Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 442 of 444
Found at i:128276882 original size:26 final size:26
Alignment explanation
Indices: 128276846--128276897 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
128276836 TCCTACTTAA
128276846 AGGTTTATTTGCCTTTCTTGAATCAC
1 AGGTTTATTTGCCTTTCTTGAATCAC
128276872 AGGTTTATTTGCCTTTCTTGAATCAC
1 AGGTTTATTTGCCTTTCTTGAATCAC
128276898 TGTTTTTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.46
Consensus pattern (26 bp):
AGGTTTATTTGCCTTTCTTGAATCAC
Found at i:128278861 original size:29 final size:27
Alignment explanation
Indices: 128278829--128278896 Score: 73
Period size: 31 Copynumber: 2.4 Consensus size: 27
128278819 ATAAATATCA
*
128278829 TAATTATACATGAATTTTGATATAATGTG
1 TAATTATACATGAACTTTGAT-T-ATGTG
*
128278858 TAATTTGATACATGAACTTTGATTTTGTG
1 TAA-TT-ATACATGAACTTTGATTATGTG
*
128278887 CAATTATACA
1 TAATTATACA
128278897 CCTTAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 5 0.15
28 2 0.06
29 9 0.26
30 3 0.09
31 15 0.44
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.44
Consensus pattern (27 bp):
TAATTATACATGAACTTTGATTATGTG
Found at i:128280102 original size:15 final size:15
Alignment explanation
Indices: 128280078--128280113 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
128280068 AAAATATTCA
128280078 AAAAAAATAAAATAT
1 AAAAAAATAAAATAT
*
128280093 AAAAATATAAAATAT
1 AAAAAAATAAAATAT
128280108 AAAAAA
1 AAAAAA
128280114 TTATAAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAAAAATAAAATAT
Found at i:128280869 original size:22 final size:22
Alignment explanation
Indices: 128280844--128280892 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
128280834 TTTTTTCTCA
128280844 TTATTTTGCTACCATTTTACTG
1 TTATTTTGCTACCATTTTACTG
* * * *
128280866 TTATGTTGTTACTATTTTATTG
1 TTATTTTGCTACCATTTTACTG
128280888 TTATT
1 TTATT
128280893 GTTTAGATAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.61
Consensus pattern (22 bp):
TTATTTTGCTACCATTTTACTG
Found at i:128280957 original size:30 final size:30
Alignment explanation
Indices: 128280921--128280982 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
128280911 AGTTATTTTA
128280921 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
**
128280951 TTGTTAATTTTGTTATTATTTTAGTGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
128280981 TT
1 TT
128280983 ACTTGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.03, G:0.11, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:128287829 original size:17 final size:18
Alignment explanation
Indices: 128287804--128287840 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
128287794 TTCTTTAAAA
128287804 ATTATAAAT-ATATAAATT
1 ATTATAAATGATA-AAATT
128287822 ATTA-AAATGATAAAATT
1 ATTATAAATGATAAAATT
128287839 AT
1 AT
128287841 ATTTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTATAAATGATAAAATT
Found at i:128293207 original size:28 final size:28
Alignment explanation
Indices: 128293146--128293216 Score: 67
Period size: 28 Copynumber: 2.5 Consensus size: 28
128293136 AATGAAATTT
* *
128293146 TATA-ATTTTT-AAAATATTAAATTAAA
1 TATATATTTTTAAAAAGATTAAAATAAA
*
128293172 TTTATATTTTTAAAAAGATTAAAATATAA
1 TATATATTTTTAAAAAGATTAAAATA-AA
128293201 TAT-TATTAATTTAAAA
1 TATATATT--TTTAAAA
128293217 TTTAATTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
26 3 0.08
27 6 0.17
28 16 0.44
29 4 0.11
30 7 0.19
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (28 bp):
TATATATTTTTAAAAAGATTAAAATAAA
Found at i:128294739 original size:21 final size:21
Alignment explanation
Indices: 128294713--128294754 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
128294703 CGATTCGACA
128294713 AATTTAAATTCAAATAGATTT
1 AATTTAAATTCAAATAGATTT
* * *
128294734 AATTTAATTTTAAATATATTT
1 AATTTAAATTCAAATAGATTT
128294755 TTTATTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
AATTTAAATTCAAATAGATTT
Found at i:128294932 original size:21 final size:21
Alignment explanation
Indices: 128294891--128294935 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
128294881 GGGGATTATG
*
128294891 ATATTTATATTCCAATTTTAA
1 ATATTTATATTCCAATATTAA
*
128294912 ATATTTAATATT-TAATATTAA
1 ATATTT-ATATTCCAATATTAA
128294933 ATA
1 ATA
128294936 ATTTTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATTTATATTCCAATATTAA
Found at i:128301722 original size:18 final size:18
Alignment explanation
Indices: 128301690--128301727 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
128301680 TATTTCATGC
*
128301690 TTATCTTTTTTTAAT-TT
1 TTATATTTTTTTAATATT
128301707 TTATATTTTTTATAATATT
1 TTATATTTTTT-TAATATT
128301726 TT
1 TT
128301728 TTGAATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 4 0.22
19 4 0.22
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATATTTTTTTAATATT
Found at i:128301734 original size:29 final size:26
Alignment explanation
Indices: 128301695--128301754 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 26
128301685 CATGCTTATC
* *
128301695 TTTTTTTAATTTTTATATTTTTTATAATA
1 TTTTTTGAATTTTGA-A-TTTTTA-AATA
128301724 TTTTTTGAATTTTGAATTTTTAAATA
1 TTTTTTGAATTTTGAATTTTTAAATA
128301750 TTTTT
1 TTTTT
128301755 ATAACTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 9 0.31
27 6 0.21
28 1 0.03
29 13 0.45
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (26 bp):
TTTTTTGAATTTTGAATTTTTAAATA
Found at i:128301763 original size:27 final size:27
Alignment explanation
Indices: 128301695--128301774 Score: 74
Period size: 27 Copynumber: 2.9 Consensus size: 27
128301685 CATGCTTATC
* *
128301695 TTTTTTTAATTTTTATATTTTTTATAATA
1 TTTTTTGAA-TTTTA-AATTTTTATAATA
*
128301724 TTTTTTGAATTTTGAATTTTTA-AATA
1 TTTTTTGAATTTTAAATTTTTATAATA
128301750 TTTTTAT-AACTTTTAAATTATTTAT
1 TTTTT-TGAA-TTTTAAATT-TTTAT
128301775 TGATGTAACA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
26 11 0.26
27 16 0.37
28 8 0.19
29 8 0.19
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (27 bp):
TTTTTTGAATTTTAAATTTTTATAATA
Found at i:128306274 original size:13 final size:13
Alignment explanation
Indices: 128306256--128306280 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
128306246 TCTTACTTTC
128306256 CTTGAATGCATGT
1 CTTGAATGCATGT
128306269 CTTGAATGCATG
1 CTTGAATGCATG
128306281 AAGAGGCGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (13 bp):
CTTGAATGCATGT
Found at i:128309880 original size:46 final size:46
Alignment explanation
Indices: 128309813--128309905 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
128309803 TTGAACTCAG
*
128309813 AATGCACTCTTTTCTATATGAGGTTGTGAGTTCAATTACATAGATT
1 AATGCACTCCTTTCTATATGAGGTTGTGAGTTCAATTACATAGATT
*
128309859 AATGCACTCCTTTCTGTATGAGGTTGTGAGTTCAATTACATAGATT
1 AATGCACTCCTTTCTATATGAGGTTGTGAGTTCAATTACATAGATT
128309905 A
1 A
128309906 CTAACATTCG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (46 bp):
AATGCACTCCTTTCTATATGAGGTTGTGAGTTCAATTACATAGATT
Found at i:128315272 original size:30 final size:30
Alignment explanation
Indices: 128315236--128315295 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
128315226 TTCACAGGGA
*
128315236 AGTTAAATTTTTTATATAAAACATAAAATT
1 AGTTAAAATTTTTATATAAAACATAAAATT
128315266 AGTTAAAATTTTTATATAAAACATAAAATT
1 AGTTAAAATTTTTATATAAAACATAAAATT
128315296 TTAGAGGGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (30 bp):
AGTTAAAATTTTTATATAAAACATAAAATT
Found at i:128315618 original size:18 final size:18
Alignment explanation
Indices: 128315597--128315631 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
128315587 TATTATAACA
128315597 TGTAAATTCATT-ATTGGT
1 TGTAAATT-ATTAATTGGT
128315615 TGTAAATTATTAATTGG
1 TGTAAATTATTAATTGG
128315632 ATATTCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.49
Consensus pattern (18 bp):
TGTAAATTATTAATTGGT
Found at i:128316095 original size:9 final size:9
Alignment explanation
Indices: 128316081--128316110 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
128316071 TTTCAATTAA
128316081 AAAAATATT
1 AAAAATATT
128316090 AAAAATATT
1 AAAAATATT
128316099 AAAAATA-T
1 AAAAATATT
128316107 AAAA
1 AAAA
128316111 TCCGGTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.24
9 16 0.76
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAAATATT
Found at i:128326235 original size:18 final size:18
Alignment explanation
Indices: 128326210--128326302 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
128326200 ACCGTTTACG
128326210 GTACTATTCACGTATACA
1 GTACTATTCACGTATACA
*
128326228 GCACTATTCACGTATACA
1 GTACTATTCACGTATACA
* *
128326246 ATACTATTCACGTATACG
1 GTACTATTCACGTATACA
* * *
128326264 GTACTATTTACGAATACG
1 GTACTATTCACGTATACA
*
128326282 GTACTGTTCACGTATACA
1 GTACTATTCACGTATACA
128326300 GTA
1 GTA
128326303 GTTGGGATTG
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (18 bp):
GTACTATTCACGTATACA
Found at i:128348415 original size:12 final size:12
Alignment explanation
Indices: 128348398--128348425 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
128348388 CTTACAAGGT
128348398 TTTTTTTTTATG
1 TTTTTTTTTATG
128348410 TTTTTTTTTATG
1 TTTTTTTTTATG
128348422 TTTT
1 TTTT
128348426 GATGTAGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTATG
Found at i:128353075 original size:75 final size:76
Alignment explanation
Indices: 128352952--128353915 Score: 852
Period size: 75 Copynumber: 13.0 Consensus size: 76
128352942 TTGCCTAGAT
* * * *
128352952 GAAGCCTGTTTACCAAACATGTTGAGTCCAGTAAGTTCACAAGGTATGGCTTG-GTGTTCAGGTT
1 GAAGCCTGTTTCCCAAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGTGTTCAGGTT
* *
128353016 CAAGAAACTTA
66 CAGGAAATTTA
* * * * *
128353027 GAAGCTTGTTTCCCAAACATGTTAAGTCCAGTGGGTTCACAAGGTATGG-TT---TG---AGGTT
1 GAAGCCTGTTTCCCAAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGTGTTCAGGTT
128353085 CAGGAAATTTA
66 CAGGAAATTTA
* ** * * *
128353096 GAAGCTTGTTTCCCGAAA-ATGTTGATTCTGGTAGGTTCGCAAGACATGG-TTCGA-AGTTCAGG
1 GAAGCCTGTTTCCC-AAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTT-GAGTGTTCAGG
*
128353158 TTCGGGAAATTTA
64 TTCAGGAAATTTA
* *
128353171 GAAGCCTGCTTCCCGAAA-TTGTTGATTCCAGT-GGATTCACAAGGCATGGCTTGA--G----GG
1 GAAGCCTGTTTCCC-AAACATGTTGATTCCAGTAGG-TTCACAAGGCATGGCTTGAGTGTTCAGG
*
128353228 -TCAGGAATTTTA
64 TTCAGGAAATTTA
* * * * * * *
128353240 GATGGCTGCTTT-CCGAACATGTTGATTCCTGTTGGTCCACAAGGCATGGCTTGAG-GTTCGGGT
1 GAAGCCTG-TTTCCCAAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGTGTTCAGGT
128353303 TCAGGAAATTTA
65 TCAGGAAATTTA
* * * *
128353315 GTAGCCTGTTTCCCAAAAATGTTGATTCCAGTTGGTTCAC-AGTGCATGGGTTGAGT-TTCAGGT
1 GAAGCCTGTTTCCCAAACATGTTGATTCCAGTAGGTTCACAAG-GCATGGCTTGAGTGTTCAGGT
128353378 TCAGGAAATTTA
65 TCAGGAAATTTA
* * *
128353390 GAAGCCTGCTTT-CCAAACATGTTGATTCCAGTTGGTTCAC-AGTGCACGGGTTGAGT-TTCAGG
1 GAAGCCTG-TTTCCCAAACATGTTGATTCCAGTAGGTTCACAAG-GCATGGCTTGAGTGTTCAGG
*
128353452 TTCGGGAAATTTA
64 TTCAGGAAATTTA
*
128353465 GAAGCCTGCTTT-CCAAACATGTTGATTCCAGCAGGTTCAC-AGTGCAT-GCTTAGAG-GTTCAG
1 GAAGCCTG-TTTCCCAAACATGTTGATTCCAGTAGGTTCACAAG-GCATGGCTT-GAGTGTTCAG
*
128353526 GTTCGGGAAATTTA
63 GTTCAGGAAATTTA
* * * * * * *
128353540 GAAGCCTGTTTTCCAAACACGTCGATTCCAATGGGTTCACAAGGTATGGCTCGAG-GTTCAGGTT
1 GAAGCCTGTTTCCCAAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGTGTTCAGGTT
*
128353604 CAGCAAATTTA
66 CAGGAAATTTA
* * * * * *
128353615 GAAGCCTGCTTCCCAAACATGTGGATTTCAGCACGTTCACAAGGCATGCCTTGAG-GTTCAGGTT
1 GAAGCCTGTTTCCCAAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGTGTTCAGGTT
128353679 CAGGAAATTTA
66 CAGGAAATTTA
* ***
128353690 GAAGCCCGTTTCCCAAACATGTTGATTCCAGTAGGTTCACACTTCATTGG-TTGAGT-TTCAGGT
1 GAAGCCTGTTTCCCAAACATGTTGATTCCAGTAGGTTCACAAGGCA-TGGCTTGAGTGTTCAGGT
128353753 TCAGGAAATTTA
65 TCAGGAAATTTA
* * ** * * * *
128353765 GAAGGCC-GCTTACCAAACATGTTGATTCCACCAGATTCACAAGGCATCGCTTGAG-GTTCATGC
1 GAA-GCCTGTTTCCCAAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGTGTTCAGGT
*
128353828 TCGGGAAATTTA
65 TCAGGAAATTTA
* * * ** * * ** * *
128353840 GAAGCCTGTTTACCAAAAACGTCAATTGCAGTGGGTTCACAAGATATAGCTTG-GGGTTCAGGTT
1 GAAGCCTGTTTCCCAAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGTGTTCAGGTT
*
128353904 CGGGAAATTTA
66 CAGGAAATTTA
128353915 G
1 G
128353916 GTGTTTGGTT
Statistics
Matches: 745, Mismatches: 110, Indels: 68
0.81 0.12 0.07
Matches are distributed among these distances:
68 2 0.00
69 101 0.14
70 10 0.01
72 3 0.00
74 24 0.03
75 590 0.79
76 15 0.02
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (76 bp):
GAAGCCTGTTTCCCAAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGTGTTCAGGTT
CAGGAAATTTA
Found at i:128356166 original size:2 final size:2
Alignment explanation
Indices: 128356159--128356187 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
128356149 TCCAAAAATA
128356159 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
128356188 ACTTACTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:128356911 original size:19 final size:19
Alignment explanation
Indices: 128356887--128356923 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
128356877 TTCGAGTTAA
128356887 TTTGAGCTAAATGATTTTG
1 TTTGAGCTAAATGATTTTG
*
128356906 TTTGAGTTAAATGATTTT
1 TTTGAGCTAAATGATTTT
128356924 AAGTTTTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.03, G:0.19, T:0.51
Consensus pattern (19 bp):
TTTGAGCTAAATGATTTTG
Found at i:128357772 original size:39 final size:39
Alignment explanation
Indices: 128357729--128357809 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
128357719 AGGAAGAATT
128357729 TTTTTTTTATTCTTCTAATAATTTAATATTTACGTTTCA
1 TTTTTTTTATTCTTCTAATAATTTAATATTTACGTTTCA
128357768 TTTTTTTTATTCTTCTAATAATTTAATATTTACGTTTCA
1 TTTTTTTTATTCTTCTAATAATTTAATATTTACGTTTCA
128357807 TTT
1 TTT
128357810 AATGCAATTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.25, C:0.10, G:0.02, T:0.63
Consensus pattern (39 bp):
TTTTTTTTATTCTTCTAATAATTTAATATTTACGTTTCA
Found at i:128359118 original size:14 final size:15
Alignment explanation
Indices: 128359099--128359132 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
128359089 TTTTGTGTAT
*
128359099 AAATATAATATAA-A
1 AAATATAAAATAATA
128359113 AAATATAAAATAATA
1 AAATATAAAATAATA
128359128 AAATA
1 AAATA
128359133 AACCTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATATAAAATAATA
Found at i:128359119 original size:9 final size:10
Alignment explanation
Indices: 128359096--128359161 Score: 50
Period size: 11 Copynumber: 6.4 Consensus size: 10
128359086 TTATTTTGTG
128359096 TATAAATATAA
1 TATAAA-ATAA
128359107 TATAAAA-AA
1 TATAAAATAA
128359116 TATAAAAT-A
1 TATAAAATAA
128359125 -ATAAAATAA
1 TATAAAATAA
128359134 -ACCTTCAAAATAA
1 TA---T-AAAATAA
128359147 TATAAAATAAA
1 TATAAAAT-AA
128359158 TATA
1 TATA
128359162 TATTTGTCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
8 7 0.15
9 12 0.26
10 6 0.13
11 13 0.28
12 1 0.02
13 7 0.15
14 1 0.02
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (10 bp):
TATAAAATAA
Found at i:128359482 original size:3 final size:3
Alignment explanation
Indices: 128359474--128359511 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
128359464 TTCTCTTTTA
128359474 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
128359512 GGATTAACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:128360344 original size:17 final size:19
Alignment explanation
Indices: 128360321--128360365 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
128360311 CTTCTAAAAA
128360321 ATATTATTTA-TATA-ATT
1 ATATTATTTATTATATATT
* *
128360338 TTATTATATATTATATATT
1 ATATTATTTATTATATATT
128360357 ATATTATTT
1 ATATTATTT
128360366 TTAATGGTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATTATTTATTATATATT
Found at i:128362504 original size:50 final size:50
Alignment explanation
Indices: 128362450--128362545 Score: 192
Period size: 50 Copynumber: 1.9 Consensus size: 50
128362440 GATATCTAAG
128362450 TCGGAGTCCTATTCAAATAAATAATATAAATTTAGATAATAAATATCATA
1 TCGGAGTCCTATTCAAATAAATAATATAAATTTAGATAATAAATATCATA
128362500 TCGGAGTCCTATTCAAATAAATAATATAAATTTAGATAATAAATAT
1 TCGGAGTCCTATTCAAATAAATAATATAAATTTAGATAATAAATAT
128362546 TTGAATATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.48, C:0.09, G:0.08, T:0.34
Consensus pattern (50 bp):
TCGGAGTCCTATTCAAATAAATAATATAAATTTAGATAATAAATATCATA
Found at i:128362917 original size:3 final size:3
Alignment explanation
Indices: 128362909--128362946 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
128362899 CATCTATTTA
128362909 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
128362947 ATTTGATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:128363327 original size:19 final size:20
Alignment explanation
Indices: 128363274--128363329 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 20
128363264 AATTTTAAAC
* *
128363274 TATATATTTTATTATTTATTA
1 TATATATTTTA-AATTAATTA
128363295 TATATTACTTTTAAATTAATT-
1 TATA-TA-TTTTAAATTAATTA
128363316 TATATATTTTAAAT
1 TATATATTTTAAAT
128363330 ACATAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 8 0.26
20 2 0.06
21 8 0.26
22 8 0.26
23 5 0.16
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TATATATTTTAAATTAATTA
Found at i:128368098 original size:22 final size:22
Alignment explanation
Indices: 128368055--128368114 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
128368045 ATCGGATATC
* *
128368055 TTCTGTAGAAAATTGTAGGAATA
1 TTCTGTA-AATATTTTAGGAATA
128368078 TTCTGTAAATATTTTAGGAATA
1 TTCTGTAAATATTTTAGGAATA
* *
128368100 TTTTGTAGATATTTT
1 TTCTGTAAATATTTT
128368115 TTTTTATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
22 26 0.79
23 7 0.21
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (22 bp):
TTCTGTAAATATTTTAGGAATA
Found at i:128372698 original size:22 final size:22
Alignment explanation
Indices: 128372670--128372714 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
128372660 AGGGGGAGTG
128372670 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
128372692 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
128372714 T
1 T
128372715 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:128376275 original size:31 final size:31
Alignment explanation
Indices: 128376240--128376305 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
128376230 GTAGTCCCTA
* *
128376240 AACTAGGTAATTGTTCCCATAATAGGGCTTG
1 AACTAGGCAATTGTTCCCACAATAGGGCTTG
** *
128376271 AACTAGGCAATTGTTTTCACAATGGGGCTTG
1 AACTAGGCAATTGTTCCCACAATAGGGCTTG
128376302 AACT
1 AACT
128376306 TTTTTTTTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.32
Consensus pattern (31 bp):
AACTAGGCAATTGTTCCCACAATAGGGCTTG
Found at i:128376547 original size:59 final size:58
Alignment explanation
Indices: 128376405--128376567 Score: 166
Period size: 59 Copynumber: 2.8 Consensus size: 58
128376395 AACATGGATA
* * * * ** *
128376405 AAAAAAAAGTTTAGGCCCTAATGTGAGAACAATTATCAAGTACAGGGATTAACTTGGAC
1 AAAAAAAAGTTCAGGCCC-AATGTGGGAACAATTGTCAAGTTCAAAGATGAACTTGGAC
* * *
128376464 AAATAGAAGTTCAAG-CCATCATGTGGGAACAATTGTCAAGTTCAAAGATGAACTTGGAC
1 AAAAAAAAGTTCAGGCCCA--ATGTGGGAACAATTGTCAAGTTCAAAGATGAACTTGGAC
* * *
128376523 AAAAAAAAGTTCAGGCTCCAATGTGGGAATATTTGTTAAGTTCAA
1 AAAAAAAAGTTCAGGC-CCAATGTGGGAACAATTGTCAAGTTCAA
128376568 GTCCTAAAAA
Statistics
Matches: 84, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
57 1 0.01
58 2 0.02
59 78 0.93
61 3 0.04
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.25
Consensus pattern (58 bp):
AAAAAAAAGTTCAGGCCCAATGTGGGAACAATTGTCAAGTTCAAAGATGAACTTGGAC
Found at i:128382298 original size:12 final size:12
Alignment explanation
Indices: 128382281--128382335 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
128382271 TCATTTTATC
128382281 ATATTAATATTT
1 ATATTAATATTT
*
128382293 ATATTAAAATTT
1 ATATTAATATTT
*
128382305 ATA-TAATATAT
1 ATATTAATATTT
*
128382316 A-ATTAA-ACTT
1 ATATTAATATTT
*
128382326 ATATTTATAT
1 ATATTAATAT
128382336 AAAATTATTA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
10 4 0.12
11 14 0.42
12 15 0.45
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (12 bp):
ATATTAATATTT
Found at i:128386527 original size:24 final size:24
Alignment explanation
Indices: 128386482--128386527 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
128386472 TGCACCAAAT
* *
128386482 CAAAGTTCATTTTTCAAATTGAAA
1 CAAAGTTCATGTATCAAATTGAAA
128386506 CAAAGTTCATGTAT-AAACTTGA
1 CAAAGTTCATGTATCAAA-TTGA
128386528 TATTTATCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (24 bp):
CAAAGTTCATGTATCAAATTGAAA
Found at i:128388582 original size:11 final size:11
Alignment explanation
Indices: 128388566--128388592 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
128388556 GCCATCAACG
128388566 TTTTTTTTCTT
1 TTTTTTTTCTT
128388577 TTTTTTTTCTT
1 TTTTTTTTCTT
128388588 TTTTT
1 TTTTT
128388593 ACACTTAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:128388972 original size:20 final size:20
Alignment explanation
Indices: 128388925--128388972 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
128388915 ATTTATAATC
*
128388925 AAATTTAATTTTAAAATTTTG
1 AAATTT-ATTTTAAAATTTAG
*
128388946 AAGTTTATTTT-AAATTTAG
1 AAATTTATTTTAAAATTTAG
128388965 ATAATTTA
1 A-AATTTA
128388973 GATATAATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 8 0.35
20 10 0.43
21 5 0.22
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (20 bp):
AAATTTATTTTAAAATTTAG
Found at i:128390965 original size:29 final size:29
Alignment explanation
Indices: 128390931--128390991 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
128390921 AAATTTTCAG
128390931 AAATCTTAAGAATTTAATGATATTTTTTT
1 AAATCTTAAGAATTTAATGATATTTTTTT
128390960 AAATCTTAAGAATTTAATGATATTTTTTT
1 AAATCTTAAGAATTTAATGATATTTTTTT
128390989 AAA
1 AAA
128390992 AAAAATTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (29 bp):
AAATCTTAAGAATTTAATGATATTTTTTT
Found at i:128392716 original size:59 final size:59
Alignment explanation
Indices: 128392641--128392797 Score: 176
Period size: 59 Copynumber: 2.7 Consensus size: 59
128392631 TCAAACAAAA
* *
128392641 AAAAAAGATTAGGTACCAAATTAGGAAAAAG-AGTTAAGTTCAG-GTAATAAATTGAACCC
1 AAAAAAGATTAGGTACCAAATTAGGAAAAAGTA-TCAAGTT-AGAGTAACAAATTGAACCC
* * * * * *
128392700 AAAAAAGATTAAGTACCAACTTAAGAAAAAGTATCAAGTTTGAGTACCAAATTGGACCC
1 AAAAAAGATTAGGTACCAAATTAGGAAAAAGTATCAAGTTAGAGTAACAAATTGAACCC
* * *
128392759 AAAAAA-ATTAGGTACCAAATTAGAAAAAAATATTAAGTT
1 AAAAAAGATTAGGTACCAAATTAGGAAAAAGTATCAAGTT
128392798 TGGATACCGA
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
58 28 0.34
59 53 0.65
60 1 0.01
ACGTcount: A:0.51, C:0.11, G:0.15, T:0.23
Consensus pattern (59 bp):
AAAAAAGATTAGGTACCAAATTAGGAAAAAGTATCAAGTTAGAGTAACAAATTGAACCC
Found at i:128397899 original size:5 final size:5
Alignment explanation
Indices: 128397889--128397917 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
128397879 ATCTGTGTGT
128397889 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
128397918 TCATACTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:128401398 original size:17 final size:17
Alignment explanation
Indices: 128401364--128401398 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
128401354 ATTCTTATTT
*
128401364 AATAAAATATAATAAAA
1 AATAAAATAAAATAAAA
128401381 AATAAAATAAAAGTAAAA
1 AATAAAATAAAA-TAAAA
128401399 TCCATATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (17 bp):
AATAAAATAAAATAAAA
Found at i:128402318 original size:8 final size:8
Alignment explanation
Indices: 128402307--128402345 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
128402297 AGTAAAAAAG
128402307 TAATTTTA
1 TAATTTTA
128402315 TAATTTTA
1 TAATTTTA
128402323 TAATTTTA
1 TAATTTTA
*
128402331 TATTTTTA
1 TAATTTTA
128402339 TAATTTT
1 TAATTTT
128402346 TAAAGAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TAATTTTA
Found at i:128402402 original size:31 final size:30
Alignment explanation
Indices: 128402329--128402409 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 30
128402319 TTTATAATTT
* * * *
128402329 TATATTTTTATAATTTTTAAAGAATTAAAT
1 TATAATTTTATTATTTTTAAAGAATCAAAG
*
128402359 TA-AATTTTTATTATTTTTAAAGAGGTCAAAG
1 TATAA-TTTTATTATTTTTAAAGA-ATCAAAG
*
128402390 TATAATTTTATTATTATTAA
1 TATAATTTTATTATTTTTAA
128402410 TTTAAAATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
29 1 0.02
30 19 0.45
31 20 0.48
32 2 0.05
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (30 bp):
TATAATTTTATTATTTTTAAAGAATCAAAG
Found at i:128410439 original size:52 final size:52
Alignment explanation
Indices: 128410361--128410465 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
128410351 GTCCCAAGAT
* *
128410361 TGCTAATATGAAAGTTTAATTTGATACCCTTGACAGTGATAGTGGCATGATG
1 TGCTAACATGAAAGTCTAATTTGATACCCTTGACAGTGATAGTGGCATGATG
*
128410413 TGCTAACATGGAAGTCTAATTTGATACCCTTGACAGTGATAGTGGCATGATG
1 TGCTAACATGAAAGTCTAATTTGATACCCTTGACAGTGATAGTGGCATGATG
128410465 T
1 T
128410466 TTTAGGATGA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (52 bp):
TGCTAACATGAAAGTCTAATTTGATACCCTTGACAGTGATAGTGGCATGATG
Found at i:128413442 original size:2 final size:2
Alignment explanation
Indices: 128413437--128413461 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
128413427 GTGTGTGGTT
128413437 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
128413462 GTACAATCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:128416469 original size:31 final size:31
Alignment explanation
Indices: 128416432--128416497 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
128416422 TTACAAAATG
128416432 GTCATTGAACTATTCAAAAGTTTTCATTTAA
1 GTCATTGAACTATTCAAAAGTTTTCATTTAA
* * *
128416463 GTCATTGAATTATTCGAAAGTTTTTATTTAA
1 GTCATTGAACTATTCAAAAGTTTTCATTTAA
128416494 GTCA
1 GTCA
128416498 CTAGATTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (31 bp):
GTCATTGAACTATTCAAAAGTTTTCATTTAA
Found at i:128419355 original size:16 final size:14
Alignment explanation
Indices: 128419334--128419367 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 14
128419324 ATTGCATATA
128419334 TTATTTGTTTTTTGTT
1 TTATTT-TTTTTT-TT
128419350 TTATTTTTTTTTTT
1 TTATTTTTTTTTTT
128419364 TTAT
1 TTAT
128419368 AGTTTCGTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 6 0.33
16 6 0.33
ACGTcount: A:0.09, C:0.00, G:0.06, T:0.85
Consensus pattern (14 bp):
TTATTTTTTTTTTT
Found at i:128425529 original size:23 final size:22
Alignment explanation
Indices: 128425503--128425546 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
128425493 ACAAAATTAA
128425503 TATTTTAAAATTTTGTATTTTTG
1 TATTTTAAAATTTT-TATTTTTG
*
128425526 TATTTTAATATTTTTATTTTT
1 TATTTTAAAATTTTTATTTTT
128425547 ATTTATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (22 bp):
TATTTTAAAATTTTTATTTTTG
Found at i:128447488 original size:48 final size:48
Alignment explanation
Indices: 128447432--128447527 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
128447422 GGAGATGTTG
*
128447432 TTGGGTTGGAGAAGAAAGAAATAAGTTCGGAAAATGGCACTGCGAGTA
1 TTGGGTTGGAGAAGAAAGAAATAAGCTCGGAAAATGGCACTGCGAGTA
*
128447480 TTGGGTTGGAGAAGAAAGAAATAGGCTCGGAAAATGGCACTGCGAGTA
1 TTGGGTTGGAGAAGAAAGAAATAAGCTCGGAAAATGGCACTGCGAGTA
128447528 CATTAAGAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.36, C:0.09, G:0.34, T:0.20
Consensus pattern (48 bp):
TTGGGTTGGAGAAGAAAGAAATAAGCTCGGAAAATGGCACTGCGAGTA
Found at i:128456099 original size:3 final size:3
Alignment explanation
Indices: 128456086--128456123 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
128456076 ATATGCTATA
* *
128456086 ATC ACC ATC ATC ATC ATC ATC ATC ATC ATC ATC TTC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
128456124 TGTTCTTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:128456693 original size:14 final size:15
Alignment explanation
Indices: 128456666--128456709 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 15
128456656 TGAATATTTA
128456666 AAAAATATAAAAATT
1 AAAAATATAAAAATT
*
128456681 AAAAATAT-CAAATT
1 AAAAATATAAAAATT
128456695 -AAAATATAAAAATT
1 AAAAATATAAAAATT
128456709 A
1 A
128456710 TTTATAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 7 0.28
14 10 0.40
15 8 0.32
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAATATAAAAATT
Found at i:128459448 original size:9 final size:9
Alignment explanation
Indices: 128459425--128459483 Score: 55
Period size: 9 Copynumber: 6.2 Consensus size: 9
128459415 TAAATATTCA
128459425 TTAGAATTTT
1 TTAG-ATTTT
*
128459435 CTAGATTTT
1 TTAGATTTT
128459444 TTAGATTTT
1 TTAGATTTT
*
128459453 TATAGATATT
1 T-TAGATTTT
*
128459463 TTAAATTTAT
1 TTAGATTT-T
*
128459473 TTTGATTTT
1 TTAGATTTT
128459482 TT
1 TT
128459484 TAATATTTGT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
9 22 0.55
10 18 0.45
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (9 bp):
TTAGATTTT
Found at i:128459453 original size:19 final size:18
Alignment explanation
Indices: 128459425--128459483 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
128459415 TAAATATTCA
*
128459425 TTAGAATTTTCTAGATTTT
1 TTAG-ATTTTTTAGATTTT
*
128459444 TTAGATTTTTATAGATATT
1 TTAGATTTTT-TAGATTTT
* *
128459463 TTAAATTTATTTTGATTTT
1 TTAGATTT-TTTAGATTTT
128459482 TT
1 TT
128459484 TAATATTTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
18 5 0.15
19 26 0.79
20 2 0.06
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (18 bp):
TTAGATTTTTTAGATTTT
Found at i:128462820 original size:23 final size:23
Alignment explanation
Indices: 128462793--128462838 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
128462783 AATATGCCTC
128462793 GTCTTACTCCTTATCGAGTTTAT
1 GTCTTACTCCTTATCGAGTTTAT
128462816 GTCTTACTCCTTATCGAGTTTAT
1 GTCTTACTCCTTATCGAGTTTAT
128462839 ATGCTCTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.22, G:0.13, T:0.48
Consensus pattern (23 bp):
GTCTTACTCCTTATCGAGTTTAT
Found at i:128465420 original size:10 final size:10
Alignment explanation
Indices: 128465386--128465420 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
128465376 AATCACTATG
128465386 ATAATGTTAC
1 ATAATGTTAC
*
128465396 AAAATGTTAC
1 ATAATGTTAC
128465406 ATAATGTTAC
1 ATAATGTTAC
*
128465416 CTAAT
1 ATAAT
128465421 AAAGTCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (10 bp):
ATAATGTTAC
Found at i:128466925 original size:4 final size:4
Alignment explanation
Indices: 128466918--128466942 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
128466908 CGTTCGTTCG
128466918 TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA T
128466943 GGAGTGTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:128476010 original size:15 final size:15
Alignment explanation
Indices: 128475990--128476019 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
128475980 AGGAAAATAA
128475990 TATTGTAATGAATGT
1 TATTGTAATGAATGT
128476005 TATTGTAATGAATGT
1 TATTGTAATGAATGT
128476020 AAATTTAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (15 bp):
TATTGTAATGAATGT
Found at i:128484832 original size:19 final size:19
Alignment explanation
Indices: 128484804--128484840 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
128484794 GCCAAAAATC
*
128484804 AGTTTTTGGTGAAATTTTG
1 AGTTTCTGGTGAAATTTTG
*
128484823 AGTTTCTGGTGAAGTTTT
1 AGTTTCTGGTGAAATTTT
128484841 TTGTTATCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.27, T:0.51
Consensus pattern (19 bp):
AGTTTCTGGTGAAATTTTG
Found at i:128486348 original size:3 final size:3
Alignment explanation
Indices: 128486340--128486367 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
128486330 AACTTGGAAT
128486340 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
128486368 TCCTTAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:128495660 original size:15 final size:15
Alignment explanation
Indices: 128495640--128495671 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
128495630 ACATAGTTAC
128495640 AATGTTCTTTCTAAA
1 AATGTTCTTTCTAAA
128495655 AATGTTCTTTCTAAA
1 AATGTTCTTTCTAAA
128495670 AA
1 AA
128495672 GGCAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (15 bp):
AATGTTCTTTCTAAA
Found at i:128500168 original size:2 final size:2
Alignment explanation
Indices: 128500161--128500186 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
128500151 AAATTTTAAA
128500161 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
128500187 CTTTTCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:128500353 original size:77 final size:74
Alignment explanation
Indices: 128500211--128500361 Score: 205
Period size: 74 Copynumber: 2.0 Consensus size: 74
128500201 CCTGCCATAT
* *
128500211 AGCTAGTTAGCACTAAGAAGAAACAAAGTTCAACAACTATATATTTCAAAATTCATACTATATCC
1 AGCTAGTTAGCACTAAGAAGAAACAAAGTTCAACAACTATATATTTCAAAATCCATACTAGATCC
*
128500276 TCATCCTCA
66 TAATCCTCA
* * *
128500285 AGCTAGTTA-CAACTAAGAAGAAACAAAGTTCAATAACAATATATTTCTTCAAACTCCATACTAG
1 AGCTAGTTAGC-ACTAAGAAGAAACAAAGTTCAACAAC--TATATAT-TTCAAAATCCATACTAG
128500349 ATCCTAATCCTCA
62 ATCCTAATCCTCA
128500362 CGTCAGCTCA
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
73 1 0.01
74 34 0.51
76 6 0.09
77 26 0.39
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (74 bp):
AGCTAGTTAGCACTAAGAAGAAACAAAGTTCAACAACTATATATTTCAAAATCCATACTAGATCC
TAATCCTCA
Found at i:128510459 original size:40 final size:40
Alignment explanation
Indices: 128510404--128510613 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
128510394 AACATTGGAA
128510404 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
128510444 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
128510484 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
128510524 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
128510563 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
128510604 CTATATCCGG
1 ATATATCCGG
128510614 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:128518585 original size:40 final size:40
Alignment explanation
Indices: 128518526--128518736 Score: 282
Period size: 40 Copynumber: 5.2 Consensus size: 40
128518516 TAACATTGAA
128518526 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
128518566 ATATAT-CGGGCTAAGGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAA-GACCCGAAGGCATTCGTGCGAGTTG
128518606 ATATATCCGGGCTAAGACCCGAAGGCATTTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCA-TTCGTGCGAGTTG
* * * *
128518647 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
128518686 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
128518727 CTATATCCGG
1 ATATATCCGG
128518737 TTAAATCCCG
Statistics
Matches: 149, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
39 10 0.07
40 92 0.62
41 47 0.32
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:128518670 original size:81 final size:80
Alignment explanation
Indices: 128518526--128518736 Score: 282
Period size: 81 Copynumber: 2.6 Consensus size: 80
128518516 TAACATTGAA
128518526 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATAT-CGGGCTAAGGACCCGAAG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATATCCGGGCTAAGGACCCGAAG
* *
128518590 GCATTCGTGCGAGTTG
66 GCATTCGTGCAAG-TC
128518606 ATATATCCGGGCTAAGACCCGAAGGCATTTCGTGCGAGTTGATATATCCGGGCTAA-GACCCGAA
1 ATATATCCGGGCTAAGACCCGAAGGCA-TTCGTGCGAGTTGATATATCCGGGCTAAGGACCCGAA
* *
128518670 GGCCTTTGTGCAAGTC
65 GGCATTCGTGCAAGTC
* * * * * * *
128518686 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCGCTATATCCGG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATATCCGG
128518737 TTAAATCCCG
Statistics
Matches: 117, Mismatches: 11, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
80 49 0.42
81 60 0.51
82 8 0.07
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (80 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATATCCGGGCTAAGGACCCGAAG
GCATTCGTGCAAGTC
Found at i:128526710 original size:40 final size:40
Alignment explanation
Indices: 128526655--128526864 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
128526645 AACATTGGAA
128526655 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
128526695 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
128526735 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
128526775 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
128526814 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
128526855 CTATATCCGG
1 ATATATCCGG
128526865 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:128532857 original size:14 final size:14
Alignment explanation
Indices: 128532838--128532864 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
128532828 TAATACGTTG
128532838 AAAAGGATTAAATA
1 AAAAGGATTAAATA
128532852 AAAAGGATTAAAT
1 AAAAGGATTAAAT
128532865 TACATCATCC
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:0.63, C:0.00, G:0.15, T:0.22
Consensus pattern (14 bp):
AAAAGGATTAAATA
Found at i:128532959 original size:2 final size:2
Alignment explanation
Indices: 128532952--128532977 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
128532942 TTATATGGAT
128532952 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
128532978 AATTTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:128533356 original size:15 final size:14
Alignment explanation
Indices: 128533305--128533359 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 14
128533295 TTCATTTTTC
*
128533305 TTTCTTTCGTTATT
1 TTTCTTTCTTTATT
128533319 TTT-TGTTCTTT-TT
1 TTTCT-TTCTTTATT
128533332 TTTCTTTTTCTTTATGT
1 TTTC--TTTCTTTAT-T
128533349 TTTCTTTCTTT
1 TTTCTTTCTTT
128533360 GAATCTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
13 6 0.18
14 8 0.24
15 13 0.38
16 2 0.06
17 5 0.15
ACGTcount: A:0.04, C:0.13, G:0.05, T:0.78
Consensus pattern (14 bp):
TTTCTTTCTTTATT
Found at i:128540448 original size:29 final size:27
Alignment explanation
Indices: 128540385--128540448 Score: 65
Period size: 30 Copynumber: 2.2 Consensus size: 27
128540375 ATTAAGTTCT
* *
128540385 CCTAAAATTTTAAAAATTATCATTAAT
1 CCTAAAATTTTAAAAATTATAATTAAA
*
128540412 CTCATAAAATTTTTAAAAATTTTAATTAGAA
1 C-C-TAAAA-TTTTAAAAATTATAATTA-AA
128540443 CCTAAA
1 CCTAAA
128540449 TTAAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 1 0.03
28 1 0.03
29 9 0.30
30 17 0.57
31 2 0.07
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (27 bp):
CCTAAAATTTTAAAAATTATAATTAAA
Found at i:128541656 original size:26 final size:26
Alignment explanation
Indices: 128541604--128541656 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
128541594 ATGATTTTAG
* *
128541604 AAGTATATCAAATACAAAACTTTTTA
1 AAGTATATCAAATACAAAACATATTA
*
128541630 AAGTATATCAAATACAAATCATATTA
1 AAGTATATCAAATACAAAACATATTA
128541656 A
1 A
128541657 TTATAGAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.32
Consensus pattern (26 bp):
AAGTATATCAAATACAAAACATATTA
Found at i:128548500 original size:14 final size:14
Alignment explanation
Indices: 128548481--128548508 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
128548471 CAACAATCAG
128548481 GAAAAAGAAATTAA
1 GAAAAAGAAATTAA
128548495 GAAAAAGAAATTAA
1 GAAAAAGAAATTAA
128548509 TTTTTTAGTG
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:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
GAAAAAGAAATTAA
Found at i:128550651 original size:14 final size:14
Alignment explanation
Indices: 128550634--128550667 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
128550624 GTTGTTGTCT
128550634 TTTTTTTTTAATAA
1 TTTTTTTTTAATAA
* *
128550648 TTTTGTTTTAATTA
1 TTTTTTTTTAATAA
128550662 TTTTTT
1 TTTTTT
128550668 AAAACAGAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (14 bp):
TTTTTTTTTAATAA
Found at i:128551010 original size:14 final size:14
Alignment explanation
Indices: 128550991--128551026 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
128550981 TATCTGCTCT
128550991 TTTTGAATATAATG
1 TTTTGAATATAATG
128551005 TTTTGAATATAATG
1 TTTTGAATATAATG
*
128551019 TTTAGAAT
1 TTTTGAAT
128551027 TACCCATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (14 bp):
TTTTGAATATAATG
Found at i:128551504 original size:84 final size:83
Alignment explanation
Indices: 128551402--128551561 Score: 241
Period size: 84 Copynumber: 1.9 Consensus size: 83
128551392 TGTGCTCCAA
* * *
128551402 AAGTTGCATACAAAAAGGTCAAGTTA-GACCCCGGGGAAAAATAAATAAATTCCCATCCCGGATG
1 AAGTTGCATACAAAAAGGTCAAGCTATG-CCCCGGGGAAAAATAAAGAAATTCCCAGCCCGGAT-
*
128551466 GTCTCTAACAATTCCAAATG
64 ATCTCTAACAATTCCAAATG
*
128551486 AAGTTGCATACAAAAAGGTCAAGCTATGCCCCGGGGAAAAGTAAAGAAATTCCCAGCCCGGATAT
1 AAGTTGCATACAAAAAGGTCAAGCTATGCCCCGGGGAAAAATAAAGAAATTCCCAGCCCGGATAT
*
128551551 CTCTGACAATT
66 CTCTAACAATT
128551562 GTCCGAGCGA
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
83 11 0.16
84 57 0.83
85 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (83 bp):
AAGTTGCATACAAAAAGGTCAAGCTATGCCCCGGGGAAAAATAAAGAAATTCCCAGCCCGGATAT
CTCTAACAATTCCAAATG
Found at i:128555442 original size:96 final size:96
Alignment explanation
Indices: 128555230--128555451 Score: 241
Period size: 96 Copynumber: 2.3 Consensus size: 96
128555220 TATCATTGCC
* * * * *
128555230 GCTTCTTTCAGTCATTGCACTGTCCAAATTTCTGCCTTTGCTCCGCCCTTTAATGTTTATAGAAA
1 GCTTCTTTCAGTCATAGCACTGTCCAGATTTCTACCTTTGCTCCGCCCTTTAATGTTCATAAAAA
* * *
128555295 GATCACAGTTTTTCTTCTTAGTCTCACAAGG
66 GAGCACAGTTTTCCTTCATAGTCTCACAAGG
* ** ** * * **
128555326 ACTTCTTTTGGTTGTCGCACTGTCCAGATTTCTACGTTTGCTCCGTGCTTTAATGTTCATAAAAA
1 GCTTCTTTCAGTCATAGCACTGTCCAGATTTCTACCTTTGCTCCGCCCTTTAATGTTCATAAAAA
* *
128555391 GAGCGCAGTTTTCCTTCATAGTCTC-C-TGCTG
66 GAGCACAGTTTTCCTTCATAGTCTCACAAG--G
128555422 GCTTCTTTCAGTCATAGCACTGTCCAGATT
1 GCTTCTTTCAGTCATAGCACTGTCCAGATT
128555452 CGCTTTAATG
Statistics
Matches: 100, Mismatches: 24, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
94 1 0.01
95 1 0.01
96 98 0.98
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (96 bp):
GCTTCTTTCAGTCATAGCACTGTCCAGATTTCTACCTTTGCTCCGCCCTTTAATGTTCATAAAAA
GAGCACAGTTTTCCTTCATAGTCTCACAAGG
Found at i:128555844 original size:135 final size:133
Alignment explanation
Indices: 128555454--128555874 Score: 457
Period size: 135 Copynumber: 3.1 Consensus size: 133
128555444 TCCAGATTCG
* * *
128555454 CTTTAATGTTCATAGAAAGATAGCAATTTTCCTTTTTAGTCTCCTGAGGGCTTCTTTCGATCATT
1 CTTTAATGTTCATA-AAAGATCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTTCTTTC-ATCATT
* * * * * *
128555519 GCATCCTTCTTAGTCTCCCGAGGGCTTCTTTCATTCATAGCACTGTCCAAATTCCTGTGC-TTGC
64 GCATCCTTCTTACTCTCCTGAGGGCTTCTTTCAGTCATCGCACTGTCCAAATTTCTG-CCTTTGC
* *
128555583 TCTGCG
128 TCCGCA
* * *
128555589 CTTTAATGTTCACAAAAAGATCACAGTTTTCCTTCTTAGTCTCCTGAGGGCTACTTTCAGTCATT
1 CTTTAATGTTCA-TAAAAGATCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTTCTTTCA-TCATT
* * * * *** *
128555654 GCATTCTCCTCACTCTCCTGAGGGCTTCTTTCTGTCATCGCACCAACCAAGTTTCTGCCTTTGCT
64 GCATCCTTCTTACTCTCCTGAGGGCTTCTTTCAGTCATCGCACTGTCCAAATTTCTGCCTTTGCT
128555719 CCGCA
129 CCGCA
* * * *
128555724 CTTTAACGTTCATAAAACGATCGCAGTTTTCCTTCTTAGTCTCTTCAGAGCTTCTTTCACTCATT
1 CTTTAATGTTCATAAAA-GATCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTTCTTTCA-TCATT
* * * ** * *
128555789 GCATCCTTCTTATTCTCCTGAGGGATTCTTTCGGTCATCTTACTGTCCAAATTTCTACGTTTGCT
64 GCATCCTTCTTACTCTCCTGAGGGCTTCTTTCAGTCATCGCACTGTCCAAATTTCTGCCTTTGCT
*
128555854 CCGCT
129 CCGCA
*
128555859 TTTTAATGTTCATAAA
1 CTTTAATGTTCATAAA
128555875 CACGGTAGCC
Statistics
Matches: 235, Mismatches: 47, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
134 6 0.03
135 228 0.97
136 1 0.00
ACGTcount: A:0.19, C:0.27, G:0.15, T:0.39
Consensus pattern (133 bp):
CTTTAATGTTCATAAAAGATCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTTCTTTCATCATTGC
ATCCTTCTTACTCTCCTGAGGGCTTCTTTCAGTCATCGCACTGTCCAAATTTCTGCCTTTGCTCC
GCA
Found at i:128558221 original size:16 final size:16
Alignment explanation
Indices: 128558202--128558260 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
128558192 AGATTAGATC
128558202 ATTTTAGA-TTCTGATT
1 ATTTTAGAGTT-TGATT
*
128558218 ATTTT-GAGTTTTATTT
1 ATTTTAGAGTTTGA-TT
128558234 ATTTTA-AGTTTTGATT
1 ATTTTAGAG-TTTGATT
128558250 ATTTTAG-GTTT
1 ATTTTAGAGTTT
128558261 AAGTCATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
15 7 0.19
16 25 0.69
17 4 0.11
ACGTcount: A:0.22, C:0.02, G:0.14, T:0.63
Consensus pattern (16 bp):
ATTTTAGAGTTTGATT
Found at i:128572447 original size:2 final size:2
Alignment explanation
Indices: 128572440--128572467 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
128572430 ACCTGTGGTT
128572440 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
128572468 AGCAGTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:128574783 original size:19 final size:19
Alignment explanation
Indices: 128574745--128574791 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
128574735 TCATTACTTA
*
128574745 TTAATTATAATTCGAGATT
1 TTAATTATAATACGAGATT
**
128574764 TTAATTATAATACGTTATT
1 TTAATTATAATACGAGATT
128574783 TTAAGTTAT
1 TTAA-TTAT
128574792 TCAAATCTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (19 bp):
TTAATTATAATACGAGATT
Found at i:128578638 original size:4 final size:4
Alignment explanation
Indices: 128578631--128578694 Score: 83
Period size: 4 Copynumber: 16.0 Consensus size: 4
128578621 GTATGTATTA
* * *
128578631 GTGC GTGC GTGC GTGC GTGC GTGC ATGT GTGC GTGC GTGC GTGT GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
* *
128578679 ATGT GTGC GTGC GTGC
1 GTGC GTGC GTGC GTGC
128578695 ATGCATGCAT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.03, C:0.20, G:0.47, T:0.30
Consensus pattern (4 bp):
GTGC
Found at i:128578667 original size:24 final size:24
Alignment explanation
Indices: 128578635--128578705 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
128578625 GTATTAGTGC
128578635 GTGCGTGCGTGCGTGCGTGCATGT
1 GTGCGTGCGTGCGTGCGTGCATGT
*
128578659 GTGCGTGCGTGCGTGTGTGCATGT
1 GTGCGTGCGTGCGTGCGTGCATGT
* *
128578683 GTGCGTGCGTGCATGCATGCATG
1 GTGCGTGCGTGCGTGCGTGCATG
128578706 CATGCATACA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.07, C:0.20, G:0.44, T:0.30
Consensus pattern (24 bp):
GTGCGTGCGTGCGTGCGTGCATGT
Found at i:128586145 original size:18 final size:20
Alignment explanation
Indices: 128586121--128586165 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
128586111 TCCGAAAAGT
*
128586121 AAGTTTAAAATTT-TATTTA
1 AAGTTTAAAATTTAAATTTA
128586140 AA-TTT-AAATTTAAATTTA
1 AAGTTTAAAATTTAAATTTA
128586158 AAGTTTAA
1 AAGTTTAA
128586166 CTCGCCTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 6 0.27
18 10 0.45
19 5 0.23
20 1 0.05
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (20 bp):
AAGTTTAAAATTTAAATTTA
Found at i:128586146 original size:6 final size:6
Alignment explanation
Indices: 128586135--128586165 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
128586125 TTAAAATTTT
128586135 ATTTAA ATTTAA ATTTAA ATTTAA AGTTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA A-TTTAA
128586166 CTCGCCTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.79
7 5 0.21
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:128587556 original size:23 final size:22
Alignment explanation
Indices: 128587518--128587562 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
128587508 AGGGTTTTGG
128587518 TCCCCTTTAAATAAAAATTTTA
1 TCCCCTTTAAATAAAAATTTTA
128587540 TCCCCTTTAAATAAAAATTTTA
1 TCCCCTTTAAATAAAAATTTTA
128587562 T
1 T
128587563 TCTATTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.18, G:0.00, T:0.42
Consensus pattern (22 bp):
TCCCCTTTAAATAAAAATTTTA
Found at i:128587614 original size:18 final size:17
Alignment explanation
Indices: 128587581--128587614 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
128587571 ATGATTAAAT
128587581 TAAAATTTAATTTAATA
1 TAAAATTTAATTTAATA
*
128587598 TAAAATTATACTTTAAT
1 TAAAATT-TAATTTAAT
128587615 TTTTAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAAATTTAATTTAATA
Found at i:128588793 original size:3 final size:3
Alignment explanation
Indices: 128588785--128588815 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
128588775 AATTGGTGAT
128588785 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
128588816 GTGATGAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:128591597 original size:17 final size:18
Alignment explanation
Indices: 128591572--128591608 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
128591562 TTATTTAAAA
128591572 ATTATAAAT-ATGTAAATT
1 ATTATAAATGATG-AAATT
128591590 ATTA-AAATGATGAAATT
1 ATTATAAATGATGAAATT
128591607 AT
1 AT
128591609 ATTTTCACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (18 bp):
ATTATAAATGATGAAATT
Found at i:128601565 original size:15 final size:15
Alignment explanation
Indices: 128601545--128601574 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
128601535 TCTCTGATTG
128601545 AAAATAACATTTATT
1 AAAATAACATTTATT
128601560 AAAATAACATTTATT
1 AAAATAACATTTATT
128601575 TCTTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATAACATTTATT
Found at i:128601893 original size:50 final size:50
Alignment explanation
Indices: 128601818--128601918 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
128601808 ACTGCCGTTG
128601818 CAGAGTATTCACATATTGTTGTTTGATAGCAATCTGATATTATTTTAAAA
1 CAGAGTATTCACATATTGTTGTTTGATAGCAATCTGATATTATTTTAAAA
128601868 CAGAGTATTCACATATTGTTGTTTGATAGCAATCTGATATTATTTTAAAA
1 CAGAGTATTCACATATTGTTGTTTGATAGCAATCTGATATTATTTTAAAA
128601918 C
1 C
128601919 CATGTGTAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.42
Consensus pattern (50 bp):
CAGAGTATTCACATATTGTTGTTTGATAGCAATCTGATATTATTTTAAAA
Found at i:128602758 original size:38 final size:38
Alignment explanation
Indices: 128602711--128602792 Score: 139
Period size: 38 Copynumber: 2.2 Consensus size: 38
128602701 ATGAACATGT
*
128602711 AGATATGGTAAAAGTACCATGGAGACCCTTATACTAAA
1 AGATTTGGTAAAAGTACCATGGAGACCCTTATACTAAA
*
128602749 AGATTTGGTAAAAGTACCATGGAGACCTTTATACTAAA
1 AGATTTGGTAAAAGTACCATGGAGACCCTTATACTAAA
128602787 AG-TTTG
1 AGATTTG
128602793 ATTACATTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
37 4 0.10
38 38 0.90
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (38 bp):
AGATTTGGTAAAAGTACCATGGAGACCCTTATACTAAA
Found at i:128603304 original size:6 final size:6
Alignment explanation
Indices: 128603293--128603325 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
128603283 CAGCGACAAT
128603293 AAAATA AAAATA AAAATA AAAATA AAAA-A AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
128603326 CATTCAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (6 bp):
AAAATA
Found at i:128605683 original size:46 final size:46
Alignment explanation
Indices: 128605631--128605719 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
128605621 TGAAATATAC
* *
128605631 TAAATTGATTATTGAATACGTTAATGTTCTCTTGTTAAATTGACTA
1 TAAATTGATCATTGAATACGTAAATGTTCTCTTGTTAAATTGACTA
* * *
128605677 TAAATTGATCATTGAATACGTAAATTTTCTTTTGTTGAATTGA
1 TAAATTGATCATTGAATACGTAAATGTTCTCTTGTTAAATTGA
128605720 TAAAAGGTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (46 bp):
TAAATTGATCATTGAATACGTAAATGTTCTCTTGTTAAATTGACTA
Found at i:128606306 original size:29 final size:29
Alignment explanation
Indices: 128606274--128606343 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
128606264 ATTAGTAAAG
128606274 ATAAAATTATACTTTAACTTCTT-AAAATT
1 ATAAAATTATA-TTTAACTTCTTAAAAATT
* *
128606303 ATAAAAAATTA-ATTTAATTTTTTAAAAATT
1 AT--AAAATTATATTTAACTTCTTAAAAATT
*
128606333 ATAAAAATATA
1 ATAAAATTATA
128606344 AATTATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
28 6 0.18
29 12 0.35
30 9 0.26
31 7 0.21
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (29 bp):
ATAAAATTATATTTAACTTCTTAAAAATT
Found at i:128606729 original size:9 final size:9
Alignment explanation
Indices: 128606697--128606741 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
128606687 ATATAAAATT
128606697 AAAT-TTAA
1 AAATATTAA
*
128606705 AAATA-TAT
1 AAATATTAA
128606713 AAATATTAA
1 AAATATTAA
*
128606722 ATATATTAA
1 AAATATTAA
128606731 AAATATTAA
1 AAATATTAA
128606740 AA
1 AA
128606742 TAAATATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
8 11 0.35
9 20 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AAATATTAA
Found at i:128606734 original size:26 final size:24
Alignment explanation
Indices: 128606686--128606750 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 24
128606676 AATATCATTT
128606686 TATATAAAATT-AA-ATTTAAAAA
1 TATATAAAATTAAATATTTAAAAA
128606708 TATATAAATATTAAATATATTAAAAA
1 TATATAAA-ATTAAATAT-TTAAAAA
128606734 TAT-TAAAA-TAAATATTT
1 TATATAAAATTAAATATTT
128606751 TTCAATAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
22 10 0.26
23 10 0.26
24 3 0.08
25 6 0.15
26 10 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TATATAAAATTAAATATTTAAAAA
Found at i:128607521 original size:15 final size:16
Alignment explanation
Indices: 128607501--128607531 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
128607491 TTAAAAAGTG
128607501 AATTAATT-ATTTTTA
1 AATTAATTAATTTTTA
128607516 AATTAATTAATTTTTA
1 AATTAATTAATTTTTA
128607532 TCGTTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTAATTAATTTTTA
Found at i:128608143 original size:14 final size:14
Alignment explanation
Indices: 128608120--128608150 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
128608110 GCCAAGGTGG
*
128608120 TGGTGGTGGTGAAC
1 TGGTGATGGTGAAC
128608134 TGGTGATGGTGAAC
1 TGGTGATGGTGAAC
128608148 TGG
1 TGG
128608151 CGGGAGATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.48, T:0.29
Consensus pattern (14 bp):
TGGTGATGGTGAAC
Found at i:128614217 original size:26 final size:27
Alignment explanation
Indices: 128614173--128614223 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
128614163 AATTTAAAAA
*
128614173 TTTTTATCTTTGAATATATATATAATC
1 TTTTTATCTTTGAATATATACATAATC
*
128614200 TTTTTATCTTTTAA-ATATACATAA
1 TTTTTATCTTTGAATATATACATAA
128614224 ATAATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (27 bp):
TTTTTATCTTTGAATATATACATAATC
Found at i:128619542 original size:35 final size:35
Alignment explanation
Indices: 128619451--128619617 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
128619441 CATGGCAAAG
*
128619451 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
*
128619486 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
128619521 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTA-T-T---ATCCATACTGAGT
** * * *
128619561 TAAGAAATATAGGTATGGCATT-TCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATTAT-CCATACTGAGT
**
128619596 TGAAAAATGTAGGTATGGTATT
1 TGTGAAATGTAGGTATGGTATT
128619618 TCAATGAGGA
Statistics
Matches: 114, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 81 0.71
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 28 0.25
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.34
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
Found at i:128619574 original size:75 final size:75
Alignment explanation
Indices: 128619451--128619621 Score: 212
Period size: 75 Copynumber: 2.4 Consensus size: 75
128619441 CATGGCAAAG
** * *
128619451 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATATAGGTATGGCATT-TC
*
128619510 CCATACTGAGC
65 CCATACCGAGC
128619521 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATATAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATATAGGTATGGCATTTCC
*
128619586 CATACCGAGT
66 CATACCGAGC
**
128619596 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
128619622 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 5 0.06
75 60 0.69
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATATAGGTATGGCATTTCC
CATACCGAGC
Found at i:128626492 original size:43 final size:43
Alignment explanation
Indices: 128626442--128626523 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
128626432 AAAGAAGACA
*
128626442 AATTAGTGAGCATATTATAAAG-TTGATTAAATTAAAATGAAAC
1 AATTAGTGAGAATATT-TAAAGTTTGATTAAATTAAAATGAAAC
128626485 AATTAGTGAGAATATTTAAAGTTTGATTAAATTAAAATG
1 AATTAGTGAGAATATTTAAAGTTTGATTAAATTAAAATG
128626524 GAGGATAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
42 5 0.14
43 32 0.86
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (43 bp):
AATTAGTGAGAATATTTAAAGTTTGATTAAATTAAAATGAAAC
Found at i:128628269 original size:24 final size:24
Alignment explanation
Indices: 128628228--128628274 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
128628218 GTTCCAATAT
128628228 TTAAATATATATAAATATTTAAAAA
1 TTAAATATATATAAATA-TTAAAAA
* *
128628253 TTAAA-ATTTATACATATTAAAA
1 TTAAATATATATAAATATTAAAA
128628275 GTCGATTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 9 0.45
25 5 0.25
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
TTAAATATATATAAATATTAAAAA
Found at i:128633062 original size:19 final size:19
Alignment explanation
Indices: 128633038--128633077 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
128633028 TCTACATTCT
128633038 TTGTTAGAGTTTAAGTGTG
1 TTGTTAGAGTTTAAGTGTG
128633057 TTGTTAGAGTTTAAGTGTG
1 TTGTTAGAGTTTAAGTGTG
128633076 TT
1 TT
128633078 AAAGTGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (19 bp):
TTGTTAGAGTTTAAGTGTG
Found at i:128633251 original size:34 final size:32
Alignment explanation
Indices: 128633175--128633274 Score: 96
Period size: 34 Copynumber: 3.0 Consensus size: 32
128633165 TCTATAATAA
*
128633175 AAATTATTATACGAATAAATTTT-T-TATTTTT
1 AAATTATTATA-AAATAAATTTTATATATTTTT
*
128633206 ATAATTTTTATAATAATAAATTTTATATATTTGTT
1 A-AATTATTATAA-AATAAATTTTATATATTT-TT
**
128633241 AAATTATTATACAAATAAAAATTATATATATTTT
1 AAATTATTATA-AAATAAATTTTATATAT-TTTT
128633275 GAAAATAACA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
31 1 0.02
32 19 0.33
33 1 0.02
34 30 0.53
35 6 0.11
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (32 bp):
AAATTATTATAAAATAAATTTTATATATTTTT
Found at i:128633677 original size:21 final size:21
Alignment explanation
Indices: 128633653--128633696 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
128633643 ATAATAAGTT
128633653 TTAAAAATA-TAATAAAAAATA
1 TTAAAAATATTAA-AAAAAATA
*
128633674 TTAAAAATATTAAAATAAATA
1 TTAAAAATATTAAAAAAAATA
128633695 TT
1 TT
128633697 TCTCAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
TTAAAAATATTAAAAAAAATA
Found at i:128633886 original size:11 final size:11
Alignment explanation
Indices: 128633872--128633901 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
128633862 AAACAGTAAG
128633872 AAAATAACAAT
1 AAAATAACAAT
*
128633883 AAAATAGCAAT
1 AAAATAACAAT
128633894 AAAATAAC
1 AAAATAAC
128633902 CTTACCTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.70, C:0.10, G:0.03, T:0.17
Consensus pattern (11 bp):
AAAATAACAAT
Found at i:128634580 original size:15 final size:15
Alignment explanation
Indices: 128634560--128634589 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
128634550 CACTCATTCT
128634560 TGGGTAAAATAAAGC
1 TGGGTAAAATAAAGC
128634575 TGGGTAAAATAAAGC
1 TGGGTAAAATAAAGC
128634590 AAGTTGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.27, T:0.20
Consensus pattern (15 bp):
TGGGTAAAATAAAGC
Found at i:128639458 original size:142 final size:143
Alignment explanation
Indices: 128639264--128639554 Score: 460
Period size: 142 Copynumber: 2.0 Consensus size: 143
128639254 TCAACTACAC
* *
128639264 TTATTAGGGAACTCAAAGAGCTCCTTAAGAGATCAAACAATTAATCACTAATGAAAGTTAAGTAT
1 TTATTAGAGAACTCAAAGAGCTCCTTAAGAGATCAAACAATTAATCACTAATGAAACTTAAGTAT
* *
128639329 TCAAACAAACATGAAACCACATAACCAAGTTCATTAGGTTCCACATACAATCAAACCACAATAAT
66 TCAAACAAACATGAAACCACATAACCAAGTTCATTAGGTTCCACATACAAGCAAACCACAACAAT
128639394 T-ACTTATTAGTTA
131 TAAC-TATTAGTTA
* *
128639407 TTATTAGAGAACTCAAAGAGCTCCTT-AGAGATCAAACAATTAATCATTAATGAAACTTCAGTAT
1 TTATTAGAGAACTCAAAGAGCTCCTTAAGAGATCAAACAATTAATCACTAATGAAACTTAAGTAT
* * * *
128639471 TCAAACAAACATTAAACCACGTAACCAAGTTCATTAGGTTCCATATACAAGCAAGCCACAACAAT
66 TCAAACAAACATGAAACCACATAACCAAGTTCATTAGGTTCCACATACAAGCAAACCACAACAAT
128639536 TAACTATTAGTTA
131 TAACTATTAGTTA
*
128639549 TAATTA
1 TTATTA
128639555 ATTTATCTGG
Statistics
Matches: 136, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
142 109 0.80
143 27 0.20
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (143 bp):
TTATTAGAGAACTCAAAGAGCTCCTTAAGAGATCAAACAATTAATCACTAATGAAACTTAAGTAT
TCAAACAAACATGAAACCACATAACCAAGTTCATTAGGTTCCACATACAAGCAAACCACAACAAT
TAACTATTAGTTA
Found at i:128644153 original size:19 final size:19
Alignment explanation
Indices: 128644129--128644170 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
128644119 TTAGAGTATA
128644129 TTTTAAAAAATATTATTGT
1 TTTTAAAAAATATTATTGT
128644148 TTTTAAAAAATATTATTGT
1 TTTTAAAAAATATTATTGT
128644167 TTTT
1 TTTT
128644171 TTTTTTTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTTAAAAAATATTATTGT
Found at i:128649484 original size:14 final size:14
Alignment explanation
Indices: 128649465--128649499 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
128649455 CTACCATTTC
128649465 ATTATTATATTGCT
1 ATTATTATATTGCT
* *
128649479 ATTATTTTATTGTT
1 ATTATTATATTGCT
128649493 ATTATTA
1 ATTATTA
128649500 AAATATTGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.63
Consensus pattern (14 bp):
ATTATTATATTGCT
Found at i:128657757 original size:26 final size:26
Alignment explanation
Indices: 128657695--128657747 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
128657685 ATCTTTAAAG
128657695 ACTAAATCAAAATTCTATCATTTTTA
1 ACTAAATCAAAATTCTATCATTTTTA
128657721 ACTAAATCAAAATTCTATCATTTTTA
1 ACTAAATCAAAATTCTATCATTTTTA
128657747 A
1 A
128657748 AGTGGTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.42
Consensus pattern (26 bp):
ACTAAATCAAAATTCTATCATTTTTA
Found at i:128658580 original size:22 final size:23
Alignment explanation
Indices: 128658544--128658587 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
128658534 AGATGATCGA
128658544 AATTAAATATATAATTTAATATG
1 AATTAAATATATAATTTAATATG
* *
128658567 AATT-AATATGTAATTTTATAT
1 AATTAAATATATAATTTAATAT
128658588 TTTTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
AATTAAATATATAATTTAATATG
Found at i:128660096 original size:26 final size:27
Alignment explanation
Indices: 128660067--128660120 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
128660057 TCTAAATAGA
128660067 GATTTTA-TGATT-TTCTTCTTCTGTGT
1 GATTTTAGTG-TTATTCTTCTTCTGTGT
128660093 GATTTTAGTGTTCATTCTTCTTCTGTGT
1 GATTTTAGTGTT-ATTCTTCTTCTGTGT
128660121 TGGTTTCCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 9 0.36
27 2 0.08
28 14 0.56
ACGTcount: A:0.11, C:0.13, G:0.17, T:0.59
Consensus pattern (27 bp):
GATTTTAGTGTTATTCTTCTTCTGTGT
Found at i:128667996 original size:7 final size:7
Alignment explanation
Indices: 128667969--128668020 Score: 61
Period size: 7 Copynumber: 7.4 Consensus size: 7
128667959 CGAATTGATC
128667969 AATTTTA
1 AATTTTA
*
128667976 ATTTTTA
1 AATTTTA
*
128667983 TACTTTTA
1 -AATTTTA
128667991 AATTTTA
1 AATTTTA
128667998 AATTTTA
1 AATTTTA
*
128668005 AATTTTC
1 AATTTTA
128668012 AA-TTTA
1 AATTTTA
128668018 AAT
1 AAT
128668021 CTAGATATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
6 5 0.13
7 27 0.71
8 6 0.16
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (7 bp):
AATTTTA
Found at i:128673077 original size:20 final size:21
Alignment explanation
Indices: 128673038--128673079 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
128673028 AATTAATTTT
*
128673038 AATATTTTATGATATAAAATA
1 AATATTCTATGATATAAAATA
*
128673059 AATATTCTAT-ATTTAAAATA
1 AATATTCTATGATATAAAATA
128673079 A
1 A
128673080 TTAAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
AATATTCTATGATATAAAATA
Found at i:128675195 original size:36 final size:36
Alignment explanation
Indices: 128675155--128675226 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
128675145 GAGATCAAAT
*
128675155 GGTATGATGCATTGACAATAAGTACTATAATCACAA
1 GGTATGATGCATTGACAACAAGTACTATAATCACAA
128675191 GGTATGATGCATTGACAACAAGTACTATAATCACAA
1 GGTATGATGCATTGACAACAAGTACTATAATCACAA
128675227 ATCATATATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (36 bp):
GGTATGATGCATTGACAACAAGTACTATAATCACAA
Found at i:128675724 original size:136 final size:134
Alignment explanation
Indices: 128675359--128675747 Score: 370
Period size: 136 Copynumber: 2.8 Consensus size: 134
128675349 TCTCGAAAAA
* * * *
128675359 TGAACTCTGGTTCAAACATTGCATATAATATTGTTGGGAAAAAC-ATCTATAACCTTCGAAAAGA
1 TGAACTCTAGTTCAAAC-TTGCATATAATATTGTTGAGAGAAACAATC-ATAACCTT-GAAAAAA
* * * * * ** *
128675423 TTTCTCTTCGTGGACCGTAAAATAAATATAGAGTAATTGGGTGTAATAGTATGTCACATTACACT
63 TTACTCTTCGTGGACCGT-AAA-AGACATAGAGCAATTGGATGTAATAGTAACTCACATAACACT
128675488 CTCGACGAG
126 CTCGACGAG
* * * * * *
128675497 GGAAATCTTA-TTTAAACCTTGCAGATAATATAGTTGAGAGAAACAATCATAACCCTCGAAAAAG
1 TGAACTC-TAGTTCAAA-CTTGCATATAATATTGTTGAGAGAAACAATCATAA-CCTTGAAAAA-
* * * * * * *
128675561 ATTATTCTTCGTGGACTGTAATAGACATAGAGCAATTGGATGTAATGGTAACTCACGTAATACTT
62 ATTACTCTTCGTGGACCGTAAAAGACATAGAGCAATTGGATGTAATAGTAACTCACATAACACTC
*
128675626 TCGAGGAG
127 TCGACGAG
* * *
128675634 TGAACTCAAGTTCAAACTTGTATATAATATTGTAGAGAGAAACAATCATAACCTTGAAAAAATTA
1 TGAACTCTAGTTCAAACTTGCATATAATATTGTTGAGAGAAACAATCATAACCTTGAAAAAATTA
* *
128675699 CTCTTCGTGGACCATAAAACGGACATATAGCAATT-GAGTGTAATAGTAA
66 CTCTTCGTGGACCGTAAAA--GACATAGAGCAATTGGA-TGTAATAGTAA
128675748 GTCAGACTAC
Statistics
Matches: 201, Mismatches: 41, Indels: 20
0.77 0.16 0.08
Matches are distributed among these distances:
134 19 0.09
135 11 0.05
136 55 0.27
137 49 0.24
138 43 0.21
139 24 0.12
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (134 bp):
TGAACTCTAGTTCAAACTTGCATATAATATTGTTGAGAGAAACAATCATAACCTTGAAAAAATTA
CTCTTCGTGGACCGTAAAAGACATAGAGCAATTGGATGTAATAGTAACTCACATAACACTCTCGA
CGAG
Found at i:128691651 original size:27 final size:28
Alignment explanation
Indices: 128691621--128691681 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 28
128691611 TATGTATATC
128691621 AGTTTTAGA-TAAAAATGTTAAAAT-TTA
1 AGTTTTA-ACTAAAAATGTTAAAATGTTA
*
128691648 AG-TTTAACTTAAAATGTTAAAATGTTA
1 AGTTTTAACTAAAAATGTTAAAATGTTA
*
128691675 AATTTTA
1 AGTTTTA
128691682 TTCAAATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 1 0.03
26 18 0.62
27 6 0.21
28 4 0.14
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.43
Consensus pattern (28 bp):
AGTTTTAACTAAAAATGTTAAAATGTTA
Done.