Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 170 of 325
Found at i:53599781 original size:30 final size:30
Alignment explanation
Indices: 53599745--53599802 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
53599735 TAAGAAAACT
* *
53599745 GAATAAAGAAATCCA-AGATAGAGAAACCCA
1 GAATAAAGAAAACCAGAG-TAAAGAAACCCA
53599775 GAATAAAGAAAACCAGAGTAAAGAAACC
1 GAATAAAGAAAACCAGAGTAAAGAAACC
53599803 TAAGATACGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.59, C:0.16, G:0.17, T:0.09
Consensus pattern (30 bp):
GAATAAAGAAAACCAGAGTAAAGAAACCCA
Found at i:53599784 original size:15 final size:15
Alignment explanation
Indices: 53599745--53599802 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
53599735 TAAGAAAACT
*
53599745 GAATAAAGAAATCCA
1 GAATAAAGAAACCCA
*
53599760 -AGATAGAGAAACCCA
1 GA-ATAAAGAAACCCA
*
53599775 GAATAAAGAAAACCA
1 GAATAAAGAAACCCA
*
53599790 GAGTAAAGAAACC
1 GAATAAAGAAACC
53599803 TAAGATACGA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 1 0.03
15 33 0.94
16 1 0.03
ACGTcount: A:0.59, C:0.16, G:0.17, T:0.09
Consensus pattern (15 bp):
GAATAAAGAAACCCA
Found at i:53602872 original size:49 final size:49
Alignment explanation
Indices: 53602816--53603040 Score: 281
Period size: 49 Copynumber: 4.5 Consensus size: 49
53602806 CTGGTACGCA
* * * *
53602816 TAGTAGCCTACACATAGTACTACACATGCGACCAATTATCCAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCAGTACACG
*
53602865 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCAGTACACG
* ** *
53602914 TAATAGCCTGCACTTAGTACTACACACGTGACCTAACCAT-CTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCAG-TACACG
* * * * *
53602964 TAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGAGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAATTATCCAGTACACG
53603015 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
53603041 TGCGACCTCA
Statistics
Matches: 153, Mismatches: 18, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
49 78 0.51
50 40 0.26
51 33 0.22
52 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCAGTACACG
Found at i:53602980 original size:99 final size:101
Alignment explanation
Indices: 53602859--53603040 Score: 289
Period size: 99 Copynumber: 1.8 Consensus size: 101
53602849 AATTATCCAG
*
53602859 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAATTATCCG-GTACACGTAATAGC
1 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAATT-TCCGAGTACACATAATAGC
53602921 CTGCACTTAGTACTACACACGTGACCTAACCATCTGA
65 CTGCACTTAGTACTACACACGTGACCTAACCATCTGA
* * * *
53602958 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGAGTACGCATAGTAGCC
1 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAATTTCCGAGTACACATAATAGCC
53603023 TGCACTTAGTACTACACA
66 TGCACTTAGTACTACACA
53603041 TGCGACCTCA
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
99 37 0.49
100 4 0.05
101 34 0.45
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (101 bp):
TACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAATTTCCGAGTACACATAATAGCC
TGCACTTAGTACTACACACGTGACCTAACCATCTGA
Found at i:53609868 original size:26 final size:27
Alignment explanation
Indices: 53609839--53609898 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
53609829 CCACATATAT
*
53609839 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
53609865 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
53609892 ATATCTG
1 ATATCTG
53609899 CCAGCCTCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:53617395 original size:48 final size:48
Alignment explanation
Indices: 53617331--53617992 Score: 964
Period size: 48 Copynumber: 14.1 Consensus size: 48
53617321 TATATATGTG
*
53617331 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
* *
53617379 TGTGGTAAAGCTGAATGGCTAGTGTGAAATATGTATGAGACATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
53617427 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGACATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
53617475 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
* *
53617523 TGTGGTAAAGCCAAATGGCTAGTGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
53617571 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGAATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
53617619 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGACATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
53617667 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
* *
53617715 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGCATGAGAGATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
53617763 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
53617811 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATA-GCCGA-A
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATG--TATA
* ** * * * *
53617859 TG-GCTAGTG-TGAAAT--ATA-TATG--AGA--TAT--G-TAT----A
1 TGTGGTAAAGCCG-AATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
53617892 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
* *
53617940 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGATGTGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
53617988 TGTGG
1 TGTGG
53617993 AAGAGGTCGT
Statistics
Matches: 557, Mismatches: 37, Indels: 40
0.88 0.06 0.06
Matches are distributed among these distances:
33 3 0.01
34 7 0.01
35 1 0.00
36 2 0.00
37 5 0.01
38 1 0.00
39 2 0.00
40 3 0.01
41 3 0.01
42 2 0.00
43 1 0.00
44 6 0.01
45 2 0.00
46 1 0.00
47 8 0.01
48 509 0.91
49 1 0.00
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.30
Consensus pattern (48 bp):
TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
Found at i:53617591 original size:144 final size:144
Alignment explanation
Indices: 53617331--53617992 Score: 1084
Period size: 144 Copynumber: 4.7 Consensus size: 144
53617321 TATATATGTG
* * *
53617331 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCTGAATG
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATG
*
53617396 GCTAGTGTGAAATATGTATGAGACATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGT
66 GCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGT
*
53617461 ATGAGACATGTATA
131 ATGAGATATGTATA
*
53617475 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCAAATG
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATG
* *
53617540 GCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGA
66 GCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGT
53617605 ATGAGATATGTATA
131 ATGAGATATGTATA
* *
53617619 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGACATATGTATATGTGGTAAAGCCGAATG
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATG
*
53617684 GCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGC
66 GCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGT
*
53617749 ATGAGAGATGTATA
131 ATGAGATATGTATA
53617763 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATG
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATG
*
53617828 GCTAGTGTGAAATATGTAT--G--A-G---A-----T--AGCCGAATGGCTAGTGTGAAATATAT
66 GCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGT
53617878 ATGAGATATGTATA
131 ATGAGATATGTATA
53617892 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATG
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATG
* *
53617957 GCTAGTGTGAAATATGTAGGAGATGTGTATATGTGG
66 GCTAGTGTGAAATATGTATGAGATATGTATATGTGG
53617993 AAGAGGTCGT
Statistics
Matches: 484, Mismatches: 21, Indels: 28
0.91 0.04 0.05
Matches are distributed among these distances:
129 120 0.25
131 2 0.00
134 1 0.00
136 1 0.00
137 1 0.00
139 1 0.00
140 1 0.00
142 1 0.00
144 356 0.74
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.30
Consensus pattern (144 bp):
TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATG
GCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGT
ATGAGATATGTATA
Found at i:53617857 original size:81 final size:81
Alignment explanation
Indices: 53617771--53617933 Score: 317
Period size: 81 Copynumber: 2.0 Consensus size: 81
53617761 TATGTGGTAA
53617771 AGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGT
1 AGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGT
*
53617836 GAAATATGTATGAGAT
66 GAAATATATATGAGAT
53617852 AGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGT
1 AGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGT
53617917 GAAATATATATGAGAT
66 GAAATATATATGAGAT
53617933 A
1 A
53617934 TGTATATGTG
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.36, C:0.07, G:0.28, T:0.29
Consensus pattern (81 bp):
AGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGT
GAAATATATATGAGAT
Found at i:53617859 original size:33 final size:33
Alignment explanation
Indices: 53617819--53617885 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
53617809 TATGTGGTAA
*
53617819 AGCCGAATGGCTAGTGTGAAATATGTATGAGAT
1 AGCCGAATGGCTAGTGTGAAATATATATGAGAT
53617852 AGCCGAATGGCTAGTGTGAAATATATATGAGAT
1 AGCCGAATGGCTAGTGTGAAATATATATGAGAT
53617885 A
1 A
53617886 TGTATATGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.27
Consensus pattern (33 bp):
AGCCGAATGGCTAGTGTGAAATATATATGAGAT
Found at i:53617869 original size:129 final size:129
Alignment explanation
Indices: 53617723--53617980 Score: 480
Period size: 129 Copynumber: 2.0 Consensus size: 129
53617713 TATGTGGTAA
*
53617723 AGCCGAATGGCTAGTGTGAAATATGCATGAGAGATGTATATGTGGTAAAGCCGAATGGCTAGTGT
1 AGCCGAATGGCTAGTGTGAAATATACATGAGAGATGTATATGTGGTAAAGCCGAATGGCTAGTGT
*
53617788 GAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAT
66 GAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAT
* *
53617852 AGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGT
1 AGCCGAATGGCTAGTGTGAAATATACATGAGAGATGTATATGTGGTAAAGCCGAATGGCTAGTGT
53617917 GAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAT
66 GAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAT
53617981 GTGTATATGT
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
129 125 1.00
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.29
Consensus pattern (129 bp):
AGCCGAATGGCTAGTGTGAAATATACATGAGAGATGTATATGTGGTAAAGCCGAATGGCTAGTGT
GAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAT
Found at i:53619381 original size:46 final size:46
Alignment explanation
Indices: 53619328--53619499 Score: 194
Period size: 46 Copynumber: 3.7 Consensus size: 46
53619318 TGGGCATCCA
53619328 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
*
53619374 AACTCGTTGAGTTGAGTCCGAGTTCGA--TA--GATG-TAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGAA-T--G--TCCG
* * *
53619421 AGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG-CCTG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC-G
*
53619467 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53619500 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 6, Indels: 24
0.78 0.04 0.17
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 59 0.55
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
Found at i:53619479 original size:93 final size:93
Alignment explanation
Indices: 53619320--53619491 Score: 283
Period size: 93 Copynumber: 1.8 Consensus size: 93
53619310 AGGATATTTG
*
53619320 GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
53619385 TTGAGTCCGAGTTCGATAGATGTAACTA
66 TTGAGTCCGAGTTCGATAGATGTAACTA
* * * *
53619413 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGA
1 GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGA
53619477 GTTGAGTCCGAGTTC
65 GTTGAGTCCGAGTTC
53619492 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCGATAGATGTAACTA
Found at i:53625653 original size:28 final size:28
Alignment explanation
Indices: 53625621--53625690 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
53625611 AATGAGATTG
53625621 GCACTAAGTGTGCGAGTTT-AAT-TGTATA
1 GCACTAAGTGTGCGAGTTTGAATAT-TA-A
*
53625649 GCACTAAGTGTGCGAGTTTGACTATTAA
1 GCACTAAGTGTGCGAGTTTGAATATTAA
53625677 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
53625691 GACTTACTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 34 0.87
29 4 0.10
30 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.31
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGAATATTAA
Found at i:53629211 original size:27 final size:26
Alignment explanation
Indices: 53629167--53629218 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
53629157 GGACTACCGA
* *
53629167 TTTACCCCTGGAGGGTAAAATGACTAT
1 TTTACCCCTCGAGCGT-AAATGACTAT
*
53629194 TTTACCCCTCGTGCGTAAATGACTA
1 TTTACCCCTCGAGCGTAAATGACTA
53629219 ACTTGTGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (26 bp):
TTTACCCCTCGAGCGTAAATGACTAT
Found at i:53629442 original size:18 final size:18
Alignment explanation
Indices: 53629419--53629462 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
53629409 ATTTTGTGAA
53629419 CTCGTGAGCGTGTGAGCG
1 CTCGTGAGCGTGTGAGCG
53629437 CTCGTGAGCGTGTGAGCG
1 CTCGTGAGCGTGTGAGCG
53629455 CTCGTGAG
1 CTCGTGAG
53629463 ACAGTTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.11, C:0.23, G:0.43, T:0.23
Consensus pattern (18 bp):
CTCGTGAGCGTGTGAGCG
Found at i:53629445 original size:10 final size:10
Alignment explanation
Indices: 53629419--53629462 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 10
53629409 ATTTTGTGAA
53629419 CTCGTGAGCG
1 CTCGTGAGCG
53629429 -T-GTGAGCG
1 CTCGTGAGCG
53629437 CTCGTGAGCG
1 CTCGTGAGCG
53629447 -T-GTGAGCG
1 CTCGTGAGCG
53629455 CTCGTGAG
1 CTCGTGAG
53629463 ACAGTTGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 14 0.47
9 4 0.13
10 12 0.40
ACGTcount: A:0.11, C:0.23, G:0.43, T:0.23
Consensus pattern (10 bp):
CTCGTGAGCG
Found at i:53629877 original size:27 final size:26
Alignment explanation
Indices: 53629833--53629884 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
53629823 TTCGCTGCAA
*
53629833 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
53629860 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
53629885 GCAGCCTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:53631739 original size:31 final size:28
Alignment explanation
Indices: 53631715--53631925 Score: 163
Period size: 29 Copynumber: 7.2 Consensus size: 28
53631705 TTTTCTTTTA
*
53631715 ATTGATGGTCAAAACCATCCCTTTTCAT
1 ATTGATGGTCGAAACCATCCCTTTTCAT
*
53631743 ATTCGATGGTCGAAGCCATCCCTTTTCAT
1 ATT-GATGGTCGAAACCATCCCTTTTCAT
* ** *
53631772 ATTCGATGATCGTCACCATCTCTTTTCAT
1 ATT-GATGGTCGAAACCATCCCTTTTCAT
*
53631801 AGTTGATGGTC-ATCACCATCCCTTTTCAT
1 A-TTGATGGTCGA-AACCATCCCTTTTCAT
* * *
53631830 AGTTGATAGTCGAAACTATCCCTTTTAATT
1 A-TTGATGGTCGAAACCATCCCTTTTCA-T
* * ** *
53631860 AATAGATGGTTGTCACAATCCCTTTTCAT
1 -ATTGATGGTCGAAACCATCCCTTTTCAT
* * * *
53631889 AGTTGATAGTTGAAACTATCCATTTTCAT
1 A-TTGATGGTCGAAACCATCCCTTTTCAT
53631918 ATTCGATG
1 ATT-GATG
53631926 CTTGTCTATA
Statistics
Matches: 147, Mismatches: 28, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
28 6 0.04
29 117 0.80
30 23 0.16
31 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (28 bp):
ATTGATGGTCGAAACCATCCCTTTTCAT
Found at i:53631855 original size:58 final size:57
Alignment explanation
Indices: 53631716--53631925 Score: 185
Period size: 58 Copynumber: 3.6 Consensus size: 57
53631706 TTTCTTTTAA
* *
53631716 TTGATGGTCAAAACCATCCCTTTTCATATTCGATGGTCGA--AGCCATCCCTTTTCATA-
1 TTGATAGTCGAAACCATCCCTTTTCATATT-GATGGTC-ATCA-CCATCCCTTTTCATAG
** *
53631773 TTCGAT-GATCGTCACCATCTCTTTTCATAGTTGATGGTCATCACCATCCCTTTTCATAG
1 TT-GATAG-TCGAAACCATCCCTTTTCATA-TTGATGGTCATCACCATCCCTTTTCATAG
* * * ** *
53631832 TTGATAGTCGAAACTATCCCTTTTAATTAATAGATGGTTGTCACAATCCCTTTTCATAG
1 TTGATAGTCGAAACCATCCCTTTTCA-T-ATTGATGGTCATCACCATCCCTTTTCATAG
* * *
53631891 TTGATAGTTGAAACTATCCATTTTCATATTCGATG
1 TTGATAGTCGAAACCATCCCTTTTCATATT-GATG
53631926 CTTGTCTATA
Statistics
Matches: 126, Mismatches: 17, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
57 6 0.05
58 64 0.51
59 55 0.44
60 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (57 bp):
TTGATAGTCGAAACCATCCCTTTTCATATTGATGGTCATCACCATCCCTTTTCATAG
Found at i:53632708 original size:5 final size:5
Alignment explanation
Indices: 53632698--53632739 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
53632688 AGATTTTCGG
53632698 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TT
53632740 ATCAAATCGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:53637246 original size:40 final size:39
Alignment explanation
Indices: 53637191--53637277 Score: 138
Period size: 40 Copynumber: 2.2 Consensus size: 39
53637181 ATACTATTTG
* *
53637191 ATTCAGTGATACCAAAGTACAAACAGGGTCACGTATGTGC
1 ATTCAG-GATACCAAAGTACAAACAGGGGCACATATGTGC
53637231 ATTCAGGCATACCAAAGTACAAACAGGGGCACATATGTGC
1 ATTCAGG-ATACCAAAGTACAAACAGGGGCACATATGTGC
53637271 ATTCAGG
1 ATTCAGG
53637278 GGCACTGAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
39 1 0.02
40 43 0.98
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21
Consensus pattern (39 bp):
ATTCAGGATACCAAAGTACAAACAGGGGCACATATGTGC
Found at i:53641157 original size:29 final size:28
Alignment explanation
Indices: 53641115--53641204 Score: 128
Period size: 29 Copynumber: 3.1 Consensus size: 28
53641105 GTGTACTAAA
*
53641115 CGATGGTCAAAACCATCCCTTCTCATATT
1 CGATGGTC-AAACCATCCCTTTTCATATT
53641144 CGATGGTCGAAACCATCCCTTTTCATATT
1 CGATGGTC-AAACCATCCCTTTTCATATT
*
53641173 CGATGGTCATCACCATCCCTTTTC-TATT
1 CGATGGTCA-AACCATCCCTTTTCATATT
53641201 CGAT
1 CGAT
53641205 AGGTGTCGAT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
28 9 0.16
29 48 0.84
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.34
Consensus pattern (28 bp):
CGATGGTCAAACCATCCCTTTTCATATT
Found at i:53647421 original size:28 final size:28
Alignment explanation
Indices: 53647358--53647455 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
53647348 ATATTAAGTC
*
53647358 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
53647385 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * *
53647413 CGCACACTTAGTGCTGA-ACAATTTAAACC
1 CGCACACTTAGTGCT-ATATAA-TCAAACT
53647442 CGCACACTTAGTGC
1 CGCACACTTAGTGC
53647456 CAATCTCATG
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 22 0.34
28 22 0.34
29 20 0.31
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:53655411 original size:28 final size:28
Alignment explanation
Indices: 53655349--53655445 Score: 126
Period size: 28 Copynumber: 3.5 Consensus size: 28
53655339 ATATTAAGTC
*
53655349 CGCACAC-CAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
53655375 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
53655403 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
53655432 CGCACACTTAGTGC
1 CGCACACTTAGTGC
53655446 CAATCTCATG
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
26 7 0.11
27 14 0.22
28 23 0.37
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:53656536 original size:11 final size:11
Alignment explanation
Indices: 53656520--53656566 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
53656510 GAAACCAACA
53656520 TTTTGTCTTTC
1 TTTTGTCTTTC
*
53656531 TTTTGTTTTTC
1 TTTTGTCTTTC
* *
53656542 TATTATCCTTTC
1 TTTTGT-CTTTC
53656554 TTTT-TCTTTC
1 TTTTGTCTTTC
53656564 TTT
1 TTT
53656567 AGCTCACGGC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
10 8 0.27
11 15 0.50
12 7 0.23
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.74
Consensus pattern (11 bp):
TTTTGTCTTTC
Found at i:53660870 original size:8 final size:8
Alignment explanation
Indices: 53660857--53660900 Score: 52
Period size: 8 Copynumber: 5.0 Consensus size: 8
53660847 TTATACAAGT
53660857 TAAAAAAA
1 TAAAAAAA
53660865 TAAAAAAA
1 TAAAAAAA
53660873 TTGAAAAAAAA
1 -T--AAAAAAA
53660884 TGAAAAAAA
1 T-AAAAAAA
53660893 TAAAAAAA
1 TAAAAAAA
53660901 AAGAGTGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 15 0.47
9 9 0.28
10 1 0.03
11 7 0.22
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.14
Consensus pattern (8 bp):
TAAAAAAA
Found at i:53660902 original size:10 final size:9
Alignment explanation
Indices: 53660858--53660901 Score: 61
Period size: 9 Copynumber: 4.8 Consensus size: 9
53660848 TATACAAGTT
53660858 AAAAAAATA
1 AAAAAAATA
*
53660867 AAAAAATTGA
1 AAAAAAAT-A
*
53660877 AAAAAAATG
1 AAAAAAATA
53660886 AAAAAAATA
1 AAAAAAATA
53660895 AAAAAAA
1 AAAAAAA
53660902 AGAGTGATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 22 0.73
10 8 0.27
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (9 bp):
AAAAAAATA
Found at i:53660902 original size:19 final size:19
Alignment explanation
Indices: 53660858--53660902 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
53660848 TATACAAGTT
*
53660858 AAAAAAATAAAAAAATTGA
1 AAAAAAATAAAAAAATTAA
53660877 AAAAAAATGAAAAAAA-TAA
1 AAAAAAAT-AAAAAAATTAA
53660896 AAAAAAA
1 AAAAAAA
53660903 GAGTGATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.84, C:0.00, G:0.04, T:0.11
Consensus pattern (19 bp):
AAAAAAATAAAAAAATTAA
Found at i:53669179 original size:24 final size:25
Alignment explanation
Indices: 53669152--53669205 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
53669142 ATGAGTGATA
*
53669152 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
53669176 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
53669200 AAAAAA
1 AAAAAA
53669206 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:53673953 original size:19 final size:19
Alignment explanation
Indices: 53673929--53673968 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
53673919 AGCTCCCATG
53673929 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
53673948 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
53673967 TA
1 TA
53673969 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:53675231 original size:14 final size:14
Alignment explanation
Indices: 53675209--53675256 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
53675199 ACCTAAACCG
* *
53675209 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
53675223 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
53675237 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
53675251 ACCATT
1 ACCATT
53675257 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:53676428 original size:18 final size:18
Alignment explanation
Indices: 53676405--53676454 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
53676395 GAAAGAAAAA
*
53676405 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* *
53676423 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
53676441 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
53676455 AAAAGAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:53676431 original size:24 final size:24
Alignment explanation
Indices: 53676398--53676479 Score: 92
Period size: 24 Copynumber: 3.4 Consensus size: 24
53676388 AAGAAATGAA
53676398 AGAAAAAGAAAAAGAGATTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
* * * *
53676422 TGAAAAAGAAAATGAGATTGAAAA
1 AGAAAAAGAAAAAGAGATTGAGAG
* * *
53676446 AGAGAATGAAAAAGAGTTTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
*
53676470 AGAGAAAGAA
1 AGAAAAAGAA
53676480 TGTGAACAAG
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (24 bp):
AGAAAAAGAAAAAGAGATTGAGAG
Found at i:53676927 original size:22 final size:22
Alignment explanation
Indices: 53676893--53676936 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
53676883 TTTGGTATTT
*
53676893 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGATACGAAATGGTAA
*
53676915 GGGATTTGATACGAAATGGTAA
1 GGGAATTGATACGAAATGGTAA
53676937 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.34, T:0.25
Consensus pattern (22 bp):
GGGAATTGATACGAAATGGTAA
Found at i:53680976 original size:20 final size:19
Alignment explanation
Indices: 53680953--53681017 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
53680943 AAGCTCAAAC
53680953 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
53680973 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
53680993 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
53681013 GAGCT
1 GAGCT
53681018 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:53684368 original size:30 final size:30
Alignment explanation
Indices: 53684334--53684430 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
53684324 AGCTCACTCC
53684334 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
53684364 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* * *
53684394 CAGCTCAACTTTAGCTCACGGGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
53684424 TAGCTCA
1 TAGCTCA
53684431 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:53685999 original size:20 final size:20
Alignment explanation
Indices: 53685970--53686023 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
53685960 CATTTTTCCC
*
53685970 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
53685990 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
53686010 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
53686024 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:53686005 original size:30 final size:30
Alignment explanation
Indices: 53685970--53686043 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
53685960 CATTTTTCCC
53685970 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
53686000 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
53686030 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
53686044 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:53686033 original size:20 final size:20
Alignment explanation
Indices: 53685970--53686034 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
53685960 CATTTTTCCC
* * * *
53685970 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
53685990 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
53686009 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
53686030 AGCTC
1 AGCTC
53686035 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:53687657 original size:11 final size:11
Alignment explanation
Indices: 53687641--53687674 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
53687631 AAAAGAGAAG
53687641 AAATTCAAAAA
1 AAATTCAAAAA
53687652 AAATTC-AAAA
1 AAATTCAAAAA
*
53687662 AAATTGAAAAA
1 AAATTCAAAAA
53687673 AA
1 AA
53687675 GGAAAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.18
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:53687663 original size:10 final size:10
Alignment explanation
Indices: 53687641--53687674 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
53687631 AAAAGAGAAG
53687641 AAATTCAAAAA
1 AAATTC-AAAA
53687652 AAATTCAAAA
1 AAATTCAAAA
*
53687662 AAATTGAAAA
1 AAATTCAAAA
53687672 AAA
1 AAA
53687675 GGAAAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 16 0.73
11 6 0.27
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.18
Consensus pattern (10 bp):
AAATTCAAAA
Found at i:53687732 original size:12 final size:12
Alignment explanation
Indices: 53687668--53687733 Score: 53
Period size: 13 Copynumber: 5.2 Consensus size: 12
53687658 AAAAAAATTG
53687668 AAAAAAAG-GAA
1 AAAAAAAGTGAA
*
53687679 AAAAAGAAGTGAC
1 AAAAA-AAGTGAA
*
53687692 AAAAAAATTGAGTTA
1 AAAAAAAGTGA---A
*
53687707 AAAAAAAGAAGAA
1 AAAAAAAG-TGAA
53687720 AAAAAAAGTGAA
1 AAAAAAAGTGAA
53687732 AA
1 AA
53687734 GTCTTGCGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
11 5 0.12
12 13 0.30
13 16 0.37
15 7 0.16
16 2 0.05
ACGTcount: A:0.73, C:0.02, G:0.17, T:0.09
Consensus pattern (12 bp):
AAAAAAAGTGAA
Found at i:53688739 original size:6 final size:6
Alignment explanation
Indices: 53688711--53688850 Score: 64
Period size: 6 Copynumber: 22.3 Consensus size: 6
53688701 CCATTGACCG
* * * * * * *
53688711 AGAAAA GGAAAA AGAGAT TGAAAA AGAAAT TGAAAGA AAACAAA AAGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAA-A AGA-AAA A-GAAAA
* * * * * * ** *
53688762 CGAAAA AGAAAA AGAAAT TGCAAA AGAAAA AGAAAT CGAAAA AGTGAG
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
* *
53688810 AGAAAA AGAAAA TGAAGAAA AGAAAA TTGAAAA AGAAAA AG
1 AGAAAA AGAAAA AG-A-AAA AGAAAA -AGAAAA AGAAAA AG
53688851 CGAAAAAAGA
Statistics
Matches: 92, Mismatches: 36, Indels: 12
0.66 0.26 0.09
Matches are distributed among these distances:
6 72 0.78
7 13 0.14
8 7 0.08
ACGTcount: A:0.69, C:0.03, G:0.20, T:0.08
Consensus pattern (6 bp):
AGAAAA
Found at i:53688739 original size:18 final size:18
Alignment explanation
Indices: 53688712--53688805 Score: 86
Period size: 18 Copynumber: 5.4 Consensus size: 18
53688702 CATTGACCGA
* * *
53688712 GAAAAGGAAAAAGAGATT
1 GAAAAAGAAAAAGAAATC
**
53688730 GAAAAAGAAATTGAAA--
1 GAAAAAGAAAAAGAAATC
* *
53688746 G-AAAACAAAAAGAAAAC
1 GAAAAAGAAAAAGAAATC
*
53688763 GAAAAAGAAAAAGAAATT
1 GAAAAAGAAAAAGAAATC
*
53688781 GCAAAAGAAAAAGAAATC
1 GAAAAAGAAAAAGAAATC
53688799 GAAAAAG
1 GAAAAAG
53688806 TGAGAGAAAA
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
15 11 0.18
16 1 0.02
17 1 0.02
18 47 0.78
ACGTcount: A:0.69, C:0.04, G:0.19, T:0.07
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAATC
Found at i:53688759 original size:11 final size:12
Alignment explanation
Indices: 53688743--53688862 Score: 75
Period size: 12 Copynumber: 9.6 Consensus size: 12
53688733 AAAGAAATTG
53688743 AAAGAAAAC-AA
1 AAAGAAAACGAA
53688754 AAAGAAAACGAA
1 AAAGAAAACGAA
*
53688766 AAAGAAAAAGAA
1 AAAGAAAACGAA
**
53688778 ATTGCAAAA-GAA
1 AAAG-AAAACGAA
*
53688790 AAAGAAATCGAA
1 AAAGAAAACGAA
* *
53688802 AAAGTGAGA-GAA
1 AAAG-AAAACGAA
*
53688814 AAAGAAAATGAAGA
1 AAAGAAAACG-A-A
*
53688828 AAAGAAAATTGAA
1 AAAGAAAA-CGAA
53688841 AAAGAAAAAGCGAAA
1 AAAG-AAAA-CG-AA
53688856 AAAGAAA
1 AAAGAAA
53688863 TTGAAAGAGA
Statistics
Matches: 86, Mismatches: 13, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
11 14 0.16
12 35 0.41
13 11 0.13
14 18 0.21
15 8 0.09
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (12 bp):
AAAGAAAACGAA
Found at i:53688796 original size:81 final size:83
Alignment explanation
Indices: 53688711--53688865 Score: 190
Period size: 81 Copynumber: 1.9 Consensus size: 83
53688701 CCATTGACCG
* ** * *
53688711 AGAAAAGGAAAAAGAGATTGAAAAAGAAATTGAAAGAAAACAAAA-AGAAAACGAAAAA-G-AAA
1 AGAAAACGAAAAAGAGAGAGAAAAAGAAAATG-AAGAAAACAAAATAGAAAAAGAAAAACGAAAA
53688773 AAGAAATTGCAAAAGAAAA
65 AAGAAATTGCAAAAGAAAA
* * * *
53688792 AGAAATCGAAAAAGTGAGAGAAAAAGAAAATGAAGAAAAGAAAATTGAAAAAGAAAAAGCGAAAA
1 AGAAAACGAAAAAGAGAGAGAAAAAGAAAATGAAGAAAACAAAATAGAAAAAGAAAAA-CGAAAA
53688857 AAGAAATTG
65 AAGAAATTG
53688866 AAAGAGAGCT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
80 11 0.18
81 37 0.61
83 1 0.02
84 12 0.20
ACGTcount: A:0.68, C:0.03, G:0.20, T:0.08
Consensus pattern (83 bp):
AGAAAACGAAAAAGAGAGAGAAAAAGAAAATGAAGAAAACAAAATAGAAAAAGAAAAACGAAAAA
AGAAATTGCAAAAGAAAA
Found at i:53688832 original size:14 final size:13
Alignment explanation
Indices: 53688811--53688848 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
53688801 AAAAGTGAGA
53688811 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
53688823 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
53688838 GAAAAAGAAAA
1 GAAAAAGAAAA
53688849 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:53688862 original size:21 final size:21
Alignment explanation
Indices: 53688812--53688862 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
53688802 AAAGTGAGAG
*
53688812 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
53688833 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
53688854 AAAAAGAAA
1 AAAAAGAAA
53688863 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:53689932 original size:14 final size:14
Alignment explanation
Indices: 53689913--53689957 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
53689903 AACTCATCTT
*
53689913 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
53689927 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
53689940 AATTTAATTTAATG
1 AGTTTAATTTAATG
53689954 AGTT
1 AGTT
53689958 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:53690965 original size:29 final size:29
Alignment explanation
Indices: 53690932--53690991 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
53690922 ATAACCAAAC
*
53690932 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
53690961 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
53690990 CT
1 CT
53690992 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:53690984 original size:15 final size:15
Alignment explanation
Indices: 53690938--53690985 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
53690928 AAACCTACAA
*
53690938 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
53690953 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
53690967 AAACTTCATATCCAT
1 AAACTTCATATCCAT
53690982 AAAC
1 AAAC
53690986 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:53693727 original size:11 final size:10
Alignment explanation
Indices: 53693702--53693762 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
53693692 ACCAATAAAA
53693702 TAAA-TGAGC
1 TAAATTGAGC
*
53693711 TGAATTGTAGC
1 TAAATTG-AGC
53693722 TAAATTGAGC
1 TAAATTGAGC
**
53693732 TCGATTGAGC
1 TAAATTGAGC
53693742 TGAAA-TGAGC
1 T-AAATTGAGC
*
53693752 TCAATTGAGC
1 TAAATTGAGC
53693762 T
1 T
53693763 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:53693763 original size:20 final size:20
Alignment explanation
Indices: 53693703--53693763 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
53693693 CCAATAAAAT
*
53693703 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
53693723 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
53693744 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
53693764 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:53696319 original size:20 final size:20
Alignment explanation
Indices: 53696273--53696319 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
53696263 AGCTCGTTTC
53696273 CAGCTCACTCAAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
*
53696293 CTA-CTCACTCAAGCTCAATT
1 C-AGCTCACTCAAGCTCAAGT
53696313 CAGCTCA
1 CAGCTCA
53696320 ATCTTAACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.04
20 22 0.92
21 1 0.04
ACGTcount: A:0.30, C:0.36, G:0.11, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:53697819 original size:11 final size:12
Alignment explanation
Indices: 53697803--53697845 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
53697793 TTGGAGTAAC
53697803 AAAAAAA-TCAA
1 AAAAAAAGTCAA
*
53697814 AAAAAAATTCGAA
1 AAAAAAAGTC-AA
*
53697827 AAAAAAAGTGAA
1 AAAAAAAGTCAA
53697839 AAAAAAA
1 AAAAAAA
53697846 TCGAGGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 7 0.25
12 11 0.39
13 10 0.36
ACGTcount: A:0.79, C:0.05, G:0.07, T:0.09
Consensus pattern (12 bp):
AAAAAAAGTCAA
Found at i:53697833 original size:24 final size:25
Alignment explanation
Indices: 53697803--53697859 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
53697793 TTGGAGTAAC
53697803 AAAAAAA-TCAAAAAAAAATTCGA-A
1 AAAAAAAGTCAAAAAAAAA-TCGAGA
*
53697827 AAAAAAAGTGAAAAAAAAATCGAGGA
1 AAAAAAAGTCAAAAAAAAATCGA-GA
53697853 AAAAAAA
1 AAAAAAA
53697860 AAGGTGAGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 11 0.38
25 10 0.34
26 8 0.28
ACGTcount: A:0.75, C:0.05, G:0.11, T:0.09
Consensus pattern (25 bp):
AAAAAAAGTCAAAAAAAAATCGAGA
Found at i:53697873 original size:31 final size:29
Alignment explanation
Indices: 53697825--53697899 Score: 91
Period size: 31 Copynumber: 2.6 Consensus size: 29
53697815 AAAAAATTCG
*
53697825 AAAAAAAAA-GTGAAAAAAAAATCGAGGA
1 AAAAAAAAAGGTGAAAAAAAAATCAAGGA
**
53697853 AAAAAAAAAGGTGAGCAAAAAAAATCAAGTT
1 AAAAAAAAAGGTGA--AAAAAAAATCAAGGA
53697884 AAAAAAAAA-GTGAAAA
1 AAAAAAAAAGGTGAAAA
53697900 GTCTTGCGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 12 0.29
29 4 0.10
30 4 0.10
31 21 0.51
ACGTcount: A:0.71, C:0.04, G:0.16, T:0.09
Consensus pattern (29 bp):
AAAAAAAAAGGTGAAAAAAAAATCAAGGA
Found at i:53698791 original size:18 final size:18
Alignment explanation
Indices: 53698770--53698804 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
53698760 AGAAAAGAAA
53698770 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
53698788 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
53698805 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:53700526 original size:20 final size:20
Alignment explanation
Indices: 53700480--53700526 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
53700470 AGCTTGTTTC
*
53700480 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
53700500 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
53700520 CAGCTCA
1 CAGCTCA
53700527 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:53702043 original size:24 final size:25
Alignment explanation
Indices: 53702009--53702070 Score: 83
Period size: 24 Copynumber: 2.5 Consensus size: 25
53701999 TATTGGAGTA
53702009 ACAAAAAAAAA-TCAAAAAAAATTCG
1 ACAAAAAAAAAGTCAAAAAAAA-TCG
*
53702034 A-AAAAAAAAAGTGAAAAAAAATCG
1 ACAAAAAAAAAGTCAAAAAAAATCG
53702058 AGCAAAAAAAAAG
1 A-CAAAAAAAAAG
53702071 GTGAGCAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 13 0.39
25 10 0.30
26 10 0.30
ACGTcount: A:0.74, C:0.08, G:0.10, T:0.08
Consensus pattern (25 bp):
ACAAAAAAAAAGTCAAAAAAAATCG
Found at i:53702049 original size:13 final size:14
Alignment explanation
Indices: 53702022--53702054 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
53702012 AAAAAAAATC
*
53702022 AAAAAAAATTCGAA
1 AAAAAAAAGTCGAA
53702036 AAAAAAAAGT-GAA
1 AAAAAAAAGTCGAA
53702049 AAAAAA
1 AAAAAA
53702055 TCGAGCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.79, C:0.03, G:0.09, T:0.09
Consensus pattern (14 bp):
AAAAAAAAGTCGAA
Found at i:53702066 original size:16 final size:16
Alignment explanation
Indices: 53702047--53702084 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
53702037 AAAAAAAGTG
53702047 AAAAAAA-ATCGAGCAA
1 AAAAAAAGAT-GAGCAA
*
53702063 AAAAAAAGGTGAGCAA
1 AAAAAAAGATGAGCAA
53702079 AAAAAA
1 AAAAAA
53702085 TCAAGTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.71, C:0.08, G:0.16, T:0.05
Consensus pattern (16 bp):
AAAAAAAGATGAGCAA
Found at i:53702999 original size:18 final size:18
Alignment explanation
Indices: 53702978--53703012 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
53702968 AGAAAAGAAA
53702978 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
53702996 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
53703013 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:53704001 original size:11 final size:10
Alignment explanation
Indices: 53703976--53704036 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
53703966 ACCAATAAAA
53703976 TAAA-TGAGC
1 TAAATTGAGC
*
53703985 TGAATTGTAGC
1 TAAATTG-AGC
53703996 TAAATTGAGC
1 TAAATTGAGC
**
53704006 TCGATTGAGC
1 TAAATTGAGC
53704016 TGAAA-TGAGC
1 T-AAATTGAGC
*
53704026 TCAATTGAGC
1 TAAATTGAGC
53704036 T
1 T
53704037 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:53704037 original size:20 final size:20
Alignment explanation
Indices: 53703977--53704037 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
53703967 CCAATAAAAT
*
53703977 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
53703997 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
53704018 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
53704038 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:53704795 original size:14 final size:14
Alignment explanation
Indices: 53704776--53704820 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
53704766 AACTCATCTT
*
53704776 AGTTTAATTAAATG
1 AGTTTAATTTAATG
53704790 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
53704803 AATTTAATTTAATG
1 AGTTTAATTTAATG
53704817 AGTT
1 AGTT
53704821 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:53711894 original size:23 final size:22
Alignment explanation
Indices: 53711843--53711894 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
53711833 CCTCGTATTT
*
53711843 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
53711865 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
53711888 TTCTTTT
1 TTCTTTT
53711895 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:53712593 original size:10 final size:10
Alignment explanation
Indices: 53712577--53712633 Score: 62
Period size: 10 Copynumber: 5.7 Consensus size: 10
53712567 CAACTCCGAC
53712577 CAGCTCAATT
1 CAGCTCAATT
* *
53712587 GAGCTCATTT
1 CAGCTCAATT
53712597 CAGCTCAA-T
1 CAGCTCAATT
*
53712606 CGGCTCAATT
1 CAGCTCAATT
*
53712616 TAGCTACAATT
1 CAGCT-CAATT
53712627 CAGCTCA
1 CAGCTCA
53712634 TTTATTTTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
9 8 0.22
10 20 0.54
11 9 0.24
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:53712600 original size:20 final size:20
Alignment explanation
Indices: 53712577--53712636 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
53712567 CAACTCCGAC
53712577 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
53712597 CAGCTCAATCG-GCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
53712617 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
53712637 ATTTTATTGG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 8 0.24
20 22 0.65
21 4 0.12
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:53714703 original size:11 final size:9
Alignment explanation
Indices: 53714669--53714702 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
53714659 TGAATTTCGT
53714669 CTTTTTTGA
1 CTTTTTTGA
53714678 -TTTTTTGA
1 CTTTTTTGA
53714686 CTTTTTTGA
1 CTTTTTTGA
53714695 CTGTTTTT
1 CT-TTTTT
53714703 TTGCGGGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.35
9 10 0.43
10 5 0.22
ACGTcount: A:0.09, C:0.09, G:0.12, T:0.71
Consensus pattern (9 bp):
CTTTTTTGA
Found at i:53718631 original size:23 final size:22
Alignment explanation
Indices: 53718579--53718631 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
53718569 TCCACGTCTT
*
53718579 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
53718601 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
53718624 TTTCTTTT
1 TTTCTTTT
53718632 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:53721398 original size:20 final size:20
Alignment explanation
Indices: 53721355--53721413 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
53721345 AACAAGCTCA
*
53721355 TGAGCTGGAATTGAGTTAGATG
1 TGAGCTGG--TTGAGCTAGATG
* *
53721377 TGAGCTTGTTGAGCTAGTTG
1 TGAGCTGGTTGAGCTAGATG
*
53721397 TGAGCTGGATGAGCTAG
1 TGAGCTGGTTGAGCTAG
53721414 GAATAAGTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 25 0.78
22 7 0.22
ACGTcount: A:0.22, C:0.08, G:0.37, T:0.32
Consensus pattern (20 bp):
TGAGCTGGTTGAGCTAGATG
Found at i:53727939 original size:9 final size:9
Alignment explanation
Indices: 53727925--53727962 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
53727915 TTTCGCACAC
*
53727925 CTTTTCACT
1 CTTTTCATT
*
53727934 CTTTTCTTT
1 CTTTTCATT
53727943 CTTTTCATT
1 CTTTTCATT
53727952 CTTTTCATT
1 CTTTTCATT
53727961 CT
1 CT
53727963 CTTTAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.08, C:0.26, G:0.00, T:0.66
Consensus pattern (9 bp):
CTTTTCATT
Found at i:53730446 original size:23 final size:22
Alignment explanation
Indices: 53730394--53730446 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
53730384 TCCACGTCTT
*
53730394 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
53730416 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
53730439 TTTCTTTT
1 TTTCTTTT
53730447 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:53736724 original size:27 final size:27
Alignment explanation
Indices: 53736686--53736797 Score: 131
Period size: 27 Copynumber: 4.1 Consensus size: 27
53736676 AGCATGGCTG
* *
53736686 CCAGA-ACAGATAATGTGACAGAGTCA
1 CCAGATACAGATAATGTGGCAGAGCCA
*
53736712 CCAGATATAGATAATCGTGGCAGAGCCA
1 CCAGATACAGATAAT-GTGGCAGAGCCA
*
53736740 CCAGA-ACAGATATATGTGGCAAAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
*
53736767 CCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGATACAGATAA-TGTGGCAGAGCCA
53736794 CCAG
1 CCAG
53736798 GACACTTCCT
Statistics
Matches: 75, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.08
27 52 0.69
28 17 0.23
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (27 bp):
CCAGATACAGATAATGTGGCAGAGCCA
Found at i:53736778 original size:54 final size:54
Alignment explanation
Indices: 53736686--53736797 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
53736676 AGCATGGCTG
* * *
53736686 CCAGAACAGATAATGTGACAGAGTCACCAGATATAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAATGTGACAAAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * *
53736740 CCAGAACAGATATATGTGGCAAAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAAAGCCACCAGATACAGATAATCGTGGCAGAGCCA
53736794 CCAG
1 CCAG
53736798 GACACTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 34 0.67
55 17 0.33
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATAATGTGACAAAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:53737239 original size:8 final size:8
Alignment explanation
Indices: 53737213--53737242 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
53737203 CAAGATACTG
53737213 GCTTTTCA
1 GCTTTTCA
*
53737221 GCATTTCA
1 GCTTTTCA
53737229 GCTTTTCA
1 GCTTTTCA
53737237 GCTTTT
1 GCTTTT
53737243 GCCGATCTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.13, C:0.23, G:0.13, T:0.50
Consensus pattern (8 bp):
GCTTTTCA
Found at i:53744392 original size:27 final size:26
Alignment explanation
Indices: 53744352--53744460 Score: 146
Period size: 27 Copynumber: 4.0 Consensus size: 26
53744342 AGCATGGCTG
* *
53744352 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
53744378 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
53744406 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
53744433 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
53744460 C
1 C
53744461 TAGGACGCTT
Statistics
Matches: 75, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
26 6 0.08
27 52 0.69
28 17 0.23
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:53744443 original size:54 final size:54
Alignment explanation
Indices: 53744352--53744460 Score: 166
Period size: 54 Copynumber: 2.0 Consensus size: 54
53744342 AGCATGGCTG
*
53744352 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * *
53744406 CCAGAACAGATATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
53744460 C
1 C
53744461 TAGGACGCTT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 32 0.64
55 18 0.36
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:53746459 original size:29 final size:29
Alignment explanation
Indices: 53746426--53746485 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
53746416 ATAACCAAAC
*
53746426 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
53746455 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
53746484 CT
1 CT
53746486 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:53746478 original size:15 final size:15
Alignment explanation
Indices: 53746432--53746479 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
53746422 AAACCTACAA
*
53746432 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
53746447 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
53746461 AAACTTCATATCCAT
1 AAACTTCATATCCAT
53746476 AAAC
1 AAAC
53746480 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:53753655 original size:30 final size:30
Alignment explanation
Indices: 53753621--53753717 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
53753611 AGCTCACTCC
*
53753621 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * *
53753651 TAGCTCAACTTTAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
53753681 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
53753711 TAGCTCA
1 TAGCTCA
53753718 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
30 47 0.90
31 5 0.10
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:53754603 original size:22 final size:20
Alignment explanation
Indices: 53754571--53754619 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
53754561 GCCGAATTTA
53754571 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
53754594 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
53754614 TGAACA
1 TGAACA
53754620 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:53756275 original size:6 final size:5
Alignment explanation
Indices: 53756251--53756307 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
53756241 AAAGAGAAAC
*
53756251 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
53756298 AAAGA AAAGA
1 AAAGA AAAGA
53756308 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:53756282 original size:15 final size:14
Alignment explanation
Indices: 53756251--53756307 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
53756241 AAAGAGAAAC
53756251 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
53756267 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
53756282 AAAGAAAACGAAATAA
1 AAAGAAAA-G-AAGAA
53756298 AAAGAAAAGA
1 AAAGAAAAGA
53756308 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:53756421 original size:30 final size:31
Alignment explanation
Indices: 53756376--53756457 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 31
53756366 TTTGAAAAGC
* * *
53756376 AAAAAGAAAAAGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAGACGAAAAAGAAATATGAGAGTG
* *
53756406 AAATAG-AGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAG-ACGAAAAAGAAATATGAGAGTG
*
53756436 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAGACGAAAAAGAAAT
53756458 TGAAACAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
29 9 0.22
30 21 0.51
31 11 0.27
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAGACGAAAAAGAAATATGAGAGTG
Found at i:53757857 original size:30 final size:31
Alignment explanation
Indices: 53757823--53757919 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
53757813 AGCTCACTCC
*
53757823 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
53757853 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
53757883 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
53757913 TAGCTCA
1 TAGCTCA
53757920 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:53758709 original size:19 final size:20
Alignment explanation
Indices: 53758682--53758726 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
53758672 TGGGGCCGAT
*
53758682 GGCCTATATGAATGTGAATG
1 GGCCTATATGAATGAGAATG
*
53758702 GGCC-ATATGAATGAGATTG
1 GGCCTATATGAATGAGAATG
53758721 GGCCTA
1 GGCCTA
53758727 GTGGTCCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (20 bp):
GGCCTATATGAATGAGAATG
Found at i:53762848 original size:16 final size:16
Alignment explanation
Indices: 53762827--53762859 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
53762817 CGACAAAATC
53762827 CTGAAATGCCGAAAAG
1 CTGAAATGCCGAAAAG
*
53762843 CTGAAATGTCGAAAAG
1 CTGAAATGCCGAAAAG
53762859 C
1 C
53762860 CAAAAGTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.15
Consensus pattern (16 bp):
CTGAAATGCCGAAAAG
Found at i:53763096 original size:28 final size:28
Alignment explanation
Indices: 53763055--53763176 Score: 113
Period size: 28 Copynumber: 4.3 Consensus size: 28
53763045 ATCGCATGAC
* *
53763055 TATGAATGTGATTGGGGTCAATAGGCCA
1 TATGAATGTGATTGGGGCCAATGGGCCA
* * *
53763083 TATGAATGTAATTGGGGCCGATGGGCGA
1 TATGAATGTGATTGGGGCCAATGGGCCA
* *
53763111 TATGAATATGATTTGGGCCTAATGGGCCA
1 TATGAATGTGATTGGGGCC-AATGGGCCA
* *
53763140 TATGAAT-TAGGTT-GGGCCTAGTGGGCCA
1 TATGAATGT-GATTGGGGCC-AATGGGCCA
*
53763168 TATGCATGT
1 TATGAATGT
53763177 ATGTAGACTT
Statistics
Matches: 78, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
28 60 0.77
29 18 0.23
ACGTcount: A:0.25, C:0.12, G:0.33, T:0.30
Consensus pattern (28 bp):
TATGAATGTGATTGGGGCCAATGGGCCA
Found at i:53763165 original size:57 final size:56
Alignment explanation
Indices: 53763055--53763171 Score: 130
Period size: 57 Copynumber: 2.1 Consensus size: 56
53763045 ATCGCATGAC
* * *
53763055 TATGAATGTGATTGGGGTCAATAGGCCATATGAATGTAATTGGGGCCGATGGGCGA
1 TATGAATATGATTGGGGCCAATAGGCCATATGAATGTAATTGGGGCCGATGGGCCA
* * * *
53763111 TATGAATATGATTTGGGCCTAATGGGCCATATGAAT-TAGGTT-GGGCCTAGTGGGCCA
1 TATGAATATGATTGGGGCC-AATAGGCCATATGAATGTA-ATTGGGGCCGA-TGGGCCA
53763168 TATG
1 TATG
53763172 CATGTATGTA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
56 24 0.47
57 27 0.53
ACGTcount: A:0.26, C:0.12, G:0.33, T:0.29
Consensus pattern (56 bp):
TATGAATATGATTGGGGCCAATAGGCCATATGAATGTAATTGGGGCCGATGGGCCA
Found at i:53765357 original size:20 final size:19
Alignment explanation
Indices: 53765334--53765398 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
53765324 AAGCTCAAAC
53765334 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
53765354 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
53765374 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
53765394 GAGCT
1 GAGCT
53765399 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:53772806 original size:30 final size:30
Alignment explanation
Indices: 53772772--53772868 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
53772762 AAAACTAAAA
53772772 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
53772802 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
53772832 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
53772861 ATGAGCTA
1 -TGAGCTA
53772869 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:53782406 original size:20 final size:20
Alignment explanation
Indices: 53782383--53782439 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
53782373 GGGTTAAGAT
*
53782383 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
53782403 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
*
53782423 TGAGCTGGAAATGAGCT
1 TGAGCT-GAATTGAGCT
53782440 AAACGGAGCT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 22 0.73
21 8 0.27
ACGTcount: A:0.25, C:0.12, G:0.35, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:53794099 original size:8 final size:9
Alignment explanation
Indices: 53794063--53794098 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
53794053 TTCAAAATAT
53794063 TTTTTTTTGA
1 TTTTTTTT-A
53794073 TTTTTTTTTA
1 -TTTTTTTTA
53794083 TTTTTTTTA
1 TTTTTTTTA
53794092 TTTTTTT
1 TTTTTTT
53794099 AATCTACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 16 0.64
10 1 0.04
11 8 0.32
ACGTcount: A:0.08, C:0.00, G:0.03, T:0.89
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:53804775 original size:49 final size:51
Alignment explanation
Indices: 53804647--53804793 Score: 194
Period size: 50 Copynumber: 3.0 Consensus size: 51
53804637 ATCTATTGTG
* **
53804647 AGGTC-GCATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCAGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* *
53804697 AGGTCA-CATGTGTAGTACTAAGTGTAGGCTACTACGTGTACCGGATAATT
1 AGGTCAGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
53804747 -GGT-AGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAA
1 AGGTCAGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA
53804794 CCTTGTCTAC
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
48 1 0.01
49 40 0.47
50 44 0.52
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (51 bp):
AGGTCAGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:53807159 original size:10 final size:10
Alignment explanation
Indices: 53807144--53807205 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
53807134 TTTGAACCAT
*
53807144 TACCAATTCG
1 TACCAATTCA
*
53807154 TACCAAATACCA
1 TACC-AAT-TCA
*
53807166 TACCATTTCA
1 TACCAATTCA
53807176 TACCAATTCCA
1 TACCAATT-CA
* *
53807187 TACCATTTCG
1 TACCAATTCA
53807197 TACCAATTC
1 TACCAATTC
53807206 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:53807189 original size:21 final size:21
Alignment explanation
Indices: 53807144--53807206 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
53807134 TTTGAACCAT
* *
53807144 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
53807166 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
53807187 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
53807207 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:53809440 original size:15 final size:15
Alignment explanation
Indices: 53809420--53809464 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
53809410 GTATCGTATC
53809420 TTGGGTTTCTTTATT
1 TTGGGTTTCTTTATT
*
53809435 TTGGGTTT-TTCTATC
1 TTGGGTTTCTT-TATT
*
53809450 TTGGATTTCTTTATT
1 TTGGGTTTCTTTATT
53809465 CGGTTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 21 0.84
16 2 0.08
ACGTcount: A:0.09, C:0.09, G:0.18, T:0.64
Consensus pattern (15 bp):
TTGGGTTTCTTTATT
Found at i:53815095 original size:17 final size:17
Alignment explanation
Indices: 53815073--53815105 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
53815063 ACTTCCCTTC
53815073 TCATCTTTTCTTTTCTT
1 TCATCTTTTCTTTTCTT
53815090 TCATCTTTTCTTTTCT
1 TCATCTTTTCTTTTCT
53815106 CCATAGCCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.70
Consensus pattern (17 bp):
TCATCTTTTCTTTTCTT
Found at i:53816048 original size:27 final size:27
Alignment explanation
Indices: 53816018--53816075 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
53816008 TACTAAAATA
* *
53816018 CCCTAAGTATG-AAAATTACCATTATGC
1 CCCTAAG-ATGCAAAATGACCATTATAC
*
53816045 CCCT-AGGTGCAAAATGACCATTATAC
1 CCCTAAGATGCAAAATGACCATTATAC
53816071 CCCTA
1 CCCTA
53816076 GAGTTGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 2 0.08
26 20 0.77
27 4 0.15
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (27 bp):
CCCTAAGATGCAAAATGACCATTATAC
Found at i:53816220 original size:28 final size:28
Alignment explanation
Indices: 53816180--53816295 Score: 173
Period size: 28 Copynumber: 4.2 Consensus size: 28
53816170 GGAGGATGCG
53816180 TTCTGGTGGCTCTGCCACAAATATCTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
53816208 TTCTGGTGGCTCTGCCACAAATATCTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
* * *
53816236 TTCTAGTGGCCCTGCCACAATTATCTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
* *
53816264 ATCTGGTGGCTCTGTCAC-AATATCTG-
1 TTCTGGTGGCTCTGCCACAAATATCTGT
53816290 TTCTGG
1 TTCTGG
53816296 CAGCCATGCT
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
26 5 0.06
27 7 0.09
28 67 0.85
ACGTcount: A:0.17, C:0.25, G:0.22, T:0.36
Consensus pattern (28 bp):
TTCTGGTGGCTCTGCCACAAATATCTGT
Found at i:53821574 original size:46 final size:47
Alignment explanation
Indices: 53821435--53821574 Score: 125
Period size: 46 Copynumber: 3.0 Consensus size: 47
53821425 TCCATAAATA
* * *
53821435 AACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CAT-CTCA-CG
1 AACTCGGACTCAACTCAACGAGTTCGGATG-CT-G-AACCATCCTAAGTG
* *
53821482 AACTCGGACTCAACTCAACGAGTTC-GA-AC--ATTCGCATCCGTAAGTG
1 AACTCGGACTCAACTCAACGAGTTCGGATGCTGA-AC-CATCC-TAAGTG
53821528 AACTCGGACTCAACTCAACGAGTTCGGATGCTGAACCATCCT-AGTG
1 AACTCGGACTCAACTCAACGAGTTCGGATGCTGAACCATCCTAAGTG
53821574 A
1 A
53821575 CATGTCACTT
Statistics
Matches: 76, Mismatches: 7, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
43 3 0.04
44 2 0.03
45 2 0.03
46 33 0.43
47 28 0.37
48 6 0.08
49 1 0.01
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (47 bp):
AACTCGGACTCAACTCAACGAGTTCGGATGCTGAACCATCCTAAGTG
Found at i:53824032 original size:30 final size:30
Alignment explanation
Indices: 53823998--53824094 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
53823988 AGCTCACTCC
53823998 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
53824028 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
53824058 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
53824088 TAGCTCA
1 TAGCTCA
53824095 TTTTAGTTTT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:53836620 original size:46 final size:45
Alignment explanation
Indices: 53836498--53836620 Score: 165
Period size: 46 Copynumber: 2.7 Consensus size: 45
53836488 AACCCGCCCC
* * * * *
53836498 TAAGTGAACTTGGACTCAACTCAACGAGCTTAGGCGTTCGTATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAG-TTCGACATTCGCATCCA
* *
53836544 TAAATGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG-ACATTCGCATCCA
53836590 TAAGTGAACTCGGACTCAACTCAACGAGTTC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC
53836621 AGATGCTCAA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 3 0.04
46 65 0.96
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.24
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGACATTCGCATCCA
Found at i:53841058 original size:23 final size:22
Alignment explanation
Indices: 53841007--53841058 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
53840997 TTCCGTCTTT
*
53841007 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
53841029 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
53841052 TTCTTTT
1 TTCTTTT
53841059 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:53845389 original size:16 final size:16
Alignment explanation
Indices: 53845368--53845399 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
53845358 ACTTCCCTTC
53845368 TCATCTTTTCTTTTCT
1 TCATCTTTTCTTTTCT
53845384 TCATCTTTTCTTTTCT
1 TCATCTTTTCTTTTCT
53845400 CCATAGCCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (16 bp):
TCATCTTTTCTTTTCT
Found at i:53846343 original size:27 final size:27
Alignment explanation
Indices: 53846313--53846370 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
53846303 TACTAAAATA
* *
53846313 CCCTAAGTATG-AAAATTACCATTATGC
1 CCCTAAG-ATGCAAAATGACCATTATAC
*
53846340 CCCT-AGGTGCAAAATGACCATTATAC
1 CCCTAAGATGCAAAATGACCATTATAC
53846366 CCCTA
1 CCCTA
53846371 GAGTTGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 2 0.08
26 20 0.77
27 4 0.15
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (27 bp):
CCCTAAGATGCAAAATGACCATTATAC
Found at i:53846515 original size:28 final size:28
Alignment explanation
Indices: 53846475--53846583 Score: 148
Period size: 28 Copynumber: 3.9 Consensus size: 28
53846465 GGAGGAAGCG
53846475 TTCTGGTGGCTCTGCCACAAATATCTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
*
53846503 TTCTGGTGGCTCTGCCACAAATATTTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
* * *
53846531 TTCTAGTGGCCCTGCCACAATTATCTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
* * *
53846559 ATCTGGTGACTCTGTCAC-AATATCT
1 TTCTGGTGGCTCTGCCACAAATATCT
53846584 ATTCTGGCAG
Statistics
Matches: 70, Mismatches: 11, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
27 6 0.09
28 64 0.91
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (28 bp):
TTCTGGTGGCTCTGCCACAAATATCTGT
Found at i:53848012 original size:50 final size:49
Alignment explanation
Indices: 53847890--53848079 Score: 200
Period size: 50 Copynumber: 3.8 Consensus size: 49
53847880 TGAGGTCGCA
* * ** *
53847890 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTAAGTGTACTAGATAA-TT-GGTCACG
* * **
53847941 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTAAGTGTACTAGATAATT-GGTCACG
* * * *
53847991 TGTGTAGTACTAAGTGTAGGCTACTAAGTGTACTGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTAAGTGTACTAGATAATTGGTCACG
* * * *
53848040 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAA
1 TGTGTAGTACTAAGTGCAGGCTACTAAGTGTACTAGATAA
53848080 CCTTGTCTAC
Statistics
Matches: 116, Mismatches: 23, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
49 39 0.34
50 44 0.38
51 33 0.28
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTAAGTGTACTAGATAATTGGTCACG
Found at i:53849502 original size:21 final size:21
Alignment explanation
Indices: 53849476--53849515 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
53849466 TTGAGCTCGT
*
53849476 TTTAGCTCGTTTGAGCTCAAA
1 TTTAGCTCGTTTCAGCTCAAA
53849497 TTTAGCTCGTTTCAGCTCA
1 TTTAGCTCGTTTCAGCTCA
53849516 TTCCTTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (21 bp):
TTTAGCTCGTTTCAGCTCAAA
Found at i:53849757 original size:13 final size:13
Alignment explanation
Indices: 53849739--53849767 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
53849729 AATAGTTGTG
53849739 TGTTATTTAATTA
1 TGTTATTTAATTA
53849752 TGTTATTTAATTA
1 TGTTATTTAATTA
53849765 TGT
1 TGT
53849768 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:53852228 original size:45 final size:43
Alignment explanation
Indices: 53852155--53852308 Score: 116
Period size: 41 Copynumber: 3.6 Consensus size: 43
53852145 ATATGCGTTC
** * * *
53852155 TCGTGTAAGACCACATTTGGGACGTTGGCATCAATATATGTGGT
1 TCGTGTAAGACCATGTCTGGGACATTGGCATC-ATATATGTGAT
* * *
53852199 TACGTGTAAGACCATGTCTGAGACATTGGCAT--TGTATTTGAT
1 T-CGTGTAAGACCATGTCTGGGACATTGGCATCATATATGTGAT
* * * *
53852241 TCGTGTAAGACCCTGTCTGGGACAGTGGCATC-GATATGAGAT
1 TCGTGTAAGACCATGTCTGGGACATTGGCATCATATATGTGAT
* * * *
53852283 AGCATGTAAAACCATGTTTGGGACAT
1 -TCGTGTAAGACCATGTCTGGGACAT
53852309 GATACGTACT
Statistics
Matches: 86, Mismatches: 21, Indels: 7
0.75 0.18 0.06
Matches are distributed among these distances:
41 27 0.31
42 14 0.16
43 19 0.22
44 1 0.01
45 25 0.29
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (43 bp):
TCGTGTAAGACCATGTCTGGGACATTGGCATCATATATGTGAT
Found at i:53854786 original size:30 final size:30
Alignment explanation
Indices: 53854752--53854848 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
53854742 AAAACTAAAA
53854752 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
53854782 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
53854812 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
53854841 ATGAGCTA
1 -TGAGCTA
53854849 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:53857021 original size:12 final size:12
Alignment explanation
Indices: 53856999--53857028 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
53856989 TTTCTTTTGC
53856999 TTTTC-AAGGCT
1 TTTTCAAAGGCT
53857010 TTTTCAAAGGCT
1 TTTTCAAAGGCT
53857022 TTTTCAA
1 TTTTCAA
53857029 GTTCTCTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.47
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:53857096 original size:15 final size:14
Alignment explanation
Indices: 53857076--53857139 Score: 56
Period size: 16 Copynumber: 4.2 Consensus size: 14
53857066 CTCTTGCCTC
53857076 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-TT
*
53857091 TCTTTTTCTTTTTCT
1 TC-TTTTCTTTTTTT
*
53857106 TCTCTTGCTTTTTCTTT
1 TCT-TTTC-TTTT-TTT
*
53857123 TCTTTTCTTTGTTT
1 TCTTTTCTTTTTTT
53857137 TCT
1 TCT
53857140 CTTTACAAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
14 7 0.17
15 11 0.28
16 17 0.43
17 5 0.12
ACGTcount: A:0.02, C:0.19, G:0.03, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTTT
Found at i:53857123 original size:20 final size:21
Alignment explanation
Indices: 53857092--53857131 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
53857082 CTTTTTATTT
53857092 CTTTTTCTTTTTCTTCTCTTG
1 CTTTTTCTTTTTCTTCTCTTG
*
53857113 CTTTTTC-TTTTCTTTTCTT
1 CTTTTTCTTTTTCTTCTCTT
53857132 TGTTTTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.75
Consensus pattern (21 bp):
CTTTTTCTTTTTCTTCTCTTG
Found at i:53857142 original size:21 final size:20
Alignment explanation
Indices: 53857076--53857143 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
53857066 CTCTTGCCTC
* *
53857076 TCTTTTCTTTTTATTTCTTTT
1 TCTTTTC-TTTTCTTTGTTTT
*
53857097 TCTTTT-TCTTCTCTTGCTTTT
1 TCTTTTCTTTTCT-TTG-TTTT
53857118 TCTTTTCTTTTCTTTGTTTT
1 TCTTTTCTTTTCTTTGTTTT
53857138 CTCTTT
1 -TCTTT
53857144 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 4 0.10
20 6 0.15
21 24 0.62
22 5 0.13
ACGTcount: A:0.01, C:0.19, G:0.03, T:0.76
Consensus pattern (20 bp):
TCTTTTCTTTTCTTTGTTTT
Found at i:53858070 original size:17 final size:17
Alignment explanation
Indices: 53858050--53858087 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
53858040 TTTAACTCGA
53858050 TTTTTTTTGTC-ACTTTT
1 TTTTTTTTGTCGA-TTTT
*
53858067 TTTTTTTTTTCGATTTT
1 TTTTTTTTGTCGATTTT
53858084 TTTT
1 TTTT
53858088 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.05, C:0.08, G:0.05, T:0.82
Consensus pattern (17 bp):
TTTTTTTTGTCGATTTT
Found at i:53858083 original size:12 final size:13
Alignment explanation
Indices: 53858068--53858107 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 13
53858058 GTCACTTTTT
53858068 TTTTTTTTTCG-A
1 TTTTTTTTTCGAA
53858080 -TTTTTTTT-GAA
1 TTTTTTTTTCGAA
53858091 TTTTTTTTTCTGAA
1 TTTTTTTTTC-GAA
53858105 TTT
1 TTT
53858108 CTTCTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 1 0.04
11 9 0.38
12 8 0.33
14 6 0.25
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.75
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Done.