Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 132 of 182
Found at i:41499502 original size:17 final size:16
Alignment explanation
Indices: 41499461--41499503 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
41499451 ACATTAAAGT
41499461 ATAAATAAAACATACC
1 ATAAATAAAACATACC
* *
41499477 ATAATATAAAATATAGC
1 ATAA-ATAAAACATACC
41499494 ATGAAATAAA
1 AT-AAATAAA
41499504 TAAAGGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 4 0.17
17 17 0.74
18 2 0.09
ACGTcount: A:0.63, C:0.09, G:0.05, T:0.23
Consensus pattern (16 bp):
ATAAATAAAACATACC
Found at i:41502032 original size:14 final size:14
Alignment explanation
Indices: 41502013--41502039 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41502003 TTGCTTAAAG
41502013 GTCCATTTACAAAA
1 GTCCATTTACAAAA
41502027 GTCCATTTACAAA
1 GTCCATTTACAAA
41502040 CTTCAAATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (14 bp):
GTCCATTTACAAAA
Found at i:41502743 original size:3 final size:3
Alignment explanation
Indices: 41502735--41502779 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
41502725 TTAATAACAT
* *
41502735 TAA TAA TAA TAA CAA TAA TAA TAA TAA GT-T TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
41502780 CCTGAAAAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 1 0.03
3 34 0.94
4 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:41502746 original size:15 final size:15
Alignment explanation
Indices: 41502726--41502776 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
41502716 TTATTTATGT
41502726 TAATAACATTAATAA
1 TAATAACATTAATAA
*
41502741 TAATAACAATAATAA
1 TAATAACATTAATAA
**
41502756 TAATAAGTTTAATAA
1 TAATAACATTAATAA
41502771 TAATAA
1 TAATAA
41502777 TAACCTGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (15 bp):
TAATAACATTAATAA
Found at i:41503962 original size:29 final size:29
Alignment explanation
Indices: 41503929--41504019 Score: 114
Period size: 30 Copynumber: 3.1 Consensus size: 29
41503919 CCCTGAAGGT
41503929 CCCCAAA-TTGTCCACAAATTACATTTTGA
1 CCCCAAACTT-TCCACAAATTACATTTTGA
*
41503958 CCCCAAACTTTCC-CAAAATTACATTTTAA
1 CCCCAAACTTTCCAC-AAATTACATTTTGA
* *
41503987 CCTCTAAACTTTCCAAAAATTACATTTTGA
1 CC-CCAAACTTTCCACAAATTACATTTTGA
41504017 CCC
1 CCC
41504020 TCGAACTTCT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
28 1 0.02
29 26 0.48
30 27 0.50
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (29 bp):
CCCCAAACTTTCCACAAATTACATTTTGA
Found at i:41503998 original size:30 final size:29
Alignment explanation
Indices: 41503929--41504043 Score: 117
Period size: 29 Copynumber: 3.9 Consensus size: 29
41503919 CCCTGAAGGT
* *
41503929 CCCCAAA-TTGTCCACAAATTACATTTTGA
1 CCCCAAACTT-TCCAAAAATTACATTTTAA
*
41503958 CCCCAAACTTTCCCAAAATTACATTTTAA
1 CCCCAAACTTTCCAAAAATTACATTTTAA
* *
41503987 CCTCTAAACTTTCCAAAAATTACATTTTGA
1 CC-CCAAACTTTCCAAAAATTACATTTTAA
* * *
41504017 CCCTCGAAC-TTCTAAAAATTCCATTTT
1 CCC-CAAACTTTCCAAAAATTACATTTT
41504044 TGACCTTGAT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
29 42 0.58
30 31 0.42
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
CCCCAAACTTTCCAAAAATTACATTTTAA
Found at i:41504016 original size:59 final size:59
Alignment explanation
Indices: 41503939--41504161 Score: 203
Period size: 59 Copynumber: 3.8 Consensus size: 59
41503929 CCCCAAATTG
* *
41503939 TCCACAAATTACATTTTGACCC-CAAACTTTCCCAAAATTA-CATTTTAACCTCTAAACTT
1 TCCAAAAATTACATTTTGACCCTCAAAC-TTCCCAAAATTACCATTTT-ACCTCTGAACTT
* ** **
41503998 TCCAAAAATTACATTTTGACCCTCGAACTTCTAAAAATT-CCATTTTTGACCT-TGATTTT
1 TCCAAAAATTACATTTTGACCCTCAAACTTCCCAAAATTACCA-TTTT-ACCTCTGAACTT
* *
41504057 TCCAAAAATTACCATTTT-ACCCTCGAACTTCCTAAAATTTACCATTTTA-CTCTCGAAC-T
1 TCCAAAAATTA-CATTTTGACCCTCAAACTTCCCAAAA-TTACCATTTTACCTCT-GAACTT
* *
41504116 TCCAAAAATTTCATTTTTGACCCT-AAAGTAT-CCAAAATTACCATTT
1 TCCAAAAATTACA-TTTTGACCCTCAAACT-TCCCAAAATTACCATTT
41504162 ACCCCTCGGG
Statistics
Matches: 137, Mismatches: 16, Indels: 23
0.78 0.09 0.13
Matches are distributed among these distances:
58 13 0.09
59 89 0.65
60 32 0.23
61 3 0.02
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.37
Consensus pattern (59 bp):
TCCAAAAATTACATTTTGACCCTCAAACTTCCCAAAATTACCATTTTACCTCTGAACTT
Found at i:41504045 original size:30 final size:29
Alignment explanation
Indices: 41503939--41504139 Score: 151
Period size: 30 Copynumber: 6.8 Consensus size: 29
41503929 CCCCAAATTG
* * *
41503939 TCCACAAATTACATTTTGACCC-CAAACTT
1 TCCAAAAATTCCATTTTGACCCTCGAAC-T
* * * *
41503968 TCCCAAAATTACATTTT-AACCTCTAAACTT
1 TCCAAAAATTCCATTTTGACCCTC-GAAC-T
*
41503998 TCCAAAAATTACATTTTGACCCTCGAACT
1 TCCAAAAATTCCATTTTGACCCTCGAACT
* * **
41504027 TCTAAAAATTCCATTTTTGA-CCTTGATTTT
1 TCCAAAAATTCCA-TTTTGACCCTCGA-ACT
41504057 TCCAAAAATTACCATTTT-ACCCTCGAACT
1 TCCAAAAATT-CCATTTTGACCCTCGAACT
* *
41504086 TCCTAAAATTTACCATTTT-ACTCTCGAACT
1 TCC-AAAAATT-CCATTTTGACCCTCGAACT
*
41504116 TCCAAAAATTTCATTTTTGACCCT
1 TCCAAAAATTCCA-TTTTGACCCT
41504140 AAAGTATCCA
Statistics
Matches: 142, Mismatches: 20, Indels: 19
0.78 0.11 0.10
Matches are distributed among these distances:
28 5 0.04
29 48 0.34
30 81 0.57
31 8 0.06
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.37
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTGACCCTCGAACT
Found at i:41504150 original size:89 final size:89
Alignment explanation
Indices: 41503939--41504165 Score: 241
Period size: 89 Copynumber: 2.6 Consensus size: 89
41503929 CCCCAAATTG
* * *
41503939 TCCACAAATTACA-TTTTGACCCCAAACTTTCCCAAAATTA-CATTTTAACCTCTAAACTTTCCA
1 TCCAAAAATTACATTTTTGACCCTAAACTTT-CCAAAATTACCATTTTACCCTCTAAACTTTCCA
41504002 AAAATTACATTTTGACCCTCGAACT
65 AAAATTACATTTTGACCCTCGAACT
* * * * ** *
41504027 TCTAAAAATTCCATTTTTGACCTTGATTTTTCCAAAAATTACCATTTTACCCTC-GAAC-TTCCT
1 TCCAAAAATTACATTTTTGACCCTAAACTTTCC-AAAATTACCATTTTACCCTCTAAACTTTCC-
* *
41504090 AAAATTTACCATTTT-ACTCTCGAACT
64 AAAAATTA-CATTTTGACCCTCGAACT
* * *
41504116 TCCAAAAATTTCATTTTTGACCCTAAAGTATCCAAAATTACCA-TTTACCC
1 TCCAAAAATTACATTTTTGACCCTAAACTTTCCAAAATTACCATTTTACCC
41504166 CTCGGGTATT
Statistics
Matches: 115, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
87 7 0.06
88 26 0.23
89 65 0.57
90 17 0.15
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.36
Consensus pattern (89 bp):
TCCAAAAATTACATTTTTGACCCTAAACTTTCCAAAATTACCATTTTACCCTCTAAACTTTCCAA
AAATTACATTTTGACCCTCGAACT
Found at i:41504266 original size:8 final size:8
Alignment explanation
Indices: 41504246--41504274 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
41504236 CATTCTTTCG
41504246 TATTTTA-
1 TATTTTAT
41504253 TATTTTAT
1 TATTTTAT
41504261 TATTTTAT
1 TATTTTAT
41504269 TATTTT
1 TATTTT
41504275 TGTGTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:41516241 original size:99 final size:98
Alignment explanation
Indices: 41516038--41516354 Score: 368
Period size: 99 Copynumber: 3.2 Consensus size: 98
41516028 CACATTCTAC
* * * * * *
41516038 AGGGAAATATTTAAGCCGCAACTGTAAATCCAGTACCACGAAAATACGAAGGGAAAGGTTCAAGT
1 AGGGAAAGATTTAAGCCGCAACAGCAAATCCAGTACCACGAAGATACGAAGGAAAAGGTTTAAGT
* * *
41516103 CGCAATGGCGAACCTTATACCTCA-AGGGACGTGA
66 CGCAATGACGAACCTTATACCTCAGA-AG-CATGA
* * * * *
41516137 TGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGTAGATAGTGGAGGAAAAGGTTTAAG
1 AGGGAAAGATTTAAGCCGCAACAGCAAATCCAGTACCACGAAGATA-CGAAGGAAAAGGTTTAAG
* * *
41516202 TCGCAACGACGAACCTTACACCTCAGAAGCTTGA
65 TCGCAATGACGAACCTTATACCTCAGAAGCATGA
* * *
41516236 AGGGAAAGATTTAAGCCGCAACAGCGAATCCAGTACCACGAAGATACGAAGGAAATGGTTTAAGC
1 AGGGAAAGATTTAAGCCGCAACAGCAAATCCAGTACCACGAAGATACGAAGGAAAAGGTTTAAGT
* * *
41516301 CGCAATGACGAGCCTTGTACCTC-GAAAGCACGA
66 CGCAATGACGAACCTTATACCTCAG-AAGCATGA
*
41516334 AGGGAAACATTTAAGCCGCAA
1 AGGGAAAGATTTAAGCCGCAA
41516355 TGACAAGTCT
Statistics
Matches: 185, Mismatches: 30, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
97 1 0.01
98 60 0.32
99 86 0.46
100 37 0.20
101 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.17
Consensus pattern (98 bp):
AGGGAAAGATTTAAGCCGCAACAGCAAATCCAGTACCACGAAGATACGAAGGAAAAGGTTTAAGT
CGCAATGACGAACCTTATACCTCAGAAGCATGA
Found at i:41516287 original size:49 final size:49
Alignment explanation
Indices: 41516038--41516354 Score: 166
Period size: 49 Copynumber: 6.4 Consensus size: 49
41516028 CACATTCTAC
* * ** *
41516038 AGGGAAATATTTAAGCCGCAACTGTAAATCCAGTACCACGAAAATACGA
1 AGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATACGA
* * * * * **
41516087 AGGGAAAGGTTCAAGTCGCAATGGCGAA-CCTTA-TACCTC-AAGGGACGTGA
1 AGGGAAAGATTTAAGCCGCAACGGCGAATCC--AGTACCACGAAGATAC--GA
* * * * *
41516137 TGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGTAGATAGTGG
1 AGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATA-CGA
* * * * * * * *
41516187 AGGAAAAGGTTTAAGTCGCAACGACGAA-CCTTA-CACCTCAGAAGCT-TGA
1 AGGGAAAGATTTAAGCCGCAACGGCGAATCC--AGTACCAC-GAAGATACGA
*
41516236 AGGGAAAGATTTAAGCCGCAACAGCGAATCCAGTACCACGAAGATACGA
1 AGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATACGA
* * * * * * *
41516285 A-GGAAATGGTTTAAGCCGCAATGACG-AGCCTTGTACCTCGAA-AGCACGA
1 AGGGAAA-GATTTAAGCCGCAACGGCGAATCC-AGTACCACGAAGA-TACGA
*
41516334 AGGGAAACATTTAAGCCGCAA
1 AGGGAAAGATTTAAGCCGCAA
41516355 TGACAAGTCT
Statistics
Matches: 196, Mismatches: 54, Indels: 36
0.69 0.19 0.13
Matches are distributed among these distances:
48 21 0.11
49 101 0.52
50 64 0.33
51 10 0.05
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.17
Consensus pattern (49 bp):
AGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATACGA
Found at i:41516399 original size:20 final size:20
Alignment explanation
Indices: 41516348--41516392 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
41516338 AAACATTTAA
41516348 GCCGCAATGACAAGTCTAGT
1 GCCGCAATGACAAGTCTAGT
41516368 GCCGCAATGACAAGTCTAGT
1 GCCGCAATGACAAGTCTAGT
41516388 GCCGC
1 GCCGC
41516393 GAAGACATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.18
Consensus pattern (20 bp):
GCCGCAATGACAAGTCTAGT
Found at i:41517002 original size:14 final size:14
Alignment explanation
Indices: 41516956--41517010 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
41516946 CTCTAGCCAC
41516956 ATTGCCACGTCAGT
1 ATTGCCACGTCAGT
* * *
41516970 A-TGTCACATCAGC
1 ATTGCCACGTCAGT
*
41516983 ATTGCCACGTCGGT
1 ATTGCCACGTCAGT
*
41516997 ATTGCCACGCCAGT
1 ATTGCCACGTCAGT
41517011 GCCACATCAT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 10 0.32
14 21 0.68
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.25
Consensus pattern (14 bp):
ATTGCCACGTCAGT
Found at i:41517595 original size:3 final size:3
Alignment explanation
Indices: 41517587--41517625 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
41517577 TTAATAACAT
41517587 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
41517626 AACCTGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:41518799 original size:29 final size:30
Alignment explanation
Indices: 41518692--41518864 Score: 197
Period size: 30 Copynumber: 5.8 Consensus size: 30
41518682 AAAGGTCCTC
* * *
41518692 AAACTATCCAAAAATTACATTTTGACCCCT
1 AAACTTTCCAAAAATTACATTTTAACCCTT
*
41518722 AAACTTTCCAAAAATTATATTTTAACCCTT
1 AAACTTTCCAAAAATTACATTTTAACCCTT
*
41518752 AAACTTTCCAAAAATTACATTTTGACCCTT
1 AAACTTTCCAAAAATTACATTTTAACCCTT
* **
41518782 AAAC-TTCCCAAAATTACATTTTAACCCCA
1 AAACTTTCCAAAAATTACATTTTAACCCTT
* * *
41518811 AAACTTTCTAAAAAATTTCATTTTATACCCTC
1 AAACTTTC-CAAAAATTACATTTTA-ACCCTT
* *
41518843 GAAC-TTCCAAAAATTCCATTTT
1 AAACTTTCCAAAAATTACATTTT
41518865 TTACCTTGAT
Statistics
Matches: 122, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
29 25 0.20
30 74 0.61
31 16 0.13
32 7 0.06
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (30 bp):
AAACTTTCCAAAAATTACATTTTAACCCTT
Found at i:41519051 original size:59 final size:58
Alignment explanation
Indices: 41518913--41519049 Score: 159
Period size: 59 Copynumber: 2.3 Consensus size: 58
41518903 GAACTTACCA
* * * * * * * *
41518913 AAAATTACCATATTACCCTCGAACTTTCAAAAATTTCATTTTTGACCCAAATTTTTCT
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCCAAATGTGTCC
*
41518971 AAAAGTTACCATTTTACCCCCGAACTTCCAAAGATTCCATTTTTAACCTCAAA-GTGTCC
1 AAAA-TTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACC-CAAATGTGTCC
*
41519030 AAAATTACCGTTTTACCCCC
1 AAAATTACCATTTTACCCCC
41519050 CGGGTATCTA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
58 19 0.28
59 44 0.66
60 4 0.06
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.34
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCCAAATGTGTCC
Found at i:41525078 original size:50 final size:50
Alignment explanation
Indices: 41525003--41525102 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
41524993 CAACAGTGGC
41525003 GTCTTTAGTGGGATGCCCTGGTCCACCCAAAATCGCTCGATTTTGGCAAT
1 GTCTTTAGTGGGATGCCCTGGTCCACCCAAAATCGCTCGATTTTGGCAAT
* *
41525053 GTCTTTAGTGGGTTGCCCTGGTCCACCCCAAATCGCTCGATTTTGGCAAT
1 GTCTTTAGTGGGATGCCCTGGTCCACCCAAAATCGCTCGATTTTGGCAAT
41525103 ACTAGTACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.18, C:0.27, G:0.24, T:0.31
Consensus pattern (50 bp):
GTCTTTAGTGGGATGCCCTGGTCCACCCAAAATCGCTCGATTTTGGCAAT
Found at i:41525642 original size:23 final size:25
Alignment explanation
Indices: 41525601--41525666 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 25
41525591 TGTTTGGTTT
* * *
41525601 AATTTATTTATAAATTTAAATTT-A
1 AATTAATTTTTAAACTTAAATTTGA
41525625 AATTAATTTTTAAA-TTAAATTTGA
1 AATTAATTTTTAAACTTAAATTTGA
41525649 AA-TAA-TTTTAAACTTAAA
1 AATTAATTTTTAAACTTAAA
41525667 AAATAAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
22 7 0.18
23 16 0.42
24 15 0.39
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
AATTAATTTTTAAACTTAAATTTGA
Found at i:41531096 original size:16 final size:15
Alignment explanation
Indices: 41531054--41531096 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
41531044 GATCATAATG
41531054 TAAATTTACAAAAAAT
1 TAAATTTA-AAAAAAT
41531070 TAAA-TTAAAAAAATT
1 TAAATTTAAAAAAA-T
*
41531085 TAAATTTTAAAA
1 TAAATTTAAAAA
41531097 GACCATAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 6 0.25
15 8 0.33
16 10 0.42
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAATTTAAAAAAAT
Found at i:41532857 original size:34 final size:34
Alignment explanation
Indices: 41532819--41532887 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
41532809 TTGAGGTATC
41532819 AAAATTTATCAAGAAGTTGAAGTGTAAAGATTAA
1 AAAATTTATCAAGAAGTTGAAGTGTAAAGATTAA
41532853 AAAATTTATCAAGAAGTTGAAGTGTAAAGATTAA
1 AAAATTTATCAAGAAGTTGAAGTGTAAAGATTAA
41532887 A
1 A
41532888 TTTTAAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.17, T:0.29
Consensus pattern (34 bp):
AAAATTTATCAAGAAGTTGAAGTGTAAAGATTAA
Found at i:41541588 original size:29 final size:29
Alignment explanation
Indices: 41541555--41541613 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
41541545 CGTCTAAGAA
41541555 ACAAGGTGCTGTGTCTCGCTCTACTTCGG
1 ACAAGGTGCTGTGTCTCGCTCTACTTCGG
* *
41541584 ACAAGGTGTTGTGTTTCGCTCTACTTCGG
1 ACAAGGTGCTGTGTCTCGCTCTACTTCGG
41541613 A
1 A
41541614 GGCTAAGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.15, C:0.24, G:0.27, T:0.34
Consensus pattern (29 bp):
ACAAGGTGCTGTGTCTCGCTCTACTTCGG
Found at i:41546021 original size:27 final size:27
Alignment explanation
Indices: 41545947--41546020 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
41545937 ATTTTTTTAC
* *
41545947 CTTTAACCTCAAACCCTAAATCTAAAA
1 CTTTAAACTCAAACCCAAAATCTAAAA
*
41545974 -TCTCAAACCTC-AACCCAAAATCTAAAA
1 CT-TTAAA-CTCAAACCCAAAATCTAAAA
41546001 CTTTAAACTCAAACTCCAAA
1 CTTTAAACTCAAAC-CCAAA
41546021 TAAATACCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
26 4 0.11
27 25 0.66
28 9 0.24
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (27 bp):
CTTTAAACTCAAACCCAAAATCTAAAA
Found at i:41546106 original size:56 final size:57
Alignment explanation
Indices: 41546053--41546187 Score: 227
Period size: 56 Copynumber: 2.4 Consensus size: 57
41546043 CCTTAAATCT
*
41546053 AAACCCTAAACCTCCAACTCATAACACATAATCCCAAATGCTTGAACCCTAAATTTC
1 AAACCCTAAACCTCAAACTCATAACACATAATCCCAAATGCTTGAACCCTAAATTTC
41546110 AAACCCTAAACC-CAAACTCATAACACATAATCCCAAATGCTTGAACCCTAAATTTC
1 AAACCCTAAACCTCAAACTCATAACACATAATCCCAAATGCTTGAACCCTAAATTTC
* *
41546166 AAACTCTAAACCTTAAATCTCA
1 AAACCCTAAACCTCAAA-CTCA
41546188 AACTCAAACC
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
56 54 0.74
57 15 0.21
58 4 0.05
ACGTcount: A:0.42, C:0.32, G:0.03, T:0.23
Consensus pattern (57 bp):
AAACCCTAAACCTCAAACTCATAACACATAATCCCAAATGCTTGAACCCTAAATTTC
Found at i:41546202 original size:20 final size:21
Alignment explanation
Indices: 41546153--41546204 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
41546143 CAAATGCTTG
*
41546153 AACCCTAAATTTCAAACTCTA
1 AACCCTAAATCTCAAACTCTA
*
41546174 AACCTTAAATCTCAAACTC-A
1 AACCCTAAATCTCAAACTCTA
41546194 AACCCTAAATC
1 AACCCTAAATC
41546205 ATGAGATTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (21 bp):
AACCCTAAATCTCAAACTCTA
Found at i:41546466 original size:17 final size:17
Alignment explanation
Indices: 41546444--41546476 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41546434 TTGTTTATGA
41546444 TTTAAAAAATTAATTAT
1 TTTAAAAAATTAATTAT
*
41546461 TTTAAATAATTAATTA
1 TTTAAAAAATTAATTA
41546477 AAGTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTAAAAAATTAATTAT
Found at i:41546642 original size:42 final size:42
Alignment explanation
Indices: 41546588--41546673 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
41546578 AAAATTATAC
41546588 TTTTTAGAATGATATTATCATAATTTATTCTCTTAGTAATTA
1 TTTTTAGAATGATATTATCATAATTTATTCTCTTAGTAATTA
41546630 TTTTTAGAATGATATTATCATAATTTATTCTCTTAGTAATTA
1 TTTTTAGAATGATATTATCATAATTTATTCTCTTAGTAATTA
41546672 TT
1 TT
41546674 GTAACAATCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (42 bp):
TTTTTAGAATGATATTATCATAATTTATTCTCTTAGTAATTA
Found at i:41549723 original size:16 final size:17
Alignment explanation
Indices: 41549692--41549728 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
41549682 GTGTTCTTTA
41549692 TTTTGTTTTAGTTATT-
1 TTTTGTTTTAGTTATTG
41549708 TTTTAGTTTTAG-TATTG
1 TTTT-GTTTTAGTTATTG
41549725 TTTT
1 TTTT
41549729 TAGGGTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.73
Consensus pattern (17 bp):
TTTTGTTTTAGTTATTG
Found at i:41558022 original size:55 final size:56
Alignment explanation
Indices: 41557938--41558052 Score: 196
Period size: 55 Copynumber: 2.1 Consensus size: 56
41557928 GTTAATAGAA
41557938 ATATATTATATTTTCACCTTCTGTTATTAG-TCCATTGAACCTATCAAACTTGATC
1 ATATATTATATTTTCACCTTCTGTTATTAGTTCCATTGAACCTATCAAACTTGATC
* * *
41557993 ATATATTATATTTTCATCTTGTGTTATTAGTTCCATTGAACTTATCAAACTTGATC
1 ATATATTATATTTTCACCTTCTGTTATTAGTTCCATTGAACCTATCAAACTTGATC
41558049 ATAT
1 ATAT
41558053 CTTGATAAAC
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
55 28 0.50
56 28 0.50
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.46
Consensus pattern (56 bp):
ATATATTATATTTTCACCTTCTGTTATTAGTTCCATTGAACCTATCAAACTTGATC
Found at i:41560390 original size:19 final size:18
Alignment explanation
Indices: 41560366--41560403 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
41560356 TGTACAATAT
41560366 AATTAAATAAATTAAATTA
1 AATTAAAT-AATTAAATTA
*
41560385 AATTAAATAATTTAATTA
1 AATTAAATAATTAAATTA
41560403 A
1 A
41560404 TTATTTACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AATTAAATAATTAAATTA
Found at i:41560404 original size:9 final size:9
Alignment explanation
Indices: 41560365--41560406 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
41560355 ATGTACAATA
41560365 TAATTAAAT
1 TAATTAAAT
*
41560374 AAATTAAAT
1 TAATTAAAT
41560383 TAAATTAAA-
1 T-AATTAAAT
*
41560392 TAATTTAAT
1 TAATTAAAT
41560401 TAATTA
1 TAATTA
41560407 TTTACCTAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
8 6 0.22
9 14 0.52
10 7 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
TAATTAAAT
Found at i:41561083 original size:15 final size:15
Alignment explanation
Indices: 41561063--41561092 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41561053 CTATATATTT
41561063 ATAAAAAAATTTAAA
1 ATAAAAAAATTTAAA
*
41561078 ATAAAATAATTTAAA
1 ATAAAAAAATTTAAA
41561093 TTATTTGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATAAAAAAATTTAAA
Found at i:41562988 original size:15 final size:13
Alignment explanation
Indices: 41562970--41563033 Score: 58
Period size: 13 Copynumber: 4.6 Consensus size: 13
41562960 TTTATAATGA
41562970 TAATAAAAATAAAT
1 TAATAAAAA-AAAT
41562984 GTAATATAAAAAAA-
1 -TAATA-AAAAAAAT
41562998 TAATAAATAAAAAAT
1 TAAT-AA-AAAAAAT
*
41563013 TAATAAATAAAAT
1 TAATAAAAAAAAT
*
41563026 TATTAAAA
1 TAATAAAA
41563034 TTAAAAGATA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
13 17 0.40
14 9 0.21
15 12 0.29
16 4 0.10
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (13 bp):
TAATAAAAAAAAT
Found at i:41563020 original size:22 final size:20
Alignment explanation
Indices: 41562993--41563062 Score: 77
Period size: 22 Copynumber: 3.3 Consensus size: 20
41562983 TGTAATATAA
*
41562993 AAAAATAATAAATAAAAAATT
1 AAAAATAA-AATTAAAAAATT
*
41563014 AATAAATAAAATTATTAAAATT
1 AA-AAATAAAATTA-AAAAATT
*
41563036 AAAAGATAAAATTAAAAAATA
1 AAAA-ATAAAATTAAAAAATT
41563057 AAAAAT
1 AAAAAT
41563063 TACACGGACA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
20 2 0.05
21 17 0.40
22 23 0.55
ACGTcount: A:0.73, C:0.00, G:0.01, T:0.26
Consensus pattern (20 bp):
AAAAATAAAATTAAAAAATT
Found at i:41563025 original size:13 final size:13
Alignment explanation
Indices: 41562970--41563059 Score: 57
Period size: 13 Copynumber: 6.9 Consensus size: 13
41562960 TTTATAATGA
*
41562970 TAATAAAAATAAAT
1 TAATAAATA-AAAT
*
41562984 GTAATATAA-AAAAA
1 -TAATA-AATAAAAT
41562998 TAATAAATAAAAAAT
1 TAATAAAT--AAAAT
41563013 TAATAAATAAAAT
1 TAATAAATAAAAT
41563026 T-AT---TAAAAT
1 TAATAAATAAAAT
41563035 TAA-AAGATAAAAT
1 TAATAA-ATAAAAT
*
41563048 TAAAAAATAAAA
1 TAATAAATAAAA
41563060 AATTACACGG
Statistics
Matches: 63, Mismatches: 2, Indels: 22
0.72 0.02 0.25
Matches are distributed among these distances:
9 7 0.11
10 1 0.02
12 4 0.06
13 26 0.41
14 5 0.08
15 18 0.29
16 2 0.03
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (13 bp):
TAATAAATAAAAT
Found at i:41563458 original size:13 final size:13
Alignment explanation
Indices: 41563440--41563473 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
41563430 AGATCATGGA
41563440 AAATTTCATATTT
1 AAATTTCATATTT
41563453 AAATTT--TATTT
1 AAATTTCATATTT
41563464 AAATTTCATA
1 AAATTTCATA
41563474 CTTTCATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (13 bp):
AAATTTCATATTT
Found at i:41563472 original size:24 final size:24
Alignment explanation
Indices: 41563440--41563487 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
41563430 AGATCATGGA
41563440 AAATTTCATA-TTTAAATTTTATTT
1 AAATTTCATACTTT-AATTTTATTT
*
41563464 AAATTTCATACTTTCATTTTATTT
1 AAATTTCATACTTTAATTTTATTT
41563488 TTTTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (24 bp):
AAATTTCATACTTTAATTTTATTT
Found at i:41565742 original size:30 final size:30
Alignment explanation
Indices: 41565703--41565763 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
41565693 AAACATTGCG
* *
41565703 ATACCATACTGAATTGGTAGTGACACTGTA
1 ATACCATACTGAACTGGCAGTGACACTGTA
* *
41565733 ATACTATACTGAACTGGCAGTGCCACTGTA
1 ATACCATACTGAACTGGCAGTGACACTGTA
41565763 A
1 A
41565764 ACACTATGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (30 bp):
ATACCATACTGAACTGGCAGTGACACTGTA
Found at i:41565768 original size:39 final size:39
Alignment explanation
Indices: 41565725--41565881 Score: 163
Period size: 39 Copynumber: 4.0 Consensus size: 39
41565715 ATTGGTAGTG
*
41565725 ACACTGTAATACTATACTGAACTGGCAGTGCCACTGTAA
1 ACACTGTAATACTATACTGAACTGGCAGTGACACTGTAA
* * * * *
41565764 ACACTATGATACTTTACTGAATTGGCAGTGACACTATAA
1 ACACTGTAATACTATACTGAACTGGCAGTGACACTGTAA
* * * *
41565803 ACACTGTGATACCATAATGAACTGGCAATGACACTGTAA
1 ACACTGTAATACTATACTGAACTGGCAGTGACACTGTAA
* * * * *
41565842 ACACTGGAATATTATA-TCGAACTAGTAGTGACACTATAA
1 ACACTGTAATACTATACT-GAACTGGCAGTGACACTGTAA
41565881 A
1 A
41565882 ATATCGCACA
Statistics
Matches: 96, Mismatches: 21, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
38 1 0.01
39 95 0.99
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (39 bp):
ACACTGTAATACTATACTGAACTGGCAGTGACACTGTAA
Found at i:41565835 original size:108 final size:108
Alignment explanation
Indices: 41565641--41565841 Score: 276
Period size: 108 Copynumber: 1.9 Consensus size: 108
41565631 TAATGAATTA
* * * * * *
41565641 GCAGTGACACTATAATCACTATGATACTTTACTTAATTAGTAGTGACATTGTAAACATTGCGATA
1 GCAGTGACACTATAAACACTATGATACTTTACTGAATTAGCAGTGACACTATAAACACTGCGATA
* * * *
41565706 CCATACTGAATTGGTAGTGACACTGTAATACTATACTGAACTG
66 CCATAATGAACTGGCAATGACACTGTAATACTATACTGAACTG
* * * *
41565749 GCAGTGCCACTGTAAACACTATGATACTTTACTGAATTGGCAGTGACACTATAAACACTGTGATA
1 GCAGTGACACTATAAACACTATGATACTTTACTGAATTAGCAGTGACACTATAAACACTGCGATA
41565814 CCATAATGAACTGGCAATGACACTGTAA
66 CCATAATGAACTGGCAATGACACTGTAA
41565842 ACACTGGAAT
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
108 79 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (108 bp):
GCAGTGACACTATAAACACTATGATACTTTACTGAATTAGCAGTGACACTATAAACACTGCGATA
CCATAATGAACTGGCAATGACACTGTAATACTATACTGAACTG
Found at i:41565872 original size:78 final size:78
Alignment explanation
Indices: 41565725--41565881 Score: 185
Period size: 78 Copynumber: 2.0 Consensus size: 78
41565715 ATTGGTAGTG
* * * * * * *
41565725 ACACTGTAATACTATACTGAACTGGCAGTGCCACTGTAAACACTATGATACTTTACTGAATTGGC
1 ACACTGTAATACCATAATGAACTGGCAATGACACTGTAAACACTAGGATACTTTACTGAACTAGC
41565790 AGTGACACTATAA
66 AGTGACACTATAA
*
41565803 ACACTGTGATACCATAATGAACTGGCAATGACACTGTAAACACT-GGAATA-TTATA-TCGAACT
1 ACACTGTAATACCATAATGAACTGGCAATGACACTGTAAACACTAGG-ATACTT-TACT-GAACT
*
41565865 AGTAGTGACACTATAA
63 AGCAGTGACACTATAA
41565881 A
1 A
41565882 ATATCGCACA
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
77 4 0.06
78 63 0.94
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (78 bp):
ACACTGTAATACCATAATGAACTGGCAATGACACTGTAAACACTAGGATACTTTACTGAACTAGC
AGTGACACTATAA
Found at i:41567715 original size:21 final size:21
Alignment explanation
Indices: 41567675--41567715 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41567665 TCTAGGCACT
* *
41567675 GGTAGAGGTGGTCCTGTTTTG
1 GGTAGAGGTGGTACTATTTTG
41567696 GGTAGAGGTGGTACTATTTT
1 GGTAGAGGTGGTACTATTTT
41567716 TGGACGAGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.07, G:0.39, T:0.39
Consensus pattern (21 bp):
GGTAGAGGTGGTACTATTTTG
Found at i:41571359 original size:14 final size:14
Alignment explanation
Indices: 41571340--41571367 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41571330 GTTTTCTTTA
41571340 TTATTTATTTATTT
1 TTATTTATTTATTT
41571354 TTATTTATTTATTT
1 TTATTTATTTATTT
41571368 ATTAGGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTATTTATTTATTT
Found at i:41571363 original size:18 final size:17
Alignment explanation
Indices: 41571336--41571370 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
41571326 TCTGGTTTTC
41571336 TTTATTATTTATTTATT
1 TTTATTATTTATTTATT
41571353 TTTATTTATTTATTTATT
1 TTTA-TTATTTATTTATT
41571371 AGGTTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTATTATTTATTTATT
Found at i:41579091 original size:15 final size:16
Alignment explanation
Indices: 41579059--41579090 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41579049 GGTAATTTTT
41579059 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
*
41579075 ATGTTAAGGGAATAAA
1 ATGTTAAAGGAATAAA
41579091 TTTGGAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:41579961 original size:195 final size:195
Alignment explanation
Indices: 41579565--41580012 Score: 541
Period size: 195 Copynumber: 2.3 Consensus size: 195
41579555 GAAACCGATG
*
41579565 CGATGGCTGAGGTACCGCATAAGTTGTGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTGAGTCA
1 CGATGGCTGAGGTACCGCATAAGTTGTGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTGACTCA
*
41579630 GGAAATGAGAAAAGAATCCAAGAATGGATTACAGGCCCTACGATGGCTGAGATTTATGCATAAGT
66 GGAAATGAGAAAAGAATCCAAGAATGGATTACAGGCCCTACGATGGCTGAGATCTATGCATAAGT
* * * * *
41579695 GTATATTCTCGACAGCTCGTGTGAGCAGTATCATTAGGGAACAGTTAGATGCACAGATACCGTAT
131 GCATACTCTCGACAGCTCGTGTGAGCAGTATCATTAGGGAACAGTTAGATACACAGACACCGTAC
* * *
41579760 CGATGGCTAAGGTA-CGACATATGTTGTGAGTCCTCGATAGCTCATGTGAGCAGCATCGTGACTC
1 CGATGGCTGAGGTACCG-CATAAGTTGTGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTGACTC
* * * * * * ** * * * *
41579824 GGGAAA-GAGATATGGATCCTA-CATGGATTATGGGCCCTATGATGGCTGGGA-CTATGCTTTA-
65 AGGAAATGAGAAAAGAATCCAAGAATGGATTACAGGCCCTACGATGGCTGAGATCTATGCATAAG
* *
41579885 TGCATACTCTCGACAGCTCGTGTGAGCA-TCATCGTTAGGGAACAGATTATAGTACAGACA-AGC
130 TGCATACTCTCGACAGCTCGTGTGAGCAGT-ATCATTAGGGAACAG-TTAGA-TAC--ACAGA-C
41579948 ACCGTAC
189 ACCGTAC
* **
41579955 CGATGGCTGAGGTACCGCATACGTTGCCAGTCCTCGATAGCTCGTGTGAGCAGCATCG
1 CGATGGCTGAGGTACCGCATAAGTTGTGAGTCCTCGATAGCTCGTGTGAGCAGCATCG
41580013 AGTACTGGTA
Statistics
Matches: 216, Mismatches: 29, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
190 1 0.00
191 40 0.19
192 11 0.05
193 27 0.12
194 14 0.06
195 121 0.56
196 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (195 bp):
CGATGGCTGAGGTACCGCATAAGTTGTGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTGACTCA
GGAAATGAGAAAAGAATCCAAGAATGGATTACAGGCCCTACGATGGCTGAGATCTATGCATAAGT
GCATACTCTCGACAGCTCGTGTGAGCAGTATCATTAGGGAACAGTTAGATACACAGACACCGTAC
Found at i:41582821 original size:16 final size:17
Alignment explanation
Indices: 41582800--41582833 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
41582790 ACTAATAATC
*
41582800 TTTAAT-TAATATATTT
1 TTTAATATAAAATATTT
41582816 TTTAATATAAAATATTT
1 TTTAATATAAAATATTT
41582833 T
1 T
41582834 GATTCACCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTAATATAAAATATTT
Found at i:41583894 original size:23 final size:22
Alignment explanation
Indices: 41583843--41583886 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
41583833 TATTTTTTTC
41583843 TATGTGAAAAATCAAGACTAAG
1 TATGTGAAAAATCAAGACTAAG
41583865 TATGTGAAAAATCAAGACTAAG
1 TATGTGAAAAATCAAGACTAAG
41583887 GGTTGTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.18, T:0.23
Consensus pattern (22 bp):
TATGTGAAAAATCAAGACTAAG
Found at i:41587551 original size:24 final size:24
Alignment explanation
Indices: 41587384--41587561 Score: 194
Period size: 24 Copynumber: 7.4 Consensus size: 24
41587374 TATCAACTTT
* * *
41587384 CACATGTTTACGCTCTTCAGCTTA
1 CACACGTTTACGCTCGTCAGCTTG
* *
41587408 CACATGTTTACGCTCGTCAGCTTA
1 CACACGTTTACGCTCGTCAGCTTG
*
41587432 TACACGTTTACGCTCGTCAGCTTG
1 CACACGTTTACGCTCGTCAGCTTG
* *
41587456 CACACGTTTACACTCGTCAGCTTA
1 CACACGTTTACGCTCGTCAGCTTG
* * * * *
41587480 TATACGTTTATGCTCATCAACTTG
1 CACACGTTTACGCTCGTCAGCTTG
*
41587504 CACATGTTTACGCTCGTCAGCTTG
1 CACACGTTTACGCTCGTCAGCTTG
* *
41587528 CACACGTTTACGCTAGTTAGCTTG
1 CACACGTTTACGCTCGTCAGCTTG
* *
41587552 TATACGTTTA
1 CACACGTTTA
41587562 TGCAGTTTGA
Statistics
Matches: 129, Mismatches: 25, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 129 1.00
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.35
Consensus pattern (24 bp):
CACACGTTTACGCTCGTCAGCTTG
Found at i:41594114 original size:24 final size:24
Alignment explanation
Indices: 41594074--41594306 Score: 268
Period size: 24 Copynumber: 9.7 Consensus size: 24
41594064 CACATTCTTT
*
41594074 CACGTTTACGCTTGTCAGCTTGCA
1 CACGTTTACGCTCGTCAGCTTGCA
* *
41594098 CACATTTATGCTCGTCAGCTTGCA
1 CACGTTTACGCTCGTCAGCTTGCA
* *
41594122 CACGTTTATGCTCGTCAGCTTGTA
1 CACGTTTACGCTCGTCAGCTTGCA
*
41594146 CACGTTTACGCTTGTCAGCTTGCA
1 CACGTTTACGCTCGTCAGCTTGCA
* * **
41594170 CATGTTTACACTCGTCAGCTTATA
1 CACGTTTACGCTCGTCAGCTTGCA
* *
41594194 TACGTTTACGCTCATCAGCTTGCA
1 CACGTTTACGCTCGTCAGCTTGCA
* * **
41594218 CAAGTTTACGCTCGTCATCTTATA
1 CACGTTTACGCTCGTCAGCTTGCA
* * *
41594242 TATGTTTACACTCGTCAGCTTGCA
1 CACGTTTACGCTCGTCAGCTTGCA
* *
41594266 CACGTTTATGCTCGTCAGTTTGCA
1 CACGTTTACGCTCGTCAGCTTGCA
*
41594290 CACATTTACGCTCGTCA
1 CACGTTTACGCTCGTCA
41594307 ACTTATATAC
Statistics
Matches: 171, Mismatches: 38, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 171 1.00
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.35
Consensus pattern (24 bp):
CACGTTTACGCTCGTCAGCTTGCA
Found at i:41594199 original size:72 final size:72
Alignment explanation
Indices: 41594074--41594306 Score: 295
Period size: 72 Copynumber: 3.2 Consensus size: 72
41594064 CACATTCTTT
* ** **
41594074 CACGTTTACGCTTGTCAGCTTGCACACATTTATGCTCGTCAGCTTGCACACGTTTATGCTCGTCA
1 CACGTTTACGCTCGTCAGCTTGCACATGTTTACACTCGTCAGCTTGCACACGTTTATGCTCGTCA
*
41594139 GCTTGTA
66 GCTTGCA
* ** * * *
41594146 CACGTTTACGCTTGTCAGCTTGCACATGTTTACACTCGTCAGCTTATATACGTTTACGCTCATCA
1 CACGTTTACGCTCGTCAGCTTGCACATGTTTACACTCGTCAGCTTGCACACGTTTATGCTCGTCA
41594211 GCTTGCA
66 GCTTGCA
* * ** *
41594218 CAAGTTTACGCTCGTCATCTTATATATGTTTACACTCGTCAGCTTGCACACGTTTATGCTCGTCA
1 CACGTTTACGCTCGTCAGCTTGCACATGTTTACACTCGTCAGCTTGCACACGTTTATGCTCGTCA
*
41594283 GTTTGCA
66 GCTTGCA
*
41594290 CACATTTACGCTCGTCA
1 CACGTTTACGCTCGTCA
41594307 ACTTATATAC
Statistics
Matches: 137, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
72 137 1.00
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.35
Consensus pattern (72 bp):
CACGTTTACGCTCGTCAGCTTGCACATGTTTACACTCGTCAGCTTGCACACGTTTATGCTCGTCA
GCTTGCA
Found at i:41596343 original size:9 final size:9
Alignment explanation
Indices: 41596329--41596390 Score: 63
Period size: 9 Copynumber: 6.7 Consensus size: 9
41596319 TATAATATAC
41596329 TACATAACA
1 TACATAACA
*
41596338 TACATAATA
1 TACATAACA
41596347 TACAT-ACA
1 TACATAACA
*
41596355 TAAACAGTAATA
1 T--ACA-TAACA
41596367 TACATAACA
1 TACATAACA
*
41596376 TACATAATA
1 TACATAACA
41596385 TACATA
1 TACATA
41596391 CTAATATACA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
8 3 0.07
9 31 0.70
10 6 0.14
11 1 0.02
12 3 0.07
ACGTcount: A:0.55, C:0.16, G:0.02, T:0.27
Consensus pattern (9 bp):
TACATAACA
Found at i:41596416 original size:25 final size:25
Alignment explanation
Indices: 41596321--41596419 Score: 77
Period size: 25 Copynumber: 4.1 Consensus size: 25
41596311 ATATAAACTA
*
41596321 TAATATAC-TACATAAC--ATACA-
1 TAATATACATACATAACAAATATAC
41596342 TAATATACATACATAAACAGTAATATAC
1 TAATATACATACAT-AACA--AATATAC
* * *
41596370 --ATA-ACATACATAATATACATAC
1 TAATATACATACATAACAAATATAC
*
41596392 TAATATACATGCATAACAAATATAC
1 TAATATACATACATAACAAATATAC
41596417 TAA
1 TAA
41596420 CAGACTGATC
Statistics
Matches: 60, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
21 8 0.13
22 10 0.17
23 3 0.05
24 6 0.10
25 26 0.43
26 3 0.05
27 4 0.07
ACGTcount: A:0.54, C:0.16, G:0.02, T:0.28
Consensus pattern (25 bp):
TAATATACATACATAACAAATATAC
Found at i:41599041 original size:24 final size:25
Alignment explanation
Indices: 41598984--41599041 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
41598974 TCACGAGCAA
* *
41598984 ACTCGTTTAAAAGCCCGTTTATTGG
1 ACTCGTTTATAAGCCCATTTATTGG
*
41599009 -CTCGTTTATAAGCTCATTTA-TGG
1 ACTCGTTTATAAGCCCATTTATTGG
41599032 ACTCGTTTAT
1 ACTCGTTTAT
41599042 TTATTAATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.10
24 26 0.90
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.41
Consensus pattern (25 bp):
ACTCGTTTATAAGCCCATTTATTGG
Found at i:41599159 original size:24 final size:23
Alignment explanation
Indices: 41599132--41599195 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
41599122 CCATTAACAT
41599132 TGTTCGTAAACATGTTCAATTATA
1 TGTTCGTAAACATGTTCAATTA-A
* * * **
41599156 TGTTCATAAAAATATTCGTTTAA
1 TGTTCGTAAACATGTTCAATTAA
*
41599179 TGTTCGTGAACATGTTC
1 TGTTCGTAAACATGTTC
41599196 GAACATGTTC
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 14 0.45
24 17 0.55
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.42
Consensus pattern (23 bp):
TGTTCGTAAACATGTTCAATTAA
Found at i:41599195 original size:12 final size:12
Alignment explanation
Indices: 41599178--41599213 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
41599168 TATTCGTTTA
41599178 ATGTTCGTGAAC
1 ATGTTCGTGAAC
41599190 ATGTTC--GAAC
1 ATGTTCGTGAAC
41599200 ATGTTCGTGAAC
1 ATGTTCGTGAAC
41599212 AT
1 AT
41599214 TAAACAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.45
12 12 0.55
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (12 bp):
ATGTTCGTGAAC
Found at i:41600851 original size:10 final size:10
Alignment explanation
Indices: 41600836--41600863 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
41600826 AGTAGTCAAT
41600836 TCATCTGCAA
1 TCATCTGCAA
41600846 TCATCTGCAA
1 TCATCTGCAA
41600856 TCATCTGC
1 TCATCTGC
41600864 CTCTGCTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.25, C:0.32, G:0.11, T:0.32
Consensus pattern (10 bp):
TCATCTGCAA
Found at i:41621375 original size:37 final size:37
Alignment explanation
Indices: 41621323--41621479 Score: 226
Period size: 37 Copynumber: 4.2 Consensus size: 37
41621313 TAAGAATTTG
*
41621323 GGCTATGTGTCTAGCAGGCTTCGTGCCGATGTATTCA
1 GGCTATGTGCCTAGCAGGCTTCGTGCCGATGTATTCA
* *
41621360 GCCTATGTGCCTAGCAGGCTTCGTGCCGGTGTATTC-
1 GGCTATGTGCCTAGCAGGCTTCGTGCCGATGTATTCA
* * *
41621396 GAGCTATGTGCCTAGCAGGCTTCGTGTCGGTGTATTCG
1 G-GCTATGTGCCTAGCAGGCTTCGTGCCGATGTATTCA
* *
41621434 GGCTATGTGCCTAACAGGCTTCGTGCCAATGTATTCA
1 GGCTATGTGCCTAGCAGGCTTCGTGCCGATGTATTCA
41621471 GGCTATGTG
1 GGCTATGTG
41621480 TCTTGTAGGC
Statistics
Matches: 108, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
36 1 0.01
37 106 0.98
38 1 0.01
ACGTcount: A:0.15, C:0.23, G:0.31, T:0.31
Consensus pattern (37 bp):
GGCTATGTGCCTAGCAGGCTTCGTGCCGATGTATTCA
Found at i:41622182 original size:20 final size:20
Alignment explanation
Indices: 41622159--41622202 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
41622149 GTAGTATCGG
41622159 TAGACTAAGCTATGTATCAA
1 TAGACTAAGCTATGTATCAA
*
41622179 TAGACTAAGTTATGTATCAA
1 TAGACTAAGCTATGTATCAA
41622199 TAGA
1 TAGA
41622203 AAAATGATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (20 bp):
TAGACTAAGCTATGTATCAA
Found at i:41622918 original size:14 final size:14
Alignment explanation
Indices: 41622901--41622927 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41622891 GTAAAACAAT
41622901 GAAAATATTTTACA
1 GAAAATATTTTACA
41622915 GAAAATATTTTAC
1 GAAAATATTTTAC
41622928 TAGCAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (14 bp):
GAAAATATTTTACA
Found at i:41623220 original size:12 final size:12
Alignment explanation
Indices: 41623203--41623228 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41623193 TCCATTTATT
41623203 TTCTTTATTTTA
1 TTCTTTATTTTA
41623215 TTCTTTATTTTA
1 TTCTTTATTTTA
41623227 TT
1 TT
41623229 TTGTTCTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (12 bp):
TTCTTTATTTTA
Found at i:41623228 original size:17 final size:16
Alignment explanation
Indices: 41623206--41623240 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
41623196 ATTTATTTTC
41623206 TTTATTTTATTCTTTAT
1 TTTATTTTATTC-TTAT
*
41623223 TTTATTTTGTTCTTAT
1 TTTATTTTATTCTTAT
41623239 TT
1 TT
41623241 AATTATTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTATTTTATTCTTAT
Found at i:41628616 original size:18 final size:18
Alignment explanation
Indices: 41628568--41628622 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
41628558 AAATTTATTT
* *
41628568 TTTTTTAAATTTA-TAAA
1 TTTTATAAAATTATTAAA
* *
41628585 TTTGAAAAACATTATTAAA
1 TTTTATAAA-ATTATTAAA
41628604 TTTTATAAAATTATTAAA
1 TTTTATAAAATTATTAAA
41628622 T
1 T
41628623 AAAATTTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 6 0.20
18 13 0.43
19 11 0.37
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
TTTTATAAAATTATTAAA
Found at i:41628652 original size:16 final size:16
Alignment explanation
Indices: 41628631--41628661 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41628621 ATAAAATTTA
*
41628631 AAAATTTTTAAAAATT
1 AAAATTATTAAAAATT
41628647 AAAATTATTAAAAAT
1 AAAATTATTAAAAAT
41628662 CAATTTAAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATTATTAAAAATT
Found at i:41631646 original size:183 final size:183
Alignment explanation
Indices: 41631338--41631887 Score: 922
Period size: 183 Copynumber: 3.0 Consensus size: 183
41631328 ATCGATGCAT
41631338 GCGCAATCGCTCGAGAGTTTGCATATTTGTGCAAGAATTGCTCTATTCACAGGCAATCTTTCGAT
1 GCGCAATCGCTCGAGAGTTTGCATATTTGTGCAAGAATTGCTCTATTCACAGGCAATCTTTCGAT
*
41631403 TTTAGTTTACTGACTGGAGATAGGTGAACGCAGTTTTGGTCAACATACGCAATCGCTCGATTTTG
66 TTTAGTTTACTGACTGGCGATAGGTGAACGCAGTTTTGGTCAACATACGCAATCGCTCGATTTTG
41631468 GAATATTGGTTCAAGCATCGGACGATCGTTGAAGGTGGTACGCCTTGTAAAAC
131 GAATATTGGTTCAAGCATCGGACGATCGTTGAAGGTGGTACGCCTTGTAAAAC
41631521 GCGCAATCGCTCGAGAGTTTGCATATTTGTGCAAGAATTGCTCTATTCACAGGCAATCTTTCGAT
1 GCGCAATCGCTCGAGAGTTTGCATATTTGTGCAAGAATTGCTCTATTCACAGGCAATCTTTCGAT
41631586 TTTAGTTTACTGACTGGCGATAGGTGAACGCAGTTTTGGTCAACATACGCAATCGCTCGATTTTG
66 TTTAGTTTACTGACTGGCGATAGGTGAACGCAGTTTTGGTCAACATACGCAATCGCTCGATTTTG
41631651 GAATATTGGTTCAAGCATCGGACGATCGTTGAAGGTGGTACGCCTTGTAAAAC
131 GAATATTGGTTCAAGCATCGGACGATCGTTGAAGGTGGTACGCCTTGTAAAAC
** * *
41631704 GCGCAATCGCTCGAGAGTTTGCATATTCATGCAAGAATTGGTCAATTCACAGGCAATCTTTCGAT
1 GCGCAATCGCTCGAGAGTTTGCATATTTGTGCAAGAATTGCTCTATTCACAGGCAATCTTTCGAT
* * * * *
41631769 TTTGGTCTACTGACTGGCGATAGATGAACGC-GATTTTGGTCCACATGCGCAATCGCTCGATTTT
66 TTTAGTTTACTGACTGGCGATAGGTGAACGCAG-TTTTGGTCAACATACGCAATCGCTCGATTTT
* * * * * * * *
41631833 GGAATATTGATTCTAGCGTCGGGCGATCGGTGAAGGTTGTACGCCCTGGAAAAC
130 GGAATATTGGTTCAAGCATCGGACGATCGTTGAAGGTGGTACGCCTTGTAAAAC
41631887 G
1 G
41631888 TGAAATCGAT
Statistics
Matches: 348, Mismatches: 18, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
182 1 0.00
183 347 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (183 bp):
GCGCAATCGCTCGAGAGTTTGCATATTTGTGCAAGAATTGCTCTATTCACAGGCAATCTTTCGAT
TTTAGTTTACTGACTGGCGATAGGTGAACGCAGTTTTGGTCAACATACGCAATCGCTCGATTTTG
GAATATTGGTTCAAGCATCGGACGATCGTTGAAGGTGGTACGCCTTGTAAAAC
Found at i:41632762 original size:9 final size:9
Alignment explanation
Indices: 41632734--41632804 Score: 52
Period size: 9 Copynumber: 7.4 Consensus size: 9
41632724 CCATGAATTT
41632734 AAAATCATTA
1 AAAATCA-TA
*
41632744 TAAATCATA
1 AAAATCATA
*
41632753 AAAATGATA
1 AAAATCATA
*
41632762 AAAAACATA
1 AAAATCATA
**
41632771 AAAAAAATA
1 AAAATCATA
41632780 TAGAAACTCATA
1 -A-AAA-TCATA
*
41632792 AAAATTATA
1 AAAATCATA
41632801 AAAA
1 AAAA
41632805 CTATTAAAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
9 32 0.65
10 10 0.20
11 4 0.08
12 3 0.06
ACGTcount: A:0.68, C:0.07, G:0.03, T:0.23
Consensus pattern (9 bp):
AAAATCATA
Found at i:41632778 original size:21 final size:21
Alignment explanation
Indices: 41632752--41632795 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
41632742 TATAAATCAT
41632752 AAAAATGATA-AAAAACATAAA
1 AAAAAT-ATAGAAAAACATAAA
**
41632773 AAAAATATAGAAACTCATAAA
1 AAAAATATAGAAAAACATAAA
41632794 AA
1 AA
41632796 TTATAAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.16
Consensus pattern (21 bp):
AAAAATATAGAAAAACATAAA
Found at i:41632816 original size:19 final size:19
Alignment explanation
Indices: 41632748--41632817 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
41632738 TCATTATAAA
*
41632748 TCATAAAAATGATAAAAAAC
1 TCATAAAAATTAT-AAAAAC
* * *
41632768 AT-AAAAAAAATATAGAAAC
1 -TCATAAAAATTATAAAAAC
41632787 TCATAAAAATTATAAAAAC
1 TCATAAAAATTATAAAAAC
41632806 T-ATTAAAAATTA
1 TCA-TAAAAATTA
41632818 CAATATTGTA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
18 2 0.05
19 29 0.73
20 8 0.20
21 1 0.03
ACGTcount: A:0.66, C:0.07, G:0.03, T:0.24
Consensus pattern (19 bp):
TCATAAAAATTATAAAAAC
Found at i:41633048 original size:19 final size:19
Alignment explanation
Indices: 41633026--41633063 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
41633016 ATATACAAAT
41633026 TATTAAAAATAATT-TTAAA
1 TATTAAAAA-AATTATTAAA
*
41633045 TATTAATAAAATTATTAAA
1 TATTAAAAAAATTATTAAA
41633064 AAGTTTAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TATTAAAAAAATTATTAAA
Found at i:41633457 original size:27 final size:28
Alignment explanation
Indices: 41633401--41633457 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
41633391 ATAAATATAT
*
41633401 ATTATACAAAAAATAAAAAATTACACAA
1 ATTATACAAAAAATAAAAAATTACAAAA
* *
41633429 ATTATA-AAAAAATAGAAAATTGCAAAA
1 ATTATACAAAAAATAAAAAATTACAAAA
41633456 AT
1 AT
41633458 CATTATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.23
Consensus pattern (28 bp):
ATTATACAAAAAATAAAAAATTACAAAA
Found at i:41633620 original size:26 final size:26
Alignment explanation
Indices: 41633591--41633649 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 26
41633581 TAAAATACAA
*
41633591 AAATTATAAAAT-TATTAAAAAG-ATAT
1 AAATT-TAAAATATA-TAAAAAGAATAC
41633617 AAATTTACAAATATATAAAAAGAATAC
1 AAATTTA-AAATATATAAAAAGAATAC
41633644 AAATTT
1 AAATTT
41633650 TAAAGAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 2 0.07
26 16 0.55
27 11 0.38
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (26 bp):
AAATTTAAAATATATAAAAAGAATAC
Found at i:41633646 original size:19 final size:18
Alignment explanation
Indices: 41633622--41633672 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
41633612 GATATAAATT
41633622 TACAAATATATAAAAAGAA
1 TACAAATATATAAAAA-AA
* *
41633641 TACAAAT-TTTAAAGAAA
1 TACAAATATATAAAAAAA
41633658 T-CAAAATATATAAAA
1 TAC-AAATATATAAAA
41633673 TTATAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
16 1 0.04
17 7 0.27
18 11 0.42
19 7 0.27
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.25
Consensus pattern (18 bp):
TACAAATATATAAAAAAA
Found at i:41633729 original size:19 final size:19
Alignment explanation
Indices: 41633693--41633731 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
41633683 AAACAATTTT
* *
41633693 ACAAACAAACAAACCAAAA
1 ACAAAAAAACAAAACAAAA
*
41633712 ACAAAAAAAGAAAACAAAA
1 ACAAAAAAACAAAACAAAA
41633731 A
1 A
41633732 TAACTATGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.79, C:0.18, G:0.03, T:0.00
Consensus pattern (19 bp):
ACAAAAAAACAAAACAAAA
Found at i:41633780 original size:20 final size:20
Alignment explanation
Indices: 41633755--41633792 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41633745 TAAAAAAAAA
41633755 CATTAACAAC-AAAACACCAT
1 CATTAAC-ACTAAAACACCAT
41633775 CATTAACACTAAAACACC
1 CATTAACACTAAAACACC
41633793 TATTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.16
Consensus pattern (20 bp):
CATTAACACTAAAACACCAT
Found at i:41648200 original size:5 final size:5
Alignment explanation
Indices: 41648125--41648183 Score: 59
Period size: 5 Copynumber: 12.2 Consensus size: 5
41648115 ACTGAAAAGC
* * * * *
41648125 TTAAT TTAAT TAAAT TTGAT TT--T ATAAT TTAAT TTAAT TTAGT TTAGT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT
41648173 TTAAT TTAAT T
1 TTAAT TTAAT T
41648184 ATATTCTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
3 2 0.04
5 43 0.96
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (5 bp):
TTAAT
Found at i:41651517 original size:18 final size:17
Alignment explanation
Indices: 41651496--41651534 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
41651486 AATGTTCTCT
*
41651496 AAATTACATAATATATAA
1 AAATGACATAATATA-AA
41651514 AAATGACATAATATAAA
1 AAATGACATAATATAAA
41651531 AAAT
1 AAAT
41651535 CATAAACTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (17 bp):
AAATGACATAATATAAA
Found at i:41651538 original size:15 final size:17
Alignment explanation
Indices: 41651500--41651539 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
41651490 TTCTCTAAAT
41651500 TACATAATATATAAAAA
1 TACATAATATATAAAAA
41651517 TGACATAATATA-AAAAA
1 T-ACATAATATATAAAAA
41651534 T-CATAA
1 TACATAA
41651540 ACTTAAAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.23
17 7 0.32
18 10 0.45
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (17 bp):
TACATAATATATAAAAA
Found at i:41656307 original size:11 final size:13
Alignment explanation
Indices: 41656290--41656345 Score: 55
Period size: 12 Copynumber: 4.5 Consensus size: 13
41656280 ATCTAAATTC
*
41656290 TATTTTTTATT-A
1 TATTTTTAATTAA
41656302 TATTTTTAATTAA
1 TATTTTTAATTAA
* *
41656315 TATTTTCAA-AAA
1 TATTTTTAATTAA
*
41656327 TATTTTTTATTAA
1 TATTTTTAATTAA
41656340 T-TTTTT
1 TATTTTT
41656346 TTTGTATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
12 24 0.67
13 12 0.33
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (13 bp):
TATTTTTAATTAA
Found at i:41656307 original size:12 final size:12
Alignment explanation
Indices: 41656290--41656355 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 12
41656280 ATCTAAATTC
41656290 TATTTTTTATTA
1 TATTTTTTATTA
*
41656302 TATTTTTAATTAA
1 TATTTTTTATT-A
** **
41656315 TATTTTCAAAAA
1 TATTTTTTATTA
41656327 TATTTTTTATTA
1 TATTTTTTATTA
* *
41656339 -ATTTTTTTTTG
1 TATTTTTTATTA
41656350 TATTTT
1 TATTTT
41656356 ATATAATTTA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 9 0.21
12 24 0.57
13 9 0.21
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (12 bp):
TATTTTTTATTA
Found at i:41657586 original size:18 final size:18
Alignment explanation
Indices: 41657563--41657597 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
41657553 TCATTGGTAG
41657563 TGTACGCTACCGTCGAGA
1 TGTACGCTACCGTCGAGA
41657581 TGTACGCTACCGTCGAG
1 TGTACGCTACCGTCGAG
41657598 TTGCACGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.20, C:0.29, G:0.29, T:0.23
Consensus pattern (18 bp):
TGTACGCTACCGTCGAGA
Found at i:41666354 original size:2 final size:2
Alignment explanation
Indices: 41666347--41666427 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
41666337 GTGACCCAAG
41666347 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
41666389 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
41666428 TGTGTGTGTG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:41669402 original size:18 final size:19
Alignment explanation
Indices: 41669369--41669408 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
41669359 CTTGTTATAT
*
41669369 ATTTTTATAAAATTTTTAAA
1 ATTTTTAT-AAATTTTAAAA
41669389 ATTTTTAT-AATTTTAAAA
1 ATTTTTATAAATTTTAAAA
41669407 AT
1 AT
41669409 ATAAATTGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
20 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTTTATAAATTTTAAAA
Found at i:41669443 original size:18 final size:17
Alignment explanation
Indices: 41669420--41669453 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
41669410 TAAATTGTGA
*
41669420 AATTTTATAAATATATTG
1 AATTTTAAAAAT-TATTG
41669438 AATTTTAAAAATTATT
1 AATTTTAAAAATTATT
41669454 TTGTATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
AATTTTAAAAATTATTG
Found at i:41669977 original size:16 final size:16
Alignment explanation
Indices: 41669958--41669993 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
41669948 AATAGGGCTA
41669958 TAATAGAATAAAGTTG
1 TAATAGAATAAAGTTG
* *
41669974 TAATGGAATTAAGTTG
1 TAATAGAATAAAGTTG
41669990 TAAT
1 TAAT
41669994 TAGTAATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.36
Consensus pattern (16 bp):
TAATAGAATAAAGTTG
Found at i:41670242 original size:61 final size:62
Alignment explanation
Indices: 41670177--41670305 Score: 197
Period size: 61 Copynumber: 2.1 Consensus size: 62
41670167 ATATAATAGG
* * * *
41670177 ATTATTATTAAATATAATTTAATAAAAATGATAATAAATAATTTAATCAT-ATTTTAATATA
1 ATTATTATGAAATATAATTTAATAAAAATAATAATAAATAATTTAATAATAATCTTAATATA
* *
41670238 ATTATTATGAAATATAATTTAATAAAAATAATCATATATAATTTAATAATAATCTTAATATA
1 ATTATTATGAAATATAATTTAATAAAAATAATAATAAATAATTTAATAATAATCTTAATATA
41670300 ATTATT
1 ATTATT
41670306 TTTATATTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
61 45 0.74
62 16 0.26
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (62 bp):
ATTATTATGAAATATAATTTAATAAAAATAATAATAAATAATTTAATAATAATCTTAATATA
Found at i:41670904 original size:22 final size:22
Alignment explanation
Indices: 41670874--41670922 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
41670864 AATTTAGATA
* *
41670874 AAATTCACATGTAATAAAATTT
1 AAATCCACACGTAATAAAATTT
**
41670896 AAATCCACACGTAATAGGATTT
1 AAATCCACACGTAATAAAATTT
41670918 AAATC
1 AAATC
41670923 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (22 bp):
AAATCCACACGTAATAAAATTT
Found at i:41672368 original size:21 final size:21
Alignment explanation
Indices: 41672344--41672444 Score: 68
Period size: 21 Copynumber: 4.9 Consensus size: 21
41672334 TATTATTTTT
41672344 ATTAAATTATATTTAATAATA
1 ATTAAATTATATTTAATAATA
* *
41672365 ATTATATTA-A---AAT-ATG
1 ATTAAATTATATTTAATAATA
* ** *
41672381 ATTAAATTATTTATTATCATTTTT
1 ATTAAATTA--TATT-TAATAATA
41672405 ATTAAATTATATTTAATAATA
1 ATTAAATTATATTTAATAATA
**
41672426 ATTTTATTATATTTAATAA
1 ATTAAATTATATTTAATAA
41672445 CAATAATAAT
Statistics
Matches: 60, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
16 10 0.17
17 3 0.05
19 1 0.02
20 1 0.02
21 29 0.48
22 4 0.07
23 2 0.03
24 10 0.17
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (21 bp):
ATTAAATTATATTTAATAATA
Found at i:41672414 original size:61 final size:59
Alignment explanation
Indices: 41672302--41672434 Score: 196
Period size: 61 Copynumber: 2.2 Consensus size: 59
41672292 TTTAATATAA
* * *
41672302 AATAATTATATTAAGAATTTTATTAAATTATATATTATTTTTATTAAATTATATTTAAT
1 AATAATTATATTAAGAATATGATTAAATTATATATCATTTTTATTAAATTATATTTAAT
41672361 AATAATTATATTAA-AATATGATTAAATTATTTATTATCATTTTTATTAAATTATATTTAAT
1 AATAATTATATTAAGAATATGATTAAATTA--TA-TATCATTTTTATTAAATTATATTTAAT
*
41672422 AATAATTTTATTA
1 AATAATTATATTA
41672435 TATTTAATAA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
58 13 0.19
59 14 0.21
60 2 0.03
61 38 0.57
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (59 bp):
AATAATTATATTAAGAATATGATTAAATTATATATCATTTTTATTAAATTATATTTAAT
Found at i:41672657 original size:16 final size:16
Alignment explanation
Indices: 41672638--41672668 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41672628 AACTCTATAC
*
41672638 CATTACAATCTTATTT
1 CATTACAACCTTATTT
41672654 CATTACAACCTTATT
1 CATTACAACCTTATT
41672669 CAATTTTAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45
Consensus pattern (16 bp):
CATTACAACCTTATTT
Found at i:41697290 original size:30 final size:30
Alignment explanation
Indices: 41697240--41697318 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 30
41697230 GTTTTTGAAC
41697240 TTTTAAAATTAGAATTAAA-TTAATAAATT
1 TTTTAAAATTAGAATTAAATTTAATAAATT
* * *
41697269 TTTTAAAGTTGAGAGTTAAATTTATTAAA-T
1 TTTTAAAATT-AGAATTAAATTTAATAAATT
* *
41697299 TTTTAGAATTAGAACTAAAT
1 TTTTAAAATTAGAATTAAAT
41697319 GATAAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
29 17 0.41
30 17 0.41
31 7 0.17
ACGTcount: A:0.46, C:0.01, G:0.09, T:0.44
Consensus pattern (30 bp):
TTTTAAAATTAGAATTAAATTTAATAAATT
Found at i:41697300 original size:31 final size:29
Alignment explanation
Indices: 41697240--41697333 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 29
41697230 GTTTTTGAAC
41697240 TTTTAAAATTAGAATTAAATTAATAAATT
1 TTTTAAAATTAGAATTAAATTAATAAATT
* * *
41697269 TTTTAAAGTTGAGAGTTAAATTTATTAAA-T
1 TTTTAAAATT-AGAATTAAA-TTAATAAATT
* * *
41697299 TTTTAGAATTAGAACTAAA-TGATAAATT
1 TTTTAAAATTAGAATTAAATTAATAAATT
*
41697327 TTGTAAA
1 TTTTAAA
41697334 TATTGAGGAT
Statistics
Matches: 51, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
27 5 0.10
28 6 0.12
29 16 0.31
30 17 0.33
31 7 0.14
ACGTcount: A:0.46, C:0.01, G:0.10, T:0.44
Consensus pattern (29 bp):
TTTTAAAATTAGAATTAAATTAATAAATT
Found at i:41697340 original size:59 final size:59
Alignment explanation
Indices: 41697240--41697415 Score: 166
Period size: 59 Copynumber: 2.9 Consensus size: 59
41697230 GTTTTTGAAC
* * * *
41697240 TTTTAAAATTAGAATTAAATTAATAAATTTTTTAAAGTTGAGAG-TTAAATTTATTAAAT
1 TTTTAGAATTAGAA-TAAATTGATAAATTTTGTAAAATTGAGAGATTAAATTTATTAAAT
41697299 TTTTAGAATTAGAACTAAA-TGATAAATTTTGTAAATATTGAG-GATTAGAATTGT-TT-AAT
1 TTTTAGAATTAGAA-TAAATTGATAAATTTTGTAAA-ATTGAGAGATTA-AATT-TATTAAAT
* * * *
41697358 TTTTAGATTTAGGATCAAATTGATAAATTATGTAAACATTG-GAGGACTAAATTTATTA
1 TTTTAGAATTAGAAT-AAATTGATAAATTTTGTAAA-ATTGAGA-GATTAAATTTATTA
41697416 TTTGGTCAAT
Statistics
Matches: 97, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
58 16 0.16
59 45 0.46
60 31 0.32
61 5 0.05
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.43
Consensus pattern (59 bp):
TTTTAGAATTAGAATAAATTGATAAATTTTGTAAAATTGAGAGATTAAATTTATTAAAT
Found at i:41702566 original size:17 final size:18
Alignment explanation
Indices: 41702534--41702569 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
41702524 TTTTAAAAAT
41702534 ACTTTTGATATAAAAAGC
1 ACTTTTGATATAAAAAGC
*
41702552 ACTTTTGA-ATTAAAAGC
1 ACTTTTGATATAAAAAGC
41702569 A
1 A
41702570 ATGCTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (18 bp):
ACTTTTGATATAAAAAGC
Found at i:41713904 original size:18 final size:18
Alignment explanation
Indices: 41713881--41713941 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
41713871 TTATAATTAC
41713881 AAAAAATAAAAAATACAT
1 AAAAAATAAAAAATACAT
** *
41713899 AAAAAATTCAAAATA-AA
1 AAAAAATAAAAAATACAT
* *
41713916 ATAAAAATATTAAAATACTT
1 A-AAAAATA-AAAAATACAT
41713936 AAAAAA
1 AAAAAA
41713942 AACTTTGAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
17 2 0.06
18 19 0.58
19 11 0.33
20 1 0.03
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAAAATAAAAAATACAT
Found at i:41713911 original size:19 final size:17
Alignment explanation
Indices: 41713890--41713941 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
41713880 CAAAAAATAA
41713890 AAAATACATAAAAAATT
1 AAAATACATAAAAAATT
*
41713907 CAAAATAAAATAAAAATATT
1 -AAAAT-ACATAAAAA-ATT
*
41713927 AAAATACTTAAAAAA
1 AAAATACATAAAAAA
41713942 AACTTTGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 1 0.03
18 12 0.41
19 13 0.45
20 3 0.10
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAATACATAAAAAATT
Found at i:41717841 original size:29 final size:29
Alignment explanation
Indices: 41717808--41718222 Score: 273
Period size: 29 Copynumber: 14.2 Consensus size: 29
41717798 CAAAAATATG
* * *
41717808 ATTTTTGGATGCTCGAGGGTAAAATGGTG
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
* * * * *
41717837 ATTTTTAGAGGTTCGAAGGCAAAACGGTA
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
* * * * *
41717866 ATTTTTGGTCA-CTCGGGGGCAAAAAT-GCA
1 ATTTTTGG-AAGTTCGAGGG-TAAAATGGTA
* * * *
41717895 ATTTTTGGAAATTTGGGGGTAAAATGGTG
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
* *
41717924 ATTTTTGGAAGTTCG-GGGATAAAAT-ATG
1 ATTTTTGGAAGTTCGAGGG-TAAAATGGTA
* **
41717952 ATTTTTGGAAGTTCGGGGGTAAAATTATA
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
* **
41717981 ATTTTTGGAAGTT-TAGGGGTAAAATCATA
1 ATTTTTGGAAGTTCGA-GGGTAAAATGGTA
*
41718010 ATTTTTGGAAGTTCGAGGTGTGAAAAT-GTG
1 ATTTTTGGAAGTTCGAGG-GT-AAAATGGTA
*
41718040 ATTTTTGGACA-CTCGAGGGTGAAAATGGTA
1 ATTTTTGGA-AGTTCGAGGGT-AAAATGGTA
* *
41718070 ATTTTT-AAATGTTC-AGAGGTAAAACGGTA
1 ATTTTTGGAA-GTTCGAG-GGTAAAATGGTA
* * *
41718099 ATTTTTGGAAAATT-TAGGGTCAAAATGAT-
1 ATTTTTGG-AAGTTCGAGGGT-AAAATGGTA
41718128 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
*
41718157 ATTTTTGGAAGATTCGA-GATCAAAAATGG-A
1 ATTTTTGGAAG-TTCGAGGGT--AAAATGGTA
**
41718187 ATTTTTGGAAGTTTAAGGGTTAAAAT-GTA
1 ATTTTTGGAAGTTCGAGGG-TAAAATGGTA
41718216 ATTTTTG
1 ATTTTTG
41718223 AAAAGTTTAG
Statistics
Matches: 310, Mismatches: 48, Indels: 56
0.75 0.12 0.14
Matches are distributed among these distances:
28 45 0.15
29 185 0.60
30 64 0.21
31 16 0.05
ACGTcount: A:0.32, C:0.06, G:0.27, T:0.35
Consensus pattern (29 bp):
ATTTTTGGAAGTTCGAGGGTAAAATGGTA
Found at i:41718190 original size:88 final size:85
Alignment explanation
Indices: 41717915--41718222 Score: 252
Period size: 88 Copynumber: 3.5 Consensus size: 85
41717905 ATTTGGGGGT
* ** * * **
41717915 AAAATGGTGATTTTTGGAAGTTCGGGGAT-AAAATATGATTTTTGGAAGTTCGGGGGTAAAATTA
1 AAAATGG-AATTTTTGGAAGTTTAGGG-TCAAAATGTGATTTTTGGAAGTTCGAGGGTAAAATGG
* *
41717979 TAATTTTTGGAAGTTTAGGGGTA
64 TAATTTTTGGAAG-TTCGAGGTA
* * *
41718002 AAATCAT--AATTTTTGGAAGTTCGAGGTGTGAAAATGTGATTTTTGGACA-CTCGAGGGTGAAA
1 AAA--ATGGAATTTTTGGAAGTT-TAGG-GTCAAAATGTGATTTTTGGA-AGTTCGAGGGT-AAA
*
41718064 ATGGTAATTTTT-AAATGTTCAGAGGT-
60 ATGGTAATTTTTGGAA-GTTC-GAGGTA
* *
41718090 AAAACGGTAATTTTTGGAAAATTTAGGGTCAAAATGAT-ATTTTTGGAAGTTCGAGGGTAAAATG
1 AAAATGG-AATTTTTGG-AAGTTTAGGGTCAAAATG-TGATTTTTGGAAGTTCGAGGGTAAAATG
*
41718154 GTAATTTTTGGAAGATTCGAGATCA
63 GTAATTTTTGGAAG-TTCGAGGT-A
* *
41718179 AAAATGGAATTTTTGGAAGTTTAAGGGTTAAAATGTAATTTTTG
1 AAAATGGAATTTTTGGAAGTTT-AGGGTCAAAATGTGATTTTTG
41718223 AAAAGTTTAG
Statistics
Matches: 179, Mismatches: 21, Indels: 41
0.74 0.09 0.17
Matches are distributed among these distances:
86 14 0.08
87 33 0.18
88 88 0.49
89 40 0.22
90 4 0.02
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.36
Consensus pattern (85 bp):
AAAATGGAATTTTTGGAAGTTTAGGGTCAAAATGTGATTTTTGGAAGTTCGAGGGTAAAATGGTA
ATTTTTGGAAGTTCGAGGTA
Found at i:41718231 original size:30 final size:29
Alignment explanation
Indices: 41717979--41718261 Score: 98
Period size: 30 Copynumber: 9.6 Consensus size: 29
41717969 GGTAAAATTA
* * *
41717979 TAATTTTTGGAAGTTT-AGGGGTAAAATCA
1 TAATTTTTGAAAGTTTAAGGGTTAAAAT-G
* ** *
41718008 TAATTTTTGGAAGTTCGAGGTGTGAAAATG
1 TAATTTTTGAAAGTTTAAGG-GTTAAAATG
* * * ** *
41718038 TGATTTTTGGACA-CTCGAGGGTGAAAATGG
1 TAATTTTT-GAAAGTTTAAGGGTTAAAAT-G
* *
41718068 TAATTTTT-AAA-TGTTCAGAGG-TAAAACGG
1 TAATTTTTGAAAGT-TTAAG-GGTTAAAA-TG
* *
41718097 TAATTTTTGGAAAATTT-AGGGTCAAAATG
1 TAATTTTT-GAAAGTTTAAGGGTTAAAATG
* **
41718126 -ATATTTTTGGAAGTTCGAGGG-TAAAATGG
1 TA-ATTTTTGAAAGTTTAAGGGTTAAAAT-G
* * * * *
41718155 TAATTTTTGGAAGATT-CGAGATCAAAAATG
1 TAATTTTTGAAAGTTTAAG-GGT-TAAAATG
* *
41718185 GAATTTTTGGAAGTTTAAGGGTTAAAATG
1 TAATTTTTGAAAGTTTAAGGGTTAAAATG
* *
41718214 TAATTTTTGAAAAGTTTAGGGGTTAAAATA
1 TAATTTTTG-AAAGTTTAAGGGTTAAAATG
* *
41718244 TGATTTTTGGATAGTTTA
1 TAATTTTT-GAAAGTTTA
41718262 GGGACCTTAT
Statistics
Matches: 196, Mismatches: 37, Indels: 41
0.72 0.14 0.15
Matches are distributed among these distances:
28 14 0.07
29 80 0.41
30 81 0.41
31 20 0.10
32 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (29 bp):
TAATTTTTGAAAGTTTAAGGGTTAAAATG
Found at i:41718234 original size:29 final size:28
Alignment explanation
Indices: 41717887--41718264 Score: 215
Period size: 29 Copynumber: 12.9 Consensus size: 28
41717877 CTCGGGGGCA
* * * *
41717887 AAAATGCAATTTTTGGAAATTTGGGGGT
1 AAAATGTAATTTTTGGAAGTTTAGGGTT
* ** *
41717915 AAAATGGTGATTTTTGGAAGTTCGGGGAT
1 AAAAT-GTAATTTTTGGAAGTTTAGGGTT
* * ** *
41717944 AAAATATGATTTTTGGAAGTTCGGGGGT
1 AAAATGTAATTTTTGGAAGTTTAGGGTT
* *
41717972 AAAATTATAATTTTTGGAAGTTTAGGGGT
1 AAAA-TGTAATTTTTGGAAGTTTAGGGTT
* * *
41718001 AAAATCATAATTTTTGGAAGTTCGAGGTGTG
1 AAAAT-GTAATTTTTGGAAGTT-TAGG-GTT
* * ** *
41718032 AAAATGTGATTTTTGGACACTCGAGGGTG
1 AAAATGTAATTTTTGGA-AGTTTAGGGTT
* *
41718061 AAAATGGTAATTTTT-AAATGTTCAGAGG-T
1 AAAAT-GTAATTTTTGGAA-GTTTAG-GGTT
* * *
41718090 AAAACGGTAATTTTTGGAAAATTTAGGGTC
1 AAAA-TGTAATTTTTGG-AAGTTTAGGGTT
*
41718120 AAAATG-ATATTTTTGGAAGTTCGAGGG-T
1 AAAATGTA-ATTTTTGGAAGTT-TAGGGTT
* * * *
41718148 AAAATGGTAATTTTTGGAAGATTCGAGATCA
1 AAAAT-GTAATTTTTGGAAGTTTAG-GGT-T
*
41718179 AAAATGGAATTTTTGGAAGTTTAAGGGTT
1 AAAATGTAATTTTTGGAAGTTT-AGGGTT
*
41718208 AAAATGTAATTTTTGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTTG-GAAGTTTA-GGGTT
* *
41718238 AAAATATGATTTTTGGATAGTTTAGGG
1 AAAATGTAATTTTTGGA-AGTTTAGGG
41718265 ACCTTATGAG
Statistics
Matches: 279, Mismatches: 47, Indels: 47
0.75 0.13 0.13
Matches are distributed among these distances:
28 43 0.15
29 137 0.49
30 83 0.30
31 16 0.06
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAGTTTAGGGTT
Found at i:41718242 original size:59 final size:58
Alignment explanation
Indices: 41717881--41718261 Score: 196
Period size: 59 Copynumber: 6.5 Consensus size: 58
41717871 TGGTCACTCG
* * ** * * *
41717881 GGGGCAAAAATGCAATTTTTGGAAATTTGGGGGTAAAATGGTGATTTTTG-GAAG-TTC
1 GGGGTAAAAATG-AATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTTGAAAAGTTTA
*** ** *
41717938 GGGGATAAAATATG-ATTTTTGGAAGTTCGGGGGTAAAATTATAATTTTTG-GAAGTTTA
1 GGGG-TAAAA-ATGAATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTTGAAAAGTTTA
** * * * * **
41717996 GGGGTAAAATCAT-AATTTTTGGAAGTTCGAGGTGTGAAAAT-GTGATTTTTGGACACTCGA
1 GGGGTAAAA--ATGAATTTTTGGAAGTTTAAGG-GT-AAAATGGTAATTTTTGAAAAGTTTA
* * * *
41718056 -GGGTGAAAATGGTAATTTTT--AAATGTTCAGAGGTAAAACGGTAATTTTTGGAAAA-TTTA
1 GGGGTAAAAAT-G-AATTTTTGGAAGT-TTAAG-GGTAAAATGGTAATTTTT-GAAAAGTTTA
* ** * * *
41718115 -GGGTCAAAATGATATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTG-GAAGATTC
1 GGGGTAAAAATGA-ATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTTGAAAAGTTTA
* *
41718172 GAGATCAAAAATGGAATTTTTGGAAGTTTAAGGGTTAAAAT-GTAATTTTTGAAAAGTTTA
1 GGGGT-AAAAAT-GAATTTTTGGAAGTTTAAGGG-TAAAATGGTAATTTTTGAAAAGTTTA
41718232 GGGGTTAAAATATG-ATTTTTGGATAGTTTA
1 GGGG-TAAAA-ATGAATTTTTGGA-AGTTTA
41718262 GGGACCTTAT
Statistics
Matches: 253, Mismatches: 44, Indels: 51
0.73 0.13 0.15
Matches are distributed among these distances:
56 2 0.01
57 50 0.20
58 62 0.25
59 88 0.35
60 48 0.19
61 3 0.01
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (58 bp):
GGGGTAAAAATGAATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTTGAAAAGTTTA
Found at i:41725608 original size:96 final size:96
Alignment explanation
Indices: 41725427--41725618 Score: 217
Period size: 96 Copynumber: 2.0 Consensus size: 96
41725417 AATTTTGAAG
* * ** * * ***
41725427 AAGGGTATTTGATTATTTCGATTTGAAGAAAGGTTGCACCTAGTGAGTTAAGGTGCACCTTTTCA
1 AAGGATATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAAATTTCA
* * *
41725492 TAACCAAAGATAAGGAAATATTGCCTTGATT
66 AAACCAAAGATAAAGAAATATTGCCTCGATT
* *
41725523 AAGGATATTCGATTATTTCGGTTTGAAGAAAAATTGTACCTAGTAAGTTAAGGCGCAAAATTTCA
1 AAGGATATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAAATTTCA
*
41725588 AAACTCGAA-ATAAA-AGAATATTGCCTCGATT
66 AAAC-CAAAGATAAAGA-AATATTGCCTCGATT
41725619 TTAAAATTTT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
95 1 0.01
96 75 0.95
97 3 0.04
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (96 bp):
AAGGATATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAAATTTCA
AAACCAAAGATAAAGAAATATTGCCTCGATT
Found at i:41725880 original size:30 final size:30
Alignment explanation
Indices: 41725846--41725919 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 30
41725836 TACTCGGGGG
41725846 CAAAATAGTAATTTTTAGTAAAA-TT-AGGGT
1 CAAAATAGTAATTTTTA--AAAAGTTAAGGGT
41725876 CAAAA-A-TGAATTTTTAAAAAGTTTAAGGGT
1 CAAAATAGT-AATTTTTAAAAAG-TTAAGGGT
41725906 -AAAAT-GTAATTTTT
1 CAAAATAGTAATTTTT
41725920 GGTGAAATCG
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
27 4 0.11
28 1 0.03
29 22 0.58
30 11 0.29
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.38
Consensus pattern (30 bp):
CAAAATAGTAATTTTTAAAAAGTTAAGGGT
Found at i:41725937 original size:29 final size:29
Alignment explanation
Indices: 41725905--41726064 Score: 95
Period size: 29 Copynumber: 5.5 Consensus size: 29
41725895 AGTTTAAGGG
41725905 TAAAATGTAATTTTTGGTGAAATCGAGGT
1 TAAAATGTAATTTTTGGTGAAATCGAGGT
* *
41725934 TAAAATG-AAATTTT-G-GAAAGTTC-AGGGG
1 TAAAATGTAATTTTTGGTGAAA--TCGA-GGT
*
41725962 T-AAATGGTAA-TTTTGGATGAAATCGGGGT
1 TAAAAT-GTAATTTTTGG-TGAAATCGAGGT
** *
41725991 TAAAAATGGGA-TTTT-G-GAAAGTTCGAGGG
1 T-AAAATGTAATTTTTGGTGAAA--TCGAGGT
*
41726020 TAAAATGGTAATTTTTGGTGAAATCGGGGT
1 TAAAAT-GTAATTTTTGGTGAAATCGAGGT
*
41726050 TAAAAATGGAATTTT
1 T-AAAATGTAATTTT
41726065 AGAAAGTTTT
Statistics
Matches: 100, Mismatches: 13, Indels: 35
0.68 0.09 0.24
Matches are distributed among these distances:
26 4 0.04
27 10 0.10
28 21 0.21
29 24 0.24
30 23 0.23
31 14 0.14
32 4 0.04
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (29 bp):
TAAAATGTAATTTTTGGTGAAATCGAGGT
Found at i:41725946 original size:58 final size:59
Alignment explanation
Indices: 41725847--41726072 Score: 264
Period size: 59 Copynumber: 3.9 Consensus size: 59
41725837 ACTCGGGGGC
* * * ** * * *
41725847 AAAATAGTAATTTTTAGTAAAATTAGGGTCAAAAAT-GAATTTTTAAAAAGTTTAAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAA-TTTTAGAAAGTTCAAGGGT
* * * *
41725906 AAAAT-GTAATTTTTGGTGAAATCGAGGTT-AAAATGAAATTTTGGAAAGTTCAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCAAGGGT
* * *
41725963 -AAATGGTAA-TTTTGGATGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCGAGGGT
1 AAAATGGTAATTTTTGG-TGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCAAGGGT
41726021 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTT
41726073 TTGAGGGTAA
Statistics
Matches: 143, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
56 10 0.07
57 36 0.25
58 44 0.31
59 47 0.33
60 6 0.04
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCAAGGGT
Found at i:41726006 original size:30 final size:30
Alignment explanation
Indices: 41725906--41726064 Score: 108
Period size: 28 Copynumber: 5.4 Consensus size: 30
41725896 GTTTAAGGGT
* *
41725906 AAAATGTAATTTTTGG-TGAAATCGAGGTT-
1 AAAATGGAA-TTTTGGATGAAATCGGGGTTA
* *
41725935 AAAATGAAATTTTGGA--AAGTTCAGGGG-T-
1 AAAATGGAATTTTGGATGAA-ATC-GGGGTTA
41725963 -AAATGGTAATTTTGGATGAAATCGGGGTTA
1 AAAATGG-AATTTTGGATGAAATCGGGGTTA
* *
41725993 AAAATGGGATTTTGGA--AAGTTCGAGGG-T-
1 AAAATGGAATTTTGGATGAA-ATCG-GGGTTA
41726021 AAAATGGTAATTTTTGG-TGAAATCGGGGTTA
1 AAAATGG-AA-TTTTGGATGAAATCGGGGTTA
41726052 AAAATGGAATTTT
1 AAAATGGAATTTT
41726065 AGAAAGTTTT
Statistics
Matches: 104, Mismatches: 9, Indels: 34
0.71 0.06 0.23
Matches are distributed among these distances:
27 7 0.07
28 31 0.30
29 26 0.25
30 25 0.24
31 15 0.14
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.33
Consensus pattern (30 bp):
AAAATGGAATTTTGGATGAAATCGGGGTTA
Found at i:41726084 original size:30 final size:29
Alignment explanation
Indices: 41726050--41726123 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
41726040 AAATCGGGGT
*
41726050 TAAAAATGGAATTTT-AGAAAGTTTTGAGGG
1 TAAAAATGCAATTTTAAG-AAGTTTT-AGGG
* *
41726080 TAAAAATGCAGTTTTAAGAAGTTTTTGGG
1 TAAAAATGCAATTTTAAGAAGTTTTAGGG
* *
41726109 TCAAAATGTAATTTT
1 TAAAAATGCAATTTT
41726124 TGAATAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 15 0.41
30 20 0.54
31 2 0.05
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.38
Consensus pattern (29 bp):
TAAAAATGCAATTTTAAGAAGTTTTAGGG
Found at i:41728169 original size:17 final size:16
Alignment explanation
Indices: 41728158--41728207 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
41728148 TATTTAAGCT
41728158 AAATTTAAATTTAGAAC
1 AAATTTAAATTTA-AAC
*
41728175 AAATTTAAATTTAAATTT
1 AAATTTAAATTTAAA--C
41728193 AAA-TTAAATTTAAAC
1 AAATTTAAATTTAAAC
41728208 TTAGAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 2 0.07
17 24 0.83
18 3 0.10
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (16 bp):
AAATTTAAATTTAAAC
Found at i:41728183 original size:23 final size:23
Alignment explanation
Indices: 41728157--41728206 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
41728147 ATATTTAAGC
41728157 TAAATTTAAATTTAGAA-CAAATT
1 TAAATTTAAATTTA-AATCAAATT
*
41728180 TAAATTTAAATTTAAATTAAATT
1 TAAATTTAAATTTAAATCAAATT
41728203 TAAA
1 TAAA
41728207 CTTAGAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAAATTTAAATTTAAATCAAATT
Found at i:41728201 original size:5 final size:6
Alignment explanation
Indices: 41728157--41728206 Score: 61
Period size: 6 Copynumber: 8.7 Consensus size: 6
41728147 ATATTTAAGC
*
41728157 TAAATT TAAATT TAGAA-- CAAATT TAAATT TAAATT TAAA-T TAAATT
1 TAAATT TAAATT TA-AATT TAAATT TAAATT TAAATT TAAATT TAAATT
41728203 TAAA
1 TAAA
41728207 CTTAGAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
4 2 0.05
5 6 0.16
6 28 0.74
7 2 0.05
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (6 bp):
TAAATT
Found at i:41728218 original size:23 final size:23
Alignment explanation
Indices: 41728175--41728219 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
41728165 AATTTAGAAC
* *
41728175 AAATTTAAATTTAAATTTAAATT
1 AAATTTAAACTTAAATATAAATT
41728198 AAATTTAAACTTAGAA-ATAAAT
1 AAATTTAAACTTA-AATATAAAT
41728220 CTGAAACCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATTTAAACTTAAATATAAATT
Found at i:41729826 original size:17 final size:17
Alignment explanation
Indices: 41729804--41729889 Score: 84
Period size: 17 Copynumber: 5.1 Consensus size: 17
41729794 GTGAGACTTT
*
41729804 TAAATTTTAATTTAAAA
1 TAAATTTAAATTTAAAA
*
41729821 TAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAA
* * *
41729838 TAAATTCAAACTCAAAA
1 TAAATTTAAATTTAAAA
* *
41729855 TGAGTTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
41729872 T-TATTTAAATTTTAAAA
1 TAAATTTAAA-TTTAAAA
41729889 T
1 T
41729890 TTAAAATTTG
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
16 6 0.11
17 49 0.89
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:41732283 original size:17 final size:18
Alignment explanation
Indices: 41732252--41732287 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
41732242 ATCTAGCAAA
41732252 ATTATATAAAAATATTAT
1 ATTATATAAAAATATTAT
*
41732270 ATTAT-TAAAGATATTAT
1 ATTATATAAAAATATTAT
41732287 A
1 A
41732288 ACAAATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
ATTATATAAAAATATTAT
Found at i:41735609 original size:37 final size:37
Alignment explanation
Indices: 41735525--41735750 Score: 292
Period size: 37 Copynumber: 6.1 Consensus size: 37
41735515 GCATCTAAAA
* * * * *
41735525 ATTCGGGCTATGTGCCTAGTAAGCTTTGTGTCGGTAT
1 ATTCGGGCTGTGTGCCTAGTAGGCTTCGTGCCGGTGT
* * *
41735562 ATTCGGGCTGTGTACCTAATAGGCTTCGTGCCGGGGT
1 ATTCGGGCTGTGTGCCTAGTAGGCTTCGTGCCGGTGT
* *
41735599 ATTTGGGCTGTGTGCCTAGTAGGCTTCGTGCTGGTGT
1 ATTCGGGCTGTGTGCCTAGTAGGCTTCGTGCCGGTGT
41735636 ATTCGGGCTGTGTGCCTAGTAGGCTTCGTGCCGGTGT
1 ATTCGGGCTGTGTGCCTAGTAGGCTTCGTGCCGGTGT
* *
41735673 ATTCGGGCTATGTGCCTAGTAGGCTTCGTGCCGATGT
1 ATTCGGGCTGTGTGCCTAGTAGGCTTCGTGCCGGTGT
* * * *
41735710 ATTCGGACTATGTGTCTAGTAGGCCTTTGTGCCGGTG-
1 ATTCGGGCTGTGTGCCTAGTAGG-CTTCGTGCCGGTGT
41735747 ATTC
1 ATTC
41735751 AAGAATAAGT
Statistics
Matches: 167, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
37 156 0.93
38 11 0.07
ACGTcount: A:0.12, C:0.19, G:0.34, T:0.35
Consensus pattern (37 bp):
ATTCGGGCTGTGTGCCTAGTAGGCTTCGTGCCGGTGT
Found at i:41736480 original size:21 final size:21
Alignment explanation
Indices: 41736454--41736494 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41736444 TACTCACTGT
*
41736454 CAATTTTAGTATCGATAGAAC
1 CAATTTAAGTATCGATAGAAC
*
41736475 CAATTTAAGTATCGGTAGAA
1 CAATTTAAGTATCGATAGAA
41736495 ATATCCAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (21 bp):
CAATTTAAGTATCGATAGAAC
Found at i:41738959 original size:10 final size:11
Alignment explanation
Indices: 41738944--41738976 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
41738934 GGAAAATATA
41738944 TTTAATTT-TT
1 TTTAATTTATT
41738954 TTTAATTTATT
1 TTTAATTTATT
*
41738965 TTGAATTTATT
1 TTTAATTTATT
41738976 T
1 T
41738977 AATGATGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (11 bp):
TTTAATTTATT
Found at i:41739138 original size:20 final size:20
Alignment explanation
Indices: 41739113--41739151 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
41739103 TTTGTGAAGT
41739113 TTATTAA-AGAGTATTTTATG
1 TTATTAATA-AGTATTTTATG
41739133 TTATTAATAAGTATTTTAT
1 TTATTAATAAGTATTTTAT
41739152 ATTTGAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (20 bp):
TTATTAATAAGTATTTTATG
Found at i:41755985 original size:8 final size:8
Alignment explanation
Indices: 41755972--41755997 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
41755962 CTTTGATTTG
41755972 TTAAGCAA
1 TTAAGCAA
41755980 TTAAGCAA
1 TTAAGCAA
41755988 TTAAGCAA
1 TTAAGCAA
41755996 TT
1 TT
41755998 CTCCATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (8 bp):
TTAAGCAA
Found at i:41759704 original size:18 final size:19
Alignment explanation
Indices: 41759671--41759747 Score: 113
Period size: 18 Copynumber: 4.2 Consensus size: 19
41759661 TGCGATCCAA
*
41759671 TATTGCTCTTACGAGCCAG
1 TATTGCTCTAACGAGCCAG
*
41759690 TATTGCTC-AACGAGCTAG
1 TATTGCTCTAACGAGCCAG
*
41759708 TATTGCTCTTACGAGCCAG
1 TATTGCTCTAACGAGCCAG
41759727 TATTGCTC-AACGAGCCAG
1 TATTGCTCTAACGAGCCAG
41759745 TAT
1 TAT
41759748 GCTATTCCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
18 28 0.54
19 24 0.46
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (19 bp):
TATTGCTCTAACGAGCCAG
Found at i:41759721 original size:37 final size:37
Alignment explanation
Indices: 41759671--41759747 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
41759661 TGCGATCCAA
*
41759671 TATTGCTCTTACGAGCCAGTATTGCTCAACGAGCTAG
1 TATTGCTCTTACGAGCCAGTATTGCTCAACGAGCCAG
41759708 TATTGCTCTTACGAGCCAGTATTGCTCAACGAGCCAG
1 TATTGCTCTTACGAGCCAGTATTGCTCAACGAGCCAG
41759745 TAT
1 TAT
41759748 GCTATTCCCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (37 bp):
TATTGCTCTTACGAGCCAGTATTGCTCAACGAGCCAG
Found at i:41761711 original size:103 final size:103
Alignment explanation
Indices: 41761604--41761798 Score: 266
Period size: 103 Copynumber: 1.9 Consensus size: 103
41761594 CTCAAATTTA
* * * *
41761604 AAATAGTATATTCGATTATTTAAGTCCAAAGAAAAATCATAACCAGTACGTTTGAGCACAACTTT
1 AAATAGGATATTCAATTACTTAAGTCCAAAGAAAAATCATAACCAGTACATTTGAGCACAA-TTT
* * *
41761669 -TCGAGTTTCCTAAATAAAGAAACATTGCCTCGTTTTTC
65 CTCAAATTCCCTAAATAAAGAAACATTGCCTCGTTTTTC
* * *
41761707 AAATAGGATATTCAATTACTTAGGTTCAAAGAAAAATCATATCCAGTACATTTGAGCACAATTTC
1 AAATAGGATATTCAATTACTTAAGTCCAAAGAAAAATCATAACCAGTACATTTGAGCACAATTTC
* *
41761772 TCAAATTCCCTAAATAACGGAACATTG
66 TCAAATTCCCTAAATAAAGAAACATTG
41761799 ACTTAATTTG
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
102 3 0.04
103 76 0.96
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.31
Consensus pattern (103 bp):
AAATAGGATATTCAATTACTTAAGTCCAAAGAAAAATCATAACCAGTACATTTGAGCACAATTTC
TCAAATTCCCTAAATAAAGAAACATTGCCTCGTTTTTC
Done.