTCC
* * * * *
31626310 AAAAAACACATTTTTGCCCTCGAACTTCT
1 AAAAATCACATTTTTACCCCCAAACTTCC
* *
31626339 AAAAATCAAATTTTTA-CCCCAAATTTTCC
1 AAAAATCACATTTTTACCCCCAAA-CTTCC
* *
31626368 CAAAATGACATTTTTACCCCCAAA
1 AAAAATCACATTTTTACCCCCAAA
31626392 AATTTTAAAA
Statistics
Matches: 176, Mismatches: 39, Indels: 21
0.75 0.17 0.09
Matches are distributed among these distances:
27 14 0.08
28 21 0.12
29 106 0.60
30 34 0.19
31 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAAATCACATTTTTACCCCCAAACTTCC
Found at i:31626355 original size:87 final size:85
Alignment explanation
Indices: 31626176--31626391 Score: 236
Period size: 87 Copynumber: 2.5 Consensus size: 85
31626166 AAAAATTACA
* * ** *
31626176 TTTTACCCCAAACTTCCAAAAAGTATTATTTTACCCCCAAAACATCCAAAAATTATATTTTTGCC
1 TTTTACCCCAAACTTCCAAAAATTA-CATTTTACCCCC-AAACATCCAAAAAACACATTTTTGCC
* * **
31626241 TCGAACTTCTTAACAATTACTT
64 TCGAACTTCTTAAAAATCAAAT
* *
31626263 TTTTACCCTCAAACTTCCAAAAATTACATCTTTGCCCCCAAACTTCCAAAAAACACATTTTTGCC
1 TTTTACCC-CAAACTTCCAAAAATTACAT-TTTACCCCCAAACATCCAAAAAACACATTTTTG-C
31626328 CTCGAACTTC-TAAAAATCAAAT
63 CTCGAACTTCTTAAAAATCAAAT
* * *
31626350 TTTTACCCCAAATTTTCCCAAAATGACATTTTTACCCCCAAA
1 TTTTACCCCAAA-CTTCCAAAAATTACA-TTTTACCCCCAAA
31626392 AATTTTAAAA
Statistics
Matches: 109, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
86 4 0.04
87 69 0.63
88 36 0.33
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (85 bp):
TTTTACCCCAAACTTCCAAAAATTACATTTTACCCCCAAACATCCAAAAAACACATTTTTGCCTC
GAACTTCTTAAAAATCAAAT
Found at i:31627221 original size:97 final size:97
Alignment explanation
Indices: 31627046--31627239 Score: 261
Period size: 97 Copynumber: 2.0 Consensus size: 97
31627036 AACCTTGGAA
* *
31627046 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTTGCACCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTTCA
31627111 AAATCAAAGATAAA-GACACATTGCCTCGATTT
66 AAATCAAAGATAAAGGA-ACATTGCCTCGATTT
* *
31627143 AAGGGTATTCGATTAT-TCTGATTTGAAGAAAAATTACGCCTAGTACA-TTAAGGCACAAATTTT
1 AAGGATATTCGATTATCTC-GATTTGAAGAAAAATTACACCTAGTA-AGTTAAGGCACAAATTTT
* * *
31627206 CAAAGCTCGAA-ATAAAGGAATATTGCCTCGATTT
64 CAAA-ATCAAAGATAAAGGAACATTGCCTCGATTT
31627240 TAAAATTTTT
Statistics
Matches: 86, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
96 2 0.02
97 77 0.90
98 7 0.08
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTTCA
AAATCAAAGATAAAGGAACATTGCCTCGATTT
Found at i:31627670 original size:29 final size:29
Alignment explanation
Indices: 31627494--31627961 Score: 214
Period size: 29 Copynumber: 15.9 Consensus size: 29
31627484 TTTCGGGGGC
* *
31627494 AAAATGGTAATTTTTAGACA-TTCGAGGGAA
1 AAAATGG-AATTTTTGGA-AGTTCGAGGGTA
** *
31627524 AAAATATAATTTTTGGACAATT-GAGGGT-
1 AAAATGGAATTTTTGGA-AGTTCGAGGGTA
* * **
31627552 AGAATGTAACTTTTAAGAAGTTCGA-GGTCA
1 AAAATGGAA-TTTTTGGAAGTTCGAGGGT-A
31627582 AAAATGGAA-TTTTGGAAGTTCGAGGGT-
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* * * * * *
31627609 AATATGCTAATTTTAGAAAATTTG-GGGTCA
1 AAAATG-GAATTTTTGGAAGTTCGAGGGT-A
31627639 AAAATGGAATTTTTGGAAGTTCGAGGGT-
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
**
31627667 AAAATGGTAATTTTTGGAAAAAAAAATCGA-GGTCA
1 AAAATGG-AATTTTTGG-----AAGTTCGAGGGT-A
* *
31627702 AAAATGAAATTTTTGGAAGTTCGGGGGT-
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*
31627730 AAAATGGTGATTTTTGGAAGTTCGA-GGTCA
1 AAAATGG-AATTTTTGGAAGTTCGAGGGT-A
* * * *
31627760 AAAATGAAATTTTTGAAAGTTTGGGGGT-
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
** * *
31627788 AAAATGGTAATTTTTGGGAAAAT-AAGGTTA
1 AAAATGG-AATTTTT-GGAAGTTCGAGGGTA
* * *
31627818 AAAATGGAATTTTTAGAGGTTTTG-GGGTA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGTA
* *** * *
31627847 AAAATGTAATTTTCAAAAAGTT-TAGGGTT
1 AAAATGGAATTTT-TGGAAGTTCGAGGGTA
** * *
31627876 AAAATATAATTTTTGGAAAGTTTGAGGGTC
1 AAAATGGAATTTTTGG-AAGTTCGAGGGTA
* *
31627906 AAAATGTAATTTTTGGAAAGTTAGAGGGT-
1 AAAATGGAATTTTTGG-AAGTTCGAGGGTA
*
31627935 AAAATGTAATTTTTGGAAAGTTC-AGGG
1 AAAATGGAATTTTTGG-AAGTTCGAGGG
31627962 GTTAAAATAT
Statistics
Matches: 338, Mismatches: 67, Indels: 68
0.71 0.14 0.14
Matches are distributed among these distances:
27 5 0.01
28 59 0.17
29 169 0.50
30 81 0.24
33 3 0.01
34 15 0.04
35 6 0.02
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:31627904 original size:30 final size:30
Alignment explanation
Indices: 31627863--31627976 Score: 144
Period size: 30 Copynumber: 3.9 Consensus size: 30
31627853 TAATTTTCAA
31627863 AAAGTTT-AGGGTTAAAATATAATTTTTGG
1 AAAGTTTGAGGGTTAAAATATAATTTTTGG
* *
31627892 AAAGTTTGAGGGTCAAAATGTAATTTTTGG
1 AAAGTTTGAGGGTTAAAATATAATTTTTGG
* *
31627922 AAAGTTAGAGGG-TAAAATGTAATTTTTGG
1 AAAGTTTGAGGGTTAAAATATAATTTTTGG
* *
31627951 AAAG-TTCAGGGGTTAAAATATGATTT
1 AAAGTTTGA-GGGTTAAAATATAATTT
31627977 CTAGACAGTT
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
28 2 0.03
29 30 0.41
30 42 0.57
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.37
Consensus pattern (30 bp):
AAAGTTTGAGGGTTAAAATATAATTTTTGG
Found at i:31627926 original size:59 final size:59
Alignment explanation
Indices: 31627488--31627956 Score: 267
Period size: 58 Copynumber: 8.0 Consensus size: 59
31627478 TGAATATTTC
* * * * ** *
31627488 GGGGGCAAAATGGTAATTTTTAGACA-TTCGAGGGAAAAAATATAATTTTTGGACAA--TT
1 GGGGGTAAAATGGTAATTTTTGGAAAGTTAGAGGTTAAAAAT-GAATTTTTGGA-AAGTTT
* * * * * * *
31627546 GAGGGTAGAAT-GTAACTTTT-AAGAAGTTCGAGGTCAAAAATGGAA-TTTTGG-AAGTTC
1 GGGGGTAAAATGGTAATTTTTGGA-AAGTTAGAGGTTAAAAAT-GAATTTTTGGAAAGTTT
* * * * * * * * *
31627603 GAGGGTAATATGCTAA-TTTTAGAAAATTTGGGGTCAAAAATGGAATTTTTGG-AAGTTC
1 GGGGGTAAAATGGTAATTTTTGGAAAGTTAGAGGTTAAAAAT-GAATTTTTGGAAAGTTT
* ** * * *
31627661 GAGGGTAAAATGGTAATTTTTGGAAAAAAAAATCGAGGTCAAAAATGAAATTTTTGG-AAGTTC
1 GGGGGTAAAATGGTAATTTTTGG----AAAGTTAGAGGTTAAAAATG-AATTTTTGGAAAGTTT
* * *
31627724 GGGGGTAAAATGGTGATTTTTGG-AAGTTCGAGGTCAAAAATGAAATTTTT-GAAAGTTT
1 GGGGGTAAAATGGTAATTTTTGGAAAGTTAGAGGTTAAAAATG-AATTTTTGGAAAGTTT
* * *
31627782 GGGGGTAAAATGGTAATTTTTGGGAAA-ATA-AGGTTAAAAATGGAATTTTTAG-AGGTTT
1 GGGGGTAAAATGGTAATTTTT-GGAAAGTTAGAGGTTAAAAAT-GAATTTTTGGAAAGTTT
* ***
31627840 TGGGGTAAAAAT-GTAATTTTCAAAAAGTTTAG-GGTTAAAATAT-AATTTTTGGAAAGTTT
1 GGGGGT-AAAATGGTAATTTTTGGAAAG-TTAGAGGTTAAAA-ATGAATTTTTGGAAAGTTT
* *
31627899 GAGGGTCAAAAT-GTAATTTTTGGAAAGTTAGAGGGT-AAAATGTAATTTTTGGAAAGTT
1 GGGGGT-AAAATGGTAATTTTTGGAAAGTTAGAGGTTAAAAATG-AATTTTTGGAAAGTT
31627957 CAGGGGTTAA
Statistics
Matches: 336, Mismatches: 48, Indels: 53
0.77 0.11 0.12
Matches are distributed among these distances:
55 2 0.01
56 1 0.00
57 54 0.16
58 153 0.46
59 69 0.21
60 4 0.01
62 1 0.00
63 52 0.15
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTTGGAAAGTTAGAGGTTAAAAATGAATTTTTGGAAAGTTT
Found at i:31627963 original size:29 final size:29
Alignment explanation
Indices: 31627437--31627969 Score: 180
Period size: 29 Copynumber: 18.2 Consensus size: 29
31627427 AACAGAGTCA
* * *
31627437 AAAATGTGATTTTTGGATA-TTCGGGGGT
1 AAAATGTAATTTTTGGAAAGTTCAGGGGT
* * * *
31627465 AAAACGGTAA-TTTT-GAATATTTCGGGGGC
1 AAAA-TGTAATTTTTGGAA-AGTTCAGGGGT
* * **
31627494 AAAATGGTAATTTTTAGACA-TTCGAGGGAA
1 AAAAT-GTAATTTTTGGAAAGTTC-AGGGGT
* *
31627524 AAAATATAATTTTTGGACAA-TTGA-GGGT
1 AAAATGTAATTTTTGGA-AAGTTCAGGGGT
* * * *
31627552 AGAATGTAACTTTT-AAGAAGTTC-GAGGT
1 AAAATGTAATTTTTGGA-AAGTTCAGGGGT
*
31627580 CAAAAATGGAA-TTTTGG-AAGTTC-GAGGGT
1 --AAAATGTAATTTTTGGAAAGTTCAG-GGGT
* * * *
31627609 AATATGCTAA-TTTTAGAAAATT-TGGGGT
1 AAAATG-TAATTTTTGGAAAGTTCAGGGGT
*
31627637 CAAAAATGGAATTTTTGG-AAGTTC-GAGGGT
1 --AAAATGTAATTTTTGGAAAGTTCAG-GGGT
** *
31627667 AAAATGGTAATTTTTGGAAAAAAAAATC-GAGGT
1 AAAAT-GTAATTTTTGG----AAAGTTCAGGGGT
* *
31627700 CAAAAATGAAATTTTTGG-AAGTTCGGGGGT
1 --AAAATGTAATTTTTGGAAAGTTCAGGGGT
* *
31627730 AAAATGGTGATTTTTGG-AAGTTC-GAGGT
1 AAAAT-GTAATTTTTGGAAAGTTCAGGGGT
* **
31627758 CAAAAATGAAATTTTT-GAAAGTTTGGGGGT
1 --AAAATGTAATTTTTGGAAAGTTCAGGGGT
* * *
31627788 AAAATGGTAATTTTTGGGAAA-AT-AAGGTT
1 AAAAT-GTAATTTTT-GGAAAGTTCAGGGGT
* * * **
31627817 AAAAATGGAATTTTTAG-AGGTTTTGGGGT
1 -AAAATGTAATTTTTGGAAAGTTCAGGGGT
*** * *
31627846 AAAAATGTAATTTTCAAAAAGTTTAGGGTT
1 -AAAATGTAATTTTTGGAAAGTTCAGGGGT
* *
31627876 AAAATATAATTTTTGGAAAGTT-TGAGGGT
1 AAAATGTAATTTTTGGAAAGTTCAG-GGGT
31627905 CAAAATGTAATTTTTGGAAAGTT-AGAGGGT
1 -AAAATGTAATTTTTGGAAAGTTCAG-GGGT
31627935 AAAATGTAATTTTTGGAAAGTTCAGGGGTT
1 AAAATGTAATTTTTGGAAAGTTCAGGGG-T
31627965 AAAAT
1 AAAAT
31627970 ATGATTTCTA
Statistics
Matches: 383, Mismatches: 75, Indels: 92
0.70 0.14 0.17
Matches are distributed among these distances:
27 11 0.03
28 68 0.18
29 175 0.46
30 100 0.26
31 6 0.02
33 3 0.01
34 15 0.04
35 5 0.01
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAAGTTCAGGGGT
Found at i:31629722 original size:17 final size:17
Alignment explanation
Indices: 31629708--31629802 Score: 82
Period size: 17 Copynumber: 5.5 Consensus size: 17
31629698 TTTAAATTTT
31629708 ATTTCAAAATAAATTTAA
1 ATTT-AAAATAAATTTAA
*
31629726 ATTTAAAATAAATGTAA
1 ATTTAAAATAAATTTAA
* * **
31629743 ACTTCAAATAAGCTTAA
1 ATTTAAAATAAATTTAA
* *
31629760 ATTTACAATAGATTTAA
1 ATTTAAAATAAATTTAA
* * * *
31629777 ACTTAAAATGACTTAAA
1 ATTTAAAATAAATTTAA
31629794 ATTTAAAAT
1 ATTTAAAAT
31629803 CTAAAATTGG
Statistics
Matches: 58, Mismatches: 19, Indels: 1
0.74 0.24 0.01
Matches are distributed among these distances:
17 54 0.93
18 4 0.07
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:31629752 original size:34 final size:34
Alignment explanation
Indices: 31629713--31629802 Score: 99
Period size: 34 Copynumber: 2.6 Consensus size: 34
31629703 ATTTTATTTC
31629713 AAAATAAATTTAAATTTAAAATAAATGTAAACTT
1 AAAATAAATTTAAATTTAAAATAAATGTAAACTT
* ** * * *
31629747 CAAATAAGCTTAAATTTACAATAGATTTAAACTT
1 AAAATAAATTTAAATTTAAAATAAATGTAAACTT
* * *
31629781 AAAATGACTTAAAATTTAAAAT
1 AAAATAAATTTAAATTTAAAAT
31629803 CTAAAATTGG
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.34
Consensus pattern (34 bp):
AAAATAAATTTAAATTTAAAATAAATGTAAACTT
Found at i:31634920 original size:20 final size:20
Alignment explanation
Indices: 31634895--31634948 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
31634885 TTTTGATTTG
* *
31634895 AGATTCGAGTTTAGGGTTCA
1 AGATTCGAATTTAAGGTTCA
*
31634915 AGATTCGAATCTAAGGTTCA
1 AGATTCGAATTTAAGGTTCA
31634935 AG-TTCGAATTTAAG
1 AGATTCGAATTTAAG
31634949 ATTCGGAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.33
Consensus pattern (20 bp):
AGATTCGAATTTAAGGTTCA
Found at i:31640787 original size:4 final size:4
Alignment explanation
Indices: 31640778--31640851 Score: 78
Period size: 4 Copynumber: 18.2 Consensus size: 4
31640768 AAATAAACGG
** * *
31640778 GAAA GAAA GAGT GGAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAG GAGAG
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA
*
31640828 GAAA GAAA G-AA GAAT GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA G
31640852 GTAATGTGTT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
3 3 0.05
4 50 0.85
5 6 0.10
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (4 bp):
GAAA
Found at i:31640831 original size:37 final size:36
Alignment explanation
Indices: 31640778--31640851 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 36
31640768 AAATAAACGG
*
31640778 GAAAGAAAGAGTGGAAAGAAAGAAAGAAAGAAAGAAA
1 GAAAGAAAGAGAGGAAAGAAAG-AAGAAAGAAAGAAA
* *
31640815 GAAAGAAGGAGAGGAAAGAAAGAAGAATGAAAGAAA
1 GAAAGAAAGAGAGGAAAGAAAGAAGAAAGAAAGAAA
31640851 G
1 G
31640852 GTAATGTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 14 0.41
37 20 0.59
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (36 bp):
GAAAGAAAGAGAGGAAAGAAAGAAGAAAGAAAGAAA
Found at i:31641108 original size:28 final size:30
Alignment explanation
Indices: 31641063--31641126 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 30
31641053 ACTGGAAGCG
* *
31641063 TTTTTTAAAATTTGAATTAGTC-CTATAATT
1 TTTTTTAAAATATGAATTAGTCAC-ATAAAT
*
31641093 TTTTTTAAAA-AT-AATTATTCACATAAAT
1 TTTTTTAAAATATGAATTAGTCACATAAAT
31641121 TTTTTT
1 TTTTTT
31641127 GGCATTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 18 0.60
29 2 0.07
30 10 0.33
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (30 bp):
TTTTTTAAAATATGAATTAGTCACATAAAT
Found at i:31642447 original size:29 final size:29
Alignment explanation
Indices: 31642414--31642611 Score: 160
Period size: 29 Copynumber: 6.9 Consensus size: 29
31642404 CAAAAACGAG
*
31642414 ATTTTGGAAAGTTCAAGGGTAAAATAGTA
1 ATTTTGGAAAGTTCGAGGGTAAAATAGTA
* * * *
31642443 TTTTTTTGTAAA-ATCG-GGGTCAAAAT-GGA
1 --ATTTTGGAAAGTTCGAGGGT-AAAATAGTA
* * *
31642472 ATTTTGGAAAGTTTGGGGGTAAAATGGTA
1 ATTTTGGAAAGTTCGAGGGTAAAATAGTA
*
31642501 ATTTTGGTAAA-ATCGAGGGTAAAAATAG-A
1 ATTTTGG-AAAGTTCGAGGGT-AAAATAGTA
*
31642530 ATTTTAGAAAGTTCGAGGGTAAAATAGTA
1 ATTTTGGAAAGTTCGAGGGTAAAATAGTA
*
31642559 ATTTTGGTAAA-ATC-AGGGTTAAAATAG-A
1 ATTTTGG-AAAGTTCGAGGG-TAAAATAGTA
* *
31642587 ATTTTAGAAAGTTCGAGAGTAAAAT
1 ATTTTGGAAAGTTCGAGGGTAAAAT
31642612 GTTCGACGGT
Statistics
Matches: 134, Mismatches: 21, Indels: 27
0.74 0.12 0.15
Matches are distributed among these distances:
27 11 0.08
28 36 0.27
29 60 0.45
30 19 0.14
31 8 0.06
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (29 bp):
ATTTTGGAAAGTTCGAGGGTAAAATAGTA
Found at i:31642478 original size:58 final size:57
Alignment explanation
Indices: 31642376--31642611 Score: 269
Period size: 58 Copynumber: 4.1 Consensus size: 57
31642366 ACCCGGGGGC
* * * * *
31642376 AAAATGGTAATTTTGGTTGAAAT-TGGGTCAAAA-ACGAGATTTTGGAAAGTTCAAGGGT
1 AAAATAGTAATTTTGG-TAAAATCGGGGTCAAAATA-GA-ATTTTAGAAAGTTCGAGGGT
* * * * * *
31642434 AAAATAGTATTTTTTTGTAAAATCGGGGTCAAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAATAGTA-ATTTTGGTAAAATCGGGGTCAAAATAGAATTTTAGAAAGTTCGAGGGT
* *
31642492 AAAATGGTAATTTTGGTAAAATCGAGGGTAAAAATAGAATTTTAGAAAGTTCGAGGGT
1 AAAATAGTAATTTTGGTAAAATCG-GGGTCAAAATAGAATTTTAGAAAGTTCGAGGGT
* * *
31642550 AAAATAGTAATTTTGGTAAAATCAGGGTTAAAATAGAATTTTAGAAAGTTCGAGAGT
1 AAAATAGTAATTTTGGTAAAATCGGGGTCAAAATAGAATTTTAGAAAGTTCGAGGGT
31642607 AAAAT
1 AAAAT
31642612 GTTCGACGGT
Statistics
Matches: 153, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
57 49 0.32
58 88 0.58
59 16 0.10
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (57 bp):
AAAATAGTAATTTTGGTAAAATCGGGGTCAAAATAGAATTTTAGAAAGTTCGAGGGT
Found at i:31642683 original size:57 final size:58
Alignment explanation
Indices: 31642619--31642752 Score: 159
Period size: 57 Copynumber: 2.3 Consensus size: 58
31642609 AATGTTCGAC
* *
31642619 GGTAAAATGGTAATTTTGGTGAAATA-AGGGGTAAAATGGAATTTT-AGAAAA-TTTGGG
1 GGTAAAATGGTAATTTTGGTAAAATAGA-GGGTAAAATAGAATTTTCA-AAAAGTTTGGG
* * *
31642676 GGTAAAATGGTAATTTTGGTAAAATCGAGGTTAAAATAGAATTTTCAAAAAGTTTTGG
1 GGTAAAATGGTAATTTTGGTAAAATAGAGGGTAAAATAGAATTTTCAAAAAGTTTGGG
*
31642734 GGTCAAAAT-ATAATTTTGG
1 GGT-AAAATGGTAATTTTGG
31642753 AGAAGTTTGG
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
57 43 0.64
58 19 0.28
59 5 0.07
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (58 bp):
GGTAAAATGGTAATTTTGGTAAAATAGAGGGTAAAATAGAATTTTCAAAAAGTTTGGG
Found at i:31642710 original size:29 final size:27
Alignment explanation
Indices: 31642619--31642720 Score: 89
Period size: 29 Copynumber: 3.6 Consensus size: 27
31642609 AATGTTCGAC
* *
31642619 GGTAAAATGGTAATTTTGGTGAAATAAGG
1 GGTAAAATGG-AATTTTGGTAAAATGA-G
* *
31642648 GGTAAAATGGAATTTTAG-AAAATTTGGG
1 GGTAAAATGGAATTTTGGTAAAA--TGAG
31642676 GGTAAAATGGTAATTTTGGTAAAATCGAG
1 GGTAAAATGG-AATTTTGGTAAAAT-GAG
* *
31642705 GTTAAAATAGAATTTT
1 GGTAAAATGGAATTTT
31642721 CAAAAAGTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
27 3 0.05
28 25 0.42
29 28 0.47
30 4 0.07
ACGTcount: A:0.39, C:0.01, G:0.26, T:0.33
Consensus pattern (27 bp):
GGTAAAATGGAATTTTGGTAAAATGAG
Found at i:31642720 original size:129 final size:131
Alignment explanation
Indices: 31642489--31642729 Score: 364
Period size: 129 Copynumber: 1.9 Consensus size: 131
31642479 AAAGTTTGGG
* *
31642489 GGTAAAATGGTAATTTTGGTAAAATCGAGGGTAAAAATAGAATTTTAGAAAGTTCGAGGGTAAAA
1 GGTAAAATGGTAATTTTGGTAAAATAGAGGGTAAAAATAGAATTTTAGAAAATTCGAGGGTAAAA
*
31642554 TAGTAATTTTGGTAAAATCAGGGTTAAAATAGAATTTT-AGAAAGTTCGAGAGTAAAATGTTCGA
66 TAGTAATTTTGGTAAAATCAGGGTTAAAATAGAATTTTCAAAAAGTTCGAGAGTAAAATGTTCGA
31642618 C
131 C
* * * *
31642619 GGTAAAATGGTAATTTTGGTGAAATA-AGGGGT-AAAATGGAATTTTAGAAAATTTGGGGGTAAA
1 GGTAAAATGGTAATTTTGGTAAAATAGA-GGGTAAAAATAGAATTTTAGAAAATTCGAGGGTAAA
*
31642682 ATGGTAATTTTGGTAAAATC-GAGGTTAAAATAGAATTTTCAAAAAGTT
65 ATAGTAATTTTGGTAAAATCAG-GGTTAAAATAGAATTTTCAAAAAGTT
31642730 TTGGGGTCAA
Statistics
Matches: 100, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
128 1 0.01
129 64 0.64
130 35 0.35
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (131 bp):
GGTAAAATGGTAATTTTGGTAAAATAGAGGGTAAAAATAGAATTTTAGAAAATTCGAGGGTAAAA
TAGTAATTTTGGTAAAATCAGGGTTAAAATAGAATTTTCAAAAAGTTCGAGAGTAAAATGTTCGA
C
Found at i:31643557 original size:21 final size:21
Alignment explanation
Indices: 31643529--31643569 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
31643519 TCTTTTCTTT
31643529 TTTGTTTT-ATTTTTTAAAAG
1 TTTGTTTTCATTTTTTAAAAG
*
31643549 TTTGATTTTCCTTTTTTAAAA
1 TTTG-TTTTCATTTTTTAAAA
31643570 AAAAACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 10 0.56
ACGTcount: A:0.24, C:0.05, G:0.07, T:0.63
Consensus pattern (21 bp):
TTTGTTTTCATTTTTTAAAAG
Found at i:31644474 original size:6 final size:6
Alignment explanation
Indices: 31644455--31644515 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
31644445 AAATTGATTC
**
31644455 AAATTT -AA-TT AAATTT AAATTT AAA-GC AAATTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
**
31644500 AAAAAT AAATTT AAAT
1 AAATTT AAATTT AAAT
31644516 CAATTTAAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
4 2 0.05
5 7 0.16
6 35 0.80
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (6 bp):
AAATTT
Found at i:31644843 original size:40 final size:40
Alignment explanation
Indices: 31644798--31644952 Score: 125
Period size: 40 Copynumber: 3.6 Consensus size: 40
31644788 TATCTTGCTC
*
31644798 TTACTATAACTTCAA-AGAGATAAAGGTTCGTTATCCAACT
1 TTACTATAACTTCAAGAG-GATAAAGGTTAGTTATCCAACT
* ***
31644838 TTACTATAATTTCAAGAGGATAAGAATTGACGTTTGAAGCTTCATCTTGCT
1 TTACTATAACTTCAAGAGGAT-A-AA--G--G-TT--AG-TT-ATCCAACT
31644889 CTTACTATAACTTC-AGAGAGATAAAGGTTAGTTATCCAACT
1 -TTACTATAACTTCAAGAG-GATAAAGGTTAGTTATCCAACT
31644930 TTACTATAACTTCAAGAGGATAA
1 TTACTATAACTTCAAGAGGATAA
31644953 GAATTGACGT
Statistics
Matches: 91, Mismatches: 9, Indels: 30
0.70 0.07 0.23
Matches are distributed among these distances:
40 35 0.38
41 12 0.13
42 4 0.04
43 2 0.02
44 1 0.01
45 2 0.02
46 2 0.02
47 2 0.02
48 1 0.01
49 1 0.01
50 4 0.04
51 10 0.11
52 15 0.16
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (40 bp):
TTACTATAACTTCAAGAGGATAAAGGTTAGTTATCCAACT
Found at i:31644946 original size:92 final size:92
Alignment explanation
Indices: 31644784--31645009 Score: 407
Period size: 92 Copynumber: 2.5 Consensus size: 92
31644774 TGATGTCAAG
* * * *
31644784 GCTTTATCTTGCTCTTACTATAACTTCAAAGAGATAAAGGTTCGTTATCCAACTTTACTATAATT
1 GCTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTAGTTATCCAACTTTACTATAACT
*
31644849 TCAAGAGGATAAGAATTGACGTTTGAA
66 TCAAGAGGATAAGAATTGACGTTTAAA
31644876 GCTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTAGTTATCCAACTTTACTATAACT
1 GCTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTAGTTATCCAACTTTACTATAACT
31644941 TCAAGAGGATAAGAATTGACGTTTAAA
66 TCAAGAGGATAAGAATTGACGTTTAAA
31644968 GCTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTT
1 GCTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTT
31645010 CGCTATTTTT
Statistics
Matches: 129, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 129 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (92 bp):
GCTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTAGTTATCCAACTTTACTATAACT
TCAAGAGGATAAGAATTGACGTTTAAA
Found at i:31656907 original size:29 final size:28
Alignment explanation
Indices: 31656864--31657021 Score: 105
Period size: 29 Copynumber: 5.5 Consensus size: 28
31656854 ACCCAGGGGC
*
31656864 AAAATGGTAACTTTGGTCAAAATTGGGTCA
1 AAAATGGTAATTTTGGT-AAAATTGGGT-A
*
31656894 AAAATGG-AATTTTGG-AAAGTATGGGGGT-
1 AAAATGGTAATTTTGGTAAA--AT-TGGGTA
**
31656922 AAAATGGTAATTTTGGTGAAATAGGGGGTA
1 AAAATGGTAATTTTGGT-AAA-ATTGGGTA
* *
31656952 AAAATGG-AATTTTAG-AAAGTTTGGGGT-
1 AAAATGGTAATTTTGGTAAA-ATT-GGGTA
*
31656979 AAAATGGTAATTTTGGTAAAATCAGGGGTA
1 AAAATGGTAATTTTGGTAAAAT--TGGGTA
31657009 AAAATGG-AATTTT
1 AAAATGGTAATTTT
31657022 AGAAAGTTTA
Statistics
Matches: 104, Mismatches: 11, Indels: 27
0.73 0.08 0.19
Matches are distributed among these distances:
27 13 0.12
28 19 0.18
29 42 0.40
30 27 0.26
31 3 0.03
ACGTcount: A:0.38, C:0.03, G:0.28, T:0.31
Consensus pattern (28 bp):
AAAATGGTAATTTTGGTAAAATTGGGTA
Found at i:31657007 original size:57 final size:56
Alignment explanation
Indices: 31656859--31657089 Score: 268
Period size: 58 Copynumber: 4.0 Consensus size: 56
31656849 TGGATACCCA
* * * * *
31656859 GGGGCAAAATGGTAACTTTGGTCAAAAT-TGGGTCAAAAATGGAATTTTGGAAAGTATG
1 GGGGTAAAATGGTAATTTTGGT-AAAATAGGGGT-AAAAATGGAATTTTAGAAAGT-TT
*
31656917 GGGGTAAAATGGTAATTTTGGTGAAATAGGGGGTAAAAATGGAATTTTAGAAAGTTT
1 GGGGTAAAATGGTAATTTTGGTAAAATA-GGGGTAAAAATGGAATTTTAGAAAGTTT
31656974 GGGGTAAAATGGTAATTTTGGTAAAATCAGGGGTAAAAATGGAATTTTAGAAAGTTT
1 GGGGTAAAATGGTAATTTTGGTAAAAT-AGGGGTAAAAATGGAATTTTAGAAAGTTT
* * * * *
31657031 AAGGGTAAAATGGTAATTTTTAGTAAAATCA-GGGTCAAAATAGAATTTTCAAAAAGTTT
1 -GGGGTAAAATGGTAA-TTTTGGTAAAAT-AGGGGTAAAAATGGAATTTT-AGAAAGTTT
31657090 CGAGGTCAAA
Statistics
Matches: 155, Mismatches: 12, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
57 59 0.38
58 71 0.46
59 25 0.16
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.31
Consensus pattern (56 bp):
GGGGTAAAATGGTAATTTTGGTAAAATAGGGGTAAAAATGGAATTTTAGAAAGTTT
Found at i:31657036 original size:29 final size:29
Alignment explanation
Indices: 31656894--31657050 Score: 132
Period size: 29 Copynumber: 5.5 Consensus size: 29
31656884 AATTGGGTCA
* * *
31656894 AAAATGG-AATTTTGGAAAGTATGGGGGT
1 AAAATGGTAATTTTAGAAAGTTTAGGGGT
*
31656922 AAAATGGTAATTTTGGTGAAA---TAGGGGGT
1 AAAATGGTAATTTT--AGAAAGTTTA-GGGGT
31656951 AAAAATGG-AATTTTAGAAAGTTT-GGGGT
1 -AAAATGGTAATTTTAGAAAGTTTAGGGGT
* * *
31656979 AAAATGGTAATTTTGGTAAA-ATCAGGGGT
1 AAAATGGTAATTTTAG-AAAGTTTAGGGGT
*
31657008 AAAAATGG-AATTTTAGAAAGTTTAAGGGT
1 -AAAATGGTAATTTTAGAAAGTTTAGGGGT
31657037 AAAATGGTAATTTT
1 AAAATGGTAATTTT
31657051 TAGTAAAATC
Statistics
Matches: 105, Mismatches: 10, Indels: 27
0.74 0.07 0.19
Matches are distributed among these distances:
27 11 0.10
28 31 0.30
29 44 0.42
30 15 0.14
31 4 0.04
ACGTcount: A:0.39, C:0.01, G:0.29, T:0.32
Consensus pattern (29 bp):
AAAATGGTAATTTTAGAAAGTTTAGGGGT
Found at i:31657071 original size:30 final size:27
Alignment explanation
Indices: 31656918--31657079 Score: 105
Period size: 29 Copynumber: 5.6 Consensus size: 27
31656908 GAAAGTATGG
* *
31656918 GGGTAAAATGGTAATTTTGGTGAAAT-A
1 GGGTAAAATGG-AATTTTAGTAAAATCA
* **
31656945 GGGGGTAAAAATGGAATTTTAG-AAAGTTTG
1 --GGGT-AAAATGGAATTTTAGTAAA-ATCA
*
31656975 GGGTAAAATGGTAATTTTGGTAAAATCA
1 GGGTAAAATGG-AATTTTAGTAAAATCA
* *
31657003 GGGGTAAAAATGGAATTTTAG-AAAGTTTAA
1 -GGGT-AAAATGGAATTTTAGTAAA--ATCA
31657033 GGGTAAAATGGTAATTTTTAGTAAAATCA
1 GGGTAAAATGG-AA-TTTTAGTAAAATCA
*
31657062 GGGTCAAAATAGAATTTT
1 GGGT-AAAATGGAATTTT
31657080 CAAAAAGTTT
Statistics
Matches: 106, Mismatches: 14, Indels: 27
0.72 0.10 0.18
Matches are distributed among these distances:
27 7 0.07
28 28 0.26
29 40 0.38
30 28 0.26
31 3 0.03
ACGTcount: A:0.40, C:0.02, G:0.27, T:0.32
Consensus pattern (27 bp):
GGGTAAAATGGAATTTTAGTAAAATCA
Found at i:31657071 original size:115 final size:115
Alignment explanation
Indices: 31656859--31657089 Score: 281
Period size: 115 Copynumber: 2.0 Consensus size: 115
31656849 TGGATACCCA
* * **
31656859 GGGGCAAAATGGTAACTTTGGTCAAAATTGGGTCAAAAATGGAATTTTGGAAAGTATGGGGGTAA
1 GGGGCAAAATGGTAACTTTGGTCAAAATGGGGTCAAAAATGGAATTTTAGAAAGTATAAGGGTAA
* * * *
31656924 AATGGTAATTTTGGTGAAATAGGGGGTAAAAATGGAATTTT-AGAAAGTTT
66 AATGGTAATTTTAGTAAAATA-GGGGTAAAAATAGAATTTTCAAAAAGTTT
* * *
31656974 GGGGTAAAATGGTAATTTTGGT-AAAATCAGGGGT-AAAAATGGAATTTTAGAAAGTTTAAGGGT
1 GGGGCAAAATGGTAACTTTGGTCAAAAT--GGGGTCAAAAATGGAATTTTAGAAAGTATAAGGGT
*
31657037 AAAATGGTAATTTTTAGTAAAATCA-GGGTCAAAATAGAATTTTCAAAAAGTTT
64 AAAATGGTAA-TTTTAGTAAAAT-AGGGGTAAAAATAGAATTTTCAAAAAGTTT
31657090 CGAGGTCAAA
Statistics
Matches: 99, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
114 5 0.05
115 71 0.72
116 22 0.22
117 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.31
Consensus pattern (115 bp):
GGGGCAAAATGGTAACTTTGGTCAAAATGGGGTCAAAAATGGAATTTTAGAAAGTATAAGGGTAA
AATGGTAATTTTAGTAAAATAGGGGTAAAAATAGAATTTTCAAAAAGTTT
Found at i:31657097 original size:30 final size:30
Alignment explanation
Indices: 31657063--31657119 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
31657053 GTAAAATCAG
31657063 GGTCAAAATAGAATTTTCAAAAAGTTTCGA
1 GGTCAAAATAGAATTTTCAAAAAGTTTCGA
* * *
31657093 GGTCAAAATATAATTTTGAAGAAGTTT
1 GGTCAAAATAGAATTTTCAAAAAGTTT
31657120 GGGGACTTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (30 bp):
GGTCAAAATAGAATTTTCAAAAAGTTTCGA
Found at i:31663792 original size:27 final size:27
Alignment explanation
Indices: 31663704--31663792 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 27
31663694 GATTTTTTGA
*
31663704 TTCAAGTTTAA-ATTTAAGGTTTAGAG
1 TTCAAGTTTAAGATTTAAGATTTAGAG
* *
31663730 TTTC-AGATTCAAGA-TTCAGATTTAGAG
1 -TTCAAG-TTTAAGATTTAAGATTTAGAG
*
31663757 TTTACAGTTTAAGATTTAAGATTT-GAAG
1 TTCA-AGTTTAAGATTTAAGATTTAG-AG
31663785 TTCAAGTT
1 TTCAAGTT
31663793 GCAAAATTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
26 4 0.08
27 29 0.59
28 16 0.33
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.42
Consensus pattern (27 bp):
TTCAAGTTTAAGATTTAAGATTTAGAG
Found at i:31665677 original size:18 final size:18
Alignment explanation
Indices: 31665656--31665693 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
31665646 TCTACATCTT
*
31665656 TATAATTTATAAAAGAAA
1 TATAATTTATAAAAAAAA
*
31665674 TATAATTTTTAAAAAAAA
1 TATAATTTATAAAAAAAA
31665692 TA
1 TA
31665694 GAAATATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
TATAATTTATAAAAAAAA
Found at i:31669979 original size:19 final size:18
Alignment explanation
Indices: 31669955--31669990 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31669945 ATTATTGTAT
*
31669955 TTTATATAGAAATTATATG
1 TTTATAT-GAAAATATATG
31669974 TTTATATGAAAATATAT
1 TTTATATGAAAATATAT
31669991 AATTAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.47
Consensus pattern (18 bp):
TTTATATGAAAATATATG
Found at i:31672441 original size:106 final size:106
Alignment explanation
Indices: 31672256--31672467 Score: 424
Period size: 106 Copynumber: 2.0 Consensus size: 106
31672246 GATATATCTT
31672256 CTTATGTTAACAAGTCTTGAATTAAACTATTTAATTGAGAGGCTCGTATAGGTTATTGTACAAAG
1 CTTATGTTAACAAGTCTTGAATTAAACTATTTAATTGAGAGGCTCGTATAGGTTATTGTACAAAG
31672321 AGTTTAAGCACTTAACTTGTTCAAGTAAAGAACTGTTTGAA
66 AGTTTAAGCACTTAACTTGTTCAAGTAAAGAACTGTTTGAA
31672362 CTTATGTTAACAAGTCTTGAATTAAACTATTTAATTGAGAGGCTCGTATAGGTTATTGTACAAAG
1 CTTATGTTAACAAGTCTTGAATTAAACTATTTAATTGAGAGGCTCGTATAGGTTATTGTACAAAG
31672427 AGTTTAAGCACTTAACTTGTTCAAGTAAAGAACTGTTTGAA
66 AGTTTAAGCACTTAACTTGTTCAAGTAAAGAACTGTTTGAA
31672468 AGTACAATTT
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 106 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (106 bp):
CTTATGTTAACAAGTCTTGAATTAAACTATTTAATTGAGAGGCTCGTATAGGTTATTGTACAAAG
AGTTTAAGCACTTAACTTGTTCAAGTAAAGAACTGTTTGAA
Found at i:31675501 original size:51 final size:50
Alignment explanation
Indices: 31675437--31675601 Score: 124
Period size: 51 Copynumber: 3.3 Consensus size: 50
31675427 TTAAGTGAAC
* *
31675437 TGTACTAGAATCACCGTTCATTTGCAGACTTTTCATTCAAAATCTTAGTAC
1 TGTATTAGAATCACC-TTCATTTGCAGACTTTTCATTCAAAATCTTAGTAA
* * * ** * *
31675488 TGTATTAGCATCA-C--CA-TGGTA-ACTATATTGGGTACAAAATTTTAGTAA
1 TGTATTAGAATCACCTTCATTTGCAGACT-T-TT-CATTCAAAATCTTAGTAA
* * *
31675536 TGTATTGGAATCGCCATTCATTTGCTGACTTTTCATTCAAAATCTTAGTAA
1 TGTATTAGAATCACC-TTCATTTGCAGACTTTTCATTCAAAATCTTAGTAA
* *
31675587 TGTATTGGCATCACC
1 TGTATTAGAATCACC
31675602 ATGGTAACTA
Statistics
Matches: 84, Mismatches: 21, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
45 3 0.04
46 4 0.05
47 4 0.05
48 23 0.27
49 1 0.01
50 1 0.01
51 38 0.45
52 4 0.05
53 3 0.04
54 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (50 bp):
TGTATTAGAATCACCTTCATTTGCAGACTTTTCATTCAAAATCTTAGTAA
Found at i:31675615 original size:99 final size:99
Alignment explanation
Indices: 31675444--31675628 Score: 316
Period size: 99 Copynumber: 1.9 Consensus size: 99
31675434 AACTGTACTA
* *
31675444 GAATCACCGTTCATTTGCAGACTTTTCATTCAAAATCTTAGTACTGTATTAGCATCACCATGGTA
1 GAATCACCATTCATTTGCAGACTTTTCATTCAAAATCTTAGTAATGTATTAGCATCACCATGGTA
*
31675509 ACTATATTGGGTACAAAATTTTAGTAATGTATTG
66 ACTATATTGAGTACAAAATTTTAGTAATGTATTG
* * *
31675543 GAATCGCCATTCATTTGCTGACTTTTCATTCAAAATCTTAGTAATGTATTGGCATCACCATGGTA
1 GAATCACCATTCATTTGCAGACTTTTCATTCAAAATCTTAGTAATGTATTAGCATCACCATGGTA
31675608 ACTATATTGAGTACAAAATTT
66 ACTATATTGAGTACAAAATTT
31675629 GGAATCACCT
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 80 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (99 bp):
GAATCACCATTCATTTGCAGACTTTTCATTCAAAATCTTAGTAATGTATTAGCATCACCATGGTA
ACTATATTGAGTACAAAATTTTAGTAATGTATTG
Found at i:31675798 original size:67 final size:66
Alignment explanation
Indices: 31675706--31675856 Score: 205
Period size: 67 Copynumber: 2.3 Consensus size: 66
31675696 CATTTCTTTG
* * * * *
31675706 CAAAATTTTAGTATT-TATTGAAATCATCATGGTAACTATATTGGAATCATCATCCATTTGCATT
1 CAAAA-TTTAATATTGTATTGAAATCACCATGATAACTATATTAGAATCACCATCCATTTGCATT
31675770 TA
65 TA
* *
31675772 CAAAATCTTAATATTGTATTGGAATCACCATGATAACTATATTAGAATCACCATTCATTTGCATT
1 CAAAAT-TTAATATTGTATTGAAATCACCATGATAACTATATTAGAATCACCATCCATTTGCATT
31675837 TA
65 TA
31675839 CAAAAGTTTAATATTGTA
1 CAAAA-TTTAATATTGTA
31675857 AATACGGTAT
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
65 1 0.01
66 12 0.16
67 61 0.81
68 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (66 bp):
CAAAATTTAATATTGTATTGAAATCACCATGATAACTATATTAGAATCACCATCCATTTGCATTT
A
Found at i:31678266 original size:25 final size:25
Alignment explanation
Indices: 31678221--31678268 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
31678211 CCTTGTTCAT
*
31678221 TCTTTCTTCCTCCTCTTTTCCCTTA
1 TCTTTCTTCCTCCTCTCTTCCCTTA
*
31678246 TCTTTCTTACTTCCT-TCTTCCCT
1 TCTTTCTT-CCTCCTCTCTTCCCT
31678269 GTTGTCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.04, C:0.40, G:0.00, T:0.56
Consensus pattern (25 bp):
TCTTTCTTCCTCCTCTCTTCCCTTA
Found at i:31682664 original size:6 final size:6
Alignment explanation
Indices: 31682653--31682687 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
31682643 ACTGCATTGA
31682653 AGGCAG AGGCAG AGGCAG AGGCAG AGGCAG AGGCA
1 AGGCAG AGGCAG AGGCAG AGGCAG AGGCAG AGGCA
31682688 AGCCATCTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.49, T:0.00
Consensus pattern (6 bp):
AGGCAG
Found at i:31689058 original size:17 final size:16
Alignment explanation
Indices: 31689018--31689063 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
31689008 GAGAATAGAT
*
31689018 TTTTAATTAAAT-AAA
1 TTTTAATTAATTAAAA
31689033 -TTTAATTAATTAAAA
1 TTTTAATTAATTAAAA
31689048 TTTTAAATTAATTAAA
1 TTTT-AATTAATTAAA
31689064 CTTTGAACTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 10 0.37
15 3 0.11
16 3 0.11
17 11 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTAATTAATTAAAA
Found at i:31693265 original size:22 final size:21
Alignment explanation
Indices: 31693210--31693265 Score: 51
Period size: 22 Copynumber: 2.5 Consensus size: 21
31693200 ATGCATGGAT
31693210 TAATTTTATTTATTTAATTCAAA
1 TAATTTTA-TT-TTTAATTCAAA
* *
31693233 TTATTTGATTTTTAAGTT-ATAA
1 TAATTTTATTTTTAA-TTCA-AA
31693255 TAATTTTATTT
1 TAATTTTATTT
31693266 ATTTTACTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
21 6 0.22
22 15 0.56
23 6 0.22
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (21 bp):
TAATTTTATTTTTAATTCAAA
Found at i:31697937 original size:145 final size:145
Alignment explanation
Indices: 31697703--31697976 Score: 354
Period size: 145 Copynumber: 1.9 Consensus size: 145
31697693 TTTTGGATAC
* * ** *
31697703 TCGGGGGCAAAATGGTAATTTTAGACTCTCGGGGGAAAATGGTAATTTTGGGAAAATTTAAGGTT
1 TCGGGGGCAAAATGATAATTTTAGACTCTCGAGGGAAAATGGTAATTTTGAAAAAATTTAAGGCT
* * *
31697768 AAAAATGACATTTTAAGCACTTGAGGGTAAAACGATAATTATTGGAAGAATCGGGATAAAAAATA
66 AAAAATGACATTTTAAGCAATTGAGGGTAAAACGATAATTATTAGAAAAATCGGGATAAAAAATA
31697833 GGACTTTTAAGATGT
131 GGACTTTTAAGATGT
* ** * *
31697848 TCGGGGGCAAAATGATAATTTTGGACT-TTTAGGGCAAATGGTAATTTTAGAAAAAATTTAGGGC
1 TCGGGGGCAAAATGATAATTTTAGACTCTCGAGGGAAAATGGTAATTTT-GAAAAAATTTAAGGC
* * * * *
31697912 TAAAAATGACATTTT-AGATAATTGAGGGTAAATCGGTAATTTTTAGAAAAATCGGGATCAAAAA
65 TAAAAATGACATTTTAAG-CAATTGAGGGTAAAACGATAATTATTAGAAAAATCGGGATAAAAAA
31697976 T
129 T
31697977 GAGATTTTTG
Statistics
Matches: 109, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
144 19 0.17
145 90 0.83
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (145 bp):
TCGGGGGCAAAATGATAATTTTAGACTCTCGAGGGAAAATGGTAATTTTGAAAAAATTTAAGGCT
AAAAATGACATTTTAAGCAATTGAGGGTAAAACGATAATTATTAGAAAAATCGGGATAAAAAATA
GGACTTTTAAGATGT
Found at i:31698073 original size:28 final size:28
Alignment explanation
Indices: 31698031--31698195 Score: 114
Period size: 28 Copynumber: 5.8 Consensus size: 28
31698021 TCGAGGTAAA
* * *
31698031 AAAATGAAATATTTGGAAGTTCGGGGGC
1 AAAATGGAATTTTTGGAAGTTCAGGGGC
* * *
31698059 AAAATGGAATTTTTGGAAATTTAGGGGT
1 AAAATGGAATTTTTGGAAGTTCAGGGGC
** *
31698087 AAAAAAGAATTTTTGAAAGTTCAGGGGC
1 AAAATGGAATTTTTGGAAGTTCAGGGGC
* * **
31698115 AAAAATGGAATGTTTGGAAGTTTTAGGGTA
1 -AAAATGGAATTTTTGGAAG-TTCAGGGGC
* ** * * *
31698145 AAAATGTAATTTTTATAAGTTTTAAGGTC
1 AAAATGGAATTTTTGGAAG-TTCAGGGGC
*
31698174 AAAAATGTAATTTTTGGAAGTT
1 -AAAATGGAATTTTTGGAAGTT
31698196 TTGGGGTAAA
Statistics
Matches: 107, Mismatches: 27, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
28 44 0.41
29 40 0.37
30 23 0.21
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTCAGGGGC
Found at i:31698125 original size:29 final size:29
Alignment explanation
Indices: 31698030--31698319 Score: 196
Period size: 29 Copynumber: 9.9 Consensus size: 29
31698020 TTCGAGGTAA
* * * **
31698030 AAAAATGAAATATTTGGAAGTTCGGGGGC
1 AAAAATGTAATTTTTGAAAGTTTAGGGGC
* *
31698059 -AAAATGGAATTTTTGGAAA-TTTAGGGGT
1 AAAAATGTAATTTTT-GAAAGTTTAGGGGC
* *
31698087 AAAAAAG-AATTTTTGAAAGTTCAGGGGC
1 AAAAATGTAATTTTTGAAAGTTTAGGGGC
* * * *
31698115 AAAAATGGAATGTTTGGAAGTTTTA-GGGT
1 AAAAATGTAATTTTTGAAAG-TTTAGGGGC
* *
31698144 AAAAATGTAATTTTT-ATAAGTTTTAAGGTC
1 AAAAATGTAATTTTTGA-AAG-TTTAGGGGC
* * *
31698174 AAAAATGTAATTTTTGGAAGTTTTGGGGT
1 AAAAATGTAATTTTTGAAAGTTTAGGGGC
* * * *
31698203 AAAAAAGTAATTTTTGTAAGTTTTAGTGTC
1 AAAAATGTAATTTTTGAAAG-TTTAGGGGC
* *
31698233 AAAAATGTAATTTTGGATAAGTTTAGGGGT
1 AAAAATGTAATTTTTGA-AAGTTTAGGGGC
* * ** * *
31698263 TAAAATATAATTTTCAAAAGTTTCAAGGTC
1 AAAAATGTAATTTTTGAAAGTTT-AGGGGC
31698293 -AAAATGTAATTTTTGGAAAGTTTAGGG
1 AAAAATGTAATTTTT-GAAAGTTTAGGG
31698320 ACCTCCAGAG
Statistics
Matches: 202, Mismatches: 47, Indels: 24
0.74 0.17 0.09
Matches are distributed among these distances:
27 4 0.02
28 38 0.19
29 86 0.43
30 71 0.35
31 3 0.01
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (29 bp):
AAAAATGTAATTTTTGAAAGTTTAGGGGC
Found at i:31698196 original size:59 final size:58
Alignment explanation
Indices: 31698059--31698319 Score: 257
Period size: 59 Copynumber: 4.4 Consensus size: 58
31698049 GTTCGGGGGC
* * * *
31698059 AAAATGGAATTTTTGGAAATTTAGGGGTAAAAAAG-AATTTTTGA-AAG-TTCAGGGGCA
1 AAAATGTAATTTTTGGAAGTTTA-GGGTAAAAAAGTAATTTTT-ATAAGTTTCAAGGTCA
* * * *
31698116 AAAATGGAATGTTTGGAAGTTTTAGGGTAAAAATGTAATTTTTATAAGTTTTAAGGTCA
1 AAAATGTAATTTTTGGAAG-TTTAGGGTAAAAAAGTAATTTTTATAAGTTTCAAGGTCA
* * *
31698175 AAAATGTAATTTTTGGAAGTTTTGGGGTAAAAAAGTAATTTTTGTAAGTTT-TAGTGTCA
1 AAAATGTAATTTTTGGAAG-TTTAGGGTAAAAAAGTAATTTTTATAAGTTTCAAG-GTCA
* * *
31698234 AAAATGTAA-TTTTGGATAAGTTTAGGGGTTAAAATA-TAATTTTCAAAAGTTTCAAGGTC-
1 AAAATGTAATTTTTGG--AAGTTTA-GGG-TAAAAAAGTAATTTTTATAAGTTTCAAGGTCA
31698293 AAAATGTAATTTTTGGAAAGTTTAGGG
1 AAAATGTAATTTTTGG-AAGTTTAGGG
31698320 ACCTCCAGAG
Statistics
Matches: 174, Mismatches: 19, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
57 28 0.16
58 25 0.14
59 85 0.49
60 28 0.16
61 8 0.05
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.37
Consensus pattern (58 bp):
AAAATGTAATTTTTGGAAGTTTAGGGTAAAAAAGTAATTTTTATAAGTTTCAAGGTCA
Found at i:31699517 original size:13 final size:13
Alignment explanation
Indices: 31699495--31699551 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 13
31699485 TCAAAATAGT
31699495 TATTATTATTTAA
1 TATTATTATTTAA
* *
31699508 TATTAATATTTAT
1 TATTATTATTTAA
* * *
31699521 TATTACTAATTAT
1 TATTATTATTTAA
31699534 TATTATTATTT-A
1 TATTATTATTTAA
31699546 TATTAT
1 TATTAT
31699552 AAATGAAATC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
12 6 0.16
13 31 0.84
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTATTATTTAA
Found at i:31700313 original size:17 final size:17
Alignment explanation
Indices: 31700291--31700371 Score: 71
Period size: 17 Copynumber: 4.8 Consensus size: 17
31700281 ATTTGTATTT
31700291 TATTAAATTTACAA-TAA
1 TATTAAATTTA-AATTAA
31700308 TATTAAATTTAAATTAA
1 TATTAAATTTAAATTAA
31700325 -ATTTAAATTTAAATTTAA
1 TA-TTAAATTTAAA-TTAA
* *
31700343 -AATAAATTTAATTTTAA
1 TATTAAATTTAA-ATTAA
*
31700360 -AGTAAATTTAAA
1 TATTAAATTTAAA
31700372 ATGGTTTGGG
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
16 3 0.05
17 48 0.86
18 5 0.09
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (17 bp):
TATTAAATTTAAATTAA
Found at i:31700321 original size:6 final size:6
Alignment explanation
Indices: 31700310--31700371 Score: 76
Period size: 6 Copynumber: 10.8 Consensus size: 6
31700300 TACAATAATA
* *
31700310 TTAAAT TTAAA- TTAAAT TTAAAT TTAAAT TTAAA- ATAAAT TTAATT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
31700356 TTAAA- GTAAAT TTAAA
1 TTAAAT TTAAAT TTAAA
31700372 ATGGTTTGGG
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
5 13 0.28
6 34 0.72
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (6 bp):
TTAAAT
Found at i:31700355 original size:28 final size:28
Alignment explanation
Indices: 31700317--31700373 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
31700307 ATATTAAATT
*
31700317 TAAATTAAA-TTTAAATTTAAATTTAAAA
1 TAAATTAAATTTTAAA-GTAAATTTAAAA
*
31700345 TAAATTTAATTTTAAAGTAAATTTAAAA
1 TAAATTAAATTTTAAAGTAAATTTAAAA
31700373 T
1 T
31700374 GGTTTGGGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
TAAATTAAATTTTAAAGTAAATTTAAAA
Found at i:31700358 original size:23 final size:23
Alignment explanation
Indices: 31700305--31700360 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
31700295 AAATTTACAA
* *
31700305 TAATATTAAATTTAAATTAAATT
1 TAATTTTAAATTTAAAATAAATT
*
31700328 TAAATTTAAATTTAAAATAAATT
1 TAATTTTAAATTTAAAATAAATT
31700351 TAATTTTAAA
1 TAATTTTAAA
31700361 GTAAATTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TAATTTTAAATTTAAAATAAATT
Found at i:31700371 original size:11 final size:11
Alignment explanation
Indices: 31700309--31700353 Score: 72
Period size: 11 Copynumber: 4.0 Consensus size: 11
31700299 TTACAATAAT
31700309 ATTAAATTTAA
1 ATTAAATTTAA
31700320 ATTAAATTTAA
1 ATTAAATTTAA
31700331 ATTTAAATTTAA
1 A-TTAAATTTAA
*
31700343 AATAAATTTAA
1 ATTAAATTTAA
31700354 TTTTAAAGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 21 0.66
12 11 0.34
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:31708559 original size:39 final size:39
Alignment explanation
Indices: 31708516--31708604 Score: 103
Period size: 39 Copynumber: 2.3 Consensus size: 39
31708506 AAATTTACGT
31708516 TAAAAATTATATAAATTTTTGAATTT-TATGAA-TTTATAA
1 TAAAAATTATATAAATTTTT--ATTTATATGAATTTTATAA
* *
31708555 TAAAATATT-TATATATTTTTATTTATATGAATTTTGTAA
1 TAAAA-ATTATATAAATTTTTATTTATATGAATTTTATAA
*
31708594 AAAAAATTATA
1 TAAAAATTATA
31708605 CTTTCATAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
37 4 0.09
38 9 0.21
39 27 0.63
40 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (39 bp):
TAAAAATTATATAAATTTTTATTTATATGAATTTTATAA
Found at i:31715429 original size:85 final size:85
Alignment explanation
Indices: 31715275--31715468 Score: 203
Period size: 85 Copynumber: 2.3 Consensus size: 85
31715265 AGATAACGCC
* * * *** * *
31715275 GCGCTTTTCCCACAAACGCCGCTAAAGACCATGTTCTTTAGCGGTGCTTTACCCAAAAACGTCGT
1 GCGCTTTTACCACAAACGCCGCTAAAGAACATGGTCTTTAGCAACGCTTTACCCAAAAACGCCGC
31715340 TAAAGAACATATCTTTAACG
66 TAAAGAACATATCTTTAACG
* ** * *
31715360 GCGCTTTTACTACAAACGCCGCTAAAGAACATGGTCTTTAGCAACGCTTTTTCCACAAATGCCGC
1 GCGCTTTTACCACAAACGCCGCTAAAGAACATGGTCTTTAGCAACGCTTTACCCAAAAACGCCGC
* * *
31715425 TAAAG-ACATGTTTTTTAGCG
66 TAAAGAACAT-ATCTTTAACG
* *
31715445 GCGC-TTTCCCACAAACGCCACTAA
1 GCGCTTTTACCACAAACGCCGCTAA
31715469 CATTAACAGA
Statistics
Matches: 89, Mismatches: 19, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
84 21 0.24
85 68 0.76
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (85 bp):
GCGCTTTTACCACAAACGCCGCTAAAGAACATGGTCTTTAGCAACGCTTTACCCAAAAACGCCGC
TAAAGAACATATCTTTAACG
Found at i:31715450 original size:42 final size:43
Alignment explanation
Indices: 31715275--31715468 Score: 214
Period size: 43 Copynumber: 4.6 Consensus size: 43
31715265 AGATAACGCC
*
31715275 GCGCTTTTCCCACAAACGCCGCTAAAGACCATGTTCTTTAGCG
1 GCGCTTTTCCCACAAACGCCGCTAAAGAACATGTTCTTTAGCG
* * * * * * *
31715318 GTGCTTTACCCAAAAACGTCGTTAAAGAACAT-ATCTTTAACG
1 GCGCTTTTCCCACAAACGCCGCTAAAGAACATGTTCTTTAGCG
* * * *
31715360 GCGCTTTTACTACAAACGCCGCTAAAGAACATGGTCTTTAGCA
1 GCGCTTTTCCCACAAACGCCGCTAAAGAACATGTTCTTTAGCG
* * * *
31715403 ACGCTTTTTCCACAAATGCCGCTAAAG-ACATGTTTTTTAGCG
1 GCGCTTTTCCCACAAACGCCGCTAAAGAACATGTTCTTTAGCG
*
31715445 GCGC-TTTCCCACAAACGCCACTAA
1 GCGCTTTTCCCACAAACGCCGCTAA
31715469 CATTAACAGA
Statistics
Matches: 121, Mismatches: 29, Indels: 4
0.79 0.19 0.03
Matches are distributed among these distances:
41 17 0.14
42 48 0.40
43 56 0.46
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (43 bp):
GCGCTTTTCCCACAAACGCCGCTAAAGAACATGTTCTTTAGCG
Found at i:31726951 original size:25 final size:23
Alignment explanation
Indices: 31726923--31726968 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
31726913 GTTGGATCCA
31726923 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
31726948 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
31726969 CCTTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:31739956 original size:167 final size:158
Alignment explanation
Indices: 31739679--31740003 Score: 551
Period size: 167 Copynumber: 2.0 Consensus size: 158
31739669 GATTCCTAAA
* *
31739679 ATAATTGGTTTAAATTTCTCATTAATTTCATCGTTTTCAGTTATTATATTAATATGATTCTATTC
1 ATAATTGGTTTAAATTTCTCATTAATTTCATCATTTTCAGTTATTATATAAATATGATTCTATTC
31739744 CATTACTTTTGCTTGGCAACTCTAAACATGTAGGTGCCTTAAGTTAGATTTTCTTCCAACCCACA
66 CATTACTTTTGCTTGGCAACTCTAAACATGTAGGTGCCTTAAGTTAGATTTTCTTCCAACCCACA
31739809 ACTCAAAAGGTGATAAAGGTTATGTATT
131 ACTCAAAAGGTGATAAAGGTTATGTATT
31739837 ATAATTGGTTTTAAATTACTCTCATTAATTTCATCATTTTCAGTTATTATACTAAATATGATTCT
1 ATAATTGG-TTTAAATT--TCTCATTAATTTCATCATTTTCAGTTATTATA-TAAATATGATTCT
31739902 ATTCCATTACTTTTTGCTTGGCATGCAACTCTAAACATGTAGGTGCCTTAAGTTAGATTTTCTTC
62 ATTCCATTAC-TTTTGCTT-G---GCAACTCTAAACATGTAGGTGCCTTAAGTTAGATTTTCTTC
31739967 CAACCCACAACTCAAAAGGTGATAAAGGTTATGTATT
122 CAACCCACAACTCAAAAGGTGATAAAGGTTATGTATT
31740004 TGAGTGTGCT
Statistics
Matches: 156, Mismatches: 2, Indels: 9
0.93 0.01 0.05
Matches are distributed among these distances:
158 8 0.05
159 8 0.05
161 31 0.20
162 22 0.14
163 8 0.05
164 1 0.01
167 78 0.50
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (158 bp):
ATAATTGGTTTAAATTTCTCATTAATTTCATCATTTTCAGTTATTATATAAATATGATTCTATTC
CATTACTTTTGCTTGGCAACTCTAAACATGTAGGTGCCTTAAGTTAGATTTTCTTCCAACCCACA
ACTCAAAAGGTGATAAAGGTTATGTATT
Found at i:31741698 original size:25 final size:23
Alignment explanation
Indices: 31741670--31741715 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
31741660 GTTAGATCCA
31741670 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
31741695 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
31741716 CCTTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:31742767 original size:11 final size:11
Alignment explanation
Indices: 31742753--31742792 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
31742743 GTCTTCTTCT
31742753 TTTTTTCTCAA
1 TTTTTTCTCAA
31742764 TTTTTT-TCAA
1 TTTTTTCTCAA
* *
31742774 TTTTTTTTCAT
1 TTTTTTCTCAA
31742785 TTTTTTCT
1 TTTTTTCT
31742793 TTTCGACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTTTCTCAA
Found at i:31759576 original size:42 final size:43
Alignment explanation
Indices: 31759400--31759593 Score: 187
Period size: 43 Copynumber: 4.6 Consensus size: 43
31759390 AGATAACACC
*
31759400 GCGCTTTTCCCACAAACGCCGCTAAAGACCATGTTCTTTAACA
1 GCGCTTTTCCCACAAACGCCGCTAAAGAACATGTTCTTTAACA
* * * * ** * * *
31759443 GTGCTTTACCTAAAAACGTTGTTAAAGAACAT-ATCTTTAACG
1 GCGCTTTTCCCACAAACGCCGCTAAAGAACATGTTCTTTAACA
* * * *
31759485 GCGCTTTTACTACAAACGCCGCTAAAGAACATGGTCTTTAGCA
1 GCGCTTTTCCCACAAACGCCGCTAAAGAACATGTTCTTTAACA
* * * *
31759528 ACGCTTTTCCCACAAACGCCGCTAAAG-ACATGTTTTTTAGCG
1 GCGCTTTTCCCACAAACGCCGCTAAAGAACATGTTCTTTAACA
* *
31759570 GTGC-TTTCCCACAAACGCCACTAA
1 GCGCTTTTCCCACAAACGCCGCTAA
31759594 CATTAACAGA
Statistics
Matches: 121, Mismatches: 29, Indels: 4
0.79 0.19 0.03
Matches are distributed among these distances:
41 19 0.16
42 47 0.39
43 55 0.45
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (43 bp):
GCGCTTTTCCCACAAACGCCGCTAAAGAACATGTTCTTTAACA
Found at i:31759576 original size:85 final size:85
Alignment explanation
Indices: 31759400--31759593 Score: 203
Period size: 85 Copynumber: 2.3 Consensus size: 85
31759390 AGATAACACC
* * ** * ** *
31759400 GCGCTTTTCCCACAAACGCCGCTAAAGACCATGTTCTTTAACAGTGCTTTACCTAAAAACGTTGT
1 GCGCTTTTCCCACAAACGCCGCTAAAGAACATGGTCTTTAACAACGCTTTACCCAAAAACGCCGC
31759465 TAAAGAACATATCTTTAACG
66 TAAAGAACATATCTTTAACG
* * * * *
31759485 GCGCTTTTACTACAAACGCCGCTAAAGAACATGGTCTTTAGCAACGCTTTTCCCACAAACGCCGC
1 GCGCTTTTCCCACAAACGCCGCTAAAGAACATGGTCTTTAACAACGCTTTACCCAAAAACGCCGC
* * *
31759550 TAAAG-ACATGTTTTTTAGCG
66 TAAAGAACAT-ATCTTTAACG
* *
31759570 GTGC-TTTCCCACAAACGCCACTAA
1 GCGCTTTTCCCACAAACGCCGCTAA
31759594 CATTAACAGA
Statistics
Matches: 88, Mismatches: 20, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
84 21 0.24
85 67 0.76
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (85 bp):
GCGCTTTTCCCACAAACGCCGCTAAAGAACATGGTCTTTAACAACGCTTTACCCAAAAACGCCGC
TAAAGAACATATCTTTAACG
Found at i:31762550 original size:15 final size:15
Alignment explanation
Indices: 31762530--31762558 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31762520 CCTGTAAATT
31762530 CAAATCCAACCAATG
1 CAAATCCAACCAATG
31762545 CAAATCCAACCAAT
1 CAAATCCAACCAAT
31762559 AACTTCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.34, G:0.03, T:0.14
Consensus pattern (15 bp):
CAAATCCAACCAATG
Found at i:31762784 original size:21 final size:21
Alignment explanation
Indices: 31762759--31762811 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
31762749 CTTGTAGCCT
* *
31762759 CTGCTTCCTTCGCTTGCCTCA
1 CTGCTGCCTCCGCTTGCCTCA
*
31762780 CTGCTGCCTCCGCTTGCCTCG
1 CTGCTGCCTCCGCTTGCCTCA
31762801 CTGCTGCCTCC
1 CTGCTGCCTCC
31762812 ACTTTAAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.02, C:0.47, G:0.19, T:0.32
Consensus pattern (21 bp):
CTGCTGCCTCCGCTTGCCTCA
Found at i:31762912 original size:66 final size:66
Alignment explanation
Indices: 31762801--31762954 Score: 227
Period size: 66 Copynumber: 2.3 Consensus size: 66
31762791 GCTTGCCTCG
* * * *
31762801 CTGCTGCCTCCACTTTAAGTTGTAGGTGGAGTTCTTCATATTTTTTTTGAGACTCTACTTCTCTC
1 CTGCAGCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTACTTCTCTC
31762866 A
66 A
* * * *
31762867 CTGCAGCCTCCTCTTTAAGTTTTAGATTGAGTTCATCATATTTTTTTTGAGCCTCTGCTTCTCTC
1 CTGCAGCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTACTTCTCTC
*
31762932 G
66 A
31762933 CTGCAGCCTCCTCTTTAAGTTG
1 CTGCAGCCTCCTCTTTAAGTTG
31762955 AGCAATTTGC
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 78 1.00
ACGTcount: A:0.16, C:0.25, G:0.16, T:0.44
Consensus pattern (66 bp):
CTGCAGCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTACTTCTCTC
A
Found at i:31768429 original size:31 final size:33
Alignment explanation
Indices: 31768387--31768453 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
31768377 TTGATTTAAA
31768387 TTTAAAA-ATATATATTACTGACAACATTTTAC
1 TTTAAAATATATATATTACTGACAACATTTTAC
*
31768419 TTTAAAATATATATATTAGTGACAACATTTTAC
1 TTTAAAATATATATATTACTGACAACATTTTAC
31768452 TT
1 TT
31768454 AAATAGTTGG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 7 0.21
33 26 0.79
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.43
Consensus pattern (33 bp):
TTTAAAATATATATATTACTGACAACATTTTAC
Found at i:31768509 original size:30 final size:29
Alignment explanation
Indices: 31768475--31768917 Score: 120
Period size: 30 Copynumber: 15.6 Consensus size: 29
31768465 CTGTTTTTAT
31768475 TAATTAAATAATTAAATATTTAATTTAATA
1 TAATTAAATAATTAAATATTTAA-TTAATA
*
31768505 TAATTAAATAATTATATATTTTCAATTAA-A
1 TAATTAAATAATTAAATA-TTT-AATTAATA
* * ** *
31768535 TAATTATAT-A-TAATTATTT-ACGAAAA
1 TAATTAAATAATTAAATATTTAATTAATA
** *
31768561 T-ATTTTA-AATTAAATAGTTAATTAAATA
1 TAATTAAATAATTAAATATTTAATT-AATA
*
31768589 TAATTAAATAATTAATCGATATTGT-TTATAAT-
1 TAATTAAATAATTAA---ATATT-TAAT-TAATA
* * *
31768621 TAAATACATAATTTAAACA--TAATTAA-A
1 TAATTAAATAA-TTAAATATTTAATTAATA
* * *
31768648 TAATTTAAT-A-TAATTATTTACTTTAATA
1 TAATTAAATAATTAAATATTTA-ATTAATA
* *
31768676 TAATTAAATAATTAAATCTTTTAACGTAAATA
1 TAATTAAATAATTAAAT-ATTTAA--TTAATA
** * *
31768708 TTTAATTAAAGGATT-ACTGTTT-A-TAAT-
1 --TAATTAAATAATTAAATATTTAATTAATA
* * * *
31768735 TAAATACATAATTAAACA--TGATTAA-A
1 TAATTAAATAATTAAATATTTAATTAATA
* *
31768761 TAATTTAAT-A-TAATTATTTACATTAATA
1 TAATTAAATAATTAAATATTTA-ATTAATA
*
31768789 TAATTAAATAATTAAATCTATTAACTTAA-A
1 TAATTAAATAATTAAATAT-TTAA-TTAATA
* * ** *
31768819 TATTTAATTAA-TCGATACTGTTTA-TAAT-
1 TAATTAAATAATTAAATA-T-TTAATTAATA
* * *
31768847 TAAATACATAATTAAACA--TAATTAA-A
1 TAATTAAATAATTAAATATTTAATTAATA
* *
31768873 TAATTTAAT-A-TAATTATTTACATTAATA
1 TAATTAAATAATTAAATATTTA-ATTAATA
31768901 TAATTAAATAATTAAAT
1 TAATTAAATAATTAAAT
31768918 CTATTAACTT
Statistics
Matches: 288, Mismatches: 74, Indels: 102
0.62 0.16 0.22
Matches are distributed among these distances:
24 13 0.05
25 23 0.08
26 34 0.12
27 28 0.10
28 49 0.17
29 14 0.05
30 62 0.22
31 19 0.07
32 19 0.07
33 14 0.05
34 13 0.05
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (29 bp):
TAATTAAATAATTAAATATTTAATTAATA
Found at i:31768602 original size:18 final size:18
Alignment explanation
Indices: 31768579--31768917 Score: 85
Period size: 18 Copynumber: 18.5 Consensus size: 18
31768569 ATTAAATAGT
31768579 TAATTAAATATAATTAAA
1 TAATTAAATATAATTAAA
* **
31768597 TAATT-AATCGATATTGTTTA
1 TAATTAAAT--ATAAT-TAAA
*
31768617 TAATTAAATA-CA-T-AA
1 TAATTAAATATAATTAAA
*
31768632 T--TTAAACATAATTAAA
1 TAATTAAATATAATTAAA
* **
31768648 TAATTTAATATAATTATT
1 TAATTAAATATAATTAAA
* *
31768666 TACTTTAATATAATTAAA
1 TAATTAAATATAATTAAA
* * *
31768684 TAATTAAATCT-TTTAACG
1 TAATTAAATATAATTAA-A
* *
31768702 TAA--ATATTTAATTAAA
1 TAATTAAATATAATTAAA
** **
31768718 GGATTACTGTTTATAATTAAA
1 TAATTA---AATATAATTAAA
* *
31768739 TACATAATTAAACATGATTAAA
1 T--A-A-TTAAATATAATTAAA
* **
31768761 TAATTTAATATAATTATT
1 TAATTAAATATAATTAAA
31768779 TACATT-AATATAATTAAA
1 TA-ATTAAATATAATTAAA
31768797 TAATTAAATCTATTAACTTAAA
1 TAATTAAA--TA-TAA-TTAAA
* * *
31768819 T-ATTTAAT-TAATCGATAC
1 TAATTAAATATAAT-TA-AA
** * *
31768837 TGTTTATAAT-TAAATACA
1 TAATTA-AATATAATTAAA
*
31768855 TAATTAAACATAATTAAA
1 TAATTAAATATAATTAAA
* **
31768873 TAATTTAATATAATTATT
1 TAATTAAATATAATTAAA
31768891 TACATT-AATATAATTAAA
1 TA-ATTAAATATAATTAAA
31768909 TAATTAAAT
1 TAATTAAAT
31768918 CTATTAACTT
Statistics
Matches: 227, Mismatches: 61, Indels: 66
0.64 0.17 0.19
Matches are distributed among these distances:
13 6 0.03
14 1 0.00
15 3 0.01
16 10 0.04
17 23 0.10
18 112 0.49
19 16 0.07
20 16 0.07
21 21 0.09
22 15 0.07
24 1 0.00
25 3 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (18 bp):
TAATTAAATATAATTAAA
Found at i:31768849 original size:46 final size:46
Alignment explanation
Indices: 31768796--31768963 Score: 122
Period size: 46 Copynumber: 3.2 Consensus size: 46
31768786 ATATAATTAA
31768796 ATAATTAAATCTATTAACTTAAATATTTAATTAATCGATACTGTTT
1 ATAATTAAATCTATTAACTTAAATATTTAATTAATCGATACTGTTT
* *
31768842 ATAATTAAATACATAATTAAACATAATTAAATAATTTAATATAATTATTTAC-ATTAATATAATT
1 ATAATTAAAT-C-T-ATT-AAC----TTAAAT-ATTTAAT-T-A--A--T-CGA-TACTGT--TT
31768906 AAATAATTAAATCTATTAACTTAAATATTTAATTAATCGATACTGTTT
1 --ATAATTAAATCTATTAACTTAAATATTTAATTAATCGATACTGTTT
31768954 ATAATTAAAT
1 ATAATTAAAT
31768964 ACATAATTAT
Statistics
Matches: 96, Mismatches: 4, Indels: 44
0.67 0.03 0.31
Matches are distributed among these distances:
46 20 0.21
47 1 0.01
48 3 0.03
49 3 0.03
50 8 0.08
51 2 0.02
53 1 0.01
54 6 0.06
55 8 0.08
56 2 0.02
57 8 0.08
58 6 0.06
59 1 0.01
61 2 0.02
62 8 0.08
63 3 0.03
64 3 0.03
65 1 0.01
66 10 0.10
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (46 bp):
ATAATTAAATCTATTAACTTAAATATTTAATTAATCGATACTGTTT
Found at i:31768877 original size:8 final size:8
Alignment explanation
Indices: 31768854--31768917 Score: 56
Period size: 9 Copynumber: 7.2 Consensus size: 8
31768844 AATTAAATAC
31768854 ATAATTAAA
1 ATAATT-AA
31768863 CATAATTAA
1 -ATAATTAA
31768872 ATAATTTAA
1 ATAA-TTAA
*
31768881 TATAATTAT
1 -ATAATTAA
*
31768890 TTACATTAA
1 ATA-ATTAA
31768899 TATAATTAA
1 -ATAATTAA
31768908 ATAATTAA
1 ATAATTAA
31768916 AT
1 AT
31768918 CTATTAACTT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
8 16 0.35
9 18 0.39
10 12 0.26
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (8 bp):
ATAATTAA
Found at i:31768894 original size:112 final size:112
Alignment explanation
Indices: 31768597--31768972 Score: 671
Period size: 112 Copynumber: 3.3 Consensus size: 112
31768587 TATAATTAAA
*
31768597 TAATTAATCGATATTGTTTATAATTAAATACATAATTTAAACATAATTAAATAATTTAATATAAT
1 TAATTAATCGATACTGTTTATAATTAAATACATAA-TTAAACATAATTAAATAATTTAATATAAT
* * *
31768662 TATTTACTTTAATATAATTAAATAATTAAATCTTTTAACGTAAATATT
65 TATTTACATTAATATAATTAAATAATTAAATCTATTAACTTAAATATT
** *
31768710 TAATTAAAGGATTACTGTTTATAATTAAATACATAATTAAACATGATTAAATAATTTAATATAAT
1 TAATTAATCGA-TACTGTTTATAATTAAATACATAATTAAACATAATTAAATAATTTAATATAAT
31768775 TATTTACATTAATATAATTAAATAATTAAATCTATTAACTTAAATATT
65 TATTTACATTAATATAATTAAATAATTAAATCTATTAACTTAAATATT
31768823 TAATTAATCGATACTGTTTATAATTAAATACATAATTAAACATAATTAAATAATTTAATATAATT
1 TAATTAATCGATACTGTTTATAATTAAATACATAATTAAACATAATTAAATAATTTAATATAATT
31768888 ATTTACATTAATATAATTAAATAATTAAATCTATTAACTTAAATATT
66 ATTTACATTAATATAATTAAATAATTAAATCTATTAACTTAAATATT
31768935 TAATTAATCGATACTGTTTATAATTAAATACATAATTA
1 TAATTAATCGATACTGTTTATAATTAAATACATAATTA
31768973 TTTAATTATT
Statistics
Matches: 252, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
112 138 0.55
113 91 0.36
114 23 0.09
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (112 bp):
TAATTAATCGATACTGTTTATAATTAAATACATAATTAAACATAATTAAATAATTTAATATAATT
ATTTACATTAATATAATTAAATAATTAAATCTATTAACTTAAATATT
Found at i:31770286 original size:9 final size:9
Alignment explanation
Indices: 31770272--31770307 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
31770262 CTTTCAAGCT
31770272 AATTATTTA
1 AATTATTTA
31770281 AATTATTT-
1 AATTATTTA
31770289 AATTATTTA
1 AATTATTTA
31770298 AATTATTTA
1 AATTATTTA
31770307 A
1 A
31770308 TAATAGTAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AATTATTTA
Found at i:31770293 original size:17 final size:17
Alignment explanation
Indices: 31770271--31770308 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
31770261 TCTTTCAAGC
31770271 TAATTATTTAAATTATT
1 TAATTATTTAAATTATT
31770288 TAATTATTTAAATTATT
1 TAATTATTTAAATTATT
31770305 TAAT
1 TAAT
31770309 AATAGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TAATTATTTAAATTATT
Found at i:31770386 original size:10 final size:10
Alignment explanation
Indices: 31770371--31770397 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
31770361 TTCCTATTTT
31770371 GAATTTATTA
1 GAATTTATTA
31770381 GAATTTATTA
1 GAATTTATTA
31770391 GAATTTA
1 GAATTTA
31770398 AAAGATTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (10 bp):
GAATTTATTA
Found at i:31772137 original size:41 final size:41
Alignment explanation
Indices: 31772080--31772402 Score: 441
Period size: 41 Copynumber: 7.9 Consensus size: 41
31772070 ATGTAAAAAT
**
31772080 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTTATCCGACC
1 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCCGACC
*
31772121 TTTAGCGGTGCTTTCCCATAAGCGCCGCTATTGCTCCGACC
1 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCCGACC
* ** *
31772162 TTTGGCGGCGCTTTCTTATAAGCGCCGCTATTGCTCAGACC
1 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCCGACC
* * *
31772203 TTTAGCAGCACTTTCCCATAAGCGCCGCTATTGCTCTGACC
1 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCCGACC
* **
31772244 TTTAGCGGCGATTTCTTATAAGCGCCGCTATTGCTCCGACC
1 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCCGACC
* *
31772285 TTTAGCGGCGCTTTCCCATAAGCGCTGCTATTGCTCTGACC
1 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCCGACC
* ** * * *
31772326 TTTAGCGGCGCATTCTTATAAGTGCCGCTATTGCTCTGATC
1 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCCGACC
31772367 TTTAGCGGCG-TTTCTCCATAAGCGCCGCTATTGCTC
1 TTTAGCGGCGCTTTC-CCATAAGCGCCGCTATTGCTC
31772403 AATCTTTTGC
Statistics
Matches: 246, Mismatches: 35, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
40 3 0.01
41 243 0.99
ACGTcount: A:0.16, C:0.31, G:0.21, T:0.32
Consensus pattern (41 bp):
TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCCGACC
Found at i:31772221 original size:82 final size:82
Alignment explanation
Indices: 31772080--31772402 Score: 486
Period size: 82 Copynumber: 3.9 Consensus size: 82
31772070 ATGTAAAAAT
** ** *
31772080 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTTATCCGACCTTTAGCGGTGCTTTCCCATAAGCG
1 TTTAGCGGCGCTTTCTTATAAGCGCCGCTATTGCTCCGACCTTTAGCGGCGCTTTCCCATAAGCG
*
31772145 CCGCTATTGCTCCGACC
66 CCGCTATTGCTCTGACC
* * * *
31772162 TTTGGCGGCGCTTTCTTATAAGCGCCGCTATTGCTCAGACCTTTAGCAGCACTTTCCCATAAGCG
1 TTTAGCGGCGCTTTCTTATAAGCGCCGCTATTGCTCCGACCTTTAGCGGCGCTTTCCCATAAGCG
31772227 CCGCTATTGCTCTGACC
66 CCGCTATTGCTCTGACC
*
31772244 TTTAGCGGCGATTTCTTATAAGCGCCGCTATTGCTCCGACCTTTAGCGGCGCTTTCCCATAAGCG
1 TTTAGCGGCGCTTTCTTATAAGCGCCGCTATTGCTCCGACCTTTAGCGGCGCTTTCCCATAAGCG
*
31772309 CTGCTATTGCTCTGACC
66 CCGCTATTGCTCTGACC
* * * *
31772326 TTTAGCGGCGCATTCTTATAAGTGCCGCTATTGCTCTGATCTTTAGCGGCG-TTTCTCCATAAGC
1 TTTAGCGGCGCTTTCTTATAAGCGCCGCTATTGCTCCGACCTTTAGCGGCGCTTTC-CCATAAGC
31772390 GCCGCTATTGCTC
65 GCCGCTATTGCTC
31772403 AATCTTTTGC
Statistics
Matches: 218, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
81 4 0.02
82 214 0.98
ACGTcount: A:0.16, C:0.31, G:0.21, T:0.32
Consensus pattern (82 bp):
TTTAGCGGCGCTTTCTTATAAGCGCCGCTATTGCTCCGACCTTTAGCGGCGCTTTCCCATAAGCG
CCGCTATTGCTCTGACC
Found at i:31787380 original size:25 final size:23
Alignment explanation
Indices: 31787352--31787397 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
31787342 GTTAGATCCA
31787352 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
31787377 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
31787398 CCTTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:31788450 original size:12 final size:12
Alignment explanation
Indices: 31788433--31788475 Score: 63
Period size: 11 Copynumber: 3.8 Consensus size: 12
31788423 TGTCTTCTTC
31788433 TTTTTTTCTCAA
1 TTTTTTTCTCAA
31788445 TTTTTTT-TCAA
1 TTTTTTTCTCAA
*
31788456 TTTTTTTTTC-A
1 TTTTTTTCTCAA
31788467 TTTTTTTCT
1 TTTTTTTCT
31788476 TTTCGACTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 20 0.69
12 9 0.31
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTTTCTCAA
Found at i:31789434 original size:17 final size:17
Alignment explanation
Indices: 31789414--31789451 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
31789404 ATTGCATAAT
31789414 TAAAATAAA-ACTAAAAA
1 TAAAATAAATA-TAAAAA
31789431 TAAAATAAATATAAAAA
1 TAAAATAAATATAAAAA
31789448 TAAA
1 TAAA
31789452 TATACTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
TAAAATAAATATAAAAA
Found at i:31789452 original size:12 final size:12
Alignment explanation
Indices: 31789414--31789455 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
31789404 ATTGCATAAT
*
31789414 TAAA-ATAAAAC
1 TAAATATAAAAA
*
31789425 TAAAAAT-AAAA
1 TAAATATAAAAA
31789436 TAAATATAAAAA
1 TAAATATAAAAA
31789448 TAAATATA
1 TAAATATA
31789456 CTATTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 13 0.48
12 14 0.52
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (12 bp):
TAAATATAAAAA
Found at i:31793254 original size:25 final size:23
Alignment explanation
Indices: 31793226--31793271 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
31793216 GTTAGATCCA
31793226 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
31793251 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
31793272 CCTTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:31803023 original size:166 final size:161
Alignment explanation
Indices: 31802699--31803025 Score: 591
Period size: 166 Copynumber: 2.0 Consensus size: 161
31802689 GATTCCTAAA
* *
31802699 ATAATTGGTTTAAATTACTCTCATTAATTTCATCGTTTTCAGTTATTATATTAAATATGATTCTA
1 ATAATTGGTTTAAATTACTCTCATTAATTTCATCATTTTCAGTTATTATACTAAATATGATTCTA
31802764 TTCCATTACTTTTGCTTGGCAACTCTAAACATGTAGGTGCCTTAAGTTAGATTTTCTTCCAACCC
66 TTCCATTACTTTTGCTTGGCAACTCTAAACATGTAGGTGCCTTAAGTTAGATTTTCTTCCAACCC
31802829 ACAACTCAAAAGGTGATAAAGGTTATGTATT
131 ACAACTCAAAAGGTGATAAAGGTTATGTATT
31802860 ATAATTGGTTTAAATTACTCTCATTAATTTCATCATTTTCAGTTATTATACTAAATATGATTCTA
1 ATAATTGGTTTAAATTACTCTCATTAATTTCATCATTTTCAGTTATTATACTAAATATGATTCTA
31802925 TTCCATTACTTTTTGCTTGGCATGCAACTCTAAACATGTAGGTGCCTTAAGTTAGATTTTCTTCC
66 TTCCATTAC-TTTTGCTT-G---GCAACTCTAAACATGTAGGTGCCTTAAGTTAGATTTTCTTCC
31802990 AACCCACAACTCAAAAGGTGATAAAGGTTATGTATT
126 AACCCACAACTCAAAAGGTGATAAAGGTTATGTATT
31803026 TGAGTGTGCT
Statistics
Matches: 159, Mismatches: 2, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
161 72 0.45
162 8 0.05
163 1 0.01
166 78 0.49
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.41
Consensus pattern (161 bp):
ATAATTGGTTTAAATTACTCTCATTAATTTCATCATTTTCAGTTATTATACTAAATATGATTCTA
TTCCATTACTTTTGCTTGGCAACTCTAAACATGTAGGTGCCTTAAGTTAGATTTTCTTCCAACCC
ACAACTCAAAAGGTGATAAAGGTTATGTATT
Found at i:31804721 original size:25 final size:23
Alignment explanation
Indices: 31804693--31804738 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
31804683 GTTAGATCCA
31804693 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
31804718 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
31804739 CCTTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:31805791 original size:11 final size:11
Alignment explanation
Indices: 31805777--31805816 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
31805767 GTCTTCTTCT
31805777 TTTTTTCTCAA
1 TTTTTTCTCAA
31805788 TTTTTT-TCAA
1 TTTTTTCTCAA
* *
31805798 TTTTTTTTCAT
1 TTTTTTCTCAA
31805809 TTTTTTCT
1 TTTTTTCT
31805817 TTTCGACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTTTCTCAA
Found at i:31822595 original size:42 final size:43
Alignment explanation
Indices: 31822419--31822612 Score: 187
Period size: 43 Copynumber: 4.6 Consensus size: 43
31822409 AAATAACGCC
*
31822419 GCGCTTTTCCCACAAACGCCGCTAAAGACCATGTTCTTTAACA
1 GCGCTTTTCCCACAAACGCCGCTAAAGAACATGTTCTTTAACA
* * * * ** * * *
31822462 GTGCTTTACCTAAAAACGTTGTTAAAGAACAT-ATCTTTAACG
1 GCGCTTTTCCCACAAACGCCGCTAAAGAACATGTTCTTTAACA
* * * *
31822504 GCGCTTTTACTACAAACGCCGCTAAAGAACATGGTCTTTAGCA
1 GCGCTTTTCCCACAAACGCCGCTAAAGAACATGTTCTTTAACA
* * * *
31822547 ACGCTTTTCCCACAAACGCCGCTAAAG-ACATGTTTTTTAGCG
1 GCGCTTTTCCCACAAACGCCGCTAAAGAACATGTTCTTTAACA
* *
31822589 GTGC-TTTCCCACAAACGCCACTAA
1 GCGCTTTTCCCACAAACGCCGCTAA
31822613 CATTAACAGA
Statistics
Matches: 121, Mismatches: 29, Indels: 4
0.79 0.19 0.03
Matches are distributed among these distances:
41 19 0.16
42 47 0.39
43 55 0.45
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (43 bp):
GCGCTTTTCCCACAAACGCCGCTAAAGAACATGTTCTTTAACA
Found at i:31822595 original size:85 final size:85
Alignment explanation
Indices: 31822419--31822612 Score: 203
Period size: 85 Copynumber: 2.3 Consensus size: 85
31822409 AAATAACGCC
* * ** * ** *
31822419 GCGCTTTTCCCACAAACGCCGCTAAAGACCATGTTCTTTAACAGTGCTTTACCTAAAAACGTTGT
1 GCGCTTTTCCCACAAACGCCGCTAAAGAACATGGTCTTTAACAACGCTTTACCCAAAAACGCCGC
31822484 TAAAGAACATATCTTTAACG
66 TAAAGAACATATCTTTAACG
* * * * *
31822504 GCGCTTTTACTACAAACGCCGCTAAAGAACATGGTCTTTAGCAACGCTTTTCCCACAAACGCCGC
1 GCGCTTTTCCCACAAACGCCGCTAAAGAACATGGTCTTTAACAACGCTTTACCCAAAAACGCCGC
* * *
31822569 TAAAG-ACATGTTTTTTAGCG
66 TAAAGAACAT-ATCTTTAACG
* *
31822589 GTGC-TTTCCCACAAACGCCACTAA
1 GCGCTTTTCCCACAAACGCCGCTAA
31822613 CATTAACAGA
Statistics
Matches: 88, Mismatches: 20, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
84 21 0.24
85 67 0.76
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (85 bp):
GCGCTTTTCCCACAAACGCCGCTAAAGAACATGGTCTTTAACAACGCTTTACCCAAAAACGCCGC
TAAAGAACATATCTTTAACG
Found at i:31828979 original size:43 final size:43
Alignment explanation
Indices: 31828855--31829048 Score: 180
Period size: 43 Copynumber: 4.6 Consensus size: 43
31828845 AGATAACGCC
* * *
31828855 GCGCTTTTCCCACAAACGCCGCTAAAGACCATGTTCTTTAGCG
1 GCGCTTTTACCACAAACGCCGCTAAAGAACATGATCTTTAGCG
* * * * * *
31828898 GTGC-TTTACCCAAAAACGTCGTTAAAAAACAT-ATCTTTAACG
1 GCGCTTTTA-CCACAAACGCCGCTAAAGAACATGATCTTTAGCG
* * *
31828940 GCGCTTTTACTACAAACGCCGCTAAAGAACATGGTCTTTAGCA
1 GCGCTTTTACCACAAACGCCGCTAAAGAACATGATCTTTAGCG
* * * *
31828983 ACGCTTTTTCCACAAACGCCGCTAAAG-ACATGTTTTTTAGCG
1 GCGCTTTTACCACAAACGCCGCTAAAGAACATGATCTTTAGCG
* * *
31829025 GCAC-TTTCCCACAAACGCCACTAA
1 GCGCTTTTACCACAAACGCCGCTAA
31829049 CATTAACAGA
Statistics
Matches: 120, Mismatches: 28, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
41 18 0.15
42 46 0.38
43 56 0.47
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (43 bp):
GCGCTTTTACCACAAACGCCGCTAAAGAACATGATCTTTAGCG
Found at i:31844031 original size:21 final size:21
Alignment explanation
Indices: 31844014--31844091 Score: 81
Period size: 22 Copynumber: 3.7 Consensus size: 21
31844004 AACAGCAATT
31844014 AAAACAGTAAAAAAAGC-ACC
1 AAAACAGTAAAAAAAGCAACC
* *
31844034 AAAATAG-AAAAAAA-TAACATC
1 AAAACAGTAAAAAAAGCAAC--C
*
31844055 AAAACAGTAAAAAACAACAACC
1 AAAACAGTAAAAAA-AGCAACC
31844077 AAAACAGTAAAAAAA
1 AAAACAGTAAAAAAA
31844092 ATACCAAAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
19 9 0.19
20 6 0.12
21 8 0.17
22 21 0.44
23 1 0.02
24 3 0.06
ACGTcount: A:0.71, C:0.15, G:0.06, T:0.08
Consensus pattern (21 bp):
AAAACAGTAAAAAAAGCAACC
Found at i:31844037 original size:20 final size:21
Alignment explanation
Indices: 31844014--31844102 Score: 101
Period size: 20 Copynumber: 4.3 Consensus size: 21
31844004 AACAGCAATT
*
31844014 AAAACAGTAAAAAA-AGCACC
1 AAAACAGTAAAAAACAACACC
* * * *
31844034 AAAATAGAAAAAAATAACATC
1 AAAACAGTAAAAAACAACACC
31844055 AAAACAGTAAAAAACAACAACC
1 AAAACAGTAAAAAACAAC-ACC
*
31844077 AAAACAGTAAAAAA-AATACC
1 AAAACAGTAAAAAACAACACC
31844097 AAAACA
1 AAAACA
31844103 ACAATATAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
20 21 0.36
21 21 0.36
22 16 0.28
ACGTcount: A:0.70, C:0.17, G:0.06, T:0.08
Consensus pattern (21 bp):
AAAACAGTAAAAAACAACACC
Found at i:31844106 original size:32 final size:32
Alignment explanation
Indices: 31843941--31844106 Score: 106
Period size: 32 Copynumber: 5.2 Consensus size: 32
31843931 ATAACATCAA
* * *
31843941 AACAACCAAAATAGCAGCAAAAATAGCAACAAAAC
1 AACAACC-AAA-A-CAGTAAAAAAAGCACCAAAAC
* *
31843976 AA-GACCAAAACAGTAAAAATAGCACCAAAAC
1 AACAACCAAAACAGTAAAAAAAGCACCAAAAC
* ** *
31844007 AGCAATTAAAACAGTAAAAAAAGCACCAAAAT
1 AACAACCAAAACAGTAAAAAAAGCACCAAAAC
** * * * *
31844039 AGA-AAAAAATAACA-TCAAAACAGTA-AAAAAC
1 A-ACAACCAA-AACAGTAAAAAAAGCACCAAAAC
**
31844070 AACAACCAAAACAGTAAAAAAAATACCAAAAC
1 AACAACCAAAACAGTAAAAAAAGCACCAAAAC
31844102 AACAA
1 AACAA
31844107 TATAATTTTT
Statistics
Matches: 102, Mismatches: 23, Indels: 15
0.73 0.16 0.11
Matches are distributed among these distances:
30 5 0.05
31 37 0.36
32 48 0.47
33 7 0.07
34 3 0.03
35 2 0.02
ACGTcount: A:0.66, C:0.19, G:0.07, T:0.08
Consensus pattern (32 bp):
AACAACCAAAACAGTAAAAAAAGCACCAAAAC
Found at i:31857319 original size:3 final size:3
Alignment explanation
Indices: 31857311--31857340 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
31857301 CCTCTTTCTT
31857311 TTG TTG TTG TTG TTG TTG TTG TTG TT- TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
31857341 GTGTGAGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.00, C:0.00, G:0.30, T:0.70
Consensus pattern (3 bp):
TTG
Found at i:31862135 original size:15 final size:14
Alignment explanation
Indices: 31862103--31862131 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
31862093 TTATGTATGG
31862103 ACATTATTCCTTAA
1 ACATTATTCCTTAA
31862117 ACATTATTCCTTAA
1 ACATTATTCCTTAA
31862131 A
1 A
31862132 ACATCTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (14 bp):
ACATTATTCCTTAA
Found at i:31866749 original size:15 final size:15
Alignment explanation
Indices: 31866700--31866750 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 15
31866690 TGTTTGATAA
*
31866700 ATTAAAAAATTAAGT
1 ATTAAAAAATTAAAT
* *
31866715 GTTGAAAAAATAAAAT
1 ATT-AAAAAATTAAAT
31866731 -TTAAAAAATTAAAT
1 ATTAAAAAATTAAAT
31866745 ATTAAA
1 ATTAAA
31866751 TTTAAATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 11 0.37
15 9 0.30
16 10 0.33
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (15 bp):
ATTAAAAAATTAAAT
Found at i:31870320 original size:58 final size:59
Alignment explanation
Indices: 31870160--31870324 Score: 188
Period size: 60 Copynumber: 2.8 Consensus size: 59
31870150 ATTTGATATT
* * ** *
31870160 TTTTCTTAATTTAGTATTTAAACCTTTTTTTTTACTCAATTTGGTATTTGAACTTGACAA
1 TTTTCTTAATTTGGTACTTAAA-CTTTTTTTAGACTCAATTTGGTACTTGAACTTGACAA
* * * * *
31870220 TTTTTTCTAATTTGGTACCTAAACTTTTTTTGGACCCAATTTGGTACTTGAACTTGGC-A
1 TTTTCT-TAATTTGGTACTTAAACTTTTTTTAGACTCAATTTGGTACTTGAACTTGACAA
* * *
31870279 TTTTCTTAATTTGGTACTTAAGCTTTTTTTAGATTCGATTTGGTAC
1 TTTTCTTAATTTGGTACTTAAACTTTTTTTAGACTCAATTTGGTAC
31870325 CTAAATTTAT
Statistics
Matches: 88, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
58 34 0.39
59 6 0.07
60 35 0.40
61 13 0.15
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (59 bp):
TTTTCTTAATTTGGTACTTAAACTTTTTTTAGACTCAATTTGGTACTTGAACTTGACAA
Found at i:31893626 original size:2 final size:2
Alignment explanation
Indices: 31893619--31893654 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
31893609 GTCGCTGGTG
31893619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31893655 TGAATCTACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31893777 original size:40 final size:40
Alignment explanation
Indices: 31893732--31893845 Score: 167
Period size: 40 Copynumber: 2.9 Consensus size: 40
31893722 GATATAATTG
* **
31893732 AAGCTACGACTTAGTAGGCTTTGAGTTGGTGATATGTCTC
1 AAGCTACGACTTAGCAGGCTTTGAGACGGTGATATGTCTC
* *
31893772 AAGCTAC-ATCTTAGCAGGCTTTGAGCCGGTGATATGTTTC
1 AAGCTACGA-CTTAGCAGGCTTTGAGACGGTGATATGTCTC
31893812 AAGCTACGACTTAGCAGGCTTTGAGACGGTGATA
1 AAGCTACGACTTAGCAGGCTTTGAGACGGTGATA
31893846 AATTTTGGGC
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
39 1 0.01
40 65 0.97
41 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.31
Consensus pattern (40 bp):
AAGCTACGACTTAGCAGGCTTTGAGACGGTGATATGTCTC
Found at i:31893858 original size:40 final size:40
Alignment explanation
Indices: 31893732--31893869 Score: 141
Period size: 40 Copynumber: 3.5 Consensus size: 40
31893722 GATATAATTG
* * ** ** *
31893732 AAGCTACGACTTAGTAGGCTTTGAGTTGGTGATATGTCTC
1 AAGCTACAACTTAGCAGGCTTTGAGACGGTGATAAATTTC
* * **
31893772 AAGCTACATCTTAGCAGGCTTTGAGCCGGTGATATGTTTC
1 AAGCTACAACTTAGCAGGCTTTGAGACGGTGATAAATTTC
* *
31893812 AAGCTACGACTTAGCAGGCTTTGAGACGGTGATAAATTTT
1 AAGCTACAACTTAGCAGGCTTTGAGACGGTGATAAATTTC
**
31893852 GGGCTACAACTTAGCAGG
1 AAGCTACAACTTAGCAGG
31893870 TTATGAGCCG
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 83 1.00
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.30
Consensus pattern (40 bp):
AAGCTACAACTTAGCAGGCTTTGAGACGGTGATAAATTTC
Found at i:31893858 original size:80 final size:80
Alignment explanation
Indices: 31893732--31893884 Score: 191
Period size: 80 Copynumber: 1.9 Consensus size: 80
31893722 GATATAATTG
* ** ** *
31893732 AAGCTACGACTTAGTAGGCTTTGAGTTGGTGATATGTCTCAAGCTACATCTTAGCAGGCTT-TGA
1 AAGCTACGACTTAGCAGGCTTTGAGACGGTGATAAATCTCAAGCTACAACTTAGCAGG-TTATGA
*
31893796 GCCGGTGATATGTTTC
65 GCCGATGATATGTTTC
* ***
31893812 AAGCTACGACTTAGCAGGCTTTGAGACGGTGATAAATTTTGGGCTACAACTTAGCAGGTTATGAG
1 AAGCTACGACTTAGCAGGCTTTGAGACGGTGATAAATCTCAAGCTACAACTTAGCAGGTTATGAG
31893877 CCGATGAT
66 CCGATGAT
31893885 GTTGTAAAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
79 2 0.03
80 59 0.97
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (80 bp):
AAGCTACGACTTAGCAGGCTTTGAGACGGTGATAAATCTCAAGCTACAACTTAGCAGGTTATGAG
CCGATGATATGTTTC
Found at i:31895973 original size:58 final size:57
Alignment explanation
Indices: 31895905--31896146 Score: 287
Period size: 58 Copynumber: 4.2 Consensus size: 57
31895895 TTGGATACTC
* * * *
31895905 GAGGGCAAAATGGTAATTTTGGTCGAAATTG-GGATAAAAA-CGAGATTTTGGAAAGTTT
1 GAGGGTAAAATGGTAATTTTGGT-GAAATCGAGG-TAAAAATGGA-ATTTTAGAAAGTTT
* * *
31895963 GAGGGTAAAATGGTAATTTTTGG-AAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTC
1 GAGGGTAAAATGGTAA-TTTTGGTGAAATCGAGGT-AAAAATGGAATTTTAGAAAGTTT
31896021 GAGGGTAAAATGGTAATTTTGGTGAAATCGAAGGTAAAAATGGAATTTTAGAAAGTTT
1 GAGGGTAAAATGGTAATTTTGGTGAAATCG-AGGTAAAAATGGAATTTTAGAAAGTTT
* *
31896079 -AGGGGTAAAATGGCAATTTTGGTGTAATC-AGGGTTAAAAATGGAATTTTAGAAAGTTT
1 GA-GGGTAAAATGGTAATTTTGGTGAAATCGA-GG-TAAAAATGGAATTTTAGAAAGTTT
31896137 GAGGGTAAAA
1 GAGGGTAAAA
31896147 ATATAATTTT
Statistics
Matches: 164, Mismatches: 10, Indels: 20
0.85 0.05 0.10
Matches are distributed among these distances:
56 1 0.01
57 15 0.09
58 135 0.82
59 13 0.08
ACGTcount: A:0.38, C:0.04, G:0.29, T:0.30
Consensus pattern (57 bp):
GAGGGTAAAATGGTAATTTTGGTGAAATCGAGGTAAAAATGGAATTTTAGAAAGTTT
Found at i:31895981 original size:29 final size:30
Alignment explanation
Indices: 31895949--31896224 Score: 158
Period size: 29 Copynumber: 9.5 Consensus size: 30
31895939 TAAAAACGAG
31895949 ATTTTGGAAAGTTTGAGGGT-AAAATGGTA
1 ATTTTGGAAAGTTTGAGGGTAAAAATGGTA
* *
31895978 ATTTTTGGAAA-ATCGA-GGTCAAAAATGG-A
1 A-TTTTGGAAAGTTTGAGGGT-AAAAATGGTA
*
31896007 ATTTTGGAAAGTTCGAGGGT-AAAATGGTA
1 ATTTTGGAAAGTTTGAGGGTAAAAATGGTA
* *
31896036 ATTTTGGTGAAA--TCGAAGGTAAAAATGG-A
1 ATTTT-G-GAAAGTTTGAGGGTAAAAATGGTA
* *
31896065 ATTTTAGAAAGTTT-AGGGGT-AAAATGGCA
1 ATTTTGGAAAGTTTGA-GGGTAAAAATGGTA
* * *
31896094 ATTTTGG--TGTAATCAGGGTTAAAAATGG-A
1 ATTTTGGAAAGT-TTGAGGG-TAAAAATGGTA
* *
31896123 ATTTTAGAAAGTTTGAGGGTAAAAAT-ATA
1 ATTTTGGAAAGTTTGAGGGTAAAAATGGTA
* * *
31896152 ATTTTAGAAAGTTTTG-GGGTTAAAAT-GTG
1 ATTTTGGAAAG-TTTGAGGGTAAAAATGGTA
* *
31896181 ATTTTAGAGGAA-TTT-AGGGTCAAAAT-GTA
1 ATTTT-G-GAAAGTTTGAGGGTAAAAATGGTA
*
31896210 TTTTTGGAGAAGTTT
1 ATTTTGGA-AAGTTT
31896225 CAAGGTCAAA
Statistics
Matches: 197, Mismatches: 24, Indels: 52
0.72 0.09 0.19
Matches are distributed among these distances:
27 7 0.04
28 34 0.17
29 104 0.53
30 43 0.22
31 9 0.05
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.34
Consensus pattern (30 bp):
ATTTTGGAAAGTTTGAGGGTAAAAATGGTA
Found at i:31896206 original size:87 final size:87
Alignment explanation
Indices: 31896051--31896244 Score: 205
Period size: 87 Copynumber: 2.2 Consensus size: 87
31896041 GGTGAAATCG
** * * *
31896051 AAGGTAAAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGCAATTTTGGTGTAATCAGGGTTAA
1 AAGGTAAAAATATAATTTTAGAAAGTTTAGGGGTAAAATGG-AATTTTAGAGGAATCAGGGTTAA
*
31896116 AAATGGAATTTTAGA-AAGTTTG
65 AAATGGAATTTTAGAGAAGTTTC
* * *
31896138 AGGGTAAAAATATAATTTTAGAAAGTTTTGGGGTTAAAATGTG-ATTTTAGAGGAATTTAGGG-T
1 AAGGTAAAAATATAATTTTAGAAAGTTTAGGGG-TAAAATG-GAATTTTAGAGGAA-TCAGGGTT
* * * *
31896201 CAAAATGTATTTTTGGAGAAGTTTC
63 AAAAATGGAATTTTAGAGAAGTTTC
*
31896226 AAGGTCAAAATATAATTTT
1 AAGGTAAAAATATAATTTT
31896245 TGGATAGTTT
Statistics
Matches: 88, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
87 52 0.59
88 35 0.40
89 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (87 bp):
AAGGTAAAAATATAATTTTAGAAAGTTTAGGGGTAAAATGGAATTTTAGAGGAATCAGGGTTAAA
AATGGAATTTTAGAGAAGTTTC
Found at i:31897121 original size:8 final size:8
Alignment explanation
Indices: 31897108--31897140 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
31897098 TACAACCTAA
31897108 ATTTTATT
1 ATTTTATT
31897116 ATTTTATT
1 ATTTTATT
31897124 ATTTTATT
1 ATTTTATT
31897132 -TATTTATT
1 AT-TTTATT
31897140 A
1 A
31897141 AATAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 1 0.04
8 22 0.96
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
ATTTTATT
Found at i:31901875 original size:8 final size:8
Alignment explanation
Indices: 31901862--31901892 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
31901852 TTCTTGCATT
31901862 TGCATTCA
1 TGCATTCA
31901870 TGCATTCA
1 TGCATTCA
31901878 TGCATTCA
1 TGCATTCA
31901886 TTGCATT
1 -TGCATT
31901893 ATCATACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.42
Consensus pattern (8 bp):
TGCATTCA
Found at i:31910288 original size:80 final size:80
Alignment explanation
Indices: 31910130--31910642 Score: 863
Period size: 80 Copynumber: 6.4 Consensus size: 80
31910120 TACCCTAACT
*
31910130 ATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAATCAGA-GGCAAGATTGAAGACCATCCGA
1 ATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGA
31910194 TCTTTTACCCCGATC
66 TCTTTTACCCCGATC
*
31910209 ATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCTGAGGGCAAGATTGAAGACCATCCGA
1 ATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGA
31910274 TCTTTTACCCCGATC
66 TCTTTTACCCCGATC
*
31910289 ATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGA
1 ATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGA
31910354 TCTTTTACCCCGATC
66 TCTTTTACCCCGATC
*
31910369 ATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAAACCATCCGA
1 ATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGA
31910434 TCTTTTACCCCGATC
66 TCTTTTACCCCGATC
* *
31910449 ATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCTGA
1 ATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGA
31910514 TCTTTTACCCCGATC
66 TCTTTTACCCCGATC
* *
31910529 ATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAAAGGGC-AGATTGAAGACCATCAGA
1 ATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGA
* * *
31910593 TCTCTTACCTCGACC
66 TCTTTTACCCCGATC
* *
31910608 ATGAGGCA-AGTTGAA-ACAATCTAATCTTTTACCCT
1 ATGGGGCAGA-TTGAAGA-AATCCAATCTTTTACCCT
31910643 TAAAGTTATA
Statistics
Matches: 414, Mismatches: 17, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
78 2 0.00
79 98 0.24
80 314 0.76
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (80 bp):
ATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGA
TCTTTTACCCCGATC
Found at i:31911521 original size:16 final size:17
Alignment explanation
Indices: 31911489--31911521 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
31911479 ATGTAATTTT
*
31911489 TTATCACACACACAAAA
1 TTATCACACACAAAAAA
31911506 TTAT-ACACACAAAAAA
1 TTATCACACACAAAAAA
31911522 AATCATATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.58, C:0.24, G:0.00, T:0.18
Consensus pattern (17 bp):
TTATCACACACAAAAAA
Found at i:31913991 original size:6 final size:6
Alignment explanation
Indices: 31913970--31914016 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
31913960 TTATAATAAT
* *
31913970 TTTAAA TTCAAA -TTAAA TTTAAA TTTAAA TTTAAA TTTAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
31914017 ATAAATTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
5 4 0.11
6 32 0.89
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (6 bp):
TTTAAA
Done.