Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 92 of 356
Found at i:28946257 original size:31 final size:31
Alignment explanation
Indices: 28946218--28946302 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 31
28946208 TATCAGAACT
* *
28946218 AGAATCAGAATCAGAATTAGAATCAGGTGAC
1 AGAATCAGAATCAGAATCAGAATCAGGTAAC
* *
28946249 AGATTCAGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGAATCAGGTAAC
* * *
28946280 AGAACCAAAATCAGAATGAGAAT
1 AGAATCAGAATCAGAATCAGAAT
28946303 GCAATCCCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.47, C:0.14, G:0.20, T:0.19
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGAATCAGGTAAC
Found at i:28946463 original size:27 final size:26
Alignment explanation
Indices: 28946415--28946474 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
28946405 GCGAGGCTGC
*
28946415 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
28946442 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
28946468 CAGATAT
1 CAGATAT
28946475 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:28946519 original size:71 final size:67
Alignment explanation
Indices: 28946442--28946583 Score: 185
Period size: 67 Copynumber: 2.1 Consensus size: 67
28946432 TCACCAGATA
* * * *
28946442 CAGATATTGTGGCTAGGCCACCAGAACAGATATATATATGTGGCGAAGCCACCAGATTGCAGTGA
1 CAGATATTGTGACGAAGCCACCAGAACAG----ATATATGTGGCGAAGCCACCAGATTGCAGCGA
*
28946507 GGCTGC
62 GGCTAC
* *
28946513 CAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCT
1 CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
28946578 AC
66 AC
28946580 CAGA
1 CAGA
28946584 ACGCTTTCTC
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
67 39 0.61
71 25 0.39
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (67 bp):
CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
AC
Found at i:28946561 original size:27 final size:26
Alignment explanation
Indices: 28946513--28946564 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
28946503 GTGAGGCTGC
*
28946513 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
28946539 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
28946565 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:28947003 original size:27 final size:27
Alignment explanation
Indices: 28946809--28946995 Score: 234
Period size: 27 Copynumber: 7.0 Consensus size: 27
28946799 GGGGTAAAAT
* * * *
28946809 GGTAATTTTACCCCACA-AGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
28946835 GGTAATTCTACCCTGCAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
28946862 AGTTATTCTACCCTACAGGGGTTTTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
28946889 GGTATTTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
28946916 GGT-ATTTTGACCCTACAGGGGTATTTC
1 GGTAATTCT-ACCCTACAGGGGTATTTC
* * *
28946943 GATATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
28946970 GGTAATTCTACCCTACAGGGGTATTT
1 GGTAATTCTACCCTACAGGGGTATTT
28946996 TAGTAATTTT
Statistics
Matches: 136, Mismatches: 22, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
26 17 0.12
27 116 0.85
28 3 0.02
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:28947171 original size:27 final size:27
Alignment explanation
Indices: 28947041--28947216 Score: 135
Period size: 27 Copynumber: 6.5 Consensus size: 27
28947031 CTGTAAATCA
* * *
28947041 GGGTACTTTGATAATTTTAC-AAGTCG
1 GGGTATTTTGATAATTTTACAAACTAG
** ** *
28947067 AGGGTATTTCAATAATTTTAC-AGGTCG
1 -GGGTATTTTGATAATTTTACAAACTAG
* *
28947094 AGGGTA-TTTCAGTAATTTCACAAA-TCAG
1 -GGGTATTTTGA-TAATTTTACAAACT-AG
*
28947122 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGATAATTTTACAAACTAG
*
28947149 GGGTATTTTGATAATTTTACAAACCAG
1 GGGTATTTTGATAATTTTACAAACTAG
* ** * *
28947176 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGATAATTTTACAAACTAG
28947203 GGGTATTTTGATAA
1 GGGTATTTTGATAA
28947217 ACTAAAGTAT
Statistics
Matches: 125, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
26 3 0.02
27 116 0.93
28 6 0.05
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.38
Consensus pattern (27 bp):
GGGTATTTTGATAATTTTACAAACTAG
Found at i:28947180 original size:81 final size:80
Alignment explanation
Indices: 28947035--28947192 Score: 176
Period size: 81 Copynumber: 2.0 Consensus size: 80
28947025 GTAATTCTGT
* * ***
28947035 AAATCAGGGTACTTTGATAATTTTACAAGTCGAGGGTATTTCAATAATTTTACAGGTCGAGGGTA
1 AAATCAGGGTACTTTGATAATTTTACAACTAGAGGGTATTTCAATAATTTTACAAACCGAGGGTA
28947100 TTTCAGTAATTTCAC
66 TTTCAGTAATTTCAC
* * **
28947115 AAATCAGGGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTTGATAATTTTACAAACC-AGGG
1 AAATCA-GGGTACTTTGATAATTTTAC-AACTAGAGGGTATTTCAATAATTTTACAAACCGA-GG
**
28947178 GTATTTTGGTAATTT
63 GTATTTCAGTAATTT
28947193 TGTAAACCAA
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
80 7 0.11
81 53 0.83
82 4 0.06
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (80 bp):
AAATCAGGGTACTTTGATAATTTTACAACTAGAGGGTATTTCAATAATTTTACAAACCGAGGGTA
TTTCAGTAATTTCAC
Found at i:28949182 original size:6 final size:6
Alignment explanation
Indices: 28949164--28949251 Score: 65
Period size: 6 Copynumber: 14.3 Consensus size: 6
28949154 AAGAAACATT
* * *
28949164 ATCAGA A-CTAGA ATCAGA ATCAGA ATTAGA ATCAG- GTGACAGA TTCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* *
28949213 ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA AT
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
28949252 GTGAATGCAA
Statistics
Matches: 65, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
5 4 0.06
6 52 0.80
7 7 0.11
8 2 0.03
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:28949212 original size:31 final size:31
Alignment explanation
Indices: 28949173--28949251 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
28949163 TATCAGAACT
* *
28949173 AGAATCAGAATCAGAATTAGAATCAGGTGAC
1 AGAATCAGAATCAGAATCAGAATCAGGTAAC
* *
28949204 AGATTCAGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGAATCAGGTAAC
*
28949235 AGAATCAAAATCAGAAT
1 AGAATCAGAATCAGAAT
28949252 GTGAATGCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGAATCAGGTAAC
Found at i:28949418 original size:27 final size:26
Alignment explanation
Indices: 28949370--28949429 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
28949360 GCGAGGCTGC
*
28949370 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
28949397 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
28949423 CAGATAT
1 CAGATAT
28949430 ATATATATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:28949826 original size:27 final size:27
Alignment explanation
Indices: 28949784--28949952 Score: 232
Period size: 27 Copynumber: 6.3 Consensus size: 27
28949774 AAACCCACAA
* * *
28949784 GGTATCTCGGTAATTCTACCCTGCAGG
1 GGTATTTCGGTATTTCTACCCTACAGG
*
28949811 GGTATTTCAGT-TATTCTACCCTACAGG
1 GGTATTTCGGTAT-TTCTACCCTACAGG
* *
28949838 GGTTTTTCGGTATTTCTACCCTACAAG
1 GGTATTTCGGTATTTCTACCCTACAGG
28949865 GGTATTTCGGTATTTCTACCCTACAGG
1 GGTATTTCGGTATTTCTACCCTACAGG
* *
28949892 GGTATTTCGATATTTCTACCCTACAAG
1 GGTATTTCGGTATTTCTACCCTACAGG
* *
28949919 GGTATTTCGGTAATTCTACCCTATAGG
1 GGTATTTCGGTATTTCTACCCTACAGG
28949946 GGTATTT
1 GGTATTT
28949953 TTAGTAATTT
Statistics
Matches: 125, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
27 124 0.99
28 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (27 bp):
GGTATTTCGGTATTTCTACCCTACAGG
Found at i:28950030 original size:27 final size:26
Alignment explanation
Indices: 28949993--28950152 Score: 117
Period size: 27 Copynumber: 5.9 Consensus size: 26
28949983 GTAATTCTGT
*
28949993 AAATCAGGGGTACTTTGATAATTTTAC
1 AAATTAGGGGTA-TTTGATAATTTTAC
* *
28950020 AAGTT-GAGGGTATTTCAATAATTTTAC
1 AAATTAG-GGGTATTT-GATAATTTTAC
** * * *
28950047 -AGGTCGAGGGTATTTCAGTAATTTCAC
1 AAATTAG-GGGTATTTGA-TAATTTTAC
*
28950074 AAATTAGGGGTATTTTGGTAATTTTAC
1 AAATTAGGGGTA-TTTGATAATTTTAC
*
28950101 AAACTAGGGGTATTTTGATAATTTTAC
1 AAATTAGGGGTA-TTTGATAATTTTAC
** *
28950128 AAACCAGGGGTATTTTGGTAATTTT
1 AAATTAGGGGTA-TTTGATAATTTT
28950153 GTAAACCAAG
Statistics
Matches: 111, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
26 8 0.07
27 97 0.87
28 6 0.05
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (26 bp):
AAATTAGGGGTATTTGATAATTTTAC
Found at i:28950058 original size:54 final size:53
Alignment explanation
Indices: 28949998--28950142 Score: 132
Period size: 54 Copynumber: 2.7 Consensus size: 53
28949988 TCTGTAAATC
* **
28949998 AGGGGTACTTTGATAATTTTACAAGTT-GAGGGTATTTCAATAATTTTACAGGTCG
1 AGGGGTA-TTTGATAATTTTACAAATTAG-GGGTATTTCAATAATTTTACA-AACG
* * *** *
28950053 A-GGGTATTTCAGTAATTTCACAAATTAGGGGTATTTTGGTAATTTTACAAACT
1 AGGGGTATTTGA-TAATTTTACAAATTAGGGGTATTTCAATAATTTTACAAACG
**
28950106 AGGGGTATTTTGATAATTTTACAAACCAGGGGTATTT
1 AGGGGTA-TTTGATAATTTTACAAATTAGGGGTATTT
28950143 TGGTAATTTT
Statistics
Matches: 73, Mismatches: 13, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
53 6 0.08
54 61 0.84
55 6 0.08
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (53 bp):
AGGGGTATTTGATAATTTTACAAATTAGGGGTATTTCAATAATTTTACAAACG
Found at i:28950139 original size:81 final size:81
Alignment explanation
Indices: 28949993--28950151 Score: 178
Period size: 81 Copynumber: 2.0 Consensus size: 81
28949983 GTAATTCTGT
* * ***
28949993 AAATCAGGGGTACTTTGATAATTTTACAAGTTGAGGGTATTTCAATAATTTTACAGGTCGAGGGT
1 AAATCAGGGGTACTTTGATAATTTTACAACTAGAGGGTATTTCAATAATTTTACAAACCGAGGGT
28950058 ATTTCAGTAATTTCAC
66 ATTTCAGTAATTTCAC
* * * **
28950074 AAATTAGGGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTTGATAATTTTACAAACC-AGGG
1 AAATCAGGGGTACTTTGATAATTTTAC-AACTAGAGGGTATTTCAATAATTTTACAAACCGA-GG
**
28950137 GTATTTTGGTAATTT
64 GTATTTCAGTAATTT
28950152 TGTAAACCAA
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
80 1 0.02
81 59 0.92
82 4 0.06
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (81 bp):
AAATCAGGGGTACTTTGATAATTTTACAACTAGAGGGTATTTCAATAATTTTACAAACCGAGGGT
ATTTCAGTAATTTCAC
Found at i:28950158 original size:27 final size:27
Alignment explanation
Indices: 28950054--28950175 Score: 154
Period size: 27 Copynumber: 4.5 Consensus size: 27
28950044 TACAGGTCGA
** * **
28950054 GGGTATTTCAGTAATTTCACAAATTAG
1 GGGTATTTTGGTAATTTTACAAACCAG
*
28950081 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACCAG
*
28950108 GGGTATTTTGATAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
** *
28950135 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAG
28950162 GGGTATTTTGGTAA
1 GGGTATTTTGGTAA
28950176 ACTAAAGTAT
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 85 1.00
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAG
Found at i:28951189 original size:13 final size:13
Alignment explanation
Indices: 28951171--28951195 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28951161 CCTACACCAT
28951171 AAGTCAAAGCATC
1 AAGTCAAAGCATC
28951184 AAGTCAAAGCAT
1 AAGTCAAAGCAT
28951196 AATAGACATT
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:0.48, C:0.20, G:0.16, T:0.16
Consensus pattern (13 bp):
AAGTCAAAGCATC
Found at i:28954383 original size:58 final size:58
Alignment explanation
Indices: 28954319--28954492 Score: 203
Period size: 58 Copynumber: 3.0 Consensus size: 58
28954309 CAAATAGGAT
* *
28954319 TATTAGTTTGCGAGTTATTTTGAGCTTAAGGAAAATTTCTAAAATCAATCGTTGGGAA
1 TATTAGTTTGCGAGTTATTTTGAGCTTAAGGAAAATTTCTAAAATCAATAGCTGGGAA
* * *
28954377 TATTAGTTTGTGAGTTGTTTTG-GACTTTAAGG-AAATCGTCTAAAATCAATAGCTGGGAA
1 TATTAGTTTGCGAGTTATTTTGAG-C-TTAAGGAAAAT-TTCTAAAATCAATAGCTGGGAA
* * *
28954436 TATTAGTTCT-CGAGCTATTTTAAGCTTAA-GAAAATTTTCTAAAATCAATAACTGGGA
1 TATTAGTT-TGCGAGTTATTTTGAGCTTAAGGAAAA-TTTCTAAAATCAATAGCTGGGA
28954493 GTTTTTAACT
Statistics
Matches: 98, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
57 2 0.02
58 51 0.52
59 43 0.44
60 2 0.02
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (58 bp):
TATTAGTTTGCGAGTTATTTTGAGCTTAAGGAAAATTTCTAAAATCAATAGCTGGGAA
Found at i:28955348 original size:211 final size:209
Alignment explanation
Indices: 28954996--28955601 Score: 603
Period size: 211 Copynumber: 2.9 Consensus size: 209
28954986 TCAGGCCTCG
* * * *
28954996 CTAACTA-TTCTGGAGGTTGCGGTATTTTACTTACGAGCCTTAACATTACAACTGGGGGCTTTGA
1 CTAACTATTTC-GGAGGCTGCGGTATTTTACCTACGAGCCTT-A-ATTACAACTGAGAGCTTTGA
* * * * * *
28955060 ACTCTCGCTAACTATTTGGGAGGTTGTGGTATTTAACCTACGAGCCTTAATAATGACAGTTGAGA
63 ACTCTCGCTAACTATTTGGG-GGCTATGATATTTAACTTACAAGCCTTAA-AATGACAGCTGAGA
* * * * *
28955125 GCTTTTAACTCTCACTAATTGTTTGGGGGGCTGTGGTATTGAACCTACGAGCCTTAACATTACAT
126 GCTTTTAACTCTCACTAACTGTTTGGGGGGCTGCGGTATTAAACCTACGAGCCTTAACAAT-CAG
*
28955190 TTGGGAGC-TTTAGCTCTCA
190 TTGGGAGCTTTTAACTCTCA
* *
28955209 CTAACTGTTTCGGAGGCTGCGGTATTTTACCTACGAGCCTTATATTACAACTGAGAGCTTTAAAC
1 CTAACTATTTCGGAGGCTGCGGTATTTTACCTACGAGCCTTA-ATTACAACTGAGAGCTTTGAAC
* *
28955274 TCTTGCTAACTATTTGGGGGCTATGATATTAAACTTACAAGCCTTAACAATGACAGCTGAGAGCT
65 TCTCGCTAACTATTTGGGGGCTATGATATTTAACTTACAAGCCTTAA-AATGACAGCTGAGAGCT
* * * * * *
28955339 TTTAACTCTCGCTAACTGTTTGGTGGGCTGCGGTATTAAACCTGCGAGTCTTAATAATGAGTTGG
129 TTTAACTCTCACTAACTGTTTGGGGGGCTGCGGTATTAAACCTACGAGCCTTAACAATCAGTTGG
*
28955404 GAGCTTTTAACTCTCG
194 GAGCTTTTAACTCTCA
* * * * * ** *
28955420 CTAACTATTTGGGGGGCTACAGTACTTTACCTATTAGCCTTAATCTA-ATAGATGAGAGCTTTGA
1 CTAACTATTTCGGAGGCTGCGGTATTTTACCTACGAGCCTTAAT-TACA-A-CTGAGAGCTTTGA
* ** * * * * * * *
28955484 ACTCTCGCTAACCATTTGAAGGCTACGGTTCTTTACCTGT--AAGCCTTAATATTACAGCTAAGA
63 ACTCTCGCTAACTATTTGGGGGCTA-TGATATTTAACT-TACAAGCCTTAAAATGACAGCTGAGA
* * * * *
28955547 GCTTTAAACTCTCACTAACTGTTT-AGGGGCTGCAGTATTTAACCTACTAGCCTTA
126 GCTTTTAACTCTCACTAACTGTTTGGGGGGCTGCGGTATTAAACCTACGAGCCTTA
28955602 GAAATAATCT
Statistics
Matches: 326, Mismatches: 60, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
210 36 0.11
211 167 0.51
212 78 0.24
213 41 0.13
214 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (209 bp):
CTAACTATTTCGGAGGCTGCGGTATTTTACCTACGAGCCTTAATTACAACTGAGAGCTTTGAACT
CTCGCTAACTATTTGGGGGCTATGATATTTAACTTACAAGCCTTAAAATGACAGCTGAGAGCTTT
TAACTCTCACTAACTGTTTGGGGGGCTGCGGTATTAAACCTACGAGCCTTAACAATCAGTTGGGA
GCTTTTAACTCTCA
Found at i:28955599 original size:70 final size:70
Alignment explanation
Indices: 28954555--28955601 Score: 549
Period size: 70 Copynumber: 14.9 Consensus size: 70
28954545 TTAGAAAGAT
* * ** * **
28954555 AGCTGGGAGCTTTTAACTCTCGCTAACTATTTGGGGGGCTGCGGCCTTAAACCTGTGAGCCTTAA
1 AGCTGAGAGCTTTTAACTCTCGCTAACTGTTT-GGGGGCTGCGGTATTTAACCTACGAGCCTTAA
* *
28954620 TAATGAT
65 T-ATTAC
* * * * * **
28954627 A-CTGAGAGCTTTTAACTCTCGTTAACTATTTGGGGGCT-CTGGTACTTCACTTGTGAGCCTTAA
1 AGCTGAGAGCTTTTAACTCTCGCTAACTGTTTGGGGGCTGC-GGTATTTAACCTACGAGCCTTAA
*
28954690 TATGAC
65 TATTAC
** * * * * * * * ***
28954696 ATTTGGGAGCTTTGAACTCTTGCTAGCTATTTAGGGGTTGCGGTACTTT-ACCTGTAAGCCTTAA
1 AGCTGAGAGCTTTTAACTCTCGCTAACTGTTTGGGGGCTGCGGTA-TTTAACCTACGAGCCTTAA
28954760 TATTAC
65 TATTAC
* * * * * * * * * * **
28954766 ATCTGGGAGCTTTGAACTTTTGCTAACTATTTAGGGGTTGTGATACTTT-ACCTGTGAGCCTTAA
1 AGCTGAGAGCTTTTAACTCTCGCTAACTGTTTGGGGGCTGCGGTA-TTTAACCTACGAGCCTTAA
*
28954830 TAGTAC
65 TATTAC
* * * * * * * **
28954836 AACT-AGAAGCTTTGAACTCTCGCTAACTATTTAGGGGTTGGGGTACTTT-ACCTGCGAGTGTTA
1 AGCTGAG-AGCTTTTAACTCTCGCTAACTGTTTGGGGGCTGCGGTA-TTTAACCTACGAGCCTTA
*
28954899 ATATTAT
64 ATATTAC
* * * * * * * * * * ** * *
28954906 GGATAAGAGCTTTGAAATCTTGCTAACTGTTTAGGGGCTACGGTATTGAACTTGTGAG-CTTGAG
1 AGCTGAGAGCTTTTAACTCTCGCTAACTGTTTGGGGGCTGCGGTATTTAACCTACGAGCCTTAAT
* *
28954970 GTTAT
66 ATTAC
* * * * * * *
28954975 AGCT-AGGAGC-TTCAGGC-CTCGCTAACTATTCTGGAGGTTGCGGTATTTTACTTACGAGCCTT
1 AGCTGA-GAGCTTTTA-ACTCTCGCTAACTGTT-TGGGGGCTGCGGTATTTAACCTACGAGCCTT
*
28955037 AACATTAC
63 AATATTAC
* * * * * * *
28955045 AACTGGGGGCTTTGAACTCTCGCTAACTATTTGGGAGGTTGTGGTATTTAACCTACGAGCCTTAA
1 AGCTGAGAGCTTTTAACTCTCGCTAACTGTTTGGG-GGCTGCGGTATTTAACCTACGAGCCTTAA
*
28955110 TAATGAC
65 T-ATTAC
* * * * *
28955117 AGTTGAGAGCTTTTAACTCTCACTAATTGTTTGGGGGGCTGTGGTATTGAACCTACGAGCCTTAA
1 AGCTGAGAGCTTTTAACTCTCGCTAACTGTTT-GGGGGCTGCGGTATTTAACCTACGAGCCTTAA
*
28955182 CATTAC
65 TATTAC
** * * * * *
28955188 ATTTGGGAGC-TTTAGCTCTCACTAACTGTTTCGGAGGCTGCGGTATTTTACCTACGAGCCTT-A
1 AGCTGAGAGCTTTTAACTCTCGCTAACTGTTT-GGGGGCTGCGGTATTTAACCTACGAGCCTTAA
28955251 TATTAC
65 TATTAC
* * * * ** * * * *
28955257 AACTGAGAGCTTTAAACTCTTGCTAACTATTTGGGGGCTATGATATTAAACTTACAAGCCTTAAC
1 AGCTGAGAGCTTTTAACTCTCGCTAACTGTTTGGGGGCTGCGGTATTTAACCTACGAGCCTTAA-
* *
28955322 AATGAC
65 TATTAC
* * *
28955328 AGCTGAGAGCTTTTAACTCTCGCTAACTGTTTGGTGGGCTGCGGTATTAAACCTGCGAGTCTTAA
1 AGCTGAGAGCTTTTAACTCTCGCTAACTGTTTGG-GGGCTGCGGTATTTAACCTACGAGCCTTAA
* *
28955393 TAAT-G
65 TATTAC
* * * * * **
28955398 AGTTGGGAGCTTTTAACTCTCGCTAACTATTTGGGGGGCTACAGTACTTT-ACCTATTAGCCTTA
1 AGCTGAGAGCTTTTAACTCTCGCTAACTGTTT-GGGGGCTGCGGTA-TTTAACCTACGAGCCTTA
* * *
28955462 ATCTAAT
64 ATATTAC
* * ** ** * * ***
28955469 AGATGAGAGCTTTGAACTCTCGCTAACCATTTGAAGGCTACGGT-TCTTTACCTGTAAGCCTTAA
1 AGCTGAGAGCTTTTAACTCTCGCTAACTGTTTGGGGGCTGCGGTAT-TTAACCTACGAGCCTTAA
28955533 TATTAC
65 TATTAC
* * * * * *
28955539 AGCTAAGAGCTTTAAACTCTCACTAACTGTTTAGGGGCTGCAGTATTTAACCTACTAGCCTTA
1 AGCTGAGAGCTTTTAACTCTCGCTAACTGTTTGGGGGCTGCGGTATTTAACCTACGAGCCTTA
28955602 GAAATAATCT
Statistics
Matches: 767, Mismatches: 181, Indels: 56
0.76 0.18 0.06
Matches are distributed among these distances:
68 16 0.02
69 78 0.10
70 436 0.57
71 155 0.20
72 79 0.10
73 3 0.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (70 bp):
AGCTGAGAGCTTTTAACTCTCGCTAACTGTTTGGGGGCTGCGGTATTTAACCTACGAGCCTTAAT
ATTAC
Found at i:28958140 original size:79 final size:81
Alignment explanation
Indices: 28957997--28958179 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 81
28957987 TACTCGTTCA
* *
28957997 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACTCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACTCGGA
* *
28958061 TTTAGTAAC-TCGCACC
66 TATAGTAACTTAGCA-C
*
28958077 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTT-AGTCCG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACT-CG
* *
28958138 GATATGGTCACTTAGCAC
64 GATATAGTAACTTAGCAC
*
28958156 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
28958180 CATCATTCGA
Statistics
Matches: 90, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
78 5 0.06
79 57 0.63
80 28 0.31
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACTCGGA
TATAGTAACTTAGCAC
Found at i:28958179 original size:40 final size:40
Alignment explanation
Indices: 28957977--28958179 Score: 227
Period size: 40 Copynumber: 5.1 Consensus size: 40
28957967 GGAATTTAAT
** *
28957977 CGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGCC
1 CGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCC
* * *
28958017 CGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACT
1 CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
* *
28958057 CGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCC
1 CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
*
28958096 CGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTC
1 CGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCC
* * *
28958136 CGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCC
1 CGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCC
28958176 CGGA
1 CGGA
28958180 CATCATTCGA
Statistics
Matches: 138, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 92 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
Found at i:28960975 original size:25 final size:25
Alignment explanation
Indices: 28960921--28960988 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
28960911 GCGATAAACA
* * *
28960921 GTAAGCTCCTCCGAGCTGAATATTG
1 GTAAGCTCATACGAGCTGAATATCG
*
28960946 ATAAGCTCATACGAGCTGCAA-ATCG
1 GTAAGCTCATACGAGCTG-AATATCG
*
28960971 GTAAGCTCATATGAGCTG
1 GTAAGCTCATACGAGCTG
28960989 TGGTGAGTCT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
25 34 0.94
26 2 0.06
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (25 bp):
GTAAGCTCATACGAGCTGAATATCG
Found at i:28968936 original size:43 final size:42
Alignment explanation
Indices: 28968875--28969052 Score: 187
Period size: 43 Copynumber: 4.2 Consensus size: 42
28968865 TGAGGAAGCA
* *
28968875 CCGCTAAAGAACGTGACCTTTAATGGTGCTTTTCACACAGATG
1 CCGCTAAAGAACGTGACCTTTAGTGG-GCTTTTCACACAAATG
* * *
28968918 CCGCTGAAGAATGTGACCTTTAGTGGGCCTTTCACACAAATG
1 CCGCTAAAGAACGTGACCTTTAGTGGGCTTTTCACACAAATG
* * * *
28968960 CCACTAAAGAACATGACCTTTAGTGGCACTTTTCACACAAATA
1 CCGCTAAAGAACGTGACCTTTAGTGG-GCTTTTCACACAAATG
* * * * * *
28969003 CCGCTAAATAACATGACCTTTAGCTGCGCTTCT-ACAAAAACG
1 CCGCTAAAGAACGTGACCTTTAG-TGGGCTTTTCACACAAATG
28969045 CCGCTAAA
1 CCGCTAAA
28969053 AGTCATGTTC
Statistics
Matches: 113, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
42 50 0.44
43 61 0.54
44 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.25
Consensus pattern (42 bp):
CCGCTAAAGAACGTGACCTTTAGTGGGCTTTTCACACAAATG
Found at i:28969052 original size:85 final size:85
Alignment explanation
Indices: 28968875--28969052 Score: 198
Period size: 85 Copynumber: 2.1 Consensus size: 85
28968865 TGAGGAAGCA
* ** * * * **
28968875 CCGCTAAAGAACGTGACCTTTAATGGTGCTTTTCACACAGATGCCGCTGAAGAATGTGACCTTTA
1 CCGCTAAAGAACATGACCTTTAATGGCACTTTTCACACAAATACCGCTAAAGAACATGACCTTTA
* * *
28968940 GTGGGCCTTTCACACAAATG
66 GTGCGCCTTTCACAAAAACG
* * *
28968960 CCACTAAAGAACATGACCTTTAGTGGCACTTTTCACACAAATACCGCTAAATAACATGACCTTTA
1 CCGCTAAAGAACATGACCTTTAATGGCACTTTTCACACAAATACCGCTAAAGAACATGACCTTTA
28969025 GCTGCG-C-TTCTACAAAAACG
66 G-TGCGCCTTTC-ACAAAAACG
28969045 CCGCTAAA
1 CCGCTAAA
28969053 AGTCATGTTC
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
84 3 0.04
85 70 0.92
86 3 0.04
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.25
Consensus pattern (85 bp):
CCGCTAAAGAACATGACCTTTAATGGCACTTTTCACACAAATACCGCTAAAGAACATGACCTTTA
GTGCGCCTTTCACAAAAACG
Found at i:28973498 original size:30 final size:31
Alignment explanation
Indices: 28973437--28973510 Score: 105
Period size: 30 Copynumber: 2.4 Consensus size: 31
28973427 ACATATACTA
*
28973437 GGCCGAAGCCTTTGCATTATTCATGTCATTG
1 GGCCGAAGCCTTTGCATTATTCATATCATTG
*
28973468 GGCCGAAGCCTTTTCATTA-TCATATCATTG
1 GGCCGAAGCCTTTGCATTATTCATATCATTG
**
28973498 GGTTGAAGCCTTT
1 GGCCGAAGCCTTT
28973511 ACTGTAAACG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 21 0.54
31 18 0.46
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (31 bp):
GGCCGAAGCCTTTGCATTATTCATATCATTG
Found at i:28973801 original size:26 final size:25
Alignment explanation
Indices: 28973731--28973801 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
28973721 CTCTTTTAAT
*
28973731 AACTAGGGCAAAGCCCTTTTTGATA
1 AACTAGGGCAAAGCCCTTTTCGATA
* *
28973756 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTAGGGCAAAGCCCTTTTCGATA
28973781 AACTAGGGCAAAAGCCCTTTT
1 AACTAGGGC-AAAGCCCTTTT
28973802 GCACTTCCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 30 0.73
26 11 0.27
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (25 bp):
AACTAGGGCAAAGCCCTTTTCGATA
Found at i:28973895 original size:10 final size:11
Alignment explanation
Indices: 28973864--28973897 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
28973854 ATGCATATCA
28973864 TACATATCATG
1 TACATATCATG
*
28973875 TGCATATCATG
1 TACATATCATG
28973886 TACA-ATCATG
1 TACATATCATG
28973896 TA
1 TA
28973898 TATCAAAGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (11 bp):
TACATATCATG
Found at i:28981430 original size:30 final size:31
Alignment explanation
Indices: 28981352--28981434 Score: 107
Period size: 30 Copynumber: 2.7 Consensus size: 31
28981342 TCAATCTCAA
*
28981352 CATAT-ACTAGGCCGAAGCCTTTGCATTATT
1 CATATCACTGGGCCGAAGCCTTTGCATTATT
* *
28981382 CATGTCACTGGGCCGAAGCCTTTTCATTA-T
1 CATATCACTGGGCCGAAGCCTTTGCATTATT
* *
28981412 CATATCATTGGGCGGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
28981435 ACTGTAAACG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 25 0.54
31 21 0.46
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTGCATTATT
Found at i:28981699 original size:24 final size:25
Alignment explanation
Indices: 28981642--28981716 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 25
28981632 CTGGAGGCCT
*
28981642 AGCCTCTTTTAAT-AACTGGGGCAA
1 AGCCTCTTTTGATAAACTGGGGCAA
* *
28981666 AACCTGTTTTGATAAACTGGGGCAA
1 AGCCTCTTTTGATAAACTGGGGCAA
* *
28981691 AGCC-CTTTTCGGTAAACTAGGGCAA
1 AGCCTCTTTT-GATAAACTGGGGCAA
28981716 A
1 A
28981717 ATCCCTTTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
24 14 0.33
25 28 0.67
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (25 bp):
AGCCTCTTTTGATAAACTGGGGCAA
Found at i:28985089 original size:9 final size:9
Alignment explanation
Indices: 28985077--28985140 Score: 55
Period size: 9 Copynumber: 7.6 Consensus size: 9
28985067 TGACATATAT
28985077 TTATGTAAG
1 TTATGTAAG
*
28985086 TTATAT-A-
1 TTATGTAAG
*
28985093 TT-TTTAAG
1 TTATGTAAG
28985101 TTATGTAAG
1 TTATGTAAG
* *
28985110 TTATAT-AT
1 TTATGTAAG
*
28985118 TTATCTAAG
1 TTATGTAAG
28985127 TTATGTAAG
1 TTATGTAAG
28985136 TTATG
1 TTATG
28985141 ATATGATATA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
6 2 0.05
7 3 0.07
8 9 0.21
9 29 0.67
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.52
Consensus pattern (9 bp):
TTATGTAAG
Found at i:28985100 original size:15 final size:17
Alignment explanation
Indices: 28985071--28985104 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
28985061 ATGATATGAC
28985071 ATATATTTATGTAAGTT
1 ATATATTTATGTAAGTT
28985088 ATATATTT-T-TAAGTT
1 ATATATTTATGTAAGTT
28985103 AT
1 AT
28985105 GTAAGTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 1 0.06
17 8 0.47
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (17 bp):
ATATATTTATGTAAGTT
Found at i:28985116 original size:26 final size:26
Alignment explanation
Indices: 28985077--28985144 Score: 113
Period size: 24 Copynumber: 2.7 Consensus size: 26
28985067 TGACATATAT
28985077 TTATGTAAGTTATATATTT-T-TAAG
1 TTATGTAAGTTATATATTTATCTAAG
28985101 TTATGTAAGTTATATATTTATCTAAG
1 TTATGTAAGTTATATATTTATCTAAG
28985127 TTATGTAAGTTATGATAT
1 TTATGTAAGTTAT-ATAT
28985145 GATATATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
24 19 0.46
25 1 0.02
26 17 0.41
27 4 0.10
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.51
Consensus pattern (26 bp):
TTATGTAAGTTATATATTTATCTAAG
Found at i:28986488 original size:33 final size:33
Alignment explanation
Indices: 28986448--28986516 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
28986438 ATATATAAGG
28986448 TTATTAGTTATCATTAGACGTATCGTTTTTCTA
1 TTATTAGTTATCATTAGACGTATCGTTTTTCTA
28986481 TTATTAGTTATCATTAGACGTATCGTTTTTCTA
1 TTATTAGTTATCATTAGACGTATCGTTTTTCTA
28986514 TTA
1 TTA
28986517 AGACTAGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.52
Consensus pattern (33 bp):
TTATTAGTTATCATTAGACGTATCGTTTTTCTA
Found at i:28988512 original size:15 final size:14
Alignment explanation
Indices: 28988488--28988529 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
28988478 TGAAATTTAT
*
28988488 TTTTAGGGTTTAAA
1 TTTTAAGGTTTAAA
28988502 GTTTTAAGGTTT-AA
1 -TTTTAAGGTTTAAA
28988516 TATTTAAGGTTTAA
1 T-TTTAAGGTTTAA
28988530 TGGATTAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 1 0.04
14 12 0.50
15 11 0.46
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (14 bp):
TTTTAAGGTTTAAA
Found at i:28988523 original size:14 final size:14
Alignment explanation
Indices: 28988504--28988530 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28988494 GGTTTAAAGT
28988504 TTTAAGGTTTAATA
1 TTTAAGGTTTAATA
28988518 TTTAAGGTTTAAT
1 TTTAAGGTTTAAT
28988531 GGATTAAGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (14 bp):
TTTAAGGTTTAATA
Found at i:28988559 original size:22 final size:23
Alignment explanation
Indices: 28988534--28988588 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
28988524 GTTTAATGGA
*
28988534 TTAAGGGTTTAGTGTC-TATAGT
1 TTAAGGGTTTAGTGGCATATAGT
* *
28988556 TTAAGGTTTTA-TGGCATATGGT
1 TTAAGGGTTTAGTGGCATATAGT
28988578 TT-AGGGTTTAG
1 TTAAGGGTTTAG
28988589 GGTTTAGAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.22, C:0.04, G:0.29, T:0.45
Consensus pattern (23 bp):
TTAAGGGTTTAGTGGCATATAGT
Found at i:28988585 original size:7 final size:7
Alignment explanation
Indices: 28988575--28988617 Score: 61
Period size: 7 Copynumber: 6.3 Consensus size: 7
28988565 TATGGCATAT
28988575 GGTTTAG
1 GGTTTAG
28988582 GGTTTAG
1 GGTTTAG
28988589 GGTTTAG
1 GGTTTAG
* *
28988596 AG-TTAT
1 GGTTTAG
28988602 GGTTTAG
1 GGTTTAG
28988609 GGTTTAG
1 GGTTTAG
28988616 GG
1 GG
28988618 ATAAACAGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 4 0.13
7 27 0.87
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (7 bp):
GGTTTAG
Found at i:28989316 original size:31 final size:33
Alignment explanation
Indices: 28989259--28989322 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
28989249 TTTGGGTCAC
* *
28989259 AACCCATAACAGAATCAATTGGGCCT-AGCCCA
1 AACCAATAACAGAATCAAGTGGGCCTAAGCCCA
28989291 AACCAATAACAGAA-CAAGTGGGCCTAAGCCCA
1 AACCAATAACAGAATCAAGTGGGCCTAAGCCCA
28989323 TTACAGTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 10 0.34
32 19 0.66
ACGTcount: A:0.41, C:0.30, G:0.17, T:0.12
Consensus pattern (33 bp):
AACCAATAACAGAATCAAGTGGGCCTAAGCCCA
Found at i:28989557 original size:32 final size:32
Alignment explanation
Indices: 28989521--28989623 Score: 75
Period size: 32 Copynumber: 3.2 Consensus size: 32
28989511 ATGCAGCTCT
28989521 AAGCCTTCAGTAGCAGTATTATAATTGGCACA
1 AAGCCTTCAGTAGCAGTATTATAATTGGCACA
* * * **
28989553 AAGCCATT-GGTAACTGTATTATGTTTGGCACA
1 AAGCC-TTCAGTAGCAGTATTATAATTGGCACA
* * * * *
28989585 TAGCCATCAG-CGACAGTAATATAATAGGCACA
1 AAGCCTTCAGTAG-CAGTATTATAATTGGCACA
*
28989617 TAGCCTT
1 AAGCCTT
28989624 GGGTAAATAT
Statistics
Matches: 52, Mismatches: 16, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
31 1 0.02
32 49 0.94
33 2 0.04
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (32 bp):
AAGCCTTCAGTAGCAGTATTATAATTGGCACA
Found at i:28989738 original size:22 final size:22
Alignment explanation
Indices: 28989690--28989749 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
28989680 GTAAATACGT
28989690 TTGGCACAAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* ** * *
28989712 ATGGCACAAAGCCATTTTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
28989734 TTGGCACAGAGCCATA
1 TTGGCACAAAGCCATA
28989750 ATCAGATTAC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:28990147 original size:27 final size:27
Alignment explanation
Indices: 28990103--28990245 Score: 117
Period size: 27 Copynumber: 5.3 Consensus size: 27
28990093 CAAAACAGTC
* * *
28990103 ATTTTACCCTACAGGGGTATTTTGGTA
1 ATTTTACACTATAAGGGTATTTTGGTA
28990130 ATTTTACACTATAAGGGTATTTTGGTA
1 ATTTTACACTATAAGGGTATTTTGGTA
* * * * **
28990157 ATATTACACTACAAGGGTACTTAGAAA
1 ATTTTACACTATAAGGGTATTTTGGTA
* * **
28990184 AATTTACA-AATCGGGGGTATTTTGGTA
1 ATTTTACACTAT-AAGGGTATTTTGGTA
* * * *
28990211 ATTTTACAATCTGAGGGTATTTTGATA
1 ATTTTACACTATAAGGGTATTTTGGTA
28990238 ATTTTACA
1 ATTTTACA
28990246 AATCAGGAGT
Statistics
Matches: 90, Mismatches: 24, Indels: 4
0.76 0.20 0.03
Matches are distributed among these distances:
26 1 0.01
27 88 0.98
28 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.39
Consensus pattern (27 bp):
ATTTTACACTATAAGGGTATTTTGGTA
Found at i:28990175 original size:54 final size:54
Alignment explanation
Indices: 28990106--28990259 Score: 143
Period size: 54 Copynumber: 2.9 Consensus size: 54
28990096 AACAGTCATT
* * * *
28990106 TTACCCTACAGGGGTATTTTGGTAATTTTACACTAT-AAGGGTATTTTGGTAATA
1 TTACACTACAAGGGTATTTTGATAATTTTACA-AATCAAGGGTATTTTGGTAATA
* * * * ** *
28990160 TTACACTACAAGGGTACTTAGAAAAATTTACAAATCGGGGGTATTTTGGTAATT
1 TTACACTACAAGGGTATTTTGATAATTTTACAAATCAAGGGTATTTTGGTAATA
* *
28990214 TTACAAT-CTGAGGGTATTTTGATAATTTTACAAATC-AGGAGTATTT
1 TTACACTAC-AAGGGTATTTTGATAATTTTACAAATCAAGG-GTATTT
28990260 CAATAATTTT
Statistics
Matches: 79, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
53 5 0.06
54 74 0.94
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.38
Consensus pattern (54 bp):
TTACACTACAAGGGTATTTTGATAATTTTACAAATCAAGGGTATTTTGGTAATA
Found at i:28990246 original size:27 final size:26
Alignment explanation
Indices: 28990117--28990273 Score: 111
Period size: 27 Copynumber: 5.8 Consensus size: 26
28990107 TACCCTACAG
*
28990117 GGGTATTTTGGTAATTTTACACTAT-AA
1 GGGTATTTTGATAATTTTACA--ATCAA
* * *
28990144 GGGTATTTTGGTAATATTACACTACAA
1 GGGTATTTTGATAATTTTACAAT-CAA
* * * * **
28990171 GGGTACTTAGAAAAATTTACAAATCGG
1 GGGTATTTTGATAATTTTAC-AATCAA
* *
28990198 GGGTATTTTGGTAATTTTACAATCTGA
1 GGGTATTTTGATAATTTTACAATC-AA
28990225 GGGTATTTTGATAATTTTACAAATC-A
1 GGGTATTTTGATAATTTTAC-AATCAA
**
28990251 GGAGTATTTCAATAATTTTACAA
1 GG-GTATTTTGATAATTTTACAA
28990274 ATCAGGAGCT
Statistics
Matches: 104, Mismatches: 20, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
25 1 0.01
26 9 0.09
27 88 0.85
28 6 0.06
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (26 bp):
GGGTATTTTGATAATTTTACAATCAA
Found at i:28990274 original size:27 final size:27
Alignment explanation
Indices: 28990186--28990281 Score: 115
Period size: 27 Copynumber: 3.6 Consensus size: 27
28990176 CTTAGAAAAA
* * *
28990186 TTTACAAATCGGGGGTATTTTGGTAAT
1 TTTACAAATCAGGAGTATTTTGATAAT
28990213 TTTAC-AATCTGAGG-GTATTTTGATAAT
1 TTTACAAATC--AGGAGTATTTTGATAAT
**
28990240 TTTACAAATCAGGAGTATTTCAATAAT
1 TTTACAAATCAGGAGTATTTTGATAAT
28990267 TTTACAAATCAGGAG
1 TTTACAAATCAGGAG
28990282 CTTAACGACC
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
26 7 0.11
27 48 0.79
28 6 0.10
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (27 bp):
TTTACAAATCAGGAGTATTTTGATAAT
Found at i:28993133 original size:41 final size:42
Alignment explanation
Indices: 28993071--28993269 Score: 201
Period size: 41 Copynumber: 4.8 Consensus size: 42
28993061 ATTCGTCGTG
* *
28993071 TTTGGA-TAAAAAATGCCACTATAGCTCAACCTTTT-GCTGCA
1 TTTGGACT-AAAAATGCCACTATTGCTCAACCTTTTAGCGGCA
* * * **
28993112 TTTGGACTAAAAACGCTACTATTGCTC-AGCTTTTAGCGGTG
1 TTTGGACTAAAAATGCCACTATTGCTCAACCTTTTAGCGGCA
* * ** *
28993153 TTTGAACAAAAAATGCCACTATTGCT-AAATTTTTAGTGGCA
1 TTTGGACTAAAAATGCCACTATTGCTCAACCTTTTAGCGGCA
**
28993194 TTTGGACTAAAAATGCCACTATTGCTCAA-CTTTTAGCGGTG
1 TTTGGACTAAAAATGCCACTATTGCTCAACCTTTTAGCGGCA
* * *
28993235 TTTGGTCTAAAAACGCCACTATTGCTCAACGTTTT
1 TTTGGACTAAAAATGCCACTATTGCTCAACCTTTT
28993270 GCAACATTTT
Statistics
Matches: 128, Mismatches: 25, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
40 6 0.05
41 115 0.90
42 7 0.05
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (42 bp):
TTTGGACTAAAAATGCCACTATTGCTCAACCTTTTAGCGGCA
Found at i:28993205 original size:82 final size:82
Alignment explanation
Indices: 28993068--28993271 Score: 261
Period size: 82 Copynumber: 2.5 Consensus size: 82
28993058 CATATTCGTC
* * * *
28993068 GTGTTTGGATAAAAAATGCCACTATAGCTCAACCTTTTGCTGCATTTGGACTAAAAACGCTACTA
1 GTGTTTGGACAAAAAATGCCACTATTGCTCAAACTTTTGCTGCATTTGGACTAAAAACGCCACTA
*
28993133 TTGCTCAGCTTTTAGCG
66 TTGCTCAACTTTTAGCG
* * *
28993150 GTGTTTGAACAAAAAATGCCACTATTGCT-AAATTTTTAG-TGGCATTTGGACTAAAAATGCCAC
1 GTGTTTGGACAAAAAATGCCACTATTGCTCAAACTTTT-GCT-GCATTTGGACTAAAAACGCCAC
28993213 TATTGCTCAACTTTTAGCG
64 TATTGCTCAACTTTTAGCG
* * *
28993232 GTGTTTGGTCTAAAAACGCCACTATTGCTC-AACGTTTTGC
1 GTGTTTGGACAAAAAATGCCACTATTGCTCAAAC-TTTTGC
28993272 AACATTTTCC
Statistics
Matches: 104, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
81 7 0.07
82 93 0.89
83 4 0.04
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (82 bp):
GTGTTTGGACAAAAAATGCCACTATTGCTCAAACTTTTGCTGCATTTGGACTAAAAACGCCACTA
TTGCTCAACTTTTAGCG
Found at i:29001323 original size:43 final size:44
Alignment explanation
Indices: 29001224--29001334 Score: 122
Period size: 42 Copynumber: 2.6 Consensus size: 44
29001214 TCTCAGACGT
* * * *
29001224 TGGCATCGAT-TTATGATTTACATGTAAGACCATGTCTGGGACAT
1 TGGCATCGATATT-TGATTTACATGTAAGACCATATATGCGACAG
* * *
29001268 TAGCATCG-TATTTGATTT-CGTGTAAGACCCTATATGCGACAG
1 TGGCATCGATATTTGATTTACATGTAAGACCATATATGCGACAG
29001310 TGGCATCGATATTTGA-TTACATGTA
1 TGGCATCGATATTTGATTTACATGTA
29001335 TGGCCACGTC
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
42 27 0.49
43 19 0.35
44 9 0.16
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (44 bp):
TGGCATCGATATTTGATTTACATGTAAGACCATATATGCGACAG
Found at i:29001357 original size:43 final size:43
Alignment explanation
Indices: 29001202--29001358 Score: 133
Period size: 43 Copynumber: 3.7 Consensus size: 43
29001192 TGTGTTTTCG
* **
29001202 TGTAAGACCACATCTCAGACGTTGGCATCGAT-TTATGATTTACA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATT-TGA-TTACA
* * * * *
29001246 TGTAAGACCATGTCTGGGACATTAGCATCG-TATTTGATTTCG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTACA
* * *
29001288 TGTAAGACC-CTATATGCGACAG-TGGCATCGATATTTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTTGATTACA
* *
29001331 TGTATGGCCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
29001359 TGTACGAGCT
Statistics
Matches: 86, Mismatches: 21, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
42 26 0.30
43 33 0.38
44 27 0.31
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTACA
Found at i:29005972 original size:53 final size:53
Alignment explanation
Indices: 29005799--29005999 Score: 182
Period size: 53 Copynumber: 3.8 Consensus size: 53
29005789 ATTAGGGTTT
* * * * *
29005799 AAGGATACTAAGTAAGACCATGCCAAGGCATGACATTGGTAAGTTTTACA-AAGG-
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG--TT-CATAAGGC
* * * *
29005853 AAGGA-ATTCATGTAAGACCATGTCAAGACATGGCATTGAT-AG---ATAAGGC
1 AAGGATA-CCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
* * * *
29005902 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
* *
29005955 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
29006000 TAAAAAGGAT
Statistics
Matches: 119, Mismatches: 20, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
47 1 0.01
48 4 0.03
49 32 0.27
50 2 0.02
53 49 0.41
54 31 0.26
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Found at i:29009958 original size:17 final size:17
Alignment explanation
Indices: 29009936--29009971 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
29009926 CAAAGACAAG
29009936 AAAACCAAACTTGTTGA
1 AAAACCAAACTTGTTGA
29009953 AAAACCAAACTTGTTGA
1 AAAACCAAACTTGTTGA
29009970 AA
1 AA
29009972 TCTAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (17 bp):
AAAACCAAACTTGTTGA
Found at i:29010660 original size:9 final size:8
Alignment explanation
Indices: 29010642--29010674 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
29010632 TTTATTATTT
29010642 TTAAAATA
1 TTAAAATA
29010650 TTAAAATTA
1 TTAAAA-TA
29010659 TTAAAATA
1 TTAAAATA
29010667 TTAAAATA
1 TTAAAATA
29010675 AAATATTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
TTAAAATA
Found at i:29010822 original size:15 final size:15
Alignment explanation
Indices: 29010802--29010843 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
29010792 CTGCACATGT
29010802 TATTAAAATATTTAA
1 TATTAAAATATTTAA
*
29010817 TATTAATAT-TTTAA
1 TATTAAAATATTTAA
*
29010831 TAAT-AAATATTTA
1 TATTAAAATATTTA
29010844 TTACAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 3 0.13
14 12 0.52
15 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTAAAATATTTAA
Found at i:29022398 original size:40 final size:40
Alignment explanation
Indices: 29022354--29022542 Score: 301
Period size: 40 Copynumber: 4.7 Consensus size: 40
29022344 GCTACTTGCT
*
29022354 CAAATGCCTTCGGGACTGAGCCCGGTTATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCACA
*
29022394 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCACA
* *
29022434 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCACA
*
29022474 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTCACT-AGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCA-CA
29022514 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
29022543 CATCCGAATA
Statistics
Matches: 140, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
39 2 0.01
40 137 0.98
41 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCACA
Found at i:29030805 original size:40 final size:40
Alignment explanation
Indices: 29030705--29030876 Score: 213
Period size: 40 Copynumber: 4.3 Consensus size: 40
29030695 GCTCCTCGTT
* * *
29030705 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
29030745 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
29030784 CGAATGCCTTTGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
29030824 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
29030864 CAAATGCCTTCGG
1 CAAATGCCTTCGG
29030877 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 35 0.30
40 78 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:29030889 original size:80 final size:78
Alignment explanation
Indices: 29030705--29030929 Score: 220
Period size: 80 Copynumber: 2.8 Consensus size: 78
29030695 GCTCCTCGTT
* * * * *
29030705 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTC-GGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
29030769 ATTTAATAACTCGCA
64 ATTTAATAACTCGCA
* * * *
29030784 CGAATGCCTTTGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCC-TTCGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
29030849 AATTT-GTATCTCGCA
63 AATTTAATAACTCGCA
* * * * *
29030864 CAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCGG
29030929 A
63 A
29030930 CAGCATTCAA
Statistics
Matches: 119, Mismatches: 20, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
78 1 0.01
79 37 0.31
80 68 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAAT
TTAATAACTCGCA
Found at i:29030938 original size:41 final size:41
Alignment explanation
Indices: 29030861--29030938 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
29030851 TTTGTATCTC
* * *
29030861 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
29030902 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
29030939 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:29038271 original size:39 final size:40
Alignment explanation
Indices: 29038223--29038394 Score: 213
Period size: 40 Copynumber: 4.3 Consensus size: 40
29038213 GCTCCTCGTT
* * * *
29038223 CAAATGCCTTCGGAACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
29038263 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
29038302 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
29038342 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
29038382 CAAATGCCTTCGG
1 CAAATGCCTTCGG
29038395 ATCTTAGTCC
Statistics
Matches: 118, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
39 34 0.29
40 80 0.68
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:29038323 original size:40 final size:39
Alignment explanation
Indices: 29038225--29038447 Score: 207
Period size: 40 Copynumber: 5.6 Consensus size: 39
29038215 TCCTCGTTCA
* * * * *
29038225 AATGCCTTCGGAACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
29038264 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
29038303 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
29038343 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
29038383 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
29038424 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
29038448 CAGCATTCAA
Statistics
Matches: 156, Mismatches: 22, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
39 39 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:29038407 original size:80 final size:78
Alignment explanation
Indices: 29038223--29038447 Score: 229
Period size: 80 Copynumber: 2.8 Consensus size: 78
29038213 GCTCCTCGTT
* * * * *
29038223 CAAATGCCTTCGGAACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGG-ACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
29038287 ATTTAATAACTCGCA
64 ATTTAATAACTCGCA
* * *
29038302 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTC-GGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
29038367 AATTT-GTATCTCGCA
63 AATTTAATAACTCGCA
* * * * *
29038382 CAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCGG
29038447 A
63 A
29038448 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 18, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
78 1 0.01
79 36 0.30
80 71 0.59
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAAT
TTAATAACTCGCA
Found at i:29038456 original size:41 final size:41
Alignment explanation
Indices: 29038379--29038456 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
29038369 TTTGTATCTC
* * *
29038379 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
29038420 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
29038457 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:29049473 original size:11 final size:11
Alignment explanation
Indices: 29049457--29049482 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29049447 GGTTAGTCAT
29049457 GTTAAGATTTA
1 GTTAAGATTTA
29049468 GTTAAGATTTA
1 GTTAAGATTTA
29049479 GTTA
1 GTTA
29049483 GAATTGAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (11 bp):
GTTAAGATTTA
Found at i:29053536 original size:10 final size:9
Alignment explanation
Indices: 29053523--29053588 Score: 71
Period size: 9 Copynumber: 6.9 Consensus size: 9
29053513 TAAAATCAAT
29053523 AAAAATATA
1 AAAAATATA
29053532 AAAAATCAT-
1 AAAAAT-ATA
29053541 AAAAATATA
1 AAAAATATA
*
29053550 GAAAATCATA
1 AAAAAT-ATA
29053560 AAAAATATA
1 AAAAATATA
29053569 TAAAAATTATA
1 -AAAAA-TATA
29053580 AACAAATAT
1 AA-AAATAT
29053589 TAAAGTGCAA
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
8 2 0.04
9 20 0.41
10 20 0.41
11 7 0.14
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.24
Consensus pattern (9 bp):
AAAAATATA
Found at i:29053564 original size:19 final size:19
Alignment explanation
Indices: 29053514--29053588 Score: 91
Period size: 18 Copynumber: 3.9 Consensus size: 19
29053504 TAAAATCATT
29053514 AAAATCA-ATAAAAATATAA
1 AAAATCATA-AAAAATATAA
*
29053533 AAAATCAT-AAAAATATAG
1 AAAATCATAAAAAATATAA
29053551 AAAATCATAAAAAATATATA
1 AAAATCATAAAAAATATA-A
*
29053571 AAAATTATAAACAAATAT
1 AAAATCATAAA-AAATAT
29053589 TAAAGTGCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
18 17 0.35
19 16 0.33
20 10 0.20
21 6 0.12
ACGTcount: A:0.69, C:0.05, G:0.01, T:0.24
Consensus pattern (19 bp):
AAAATCATAAAAAATATAA
Found at i:29053780 original size:19 final size:20
Alignment explanation
Indices: 29053758--29053800 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
29053748 AAAATTATGT
29053758 AAAATATTT-AAAATATAGA
1 AAAATATTTAAAAATATAGA
29053777 AAAATATTTAAAAAATATAGA
1 AAAATATTT-AAAAATATAGA
29053798 AAA
1 AAA
29053801 GTGAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 9 0.41
21 13 0.59
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAATATTTAAAAATATAGA
Found at i:29053793 original size:21 final size:21
Alignment explanation
Indices: 29053734--29053800 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 21
29053724 TATAAATTAT
*
29053734 GAAAAAAATTGTAAAAAAT-TA
1 GAAAAATATT-TAAAAAATATA
*
29053755 TGTAAAATATTT--AAAATATA
1 -GAAAAATATTTAAAAAATATA
29053775 GAAAAATATTTAAAAAATATA
1 GAAAAATATTTAAAAAATATA
29053796 GAAAA
1 GAAAA
29053801 GTGAAAATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
19 15 0.38
20 2 0.05
21 14 0.36
22 8 0.21
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.28
Consensus pattern (21 bp):
GAAAAATATTTAAAAAATATA
Found at i:29053827 original size:19 final size:19
Alignment explanation
Indices: 29053803--29053840 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
29053793 ATAGAAAAGT
29053803 GAAAATTATAAAAAATATA
1 GAAAATTATAAAAAATATA
*
29053822 GAAAATTATGAAAAATATA
1 GAAAATTATAAAAAATATA
29053841 TTACAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (19 bp):
GAAAATTATAAAAAATATA
Found at i:29054257 original size:8 final size:8
Alignment explanation
Indices: 29054246--29054342 Score: 56
Period size: 8 Copynumber: 11.6 Consensus size: 8
29054236 TTTTTAATAT
29054246 TTTTATAA
1 TTTTATAA
29054254 TTTTTCATAA
1 -TTTT-ATAA
*
29054264 -TTTATAT
1 TTTTATAA
29054271 TTTTAT-A
1 TTTTATAA
29054278 TTTTATAA
1 TTTTATAA
*
29054286 TTTTTAGTTA
1 -TTTTA-TAA
*
29054296 TTTTAAAA
1 TTTTATAA
29054304 TTTATATAA
1 TTT-TATAA
* **
29054313 ATTTATTC
1 TTTTATAA
29054321 TTTTATAA
1 TTTTATAA
29054329 TATTT-TATA
1 T-TTTATA-A
29054338 TTTTA
1 TTTTA
29054343 ATGATTTTTT
Statistics
Matches: 67, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
7 9 0.13
8 27 0.40
9 25 0.37
10 6 0.09
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (8 bp):
TTTTATAA
Found at i:29054334 original size:10 final size:10
Alignment explanation
Indices: 29054154--29054337 Score: 56
Period size: 10 Copynumber: 18.5 Consensus size: 10
29054144 TTTATTCTTC
*
29054154 TTATAATATG
1 TTATAATATT
29054164 TTATAATATAT
1 TTATAATAT-T
* *
29054175 ATTTTAATTTT
1 -TTATAATATT
*
29054186 TTATTAA-GTT
1 TTA-TAATATT
29054196 TTA-AATATT
1 TTATAATATT
29054205 TT-TAATAATT
1 TTATAAT-ATT
**
29054215 TT-CCATATT
1 TTATAATATT
29054224 TTAAAATAATATT
1 TT---ATAATATT
*
29054237 TTTTAATATTT
1 TTATAATA-TT
29054248 TTATAAT-TT
1 TTATAATATT
29054257 TTCATAATTTATAT
1 TT-ATAA--TAT-T
*
29054271 TT-TTATATT
1 TTATAATATT
29054280 TTATAAT-TT
1 TTATAATATT
29054289 TTAGT--TATT
1 TTA-TAATATT
29054298 TTA-AA-ATT
1 TTATAATATT
29054306 TATATAA-A-T
1 T-TATAATATT
*
29054315 TTAT--TCTT
1 TTATAATATT
29054323 TTATAATATT
1 TTATAATATT
29054333 TTATA
1 TTATA
29054338 TTTTAATGAT
Statistics
Matches: 131, Mismatches: 16, Indels: 54
0.65 0.08 0.27
Matches are distributed among these distances:
8 15 0.11
9 33 0.25
10 50 0.38
11 12 0.09
12 10 0.08
13 8 0.06
14 3 0.02
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (10 bp):
TTATAATATT
Found at i:29054367 original size:42 final size:42
Alignment explanation
Indices: 29054262--29054376 Score: 112
Period size: 42 Copynumber: 2.8 Consensus size: 42
29054252 AATTTTTCAT
29054262 AATTTATAT--TTTTATATTTTATAAT-TTTTAGTTATTTTAA
1 AATTTATATAATTTTATATTTTATAATATTTTAG-TATTTTAA
* *
29054302 AATTTATATAAATTTATTCTTTTATAATATTTTA-TATTTTAA
1 AATTTATATAATTTTA-TATTTTATAATATTTTAGTATTTTAA
* * * * *
29054344 TGATTTTTTTCATTTTATATTTTAAAATATTTT
1 -AATTTATATAATTTTATATTTTATAATATTTT
29054377 TATAACTGTA
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
40 9 0.15
42 26 0.43
43 21 0.34
44 5 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (42 bp):
AATTTATATAATTTTATATTTTATAATATTTTAGTATTTTAA
Found at i:29054376 original size:25 final size:25
Alignment explanation
Indices: 29054330--29054377 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
29054320 CTTTTATAAT
*
29054330 ATTTTATATTTTAATGATTTTTTTC
1 ATTTTATATTTTAATAATTTTTTTC
*
29054355 ATTTTATATTTTAA-AATATTTTT
1 ATTTTATATTTTAATAATTTTTTT
29054378 ATAACTGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (25 bp):
ATTTTATATTTTAATAATTTTTTTC
Found at i:29054428 original size:22 final size:22
Alignment explanation
Indices: 29054401--29054446 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
29054391 ATTTTTACTA
*
29054401 TTTTTATTATTTTCTA-TAATTT
1 TTTTTATAATTTT-TATTAATTT
29054423 TTTTTATAATTTTTATTAATTT
1 TTTTTATAATTTTTATTAATTT
29054445 TT
1 TT
29054447 ACTAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTTATAATTTTTATTAATTT
Found at i:29054435 original size:31 final size:32
Alignment explanation
Indices: 29054392--29054453 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
29054382 CTGTAATATA
29054392 TTTTTACTATTTTTATT-ATTTTCTA-TAATTT
1 TTTTTACTATTTTTATTAATTTT-TACTAATTT
29054423 TTTTTA-TAATTTTTATTAATTTTTACTAATT
1 TTTTTACT-ATTTTTATTAATTTTTACTAATT
29054454 ATAGATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
30 1 0.04
31 17 0.61
32 10 0.36
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (32 bp):
TTTTTACTATTTTTATTAATTTTTACTAATTT
Found at i:29054437 original size:9 final size:9
Alignment explanation
Indices: 29054244--29054453 Score: 86
Period size: 9 Copynumber: 23.3 Consensus size: 9
29054234 ATTTTTTAAT
29054244 ATTTTTATA
1 ATTTTTATA
29054253 ATTTTTCATA
1 ATTTTT-ATA
29054263 A--TTTAT-
1 ATTTTTATA
29054269 ATTTTTAT-
1 ATTTTTATA
29054277 A-TTTTATA
1 ATTTTTATA
*
29054285 ATTTTTAGTT
1 ATTTTTA-TA
*
29054295 A-TTTTAAA
1 ATTTTTATA
*
29054303 ATTTATATA
1 ATTTTTATA
*
29054312 A-ATTTAT-
1 ATTTTTATA
29054319 -TCTTTTATA
1 AT-TTTTATA
29054328 ATATTTTAT-
1 AT-TTTTATA
* *
29054337 ATTTTAATG
1 ATTTTTATA
* *
29054346 ATTTTTTTC
1 ATTTTTATA
29054355 A-TTTTAT-
1 ATTTTTATA
* *
29054362 ATTTTAAAA
1 ATTTTTATA
29054371 TATTTTTATA
1 -ATTTTTATA
* * *
29054381 ACTGTAATA
1 ATTTTTATA
29054390 TATTTTTACT-
1 -ATTTTTA-TA
*
29054400 ATTTTTATT
1 ATTTTTATA
29054409 ATTTTCTATA
1 ATTTT-TATA
29054419 ATTTTTTTTATA
1 A---TTTTTATA
29054431 ATTTTTATTA
1 ATTTTTA-TA
29054441 ATTTTTACTA
1 ATTTTTA-TA
29054451 ATT
1 ATT
29054454 ATAGATATAT
Statistics
Matches: 152, Mismatches: 26, Indels: 45
0.68 0.12 0.20
Matches are distributed among these distances:
6 1 0.01
7 9 0.06
8 35 0.23
9 55 0.36
10 42 0.28
11 1 0.01
12 5 0.03
13 4 0.03
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (9 bp):
ATTTTTATA
Found at i:29055119 original size:32 final size:32
Alignment explanation
Indices: 29055083--29055143 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
29055073 TAAATAATGA
29055083 TAGACTCTAAATCGGCCCGATTTGGACAAAGT
1 TAGACTCTAAATCGGCCCGATTTGGACAAAGT
*
29055115 TAGACTCTAAATTGGCCCGATTTGGACAA
1 TAGACTCTAAATCGGCCCGATTTGGACAA
29055144 GGTTTTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (32 bp):
TAGACTCTAAATCGGCCCGATTTGGACAAAGT
Found at i:29055414 original size:19 final size:20
Alignment explanation
Indices: 29055388--29055428 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
29055378 TTAAATATTT
29055388 ATATATTTATATATTTTAAAA
1 ATAT-TTTATATATTTTAAAA
* *
29055409 ATATTTTTTATTTTTTAAAA
1 ATATTTTATATATTTTAAAA
29055429 TTTTAAAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATTTTATATATTTTAAAA
Found at i:29062146 original size:12 final size:12
Alignment explanation
Indices: 29062129--29062153 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29062119 AGCTTGAAAT
29062129 GCTGGTGAGCTC
1 GCTGGTGAGCTC
29062141 GCTGGTGAGCTC
1 GCTGGTGAGCTC
29062153 G
1 G
29062154 TACTTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.24, G:0.44, T:0.24
Consensus pattern (12 bp):
GCTGGTGAGCTC
Found at i:29065786 original size:25 final size:24
Alignment explanation
Indices: 29065758--29065827 Score: 88
Period size: 24 Copynumber: 2.9 Consensus size: 24
29065748 CTAAATAACG
*
29065758 GGAAGCTCGTGAGAGCCAAGTATTA
1 GGAAGCTCATGAGAGCCAA-TATTA
*
29065783 GGAAGCTCAAGAGAGCCAATATTA
1 GGAAGCTCATGAGAGCCAATATTA
*
29065807 -GAATGCTCATGAGAGCTAATA
1 GGAA-GCTCATGAGAGCCAATA
29065828 ACGGATGCTC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 3 0.08
24 20 0.50
25 17 0.43
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (24 bp):
GGAAGCTCATGAGAGCCAATATTA
Found at i:29066746 original size:13 final size:14
Alignment explanation
Indices: 29066730--29066759 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29066720 TATTATTTAT
29066730 TTTA-TTTATCATC
1 TTTATTTTATCATC
29066743 TTTATTTTATCATC
1 TTTATTTTATCATC
29066757 TTT
1 TTT
29066760 CCAATTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATTTTATCATC
Found at i:29070052 original size:20 final size:22
Alignment explanation
Indices: 29070024--29070065 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
29070014 GTTAAAGGCA
29070024 TTACAGAACAAATCAA-AACAT
1 TTACAGAACAAATCAATAACAT
*
29070045 TTAC-GAACAATTCAATAACAT
1 TTACAGAACAAATCAATAACAT
29070066 CATCCACAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.52, C:0.19, G:0.05, T:0.24
Consensus pattern (22 bp):
TTACAGAACAAATCAATAACAT
Found at i:29071651 original size:44 final size:42
Alignment explanation
Indices: 29071496--29071657 Score: 148
Period size: 43 Copynumber: 3.8 Consensus size: 42
29071486 GGAAAGCTCG
* * * ** *
29071496 TACAATGCCAATGTCTCAGACGTGGTCTTACTTGTAATCAAA
1 TACAATGCCAACGTCCCAGACATGGTCTTACACGAAATCAAA
*
29071538 TATCAATGCC-ACTATCCCAGACATGGTCTTACACGAAATCAAA
1 TA-CAATGCCAAC-GTCCCAGACATGGTCTTACACGAAATCAAA
* * *
29071581 TACGATGCCAACGTCCCAGACGTGGTCTTACATGTAAATACCAAA
1 TACAATGCCAACGTCCCAGACATGGTCTTACACG-AAAT--CAAA
* * *
29071626 T-CAATGCGAACGTCCTAGACCTGGTCTTACAC
1 TACAATGCCAACGTCCCAGACATGGTCTTACAC
29071658 AAAAATACAT
Statistics
Matches: 98, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
42 28 0.29
43 39 0.40
44 26 0.27
45 5 0.05
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (42 bp):
TACAATGCCAACGTCCCAGACATGGTCTTACACGAAATCAAA
Found at i:29071665 original size:44 final size:44
Alignment explanation
Indices: 29071534--29071661 Score: 120
Period size: 44 Copynumber: 2.9 Consensus size: 44
29071524 TACTTGTAAT
* *
29071534 CAAATATCAATGCC-ACTATCCCAGACATGGTCTTACACGAAAT--
1 CAAATA-CAATGCCAAC-GTCCCAGACATGGTCTTACACAAAATAC
* * **
29071577 CAAATACGATGCCAACGTCCCAGACGTGGTCTTACATGTAAATAC
1 CAAATACAATGCCAACGTCCCAGACATGGTCTTACA-CAAAATAC
* * *
29071622 CAAAT-CAATGCGAACGTCCTAGACCTGGTCTTACACAAAA
1 CAAATACAATGCCAACGTCCCAGACATGGTCTTACACAAAA
29071662 ATACATATAA
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
42 24 0.34
43 15 0.21
44 26 0.37
45 5 0.07
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (44 bp):
CAAATACAATGCCAACGTCCCAGACATGGTCTTACACAAAATAC
Found at i:29086252 original size:17 final size:17
Alignment explanation
Indices: 29086230--29086265 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
29086220 ACTTCTTCTG
*
29086230 TTTGTTGTTTGTTGCAA
1 TTTGTTGTTTGCTGCAA
29086247 TTTGTTGTTTGCTGCAA
1 TTTGTTGTTTGCTGCAA
29086264 TT
1 TT
29086266 CTATTAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.08, G:0.22, T:0.58
Consensus pattern (17 bp):
TTTGTTGTTTGCTGCAA
Found at i:29089433 original size:21 final size:21
Alignment explanation
Indices: 29089358--29089423 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 21
29089348 GTCTTGAATT
29089358 TGTTAGATATTGAATTTATTA
1 TGTTAGATATTGAATTTATTA
* *
29089379 TGTTTTAAGCTTGTTGAATTTATTA
1 TG--TT-AG-ATATTGAATTTATTA
29089404 TGTTAGATATTGAATTTATT
1 TGTTAGATATTGAATTTATT
29089424 TGGTTGGATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 14 0.38
22 2 0.05
23 4 0.11
24 2 0.05
25 15 0.41
ACGTcount: A:0.29, C:0.02, G:0.15, T:0.55
Consensus pattern (21 bp):
TGTTAGATATTGAATTTATTA
Found at i:29090693 original size:28 final size:28
Alignment explanation
Indices: 29090661--29090719 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
29090651 ACAATATATG
* * *
29090661 TAAAAAATATTTTAAAGTATAAATTTAT
1 TAAAAAACAATTTAAAATATAAATTTAT
29090689 TAAAAAACAATTTAAAATATAAATTTAT
1 TAAAAAACAATTTAAAATATAAATTTAT
29090717 TAA
1 TAA
29090720 TATATGTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (28 bp):
TAAAAAACAATTTAAAATATAAATTTAT
Found at i:29091736 original size:43 final size:43
Alignment explanation
Indices: 29091645--29092250 Score: 374
Period size: 43 Copynumber: 14.1 Consensus size: 43
29091635 ACAGGTTATA
* * * * * *
29091645 CTTCGGTTTATCTGATGATGCCTCTGTATGTGCCAGTATATTTT
1 CTTCGGTTTGTCCGATGATG-CACTGTGTGTGCCAGTATAGTTG
* *
29091689 CTTAGGTTTGCCCGATGATGCACTGTGTGTGCCAGTATAGTTG
1 CTTCGGTTTGTCCGATGATGCACTGTGTGTGCCAGTATAGTTG
* * * * * * * * *
29091732 CTTAGATATATCTGATGATGCACTGTATGTACCAGTATATTTT
1 CTTCGGTTTGTCCGATGATGCACTGTGTGTGCCAGTATAGTTG
* * * * * * *
29091775 ATTCGGTTTGTCCAATAATGCACT-TCATTTGCTAGTATAGTTA
1 CTTCGGTTTGTCCGATGATGCACTGT-GTGTGCCAGTATAGTTG
* * * * *
29091818 CTTCGATATATCCGATGATGCACTGTGTGTGCCAGTATATTTT
1 CTTCGGTTTGTCCGATGATGCACTGTGTGTGCCAGTATAGTTG
* *** * *
29091861 CTTCGGCTTGTTTAATGATGCACTGCGTGTGCCAATATAGTTG
1 CTTCGGTTTGTCCGATGATGCACTGTGTGTGCCAGTATAGTTG
* * * * *
29091904 CTTTGATATT-TCCGATAATGCACTGTGTGTGCCAGTATATTTT
1 CTTCGGT-TTGTCCGATGATGCACTGTGTGTGCCAGTATAGTTG
* * * *
29091947 CTTCTGTTTTTCCAATGATGCACTGTGTGTGCCAATATAGTTG
1 CTTCGGTTTGTCCGATGATGCACTGTGTGTGCCAGTATAGTTG
* * * * * * * *
29091990 CTTTGGTATATCTGATGATACACTGTGTGTACCAGTATATTTT
1 CTTCGGTTTGTCCGATGATGCACTGTGTGTGCCAGTATAGTTG
* * * * *
29092033 CTTCGATTTGTCTGATGGTGCACTATGTGTGCTAGTATAGTTG
1 CTTCGGTTTGTCCGATGATGCACTGTGTGTGCCAGTATAGTTG
* * * ***** * *
29092076 CTTCTGTATATCCGATGATGCACTAAAAATGCCAATATATGCT-
1 CTTCGGTTTGTCCGATGATGCACTGTGTGTGCCAGTATA-GTTG
* * * *
29092119 CTTCAGTTTGTCCAATGATGCACTGTGTGTACCAATATAGTTG
1 CTTCGGTTTGTCCGATGATGCACTGTGTGTGCCAGTATAGTTG
* * * * * * * *
29092162 TTTTGGTAT-ACACGATGATGCACTGTGGGTGCTAGTATATTTT
1 CTTCGGTTTGTC-CGATGATGCACTGTGTGTGCCAGTATAGTTG
* ** * **
29092205 CTTCGGTTTGTCCAACAATGCACTGTCTGTGCCAACATAGTTG
1 CTTCGGTTTGTCCGATGATGCACTGTGTGTGCCAGTATAGTTG
29092248 CTT
1 CTT
29092251 TGGTACATTC
Statistics
Matches: 411, Mismatches: 143, Indels: 17
0.72 0.25 0.03
Matches are distributed among these distances:
42 6 0.01
43 383 0.93
44 22 0.05
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (43 bp):
CTTCGGTTTGTCCGATGATGCACTGTGTGTGCCAGTATAGTTG
Found at i:29092253 original size:86 final size:86
Alignment explanation
Indices: 29091653--29092269 Score: 637
Period size: 86 Copynumber: 7.2 Consensus size: 86
29091643 TACTTCGGTT
* * * * * *
29091653 TATCTGATGATGCCTCTGTATGTGCCAGTATATTTTCTTAGGTTTGCCCGATGATGCACTGTGTG
1 TATCCGATGATG-CACTGTGTGTGCCAGTATATTTTCTTCGGTTTGTCCAATGATGCACTGTGTG
* * *
29091718 TGCCAGTATAGTTGCTTAGATA
65 TGCCAATATAGTTGCTTTGGTA
* * * * * * *
29091740 TATCTGATGATGCACTGTATGTACCAGTATATTTTATTCGGTTTGTCCAATAATGCACT-TCATT
1 TATCCGATGATGCACTGTGTGTGCCAGTATATTTTCTTCGGTTTGTCCAATGATGCACTGT-GTG
* * * * *
29091804 TGCTAGTATAGTTACTTCGATA
65 TGCCAATATAGTTGCTTTGGTA
* ** *
29091826 TATCCGATGATGCACTGTGTGTGCCAGTATATTTTCTTCGGCTTGTTTAATGATGCACTGCGTGT
1 TATCCGATGATGCACTGTGTGTGCCAGTATATTTTCTTCGGTTTGTCCAATGATGCACTGTGTGT
*
29091891 GCCAATATAGTTGCTTTGATA
66 GCCAATATAGTTGCTTTGGTA
* * * *
29091912 TTTCCGATAATGCACTGTGTGTGCCAGTATATTTTCTTCTGTTTTTCCAATGATGCACTGTGTGT
1 TATCCGATGATGCACTGTGTGTGCCAGTATATTTTCTTCGGTTTGTCCAATGATGCACTGTGTGT
29091977 GCCAATATAGTTGCTTTGGTA
66 GCCAATATAGTTGCTTTGGTA
* * * * ** * *
29091998 TATCTGATGATACACTGTGTGTACCAGTATATTTTCTTCGATTTGTCTGATGGTGCACTATGTGT
1 TATCCGATGATGCACTGTGTGTGCCAGTATATTTTCTTCGGTTTGTCCAATGATGCACTGTGTGT
* *
29092063 GCTAGTATAGTTGCTTCT-GTA
66 GCCAATATAGTTGCTT-TGGTA
***** * ** *
29092084 TATCCGATGATGCACTAAAAATGCCAATATATGCTCTTCAGTTTGTCCAATGATGCACTGTGTGT
1 TATCCGATGATGCACTGTGTGTGCCAGTATATTTTCTTCGGTTTGTCCAATGATGCACTGTGTGT
* *
29092149 ACCAATATAGTTGTTTTGGTA
66 GCCAATATAGTTGCTTTGGTA
* * ** *
29092170 TA-CACGATGATGCACTGTGGGTGCTAGTATATTTTCTTCGGTTTGTCCAACAATGCACTGTCTG
1 TATC-CGATGATGCACTGTGTGTGCCAGTATATTTTCTTCGGTTTGTCCAATGATGCACTGTGTG
*
29092234 TGCCAACATAGTTGCTTTGGTA
65 TGCCAATATAGTTGCTTTGGTA
* * *
29092256 CATTCAATGATGCA
1 TATCCGATGATGCA
29092270 AGTATGATGA
Statistics
Matches: 434, Mismatches: 90, Indels: 13
0.81 0.17 0.02
Matches are distributed among these distances:
85 3 0.01
86 418 0.96
87 13 0.03
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (86 bp):
TATCCGATGATGCACTGTGTGTGCCAGTATATTTTCTTCGGTTTGTCCAATGATGCACTGTGTGT
GCCAATATAGTTGCTTTGGTA
Found at i:29095730 original size:18 final size:18
Alignment explanation
Indices: 29095709--29095746 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
29095699 TCTCTTTGTT
*
29095709 CTCTTCGTTCTCAGCTTC
1 CTCTTCGTTCTCAACTTC
*
29095727 CTCTTCTTTCTCAACTTC
1 CTCTTCGTTCTCAACTTC
29095745 CT
1 CT
29095747 ATTTGTTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.39, G:0.05, T:0.47
Consensus pattern (18 bp):
CTCTTCGTTCTCAACTTC
Found at i:29096918 original size:59 final size:60
Alignment explanation
Indices: 29096855--29096977 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 60
29096845 GACAAAATTG
* *
29096855 AATAGTTGGGTGATTATTTTCT-ATTTTTTCATAGTT-GA-GTAACAAAAAAGAAATTTAAT
1 AATAGTTGGGCGATCATTTTCTAATTTTTT-ATAGTTGGATG-AACAAAAAAGAAATTTAAT
* * ** *
29096914 AATAGTTGGGCGATCATTTTGTAATTTTTTATATTTGGATGATTAAAAAAGAAATTTACT
1 AATAGTTGGGCGATCATTTTCTAATTTTTTATAGTTGGATGAACAAAAAAGAAATTTAAT
29096974 AATA
1 AATA
29096978 ATTTAATGAT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
59 24 0.44
60 29 0.54
61 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.42
Consensus pattern (60 bp):
AATAGTTGGGCGATCATTTTCTAATTTTTTATAGTTGGATGAACAAAAAAGAAATTTAAT
Found at i:29101430 original size:15 final size:16
Alignment explanation
Indices: 29101399--29101434 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
29101389 TATTACATAC
29101399 ATTAAATAAATAATAT
1 ATTAAATAAATAATAT
*
29101415 ATTAAAT-AATACTAT
1 ATTAAATAAATAATAT
29101430 ATTAA
1 ATTAA
29101435 GTTTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTAAATAAATAATAT
Found at i:29101981 original size:30 final size:29
Alignment explanation
Indices: 29101947--29102004 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
29101937 GACTTTCATG
29101947 TATAT-ATTTGAACTAAATCAAATATTTATA
1 TATATAATTT-AACTAAATCAAA-ATTTATA
* *
29101977 TATATAATTTCACTAAATTAAAATTTAT
1 TATATAATTTAACTAAATCAAAATTTAT
29102005 GTATCAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.24
30 15 0.60
31 4 0.16
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.45
Consensus pattern (29 bp):
TATATAATTTAACTAAATCAAAATTTATA
Found at i:29102659 original size:21 final size:21
Alignment explanation
Indices: 29102621--29102678 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
29102611 GTTTTAAGAA
*
29102621 TTGTTTTAGTATCATTTTTAT
1 TTGTTTTAATATCATTTTTAT
**
29102642 TTGTTTTAATATTTTTTTTAT
1 TTGTTTTAATATCATTTTTAT
*
29102663 GTT-TTTAAATAT-ATTT
1 -TTGTTTTAATATCATTT
29102679 GATTTATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 3 0.10
21 26 0.84
22 2 0.06
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (21 bp):
TTGTTTTAATATCATTTTTAT
Found at i:29105293 original size:37 final size:38
Alignment explanation
Indices: 29105224--29105350 Score: 157
Period size: 38 Copynumber: 3.4 Consensus size: 38
29105214 ATAATACTAA
* * *
29105224 AACAGTAGACATGCTTAACGTGTATTCAGTTCAAC-AT
1 AACAATAGACATGCTTAACATGTATTCGGTTCAACAAT
* * * *
29105261 AACAATAGACATGCTTATCATGTTTTTGGTTCAACGAT
1 AACAATAGACATGCTTAACATGTATTCGGTTCAACAAT
* *
29105299 AATAATAGACATGTTTAACATGTATTCGGTTCAACAAT
1 AACAATAGACATGCTTAACATGTATTCGGTTCAACAAT
*
29105337 AACAATAGGCATGC
1 AACAATAGACATGC
29105351 AACTATTAAT
Statistics
Matches: 74, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
37 29 0.39
38 45 0.61
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (38 bp):
AACAATAGACATGCTTAACATGTATTCGGTTCAACAAT
Found at i:29107142 original size:47 final size:46
Alignment explanation
Indices: 29107070--29107380 Score: 164
Period size: 47 Copynumber: 6.6 Consensus size: 46
29107060 TCATTTGTGC
*
29107070 GCTAGTGTAAGA-CATGTCTGAGACATGCATCGACCACATTATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGCATCG-CCACATTATGAGA
* *
29107116 GCTAGTGTAAGACCATGTCTGGGACATGGCATCG--GCATTAAGACAAGA
1 GCTAGTGTAAGACCATGTCTGGGACAT-GCATCGCCACATTATG---AGA
* * * *
29107164 GCTAATGTAAGA-CATGTCTGGGACATGCTTCGGCTAC--GA-GAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGCATC-GCCACATTATGAGA
* * * *
29107207 TG-TCAGTGTAAGACCATGTTTGGGATATGGCATCGGCACGGATATGTGAGA
1 -GCT-AGTGTAAGACCATGTCTGGGACAT-GCATCGCCAC--AT-TATGAGA
* * * *
29107258 GCTAGTGTAAGACCATGTAT-GGACATGGCGTCGGCCTCGATT-TCGATA
1 GCTAGTGTAAGACCATGTCTGGGACAT-GCATC-GCCAC-ATTAT-GAGA
* *
29107306 G-TCAGTGTAAGACCATGTCTAGGACATGACATCG--TC-TTGATGGATGA
1 GCT-AGTGTAAGACCATGTCTGGGACATG-CATCGCCACATT-AT-GA-GA
* *
29107353 GCCAGTGTAAGACCATGTCTGTGACATG
1 GCTAGTGTAAGACCATGTCTGGGACATG
29107381 GCAGTGGCAT
Statistics
Matches: 209, Mismatches: 28, Indels: 55
0.72 0.10 0.19
Matches are distributed among these distances:
43 4 0.02
44 11 0.05
45 21 0.10
46 26 0.12
47 56 0.27
48 43 0.21
49 23 0.11
50 20 0.10
51 5 0.02
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (46 bp):
GCTAGTGTAAGACCATGTCTGGGACATGCATCGCCACATTATGAGA
Found at i:29107270 original size:94 final size:93
Alignment explanation
Indices: 29107070--29107244 Score: 221
Period size: 92 Copynumber: 1.9 Consensus size: 93
29107060 TCATTTGTGC
* *
29107070 GCTAGTGTAAGACATGTCTGAGACATGCATCGACCACATTATGAGAGCTAGTGTAAGACCATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACCACA-GATGAGAGCTAGTGTAAGACCATGTC
*
29107135 TGGGACATGGCATCGGCATTAAGACAAGA
65 TGGGACATGGCATCGGCAATAAGACAAGA
* * * *
29107164 GCTAATGTAAGACATGTCTGGGACATGCTTCGGCTAC-GA-GAGATG-TCAGTGTAAGACCATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACCACAGATGAGA-GCT-AGTGTAAGACCATGT
* *
29107226 TTGGGATATGGCATCGGCA
64 CTGGGACATGGCATCGGCA
29107245 CGGATATGTG
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
91 5 0.07
92 34 0.48
94 32 0.45
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (93 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGACCACAGATGAGAGCTAGTGTAAGACCATGTCT
GGGACATGGCATCGGCAATAAGACAAGA
Found at i:29110269 original size:12 final size:12
Alignment explanation
Indices: 29110231--29110268 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
29110221 TTTTTCTCTC
*
29110231 TTTCTTCTTCTT
1 TTTCTTCTTTTT
*
29110243 TTCCTTCTTTTT
1 TTTCTTCTTTTT
29110255 TTTCTT-TTTTT
1 TTTCTTCTTTTT
29110266 TTT
1 TTT
29110269 TAATTTACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTCTTCTTTTT
Found at i:29117208 original size:51 final size:51
Alignment explanation
Indices: 29117148--29117249 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
29117138 GGATGCTTTT
29117148 AAGTGAAACCTCAACCCTCCATACAAAGACCCCCAAAGACCAACAAACAGG
1 AAGTGAAACCTCAACCCTCCATACAAAGACCCCCAAAGACCAACAAACAGG
29117199 AAGTGAAACCTCAACCCTCCATACAAAGACCCCCAAAGACCAACAAACAGG
1 AAGTGAAACCTCAACCCTCCATACAAAGACCCCCAAAGACCAACAAACAGG
29117250 CATACAACAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.45, C:0.35, G:0.12, T:0.08
Consensus pattern (51 bp):
AAGTGAAACCTCAACCCTCCATACAAAGACCCCCAAAGACCAACAAACAGG
Found at i:29127881 original size:2 final size:2
Alignment explanation
Indices: 29127874--29127923 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
29127864 TTTATTAAAA
29127874 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
29127916 AG AG AG AG
1 AG AG AG AG
29127924 GATGGTTTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29128470 original size:27 final size:27
Alignment explanation
Indices: 29128418--29128478 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
29128408 TGTGTGTTTA
* *
29128418 AAAATAATATATAATTATCAACTAATG
1 AAAATAATATAAAATTATAAACTAATG
* *
29128445 AAAATAATA-AAAATATATAAATTAATT
1 AAAATAATATAAAAT-TATAAACTAATG
29128472 AAAATAA
1 AAAATAA
29128479 AACTTTAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 4 0.14
27 25 0.86
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (27 bp):
AAAATAATATAAAATTATAAACTAATG
Found at i:29129660 original size:31 final size:31
Alignment explanation
Indices: 29129621--29129689 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
29129611 AATTGGTTCC
* *
29129621 TAAATTTGAGACTTTTTCTCAATTTAGTA-T
1 TAAATTTGACACTTTTTCTCAAGTTAGTAGT
* *
29129651 TGAAATTTGACATTTTTTCTTAAGTTAGTAGT
1 T-AAATTTGACACTTTTTCTCAAGTTAGTAGT
29129683 TAAATTT
1 TAAATTT
29129690 TTCGGGATCC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.03
31 30 0.91
32 2 0.06
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (31 bp):
TAAATTTGACACTTTTTCTCAAGTTAGTAGT
Found at i:29130160 original size:26 final size:28
Alignment explanation
Indices: 29130107--29130166 Score: 81
Period size: 30 Copynumber: 2.2 Consensus size: 28
29130097 AACATCTAAT
29130107 AAATTTAGGTACCAAATTAAACGTAAAAA
1 AAATTTAGGTACCAAATT-AACGTAAAAA
29130136 AAATCTTAGGTACCAAATT-A-G-AAAAA
1 AAAT-TTAGGTACCAAATTAACGTAAAAA
29130162 AAATT
1 AAATT
29130167 GCTAAGTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
25 1 0.03
26 9 0.30
27 1 0.03
28 1 0.03
29 4 0.13
30 14 0.47
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.25
Consensus pattern (28 bp):
AAATTTAGGTACCAAATTAACGTAAAAA
Found at i:29131177 original size:22 final size:21
Alignment explanation
Indices: 29131137--29131177 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
29131127 CAAAAGTTAT
*
29131137 AAAATAAAGTTAAATTTTTTC
1 AAAATAAAGTTAAAATTTTTC
*
29131158 AAAATAAAATTTAAAATTTT
1 AAAAT-AAAGTTAAAATTTT
29131178 AAAACCTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
AAAATAAAGTTAAAATTTTTC
Found at i:29135887 original size:39 final size:39
Alignment explanation
Indices: 29135828--29135920 Score: 150
Period size: 39 Copynumber: 2.4 Consensus size: 39
29135818 TAGAATCAAA
* * *
29135828 ATAGTAAAACTAGTCCTATTCACCCTTTACTTCCTATAAT
1 ATAG-AAAACTACTCCTATTCACCATCTACTTCCTATAAT
29135868 ATAGAAAACTACTCCTATTCACCATCTACTTCCTATAAT
1 ATAGAAAACTACTCCTATTCACCATCTACTTCCTATAAT
29135907 ATAGAAAACTACTC
1 ATAGAAAACTACTC
29135921 TTAAAATAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
39 46 0.92
40 4 0.08
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (39 bp):
ATAGAAAACTACTCCTATTCACCATCTACTTCCTATAAT
Found at i:29146751 original size:79 final size:81
Alignment explanation
Indices: 29146615--29146799 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
29146605 TTGAATGATG
* *
29146615 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
29146679 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
29146694 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
29146756 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
29146774 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
29146800 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:29146813 original size:40 final size:40
Alignment explanation
Indices: 29146616--29146799 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
29146606 TGAATGATGT
* * * *
29146616 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
29146656 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
29146696 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
29146734 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
29146775 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
29146800 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:29146821 original size:79 final size:79
Alignment explanation
Indices: 29146668--29146832 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
29146658 GGACTAAGAT
* * **
29146668 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
29146733 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
29146747 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
29146810 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
29146826 CCGAAGG
1 CCGAAGG
29146833 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:29154950 original size:79 final size:81
Alignment explanation
Indices: 29154818--29154998 Score: 210
Period size: 79 Copynumber: 2.3 Consensus size: 81
29154808 ATGATGTCCG
* *
29154818 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTG
1 GGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATTGTG
*
29154882 CGAGATACTA-ATTCCA
66 CGAGATACTATA-ACCA
* * * **
29154898 GGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAATTGT
1 GGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAATTGT
* *
29154960 GCGAGTTACTATAACCG
65 GCGAGATACTATAACCA
*
29154977 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
29154999 AACGAGTAGC
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
78 1 0.01
79 56 0.65
80 29 0.34
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
GGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATTGTG
CGAGATACTATAACCA
Found at i:29155005 original size:40 final size:40
Alignment explanation
Indices: 29154814--29154998 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
29154804 TTGAATGATG
* * * *
29154814 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
29154854 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
29154894 TCCAGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
29154933 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
29154974 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
29154999 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 34 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:29155020 original size:79 final size:79
Alignment explanation
Indices: 29154867--29155031 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
29154857 GGACTAAGAT
* * **
29154867 CCGAAGGCATTTGTGCGAGATACTAATTCCAGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCAGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
29154932 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
29154946 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCAGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
29155009 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
29155025 CCGAAGG
1 CCGAAGG
29155032 TACGTGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 46 0.63
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCAGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:29158071 original size:39 final size:39
Alignment explanation
Indices: 29158010--29158105 Score: 147
Period size: 39 Copynumber: 2.4 Consensus size: 39
29158000 TGGAATCAAA
* *
29158010 ATAGTAAAACTACTCATATTTGCCCTCTACTTCCTATAAT
1 ATAG-AAAACTACTCCTATTTGCCCTCTACCTCCTATAAT
* *
29158050 ATAGAAAACTAATCCTGTTTGCCCTCTACCTCCTATAAT
1 ATAGAAAACTACTCCTATTTGCCCTCTACCTCCTATAAT
29158089 ATAGAAAACTACTCCTA
1 ATAGAAAACTACTCCTA
29158106 AAATAAATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
39 46 0.92
40 4 0.08
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.33
Consensus pattern (39 bp):
ATAGAAAACTACTCCTATTTGCCCTCTACCTCCTATAAT
Found at i:29158532 original size:24 final size:24
Alignment explanation
Indices: 29158505--29158553 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
29158495 TATATTTCAT
*
29158505 ATTGAATATCCACTTAATATCTCC
1 ATTGAATATCCACTTAATACCTCC
* * *
29158529 ATTGAGTATTCATTTAATACCTCC
1 ATTGAATATCCACTTAATACCTCC
29158553 A
1 A
29158554 AACTGAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (24 bp):
ATTGAATATCCACTTAATACCTCC
Found at i:29158935 original size:34 final size:34
Alignment explanation
Indices: 29158859--29158936 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
29158849 CAACTTCCTT
* *
29158859 ATAAC-ATACATATAATGTATTCAACAATTGATA
1 ATAACTATACATATAACGCATTCAACAATTGATA
** * *
29158892 ATAGTTATACATATAACGCATTCAATAATTGGTA
1 ATAACTATACATATAACGCATTCAACAATTGATA
29158926 ATAACTATACA
1 ATAACTATACA
29158937 AGCATAATAT
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
33 3 0.08
34 33 0.92
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (34 bp):
ATAACTATACATATAACGCATTCAACAATTGATA
Found at i:29159471 original size:58 final size:57
Alignment explanation
Indices: 29159397--29159561 Score: 190
Period size: 58 Copynumber: 2.8 Consensus size: 57
29159387 AAGGTTTAAC
*
29159397 TTTTTTTAGTCCAAGTTAGTCCTTGAACTAGACAATTATTCTCACATTGAGCTT-GAACT
1 TTTTTTTA-TCTAAGTTAGT-CTTGAACTAGACAATTATTCTCACATTGAGCTTGGAA-T
* * * * *
29159456 TTTTTTTATCTAAGTTAGTCTCTAAACTTGGCAACTATTCTCACACTGAGCTTGGAAT
1 TTTTTTTATCTAAGTTAGTCT-TGAACTAGACAATTATTCTCACATTGAGCTTGGAAT
* *
29159514 TTTTTTTAT-TAAAGTTAGTTCTTGAACTAGACAATTGTTTTCACATTG
1 TTTTTTTATCT-AAGTTAG-TCTTGAACTAGACAATTATTCTCACATTG
29159562 GTGACATAAA
Statistics
Matches: 89, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
57 3 0.03
58 72 0.81
59 14 0.16
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (57 bp):
TTTTTTTATCTAAGTTAGTCTTGAACTAGACAATTATTCTCACATTGAGCTTGGAAT
Found at i:29159729 original size:59 final size:59
Alignment explanation
Indices: 29159650--29159793 Score: 163
Period size: 59 Copynumber: 2.4 Consensus size: 59
29159640 CTATATTAAA
* * *
29159650 GCTTAACTTTTTTTTAGTCCAAGTTAGTA-TC-TAAACTTGGTAATTATTCTCACACTAAG
1 GCTTAAC-TTTTTTT-GTCCAAGTTAGTACCCTTAAACTTAGAAATTATTCTCACACTAAG
* *
29159709 GCTTAAGCTTTTTTTGGTCCAAGTTA--ACCCTTGAACTTAGAAATTATTCTCACATTAAG
1 GCTTAA-CTTTTTTT-GTCCAAGTTAGTACCCTTAAACTTAGAAATTATTCTCACACTAAG
29159768 GCTTGAACTTTTTTT-TCCAAGTTAGT
1 GCTT-AACTTTTTTTGTCCAAGTTAGT
29159794 TCATTATATT
Statistics
Matches: 73, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
57 10 0.14
58 1 0.01
59 59 0.81
60 3 0.04
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.42
Consensus pattern (59 bp):
GCTTAACTTTTTTTGTCCAAGTTAGTACCCTTAAACTTAGAAATTATTCTCACACTAAG
Found at i:29159792 original size:261 final size:261
Alignment explanation
Indices: 29159326--29159795 Score: 558
Period size: 261 Copynumber: 1.8 Consensus size: 261
29159316 TCTTTACACC
* * * *
29159326 ATTATAATAAAAAAGGTTAATGCACTATTTTGGGCCTAAACTTGGCAAGTGTTCTCATATTAAGG
1 ATTATAATAAAAAAGGTTAACGCACTAGTTGGGGCCTAAACTTGGCAAGTGTTCTCATATTAAAG
* * * *
29159391 TTTAACTTTTTTTAGTCCAAGTTAGTCCTTGAACTAGACAATTATTCTCACATTGAGCTTGAACT
66 CTTAACTTTTTTTAGTCCAAGTTAGTCCTTAAACTAGACAATTATTCTCACACTAAGCTTGAACT
* * ** * * * *
29159456 TTTTTTTATCTAAGTTAGTCTCTAAACTTGGCAACTATTCTCACACTGAGCTTGGAATTTTTTTT
131 TTTTTTGATCCAAGTTACCCTCTAAACTTAGAAACTATTCTCACACTAAGCTTGGAACTTTTTTT
*
29159521 ATTAAAGTTAGTTCTTGAACTAGACAATTGTTTTCACATTGGTGACATAAACTTTTTTTTTACAA
196 ATCAAAGTTAGTTCTTGAACTAGACAATTGTTTTCACATTGGTGACATAAACTTTTTTTTTACAA
29159586 T
261 T
* * * *
29159587 ATTATAATAAAAAGGGTTAACGCATTGGTTGGGGCCTAAACTT-GTAAGTGTTC-CTATATTAAA
1 ATTATAATAAAAAAGGTTAACGCACTAGTTGGGGCCTAAACTTGGCAAGTGTTCTC-ATATTAAA
* * **
29159650 GCTTAACTTTTTTTTAGTCCAAGTTAGT-ATCTAAACTTGGTAATTATTCTCACACTAAGGCTT-
65 GCTTAAC-TTTTTTTAGTCCAAGTTAGTCCT-TAAACTAGACAATTATTCTCACACTAA-GCTTG
* * * *
29159713 AAGCTTTTTTTGGTCCAAGTTAACCCT-TGAACTTAGAAATTATTCTCACATTAAGGCTT-GAAC
127 AA-CTTTTTTTGATCCAAGTT-ACCCTCTAAACTTAGAAACTATTCTCACACTAA-GCTTGGAAC
*
29159776 TTTTTTT-TCCAAGTTAGTTC
189 TTTTTTTATCAAAGTTAGTTC
29159796 ATTATATTTC
Statistics
Matches: 172, Mismatches: 30, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
259 1 0.01
260 23 0.13
261 91 0.53
262 50 0.29
263 7 0.04
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.41
Consensus pattern (261 bp):
ATTATAATAAAAAAGGTTAACGCACTAGTTGGGGCCTAAACTTGGCAAGTGTTCTCATATTAAAG
CTTAACTTTTTTTAGTCCAAGTTAGTCCTTAAACTAGACAATTATTCTCACACTAAGCTTGAACT
TTTTTTGATCCAAGTTACCCTCTAAACTTAGAAACTATTCTCACACTAAGCTTGGAACTTTTTTT
ATCAAAGTTAGTTCTTGAACTAGACAATTGTTTTCACATTGGTGACATAAACTTTTTTTTTACAA
T
Found at i:29161966 original size:43 final size:43
Alignment explanation
Indices: 29161919--29162017 Score: 121
Period size: 42 Copynumber: 2.3 Consensus size: 43
29161909 TCCCTGACGT
* *
29161919 GGTCTTACATGTAA-TCAAACATCGATGCCATTGTCCCAAACAG
1 GGTCTTACACGTAACTCAAACA-CGATGCCAATGTCCCAAACAG
* * *
29161962 GGTCTTACACG-AACTCAGATACGATGCCAATGTCCCAAACAT
1 GGTCTTACACGTAACTCAAACACGATGCCAATGTCCCAAACAG
*
29162004 GGACTTACACGTAA
1 GGTCTTACACGTAA
29162018 AACAAAAGTC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
42 31 0.65
43 17 0.35
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.23
Consensus pattern (43 bp):
GGTCTTACACGTAACTCAAACACGATGCCAATGTCCCAAACAG
Found at i:29170657 original size:24 final size:24
Alignment explanation
Indices: 29170630--29170675 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
29170620 TGAAGCCAAA
*
29170630 TATGAATTAACCATAGTTTATTAG
1 TATGAATTAACCATAATTTATTAG
*
29170654 TATGGATTAACCATAATTTATT
1 TATGAATTAACCATAATTTATT
29170676 CTTCACTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (24 bp):
TATGAATTAACCATAATTTATTAG
Found at i:29180306 original size:21 final size:20
Alignment explanation
Indices: 29180279--29180325 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
29180269 ATGATTTTTA
*
29180279 TTTTTTTTAGATTTTTTGAG
1 TTTTTTTTAGATTTTTTCAG
**
29180299 TATTTTTTTATTTTTTTTCAG
1 T-TTTTTTTAGATTTTTTCAG
29180320 TTTTTT
1 TTTTTT
29180326 AAATTTATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.13, C:0.02, G:0.09, T:0.77
Consensus pattern (20 bp):
TTTTTTTTAGATTTTTTCAG
Found at i:29180323 original size:11 final size:10
Alignment explanation
Indices: 29180273--29180325 Score: 56
Period size: 9 Copynumber: 5.3 Consensus size: 10
29180263 TTTTATATGA
29180273 TTTTTA-TTT
1 TTTTTAGTTT
*
29180282 TTTTTAGATT
1 TTTTTAGTTT
*
29180292 TTTTGAGTATT
1 TTTTTAGT-TT
29180303 TTTTTA-TTT
1 TTTTTAGTTT
29180312 TTTTTCAGTTT
1 TTTTT-AGTTT
29180323 TTT
1 TTT
29180326 AAATTTATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 13 0.36
10 10 0.28
11 13 0.36
ACGTcount: A:0.13, C:0.02, G:0.08, T:0.77
Consensus pattern (10 bp):
TTTTTAGTTT
Found at i:29188043 original size:48 final size:48
Alignment explanation
Indices: 29187988--29188083 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
29187978 GTCGATACCG
*
29187988 TATCGATACTTGGTAAGTCATTTTCAAGTTAGTAGCCTATTATGGTAT
1 TATCGATACTTGGTAACTCATTTTCAAGTTAGTAGCCTATTATGGTAT
* *
29188036 TATCGATACTTGGTAACTGATTTTCAAGTTAGTAGCCTATTTTGGTAT
1 TATCGATACTTGGTAACTCATTTTCAAGTTAGTAGCCTATTATGGTAT
29188084 CGATTTCTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.43
Consensus pattern (48 bp):
TATCGATACTTGGTAACTCATTTTCAAGTTAGTAGCCTATTATGGTAT
Found at i:29192327 original size:6 final size:6
Alignment explanation
Indices: 29192311--29192341 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
29192301 CATTATCAGG
29192311 ATATCAA ATATAA ATATAA ATATAA ATATAA
1 ATAT-AA ATATAA ATATAA ATATAA ATATAA
29192342 GAATGGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Done.