Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 91 of 221
Found at i:27653366 original size:23 final size:23
Alignment explanation
Indices: 27653336--27653392 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
27653326 GGAAACCAAT
*
27653336 TTTTTTTTGAATTTTTTTTTGAA
1 TTTTTTTTGAATTTCTTTTTGAA
27653359 TTTTTTTTGAATTTCTTTTTGAA
1 TTTTTTTTGAATTTCTTTTTGAA
27653382 TTTTTTTTGAA
1 TTTTTTTTGAA
27653393 GAAACTACTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.02, G:0.09, T:0.72
Consensus pattern (23 bp):
TTTTTTTTGAATTTCTTTTTGAA
Found at i:27654428 original size:21 final size:23
Alignment explanation
Indices: 27654383--27654429 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
27654373 TCACCTGCAA
* *
27654383 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
27654406 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
27654427 TAA
1 TAA
27654430 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:27655617 original size:20 final size:20
Alignment explanation
Indices: 27655592--27655638 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
27655582 AGCTCATTTC
27655592 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCGAGCTCAAGT
* * * *
27655612 CAGCTCATTTGAGTTCAATT
1 CAGCTCACTCGAGCTCAAGT
27655632 CAGCTCA
1 CAGCTCA
27655639 ACCTCAACCC
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:0.26, C:0.30, G:0.17, T:0.28
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAAGT
Found at i:27658713 original size:24 final size:23
Alignment explanation
Indices: 27658682--27658726 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
27658672 GATTGAGAGT
27658682 GAAAATGAAATT-GAAGAAAGAAGA
1 GAAAATG-AATTAGAA-AAAGAAGA
27658706 GAAAATGAATTAGAAAAAGAA
1 GAAAATGAATTAGAAAAAGAA
27658727 ACAAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.64, C:0.00, G:0.22, T:0.13
Consensus pattern (23 bp):
GAAAATGAATTAGAAAAAGAAGA
Found at i:27666407 original size:21 final size:21
Alignment explanation
Indices: 27666362--27666424 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
27666352 TTTGAACCAT
* *
27666362 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
27666384 TACCATTTTGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
27666405 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
27666425 CAAATACCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 23 0.66
22 12 0.34
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:27668010 original size:12 final size:13
Alignment explanation
Indices: 27667988--27668012 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27667978 ATAGTAGTTT
27667988 CTCGAAAAAAAAA
1 CTCGAAAAAAAAA
27668001 CTCGAAAAAAAA
1 CTCGAAAAAAAA
27668013 TTGGTTTCCA
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:0.68, C:0.16, G:0.08, T:0.08
Consensus pattern (13 bp):
CTCGAAAAAAAAA
Found at i:27668072 original size:16 final size:16
Alignment explanation
Indices: 27668051--27668108 Score: 89
Period size: 16 Copynumber: 3.6 Consensus size: 16
27668041 GATATCAAGT
27668051 TGAAAAAAAAATTTCG
1 TGAAAAAAAAATTTCG
*
27668067 TGAAAAAAAAAATTCG
1 TGAAAAAAAAATTTCG
*
27668083 TGAAAAAAAAAATTTCT
1 TG-AAAAAAAAATTTCG
27668100 TGAAAAAAA
1 TGAAAAAAA
27668109 GAAGAAGAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 24 0.63
17 14 0.37
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.22
Consensus pattern (16 bp):
TGAAAAAAAAATTTCG
Found at i:27668075 original size:17 final size:17
Alignment explanation
Indices: 27668053--27668108 Score: 96
Period size: 17 Copynumber: 3.4 Consensus size: 17
27668043 TATCAAGTTG
27668053 AAAAAAAAATTTCGTGA
1 AAAAAAAAATTTCGTGA
27668070 AAAAAAAAA-TTCGTGA
1 AAAAAAAAATTTCGTGA
*
27668086 AAAAAAAAATTTCTTGA
1 AAAAAAAAATTTCGTGA
27668103 AAAAAA
1 AAAAAA
27668109 GAAGAAGAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
16 16 0.43
17 21 0.57
ACGTcount: A:0.64, C:0.05, G:0.09, T:0.21
Consensus pattern (17 bp):
AAAAAAAAATTTCGTGA
Found at i:27668485 original size:30 final size:30
Alignment explanation
Indices: 27668451--27668547 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
27668441 AGCTCACTCC
27668451 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * * *
27668481 TAGCTCAACTTCAGCTTAGGAGTTTAGCAT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
27668511 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
27668541 TAGCTCA
1 TAGCTCA
27668548 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
29 1 0.02
30 48 0.98
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:27671909 original size:10 final size:10
Alignment explanation
Indices: 27671896--27671933 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
27671886 AAGAAGCTAA
27671896 ATTGAGCTCG
1 ATTGAGCTCG
27671906 ATTGAGCT-G
1 ATTGAGCTCG
27671915 ACTTGAGCTCG
1 A-TTGAGCTCG
*
27671926 AGTGAGCT
1 ATTGAGCT
27671934 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:27671920 original size:20 final size:20
Alignment explanation
Indices: 27671897--27671934 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
27671887 AGAAGCTAAA
*
27671897 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
27671917 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
27671935 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:27673598 original size:18 final size:18
Alignment explanation
Indices: 27673577--27673611 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
27673567 TTTTTCTTTT
27673577 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
27673595 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
27673612 TTTCTTTTCT
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:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:27674526 original size:18 final size:17
Alignment explanation
Indices: 27674505--27674547 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
27674495 TTTAACTTGA
27674505 TTTTTTTTTGCTC-ACCTT
1 TTTTTTTTTGCTCGA--TT
27674523 TTTTTTTTTGCTCGATT
1 TTTTTTTTTGCTCGATT
27674540 TTTTTTTT
1 TTTTTTTT
27674548 CACTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.42
18 13 0.54
19 1 0.04
ACGTcount: A:0.05, C:0.14, G:0.07, T:0.74
Consensus pattern (17 bp):
TTTTTTTTTGCTCGATT
Found at i:27674567 original size:12 final size:14
Alignment explanation
Indices: 27674523--27674612 Score: 84
Period size: 13 Copynumber: 6.5 Consensus size: 14
27674513 TGCTCACCTT
27674523 TTTTTTTTTGCTCG-A
1 TTTTTTTTT--TCGAA
*
27674538 TTTTTTTTTTC-AC
1 TTTTTTTTTTCGAA
27674551 TTTTTTTTTT-GAA
1 TTTTTTTTTTCGAA
27674564 TTTTTTTTTTC-AA
1 TTTTTTTTTTCGAA
27674577 TCAATTTTTTTTTCGAA
1 T---TTTTTTTTTCGAA
27674594 TTTTTTTTTT-G-A
1 TTTTTTTTTTCGAA
27674606 TTTTTTT
1 TTTTTTT
27674613 GTTACTCCAA
Statistics
Matches: 66, Mismatches: 2, Indels: 17
0.78 0.02 0.20
Matches are distributed among these distances:
12 8 0.12
13 27 0.41
14 9 0.14
15 9 0.14
16 10 0.15
17 3 0.05
ACGTcount: A:0.12, C:0.08, G:0.06, T:0.74
Consensus pattern (14 bp):
TTTTTTTTTTCGAA
Found at i:27674572 original size:30 final size:30
Alignment explanation
Indices: 27674524--27674603 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
27674514 GCTCACCTTT
27674524 TTTTTTTTGCTCG-ATTTTTTTTTTC-A-C--
1 TTTTTTTT--TCGAATTTTTTTTTTCAATCAA
*
27674551 TTTTTTTTTTGAATTTTTTTTTTCAATCAA
1 TTTTTTTTTCGAATTTTTTTTTTCAATCAA
27674581 TTTTTTTTTCGAATTTTTTTTTT
1 TTTTTTTTTCGAATTTTTTTTTT
27674604 GATTTTTTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
25 2 0.04
26 12 0.26
27 9 0.20
28 1 0.02
30 22 0.48
ACGTcount: A:0.12, C:0.09, G:0.05, T:0.74
Consensus pattern (30 bp):
TTTTTTTTTCGAATTTTTTTTTTCAATCAA
Found at i:27676278 original size:10 final size:10
Alignment explanation
Indices: 27676265--27676302 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
27676255 AAGAAGCTAA
27676265 ATTGAGCTCG
1 ATTGAGCTCG
27676275 ATTGAGCT-G
1 ATTGAGCTCG
27676284 ACTTGAGCTCG
1 A-TTGAGCTCG
*
27676295 AGTGAGCT
1 ATTGAGCT
27676303 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:27676289 original size:20 final size:20
Alignment explanation
Indices: 27676266--27676303 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
27676256 AGAAGCTAAA
*
27676266 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
27676286 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
27676304 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:27676989 original size:21 final size:23
Alignment explanation
Indices: 27676944--27676990 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
27676934 TCACCTGCAA
* *
27676944 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
27676967 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
27676988 TAA
1 TAA
27676991 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:27680215 original size:40 final size:40
Alignment explanation
Indices: 27680115--27680379 Score: 286
Period size: 40 Copynumber: 6.7 Consensus size: 40
27680105 GCTCCTCGTT
* * * *
27680115 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* **
27680155 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
27680194 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
27680234 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
27680274 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
27680314 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
27680355 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
27680380 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
39 39 0.20
40 143 0.73
41 15 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:27680339 original size:80 final size:80
Alignment explanation
Indices: 27680082--27680379 Score: 263
Period size: 80 Copynumber: 3.7 Consensus size: 80
27680072 AAATCACGTA
* ** * * *
27680082 CCTTCGGGATTTAA-CCGGATATAGCTC-CTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTTT
1 CCTTCGGGACTTAACCCGGATATAG-TCACTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
27680144 AGTAACTCACAC-AATG
64 AATAACTCGCACAAATG
* * * *
27680160 CCTTCGGGACATAACCCGGATTTA-ACAACTCGCACGAATGCCTTCGGGACTTAACCCGG-ATTT
1 CCTTCGGGACTTAACCCGGATATAGTC-ACTCGCAC-AAAGCCTTCGGGACTTAACCCGGAATTT
*
27680223 AATAACTCGCACGAATG
64 AATAACTCGCACAAATG
* *
27680240 CCTTCGGGACTTAACCCGGATTTAGT-ATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAATTT
1 CCTTCGGGACTTAACCCGGATATAGTCA-CTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
27680304 -GTATCTCGCACAAATG
64 AATAACTCGCACAAATG
** * * *
27680320 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTAACCCGGATATAGTCAC-TCGCACAAAGCCTTCGGGACTTAACCCGGA
27680380 CAGCATTCAA
Statistics
Matches: 182, Mismatches: 26, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
77 1 0.01
78 12 0.07
79 50 0.27
80 106 0.58
81 13 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (80 bp):
CCTTCGGGACTTAACCCGGATATAGTCACTCGCACAAAGCCTTCGGGACTTAACCCGGAATTTAA
TAACTCGCACAAATG
Found at i:27680388 original size:41 final size:41
Alignment explanation
Indices: 27680311--27680388 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
27680301 TTTGTATCTC
* * *
27680311 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
27680352 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
27680389 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:27688081 original size:40 final size:40
Alignment explanation
Indices: 27687981--27688192 Score: 232
Period size: 40 Copynumber: 5.3 Consensus size: 40
27687971 GCTCCTCGTT
* * ** *
27687981 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGAATTTAGTAACTCGCA
* **
27688021 C-AATGCCTTCGGGACATAACCCGAATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGAATTTAGTAACTCGCA
* * * *
27688060 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGAATTTAGTAACTCGCA
* *
27688100 CGAATGCCTTCGGGACTTAACCC-AGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGA-ATTTAGTAACTCGCA
* * *
27688140 CAAAGGCCTTCGGGGCTTAACCCGAAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCG-AATTTAGTAACTCGCA
27688180 CAAATGCCTTCGG
1 CAAATGCCTTCGG
27688193 ATCTTAGTCC
Statistics
Matches: 150, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
39 33 0.22
40 112 0.75
41 4 0.03
42 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGAATTTAGTAACTCGCA
Found at i:27688205 original size:120 final size:119
Alignment explanation
Indices: 27687983--27688238 Score: 275
Period size: 120 Copynumber: 2.1 Consensus size: 119
27687973 TCCTCGTTCA
* * * * *
27687983 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGAATT
1 AATGCCTTCGGGACTTAACCCAGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGAATT
* *
27688048 TAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCA-CAC
66 TAACAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTCAGCAC
* * * *
27688101 GAATGCCTTCGGGACTTAACCCAGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGAA
1 -AATGCCTTCGGGACTTAACCCAGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCG-A
** * ** * * *
27688166 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAACAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAACTCAGCAC
*
27688222 AAAGCCTTCGGGACTTA
1 AATGCCTTCGGGACTTA
27688239 GCCCGGACAG
Statistics
Matches: 113, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
119 36 0.32
120 69 0.61
121 8 0.07
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAACCCAGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGAATT
TAACAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTCAGCAC
Found at i:27688254 original size:41 final size:41
Alignment explanation
Indices: 27688177--27688254 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
27688167 TTTGTATCTC
* * *
27688177 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
27688218 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
27688255 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:27696206 original size:23 final size:22
Alignment explanation
Indices: 27696155--27696206 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
27696145 CCTCGTCTTT
*
27696155 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
27696177 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
27696200 TTCTTTT
1 TTCTTTT
27696207 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:27698018 original size:20 final size:19
Alignment explanation
Indices: 27697995--27698059 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
27697985 AAGCTCAAAC
27697995 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
27698015 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
27698035 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
27698055 GAGCT
1 GAGCT
27698060 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:27699834 original size:20 final size:20
Alignment explanation
Indices: 27699787--27699834 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
27699777 AGTAAGCTCG
27699787 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
27699807 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
27699827 GTTGAGCT
1 GTTGAGCT
27699835 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:27703750 original size:21 final size:23
Alignment explanation
Indices: 27703705--27703751 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
27703695 TCACCTGCAA
* *
27703705 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
27703728 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
27703749 TAA
1 TAA
27703752 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:27707114 original size:13 final size:12
Alignment explanation
Indices: 27707096--27707141 Score: 58
Period size: 13 Copynumber: 3.7 Consensus size: 12
27707086 ACGGTATTGT
27707096 AAAAAAAATAT-A
1 AAAAAAAAT-TCA
27707108 AAAAAAAATTCAA
1 AAAAAAAATTC-A
27707121 AAAAAAAATTCGA
1 AAAAAAAATTC-A
27707134 AAAAAAAA
1 AAAAAAAA
27707142 GTTTGTATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
11 1 0.03
12 9 0.29
13 21 0.68
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.13
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:27707124 original size:14 final size:14
Alignment explanation
Indices: 27707107--27707141 Score: 63
Period size: 13 Copynumber: 2.6 Consensus size: 14
27707097 AAAAAAATAT
27707107 AAAAAAAAATTC-A
1 AAAAAAAAATTCGA
27707120 AAAAAAAAATTCGA
1 AAAAAAAAATTCGA
27707134 AAAAAAAA
1 AAAAAAAA
27707142 GTTTGTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.80, C:0.06, G:0.03, T:0.11
Consensus pattern (14 bp):
AAAAAAAAATTCGA
Found at i:27708164 original size:20 final size:21
Alignment explanation
Indices: 27708141--27708185 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
27708131 AATCTTGAAT
*
27708141 GAAATTGAGAGAAGA-AAAAA
1 GAAATTGAGAGAAAAGAAAAA
27708161 GAAA-TGAGAGAAAAGAAAAA
1 GAAATTGAGAGAAAAGAAAAA
27708181 GAAAT
1 GAAAT
27708186 AAAAGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (21 bp):
GAAATTGAGAGAAAAGAAAAA
Found at i:27708192 original size:20 final size:20
Alignment explanation
Indices: 27708156--27708194 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27708146 TGAGAGAAGA
* *
27708156 AAAAAGAAATGAGAGAAAAG
1 AAAAAGAAATAAAAGAAAAG
27708176 AAAAAGAAATAAAAGAAAA
1 AAAAAGAAATAAAAGAAAA
27708195 AGATGAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (20 bp):
AAAAAGAAATAAAAGAAAAG
Found at i:27715420 original size:18 final size:18
Alignment explanation
Indices: 27715364--27715421 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
27715354 AGTGCGAACG
27715364 AGAAAAAGAAATCAAAAGAAA
1 AGAAAAAGAAATC--AA-AAA
* **
27715385 AGAAAAAGAGATTGAAAA
1 AGAAAAAGAAATCAAAAA
27715403 AGAAAAAGAAATCAAAAA
1 AGAAAAAGAAATCAAAAA
27715421 A
1 A
27715422 AAGAGTGAGG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 19 0.61
19 1 0.03
21 11 0.35
ACGTcount: A:0.74, C:0.03, G:0.16, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAAATCAAAAA
Found at i:27717663 original size:34 final size:33
Alignment explanation
Indices: 27717599--27717664 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
27717589 TTAAAGATGT
* *
27717599 TGTTCTACATGCATGGAACGGCAATTAATGAGA
1 TGTTCCACATGCATGGAACGACAATTAATGAGA
*
27717632 TGTTCCACATGCAATGG-ACGACATTTAAATGAG
1 TGTTCCACATGC-ATGGAACGACAATT-AATGAG
27717665 GGAGAGTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (33 bp):
TGTTCCACATGCATGGAACGACAATTAATGAGA
Found at i:27718367 original size:20 final size:20
Alignment explanation
Indices: 27718321--27718367 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
27718311 AGCTTGTTTC
*
27718321 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
27718341 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
27718361 CAGCTCA
1 CAGCTCA
27718368 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:27722647 original size:20 final size:20
Alignment explanation
Indices: 27722601--27722647 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
27722591 AGCTCGTTTC
*
27722601 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
27722621 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
27722641 CAGCTCA
1 CAGCTCA
27722648 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:27727290 original size:12 final size:13
Alignment explanation
Indices: 27727270--27727305 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
27727260 ATGGAAACCA
27727270 AATTTTTTTTTTG
1 AATTTTTTTTTTG
27727283 AATTTTTTTTTTG
1 AATTTTTTTTTTG
*
27727296 AGTTTTTTTT
1 AATTTTTTTT
27727306 GAGAAACTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (13 bp):
AATTTTTTTTTTG
Found at i:27735748 original size:18 final size:18
Alignment explanation
Indices: 27735727--27735761 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
27735717 TTTTTCTTTT
27735727 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
27735745 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
27735762 TTTCTTTTCT
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:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:27736681 original size:30 final size:28
Alignment explanation
Indices: 27736636--27736723 Score: 78
Period size: 30 Copynumber: 3.2 Consensus size: 28
27736626 CTCGCAAGAC
* *
27736636 TTTTCACTTTTTTTTTTAACTTGATTTTTT
1 TTTTCAC-CTTTTTTTTAACTCGA-TTTTT
**
27736666 TTTGTCACCTTTTTTTTTGCTCGATTTTT
1 TTT-TCACCTTTTTTTTAACTCGATTTTT
27736695 TTTTCA-CTTTTTTTT---T-GATTTTT
1 TTTTCACCTTTTTTTTAACTCGATTTTT
27736718 TTTTCA
1 TTTTCA
27736724 ATCAATTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
23 13 0.25
24 1 0.02
27 9 0.17
28 3 0.06
29 8 0.15
30 15 0.28
31 4 0.08
ACGTcount: A:0.10, C:0.12, G:0.06, T:0.72
Consensus pattern (28 bp):
TTTTCACCTTTTTTTTAACTCGATTTTT
Found at i:27736705 original size:12 final size:12
Alignment explanation
Indices: 27736661--27736723 Score: 56
Period size: 14 Copynumber: 4.9 Consensus size: 12
27736651 TTAACTTGAT
27736661 TTTTTTTTGTCACC
1 TTTTTTTT-TCA-C
*
27736675 TTTTTTTTTGCTC
1 TTTTTTTTT-CAC
27736688 GATTTTTTTTTCAC
1 --TTTTTTTTTCAC
*
27736702 TTTTTTTTTGA-
1 TTTTTTTTTCAC
27736713 TTTTTTTTTCA
1 TTTTTTTTTCA
27736724 ATCAATTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
11 10 0.24
12 10 0.24
13 2 0.05
14 11 0.26
15 9 0.21
ACGTcount: A:0.08, C:0.13, G:0.06, T:0.73
Consensus pattern (12 bp):
TTTTTTTTTCAC
Found at i:27736732 original size:23 final size:23
Alignment explanation
Indices: 27736688--27736733 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
27736678 TTTTTTGCTC
* ***
27736688 GATTTTTTTTTCACTTTTTTTTT
1 GATTTTTTTTTCAATCAATTTTT
27736711 GATTTTTTTTTCAATCAATTTTT
1 GATTTTTTTTTCAATCAATTTTT
27736734 TTTTCGAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.15, C:0.09, G:0.04, T:0.72
Consensus pattern (23 bp):
GATTTTTTTTTCAATCAATTTTT
Found at i:27736737 original size:27 final size:23
Alignment explanation
Indices: 27736656--27736723 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 23
27736646 TTTTTTTAAC
27736656 TTGATTTTTTTTTGTCACCTTTTTTTT
1 TTGA-TTTTTTTT-TCA-C-TTTTTTT
27736683 TGCTCGATTTTTTTTTCACTTTTTTT
1 T--T-GATTTTTTTTTCACTTTTTTT
27736709 TTGATTTTTTTTTCA
1 TTGATTTTTTTTTCA
27736724 ATCAATTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
23 13 0.34
24 1 0.03
26 8 0.21
27 2 0.05
28 3 0.08
29 9 0.24
30 2 0.05
ACGTcount: A:0.09, C:0.12, G:0.07, T:0.72
Consensus pattern (23 bp):
TTGATTTTTTTTTCACTTTTTTT
Found at i:27743437 original size:18 final size:18
Alignment explanation
Indices: 27743416--27743450 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
27743406 TTTTTCTTTT
27743416 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
27743434 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
27743451 TTTCTTTTCT
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:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:27746663 original size:10 final size:10
Alignment explanation
Indices: 27746650--27746687 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
27746640 AAGAAGCTAA
27746650 ATTGAGCTCG
1 ATTGAGCTCG
27746660 ATTGAGCT-G
1 ATTGAGCTCG
27746669 ACTTGAGCTCG
1 A-TTGAGCTCG
*
27746680 AGTGAGCT
1 ATTGAGCT
27746688 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:27746674 original size:20 final size:20
Alignment explanation
Indices: 27746651--27746688 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
27746641 AGAAGCTAAA
*
27746651 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
27746671 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
27746689 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:27749596 original size:18 final size:18
Alignment explanation
Indices: 27749575--27749609 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
27749565 TTTTTCTTTT
27749575 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
27749593 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
27749610 TTTCTTTTCT
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:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:27750606 original size:12 final size:13
Alignment explanation
Indices: 27750538--27750614 Score: 75
Period size: 13 Copynumber: 5.7 Consensus size: 13
27750528 TTTTGCTCGA
* *
27750538 TTTTTTTTCACTT
1 TTTTTTTTGAATT
27750551 TTTTTTTTGAATT
1 TTTTTTTTGAATT
*
27750564 TTTTTTTCAATCAATT
1 TTTTTTT---TGAATT
*
27750580 TTTTTTTCCGAATT
1 TTTTTTT-TGAATT
27750594 TTTTTTTTG-ATT
1 TTTTTTTTGAATT
27750606 TTTTTTTTG
1 TTTTTTTTG
27750615 TTACTCCAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
12 12 0.22
13 19 0.35
14 11 0.20
16 12 0.22
ACGTcount: A:0.13, C:0.08, G:0.05, T:0.74
Consensus pattern (13 bp):
TTTTTTTTGAATT
Found at i:27752281 original size:10 final size:10
Alignment explanation
Indices: 27752268--27752305 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
27752258 AAGAAGCTAA
27752268 ATTGAGCTCG
1 ATTGAGCTCG
27752278 ATTGAGCT-G
1 ATTGAGCTCG
27752287 ACTTGAGCTCG
1 A-TTGAGCTCG
*
27752298 AGTGAGCT
1 ATTGAGCT
27752306 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:27752292 original size:20 final size:20
Alignment explanation
Indices: 27752269--27752306 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
27752259 AGAAGCTAAA
*
27752269 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
27752289 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
27752307 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:27753875 original size:21 final size:21
Alignment explanation
Indices: 27753830--27753892 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
27753820 TTTGAACCAT
* *
27753830 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
27753852 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
27753873 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
27753893 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:27755042 original size:18 final size:19
Alignment explanation
Indices: 27754985--27755042 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 19
27754975 AATTTCAACT
27754985 CACT-TTTTCTTTTGTTTTC
1 CACTCTTTTCTTTT-TTTTC
27755004 TCACTCTTTT-TTTCTTTTTC
1 -CACTCTTTTCTTT-TTTTTC
*
27755024 CA-TCTTTTCTTTTTGTTC
1 CACTCTTTTCTTTTTTTTC
27755042 C
1 C
27755043 TTTGCCTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 12 0.35
19 5 0.15
20 12 0.35
21 5 0.15
ACGTcount: A:0.05, C:0.24, G:0.03, T:0.67
Consensus pattern (19 bp):
CACTCTTTTCTTTTTTTTC
Found at i:27758920 original size:20 final size:19
Alignment explanation
Indices: 27758897--27758961 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
27758887 AAGCTCAAAC
27758897 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
27758917 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
27758937 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
27758957 GAGCT
1 GAGCT
27758962 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:27760248 original size:17 final size:18
Alignment explanation
Indices: 27760226--27760259 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27760216 ACAATACTCC
*
27760226 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
27760243 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
27760260 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:27761406 original size:14 final size:14
Alignment explanation
Indices: 27761333--27761413 Score: 78
Period size: 13 Copynumber: 5.6 Consensus size: 14
27761323 TGGTCACCTT
27761333 TTTTTTTTTGCTCG-A
1 TTTTTTTTT--TCGAA
*
27761348 TTTTTTTTTTC-AC
1 TTTTTTTTTTCGAA
27761361 TTTTTTTTTT-GAA
1 TTTTTTTTTTCGAA
*
27761374 TTTTTTTTTTCAATCAA
1 TTTTTTTTTTC---GAA
27761391 TTTTTTTTTTCGAA
1 TTTTTTTTTTCGAA
27761405 TTTTTTTTT
1 TTTTTTTTT
27761414 GATTTTTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
13 23 0.41
14 11 0.20
15 9 0.16
17 13 0.23
ACGTcount: A:0.12, C:0.09, G:0.05, T:0.74
Consensus pattern (14 bp):
TTTTTTTTTTCGAA
Found at i:27761418 original size:11 final size:13
Alignment explanation
Indices: 27761334--27761423 Score: 60
Period size: 17 Copynumber: 6.6 Consensus size: 13
27761324 GGTCACCTTT
*
27761334 TTTTTTTTGCTCGAT
1 TTTTTTTT--TCGAA
*
27761349 TTTTTTTTTC-AC
1 TTTTTTTTTCGAA
*
27761361 TTTTTTTTTTGAA
1 TTTTTTTTTCGAA
*
27761374 TTTTTTTTTTCAATCAA
1 -TTTTTTTTTC---GAA
27761391 TTTTTTTTTTCGAA
1 -TTTTTTTTTCGAA
27761405 TTTTTTTTT-G-A
1 TTTTTTTTTCGAA
27761416 TTTTTTTT
1 TTTTTTTT
27761424 GTTACTCCAA
Statistics
Matches: 64, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
11 9 0.14
12 11 0.17
13 12 0.19
14 11 0.17
15 8 0.12
17 13 0.20
ACGTcount: A:0.12, C:0.08, G:0.06, T:0.74
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:27761421 original size:13 final size:13
Alignment explanation
Indices: 27761348--27761423 Score: 55
Period size: 13 Copynumber: 5.5 Consensus size: 13
27761338 TTTTGCTCGA
* *
27761348 TTTTTTTTTTCAC
1 TTTTTTTTTTGAT
27761361 TTTTTTTTTTGAAT
1 TTTTTTTTTTG-AT
*
27761375 TTTTTTTTTCAATCAAT
1 TTTTTTTTT---T-GAT
*
27761392 TTTTTTTTTCGA-
1 TTTTTTTTTTGAT
*
27761404 ATTTTTTTTTGAT
1 TTTTTTTTTTGAT
27761417 TTTTTTT
1 TTTTTTT
27761424 GTTACTCCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
12 10 0.20
13 17 0.35
14 10 0.20
17 12 0.24
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTTGAT
Found at i:27763054 original size:20 final size:19
Alignment explanation
Indices: 27763031--27763095 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
27763021 AAGCTCAAAC
27763031 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
27763051 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
27763071 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
27763091 GAGCT
1 GAGCT
27763096 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:27763660 original size:20 final size:21
Alignment explanation
Indices: 27763625--27763663 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
27763615 CAGCTCGTTG
27763625 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
27763646 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
27763664 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:27764070 original size:13 final size:13
Alignment explanation
Indices: 27764052--27764077 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27764042 TGTGTCCTAA
27764052 TATGAATTAAATT
1 TATGAATTAAATT
27764065 TATGAATTAAATT
1 TATGAATTAAATT
27764078 GCTTTCAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:27770072 original size:12 final size:11
Alignment explanation
Indices: 27770052--27770107 Score: 76
Period size: 11 Copynumber: 5.0 Consensus size: 11
27770042 TAGTAGTTTC
*
27770052 TTCAAAAAAAT
1 TTCAAAAAAAA
27770063 TTCAAAAAAAAA
1 TTC-AAAAAAAA
27770075 TTCAAAAAAAA
1 TTCAAAAAAAA
*
27770086 TTGAAAAAAAA
1 TTCAAAAAAAA
*
27770097 TTGAAAAAAAA
1 TTCAAAAAAAA
27770108 AATTTGGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
11 32 0.76
12 10 0.24
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.20
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:27770170 original size:15 final size:15
Alignment explanation
Indices: 27770150--27770203 Score: 90
Period size: 15 Copynumber: 3.5 Consensus size: 15
27770140 ATATCAAGTA
27770150 GAAAAAAAATTTCGT
1 GAAAAAAAATTTCGT
*
27770165 GAAAAAAAAATTCGT
1 GAAAAAAAATTTCGT
27770180 GAAAAAAAATTTTCGT
1 GAAAAAAAA-TTTCGT
27770196 GAAAAAAA
1 GAAAAAAA
27770204 GAAGAAGCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
15 23 0.64
16 13 0.36
ACGTcount: A:0.59, C:0.06, G:0.13, T:0.22
Consensus pattern (15 bp):
GAAAAAAAATTTCGT
Found at i:27770172 original size:16 final size:16
Alignment explanation
Indices: 27770151--27770203 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
27770141 TATCAAGTAG
27770151 AAAAAAAATTTCGTGA
1 AAAAAAAATTTCGTGA
27770167 AAAAAAAA-TTCGTGA
1 AAAAAAAATTTCGTGA
*
27770182 AAAAAAATTTTCGTGA
1 AAAAAAAATTTCGTGA
27770198 AAAAAA
1 AAAAAA
27770204 GAAGAAGCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
15 14 0.40
16 21 0.60
ACGTcount: A:0.60, C:0.06, G:0.11, T:0.23
Consensus pattern (16 bp):
AAAAAAAATTTCGTGA
Found at i:27772246 original size:12 final size:12
Alignment explanation
Indices: 27772224--27772255 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
27772214 CATAAAAATT
27772224 TAAACTAAGTAAA
1 TAAA-TAAGTAAA
27772237 TAAATAAGTAAA
1 TAAATAAGTAAA
27772249 TAAATAA
1 TAAATAA
27772256 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.25
Consensus pattern (12 bp):
TAAATAAGTAAA
Found at i:27773667 original size:23 final size:22
Alignment explanation
Indices: 27773615--27773667 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
27773605 TCCACGTCTT
*
27773615 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
27773637 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
27773660 TTTCTTTT
1 TTTCTTTT
27773668 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:27776042 original size:12 final size:12
Alignment explanation
Indices: 27776020--27776051 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
27776010 CATAAAAATT
27776020 TAAACTAAGTAAA
1 TAAA-TAAGTAAA
27776033 TAAATAAGTAAA
1 TAAATAAGTAAA
27776045 TAAATAA
1 TAAATAA
27776052 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.25
Consensus pattern (12 bp):
TAAATAAGTAAA
Found at i:27777508 original size:46 final size:46
Alignment explanation
Indices: 27777456--27777549 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
27777446 ATAGTGTGGC
*
27777456 GTTCATCATATACCAAGGTTCTTATCA-TCATTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATTC-TTGATAGTGGGTCGAG
27777502 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
27777548 GT
1 GT
27777550 CTTTTCTTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 44 0.96
47 2 0.04
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (46 bp):
GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
Found at i:27777884 original size:12 final size:12
Alignment explanation
Indices: 27777867--27777909 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
27777857 TAGTTTCTTG
*
27777867 AAAAAAACTCGA
1 AAAAAAATTCGA
27777879 AAAAAAATTC-A
1 AAAAAAATTCGA
27777890 AAAAAAATTTCGA
1 AAAAAAA-TTCGA
27777903 AAAAAAA
1 AAAAAAA
27777910 AAGTTTCCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 8 0.29
12 12 0.43
13 8 0.29
ACGTcount: A:0.72, C:0.09, G:0.05, T:0.14
Consensus pattern (12 bp):
AAAAAAATTCGA
Found at i:27777970 original size:14 final size:13
Alignment explanation
Indices: 27777946--27777984 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
27777936 GGATATCAAG
*
27777946 TTGTGAAAAAAAA
1 TTGTAAAAAAAAA
*
27777959 TTTTGAAAAAAAAA
1 TTGT-AAAAAAAAA
27777973 TTGTAAAAAAAA
1 TTGTAAAAAAAA
27777985 GAGCTAGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (13 bp):
TTGTAAAAAAAAA
Found at i:27783398 original size:46 final size:46
Alignment explanation
Indices: 27783346--27783439 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
27783336 ATAGTGTGGC
*
27783346 GTTCATCATATACCAAGGTTCTTATCA-TCATTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATTC-TTGATAGTGGGTCGAG
27783392 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
27783438 GT
1 GT
27783440 CTTTTCTTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 44 0.96
47 2 0.04
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (46 bp):
GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
Found at i:27785003 original size:10 final size:10
Alignment explanation
Indices: 27784987--27785044 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
27784977 CAACTCCGAC
27784987 CAGCTCAATT
1 CAGCTCAATT
* *
27784997 GAGCTCATTT
1 CAGCTCAATT
27785007 CAGCTCAA-T
1 CAGCTCAATT
27785016 CGAGCTCAATT
1 C-AGCTCAATT
*
27785027 TAGCTACAATT
1 CAGCT-CAATT
27785038 CAGCTCA
1 CAGCTCA
27785045 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:27785010 original size:20 final size:20
Alignment explanation
Indices: 27784987--27785047 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
27784977 CAACTCCGAC
27784987 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
27785007 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
27785028 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
27785048 ATTTTATTGG
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:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:27787104 original size:13 final size:13
Alignment explanation
Indices: 27787086--27787110 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27787076 TGGTCATCAT
27787086 GGTGTGAACACAA
1 GGTGTGAACACAA
27787099 GGTGTGAACACA
1 GGTGTGAACACA
27787111 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:27788026 original size:12 final size:13
Alignment explanation
Indices: 27788009--27788055 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
27787999 TTGGAGTAAC
27788009 AAAAAAATC-AAA
1 AAAAAAATCGAAA
*
27788021 AAAAAATTCGAAA
1 AAAAAAATCGAAA
*
27788034 AAAAAAATTGATTAA
1 AAAAAAATCGA--AA
27788049 AAAAAAA
1 AAAAAAA
27788056 ATTCAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.28
13 12 0.41
15 9 0.31
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (13 bp):
AAAAAAATCGAAA
Found at i:27788050 original size:13 final size:14
Alignment explanation
Indices: 27788018--27788066 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 14
27788008 CAAAAAAATC
27788018 AAAAAAAAATTCGA
1 AAAAAAAAATTCGA
27788032 AAAAAAAAATT-GATTA
1 AAAAAAAAATTCG---A
27788048 AAAAAAAAATTC-A
1 AAAAAAAAATTCGA
27788061 AAAAAA
1 AAAAAA
27788067 GTGAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
13 8 0.26
14 11 0.35
16 12 0.39
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (14 bp):
AAAAAAAAATTCGA
Found at i:27789020 original size:18 final size:18
Alignment explanation
Indices: 27788999--27789033 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
27788989 AGAAAAGAAA
27788999 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
27789017 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
27789034 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:27791121 original size:10 final size:10
Alignment explanation
Indices: 27791105--27791162 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
27791095 CAACTCCGAC
27791105 CAGCTCAATT
1 CAGCTCAATT
* *
27791115 GAGCTCATTT
1 CAGCTCAATT
27791125 CAGCTCAA-T
1 CAGCTCAATT
27791134 CGAGCTCAATT
1 C-AGCTCAATT
*
27791145 TAGCTACAATT
1 CAGCT-CAATT
27791156 CAGCTCA
1 CAGCTCA
27791163 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:27791128 original size:20 final size:20
Alignment explanation
Indices: 27791105--27791165 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
27791095 CAACTCCGAC
27791105 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
27791125 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
27791146 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
27791166 ATTTTATTGG
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:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:27796803 original size:15 final size:16
Alignment explanation
Indices: 27796783--27796821 Score: 71
Period size: 15 Copynumber: 2.5 Consensus size: 16
27796773 CAAAAAAAAA
27796783 TTTTTTCACGAAATTT
1 TTTTTTCACGAAATTT
27796799 TTTTTTCACG-AATTT
1 TTTTTTCACGAAATTT
27796814 TTTTTTCA
1 TTTTTTCA
27796822 ACTTGATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.21, C:0.13, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTTTTCACGAAATTT
Found at i:27796879 original size:12 final size:12
Alignment explanation
Indices: 27796862--27796891 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
27796852 GAAACCAATT
27796862 TTTTTTTTTGAA
1 TTTTTTTTTGAA
27796874 TTTTTTTTTGAA
1 TTTTTTTTTGAA
27796886 TTTTTT
1 TTTTTT
27796892 AAAAAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:27797594 original size:22 final size:23
Alignment explanation
Indices: 27797568--27797612 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
27797558 TTAATTGATC
* *
27797568 AACAACTT-ATTTATTAAACTAA
1 AACAACTTAATTAATAAAACTAA
*
27797590 AACAAGTTAATTAATAAAACTAA
1 AACAACTTAATTAATAAAACTAA
27797613 TTCAGCTTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31
Consensus pattern (23 bp):
AACAACTTAATTAATAAAACTAA
Found at i:27802983 original size:11 final size:12
Alignment explanation
Indices: 27802958--27803005 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 12
27802948 ATGCAATTTT
27802958 TTTTTCTTTTCAA
1 TTTTT-TTTTCAA
27802971 TTTTTTTTT-AA
1 TTTTTTTTTCAA
27802982 TTTTTTTTTCGAA
1 TTTTTTTTTC-AA
27802995 CTCTTTTTTTT
1 -T-TTTTTTTT
27803006 ACGTACCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 11 0.35
12 4 0.13
13 7 0.23
14 1 0.03
15 8 0.26
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.75
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:27802985 original size:18 final size:17
Alignment explanation
Indices: 27802951--27802985 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
27802941 AAACCGTATG
*
27802951 CAATTTTTTTTTCTTTT
1 CAATTTTTTTTTATTTT
27802968 CAATTTTTTTTTAATTTT
1 CAATTTTTTTTT-ATTTT
27802986 TTTTTCGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (17 bp):
CAATTTTTTTTTATTTT
Found at i:27807256 original size:15 final size:14
Alignment explanation
Indices: 27807236--27807274 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
27807226 AAACCGTATG
27807236 CAATTTTTTTTCTTT
1 CAATTTTTTTT-TTT
27807251 CAA-TTTTTTTTTT
1 CAATTTTTTTTTTT
27807264 -AATTTTTTTTT
1 CAATTTTTTTTT
27807275 CGAACTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.09
13 11 0.48
14 7 0.30
15 3 0.13
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (14 bp):
CAATTTTTTTTTTT
Found at i:27807259 original size:13 final size:12
Alignment explanation
Indices: 27807241--27807289 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
27807231 GTATGCAATT
27807241 TTTTTTCTTTCAA
1 TTTTTT-TTTCAA
*
27807254 TTTTTTTTTTAA
1 TTTTTTTTTCAA
27807266 TTTTTTTTTCGAA
1 TTTTTTTTTC-AA
27807279 CTCTTTTTTTT
1 -T-TTTTTTTT
27807290 ACGTACCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 14 0.45
13 8 0.26
14 1 0.03
15 8 0.26
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:27807267 original size:12 final size:13
Alignment explanation
Indices: 27807240--27807274 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
27807230 CGTATGCAAT
27807240 TTTTTTTCTTTCAA
1 TTTTTTT-TTTCAA
27807254 TTTTTTTTTT-AA
1 TTTTTTTTTTCAA
27807266 TTTTTTTTT
1 TTTTTTTTT
27807275 CGAACTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 11 0.52
13 3 0.14
14 7 0.33
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTTTTTCAA
Found at i:27815020 original size:12 final size:12
Alignment explanation
Indices: 27815004--27815038 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
27814994 TTTTTCTTTG
27815004 ATTTTTTTTCAA
1 ATTTTTTTTCAA
*
27815016 TTTTTTTTTCAA
1 ATTTTTTTTCAA
27815028 ATTTTTTTTCA
1 ATTTTTTTTCA
27815039 CGAATCTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (12 bp):
ATTTTTTTTCAA
Found at i:27815021 original size:13 final size:13
Alignment explanation
Indices: 27815005--27815036 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
27814995 TTTTCTTTGA
27815005 TTTTTTTTC-AAT
1 TTTTTTTTCAAAT
27815017 TTTTTTTTCAAAT
1 TTTTTTTTCAAAT
27815030 TTTTTTT
1 TTTTTTT
27815037 CACGAATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTTTTCAAAT
Found at i:27817073 original size:20 final size:20
Alignment explanation
Indices: 27817044--27817097 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
27817034 GTTTTTTTCC
*
27817044 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
27817064 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
27817084 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
27817098 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:27817079 original size:30 final size:30
Alignment explanation
Indices: 27817044--27817117 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
27817034 GTTTTTTTCC
27817044 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
27817074 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
27817104 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
27817118 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:27817107 original size:20 final size:20
Alignment explanation
Indices: 27817044--27817108 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
27817034 GTTTTTTTCC
* * * *
27817044 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
27817064 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
27817083 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
27817104 AGCTC
1 AGCTC
27817109 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:27822002 original size:21 final size:21
Alignment explanation
Indices: 27821957--27822019 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
27821947 TTTGAACCAT
* *
27821957 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
27821979 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
*
27822000 TACCATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
27822020 CAAATACCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 25 0.66
22 13 0.34
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.29
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:27823794 original size:10 final size:10
Alignment explanation
Indices: 27823778--27823835 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
27823768 CAACTCCGAC
27823778 CAGCTCAATT
1 CAGCTCAATT
* *
27823788 GAGCTCATTT
1 CAGCTCAATT
27823798 CAGCTCAA-T
1 CAGCTCAATT
27823807 CGAGCTCAATT
1 C-AGCTCAATT
*
27823818 TAGCTACAATT
1 CAGCT-CAATT
27823829 CAGCTCA
1 CAGCTCA
27823836 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:27823801 original size:20 final size:20
Alignment explanation
Indices: 27823778--27823838 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
27823768 CAACTCCGAC
27823778 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
27823798 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
27823819 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
27823839 ATTTTATTGG
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:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:27826899 original size:10 final size:10
Alignment explanation
Indices: 27826883--27826940 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
27826873 CAACTCCGAC
27826883 CAGCTCAATT
1 CAGCTCAATT
* *
27826893 GAGCTCATTT
1 CAGCTCAATT
27826903 CAGCTCAA-T
1 CAGCTCAATT
27826912 CGAGCTCAATT
1 C-AGCTCAATT
*
27826923 TAGCTACAATT
1 CAGCT-CAATT
27826934 CAGCTCA
1 CAGCTCA
27826941 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:27826906 original size:20 final size:20
Alignment explanation
Indices: 27826883--27826943 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
27826873 CAACTCCGAC
27826883 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
27826903 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
27826924 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
27826944 ATTTTATTGG
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:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:27828230 original size:10 final size:11
Alignment explanation
Indices: 27828200--27828229 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
27828190 GTTCGTAACG
*
27828200 AAAAAAAAGTC
1 AAAAAAAAATC
27828211 AAAAAAAAATC
1 AAAAAAAAATC
27828222 AAAAAAAA
1 AAAAAAAA
27828230 TTTGAGTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.83, C:0.07, G:0.03, T:0.07
Consensus pattern (11 bp):
AAAAAAAAATC
Found at i:27828329 original size:10 final size:10
Alignment explanation
Indices: 27828314--27828351 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
27828304 AGAAATTCAA
27828314 AAAAAAAATC
1 AAAAAAAATC
27828324 AAAAAAAATC
1 AAAAAAAATC
*
27828334 GAAAAAAAA-G
1 -AAAAAAAATC
27828344 AAAAAAAA
1 AAAAAAAA
27828352 AAAAGTGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 8 0.31
10 10 0.38
11 8 0.31
ACGTcount: A:0.84, C:0.05, G:0.05, T:0.05
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:27828412 original size:38 final size:38
Alignment explanation
Indices: 27828312--27828397 Score: 117
Period size: 38 Copynumber: 2.4 Consensus size: 38
27828302 GAAGAAATTC
* *
27828312 AAAAAAAAAA-TCA-AAAAAAATCGA--AAAAAAAGAA
1 AAAAAAAAAAGTGACAAAAAAATCGAGTTAAAAAAGAA
27828346 AAAAAAAAAAGTGACAAAAAAATCGAGTTAAAAAAGAA
1 AAAAAAAAAAGTGACAAAAAAATCGAGTTAAAAAAGAA
*
27828384 GAAAAAAAAAGTGA
1 AAAAAAAAAAGTGA
27828398 AAAGTCTTGC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
34 10 0.22
35 2 0.04
36 11 0.24
38 22 0.49
ACGTcount: A:0.76, C:0.05, G:0.12, T:0.08
Consensus pattern (38 bp):
AAAAAAAAAAGTGACAAAAAAATCGAGTTAAAAAAGAA
Found at i:27830248 original size:21 final size:21
Alignment explanation
Indices: 27830222--27830267 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
27830212 CCGACACTAC
*
27830222 CAAATGTGGAGATAAGAAATG
1 CAAATGTGGAGACAAGAAATG
27830243 CAAATGTGGAGACAAGAAATG
1 CAAATGTGGAGACAAGAAATG
27830264 CAAA
1 CAAA
27830268 GGATAATGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.50, C:0.09, G:0.26, T:0.15
Consensus pattern (21 bp):
CAAATGTGGAGACAAGAAATG
Found at i:27830871 original size:18 final size:18
Alignment explanation
Indices: 27830845--27830945 Score: 69
Period size: 18 Copynumber: 5.4 Consensus size: 18
27830835 AAATTGAAAG
*
27830845 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
27830863 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
27830881 AAAAGAAAAAGAAATC-A
1 AAAAGAAAAAGAAAACGA
** *
27830898 AAATAGTGAAAGAAAAAGA
1 AAA-AGAAAAAGAAAACGA
* *
27830917 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
27830938 AAAAGAAA
1 AAAAGAAA
27830946 TTGAGATTGA
Statistics
Matches: 63, Mismatches: 15, Indels: 9
0.72 0.17 0.10
Matches are distributed among these distances:
17 3 0.05
18 39 0.62
19 6 0.10
20 9 0.14
21 6 0.10
ACGTcount: A:0.72, C:0.04, G:0.16, T:0.08
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:27830873 original size:6 final size:6
Alignment explanation
Indices: 27830841--27830945 Score: 61
Period size: 6 Copynumber: 17.2 Consensus size: 6
27830831 AAAGAAATTG
* * ** *
27830841 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* * ** * *
27830888 AAAGAA ATCA-AA ATAGTG AAAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
27830939 AAAGAA A
1 AAAGAA A
27830946 TTGAGATTGA
Statistics
Matches: 73, Mismatches: 21, Indels: 11
0.70 0.20 0.10
Matches are distributed among these distances:
5 4 0.05
6 57 0.78
7 8 0.11
8 4 0.05
ACGTcount: A:0.72, C:0.04, G:0.16, T:0.08
Consensus pattern (6 bp):
AAAGAA
Found at i:27830888 original size:24 final size:23
Alignment explanation
Indices: 27830855--27830949 Score: 74
Period size: 24 Copynumber: 4.1 Consensus size: 23
27830845 AAAACAAAAA
27830855 GAAAACGAAAAAGAAAAAGAAATT
1 GAAAA-GAAAAAGAAAAAGAAATT
*
27830879 GCAAAAGAAAAAGAAATCAA-AATAGT
1 G-AAAAGAAAAAGAAA--AAGAA-ATT
*
27830905 G-AAAGAAAAAGAAAATG-AA--
1 GAAAAGAAAAAGAAAAAGAAATT
*
27830924 GAAAAGAAAATTGAAAAAGAAATT
1 GAAAAGAAAA-AGAAAAAGAAATT
27830948 GA
1 GA
27830950 GATTGAGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
19 1 0.02
20 8 0.14
21 7 0.12
22 4 0.07
24 26 0.46
25 6 0.11
26 5 0.09
ACGTcount: A:0.68, C:0.03, G:0.18, T:0.11
Consensus pattern (23 bp):
GAAAAGAAAAAGAAAAAGAAATT
Found at i:27830944 original size:27 final size:28
Alignment explanation
Indices: 27830909--27830975 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
27830899 AATAGTGAAA
27830909 GAAAAAGAAAATGA-A-GAAAAGAAAATT
1 GAAAAAGAAAATGAGATGAAAA-AAAATT
* *
27830936 GAAAAAGAAATTGAGATTGAGAAAAAATT
1 GAAAAAGAAAATGAGA-TGAAAAAAAATT
27830965 GAAAAAGAAAA
1 GAAAAAGAAAA
27830976 AGATGTTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 13 0.38
28 1 0.03
29 16 0.47
30 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.13
Consensus pattern (28 bp):
GAAAAAGAAAATGAGATGAAAAAAAATT
Found at i:27830965 original size:17 final size:18
Alignment explanation
Indices: 27830933--27830966 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27830923 AGAAAAGAAA
27830933 ATTGAAAAAGAAATTGAG
1 ATTGAAAAAGAAATTGAG
*
27830951 ATTGAGAAA-AAATTGA
1 ATTGAAAAAGAAATTGA
27830967 AAAAGAAAAA
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:0.56, C:0.00, G:0.21, T:0.24
Consensus pattern (18 bp):
ATTGAAAAAGAAATTGAG
Found at i:27833051 original size:10 final size:10
Alignment explanation
Indices: 27833035--27833092 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
27833025 CAACTCCGAC
27833035 CAGCTCAATT
1 CAGCTCAATT
* *
27833045 GAGCTCATTT
1 CAGCTCAATT
27833055 CAGCTCAA-T
1 CAGCTCAATT
27833064 CGAGCTCAATT
1 C-AGCTCAATT
*
27833075 TAGCTACAATT
1 CAGCT-CAATT
27833086 CAGCTCA
1 CAGCTCA
27833093 TTTGTTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:27833058 original size:20 final size:20
Alignment explanation
Indices: 27833035--27833095 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
27833025 CAACTCCGAC
27833035 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
27833055 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
27833076 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
27833096 GTTTTATTGG
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:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:27838070 original size:13 final size:13
Alignment explanation
Indices: 27838052--27838077 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27838042 ACCTGAAAGC
27838052 AATTTAATTCATA
1 AATTTAATTCATA
27838065 AATTTAATTCATA
1 AATTTAATTCATA
27838078 TTAGGACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATTCATA
Found at i:27838492 original size:20 final size:21
Alignment explanation
Indices: 27838467--27838505 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
27838457 TCAAACAAGC
27838467 AAATGAGCTCAA-TGAGCTGG
1 AAATGAGCTCAATTGAGCTGG
*
27838487 AAATGAGCTGAATTGAGCT
1 AAATGAGCTCAATTGAGCT
27838506 CAACGAGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (21 bp):
AAATGAGCTCAATTGAGCTGG
Found at i:27839780 original size:17 final size:17
Alignment explanation
Indices: 27839760--27839813 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
27839750 CTTCACTCGT
27839760 TTTCTTTTCAAACTCTC
1 TTTCTTTTCAAACTCTC
*
27839777 TTTCTTTTTCAATCTCAT-
1 TTTC-TTTTCAAACTC-TC
27839795 TTTGCTTTTC--ACTCTC
1 TTT-CTTTTCAAACTCTC
27839811 TTT
1 TTT
27839814 TGTTTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
15 1 0.03
16 6 0.19
17 4 0.13
18 18 0.58
19 2 0.06
ACGTcount: A:0.13, C:0.26, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTCTTTTCAAACTCTC
Found at i:27839803 original size:18 final size:18
Alignment explanation
Indices: 27839782--27839833 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
27839772 CTCTCTTTCT
27839782 TTTTCAATCTCATTTTGC
1 TTTTCAATCTCATTTTGC
* *
27839800 TTTTCACTCTC-TTTTGT
1 TTTTCAATCTCATTTTGC
*
27839817 TTTTGAAATCTCATTTT
1 TTTT-CAATCTCATTTT
27839834 CATATTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 9 0.32
18 15 0.54
19 4 0.14
ACGTcount: A:0.15, C:0.19, G:0.06, T:0.60
Consensus pattern (18 bp):
TTTTCAATCTCATTTTGC
Found at i:27839847 original size:6 final size:6
Alignment explanation
Indices: 27839838--27839936 Score: 65
Period size: 6 Copynumber: 16.0 Consensus size: 6
27839828 CATTTTCATA
* * * **
27839838 TTTTTC TTTTTC AATTTTC TTTTCTTC ATTTTC TTTTTC TCTCAC TTTTTC
1 TTTTTC TTTTTC -TTTTTC -TTT-TTC TTTTTC TTTTTC TTTTTC TTTTTC
* * * **
27839889 GTTTTC GTTTTC TTTTT- TGTTTTC TTTTTC TTCTTC ACTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC TTTTTC TTTTTC
27839937 GAATTCATTA
Statistics
Matches: 70, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
5 1 0.01
6 56 0.80
7 10 0.14
8 3 0.04
ACGTcount: A:0.05, C:0.20, G:0.03, T:0.72
Consensus pattern (6 bp):
TTTTTC
Found at i:27842057 original size:13 final size:13
Alignment explanation
Indices: 27842039--27842064 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27842029 ACCTGAAAGC
27842039 AATTTAATTCATA
1 AATTTAATTCATA
27842052 AATTTAATTCATA
1 AATTTAATTCATA
27842065 TTAGGACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATTCATA
Found at i:27842479 original size:20 final size:21
Alignment explanation
Indices: 27842454--27842492 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
27842444 TCAAACAAGC
27842454 AAATGAGCTCAA-TGAGCTGG
1 AAATGAGCTCAATTGAGCTGG
*
27842474 AAATGAGCTGAATTGAGCT
1 AAATGAGCTCAATTGAGCT
27842493 CAACGAGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (21 bp):
AAATGAGCTCAATTGAGCTGG
Found at i:27844492 original size:21 final size:21
Alignment explanation
Indices: 27844466--27844528 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
27844456 TTGGTATTTG
27844466 GGAATTGGTTCGAAATGGTAT
1 GGAATTGGTTCGAAATGGTAT
27844487 GGAATTGGTAT-GAAATGGTAT
1 GGAATTGGT-TCGAAATGGTAT
* * *
27844508 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTTCGAAATGGTA
27844529 ATGGTTCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 21 0.58
22 15 0.42
ACGTcount: A:0.29, C:0.03, G:0.33, T:0.35
Consensus pattern (21 bp):
GGAATTGGTTCGAAATGGTAT
Found at i:27844497 original size:11 final size:11
Alignment explanation
Indices: 27844466--27844528 Score: 51
Period size: 10 Copynumber: 5.9 Consensus size: 11
27844456 TTGGTATTTG
27844466 GGAATTGGT-T
1 GGAATTGGTAT
* *
27844476 CGAAATGGTAT
1 GGAATTGGTAT
27844487 GGAATTGGTAT
1 GGAATTGGTAT
*
27844498 -GAAATGGTAT
1 GGAATTGGTAT
*
27844508 GGTATTTGGTA-
1 GG-AATTGGTAT
*
27844519 CGAATTGGTA
1 GGAATTGGTA
27844529 ATGGTTCAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
10 23 0.56
11 12 0.29
12 6 0.15
ACGTcount: A:0.29, C:0.03, G:0.33, T:0.35
Consensus pattern (11 bp):
GGAATTGGTAT
Found at i:27847004 original size:12 final size:12
Alignment explanation
Indices: 27846987--27847020 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
27846977 GAGGAAATTT
27846987 GAAAAAAAAATC
1 GAAAAAAAAATC
*
27846999 G-AAAAAAAATT
1 GAAAAAAAAATC
27847010 GAAAAAAAAAT
1 GAAAAAAAAAT
27847021 TGAAGTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.76, C:0.03, G:0.09, T:0.12
Consensus pattern (12 bp):
GAAAAAAAAATC
Found at i:27847021 original size:12 final size:12
Alignment explanation
Indices: 27846985--27847024 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
27846975 AAGAGGAAAT
27846985 TTGAAAAAAAAA
1 TTGAAAAAAAAA
*
27846997 TCG-AAAAAAAA
1 TTGAAAAAAAAA
27847008 TTGAAAAAAAAA
1 TTGAAAAAAAAA
27847020 TTGAA
1 TTGAA
27847025 GTATTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.70, C:0.03, G:0.10, T:0.17
Consensus pattern (12 bp):
TTGAAAAAAAAA
Found at i:27848107 original size:33 final size:33
Alignment explanation
Indices: 27848070--27848132 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
27848060 AAATTGAAAA
27848070 TGAGA-GAGAAAATGAAAAGAGAAAAAAAGAAGT
1 TGAGATGAGAAAA-GAAAAGAGAAAAAAAGAAGT
* * *
27848103 TGAGATTAGAAAAGAAACGAGAGAAAAAGA
1 TGAGATGAGAAAAGAAAAGAGAAAAAAAGA
27848133 GATAAACGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 20 0.77
34 6 0.23
ACGTcount: A:0.62, C:0.02, G:0.27, T:0.10
Consensus pattern (33 bp):
TGAGATGAGAAAAGAAAAGAGAAAAAAAGAAGT
Found at i:27850169 original size:28 final size:28
Alignment explanation
Indices: 27850129--27850191 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
27850119 TGGCCAAGGC
27850129 CCACGAGCATTAGTCAAGTTCGAAGCTT
1 CCACGAGCATTAGTCAAGTTCGAAGCTT
27850157 CCACGAGCATTAGTCAAGTTCGAAGCTT
1 CCACGAGCATTAGTCAAGTTCGAAGCTT
27850185 CCACGAG
1 CCACGAG
27850192 GAGCACCGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (28 bp):
CCACGAGCATTAGTCAAGTTCGAAGCTT
Found at i:27850415 original size:10 final size:9
Alignment explanation
Indices: 27850370--27850405 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
27850360 AGAAGTGAGC
27850370 AAAAAAAGA
1 AAAAAAAGA
27850379 AAAAAAAGTA
1 AAAAAAAG-A
27850389 AAAAAAAGA
1 AAAAAAAGA
27850398 ACAAAAAA
1 A-AAAAAA
27850406 AAAGTGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.40
10 15 0.60
ACGTcount: A:0.86, C:0.03, G:0.08, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Done.