Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014717.1 Kokia drynarioides strain JFW-HI SEQ_129756, whole genome shotgun sequence
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: 79542
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:923 original size:29 final size:28
Alignment explanation
Indices: 883--1305 Score: 351
Period size: 29 Copynumber: 14.5 Consensus size: 28
873 GGAGGTCCTT
883 AAACTCTCCAAAAATTACCATTTTACCCTC
1 AAACT-TCCAAAAATTACCATTTTACCC-C
* * * *
913 GAATTTCCAAAAA-TCCCATTTTTGACCCT
1 AAACTTCCAAAAATTACCA-TTTT-ACCCC
*
942 AAACTTTCTAAAAATTACCATTTTACTCCC
1 AAAC-TTCCAAAAATTACCATTTTAC-CCC
*
972 AAACTTCCAAAAA-TCCCATTTTTAACCCC
1 AAACTTCCAAAAATTACCA-TTTT-ACCCC
* * * *
1001 GAACCTTCTAAAAATTATCATTTAACCCCC
1 -AAACTTCCAAAAATTACCATTTTA-CCCC
*
1031 AAACTTCCAAAAATTACCATTTTACCCTT
1 AAACTTCCAAAAATTACCATTTTACCC-C
*
1060 AAACTTCCAAAAA-T-CTCATTTTTAACCCT
1 AAACTTCCAAAAATTAC-CA-TTTT-ACCCC
* *
1089 AAACTTTCTAAAAATTACCATTTTATTCCC
1 AAAC-TTCCAAAAATTACCATTTTA-CCCC
* *
1119 AAACTTCCAAAAA-TCCCATTTTGACCTCG
1 AAACTTCCAAAAATTACCATTTT-ACC-CC
* *
1148 AACCTTCTAAAAATTACCATTTTACCCC
1 AAACTTCCAAAAATTACCATTTTACCCC
1176 TAAACTTCCAAAAA-T-CTCATTTTGACCCC
1 -AAACTTCCAAAAATTAC-CATTTT-ACCCC
1205 AAACTTTCCAAAAATTACCATTTTACCCC
1 AAAC-TTCCAAAAATTACCATTTTACCCC
*
1234 TAAACTTCCAAAAA-TCCCATTTTTGACCCC
1 -AAACTTCCAAAAATTACCA-TTTT-ACCCC
*
1264 AAACATT-CTAAAATTACCATTTTACCCCC
1 AAAC-TTCCAAAAATTACCATTTTA-CCCC
*
1293 GAACTTCCAAAAA
1 AAACTTCCAAAAA
1306 CCTAATTTTT
Statistics
Matches: 320, Mismatches: 39, Indels: 69
0.75 0.09 0.16
Matches are distributed among these distances:
27 2 0.01
28 42 0.13
29 167 0.52
30 97 0.30
31 11 0.03
32 1 0.00
ACGTcount: A:0.37, C:0.30, G:0.02, T:0.32
Consensus pattern (28 bp):
AAACTTCCAAAAATTACCATTTTACCCC
Found at i:980 original size:59 final size:57
Alignment explanation
Indices: 882--1290 Score: 263
Period size: 59 Copynumber: 7.0 Consensus size: 57
872 CGGAGGTCCT
* * *
882 TAAACTCTCCAAAAATTACCATTTTACCCTCGAATTTCCAAAAATCCCATTTTTGACCC
1 TAAACTTTCCAAAAATTACCATTTTACCC-CAAACTTCCAAAAATCCCATTTTT-ACCC
*
941 TAAACTTTCTAAAAATTACCATTTTACTCCCAAACTTCCAAAAATCCCATTTTTAACCC
1 TAAACTTTCCAAAAATTACCATTTTAC-CCCAAACTTCCAAAAATCCCATTTTT-ACCC
** * * * * *
1000 CGAACCTTCTAAAAATTATCATTTAACCCCCAAACTTCCAAAAATTACCA-TTTTACCC
1 TAAACTTTCCAAAAATTACCATTTTA-CCCCAAACTTCCAAAAA-TCCCATTTTTACCC
* * * *
1058 TTAAAC-TTCCAAAAA-T-CTCATTTTTAACCCTAAACTTTCTAAAAATTACCATTTTATTCCC
1 -TAAACTTTCCAAAAATTAC-CA-TTTT-ACCCCAAAC-TTCCAAAAA-TCCCATTTT-TACCC
* * * * *
1119 -AAAC-TTCCAAAAA-TCCCATTTTGACCTCGAACCTTCTAAAAATTACCA-TTTTACCCC
1 TAAACTTTCCAAAAATTACCATTTT-ACC-CCAAACTTCCAAAAA-TCCCATTTTTA-CCC
*
1176 TAAAC-TTCCAAAAA-T-CTCATTTTGACCCCAAACTTTCCAAAAATTACCA-TTTTACCCC
1 TAAACTTTCCAAAAATTAC-CATTTT-ACCCCAAAC-TTCCAAAAA-TCCCATTTTTA-CCC
* * * *
1234 TAAAC-TTCCAAAAA-TCCCATTTTTGACCCCAAACATTCTAAAATTACCA-TTTTACCC
1 TAAACTTTCCAAAAATTACCA-TTTT-ACCCCAAAC-TTCCAAAAATCCCATTTTTACCC
1291 CCGAACTTCC
Statistics
Matches: 303, Mismatches: 29, Indels: 38
0.82 0.08 0.10
Matches are distributed among these distances:
56 1 0.00
57 17 0.06
58 118 0.39
59 152 0.50
60 11 0.04
61 4 0.01
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.33
Consensus pattern (57 bp):
TAAACTTTCCAAAAATTACCATTTTACCCCAAACTTCCAAAAATCCCATTTTTACCC
Found at i:1043 original size:88 final size:87
Alignment explanation
Indices: 942--1305 Score: 402
Period size: 88 Copynumber: 4.1 Consensus size: 87
932 TTTTGACCCT
* *
942 AAACTTTCTAAAAATTACCATTTTACTCCCAAACTTCCAAAAATCCCATTTTTAACCCCGAACCT
1 AAAC-TTCCAAAAATTACCATTTTAC-CCCAAACTTCCAAAAATCCCATTTTTAACCCCAAACCT
* *
1007 TCTAAAAATTATCATTTAACCCCC
64 TCTAAAAATTACCATTTTACCCCC
* * * *
1031 AAACTTCCAAAAATTACCATTTTACCCTTAAACTTCCAAAAATCTCATTTTTAACCCTAAACTTT
1 AAACTTCCAAAAATTACCATTTTACCC-CAAACTTCCAAAAATCCCATTTTTAACCCCAAACCTT
**
1096 CTAAAAATTACCATTTTATTCCC
65 CTAAAAATTACCATTTTACCCCC
* * * * *
1119 AAACTTCCAAAAA-TCCCATTTTGACCTCGAACCTTCTAAAAATTACCA-TTTT-ACCCCTAAA-
1 AAACTTCCAAAAATTACCATTTT-ACC-CCAAACTTCCAAAAA-TCCCATTTTTAACCCC-AAAC
*
1180 CTTCCAAAAA-T-CTCATTTTGA-CCCC
62 CTTCTAAAAATTAC-CATTTT-ACCCCC
* *
1205 AAACTTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAACAT
1 AAAC-TTCCAAAAATTACCATTTTACCCC-AAACTTCCAAAAATCCCATTTTTAACCCCAAACCT
1270 TCT-AAAATTACCATTTTACCCCC
64 TCTAAAAATTACCATTTTACCCCC
*
1293 GAACTTCCAAAAA
1 AAACTTCCAAAAA
1306 CCTAATTTTT
Statistics
Matches: 231, Mismatches: 28, Indels: 34
0.79 0.10 0.12
Matches are distributed among these distances:
85 1 0.00
86 19 0.08
87 67 0.29
88 135 0.58
89 9 0.04
ACGTcount: A:0.37, C:0.30, G:0.02, T:0.32
Consensus pattern (87 bp):
AAACTTCCAAAAATTACCATTTTACCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAACCTTC
TAAAAATTACCATTTTACCCCC
Found at i:1249 original size:116 final size:118
Alignment explanation
Indices: 1027--1334 Score: 428
Period size: 116 Copynumber: 2.6 Consensus size: 118
1017 ATCATTTAAC
* * *
1027 CCCCAAA-CTTCCAAAAATTACCATTTTACCCTTAAACTTCCAAAAATCTCATTTTTAACCCTAA
1 CCCCAAACCTTCTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCATTTTTAACCCCAA
* *
1091 ACTTTCTAAAAATTACCATTTTATTCCCAAACTTCCAAAAATCCCA-TTTTGA
66 ACTTTCCAAAAATTACCATTTTATCCCCAAACTTCCAAAAATCCCATTTTTGA
* * *
1143 CCTCGAACCTTCTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCA-TTTTGACCCCAA
1 CCCCAAACCTTCTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCATTTTTAACCCCAA
1207 ACTTTCCAAAAATTACCATTTTA-CCCCTAAACTTCCAAAAATCCCATTTTTGA
66 ACTTTCCAAAAATTACCATTTTATCCCC-AAACTTCCAAAAATCCCATTTTTGA
* ** * * * *
1260 CCCCAAACATTCT-AAAATTACCATTTTACCCCCGAACTTCCAAAAACCTAATTTTTTACCCCGA
1 CCCCAAACCTTCTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCATTTTTAACCCCAA
*
1324 ACCTTCCAAAA
66 ACTTTCCAAAA
1335 CAACCATTTT
Statistics
Matches: 170, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
115 3 0.02
116 89 0.52
117 78 0.46
ACGTcount: A:0.36, C:0.31, G:0.02, T:0.31
Consensus pattern (118 bp):
CCCCAAACCTTCTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCATTTTTAACCCCAA
ACTTTCCAAAAATTACCATTTTATCCCCAAACTTCCAAAAATCCCATTTTTGA
Found at i:1341 original size:58 final size:58
Alignment explanation
Indices: 1027--1350 Score: 327
Period size: 58 Copynumber: 5.6 Consensus size: 58
1017 ATCATTTAAC
* ** * *
1027 CCCCAAA-CTTCCAAAAATTACCATTTTACCCTTAAACTTCCAAAAATCTCATTTTTAA
1 CCCCAAACCTTCTAAAAA-TACCATTTTACCCCCAAACTTCCAAAAACCTCATTTTTGA
* * **
1085 CCCTAAACTTTCTAAAAATTACCATTTTATTCCCAAACTTCCAAAAATCC-CA-TTTTGA
1 CCCCAAACCTTCTAAAAA-TACCATTTTACCCCCAAACTTCCAAAAA-CCTCATTTTTGA
* * * *
1143 CCTCGAACCTTCTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCA-TTTTGA
1 CCCCAAACCTTCTAAAAA-TACCATTTTACCCCCAAACTTCCAAAAACCTCATTTTTGA
* * *
1201 CCCCAAACTTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCC-CATTTTTGA
1 CCCCAAACCTTCTAAAAA-TACCATTTTACCCCCAAACTTCCAAAAA-CCTCATTTTTGA
* * * * *
1260 CCCCAAACATTCTAAAATTACCATTTTACCCCCGAACTTCCAAAAACCTAATTTTTTA
1 CCCCAAACCTTCTAAAAATACCATTTTACCCCCAAACTTCCAAAAACCTCATTTTTGA
* * *
1318 CCCCGAACCTTCCAAAACA-ACCATTTTGCCCCC
1 CCCCAAACCTTCTAAAA-ATACCATTTTACCCCC
1351 CCGAGCATCC
Statistics
Matches: 225, Mismatches: 34, Indels: 14
0.82 0.12 0.05
Matches are distributed among these distances:
57 3 0.01
58 164 0.73
59 57 0.25
60 1 0.00
ACGTcount: A:0.35, C:0.32, G:0.02, T:0.31
Consensus pattern (58 bp):
CCCCAAACCTTCTAAAAATACCATTTTACCCCCAAACTTCCAAAAACCTCATTTTTGA
Found at i:1341 original size:116 final size:113
Alignment explanation
Indices: 969--1349 Score: 401
Period size: 116 Copynumber: 3.3 Consensus size: 113
959 CCATTTTACT
* * * ** *
969 CCCAAAC-TTCCAAAAATCCCATTTTTAACCCCGAACCTTCTAAAAATTATCA-TTTAACCCCCA
1 CCCAAACTTTCCAAAAATACCA-TTTT-ACCCC-AAACTTCCAAAAA-TCCCATTTTGA-CCCCA
* *
1032 AACTTCCAAAAATTACCATTTTACCCTTAAACTTCCAAAAATCTCATTTTTAAC
61 AACTT-CTAAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCATTTTTAAC
* * * * *
1086 CCTAAACTTTCTAAAAATTACCATTTTATTCCCAAACTTCCAAAAATCCCATTTTGACCTCGAAC
1 CCCAAACTTTCCAAAAA-TACCATTTTA-CCCCAAACTTCCAAAAATCCCATTTTGACC-CCAAA
*
1151 CTTCTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCA-TTTTGAC
63 CTTCT-AAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCATTTTTAAC
1202 CCCAAACTTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAA
1 CCCAAACTTTCCAAAAA-TACCATTTTACCCC-AAACTTCCAAAAATCCCA-TTTTGACCCCAAA
** * * *
1267 CATTCTAAAATTACCATTTTACCCCCGAACTTCCAAAAACCTAATTTTTTAC
63 C-TTCTAAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCATTTTTAAC
* * *
1319 CCCGAACCTTCCAAAACA-ACCATTTTGCCCC
1 CCCAAACTTTCCAAAA-ATACCATTTTACCCC
1350 CCCGAGCATC
Statistics
Matches: 226, Mismatches: 27, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
115 3 0.01
116 106 0.47
117 97 0.43
118 16 0.07
119 4 0.02
ACGTcount: A:0.36, C:0.31, G:0.02, T:0.31
Consensus pattern (113 bp):
CCCAAACTTTCCAAAAATACCATTTTACCCCAAACTTCCAAAAATCCCATTTTGACCCCAAACTT
CTAAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCATTTTTAAC
Found at i:1342 original size:88 final size:87
Alignment explanation
Indices: 883--1344 Score: 349
Period size: 88 Copynumber: 5.3 Consensus size: 87
873 GGAGGTCCTT
* * * * *
883 AAACTCTCCAAAAATTACCA-TTTT-ACCCTCGAATTTCCAAAAA-TCCCATTTTTGA-CCCTAA
1 AAACT-TCCAAAAA-TACCATTTTTAACCC-CAAACTTCTAAAAATTACCA-TTTT-ACCCCCAA
* * *
944 ACTTTCTAAAAATTACCATTTTACTCCC-
61 AC-TTCCAAAAACTAACATTTTAC-CCCG
* * * *
972 AAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCTAAAAATTATCATTTAACCCCCAAACTT
1 AAACTTCCAAAAATACCATTTTTAACCCC-AAACTTCTAAAAATTACCATTTTACCCCCAAACTT
* * **
1037 CCAAAAATTACCATTTTACCCTT
65 CCAAAAACTAACATTTTACCCCG
* **
1060 AAACTTCCAAAAAT-CTCATTTTTAACCCTAAACTTTCTAAAAATTACCATTTTATTCCCAAACT
1 AAACTTCCAAAAATAC-CATTTTTAACCCCAAAC-TTCTAAAAATTACCATTTTACCCCCAAACT
** *
1124 TCCAAAAA-TCCCATTTTGACCTCG
64 TCCAAAAACTAACATTTT-ACCCCG
* * *
1148 AACCTTCTAAAAATTACCA-TTTT-ACCCCTAAACTTCCAAAAA-T-CTCATTTTGA-CCCCAAA
1 AAACTTCCAAAAA-TACCATTTTTAACCCC-AAACTTCTAAAAATTAC-CATTTT-ACCCCCAAA
* * *
1208 CTTTCCAAAAATTACCATTTTACCCCT
62 C-TTCCAAAAACTAACATTTTACCCCG
* * *
1235 AAACTTCCAAAAATCCCATTTTTGACCCCAAACATTCT-AAAATTACCATTTTACCCCCGAACTT
1 AAACTTCCAAAAATACCATTTTTAACCCCAAAC-TTCTAAAAATTACCATTTTACCCCCAAACTT
**
1299 CCAAAAACCTAATTTTTTACCCCG
65 CCAAAAA-CTAACATTTTACCCCG
*
1323 AACCTTCCAAAACA-ACCATTTT
1 AAACTTCCAAAA-ATACCATTTT
1345 GCCCCCCCGA
Statistics
Matches: 308, Mismatches: 41, Indels: 49
0.77 0.10 0.12
Matches are distributed among these distances:
85 1 0.00
86 18 0.06
87 77 0.25
88 175 0.57
89 33 0.11
90 4 0.01
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.32
Consensus pattern (87 bp):
AAACTTCCAAAAATACCATTTTTAACCCCAAACTTCTAAAAATTACCATTTTACCCCCAAACTTC
CAAAAACTAACATTTTACCCCG
Found at i:2608 original size:31 final size:31
Alignment explanation
Indices: 2517--2592 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
2507 ATTTGATTAT
*
2517 TAAACTATTCAAAAGTTTTCATTTAAGTAAC
1 TAAACTATTCAAAAGTTTTCATTTAAGTCAC
* *
2548 TAAACCATTCAAGAGTTTTCATTTAAGTCAC
1 TAAACTATTCAAAAGTTTTCATTTAAGTCAC
2579 TAAACTATTCAAAA
1 TAAACTATTCAAAA
2593 AATTTTATCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.36
Consensus pattern (31 bp):
TAAACTATTCAAAAGTTTTCATTTAAGTCAC
Found at i:3090 original size:16 final size:17
Alignment explanation
Indices: 3069--3105 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3059 TTATTTAATC
*
3069 AATAAAAT-AATTTTAA
1 AATAAAATAAATTATAA
3085 AATAAAATAAATTATAA
1 AATAAAATAAATTATAA
3102 AATA
1 AATA
3106 TATTAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAAAATAAATTATAA
Found at i:4010 original size:13 final size:13
Alignment explanation
Indices: 3994--4018 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3984 AAATAGCGTA
3994 AATAATAATAATT
1 AATAATAATAATT
4007 AATAATAATAAT
1 AATAATAATAAT
4019 AAACAAATAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATAATAATAATT
Found at i:4973 original size:29 final size:29
Alignment explanation
Indices: 4924--4985 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
4914 CCTTAGAGGT
*
4924 CCCTAAACTGTCTAGAAATTATATTTTAA
1 CCCTAAACTGTCTACAAATTATATTTTAA
*
4953 CCCTAAACT-TCTCCAACATTATATTTTAA
1 CCCTAAACTGTCTACAA-ATTATATTTTAA
4982 CCCT
1 CCCT
4986 CGAACTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 5 0.17
29 25 0.83
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (29 bp):
CCCTAAACTGTCTACAAATTATATTTTAA
Found at i:5009 original size:30 final size:29
Alignment explanation
Indices: 4939--5044 Score: 88
Period size: 29 Copynumber: 3.6 Consensus size: 29
4929 AACTGTCTAG
4939 AAATTATATTTTAACCCTAAACTTCTCCA
1 AAATTATATTTTAACCCTAAACTTCTCCA
* * * **
4968 ACATTATATTTTAACCCTCGAACTTTTTGA
1 AAATTATATTTTAACCCT-AAACTTCTCCA
* * *
4998 AAATTACATTTTTACCCCCTAAACTTC-CAA
1 AAATTATA-TTTTA-ACCCTAAACTTCTCCA
**
5028 AAATTCCATTTTAACCC
1 AAATTATATTTTAACCC
5045 CTATTTTTCC
Statistics
Matches: 60, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
28 3 0.05
29 22 0.37
30 21 0.35
31 10 0.17
32 4 0.07
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (29 bp):
AAATTATATTTTAACCCTAAACTTCTCCA
Found at i:5045 original size:30 final size:28
Alignment explanation
Indices: 4997--5095 Score: 112
Period size: 29 Copynumber: 3.5 Consensus size: 28
4987 GAACTTTTTG
*
4997 AAAATTACATTTTTACCCCCTAAACTTCCA
1 AAAATTCCA-TTTTA-CCCCTAAACTTCCA
***
5027 AAAATTCCATTTTAACCCCTATTTTTCCA
1 AAAATTCCATTTT-ACCCCTAAACTTCCA
5056 AAAATTACCA-TTTACCCCTAAACTTCC-
1 AAAATT-CCATTTTACCCCTAAACTTCCA
5083 AAAATTCCATTTT
1 AAAATTCCATTTT
5096 TGATCTCGAT
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
26 3 0.05
27 9 0.15
28 11 0.19
29 24 0.41
30 12 0.20
ACGTcount: A:0.35, C:0.28, G:0.00, T:0.36
Consensus pattern (28 bp):
AAAATTCCATTTTACCCCTAAACTTCCA
Found at i:5079 original size:57 final size:58
Alignment explanation
Indices: 4997--5366 Score: 276
Period size: 58 Copynumber: 6.3 Consensus size: 58
4987 GAACTTTTTG
4997 AAAATTA-CATTTTTACCCCCTAAACTTCCAAAAATTCCA-TTTTAACCCCTATTTTTCCA
1 AAAATTACCA-TTTTA-CCCCTAAACTTCCAAAAATTCCATTTTTAA-CCCTATTTTTCCA
* * * *
5056 AAAATTACCA-TTTACCCCTAAACTTCC-AAAATTCCATTTTTGATCTCGATTTTTGCA
1 AAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTT-AACCCTATTTTTCCA
* * * * * * ***
5113 AAAACTACAATTTTA-TCCTCGAACTTCCAAAAAATCCATTTTTAACCCTAATTTAAAA
1 AAAATTACCATTTTACCCCT-AAACTTCCAAAAATTCCATTTTTAACCCTATTTTTCCA
* * *
5171 AAAAATACCATTTTA-CCCTCAAACTTCCTAAAATTCCA-TTTTAACCTCAAATTTTTTTCCA
1 AAAATTACCATTTTACCCCT-AAACTTCCAAAAATTCCATTTTTAACC-C---TATTTTTCCA
* * * *
5232 AAAATTACCATTTTACCCCCGAAA-TTCCAAAAATTTCATTTTTGACCTTGATTTTTCC-
1 AAAATTACCATTTTA-CCCCTAAACTTCCAAAAATTCCATTTTTAACCCT-ATTTTTCCA
* * * * * ** *
5290 AAAATTACCATTTTACCCCCT-GA-TGCCTAAAATTCCATTTTAAACCTTGAACTTTCCC
1 AAAATTACCATTTTA-CCCCTAAACTTCCAAAAATTCCATTTTTAACCCT-ATTTTTCCA
*
5348 AAAATTACCATTTTCCCCC
1 AAAATTACCATTTTACCCC
5367 GAGTGTCTAA
Statistics
Matches: 252, Mismatches: 44, Indels: 32
0.77 0.13 0.10
Matches are distributed among these distances:
56 9 0.04
57 78 0.31
58 92 0.37
59 27 0.11
60 2 0.01
61 31 0.12
62 10 0.04
63 3 0.01
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.36
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCCTATTTTTCCA
Found at i:5154 original size:28 final size:28
Alignment explanation
Indices: 5122--5221 Score: 85
Period size: 29 Copynumber: 3.5 Consensus size: 28
5112 AAAAACTACA
* *
5122 ATTTTATCCTCGAACTTCCAAAAAATCC
1 ATTTTAACCTCAAACTTCCAAAAAATCC
* * **
5150 ATTTTTAACC-CTAATTTAAAAAAAAATACC
1 A-TTTTAACCTCAAACTT-CCAAAAAAT-CC
* * *
5180 ATTTTACCCTCAAACTTCCTAAAATTCC
1 ATTTTAACCTCAAACTTCCAAAAAATCC
5208 ATTTTAACCTCAAA
1 ATTTTAACCTCAAA
5222 TTTTTTTCCA
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
28 21 0.38
29 26 0.47
30 8 0.15
ACGTcount: A:0.40, C:0.25, G:0.01, T:0.34
Consensus pattern (28 bp):
ATTTTAACCTCAAACTTCCAAAAAATCC
Found at i:5350 original size:58 final size:56
Alignment explanation
Indices: 5226--5388 Score: 184
Period size: 58 Copynumber: 2.8 Consensus size: 56
5216 CTCAAATTTT
* * * * ** *
5226 TTTCCAAAAATTACCATTTTACCCCCGAAATTCCAAAAATTTCATTTTTGACCTTGAT
1 TTTCCCAAAATTACCATTTTACCCCCG--ATGCCTAAAATTCCATTTTAAACCTTGAC
*
5284 TTTTCCAAAATTACCATTTTACCCCCTGATGCCTAAAATTCCATTTTAAACCTTGAAC
1 TTTCCCAAAATTACCATTTTACCCCC-GATGCCTAAAATTCCATTTTAAACCTTG-AC
*
5342 TTTCCCAAAATTACCATTTT-CCCCCGAGTGTCTAAAATTACCATTTT
1 TTTCCCAAAATTACCATTTTACCCCCGA-TGCCTAAAATT-CCATTTT
5389 TCCCCCTAGG
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
56 2 0.02
57 37 0.41
58 51 0.56
59 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.37
Consensus pattern (56 bp):
TTTCCCAAAATTACCATTTTACCCCCGATGCCTAAAATTCCATTTTAAACCTTGAC
Found at i:12426 original size:50 final size:49
Alignment explanation
Indices: 12275--12432 Score: 158
Period size: 51 Copynumber: 3.2 Consensus size: 49
12265 CTACAGGTCT
* * * *
12275 CAGTACCATGAAGACATGAAGGGAAAGGTCTAAGTCACAACGGTAAGA-C
1 CAGTACCATGAAGACATGAAGGGAAAGATCTAAGCCGCAACGG-AGGATC
* * * * *
12324 CGTGTACC-TCAGAAGACACGAAGGGAAAGATTTAAGCCGCAACGGTGAATC
1 C-AGTACCAT--GAAGACATGAAGGGAAAGATCTAAGCCGCAACGGAGGATC
* *
12375 CAGTACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAATGGCGGATC
1 CAGTACCATGAAGACATGAAGGGAAAGATCTAAG-CCGCAACGGAGGATC
12425 CAGTACCA
1 CAGTACCA
12433 CAAAGATACA
Statistics
Matches: 88, Mismatches: 15, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
49 25 0.28
50 31 0.35
51 32 0.36
ACGTcount: A:0.38, C:0.21, G:0.27, T:0.15
Consensus pattern (49 bp):
CAGTACCATGAAGACATGAAGGGAAAGATCTAAGCCGCAACGGAGGATC
Found at i:12448 original size:100 final size:100
Alignment explanation
Indices: 12275--12459 Score: 223
Period size: 100 Copynumber: 1.9 Consensus size: 100
12265 CTACAGGTCT
* * * *
12275 CAGTACCATGAAGACATGAAGGGAAAGGTCTAAGTCACAACGGTAAGACCGTGTACCTCAGAAGA
1 CAGTACCATGAAGACATGAAGGGAAAGATCTAAGCCACAACGGTAAGACCGAGTACCACAGAAGA
*
12340 CACGAAGGGAAAGATTTAAGCCGCAACGGTGAATC
66 CACAAAGGGAAAGATTTAAGCCGCAACGGTGAATC
* * **
12375 CAGTACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAATGG-CGGATCC-AGTACCACA-AA
1 CAGTACCATGAAGACATGAAGGGAAAGATCTAAG-CCACAACGGTAAGA-CCGAGTACCACAGAA
* *
12437 GATACAAAAGGGAAAGGTTTAAG
64 GACAC-AAAGGGAAAGATTTAAG
12460 TCATTACGGC
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
99 6 0.08
100 57 0.80
101 8 0.11
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.15
Consensus pattern (100 bp):
CAGTACCATGAAGACATGAAGGGAAAGATCTAAGCCACAACGGTAAGACCGAGTACCACAGAAGA
CACAAAGGGAAAGATTTAAGCCGCAACGGTGAATC
Found at i:12565 original size:50 final size:49
Alignment explanation
Indices: 12335--12580 Score: 199
Period size: 50 Copynumber: 4.9 Consensus size: 49
12325 GTGTACCTCA
* * * *
12335 GAAGACACGAAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCAT
1 GAAGACATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCAC
* * * *
12384 GAAGACATGAAGGGAAAGATCTAAGACCGCAATGGCGGATCCAGTACCAC
1 GAAGACATGAAGGGAAAGATTTAAG-CCGTAACGGCGAATCCAGTACCAC
* * * * * * * * *
12434 AAAGATACA-AAAGGGAAAGGTTTAAGTCATTACGGCGGA-CCGTGTACCTC
1 GAAG--ACATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCC-AGTACCAC
*
12484 AGAAGACAAGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCAC
1 -GAAGACATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCAC
** * * * * *
12534 GAAGATTTGAAGGGGAAAGGTTTAAGTCGTAATGGAGAACCCAGTAC
1 GAAGACATGAA-GGGAAAGATTTAAGCCGTAACGGCGAATCCAGTAC
12581 TTTAAAAACA
Statistics
Matches: 155, Mismatches: 34, Indels: 15
0.76 0.17 0.07
Matches are distributed among these distances:
49 36 0.23
50 97 0.63
51 19 0.12
52 3 0.02
ACGTcount: A:0.38, C:0.18, G:0.28, T:0.16
Consensus pattern (49 bp):
GAAGACATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCAC
Found at i:12578 original size:150 final size:151
Alignment explanation
Indices: 12293--12580 Score: 391
Period size: 150 Copynumber: 1.9 Consensus size: 151
12283 TGAAGACATG
*
12293 AAGGGAAAGGTCTAAGTCACAACGGTAAGACCGTGTACCTCAGAAGACACGAAGGGAAAGATTTA
1 AAGGGAAAGGTCTAAGTCACAACGGTAAGACCGTGTACCTCAGAAGACAAGAAGGGAAAGATTTA
* * * *
12358 AGCCGCAACGGTGAATCCAGTACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAATGGCGGA
66 AGCCGCAACGGCGAATCCAGTACCACGAAGACATGAAGGGAAAGATCTAAGACCGCAATGGAGAA
*
12423 TCCAGTACCACAAAGATACAA
131 CCCAGTACCACAAAGATACAA
* ** **
12444 AAGGGAAAGGTTTAAGTCATTACGG-CGGACCGTGTACCTCAGAAGACAAGAAGGGAAAGATTTA
1 AAGGGAAAGGTCTAAGTCACAACGGTAAGACCGTGTACCTCAGAAGACAAGAAGGGAAAGATTTA
* ** * * * *
12508 AGCCGTAACGGCGAATCCAGTACCACGAAGATTTGAAGGGGAAAGGTTTAAG-TCGTAATGGAGA
66 AGCCGCAACGGCGAATCCAGTACCACGAAGACATGAA-GGGAAAGATCTAAGACCGCAATGGAGA
12572 ACCCAGTAC
130 ACCCAGTAC
12581 TTTAAAAACA
Statistics
Matches: 118, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
150 84 0.71
151 34 0.29
ACGTcount: A:0.38, C:0.19, G:0.27, T:0.16
Consensus pattern (151 bp):
AAGGGAAAGGTCTAAGTCACAACGGTAAGACCGTGTACCTCAGAAGACAAGAAGGGAAAGATTTA
AGCCGCAACGGCGAATCCAGTACCACGAAGACATGAAGGGAAAGATCTAAGACCGCAATGGAGAA
CCCAGTACCACAAAGATACAA
Found at i:12852 original size:101 final size:101
Alignment explanation
Indices: 12666--12860 Score: 248
Period size: 101 Copynumber: 1.9 Consensus size: 101
12656 AACTACAATG
* * * * *
12666 GCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTTAACGTCAATTCCTATCC
1 GCAAGTCTTTATCTCTCTAAAATTGTAGTAAGAGCAAGATGAAGCTTCAACATCAAATCCTATCC
* ** *
12731 TCTTGAGGTTACAGTAAAGTTGGATTAAAAATAATA
66 TCTGGAGGTTACAACAAAGTTGGAATAAAAATAATA
* *
12767 GCAAGTTTTTATCTCTCTAAAATTGTAGTAAGAGCAAGATGAAGCTTCAACATTAAATCCTATCT
1 GCAAGTCTTTATCTCTCTAAAATTGTAGTAAGAGCAAGATGAAGCTTCAACATCAAATCCTATC-
* * *
12832 TTCTGGA-GTTGCAACGAAGTTGGAATAAA
65 CTCTGGAGGTTACAACAAAGTTGGAATAAA
12861 TCTATAGCAG
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
101 74 0.94
102 5 0.06
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (101 bp):
GCAAGTCTTTATCTCTCTAAAATTGTAGTAAGAGCAAGATGAAGCTTCAACATCAAATCCTATCC
TCTGGAGGTTACAACAAAGTTGGAATAAAAATAATA
Found at i:13055 original size:39 final size:39
Alignment explanation
Indices: 12916--13148 Score: 159
Period size: 39 Copynumber: 6.0 Consensus size: 39
12906 AGTGAAGTTA
*
12916 CATCGTCAACCAATCTCTTACCCCGAGCATGGGGCAGAT
1 CATCGTCAACCAATCTCTTACCCCGAGCCTGGGGCAGAT
** * *
12955 CATTATCAACCAATCTCTTACCCCGAGCTTGGGGTAGAT
1 CATCGTCAACCAATCTCTTACCCCGAGCCTGGGGCAGAT
** * * **** *
12994 TGTAGCCATTTGATCTTTTACCCCGAGCCTGGGGCAGAT
1 CATCGTCAACCAATCTCTTACCCCGAGCCTGGGGCAGAT
* * * *
13033 CATCGTCAACCAATTTCGTACCCAGAGCC-AGGGCAGAT
1 CATCGTCAACCAATCTCTTACCCCGAGCCTGGGGCAGAT
* * ** * * *
13071 TA-CAGCCATTCGATCTCTTACCCCGAGCTTGGGGAAGAT
1 CATC-GTCAACCAATCTCTTACCCCGAGCCTGGGGCAGAT
* * *
13110 CACCGTCAACCAATTTGC-TACCCCGATCAC-GGGGCAGAT
1 CATCGTCAACCAATCT-CTTACCCCGAGC-CTGGGGCAGAT
13149 TGCAATTTTC
Statistics
Matches: 140, Mismatches: 49, Indels: 10
0.70 0.25 0.05
Matches are distributed among these distances:
37 1 0.01
38 26 0.19
39 111 0.79
40 2 0.01
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.24
Consensus pattern (39 bp):
CATCGTCAACCAATCTCTTACCCCGAGCCTGGGGCAGAT
Found at i:13132 original size:77 final size:78
Alignment explanation
Indices: 12928--13125 Score: 245
Period size: 77 Copynumber: 2.6 Consensus size: 78
12918 TCGTCAACCA
** * * * ** *
12928 ATCTCTTACCCCGAGCATGGGGCAGATCATTATCAACCAATCTCTTACCCCGAGCTTGGGGTAGA
1 ATCTCTTACCCCGAGCATGGGGCAGATCATCGTCAACCAATTTCGTACCCAGAGCTCAGGGCAGA
** *
12993 TTGTAGCCATTTG
66 TTACAGCCATTCG
* *
13006 ATCTTTTACCCCGAGCCTGGGGCAGATCATCGTCAACCAATTTCGTACCCAGAGC-CAGGGCAGA
1 ATCTCTTACCCCGAGCATGGGGCAGATCATCGTCAACCAATTTCGTACCCAGAGCTCAGGGCAGA
13070 TTACAGCCATTCG
66 TTACAGCCATTCG
* * *
13083 ATCTCTTACCCCGAGCTTGGGGAAGATCACCGTCAACCAATTT
1 ATCTCTTACCCCGAGCATGGGGCAGATCATCGTCAACCAATTT
13126 GCTACCCCGA
Statistics
Matches: 103, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
77 55 0.53
78 48 0.47
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.25
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCATGGGGCAGATCATCGTCAACCAATTTCGTACCCAGAGCTCAGGGCAGA
TTACAGCCATTCG
Found at i:13515 original size:194 final size:193
Alignment explanation
Indices: 13166--14005 Score: 1072
Period size: 194 Copynumber: 4.3 Consensus size: 193
13156 TTCCACAAAT
* * *
13166 AGTGAAGCGGTCGTCTTCCTGATGAGATACAAAGAAGTATACCATCTCAAGGTTCAATACGAGCA
1 AGTG-AGCGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTCAAGG-------CGAACA
* *
13231 AATCTTCGAACCCCAACTTTCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGC
58 AATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGC
* * *
13296 TTCCTAATGAGATACTGAGAAGTGGACCAAATTCGTTTTCCTGATGAGGTATAGAGAAGCGGATT
123 TTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATT
13361 GAAACA
188 GAAACA
13367 AGTGACGCGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTCAAGGCGAACAAATCTTC
1 AGTGA-GCGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTCAAGGCGAACAAATCTTC
* *
13432 GAACCCCAGCTTCCTGATGAAATACTGAGAAGCAGAGT-GAAGCAATAAAAAGGTTAGCTTCCTG
65 GAACCCCAACTTCCTGATGAGATACTGAGAAGCAG-GTCGAAGCAATAAAAAGGTTAGCTTCCTG
* * *
13496 ATGAGATACTTAGAAGTGGACTAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAATA
129 ATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACA
* * * * *
13561 AGTGAGGCGATCATCTTCTTGATGAGATGCAGAGAAGTATACCAACTCAATGCGAACAAATCTTC
1 AGTGA-GCGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTCAAGGCGAACAAATCTTC
* * *
13626 AAACCCCAACTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAATGGTTAGCTTCCTGA
65 GAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTGA
*
13691 TGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGTTACAGAGAAGCGGATTGAAACAA
130 TGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAAC-A
** * * *
13756 ACG-GAGCGGTTGTCTTCCTGATGAGATACAGAGGAGTATACCAACTCAGAGCTCGATGTGAGCA
1 A-GTGAGCGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTCA-AG-GCGA----A-CA
* * * * * *
13820 AATCTTTGAATCACAGCTTCCTGATGAGATACTTAGAAGCAGGTCGAAGCAATAAAATGGTTAGC
58 AATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGC
* * ** * *
13885 TTCTTGATGAAATACTGAGAAGTAAACCAAATTCATCTTCCTGATAAGGTACAGAGAAGCGGATT
123 TTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATT
13950 GAAACA
188 GAAACA
* * * * * *
13956 AGCGATGCAGTCATCTTCCTGATAAGATACTAAGAAGTAGACCAAATCAA
1 AGTGA-GCGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTCAA
14006 CGACACCAAA
Statistics
Matches: 566, Mismatches: 59, Indels: 29
0.87 0.09 0.04
Matches are distributed among these distances:
193 2 0.00
194 341 0.60
195 6 0.01
196 4 0.01
199 1 0.00
200 7 0.01
201 205 0.36
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (193 bp):
AGTGAGCGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTCAAGGCGAACAAATCTTCG
AACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTGAT
GAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACA
Found at i:14532 original size:16 final size:16
Alignment explanation
Indices: 14511--14551 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
14501 AATACACCCA
*
14511 AACCCAATTAT-AGAT
1 AACCCAATTATCAAAT
14526 GAACCCAA-TATCAAAT
1 -AACCCAATTATCAAAT
14542 AACCCAATTA
1 AACCCAATTA
14552 GCCCCAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.49, C:0.24, G:0.05, T:0.22
Consensus pattern (16 bp):
AACCCAATTATCAAAT
Found at i:14996 original size:19 final size:19
Alignment explanation
Indices: 14969--15023 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
14959 CATTAAATTT
*
14969 ATAATTAATAATAAATAAC
1 ATAAATAATAATAAATAAC
*
14988 ATAAATAATAATTAAT-A-
1 ATAAATAATAATAAATAAC
15005 AT-AATAATAATAAAATAAC
1 ATAAATAATAAT-AAATAAC
15024 GTTTTTAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 9 0.30
17 5 0.17
18 2 0.07
19 14 0.47
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAAATAATAATAAATAAC
Found at i:15010 original size:16 final size:16
Alignment explanation
Indices: 14964--15015 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
14954 AAGTACATTA
*
14964 AATTTATAATTAATAAT
1 AATTAATAA-TAATAAT
* *
14981 AAATAA-CATAAATAAT
1 AATTAATAAT-AATAAT
14997 AATTAATAATAATAAT
1 AATTAATAATAATAAT
15013 AAT
1 AAT
15016 AAAATAACGT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 1 0.04
16 21 0.75
17 6 0.21
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTAATAATAATAAT
Found at i:15017 original size:26 final size:26
Alignment explanation
Indices: 14969--15018 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
14959 CATTAAATTT
*
14969 ATAATTAATAATAAATAACATAAATA
1 ATAATTAATAATAAATAAAATAAATA
14995 ATAATTAATAAT-AATAATAATAAA
1 ATAATTAATAATAAATAA-AATAAA
15019 ATAACGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (26 bp):
ATAATTAATAATAAATAAAATAAATA
Found at i:16164 original size:30 final size:30
Alignment explanation
Indices: 16099--16206 Score: 94
Period size: 30 Copynumber: 3.5 Consensus size: 30
16089 GGAGGTCCCT
*
16099 AAACTGTC-CAAAAATCATATTTTGACCCCA
1 AAACT-TCTCAAAAATTATATTTTGACCCCA
* *
16129 AAACTTCTCCAAAATTATATTTTGACCCCC
1 AAACTTCTCAAAAATTATATTTTGACCCCA
* * * * *
16159 GAACTTTTCAAAAATTCCATTTTTTTACCCCCT
1 AAACTTCTCAAAAATT--ATATTTTGA-CCCCA
16192 AAACTT-TCAAAAATT
1 AAACTTCTCAAAAATT
16207 CCAATTTTAA
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
29 2 0.03
30 37 0.58
32 16 0.25
33 9 0.14
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (30 bp):
AAACTTCTCAAAAATTATATTTTGACCCCA
Found at i:16301 original size:58 final size:56
Alignment explanation
Indices: 16201--16642 Score: 444
Period size: 59 Copynumber: 7.7 Consensus size: 56
16191 TAAACTTTCA
* * *
16201 AAAATTCCAATTTTAACCTTAATTTTTCAAAAAATTACCATTTTACCCTCGAACATTCC
1 AAAATTCCATTTTTAACCTCAATTTTTC-CAAAATTACCATTTTACCC-CGAAC-TTCC
* *
16260 AAAATTCCATTTTTGACCTCGATTTTTCCAAAATTACCATTTTACCCCTGAACTTCC
1 AAAATTCCATTTTTAACCTCAATTTTTCCAAAATTACCATTTTACCCC-GAACTTCC
* * * * *
16317 AAAAATTCCATTTTTAACCCCTATTTTTCC-AAATTACTATTTTGCCCCCAAACTTCCC
1 -AAAATTCCATTTTTAACCTCAATTTTTCCAAAATTACCATTTT-ACCCCGAACTT-CC
* * * * *
16375 AAAATTCCAATTTT-ACCTTAATTTTT-TAAAATTACCATTTTACCCCTAAACTTCTT
1 AAAATTCCATTTTTAACCTCAATTTTTCCAAAATTACCATTTTACCCC-GAACTTC-C
* *
16431 AAAATTCCATTTTTAACCTTAATTTTTCCAAAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATTCCATTTTTAACCTCAATTTTTCC-AAAATTACCATTTTA-CCCCGAAC-TTCC
*
16490 AAAATTCCATTTTTAACCTCAATTTTTCAAAAAGTTACCA-TTTACCCCTGAACTTCTC
1 AAAATTCCATTTTTAACCTCAATTTTTCCAAAA-TTACCATTTTACCCC-GAACTTC-C
** * * * * *
16548 AAAAATTTTATTTTTTACCCCAATTTTTCTAAAATTACCATTTTACCCTGAA-TGCC
1 -AAAATTCCATTTTTAACCTCAATTTTTCCAAAATTACCATTTTACCCCGAACTTCC
* *
16604 TAAAATTCCATTTTTAACCTCGAACTTTTCTAAAATTAC
1 -AAAATTCCATTTTTAACCTC-AATTTTTCCAAAATTAC
16643 TAGTTTGCCC
Statistics
Matches: 327, Mismatches: 38, Indels: 38
0.81 0.09 0.09
Matches are distributed among these distances:
55 5 0.02
56 57 0.17
57 72 0.22
58 75 0.23
59 111 0.34
60 7 0.02
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.40
Consensus pattern (56 bp):
AAAATTCCATTTTTAACCTCAATTTTTCCAAAATTACCATTTTACCCCGAACTTCC
Found at i:16503 original size:29 final size:29
Alignment explanation
Indices: 16099--16504 Score: 170
Period size: 29 Copynumber: 13.8 Consensus size: 29
16089 GGAGGTCCCT
* * *
16099 AAACTGTCCAAAAAT-CATATTTTGACCCCA
1 AAACTTTCCAAAATTCCAT-TTTT-ACCCCC
** *
16129 AAACTTCTCCAAAATTATATTTTGACCCCC
1 AAACTT-TCCAAAATTCCATTTTTACCCCC
* *
16159 GAACTTTTCAAAAATTCCATTTTTTTACCCCC
1 AAAC-TTTCCAAAATTCCA--TTTTTACCCCC
* * * **
16191 TAAACTTTCAAAAATTCCAATTTTAACCTT
1 -AAACTTTCCAAAATTCCATTTTTACCCCC
** * *
16221 AATTTTTCAAAAAATTACCA-TTTTACCCTC
1 AAACTTTC-CAAAATT-CCATTTTTACCCCC
* * *
16251 GAACATTCCAAAATTCCATTTTTGA-CCTC
1 AAACTTTCCAAAATTCCATTTTT-ACCCCC
* ** *
16280 GATTTTTCCAAAATTACCA-TTTTACCCCT
1 AAACTTTCCAAAATT-CCATTTTTACCCCC
* *
16309 GAAC-TTCCAAAAATTCCATTTTTAACCCC
1 AAACTTTCC-AAAATTCCATTTTTACCCCC
* ** * *
16338 TATTTTTCC-AAATTAC-TATTTTGCCCCC
1 AAACTTTCCAAAATTCCAT-TTTTACCCCC
* * *
16366 AAACTTCCCAAAATTCCAATTTTA--CCT
1 AAACTTTCCAAAATTCCATTTTTACCCCC
* * ** *
16393 TAATTTTTTAAAATTACCA-TTTTACCCCT
1 AAACTTTCCAAAATT-CCATTTTTACCCCC
* * **
16422 AAAC-TTCTTAAAATTCCATTTTTAACCTT
1 AAACTTTC-CAAAATTCCATTTTTACCCCC
**
16451 AATTTTTCCAAAAATTACCA-TTTTACCCCC
1 AAACTTTCC-AAAATT-CCATTTTTACCCCC
16481 AAACTTTCCAAAATTCCATTTTTA
1 AAACTTTCCAAAATTCCATTTTTA
16505 ACCTCAATTT
Statistics
Matches: 284, Mismatches: 65, Indels: 55
0.70 0.16 0.14
Matches are distributed among these distances:
27 18 0.06
28 41 0.14
29 98 0.35
30 79 0.28
31 19 0.07
32 26 0.09
33 3 0.01
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.38
Consensus pattern (29 bp):
AAACTTTCCAAAATTCCATTTTTACCCCC
Found at i:16611 original size:230 final size:234
Alignment explanation
Indices: 16117--16642 Score: 633
Period size: 230 Copynumber: 2.2 Consensus size: 234
16107 CAAAAATCAT
* * * *
16117 ATTTTGACCCCAAAACTTCTCCAAAATT--ATATTTTGACCCCCGAACTTTTCAAAAATT-CCAT
1 ATTTTGACCCC-AAACTGC-CCAAAATTCCA-ATTTT-AACCTCGAACTTTTCTAAAATTACCA-
16179 TTTTTTACCCCCTAAACTTTCAAAAATTCCAATTTTAACCTTAATTTTTCAAAAAATTACCATTT
61 --TTTTACCCCCTAAACTTTCAAAAATTCCAATTTTAACCTTAATTTTTCAAAAAATTACCATTT
* * * * *
16244 TACCCTCGAACATTCCAAAATTCCATTTTTGACCTCGATTTTTCCAAAATTACCATTTTACCCCT
124 TACCCCCAAACATTCCAAAATTCCATTTTTAACCTCAATTTTTCAAAAATTACCATTTTACCCCT
* * *
16309 GAACTTCCAAAAATTCCATTTTTAACCCCTATTTTTCCAAATTACT
189 GAACTTCCAAAAATTCCATTTTTAACCCCAATTTTTCAAAATTACC
* * * *
16355 ATTTTGCCCCCAAACTTCCCAAAATTCCAATTTT-ACCT-TAA-TTTTTTAAAATTACCATTTTA
1 ATTTTGACCCCAAACTGCCCAAAATTCCAATTTTAACCTCGAACTTTTCTAAAATTACCATTTTA
* * *
16417 -CCCCTAAAC-TTCTTAAAATTCCATTTTTAACCTTAATTTTTCCAAAAATTACCATTTTACCCC
66 CCCCCTAAACTTTC-AAAAATTCCAATTTTAACCTTAATTTTTCAAAAAATTACCATTTTACCCC
*
16480 CAAACTTTCCAAAATTCCATTTTTAACCTCAATTTTTCAAAAAGTTACCA-TTTACCCCTGAACT
130 CAAACATTCCAAAATTCCATTTTTAACCTCAATTTTTCAAAAA-TTACCATTTTACCCCTGAACT
** *
16544 TCTCAAAAATTTTATTTTTTACCCCAATTTTTCTAAAATTACC
194 TC-CAAAAATTCCATTTTTAACCCCAATTTTTC-AAAATTACC
** * *
16587 ATTTT-ACCCTGAA-TGCCTAAAATTCCATTTTTAACCTCGAACTTTTCTAAAATTAC
1 ATTTTGACCCCAAACTGCCCAAAATTCCAATTTTAACCTCGAACTTTTCTAAAATTAC
16643 TAGTTTGCCC
Statistics
Matches: 249, Mismatches: 29, Indels: 25
0.82 0.10 0.08
Matches are distributed among these distances:
229 3 0.01
230 125 0.50
231 46 0.18
232 14 0.06
233 23 0.09
234 5 0.02
235 2 0.01
236 8 0.03
237 12 0.05
238 11 0.04
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (234 bp):
ATTTTGACCCCAAACTGCCCAAAATTCCAATTTTAACCTCGAACTTTTCTAAAATTACCATTTTA
CCCCCTAAACTTTCAAAAATTCCAATTTTAACCTTAATTTTTCAAAAAATTACCATTTTACCCCC
AAACATTCCAAAATTCCATTTTTAACCTCAATTTTTCAAAAATTACCATTTTACCCCTGAACTTC
CAAAAATTCCATTTTTAACCCCAATTTTTCAAAATTACC
Found at i:17934 original size:54 final size:54
Alignment explanation
Indices: 17852--17955 Score: 190
Period size: 54 Copynumber: 1.9 Consensus size: 54
17842 ACCCAGTACC
17852 GTCTTGCCATTTAACAATCCGGTTCAACGTTCCTTTTCCTTTGACCCTGCTACA
1 GTCTTGCCATTTAACAATCCGGTTCAACGTTCCTTTTCCTTTGACCCTGCTACA
* *
17906 GTCTTGCCATTTGACAATCCGGTTCAACGTTCCTTTTCCTTTGGCCCTGC
1 GTCTTGCCATTTAACAATCCGGTTCAACGTTCCTTTTCCTTTGACCCTGC
17956 AGAAGTTTCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.15, C:0.32, G:0.15, T:0.38
Consensus pattern (54 bp):
GTCTTGCCATTTAACAATCCGGTTCAACGTTCCTTTTCCTTTGACCCTGCTACA
Found at i:20128 original size:20 final size:20
Alignment explanation
Indices: 20070--20131 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 20
20060 ATTTCGAAAT
20070 AAAAGTTTTGAGTTTTTAAAA
1 AAAAG-TTTGAGTTTTTAAAA
*
20091 AAATAG--TGATTTTCTTAAAA
1 AAA-AGTTTGAGTTT-TTAAAA
20111 AAAAGTTT-AGATTTTTAAAA
1 AAAAGTTTGAG-TTTTTAAAA
20131 A
1 A
20132 TAAAAATAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
19 8 0.24
20 17 0.50
21 7 0.21
22 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (20 bp):
AAAAGTTTGAGTTTTTAAAA
Found at i:20136 original size:22 final size:20
Alignment explanation
Indices: 20070--20136 Score: 57
Period size: 22 Copynumber: 3.2 Consensus size: 20
20060 ATTTCGAAAT
20070 AAAAGTTTTGAGTTTTTAAAAA
1 AAAAG-TTTGA-TTTTTAAAAA
* *
20092 AATAG--TGATTTTCTTAAAA
1 AAAAGTTTGATTTT-TAAAAA
20111 AAAAGTTTAGATTTTTAAAAA
1 AAAAGTTT-GATTTTTAAAAA
20132 TAAAA
1 -AAAA
20137 ATAAGTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
18 4 0.11
19 12 0.33
21 6 0.17
22 14 0.39
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.39
Consensus pattern (20 bp):
AAAAGTTTGATTTTTAAAAA
Found at i:24906 original size:37 final size:38
Alignment explanation
Indices: 24855--24928 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 38
24845 ATTTAACTTT
*
24855 TCACATTTGGATATATTCCATTTAT-GGTGCATCATTG
1 TCACATTTGGATATATTCCATTTATGGGTGCAACATTG
* *
24892 TCACATTTGTATATATTGCATTTATGGGTGCAACATT
1 TCACATTTGGATATATTCCATTTATGGGTGCAACATT
24929 ATCATCTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 23 0.70
38 10 0.30
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (38 bp):
TCACATTTGGATATATTCCATTTATGGGTGCAACATTG
Found at i:26252 original size:8 final size:7
Alignment explanation
Indices: 26214--26259 Score: 56
Period size: 7 Copynumber: 6.0 Consensus size: 7
26204 ATTTTTTAAA
26214 AATATTT
1 AATATTT
26221 ATATTATTTT
1 A-A-TA-TTT
26231 AATATTT
1 AATATTT
26238 AATATTT
1 AATATTT
26245 AATAATTT
1 AAT-ATTT
26253 AATATTT
1 AATATTT
26260 TTTTATTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 18 0.51
8 10 0.29
9 3 0.09
10 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATATTT
Found at i:26252 original size:15 final size:14
Alignment explanation
Indices: 26214--26259 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 14
26204 ATTTTTTAAA
26214 AATATTTATATTATTTT
1 AATATTTA-A-TA-TTT
26231 AATATTTAATATTT
1 AATATTTAATATTT
26245 AATAATTTAATATTT
1 AAT-ATTTAATATTT
26260 TTTTATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.21
15 13 0.46
16 1 0.04
17 8 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AATATTTAATATTT
Found at i:26305 original size:59 final size:60
Alignment explanation
Indices: 26194--26313 Score: 140
Period size: 61 Copynumber: 2.0 Consensus size: 60
26184 CCACCCATAT
* *
26194 TATTTTTTTAATTTTTTAAAAATATTTATATTATTTTAATATTTAATATTTAATAATTTAA
1 TATTTTTTTAATTTATTAAAAATATTTATATTATCTTAATATTTAATATTTAAT-ATTTAA
* * *
26255 TATTTTTTT-ATTTATTAAAATTTTTATATAGTTATCTTAATA-TT-GT-TTTAATATTTAA
1 TATTTTTTTAATTTATTAAAAATATT-TATA-TTATCTTAATATTTAATATTTAATATTTAA
26313 T
1 T
26314 TAACGTAGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
58 7 0.13
59 6 0.12
60 14 0.27
61 15 0.29
62 10 0.19
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.62
Consensus pattern (60 bp):
TATTTTTTTAATTTATTAAAAATATTTATATTATCTTAATATTTAATATTTAATATTTAA
Found at i:30045 original size:29 final size:30
Alignment explanation
Indices: 30007--30070 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
29997 GGTTAATGTG
30007 CAATTGTATACAT-AAACTTTGAGTTGATA
1 CAATTGTATACATAAAACTTTGAGTTGATA
* * * *
30036 CAATTTTATACATAAAATTTTGATTTGATC
1 CAATTGTATACATAAAACTTTGAGTTGATA
30066 CAATT
1 CAATT
30071 CTTGTAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 12 0.40
30 18 0.60
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (30 bp):
CAATTGTATACATAAAACTTTGAGTTGATA
Found at i:33477 original size:30 final size:29
Alignment explanation
Indices: 33442--33634 Score: 108
Period size: 30 Copynumber: 6.6 Consensus size: 29
33432 TTCGGGGGTG
*
33442 AAATGGTAA-TTTTGGAAAAATCGAGATAAA
1 AAATGG-AAGTTTTGG-AAAATCGAGGTAAA
** ***
33472 AAATGGAAGTTTTGGAAGTTCGAGGGGTA
1 AAATGGAAGTTTTGGAAAATCGAGGTAAA
* * *
33501 AAATGGTAATTTTTGGAAAATCGGGGTTAA
1 AAATGG-AAGTTTTGGAAAATCGAGGTAAA
* *
33531 AAATGGAA-TTTTGGAAAGTTCAGGGGT-AA
1 AAATGGAAGTTTTGGAAA-ATC-GAGGTAAA
* * * *
33560 AAATGTAATTTTTAGAAAATAG-GGTAAA
1 AAATGGAAGTTTTGGAAAATCGAGGTAAA
* * * * *
33588 AAATGTAATTTTTAGAAAAATCAAGGTCAA
1 AAATGGAAGTTTT-GGAAAATCGAGGTAAA
*
33618 TAATGGAA-TTTTGGAAA
1 AAATGGAAGTTTTGGAAA
33635 GTTTGGCAGG
Statistics
Matches: 129, Mismatches: 26, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
27 3 0.02
28 29 0.22
29 39 0.30
30 58 0.45
ACGTcount: A:0.42, C:0.03, G:0.24, T:0.30
Consensus pattern (29 bp):
AAATGGAAGTTTTGGAAAATCGAGGTAAA
Found at i:33521 original size:59 final size:59
Alignment explanation
Indices: 33316--33604 Score: 272
Period size: 58 Copynumber: 5.0 Consensus size: 59
33306 TTTTGGTCAC
* ** *
33316 TCGA-GGGTAAAATGGTAATTTTGGGAAGTTCGAGGTAAAAAATAGAATTTTTAGACA--
1 TCGAGGGGTAAAATGGTAATTTTTGGAAAATCGAGGTAAAAAATGGAATTTTTAGA-AGT
* * * ** ** *
33373 TCGGGGGGTAAAATGGTAATTTTAGGAAAGTTTAGGGTTTAAAATGGAATTTTTAGATGT
1 TCGAGGGGTAAAATGGTAATTTTTGGAAAATCGA-GGTAAAAAATGGAATTTTTAGAAGT
* * * *
33433 TCG-GGGGTGAAATGGTAA-TTTTGGAAAAATCGAGATAAAAAATGGAAGTTTTGGAAGT
1 TCGAGGGGTAAAATGGTAATTTTTGG-AAAATCGAGGTAAAAAATGGAATTTTTAGAAGT
* * *
33491 TCGAGGGGTAAAATGGTAATTTTTGGAAAATCGGGGTTAAAAATGGAA-TTTTGGAAAGT
1 TCGAGGGGTAAAATGGTAATTTTTGGAAAATCGAGGTAAAAAATGGAATTTTTAG-AAGT
* * *
33550 TC-AGGGGTAAAAAT-GTAATTTTTAGAAAATAG-GGTAAAAAATGTAATTTTTAGAA
1 TCGAGGGGT-AAAATGGTAATTTTTGGAAAATCGAGGTAAAAAATGGAATTTTTAGAA
33605 AAATCAAGGT
Statistics
Matches: 192, Mismatches: 30, Indels: 20
0.79 0.12 0.08
Matches are distributed among these distances:
57 17 0.09
58 84 0.44
59 82 0.43
60 9 0.05
ACGTcount: A:0.38, C:0.03, G:0.28, T:0.31
Consensus pattern (59 bp):
TCGAGGGGTAAAATGGTAATTTTTGGAAAATCGAGGTAAAAAATGGAATTTTTAGAAGT
Found at i:33571 original size:58 final size:58
Alignment explanation
Indices: 33320--33599 Score: 223
Period size: 59 Copynumber: 4.8 Consensus size: 58
33310 GGTCACTCGA
* ** * * * * *
33320 GGGTAAAATGGTAATTTTGGGAAGTTCGAGGTAAAAAATAGAATTTTTAGACA--TCGGG
1 GGGTAAAATGGTAATTTTTGGAAAATCGGGGTAAAAAATGGAA-TTTTGGAAAGTTC-AG
* * ** ** * * *
33378 GGGTAAAATGGTAATTTTAGGAAAGTTTAGGGTTTAAAATGGAATTTT-TAGATGTTCGG
1 GGGTAAAATGGTAATTTTTGGAAA-ATCGGGGTAAAAAATGGAATTTTGGA-AAGTTCAG
* * *
33437 GGGTGAAATGGTAA-TTTTGGAAAAATCGAGATAAAAAATGGAAGTTTTGG-AAGTTCGAG
1 GGGTAAAATGGTAATTTTTGG-AAAATCGGGGTAAAAAATGGAA-TTTTGGAAAGTTC-AG
*
33496 GGGTAAAATGGTAATTTTTGGAAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCAG
1 GGGTAAAATGGTAATTTTTGGAAAATCGGGGTAAAAAATGGAATTTTGGAAAGTTCAG
* * *
33554 GGGTAAAAAT-GTAATTTTTAGAAAAT-AGGGTAAAAAATGTAATTTT
1 GGGT-AAAATGGTAATTTTTGGAAAATCGGGGTAAAAAATGGAATTTT
33600 TAGAAAAATC
Statistics
Matches: 180, Mismatches: 31, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
57 18 0.10
58 75 0.42
59 79 0.44
60 8 0.04
ACGTcount: A:0.38, C:0.03, G:0.28, T:0.32
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGGAAAATCGGGGTAAAAAATGGAATTTTGGAAAGTTCAG
Found at i:33592 original size:28 final size:28
Alignment explanation
Indices: 33496--33687 Score: 115
Period size: 30 Copynumber: 6.6 Consensus size: 28
33486 GAAGTTCGAG
* *
33496 GGGT-AAAATGGTAATTTTTGGAAAATCG
1 GGGTAAAAAT-GTAATTTTTAGAAAATCA
* * *
33524 GGGTTAAAAATGGAA-TTTTGGAAAGTTCA
1 GGG-TAAAAATGTAATTTTTAGAAA-ATCA
33553 GGGGTAAAAATGTAATTTTTAGAAAAT-A
1 -GGGTAAAAATGTAATTTTTAGAAAATCA
33581 GGGTAAAAAATGTAATTTTTAGAAAAATCA
1 GGGT-AAAAATGTAATTTTTAG-AAAATCA
* * * * * **
33611 AGGTCAATAATGGAA-TTTTGGAAAGTTT
1 GGGT-AAAAATGTAATTTTTAGAAAATCA
* *
33639 GGCAG-GAAAATGTAATTTTTAAAAAAATCA
1 GG--GTAAAAATGTAATTTTT-AGAAAATCA
*
33669 GGGTTAAAAATGGAATTTT
1 GGG-TAAAAATGTAATTTT
33688 GGAAAAGTTT
Statistics
Matches: 125, Mismatches: 25, Indels: 26
0.71 0.14 0.15
Matches are distributed among these distances:
27 4 0.03
28 43 0.34
29 31 0.25
30 47 0.38
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.32
Consensus pattern (28 bp):
GGGTAAAAATGTAATTTTTAGAAAATCA
Found at i:33628 original size:58 final size:59
Alignment explanation
Indices: 33558--33687 Score: 147
Period size: 58 Copynumber: 2.2 Consensus size: 59
33548 GTTCAGGGGT
* * *
33558 AAAAATGTAATTTTTAGAAAATAGGGTA-AAAAATGTAATTTTTAGAAAAATCAAGGTC
1 AAAAATGGAATTTTTAGAAAATAGGGCAGAAAAATGTAATTTTTAAAAAAATCAAGGTC
* * * ** * * *
33616 AATAATGGAA-TTTTGGAAAGTTTGGCAGGAAAATGTAATTTTTAAAAAAATCAGGGTT
1 AAAAATGGAATTTTTAGAAAATAGGGCAGAAAAATGTAATTTTTAAAAAAATCAAGGTC
33674 AAAAATGGAATTTT
1 AAAAATGGAATTTT
33688 GGAAAAGTTT
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
57 12 0.21
58 43 0.74
59 3 0.05
ACGTcount: A:0.46, C:0.03, G:0.18, T:0.32
Consensus pattern (59 bp):
AAAAATGGAATTTTTAGAAAATAGGGCAGAAAAATGTAATTTTTAAAAAAATCAAGGTC
Found at i:33688 original size:58 final size:59
Alignment explanation
Indices: 33587--33697 Score: 179
Period size: 58 Copynumber: 1.9 Consensus size: 59
33577 AATAGGGTAA
* *
33587 AAAATGTAATTTTTAGAAAAATCAAGGTCAATAATGGAATTTTGG-AAAGTTTGGCAGG
1 AAAATGTAATTTTTAAAAAAATCAAGGTCAAAAATGGAATTTTGGAAAAGTTTGGCAGG
* *
33645 AAAATGTAATTTTTAAAAAAATCAGGGTTAAAAATGGAATTTTGGAAAAGTTT
1 AAAATGTAATTTTTAAAAAAATCAAGGTCAAAAATGGAATTTTGGAAAAGTTT
33698 AGTGGTCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
58 41 0.85
59 7 0.15
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.32
Consensus pattern (59 bp):
AAAATGTAATTTTTAAAAAAATCAAGGTCAAAAATGGAATTTTGGAAAAGTTTGGCAGG
Found at i:33693 original size:29 final size:29
Alignment explanation
Indices: 33442--33693 Score: 131
Period size: 29 Copynumber: 8.6 Consensus size: 29
33432 TTCGGGGGTG
* *
33442 AAATGGTAATTTTGGAAAAATC-GAGATAAA
1 AAATGG-AATTTTGGAAAAATCAG-GGTTAA
** *
33472 AAATGGAAGTTTTGG-AAGTTCGAGGGGT-A
1 AAATGGAA-TTTTGGAAAAATC-AGGGTTAA
*
33501 AAATGGTAATTTTTGG-AAAATCGGGGTTAA
1 AAATGG-AA-TTTTGGAAAAATCAGGGTTAA
** *
33531 AAATGGAATTTTGGAAAGTTCAGGGGTAA
1 AAATGGAATTTTGGAAAAATCAGGGTTAA
* * *
33560 AAATGTAATTTT-TAGAAAAT-AGGGTAAA
1 AAATGGAATTTTGGA-AAAATCAGGGTTAA
* * * *
33588 AAATGTAATTTTTAGAAAAATCAAGGTCAA
1 AAATGGAA-TTTTGGAAAAATCAGGGTTAA
* * ** ****
33618 TAATGGAATTTTGG-AAAGTTTGGCAGGA
1 AAATGGAATTTTGGAAAAATCAGGGTTAA
* **
33646 AAATGTAATTTTTAAAAAAATCAGGGTTAA
1 AAATGGAA-TTTTGGAAAAATCAGGGTTAA
33676 AAATGGAATTTTGGAAAA
1 AAATGGAATTTTGGAAAA
33694 GTTTAGTGGT
Statistics
Matches: 162, Mismatches: 48, Indels: 25
0.69 0.20 0.11
Matches are distributed among these distances:
28 33 0.20
29 69 0.43
30 59 0.36
31 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.24, T:0.30
Consensus pattern (29 bp):
AAATGGAATTTTGGAAAAATCAGGGTTAA
Found at i:34882 original size:13 final size:13
Alignment explanation
Indices: 34815--34875 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 13
34805 CTCTTCCTCT
34815 TTTATTATTAATA
1 TTTATTATTAATA
* **
34828 TTTATTAATGCTA
1 TTTATTATTAATA
** *
34841 TTTATTACCACTA
1 TTTATTATTAATA
*
34854 TTTATAATTAATA
1 TTTATTATTAATA
34867 -TTATTATTA
1 TTTATTATTA
34876 TTTATTAAAA
Statistics
Matches: 37, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
12 8 0.22
13 29 0.78
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (13 bp):
TTTATTATTAATA
Found at i:35626 original size:17 final size:17
Alignment explanation
Indices: 35596--35658 Score: 99
Period size: 17 Copynumber: 3.7 Consensus size: 17
35586 TCTATTTAAT
35596 TTAAAATAAATTTAAAC
1 TTAAAATAAATTTAAAC
* * *
35613 TTAAAGTAAGTTTAAAT
1 TTAAAATAAATTTAAAC
35630 TTAAAATAAATTTAAAC
1 TTAAAATAAATTTAAAC
35647 TTAAAATAAATT
1 TTAAAATAAATT
35659 AAAGTTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
TTAAAATAAATTTAAAC
Found at i:36547 original size:97 final size:98
Alignment explanation
Indices: 36070--36549 Score: 481
Period size: 97 Copynumber: 4.9 Consensus size: 98
36060 CTTTAATATG
** * * * * * *
36070 CGTGGTACTAAATTCGCCGTTGTGACTTAAAT-TTTCCTTTTATGCTTCTGAGGTA-TAAGGTTT
1 CGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTACT-AGGTTC
* * *
36133 ACCATTGCGAATTAAACCTTTCTCTT-GTGTCTT
65 GCCATTGCGACTTAAACCTTTCCCTTCGTGTCTT
* * *
36166 CGTGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTCTCCT-AGGGACTAGGTTC
1 CGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGT-TTCTGAGGTACTAGGTTC
** * *
36230 ATCGTTGCGACTTAAACCTTTCCTTTCGTGTCTT
65 GCCATTGCGACTTAAACCTTTCCCTTCGTGTCTT
* * * *
36264 CATGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTGTTC-GTGGTACT-GGATT
1 CGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGT-TTCTGAGGTACTAGG-TT
* * * *
36327 CGCCATTGCGGCTTTAAATCTTTTCCCTTCATGTCTC
64 CGCCATTGCGAC-TTAAA-CCTTTCCCTTCGTGTCTT
* * * * * * * * * * *
36364 CGAGGTACTAGG-TTTGCCATCGCGACTTAAACCTATCCCTTCATGTCTCTGGGGTATTAGGTTT
1 CGTGGTACT-GGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTACTAGGTTC
*
36428 GTCATTGCGACTTAAACCTTTCCCTT-GTGTCTT
65 GCCATTGCGACTTAAACCTTTCCCTTCGTGTCTT
* *
36461 CGTGGTACTGGATTCGCCGTTACGGCTTAAATCTTTCCCTTCATGTTTCAGAGGTACTAGGTTCG
1 CGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTACTAGGTTCG
36526 CCATTGCGACTTAAACCTTTCCCT
66 CCATTGCGACTTAAACCTTTCCCT
36550 CCATGTTTTG
Statistics
Matches: 307, Mismatches: 65, Indels: 23
0.78 0.16 0.06
Matches are distributed among these distances:
96 29 0.09
97 119 0.39
98 79 0.26
99 12 0.04
100 64 0.21
101 4 0.01
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (98 bp):
CGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTACTAGGTTCG
CCATTGCGACTTAAACCTTTCCCTTCGTGTCTT
Found at i:36556 original size:49 final size:48
Alignment explanation
Indices: 36134--36557 Score: 338
Period size: 49 Copynumber: 8.7 Consensus size: 48
36124 ATAAGGTTTA
* * *
36134 CCATTGCGAATTAAACCTTTCTCTT-GTGTCTTCGTGGTACTGGATTCG
1 CCATTGCGACTTAAACCTTTCCCTTCATGT-TTCGTGGTACTGGATTCG
* * * * * *
36182 CCATTGCGGCTTAAATCTTTCCCTTCATGTCTCCTAGGGACTAGG-TTCA
1 CCATTGCGACTTAAACCTTTCCCTTCATGTTTCGT-GGTACT-GGATTCG
* * * * * *
36231 TCGTTGCGACTTAAACCTTTCCTTTCGTGTCTTCATGGTACTGGATCCG
1 CCATTGCGACTTAAACCTTTCCCTTCATGT-TTCGTGGTACTGGATTCG
* * * *
36280 CCGTTGCGGCTTAGATCTTTCCCTTCATGTGTTCGTGGTACTGGATTCG
1 CCATTGCGACTTAAACCTTTCCCTTCATGT-TTCGTGGTACTGGATTCG
* * * * *
36329 CCATTGCGGCTTTAAATCTTTTCCCTTCATGTCTCCGAGGTACTAGG-TTTG
1 CCATTGCGAC-TTAAA-CCTTTCCCTTCATGT-TTCGTGGTACT-GGATTCG
* * * * * *
36380 CCATCGCGACTTAAACCTATCCCTTCATGTCTCTGGGGTATTAGG-TTTG
1 CCATTGCGACTTAAACCTTTCCCTTCATGTTTC-GTGGTACT-GGATTCG
* *
36429 TCATTGCGACTTAAACCTTTCCCTT-GTGTCTTCGTGGTACTGGATTCG
1 CCATTGCGACTTAAACCTTTCCCTTCATGT-TTCGTGGTACTGGATTCG
* * * * *
36477 CCGTTACGGCTTAAATCTTTCCCTTCATGTTTCAGAGGTACTAGG-TTCG
1 CCATTGCGACTTAAACCTTTCCCTTCATGTTTC-GTGGTACT-GGATTCG
*
36526 CCATTGCGACTTAAACCTTTCCCTCCATGTTT
1 CCATTGCGACTTAAACCTTTCCCTTCATGTTT
36558 TGCGATACTG
Statistics
Matches: 297, Mismatches: 65, Indels: 27
0.76 0.17 0.07
Matches are distributed among these distances:
47 2 0.01
48 62 0.21
49 182 0.61
50 16 0.05
51 33 0.11
52 2 0.01
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.38
Consensus pattern (48 bp):
CCATTGCGACTTAAACCTTTCCCTTCATGTTTCGTGGTACTGGATTCG
Found at i:37012 original size:18 final size:18
Alignment explanation
Indices: 36986--37020 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
36976 AAAATTGTCG
*
36986 AATATTTACAAGGAACAA
1 AATAATTACAAGGAACAA
37004 AATAATTACAAGGAACA
1 AATAATTACAAGGAACA
37021 GTATTAGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.20
Consensus pattern (18 bp):
AATAATTACAAGGAACAA
Found at i:47909 original size:97 final size:97
Alignment explanation
Indices: 47734--47927 Score: 250
Period size: 97 Copynumber: 2.0 Consensus size: 97
47724 AACTTTGGAA
* * *
47734 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTCACACCTAATAAGTTAAGGAACAAATTTTCA
1 AAGGATATTCGACTATCTCGATTTGAAGAAAAATCACACCTAACAAGTTAAGGAACAAATTTTCA
* *
47799 GAATCAGAGAT-AAAGAAACATTGCCTCGATTT
66 AAATCAGAAATAAAAG-AACATTGCCTCGATTT
* * *
47831 AAGGGTATTCGACTAT-TCCGATTTGAAGAAAAATCGCACCTAACAAGTTAAGGCACAAATTTTC
1 AAGGATATTCGACTATCT-CGATTTGAAGAAAAATCACACCTAACAAGTTAAGGAACAAATTTTC
* *
47895 AAAACTC-GAAATAAAAGAATATTGCCTTGATTT
65 AAAA-TCAGAAATAAAAGAACATTGCCTCGATTT
47928 TGAAGTTTTC
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
96 1 0.01
97 77 0.92
98 6 0.07
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (97 bp):
AAGGATATTCGACTATCTCGATTTGAAGAAAAATCACACCTAACAAGTTAAGGAACAAATTTTCA
AAATCAGAAATAAAAGAACATTGCCTCGATTT
Found at i:48261 original size:29 final size:28
Alignment explanation
Indices: 48160--48381 Score: 132
Period size: 30 Copynumber: 7.6 Consensus size: 28
48150 ATACCCAAAG
* **
48160 GGGTAAAATGGTAA-TTTTGGACACTCGA
1 GGGTAAAATGGTAATTTTTAGACA-TTTA
* * * * *
48188 GGGAAAAAT-GTAATTTTGAGAAAGTTC
1 GGGTAAAATGGTAATTTTTAGACATTTA
48215 GAGGTCAAAAATGG-AATTTTTAGACATTTAA
1 G-GGT--AAAATGGTAATTTTTAGACATTT-A
* * *
48246 GGGTAAAATGGTAATTTTTGGAAAGTTTG
1 GGGTAAAATGGTAATTTTTAGACA-TTTA
*
48275 GGGTTTAAAAT-GAAATTTTTAGACATTTGA
1 GGG--TAAAATGGTAATTTTTAGACATTT-A
*
48305 GGGTAAAATGGTATTTTTTAGGA-AGTTTA
1 GGGTAAAATGGTAATTTTTA-GACA-TTTA
**
48334 GGGTTTAAAATGG-AATTTTTAGACATATGG
1 GGG--TAAAATGGTAATTTTTAGACAT-TTA
*
48364 GGGTAAAATGGTTATTTT
1 GGGTAAAATGGTAATTTT
48382 AAGAAAAATA
Statistics
Matches: 149, Mismatches: 26, Indels: 37
0.70 0.12 0.17
Matches are distributed among these distances:
27 5 0.03
28 37 0.25
29 37 0.25
30 54 0.36
31 16 0.11
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.36
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTTAGACATTTA
Found at i:48270 original size:59 final size:58
Alignment explanation
Indices: 48163--48381 Score: 230
Period size: 59 Copynumber: 3.7 Consensus size: 58
48153 CCCAAAGGGG
* * * * *
48163 TAAAATGGTAA-TTTTGGACACTCGAGGGAAAAAT-GTAA-TTTTGAGAAAGTTCGAGGTC
1 TAAAATGG-AATTTTTAGACATTTGAGGGTAAAATGGTAATTTTTG-GAAAGTT-GAGGTT
* * *
48221 AAAAATGGAATTTTTAGACATTTAAGGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTT
1 TAAAATGGAATTTTTAGACATTTGAGGGTAAAATGGTAATTTTTGGAAAG-TTGAGGTT
* * *
48280 TAAAATGAAATTTTTAGACATTTGAGGGTAAAATGGTATTTTTTAGG-AAGTTTAGGGTT
1 TAAAATGGAATTTTTAGACATTTGAGGGTAAAATGGTAATTTTT-GGAAAGTTGA-GGTT
* * *
48339 TAAAATGGAATTTTTAGACATATGGGGGTAAAATGGTTATTTT
1 TAAAATGGAATTTTTAGACATTTGAGGGTAAAATGGTAATTTT
48382 AAGAAAAATA
Statistics
Matches: 136, Mismatches: 19, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
57 2 0.01
58 27 0.20
59 98 0.72
60 9 0.07
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.37
Consensus pattern (58 bp):
TAAAATGGAATTTTTAGACATTTGAGGGTAAAATGGTAATTTTTGGAAAGTTGAGGTT
Found at i:48355 original size:30 final size:29
Alignment explanation
Indices: 48222--48374 Score: 113
Period size: 29 Copynumber: 5.2 Consensus size: 29
48212 TTCGAGGTCA
48222 AAAATGGAATTTTTA-GACATTTAAGGGT
1 AAAATGGAATTTTTAGGACATTTAAGGGT
* *
48250 AAAATGGTAATTTTT-GGAAAGTTT-GGGGTTT
1 AAAATGG-AATTTTTAGGACA-TTTAAGGG--T
* *
48281 AAAATGAAATTTTTA-GACATTTGAGGGT
1 AAAATGGAATTTTTAGGACATTTAAGGGT
*
48309 AAAATGGTATTTTTTAGGA-AGTTT-AGGGTTT
1 AAAATGG-AATTTTTAGGACA-TTTAAGGG--T
* **
48340 AAAATGGAATTTTTA-GACATATGGGGGT
1 AAAATGGAATTTTTAGGACATTTAAGGGT
48368 AAAATGG
1 AAAATGG
48375 TTATTTTAAG
Statistics
Matches: 101, Mismatches: 10, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
28 22 0.22
29 32 0.32
30 32 0.32
31 15 0.15
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.37
Consensus pattern (29 bp):
AAAATGGAATTTTTAGGACATTTAAGGGT
Found at i:48409 original size:29 final size:29
Alignment explanation
Indices: 48340--48469 Score: 102
Period size: 29 Copynumber: 4.4 Consensus size: 29
48330 TTTAGGGTTT
* * * *
48340 AAAATGGAATTTTTAGACATATGGGGGT-
1 AAAATGGAATTTTAAGAAAAATAGGGGTA
*
48368 AAAATGGTTATTTTAAGAAAAATAGGGGTA
1 AAAATGG-AATTTTAAGAAAAATAGGGGTA
** *
48398 AAAATGGAATTTTAA-AAAGTTCAAGGGTA
1 AAAATGGAATTTTAAGAAAAAT-AGGGGTA
* * * *
48427 AAAATGTAATTTCAAAAAAAATTAGGGTTA
1 AAAATGGAATTTTAAGAAAAA-TAGGGGTA
*
48457 AAAATAGAATTTT
1 AAAATGGAATTTT
48470 GGAAAAGTTT
Statistics
Matches: 79, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
28 11 0.14
29 42 0.53
30 25 0.32
31 1 0.01
ACGTcount: A:0.47, C:0.02, G:0.20, T:0.31
Consensus pattern (29 bp):
AAAATGGAATTTTAAGAAAAATAGGGGTA
Found at i:48510 original size:30 final size:30
Alignment explanation
Indices: 48390--48503 Score: 88
Period size: 30 Copynumber: 3.8 Consensus size: 30
48380 TTAAGAAAAA
* *
48390 TAGGGGTAAAAATGGAATTTT-AAAAAGTT
1 TAGGGGTAAAAATAGAATTTTGGAAAAGTT
* * *** **
48419 CAAGGGTAAAAAT-GTAATTTCAAAAAAAAT
1 TAGGGGTAAAAATAG-AATTTTGGAAAAGTT
*
48449 TAGGGTTAAAAATAGAATTTTGGAAAAGTT
1 TAGGGGTAAAAATAGAATTTTGGAAAAGTT
* *
48479 TAGGGGTGAAAATATGATTTTTGGA
1 TAGGGGTAAAAATA-GAATTTTGGA
48504 TAGTTTAAGG
Statistics
Matches: 65, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
28 1 0.02
29 16 0.25
30 38 0.58
31 10 0.15
ACGTcount: A:0.45, C:0.02, G:0.23, T:0.31
Consensus pattern (30 bp):
TAGGGGTAAAAATAGAATTTTGGAAAAGTT
Found at i:50475 original size:23 final size:23
Alignment explanation
Indices: 50431--50477 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
50421 AATTCTAAAA
*
50431 TAAATTTAAACTTAAAGTAAGTT
1 TAAATTTAAACATAAAGTAAGTT
*
50454 TAAATTTAAA-ATAAATTAAAGTT
1 TAAATTTAAACATAAAGT-AAGTT
50477 T
1 T
50478 TAAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.40
Consensus pattern (23 bp):
TAAATTTAAACATAAAGTAAGTT
Found at i:50482 original size:18 final size:17
Alignment explanation
Indices: 50400--50470 Score: 99
Period size: 17 Copynumber: 4.2 Consensus size: 17
50390 TTTTAATTCT
50400 ATTT-AATTTAAAATAA
1 ATTTAAATTTAAAATAA
50416 ATTTAAATTCTAAAATAA
1 ATTTAAATT-TAAAATAA
* *
50434 ATTTAAACTTAAAGTAA
1 ATTTAAATTTAAAATAA
*
50451 GTTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
50468 ATT
1 ATT
50471 AAAGTTTTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
16 4 0.09
17 27 0.57
18 16 0.34
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:51032 original size:31 final size:30
Alignment explanation
Indices: 50996--51068 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 30
50986 GATTAAATAG
*
50996 AAATTAAAGTTTCA-AGTATATATTTGAACC
1 AAATTAAAGTTTCATA-TATATAATTGAACC
* * * *
51026 ACAATTAGATTTTTATATATATAATTGCACC
1 A-AATTAAAGTTTCATATATATAATTGAACC
51057 AAATTAAAGTTT
1 AAATTAAAGTTT
51069 ATGTATACAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
30 10 0.29
31 23 0.68
32 1 0.03
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (30 bp):
AAATTAAAGTTTCATATATATAATTGAACC
Found at i:51069 original size:29 final size:29
Alignment explanation
Indices: 50996--51080 Score: 73
Period size: 31 Copynumber: 2.8 Consensus size: 29
50986 GATTAAATAG
*
50996 AAATTAAAGTTTCA-AGTATATATTTGAACC
1 AAATTAAAGTTT-ATA-TATATAATTGAACC
** *
51026 ACAATTAGATTTTTATATATATAATTGCACC
1 A-AATTA-AAGTTTATATATATAATTGAACC
* *
51057 AAATTAAAGTTTATGTATACAATT
1 AAATTAAAGTTTATATATATAATT
51081 TCACATTAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
29 14 0.32
30 6 0.14
31 19 0.43
32 5 0.11
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.40
Consensus pattern (29 bp):
AAATTAAAGTTTATATATATAATTGAACC
Found at i:52432 original size:18 final size:18
Alignment explanation
Indices: 52399--52451 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
52389 TCTCACATCC
52399 TTGTTTTAG-A-TTAAAT
1 TTGTTTTAGAATTTAAAT
52415 TTGTTTTAGAATTTAAAT
1 TTGTTTTAGAATTTAAAT
*
52433 TTATTTTA-AATTTAAAT
1 TTGTTTTAGAATTTAAAT
52450 TT
1 TT
52452 AATTTAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
16 9 0.26
17 12 0.35
18 13 0.38
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (18 bp):
TTGTTTTAGAATTTAAAT
Found at i:52446 original size:17 final size:17
Alignment explanation
Indices: 52409--52501 Score: 96
Period size: 17 Copynumber: 5.4 Consensus size: 17
52399 TTGTTTTAGA
*
52409 TTAAATTTGTTTTAGAAT
1 TTAAATTTATTTTA-AAT
52427 TTAAATTTATTTTAAAT
1 TTAAATTTATTTTAAAT
* *
52444 TTAAATTTAATTTAAGT
1 TTAAATTTATTTTAAAT
* *
52461 TTAGATTCATTTTCAAAT
1 TTAAATTTATTTT-AAAT
* *
52479 TTAAAATTATTATAAAT
1 TTAAATTTATTTTAAAT
*
52496 TAAAAT
1 TTAAAT
52502 AAATAAAATT
Statistics
Matches: 61, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
17 36 0.59
18 25 0.41
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (17 bp):
TTAAATTTATTTTAAAT
Found at i:52448 original size:35 final size:35
Alignment explanation
Indices: 52409--52501 Score: 91
Period size: 35 Copynumber: 2.7 Consensus size: 35
52399 TTGTTTTAGA
** *
52409 TTAAATTTGTTTTAGAATTTAAATTTATTTT-AAAT
1 TTAAATTTAATTTA-AATTTAAATTCATTTTCAAAT
* *
52444 TTAAATTTAATTTAAGTTTAGATTCATTTTCAAAT
1 TTAAATTTAATTTAAATTTAAATTCATTTTCAAAT
* *
52479 TTAAAATT-ATTATAAATTAAAAT
1 TTAAATTTAATT-TAAATTTAAAT
52502 AAATAAAATT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
34 16 0.34
35 31 0.66
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (35 bp):
TTAAATTTAATTTAAATTTAAATTCATTTTCAAAT
Found at i:53178 original size:3 final size:3
Alignment explanation
Indices: 53170--53242 Score: 76
Period size: 3 Copynumber: 24.0 Consensus size: 3
53160 AAATGGTTAT
* ** * *
53170 TAA TAA TAA TAT TAA TAA TAA TAA -ATA TTG TAA TAA TGA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
53215 TAA TTAA TAA TAA TAA TAA TAA TAA TAA
1 TAA -TAA TAA TAA TAA TAA TAA TAA TAA
53243 AAGTCGAAAC
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
2 1 0.02
3 53 0.93
4 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:54289 original size:29 final size:29
Alignment explanation
Indices: 54256--54541 Score: 247
Period size: 29 Copynumber: 9.7 Consensus size: 29
54246 CTAAACTATT
54256 CAAAAATTCCATTTTTACCCTCGAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTC
* *
54285 CAAAAAAATCACATTTTTACCCCCGAACTTC
1 C-AAAAATTC-CATTTTTACCCTCGAACTTC
* * *
54316 TAAAAATCCCATTTTTGACCC-CAAAACTTC
1 CAAAAATTCCATTTTT-ACCCTC-GAACTTC
* *
54346 CAAAAATTTCATTTTTACCCTTGAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTC
** **
54375 CAAAAACCCCATTTTTAACCCTAAAACTTC
1 CAAAAATTCCATTTTT-ACCCTCGAACTTC
*
54405 CAAAAATTCCTTTTTTACCCTCGAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTC
* * * **
54434 TAAAAATCCCATTTTGACCCTAAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTC
* * *
54463 C-AAATTTTCATTTTTACCC-CTAAACTTC
1 CAAAAATTCCATTTTTACCCTC-GAACTTC
* * * *
54491 CAAAAATCCCATTTTTAACCTTGAATTTTCC
1 CAAAAATTCCATTTTTACCCTCGAA-CTT-C
54522 CAAAAATTACCA-TTTTACCC
1 CAAAAATT-CCATTTTTACCC
54542 CCAGGTATCC
Statistics
Matches: 203, Mismatches: 42, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
28 22 0.11
29 82 0.40
30 62 0.31
31 34 0.17
32 3 0.01
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.34
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCTCGAACTTC
Found at i:54372 original size:59 final size:59
Alignment explanation
Indices: 54256--54506 Score: 285
Period size: 59 Copynumber: 4.3 Consensus size: 59
54246 CTAAACTATT
* * **
54256 CAAAAATTCCATTTTT-ACCCTC-GAACTTCCAAAAAAATCACATTTTTACCCCCGAACTTC
1 CAAAAATCCCATTTTTGACCC-CAAAACTTCC--AAAAATTTCATTTTTACCCCCGAACTTC
* **
54316 TAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTTCATTTTTACCCTTGAACTTC
1 CAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTTCATTTTTACCCCCGAACTTC
* * * * * *
54375 CAAAAACCCCATTTTTAACCCTAAAACTTCCAAAAATTCCTTTTTTACCCTCGAACTTC
1 CAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTTCATTTTTACCCCCGAACTTC
* * * **
54434 TAAAAATCCCA-TTTTGACCCTAAAACTTCC-AAATTTTCATTTTTACCCCTAAACTTC
1 CAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTTCATTTTTACCCCCGAACTTC
54491 CAAAAATCCCATTTTT
1 CAAAAATCCCATTTTT
54507 AACCTTGAAT
Statistics
Matches: 164, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
57 31 0.19
58 22 0.13
59 85 0.52
60 15 0.09
61 11 0.07
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.34
Consensus pattern (59 bp):
CAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTTCATTTTTACCCCCGAACTTC
Found at i:59737 original size:16 final size:16
Alignment explanation
Indices: 59716--59746 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59706 ATATTTACAG
*
59716 GGAAAAATAATATAAT
1 GGAAAAATAAAATAAT
59732 GGAAAAATAAAATAA
1 GGAAAAATAAAATAA
59747 AAAAGTACCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (16 bp):
GGAAAAATAAAATAAT
Found at i:63466 original size:83 final size:84
Alignment explanation
Indices: 63128--63560 Score: 362
Period size: 83 Copynumber: 5.0 Consensus size: 84
63118 ATTTTGAAGT
* * * * *
63128 TGGTAAGTGTTTCTTTTCTGTTTATATAAAAAAGTTCTATTTTTTAGGTTTTGTTTGGATGGTCG
1 TGGTAAGTGTTT-TTTTCTGTTCATATAAAAAA-TTGTATATTTTGGGTTTTGTTTGGATGGTCT
* *
63193 GAAAAAGCAAGAAAATAATTG
64 GAAAATGCAAGAAAATAATGG
* * * *
63214 TGGTAAGTGTTTATCTTTTTCTGTTCATATAAAAAAATGTCTCCTTTTCTGAGTTTTGTTTGGAT
1 TGGTAAGTG--T-T-TTTTTCTGTTCATATAAAAAATTGTAT--ATTT-TGGGTTTTGTTTGGAT
** *
63279 TATCTGAAAATGCAAGAAAATAACGG
59 GGTCTGAAAATGCAAGAAAATAATGG
** * ** *
63305 TTATAAGTGTTTTTTTTTTTTCTGTTCATATAAAAAA-AGTATA-----CATTTTGTTTAGATGG
1 TGGTAAGTG-----TTTTTTTCTGTTCATATAAAAAATTGTATATTTTGGGTTTTGTTTGGATGG
63364 TCTGAAAATGCAAGAAAATAATGG
61 TCTGAAAATGCAAGAAAATAATGG
* *
63388 TGGTAAGTGTTTTTTTCTGTTCATATAAAAAATTGTATATTTTGGGTTTTGTTTGGATGCTCCGA
1 TGGTAAGTGTTTTTTTCTGTTCATATAAAAAATTGTATATTTTGGGTTTTGTTTGGATGGTCTGA
63453 AAATGCAAG-AAATAATGG
66 AAATGCAAGAAAATAATGG
* ** *** * *
63471 TAGTATCT-TTTTTTTCTGTTCATATAGAAAAAGCCTCAT-TTTATGGGTTTTGATTGGATGGTT
1 TGGTAAGTGTTTTTTTCTGTTCATATA-AAAAATTGT-ATATTT-TGGGTTTTGTTTGGATGGTC
*
63534 TGAAAATACAAGAAAAATAATGG
63 TGAAAATGCAAG-AAAATAATGG
63557 TGGT
1 TGGT
63561 GAGTAGAGTT
Statistics
Matches: 283, Mismatches: 43, Indels: 42
0.77 0.12 0.11
Matches are distributed among these distances:
78 23 0.08
79 5 0.02
82 18 0.06
83 64 0.23
84 54 0.19
86 21 0.07
88 4 0.01
89 20 0.07
90 5 0.02
91 44 0.16
92 21 0.07
93 1 0.00
94 3 0.01
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (84 bp):
TGGTAAGTGTTTTTTTCTGTTCATATAAAAAATTGTATATTTTGGGTTTTGTTTGGATGGTCTGA
AAATGCAAGAAAATAATGG
Found at i:66051 original size:96 final size:96
Alignment explanation
Indices: 65872--66058 Score: 211
Period size: 96 Copynumber: 1.9 Consensus size: 96
65862 GCGAAAAAGA
* ** * * *
65872 TATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCATAATATTTCGGAATC
1 TATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCATAATATTTCGAAACC
*
65937 GAAGATAAGGAAACATTGCCTCGATTAAGGG
66 GAAGATAAAGAAACATTGCCTCGATTAAGGG
* *
65968 TATTCGATTATTTCGATTTGAAGAAAAATTACACCTAGTGAGTTAAGGCGGA-AAT-TTTCGAAA
1 TATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGC--ATAATATTTCGAAA
* *
66031 CCCGAA-ATAAA-AGAATATTGCCTTGATT
64 -CCGAAGATAAAGA-AACATTGCCTCGATT
66059 TTAAAGTTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
95 1 0.01
96 67 0.88
97 7 0.09
98 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (96 bp):
TATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCATAATATTTCGAAACC
GAAGATAAAGAAACATTGCCTCGATTAAGGG
Found at i:66394 original size:29 final size:30
Alignment explanation
Indices: 66349--66762 Score: 289
Period size: 30 Copynumber: 14.0 Consensus size: 30
66339 AAACATTCAG
*
66349 GGGTAAAAGGGTAA-TTTTGGAAAGTT-GA
1 GGGTAAAATGGTAATTTTTGGAAAGTTCGA
*
66377 GGGTCAAAAATGG-GATTTTTGG-AAGTTC-A
1 GGGT--AAAATGGTAATTTTTGGAAAGTTCGA
*
66406 GGGGTAAAATGGTAATTTTTGGAAAGTT-GG
1 -GGGTAAAATGGTAATTTTTGGAAAGTTCGA
* * *
66436 GGGTCAAAAATGG-GACTTTTGG-AAGTTCGG
1 GGGT--AAAATGGTAATTTTTGGAAAGTTCGA
66466 GGGTAAAATGGTAA-TTTT-GAAAGGTTCG-
1 GGGTAAAATGGTAATTTTTGGAAA-GTTCGA
* *
66494 GGGTCAAAAAT-G-AGATTTTTTG-AAGTTCGG
1 GGGT--AAAATGGTA-ATTTTTGGAAAGTTCGA
*
66524 GGGTAAAATGGTAA-TTTTGGAAGGTTCG-
1 GGGTAAAATGGTAATTTTTGGAAAGTTCGA
*
66552 GGGTTAAAATGGTAA-TTTTGGAAGGTTC-A
1 GGG-TAAAATGGTAATTTTTGGAAAGTTCGA
* * * * *
66581 GGATCAAAAATGG-GACTTTTGGGAAGTTCGG
1 GGGT--AAAATGGTAATTTTTGGAAAGTTCGA
*
66612 GGGTAAAATGGTAATTTTTGGAAGGTTCG-
1 GGGTAAAATGGTAATTTTTGGAAAGTTCGA
* * * * *
66641 GGGTTGAAAATGG-GACTTTTGGGAAGTTTGG
1 GGG-T-AAAATGGTAATTTTTGGAAAGTTCGA
*
66672 GGGTAAAATGGTAATTTTTGGAAGGTTCG-
1 GGGTAAAATGGTAATTTTTGGAAAGTTCGA
* * *
66701 GGGTCGAAAATGG-GACTTTTGGGAAGTTCGA
1 GGGT--AAAATGGTAATTTTTGGAAAGTTCGA
*
66732 GGGTAAAATGGTAATTTTTGGAAGGTTCGA
1 GGGTAAAATGGTAATTTTTGGAAAGTTCGA
66762 G
1 G
66763 ATCAAAAATG
Statistics
Matches: 311, Mismatches: 37, Indels: 74
0.74 0.09 0.18
Matches are distributed among these distances:
27 1 0.00
28 43 0.14
29 100 0.32
30 135 0.43
31 32 0.10
ACGTcount: A:0.29, C:0.05, G:0.35, T:0.31
Consensus pattern (30 bp):
GGGTAAAATGGTAATTTTTGGAAAGTTCGA
Found at i:66444 original size:59 final size:56
Alignment explanation
Indices: 66344--66755 Score: 350
Period size: 60 Copynumber: 7.0 Consensus size: 56
66334 ATTTCAAACA
* * *
66344 TTCAGGGGTAAAAGGGTAATTTTGGAAAGTTGAGGGTCAAAAATGGGATTTTTGGAAG
1 TTCAGGGGTAAAATGGTAATTTTGGAAAGTTGGGGGT--AAAATGGAATTTTTGGAAG
* *
66402 TTCAGGGGTAAAATGGTAATTTTTGGAAAGTTGGGGGTCAAAAATGGGACTTTTGGAAG
1 TTCAGGGGTAAAATGGTAA-TTTTGGAAAGTTGGGGGT--AAAATGGAATTTTTGGAAG
* * *
66461 TTCGGGGGTAAAATGGTAATTTT-GAAAGGTTCGGGGTCAAAAAT-GAGATTTTTTGAAG
1 TTCAGGGGTAAAATGGTAATTTTGGAAA-GTTGGGGGT--AAAATGGA-ATTTTTGGAAG
* * *
66519 TTCGGGGGTAAAATGGTAATTTTGGAAGGTTCGGGGTTAAAATGGTAA-TTTTGGAAGG
1 TTCAGGGGTAAAATGGTAATTTTGGAAAGTT-GGGGGTAAAATGG-AATTTTTGGAA-G
* * * *
66577 TTCA-GGATCAAAAATGGGACTTTTGGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGG
1 TTCAGGGGT--AAAATGGTAATTTTGGAAAGTT-GGGGGTAAAATGG-AATTTTTGGAA-G
* * *
66637 TTC-GGGGTTGAAAATGGGACTTTTGGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAGG
1 TTCAGGGG-T-AAAATGGTAATTTTGGAAAG-TTGGGGGTAAAATGG-AATTTTTGGAA-G
* * * *
66697 TTC-GGGGTCGAAAATGGGACTTTTGGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAG
1 TTCAGGGGT--AAAATGGTAATTTTGGAAAGTT-GGGGGTAAAATGG-AATTTTTGGAAG
66756 GTTCGAGATC
Statistics
Matches: 316, Mismatches: 22, Indels: 31
0.86 0.06 0.08
Matches are distributed among these distances:
57 20 0.06
58 78 0.25
59 101 0.32
60 114 0.36
61 3 0.01
ACGTcount: A:0.29, C:0.05, G:0.35, T:0.31
Consensus pattern (56 bp):
TTCAGGGGTAAAATGGTAATTTTGGAAAGTTGGGGGTAAAATGGAATTTTTGGAAG
Found at i:66635 original size:60 final size:60
Alignment explanation
Indices: 66528--66782 Score: 370
Period size: 60 Copynumber: 4.3 Consensus size: 60
66518 GTTCGGGGGT
* * * *
66528 AAAATGGTAATTTT-GGAAGGTTCGGGGTTAAAATGGTAA-TTTTGGAAGGTTCAGGATCA
1 AAAATGGGACTTTTGGGAA-GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGATCA
* **
66587 AAAATGGGACTTTTGGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTG
1 AAAATGGGACTTTTGGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGATCA
* * *
66647 AAAATGGGACTTTTGGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCG
1 AAAATGGGACTTTTGGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGATCA
* *
66707 AAAATGGGACTTTTGGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGATCA
1 AAAATGGGACTTTTGGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGATCA
*
66767 AAAATGGGATTTTTGG
1 AAAATGGGACTTTTGG
66783 ACAATCTGGG
Statistics
Matches: 179, Mismatches: 15, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
59 31 0.17
60 148 0.83
ACGTcount: A:0.29, C:0.05, G:0.35, T:0.32
Consensus pattern (60 bp):
AAAATGGGACTTTTGGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGATCA
Found at i:66711 original size:120 final size:118
Alignment explanation
Indices: 66363--66760 Score: 390
Period size: 117 Copynumber: 3.4 Consensus size: 118
66353 AAAAGGGTAA
* * * *
66363 TTTTGGAAAGTT-GAGGGTCAAAAATGG-GATTTTTGGAA-GTTCAGGGGTAAAATGGTAATTTT
1 TTTTGGGAAGTTCGAGGGT--AAAATGGTAATTTTTGGAAGGTTCGGGGGTAAAATGGGAA-TTT
* * * * * * *
66425 TGGAAAGTT-GGGGGTCAAAAATGGGACTTTTGGAA-GTTCGGGGGT--AAAATGGTAA
63 TGGAAGGTTCGGGGGT--AAAATGGTAATTTTGGAAGGTTC-AGGATCAAAAATGGGAC
* * *
66480 TTTT-GAAAGGTTCG-GGGTCAAAAAT-G-AGATTTTTTGAA-GTTCGGGGGTAAAATGGTAATT
1 TTTTGGGAA-GTTCGAGGGT--AAAATGGTA-ATTTTTGGAAGGTTCGGGGGTAAAATGGGAATT
*
66540 TTGGAAGGTTCGGGGTTAAAATGGTAATTTTGGAAGGTTCAGGATCAAAAATGGGAC
62 TTGGAAGGTTCGGGGGTAAAATGGTAATTTTGGAAGGTTCAGGATCAAAAATGGGAC
* * *
66597 TTTTGGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTGAAAATGGGACTTTTG
1 TTTTGGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGGT-AAAATGGGAATTTT-
* * * *
66662 GGAA-GTTTGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCGAAAATGGGAC
64 GGAAGGTTCGGGGGTAAAATGGTAA-TTTTGGAAGGTTCAGGATCAAAAATGGGAC
66717 TTTTGGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCG
1 TTTTGGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCG
66761 AGATCAAAAA
Statistics
Matches: 244, Mismatches: 22, Indels: 27
0.83 0.08 0.09
Matches are distributed among these distances:
115 19 0.08
116 25 0.10
117 78 0.32
118 18 0.07
119 30 0.12
120 74 0.30
ACGTcount: A:0.28, C:0.05, G:0.35, T:0.32
Consensus pattern (118 bp):
TTTTGGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGGTAAAATGGGAATTTTGG
AAGGTTCGGGGGTAAAATGGTAATTTTGGAAGGTTCAGGATCAAAAATGGGAC
Found at i:66779 original size:29 final size:29
Alignment explanation
Indices: 66348--66760 Score: 350
Period size: 29 Copynumber: 14.0 Consensus size: 29
66338 CAAACATTCA
* *
66348 GGGGTAAAAGGGTAA-TTTTGGAAAGTT-
1 GGGGTAAAATGGTAATTTTTGGAAGGTTC
*
66375 GAGGGTCAAAAATGG-GATTTTTGGAA-GTTC
1 G-GGGT--AAAATGGTAATTTTTGGAAGGTTC
* *
66405 AGGGGTAAAATGGTAATTTTTGGAAAGTTG
1 -GGGGTAAAATGGTAATTTTTGGAAGGTTC
* *
66435 GGGGTCAAAAATGG-GACTTTTGGAA-GTTC
1 GGGGT--AAAATGGTAATTTTTGGAAGGTTC
*
66464 GGGGGTAAAATGGTAA-TTTTGAAAGGTTC
1 -GGGGTAAAATGGTAATTTTTGGAAGGTTC
*
66493 GGGGTCAAAAAT-G-AGATTTTTTGAA-GTTC
1 GGGGT--AAAATGGTA-ATTTTTGGAAGGTTC
66522 GGGGGTAAAATGGTAA-TTTTGGAAGGTTC
1 -GGGGTAAAATGGTAATTTTTGGAAGGTTC
66551 GGGGTTAAAATGGTAA-TTTTGGAAGGTTC
1 GGGG-TAAAATGGTAATTTTTGGAAGGTTC
* * * * *
66580 AGGATCAAAAATGGGACTTTTGGGAA-GTTC
1 GGGGT--AAAATGGTAATTTTTGGAAGGTTC
66610 GGGGGTAAAATGGTAATTTTTGGAAGGTTC
1 -GGGGTAAAATGGTAATTTTTGGAAGGTTC
* * * * *
66640 GGGGTTGAAAATGGGACTTTTGGGAAGTTTG
1 GGGG-T-AAAATGGTAATTTTTGGAAGGTTC
66671 GGGGTAAAATGGTAATTTTTGGAAGGTTC
1 GGGGTAAAATGGTAATTTTTGGAAGGTTC
* * *
66700 GGGGTCGAAAATGGGACTTTTGGGAA-GTTC
1 GGGGT--AAAATGGTAATTTTTGGAAGGTTC
66730 GAGGGTAAAATGGTAATTTTTGGAAGGTTC
1 G-GGGTAAAATGGTAATTTTTGGAAGGTTC
66760 G
1 G
66761 AGATCAAAAA
Statistics
Matches: 315, Mismatches: 38, Indels: 63
0.76 0.09 0.15
Matches are distributed among these distances:
27 1 0.00
28 48 0.15
29 125 0.40
30 80 0.25
31 61 0.19
ACGTcount: A:0.29, C:0.05, G:0.35, T:0.31
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTTGGAAGGTTC
Found at i:67987 original size:7 final size:7
Alignment explanation
Indices: 67975--68013 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
67965 CCCCCCTTTT
67975 TTATTAA
1 TTATTAA
67982 TTATTAA
1 TTATTAA
*
67989 TTAATAA
1 TTATTAA
67996 TTATTAA
1 TTATTAA
68003 -TATT-A
1 TTATTAA
68008 TTATTA
1 TTATTA
68014 TTAATATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 1 0.04
6 8 0.29
7 19 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTATTAA
Found at i:68015 original size:15 final size:15
Alignment explanation
Indices: 67975--68020 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
67965 CCCCCCTTTT
67975 TTATTAATTATTAAT-
1 TTATT-ATTATTAATA
* *
67990 TAATAATTATTAATA
1 TTATTATTATTAATA
68005 TTATTATTATTAATA
1 TTATTATTATTAATA
68020 T
1 T
68021 CAAAACATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTATTATTAATA
Found at i:68814 original size:18 final size:18
Alignment explanation
Indices: 68758--68872 Score: 146
Period size: 17 Copynumber: 6.5 Consensus size: 18
68748 ATTTATTTTA
*
68758 AAATTTAAATTTGAAAAT
1 AAATTTAAATTTTAAAAT
* * *
68776 AATTTTTAAA-CTTAAATT
1 AA-ATTTAAATTTTAAAAT
68794 AAATTTAAATTTTAAAAT
1 AAATTTAAATTTTAAAAT
68812 AAATTTAAA-TTTAAAAT
1 AAATTTAAATTTTAAAAT
* *
68829 AAATTTAAATTTTTAAAC
1 AAATTTAAATTTTAAAAT
68847 AAATTT-AATTTTAAAAT
1 AAATTTAAATTTTAAAAT
68864 AAATTTAAA
1 AAATTTAAA
68873 GGGAGTATGG
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
17 38 0.46
18 38 0.46
19 6 0.07
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (18 bp):
AAATTTAAATTTTAAAAT
Found at i:68819 original size:24 final size:24
Alignment explanation
Indices: 68752--68826 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 24
68742 GGTTTTATTT
*
68752 ATTTTAAAATTTAAATTTGAAA-ATAA
1 ATTTTAAAA--TAAATTT-AAATTTAA
* *
68778 TTTTTAAACTTAAA-TTAAATTTAA
1 ATTTTAAA-ATAAATTTAAATTTAA
68802 ATTTTAAAATAAATTTAAATTTAA
1 ATTTTAAAATAAATTTAAATTTAA
68826 A
1 A
68827 ATAAATTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
23 7 0.17
24 23 0.56
25 4 0.10
26 7 0.17
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (24 bp):
ATTTTAAAATAAATTTAAATTTAA
Found at i:68826 original size:35 final size:35
Alignment explanation
Indices: 68758--68872 Score: 158
Period size: 35 Copynumber: 3.3 Consensus size: 35
68748 ATTTATTTTA
* * * *
68758 AAATTTAAATTTGAAAATAATTTTTAAACTTAAATT
1 AAATTTAAATTTTAAAATAA-ATTTAAATTTAAAAT
68794 AAATTTAAATTTTAAAATAAATTTAAATTTAAAAT
1 AAATTTAAATTTTAAAATAAATTTAAATTTAAAAT
* * *
68829 AAATTTAAATTTTTAAACAAATTTAATTTTAAAAT
1 AAATTTAAATTTTAAAATAAATTTAAATTTAAAAT
68864 AAATTTAAA
1 AAATTTAAA
68873 GGGAGTATGG
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 53 0.74
36 19 0.26
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (35 bp):
AAATTTAAATTTTAAAATAAATTTAAATTTAAAAT
Found at i:68872 original size:6 final size:6
Alignment explanation
Indices: 68758--68840 Score: 66
Period size: 6 Copynumber: 14.0 Consensus size: 6
68748 ATTTATTTTA
* * *
68758 AAATTT AAATTT GAAA-AT AATTTTT AAACTT AAA-TT AAATTT AAATTTT
1 AAATTT AAATTT -AAATTT AA-ATTT AAATTT AAATTT AAATTT AAA-TTT
* *
68807 AAA-AT AAATTT AAATTT AAA-AT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
68841 TTAAACAAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 14
0.73 0.11 0.17
Matches are distributed among these distances:
5 15 0.25
6 34 0.56
7 12 0.20
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (6 bp):
AAATTT
Found at i:69953 original size:209 final size:209
Alignment explanation
Indices: 69224--69960 Score: 1285
Period size: 209 Copynumber: 3.5 Consensus size: 209
69214 TGCTTCGACC
* * *
69224 TGCTTCTCAGTACCTCATCAGGAAACTGTGGTTCGAAGATTTGCTCACATCGAGCGTGAGTTTGG
1 TGCTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGG
* * * *
69289 TTTGGTCTTCTTCTCAGTATCTCATCAGGCAGATGACTGCGTTGTCTGTTTCAATTCGCTTCTCT
66 TTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCGTCGTCTGTTTCAATTCGCTTCTCT
*
69354 GTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTGTACCTCATCGGGAAGATGGTCAGGAAA
131 GTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTGTACCTCATCGGGAAGATGGTCAGGAAG
69419 CTAACCGTTTGACT
196 CTAACCGTTTGACT
*
69433 TGCTTCTTAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGG
1 TGCTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGG
* * *
69498 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATCGCGTCATCTGTTTCAATTCGCTTCTCT
66 TTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCGTCGTCTGTTTCAATTCGCTTCTCT
*
69563 GTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTGTACCTCATCGGGAAGATGGTCAAGAAG
131 GTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTGTACCTCATCGGGAAGATGGTCAGGAAG
69628 CTAACCGTTTGACT
196 CTAACCGTTTGACT
* *
69642 TGCTTCTTAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGATCACATCGAGCGTGGGTTTGG
1 TGCTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGG
69707 TTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCGTCGTCTGTTTCAATTCGCTTCTCT
66 TTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCGTCGTCTGTTTCAATTCGCTTCTCT
*
69772 GTATCTCATCAGGAAGACGAATTTGATCCACTTCTCTGTACCTCATCGGGAAGATGGTCAGGAAG
131 GTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTGTACCTCATCGGGAAGATGGTCAGGAAG
* * *
69837 TTAATCGATTGACT
196 CTAACCGTTTGACT
*
69851 TGCTTCTCAGTATCGCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGG
1 TGCTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGG
*
69916 TTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGTGTCGT
66 TTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCGTCGT
69961 TTTGTTGGAT
Statistics
Matches: 504, Mismatches: 24, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
209 504 1.00
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (209 bp):
TGCTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGG
TTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCGTCGTCTGTTTCAATTCGCTTCTCT
GTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTGTACCTCATCGGGAAGATGGTCAGGAAG
CTAACCGTTTGACT
Found at i:70483 original size:27 final size:27
Alignment explanation
Indices: 70453--70513 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
70443 CAAGAATTCT
* *
70453 TATTAAAAAGAGGATCGAATGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
*
70480 TATTAAAAGGAGGATCAAAGGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
70507 TCATTAA
1 T-ATTAA
70514 TTGAATATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.54, C:0.08, G:0.18, T:0.20
Consensus pattern (27 bp):
TATTAAAAAGAGGATCAAAGGAAACAA
Done.