Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 66 of 132
Found at i:18470981 original size:124 final size:123
Alignment explanation
Indices: 18470693--18471073 Score: 469
Period size: 124 Copynumber: 3.1 Consensus size: 123
18470683 AGAAGACGGA
* * * * * * * * *
18470693 TTTGTTCCACTTCTCTGTATCTCATTAGGAAGATGACCGCTTTATTACTTTGA-CGTACTTCTCT
1 TTTGGTCCATTTCTCTATATCTCATCAAGAAGATGACCGCTTCATCATTTTGATC-CACTTCTCT
* * * * *
18470757 GTATCTCATCAGGAAGATGGAGTTTGAAGTTTCACTTACATTGAACTTCGCTTCATTGA-
65 GTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACGTTGAGCTTCACTTCATT-AT
* * * * * *
18470816 TTTGCTCTACTTCTCTGTATCTCGTCAAGAAGATGACCGCTTCATCGTTTTGATCCACTTCTCTG
1 TTTGGTCCATTTCTCTATATCTCATCAAGAAGATGACCGCTTCATCATTTTGATCCACTTCTCTG
* * *
18470881 TATATCATCAGGAAGATGGGGGTGTGAAGTTTCACTCACGTTGAGTTTCACTTCATTAT
66 TATCTCATCAGGAAGAT-GGGGTTTGAAGTTTCACTCACGTTGAGCTTCACTTCATTAT
*
18470940 TTTGGTCCATTTCTCTATATCTCATCAAGAAGATGATCGCTTCATCATTTTGATCCACTTCTCTG
1 TTTGGTCCATTTCTCTATATCTCATCAAGAAGATGACCGCTTCATCATTTTGATCCACTTCTCTG
* * *
18471005 TATCTCATCAGGAAGATAGAGGTTTGAAGTTTCACTCACGTTGAGCTCCACTTTATTAT
66 TATCTCATCAGGAAGAT-GGGGTTTGAAGTTTCACTCACGTTGAGCTTCACTTCATTAT
18471064 TTTGGTCCAT
1 TTTGGTCCAT
18471074 GATATCATTA
Statistics
Matches: 223, Mismatches: 32, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
123 70 0.31
124 153 0.69
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.39
Consensus pattern (123 bp):
TTTGGTCCATTTCTCTATATCTCATCAAGAAGATGACCGCTTCATCATTTTGATCCACTTCTCTG
TATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACGTTGAGCTTCACTTCATTAT
Found at i:18476576 original size:435 final size:434
Alignment explanation
Indices: 18475761--18476633 Score: 1478
Period size: 435 Copynumber: 2.0 Consensus size: 434
18475751 TTCTGACAGT
* *
18475761 AATTGGGTGAGCCCCGTCCAATGTGTGCCAAAGAAGAGTGGTTTCATAGTCATGGCCAATGATAA
1 AATTGAGTGAGCCCCGTCCAATGTGTGCCAAAGAAGAGTGGTTTCATAGTCATGACCAATGATAA
* *
18475826 GAACGAGTTGATCCCTACTTGAATTCGACTGGTTGGCGAGTATGCATGGATTATCGTCGACTGAA
66 GAACGAGTTGATCCCTACTTCAATTCAACTGGTTGGCGAGTATGCATGGATTATCGTCGACTGAA
* *
18475891 TGCGGCCATAAAGAAGGACCATTTCCCACTACCTTCCATTGACTAGATGCTAGATAGGCTAGCTA
131 TGCGGCCACAAAGAAGGACCATTTCCCACTACCTTCCATTGACCAGATGCTAGATAGGCTAGCTA
* *
18475956 GTAAAGCCTATTATTGCTTCTTAGATGGCTATTCTAGGTACAACCAAATTGCTATTGCATCGGAA
196 GTAAAGCCTATTATTGCTTCTTAGATGGCTATTCTAGGTACAACCAAATTGCCATTGCACCGGAA
18476021 GATCAAGTAAAAAAAACATTCACATGCCCTTTTCGAACCTTTACCTTCCGACGTATACCGTTTGG
261 GATCAAGTAAAAAAAACATTCACATGCCCTTTTCGAACCTTTACCTTCCGACGTATACCGTTTGG
* *
18476086 GTTGTACAATGCGCCAGCAACATTCTAGAGGTGTATGATGACGATCTTCTCGAACATGATCGAGG
326 GTTATACAATGCGCCAGCAACATTCTAGAGGTGTATGATGACGATCTTCTCGAACATAATCGAGG
18476151 ACTCTCTAGAGGTATTCATGAATGATTTCTTTGTTTATGGATAA
391 ACTCTCTAGAGGTATTCATGAATGATTTCTTTGTTTATGGATAA
18476195 AATTGAGTGAGCCCCGTCCAATGTGTGCCAAAGAAGAGTGGTTTCATAGTCATGACCAATGATAA
1 AATTGAGTGAGCCCCGTCCAATGTGTGCCAAAGAAGAGTGGTTTCATAGTCATGACCAATGATAA
*
18476260 GAACGAGTTGATCCCTAC-TCACATTGCAATTGGTTGGCGAGTATGCATGGATTATCGTCGACTG
66 GAACGAGTTGATCCCTACTTCA-ATT-CAACTGGTTGGCGAGTATGCATGGATTATCGTCGACTG
* *
18476324 AATGCGGCCACAAAGAAGGACCATTTCCCACTATCTTCCATTGACCAGATGCTGGATAGGCTAGC
129 AATGCGGCCACAAAGAAGGACCATTTCCCACTACCTTCCATTGACCAGATGCTAGATAGGCTAGC
* * * **
18476389 TGGTAAAGCCTATTATTGCTTCTTAGATGGTTATTCTGGGTACAACCAAATTGCCATTGTGCCGG
194 TAGTAAAGCCTATTATTGCTTCTTAGATGGCTATTCTAGGTACAACCAAATTGCCATTGCACCGG
** * * * **
18476454 AAGATCAAGTAAAAACGACATTCACATGCCCTTTTGGAACCTTTGCCTTTCGACGTATGTCGTTT
259 AAGATCAAGTAAAAAAAACATTCACATGCCCTTTTCGAACCTTTACCTTCCGACGTATACCGTTT
* *
18476519 GGGTTATGCAATGCGCCAGCAACATTCTAGAGGTGTATGATGGCGATCTTCTCGAACATAATCGA
324 GGGTTATACAATGCGCCAGCAACATTCTAGAGGTGTATGATGACGATCTTCTCGAACATAATCGA
18476584 GGACTCTCTAGAGGTATTCATGAATGATTTCTTTGTTTATGGATAA
389 GGACTCTCTAGAGGTATTCATGAATGATTTCTTTGTTTATGGATAA
18476630 AATT
1 AATT
18476634 TTGACCAATG
Statistics
Matches: 410, Mismatches: 27, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
433 2 0.00
434 84 0.20
435 324 0.79
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (434 bp):
AATTGAGTGAGCCCCGTCCAATGTGTGCCAAAGAAGAGTGGTTTCATAGTCATGACCAATGATAA
GAACGAGTTGATCCCTACTTCAATTCAACTGGTTGGCGAGTATGCATGGATTATCGTCGACTGAA
TGCGGCCACAAAGAAGGACCATTTCCCACTACCTTCCATTGACCAGATGCTAGATAGGCTAGCTA
GTAAAGCCTATTATTGCTTCTTAGATGGCTATTCTAGGTACAACCAAATTGCCATTGCACCGGAA
GATCAAGTAAAAAAAACATTCACATGCCCTTTTCGAACCTTTACCTTCCGACGTATACCGTTTGG
GTTATACAATGCGCCAGCAACATTCTAGAGGTGTATGATGACGATCTTCTCGAACATAATCGAGG
ACTCTCTAGAGGTATTCATGAATGATTTCTTTGTTTATGGATAA
Found at i:18483616 original size:47 final size:48
Alignment explanation
Indices: 18483543--18483667 Score: 189
Period size: 48 Copynumber: 2.6 Consensus size: 48
18483533 CACGATCAGT
* * * *
18483543 CCACTTTTTTGTATCCCATCAAGAAGATGATCACTTCA-TGTTTTGAC
1 CCACTTCTCTGTATCTCATCAGGAAGATGATCACTTCATTGTTTTGAC
**
18483590 CCACTTCTCTGTATCTCATCAGGAAGATGATTGCTTCATTGTTTTGAC
1 CCACTTCTCTGTATCTCATCAGGAAGATGATCACTTCATTGTTTTGAC
18483638 CCACTTCTCTGTATCTCATCAGGAAGATGA
1 CCACTTCTCTGTATCTCATCAGGAAGATGA
18483668 GGTTTGAAGT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
47 32 0.45
48 39 0.55
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (48 bp):
CCACTTCTCTGTATCTCATCAGGAAGATGATCACTTCATTGTTTTGAC
Found at i:18483776 original size:48 final size:49
Alignment explanation
Indices: 18483705--18483811 Score: 153
Period size: 48 Copynumber: 2.2 Consensus size: 49
18483695 CTGCTAAATT
* * *
18483705 ATTTTGGTCCACTTCTCTGTATCTCATCAGGAAAATGATCGCTTCA-TC
1 ATTTTGATCTACTTCTCTGTATCTCATCAGGAAAATGATCACTTCATTC
* * *
18483753 ATTTTGATCTACTTCTCTGTATCTCATTAGGAAGATGATCACTTCATTT
1 ATTTTGATCTACTTCTCTGTATCTCATCAGGAAAATGATCACTTCATTC
18483802 ATTTTGATCT
1 ATTTTGATCT
18483812 GACCCACTAC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
48 41 0.79
49 11 0.21
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (49 bp):
ATTTTGATCTACTTCTCTGTATCTCATCAGGAAAATGATCACTTCATTC
Found at i:18483972 original size:21 final size:20
Alignment explanation
Indices: 18483920--18483973 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
18483910 TAGGGACGTA
*
18483920 AGATTCACCTTTACAACTTC
1 AGATTTACCTTTACAACTTC
*
18483940 A-ATTTAGCCCTTTACATCTTC
1 AGATTTA--CCTTTACAACTTC
18483961 GAGATTTACCTTT
1 -AGATTTACCTTT
18483974 GTAACTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 4 0.14
20 1 0.04
21 17 0.61
22 1 0.04
23 5 0.18
ACGTcount: A:0.26, C:0.26, G:0.07, T:0.41
Consensus pattern (20 bp):
AGATTTACCTTTACAACTTC
Found at i:18484096 original size:49 final size:48
Alignment explanation
Indices: 18484040--18484395 Score: 216
Period size: 49 Copynumber: 7.3 Consensus size: 48
18484030 TTTCATCTTC
*
18484040 AGGGTATAAGATTCGCAGTTGTGGCCTCAATCTTTCCCTTCACATCTCT
1 AGGGTATAAGATTCGC-GTTGCGGCCTCAATCTTTCCCTTCACATCTCT
* * * ** *
18484089 AGGGTATAAGGTCTAC-CATTGCGGCCTCAACCTTTTTCTTCACATCTTT
1 AGGGTATAAGAT-T-CGCGTTGCGGCCTCAATCTTTCCCTTCACATCTCT
* * * ** * ** *
18484138 AGGGTTTAAGATTCGCCATTGCGGCTTCAATC-TGGCTTTCTTATTTCT
1 AGGGTATAAGATTCG-CGTTGCGGCCTCAATCTTTCCCTTCACATCTCT
* * * * *
18484186 AAGGTATAAGGTTTGTCGTTGCGGTCTCAACCTTTCCCTTCACATCTCT
1 AGGGTATAAGATTCG-CGTTGCGGCCTCAATCTTTCCCTTCACATCTCT
* * * * * **
18484235 AGGGTACAAGATTCATCGTAGTGGCTTCAATCTTTCCCTTCGTAT-TCTT
1 AGGGTATAAGATTC-GCGTTGCGGCCTCAATCTTTCCCTTCACATCTC-T
* * * **
18484284 AATGGTATGAGATTCACCGTTGCGATCTCAATCTTTCCCTTCACAT-TCCT
1 -AGGGTATAAGATTC-GCGTTGCGGCCTCAATCTTTCCCTTCACATCT-CT
** * * * *
18484334 AGGGTACGAGATTCATCGTTGTGGCCTCAATCTTTCCCTTCACGTCTTT
1 AGGGTATAAGATTC-GCGTTGCGGCCTCAATCTTTCCCTTCACATCTCT
* *
18484383 AGAGTATATGATT
1 AGGGTATAAGATT
18484396 TGACATTTCC
Statistics
Matches: 228, Mismatches: 69, Indels: 20
0.72 0.22 0.06
Matches are distributed among these distances:
47 1 0.00
48 34 0.15
49 152 0.67
50 39 0.17
51 2 0.01
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.37
Consensus pattern (48 bp):
AGGGTATAAGATTCGCGTTGCGGCCTCAATCTTTCCCTTCACATCTCT
Found at i:18484261 original size:97 final size:98
Alignment explanation
Indices: 18484107--18484366 Score: 256
Period size: 99 Copynumber: 2.7 Consensus size: 98
18484097 AGGTCTACCA
* ** * ** ** * *
18484107 TTGCGGCCTCAACCTTTTTCTTCACATCTTTAGGGTTTAAGATTCGCCATTGCGGCTTCAATCTG
1 TTGCGGTCTCAACCTTTCCCTTCACATCTCTAGGGTACAAGATTCATCGTTGTGGCTTCAATCTG
* * * * ***
18484172 GCTTTCTTATT-TCTAA-GGTATAAGGTTTGTCG
66 CCCTTCGTATTCT-TAATGGTATAAGATTCACCG
*
18484204 TTGCGGTCTCAACCTTTCCCTTCACATCTCTAGGGTACAAGATTCATCGTAGTGGCTTCAATCTT
1 TTGCGGTCTCAACCTTTCCCTTCACATCTCTAGGGTACAAGATTCATCGTTGTGGCTTCAATC-T
* *
18484269 TCCCTTCGTATTCTTAATGGTATGAGATTCACCG
65 GCCCTTCGTATTCTTAATGGTATAAGATTCACCG
* * * *
18484303 TTGCGATCTCAATCTTTCCCTTCACAT-TCCTAGGGTACGAGATTCATCGTTGTGGCCTCAATCT
1 TTGCGGTCTCAACCTTTCCCTTCACATCT-CTAGGGTACAAGATTCATCGTTGTGGCTTCAATCT
18484367 TTCCCTTCAC
Statistics
Matches: 134, Mismatches: 25, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
97 52 0.39
98 14 0.10
99 68 0.51
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (98 bp):
TTGCGGTCTCAACCTTTCCCTTCACATCTCTAGGGTACAAGATTCATCGTTGTGGCTTCAATCTG
CCCTTCGTATTCTTAATGGTATAAGATTCACCG
Found at i:18486177 original size:82 final size:84
Alignment explanation
Indices: 18486063--18486225 Score: 276
Period size: 82 Copynumber: 2.0 Consensus size: 84
18486053 TCATCTTGAC
**
18486063 TTTTCCTTCTTTTCTTTGCTTTTCTTTCTCTTTTCCTTTTCTTGGGTTTTAAGATGTCCCTTGTG
1 TTTTCCTTCTTTTCTTTGCTTTTCTTTCTCTTTTCCTTTTCTTGGGTTTTAAGATGTCCCTTACG
*
18486128 GTTTTTTTATCATCTCAAA
66 ATTTTTTTATCATCTCAAA
*
18486147 TTTT-CTTTTTTTCTTTGC-TTTCTTTCTCTTTTCCTTTTCTTGGGTTTTAAGATGTCCCTTACG
1 TTTTCCTTCTTTTCTTTGCTTTTCTTTCTCTTTTCCTTTTCTTGGGTTTTAAGATGTCCCTTACG
18486210 ATTTTTTTATCATCTC
66 ATTTTTTTATCATCTC
18486226 GACCCCTTTT
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
82 58 0.77
83 13 0.17
84 4 0.05
ACGTcount: A:0.09, C:0.20, G:0.10, T:0.61
Consensus pattern (84 bp):
TTTTCCTTCTTTTCTTTGCTTTTCTTTCTCTTTTCCTTTTCTTGGGTTTTAAGATGTCCCTTACG
ATTTTTTTATCATCTCAAA
Found at i:18486253 original size:18 final size:18
Alignment explanation
Indices: 18486232--18486269 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
18486222 TCTCGACCCC
18486232 TTTTCTT-TTTCTTTCTTT
1 TTTTCTTCTTTCTTT-TTT
18486250 TTTTCTTCTTTCTTTTTT
1 TTTTCTTCTTTCTTTTTT
18486268 TT
1 TT
18486270 CCTCTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTCTTCTTTCTTTTTT
Found at i:18486255 original size:82 final size:81
Alignment explanation
Indices: 18486063--18486260 Score: 256
Period size: 82 Copynumber: 2.4 Consensus size: 81
18486053 TCATCTTGAC
**
18486063 TTTTCCTTCTTTTCTTTGCTTTTCTTTCTCTTTTCCTTTTCTTGGGTTTTAAGATGTCCCTTGTG
1 TTTT-CTT-TTTTCTTTGCTTTT-TTTCTCTTTTCCTTTTCTTGGGTTTTAAGATGTCCCTTACG
*
18486128 GTTTTTTTATCATCTCAAA
63 ATTTTTTTATCATCTCAAA
*
18486147 TTTTCTTTTTTTCTTTGCTTTCTTTCTCTTTTCCTTTTCTTGGGTTTTAAGATGTCCCTTACGAT
1 TTTTC-TTTTTTCTTTGCTTTTTTTCTCTTTTCCTTTTCTTGGGTTTTAAGATGTCCCTTACGAT
**
18486212 TTTTTTATCATCTCGACCCC
65 TTTTTTATCATCTC-A--AA
18486232 TTTTC-TTTTTCTTT-CTTTTTTTCTTCTTT
1 TTTTCTTTTTTCTTTGCTTTTTTTC-TCTTT
18486261 CTTTTTTTTC
Statistics
Matches: 102, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
82 62 0.61
83 29 0.28
84 6 0.06
85 5 0.05
ACGTcount: A:0.08, C:0.21, G:0.09, T:0.62
Consensus pattern (81 bp):
TTTTCTTTTTTCTTTGCTTTTTTTCTCTTTTCCTTTTCTTGGGTTTTAAGATGTCCCTTACGATT
TTTTTATCATCTCAAA
Found at i:18486258 original size:15 final size:14
Alignment explanation
Indices: 18486231--18486269 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 14
18486221 ATCTCGACCC
18486231 CTTTTCTTTTTCTTT
1 CTTTT-TTTTTCTTT
18486246 CTTTTTTTCTTCTTT
1 CTTTTTTT-TTCTTT
18486261 CTTTTTTTT
1 CTTTTTTTT
18486270 CCTCTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
CTTTTTTTTTCTTT
Found at i:18486266 original size:16 final size:16
Alignment explanation
Indices: 18486231--18486276 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
18486221 ATCTCGACCC
*
18486231 CTTTTCTTT-TTCTTT
1 CTTTTTTTTCTTCTTT
18486246 C-TTTTTTTCTTCTTT
1 CTTTTTTTTCTTCTTT
*
18486261 CTTTTTTTTCCTCTTT
1 CTTTTTTTTCTTCTTT
18486277 TTTGACCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 6 0.22
15 8 0.30
16 13 0.48
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
CTTTTTTTTCTTCTTT
Found at i:18486275 original size:19 final size:18
Alignment explanation
Indices: 18486235--18486278 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
18486225 CGACCCCTTT
*
18486235 TCTTTTTCTTTCTTTTTT
1 TCTTTTTCTTTCTTTTTC
18486253 TCTTCTTTCTTT-TTTTTCC
1 TCTT-TTTCTTTCTTTTT-C
18486272 TCTTTTT
1 TCTTTTT
18486279 TGACCTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TCTTTTTCTTTCTTTTTC
Found at i:18491030 original size:30 final size:30
Alignment explanation
Indices: 18490975--18491113 Score: 172
Period size: 30 Copynumber: 4.6 Consensus size: 30
18490965 GGAGAATTTT
* *
18490975 GGGGTTAAAATGTAATTTTGGAAAAGTTTA
1 GGGGTCAAAATGTAATTTTGAAAAAGTTTA
* * *
18491005 GGGGTTAAAATATAATTTTCAAAAAGTTTA
1 GGGGTCAAAATGTAATTTTGAAAAAGTTTA
* *
18491035 GGGGTCAAATTGTAATTTTGAGAAAGTTTA
1 GGGGTCAAAATGTAATTTTGAAAAAGTTTA
*
18491065 TGGGTCAAAATGTAATTTTAGAAAAA-TTTA
1 GGGGTCAAAATGTAATTTT-GAAAAAGTTTA
* *
18491095 AGGGTCAAAATATAATTTT
1 GGGGTCAAAATGTAATTTT
18491114 TAAATAAAAC
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
30 90 0.95
31 5 0.05
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.37
Consensus pattern (30 bp):
GGGGTCAAAATGTAATTTTGAAAAAGTTTA
Found at i:18494031 original size:15 final size:17
Alignment explanation
Indices: 18494001--18494032 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
18493991 TAGTAAAAAT
18494001 ATAATTTTATTATTTTA
1 ATAATTTTATTATTTTA
18494018 ATAA-TTTA-TATTTTA
1 ATAATTTTATTATTTTA
18494033 TCATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATAATTTTATTATTTTA
Found at i:18501414 original size:17 final size:18
Alignment explanation
Indices: 18501384--18501421 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
18501374 CAGTATATAA
18501384 AAATATTAATAT-AATTT
1 AAATATTAATATAAATTT
18501401 AAAT-TTAATAATAAATTT
1 AAATATTAAT-ATAAATTT
18501419 AAA
1 AAA
18501422 AACAAATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.26
17 6 0.32
18 8 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATTAATATAAATTT
Found at i:18501802 original size:21 final size:21
Alignment explanation
Indices: 18501778--18501832 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
18501768 GAAATTTAAA
*
18501778 ACAAACATAATGAGGACATTT
1 ACAAACATAATGAGGACAGTT
* * *
18501799 ACAAAACATTATGATGAGAGTT
1 AC-AAACATAATGAGGACAGTT
18501821 ACAAACATAATG
1 ACAAACATAATG
18501833 TTTTTTAGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.24
Consensus pattern (21 bp):
ACAAACATAATGAGGACAGTT
Found at i:18513535 original size:2 final size:2
Alignment explanation
Indices: 18513528--18513618 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
18513518 GGTACCTCCA
18513528 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
18513570 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
18513612 CT CT CT C
1 CT CT CT C
18513619 CATCTTTAAA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:18521057 original size:43 final size:43
Alignment explanation
Indices: 18520980--18521270 Score: 342
Period size: 43 Copynumber: 6.8 Consensus size: 43
18520970 TGAATTAACC
** *
18520980 TATGCTCCCACCGAGTCATAAGTTCTTCCATTTACAATAATCT
1 TATGCTCTTACCGAGACATAAGTTCTTCCATTTACAATAATCT
* * *
18521023 TATACTCTTACTGAGACATAAGTTCTCCCATTTACAATAATCT
1 TATGCTCTTACCGAGACATAAGTTCTTCCATTTACAATAATCT
*
18521066 TATGCTTTTACCGAGACATAAGTTCTTCCATTTACAATAATCT
1 TATGCTCTTACCGAGACATAAGTTCTTCCATTTACAATAATCT
* *
18521109 TATGCTCTTACAGAGACATAATTTCTTCCATTTACAATAATCT
1 TATGCTCTTACCGAGACATAAGTTCTTCCATTTACAATAATCT
*
18521152 TATGCTCTTACCGAGACATAAG-TCTTCCATTTATACATAAT-T
1 TATGCTCTTACCGAGACATAAGTTCTTCCATTTACA-ATAATCT
* * *
18521194 TCATGCTCAT-CTCGAGACATGAG-TCTTCCATTTATATATAATCT
1 T-ATGCTCTTAC-CGAGACATAAGTTCTTCCATTTACA-ATAATCT
* * * *
18521238 CATGCTCAT-CCTGAGACTTGAG-TCTTCCATTTA
1 TATGCTCTTACC-GAGACATAAGTTCTTCCATTTA
18521271 TATATTAAGT
Statistics
Matches: 222, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
42 16 0.07
43 205 0.92
44 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (43 bp):
TATGCTCTTACCGAGACATAAGTTCTTCCATTTACAATAATCT
Found at i:18521791 original size:19 final size:19
Alignment explanation
Indices: 18521767--18521805 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
18521757 AACCCAAAAG
18521767 TTAGTGGATGATAATCATA
1 TTAGTGGATGATAATCATA
18521786 TTAGTGGATGATAATCATA
1 TTAGTGGATGATAATCATA
18521805 T
1 T
18521806 CCACCACCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (19 bp):
TTAGTGGATGATAATCATA
Found at i:18522589 original size:35 final size:35
Alignment explanation
Indices: 18522496--18522598 Score: 107
Period size: 40 Copynumber: 2.8 Consensus size: 35
18522486 CCGTGAAAGA
*
18522496 ATTTGCGCCCAACGCTAGTCGGATAAACCAATAAT
1 ATTTGCGCCCAACGCTAGTCGGATAAACCAACAAT
* * * * *
18522531 ATTAAATGTGAGCCCAACTCTAGTTGGATAAACCGACGAT
1 A-T---T-TGCGCCCAACGCTAGTCGGATAAACCAACAAT
18522571 ATTTGCGCCCAACGCTAGTCGGATAAAC
1 ATTTGCGCCCAACGCTAGTCGGATAAAC
18522599 TGAAAAATGT
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
35 23 0.43
36 2 0.04
39 2 0.04
40 27 0.50
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.23
Consensus pattern (35 bp):
ATTTGCGCCCAACGCTAGTCGGATAAACCAACAAT
Found at i:18523589 original size:7 final size:7
Alignment explanation
Indices: 18523577--18523611 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
18523567 CATTCATTTG
18523577 ATTCATC
1 ATTCATC
18523584 ATTCATC
1 ATTCATC
18523591 ATTCATC
1 ATTCATC
*
18523598 ATTTATC
1 ATTCATC
18523605 A-TCATC
1 ATTCATC
18523611 A
1 A
18523612 CATGCAAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.43
Consensus pattern (7 bp):
ATTCATC
Found at i:18530911 original size:57 final size:57
Alignment explanation
Indices: 18530823--18530947 Score: 232
Period size: 57 Copynumber: 2.2 Consensus size: 57
18530813 CAAAACAAAT
*
18530823 CAATTAATTAAAGGACCAAAAAATAAAATTAACCCAATTTAAATAATTAATTAAACC
1 CAATTAATTAAAAGACCAAAAAATAAAATTAACCCAATTTAAATAATTAATTAAACC
18530880 CAATTAATTAAAAGACCAAAAAATAAAATTAACCCAATTTAAATAATTAATTAAACC
1 CAATTAATTAAAAGACCAAAAAATAAAATTAACCCAATTTAAATAATTAATTAAACC
*
18530937 CAATTTATTAA
1 CAATTAATTAA
18530948 TGAAATATTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 66 1.00
ACGTcount: A:0.56, C:0.14, G:0.02, T:0.28
Consensus pattern (57 bp):
CAATTAATTAAAAGACCAAAAAATAAAATTAACCCAATTTAAATAATTAATTAAACC
Found at i:18532893 original size:16 final size:17
Alignment explanation
Indices: 18532862--18532894 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
18532852 AATTTTTATT
*
18532862 ACTTGCACATAAATAAA
1 ACTTGCACAAAAATAAA
18532879 ACTTG-ACAAAAATAAA
1 ACTTGCACAAAAATAAA
18532895 CTGATTAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.58, C:0.15, G:0.06, T:0.21
Consensus pattern (17 bp):
ACTTGCACAAAAATAAA
Found at i:18545251 original size:15 final size:15
Alignment explanation
Indices: 18545230--18545259 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
18545220 AATCACATAT
18545230 AAAAAAAGAGAAAAAG
1 AAAAAAA-AGAAAAAG
18545246 AAAAAAAAGAAAAA
1 AAAAAAAAGAAAAA
18545260 AAATTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:18545253 original size:10 final size:9
Alignment explanation
Indices: 18545230--18545262 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
18545220 AATCACATAT
18545230 AAAAAAAG-
1 AAAAAAAGA
*
18545238 AGAAAAAGA
1 AAAAAAAGA
18545247 AAAAAAAGA
1 AAAAAAAGA
18545256 AAAAAAA
1 AAAAAAA
18545263 TTATATTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:18549857 original size:20 final size:22
Alignment explanation
Indices: 18549834--18549873 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
18549824 TTCTAATTAA
*
18549834 TATTTTAAAC-TT-CTCTAAAT
1 TATTGTAAACATTGCTCTAAAT
18549854 TATTGTAAACATTGCTCTAA
1 TATTGTAAACATTGCTCTAA
18549874 TAAATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (22 bp):
TATTGTAAACATTGCTCTAAAT
Found at i:18550946 original size:31 final size:29
Alignment explanation
Indices: 18550908--18550975 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 29
18550898 TAAATGTGAC
* *
18550908 AAAGTAAAGTGCAAGAAAATAAATTGCAAG
1 AAAGTAAAGTACAAGAAAAT-AACTGCAAG
* *
18550938 AAAAGTAAATTACAAGAAAGTAACTGCAAG
1 -AAAGTAAAGTACAAGAAAATAACTGCAAG
18550968 AAAGTAAA
1 AAAGTAAA
18550976 TTGGTAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 8 0.24
30 8 0.24
31 17 0.52
ACGTcount: A:0.59, C:0.07, G:0.18, T:0.16
Consensus pattern (29 bp):
AAAGTAAAGTACAAGAAAATAACTGCAAG
Found at i:18550969 original size:14 final size:15
Alignment explanation
Indices: 18550908--18550978 Score: 90
Period size: 15 Copynumber: 4.7 Consensus size: 15
18550898 TAAATGTGAC
*
18550908 AAAGTAAAGTGCAAG
1 AAAGTAAATTGCAAG
*
18550923 AAAATAAATTGCAAG
1 AAAGTAAATTGCAAG
*
18550938 AAAAGTAAATTACAAG
1 -AAAGTAAATTGCAAG
*
18550954 AAAGT-AACTGCAAG
1 AAAGTAAATTGCAAG
18550968 AAAGTAAATTG
1 AAAGTAAATTG
18550979 GTAAATAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
14 12 0.26
15 22 0.47
16 13 0.28
ACGTcount: A:0.56, C:0.07, G:0.18, T:0.18
Consensus pattern (15 bp):
AAAGTAAATTGCAAG
Found at i:18552789 original size:14 final size:14
Alignment explanation
Indices: 18552750--18552795 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
18552740 AAAAATTTTC
18552750 TAAATCT-TTTAAA
1 TAAATCTCTTTAAA
*
18552763 AAGAATCTACTTTAAA
1 TA-AATCT-CTTTAAA
18552779 TAAATCTCTTT-AA
1 TAAATCTCTTTAAA
18552792 TAAA
1 TAAA
18552796 CAAAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 7 0.25
14 9 0.32
15 5 0.18
16 7 0.25
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (14 bp):
TAAATCTCTTTAAA
Found at i:18554352 original size:20 final size:21
Alignment explanation
Indices: 18554314--18554352 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18554304 GCCAAGCTTC
*
18554314 ACTAAGTTAGAAAATACAATA
1 ACTAAGTTAGAAAAGACAATA
18554335 ACTAAGTTA-AAAAGACAA
1 ACTAAGTTAGAAAAGACAA
18554353 AAAATGCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.21
Consensus pattern (21 bp):
ACTAAGTTAGAAAAGACAATA
Found at i:18557484 original size:20 final size:20
Alignment explanation
Indices: 18557459--18557498 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
18557449 AAGACTAAGA
*
18557459 AAAAT-AACTGAAATATAAAT
1 AAAATAAACT-AAAAATAAAT
18557479 AAAATAAACTAAAAATAAAT
1 AAAATAAACTAAAAATAAAT
18557499 GATAAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.23
Consensus pattern (20 bp):
AAAATAAACTAAAAATAAAT
Found at i:18575149 original size:106 final size:106
Alignment explanation
Indices: 18575013--18575232 Score: 341
Period size: 106 Copynumber: 2.1 Consensus size: 106
18575003 TTTACTGAAT
* * *
18575013 ATAATTTAACGCAATTACAATTATTAATTATAATGATTTCATTAAATATTAAAACATGGAAGTTA
1 ATAATTTAACGCAATTACAATTATTAATTATAATAATTTCATTAAATATTAAAACATGAAAGATA
*
18575078 ATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCC
66 ATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCC
** * * *
18575119 ATAATTTAACGTGATTATAATTATTAATTATAATAATTTCGTTAAATATTAAAATATGAAAGATA
1 ATAATTTAACGCAATTACAATTATTAATTATAATAATTTCATTAAATATTAAAACATGAAAGATA
*
18575184 ATATCCTTTTGGAAATGATATAATATTTTAATAAACCTTCC
66 ATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCC
18575225 ATATATTT
1 ATA-ATTT
18575233 CTTTAAAGGA
Statistics
Matches: 103, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
106 99 0.96
107 4 0.04
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (106 bp):
ATAATTTAACGCAATTACAATTATTAATTATAATAATTTCATTAAATATTAAAACATGAAAGATA
ATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCC
Found at i:18575306 original size:123 final size:126
Alignment explanation
Indices: 18575163--18575405 Score: 359
Period size: 123 Copynumber: 1.9 Consensus size: 126
18575153 AATTTCGTTA
* *
18575163 AATATTAAAATATGAAAGATAATATCCTTTTGGAAATGATATAATATTTTAATAAACCTTCCATA
1 AATATTAAAACATGAAAGATAATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCCATA
* *
18575228 TATTTCTTTAAAG-G-A-ATATTTCCATTTTAATATAAGATATT-ATATAAAAGAAAATTG
66 TATTTCTCTAAAGAGAATATATTTCCATTTTAATATAAGATATTAAAATAAAAGAAAATTG
* *
18575285 AATATTAAAAACATGAAAGATAATATCCTTTTGGAGAGGATATAATGTTTTAATAAACCTTCCAT
1 AATATT-AAAACATGAAAGATAATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCCAT
** *
18575350 ATATTTCTCTAAAGAGATATATATTTTTATTTTAATATGAGATATTAAAATAAAAG
65 ATATTTCTCTAAAGAGA-ATATATTTCCATTTTAATATAAGATATTAAAATAAAAG
18575406 GAAAGATAGC
Statistics
Matches: 106, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
122 6 0.06
123 67 0.63
124 1 0.01
126 1 0.01
127 23 0.22
128 8 0.08
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.39
Consensus pattern (126 bp):
AATATTAAAACATGAAAGATAATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCCATA
TATTTCTCTAAAGAGAATATATTTCCATTTTAATATAAGATATTAAAATAAAAGAAAATTG
Found at i:18579558 original size:21 final size:21
Alignment explanation
Indices: 18579532--18579607 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
18579522 CATCATAATT
*
18579532 AGATGCATCCACAGCAAAGTC
1 AGATGCATCCACAACAAAGTC
*
18579553 AGATGCATCCACAACAAAGCC
1 AGATGCATCCACAACAAAGTC
* * *
18579574 AGATGTAGCCACATCAGAA-TC
1 AGATGCATCCACAACA-AAGTC
*
18579595 AGATGCAACCACA
1 AGATGCATCCACA
18579608 CCAGAATCGG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 44 0.96
22 2 0.04
ACGTcount: A:0.41, C:0.29, G:0.17, T:0.13
Consensus pattern (21 bp):
AGATGCATCCACAACAAAGTC
Found at i:18579612 original size:21 final size:21
Alignment explanation
Indices: 18579532--18579632 Score: 80
Period size: 21 Copynumber: 4.8 Consensus size: 21
18579522 CATCATAATT
* *
18579532 AGATGCATCCACAGCAAAGTC
1 AGATGCAGCCACAACAAAGTC
* *
18579553 AGATGCATCCACAACAAAGCC
1 AGATGCAGCCACAACAAAGTC
* *
18579574 AGATGTAGCCACATCAGAA-TC
1 AGATGCAGCCACAACA-AAGTC
* *
18579595 AGATGCAACCACACCAGAA-TC
1 AGATGCAGCCACAACA-AAGTC
* *
18579616 GGATGCAGCCACTACAA
1 AGATGCAGCCACAACAA
18579633 TATGCAATGT
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 1 0.02
21 63 0.95
22 2 0.03
ACGTcount: A:0.40, C:0.30, G:0.18, T:0.13
Consensus pattern (21 bp):
AGATGCAGCCACAACAAAGTC
Found at i:18601026 original size:27 final size:27
Alignment explanation
Indices: 18600988--18601045 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
18600978 TATGAGATGT
18600988 AAGAAGCATCCTAGTATGAAATTTATG
1 AAGAAGCATCCTAGTATGAAATTTATG
* *
18601015 AAGAAGCGTCCTAGTATGAATTTTATG
1 AAGAAGCATCCTAGTATGAAATTTATG
18601042 AAGA
1 AAGA
18601046 TTTGGGGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (27 bp):
AAGAAGCATCCTAGTATGAAATTTATG
Found at i:18603888 original size:30 final size:30
Alignment explanation
Indices: 18603854--18603912 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
18603844 AACGAAAAAC
18603854 AAAATAAAACAGTAAATTTTAAAAAGGATA
1 AAAATAAAACAGTAAATTTTAAAAAGGATA
* * *
18603884 AAAATGAAAGAGTTAATTTTAAAAAGGAT
1 AAAATAAAACAGTAAATTTTAAAAAGGAT
18603913 TTGCTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.59, C:0.02, G:0.14, T:0.25
Consensus pattern (30 bp):
AAAATAAAACAGTAAATTTTAAAAAGGATA
Found at i:18605858 original size:50 final size:50
Alignment explanation
Indices: 18605754--18605878 Score: 128
Period size: 50 Copynumber: 2.5 Consensus size: 50
18605744 TACAACTTTG
* * * * *
18605754 AGATTCACCTTTACGGCTTCAATCTGCTTCTTCATAGCTTTAGGGGTGTG
1 AGATTCACCTTTGCGGCTTCAATCTGCCTCTACATAGCTTTAGGGGTATA
** *
18605804 AGATTTGCCTTTGCGGCTTCAATCTAGCCCTCTACA-ATCTTTA-GGGTATA
1 AGATTCACCTTTGCGGCTTCAATCT-G-CCTCTACATAGCTTTAGGGGTATA
* *
18605854 AGATTCACCGTTGCGACTTCAATCT
1 AGATTCACCTTTGCGGCTTCAATCT
18605879 TTACCTCCAC
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
50 48 0.79
51 7 0.11
52 6 0.10
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (50 bp):
AGATTCACCTTTGCGGCTTCAATCTGCCTCTACATAGCTTTAGGGGTATA
Found at i:18605917 original size:49 final size:49
Alignment explanation
Indices: 18605804--18606370 Score: 530
Period size: 49 Copynumber: 11.6 Consensus size: 49
18605794 TAGGGGTGTG
* * ** * *
18605804 AGATTTGCCTTTGCGGCTTCAATCTAGCCC-TCTACAATCTTTAGGGTATA
1 AGATTCGCCATTGCGGCTTCAATCTTTCCCTTC-AC-ATCTCTAGGGTACA
* * * * * * *
18605854 AGATTCACCGTTGCGACTTCAATCTTTACCTCCACATTTCTAGGGTGCA
1 AGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTACA
* * * * * *
18605903 AGATCCGCCATTGCGGCTTTAATATTTTCCTCCATATCTCTAGGGTACA
1 AGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTACA
** * * * *
18605952 AGATTCTTCATTGTGACTTCAATCTTTCCCTTCACATTTCTAGGGTGCA
1 AGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTACA
* * * * * *
18606001 AGATTTGCCATTACGGCTTCAATCTTTCTCTTCACGTCTCCAAGGTACA
1 AGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTACA
* * * *
18606050 AGATTGGCCATTGTGGCTTCAATC-TTCCCTTCATATCTCTAGGGTGCA
1 AGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTACA
* * *
18606098 AGATTCGTCATTGCGGCTTCGATCTTTCCCTTCACATCTCTAAGGTACA
1 AGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTACA
* * * *
18606147 AGATTTGCCATTGTGGCTTCAATCTTTCCCTTCACATTTCTAGGGTGCA
1 AGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTACA
** ** * * * *
18606196 AGATTTTCCATTGCAACTTCAATCTTTCCCTTTACATCTCCAAGGTATA
1 AGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTACA
* * *
18606245 AGATTCGCCATTACGGCTTCAATC-TTCTCTTCACATCTCTAGGGAACA
1 AGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTACA
** * * *
18606293 AGATTCTTC-TATGCGGCTTCAATCTTTCCCTTCACATTTCTAAGGTGCA
1 AGATTCGCCAT-TGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTACA
* * *
18606342 AGATTTGCCATAGCGACTTCAATCTTTCC
1 AGATTCGCCATTGCGGCTTCAATCTTTCC
18606371 GTCTTTAGGG
Statistics
Matches: 409, Mismatches: 103, Indels: 11
0.78 0.20 0.02
Matches are distributed among these distances:
47 1 0.00
48 75 0.18
49 306 0.75
50 26 0.06
51 1 0.00
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.36
Consensus pattern (49 bp):
AGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTACA
Found at i:18606112 original size:195 final size:195
Alignment explanation
Indices: 18605870--18606370 Score: 655
Period size: 195 Copynumber: 2.6 Consensus size: 195
18605860 ACCGTTGCGA
* * * * * * * * *
18605870 CTTCAATCTTTACCTCCACATTTCTAGGGTGCAAGATCCGCCATTGCGGCTTTAATATTTTCCTC
1 CTTCAATC-TTCCCTTCACATCTCTAGGGTGCAAGATTCGTCATTGCGGCTTCAATCTTTCCCTT
* * *
18605935 CATATCTCTAGGGTACAAGATTCT-TCATTGTGACTTCAATCTTTCCCTTCACATTTCTAGGGTG
65 CACATCTCTAAGGTACAAGATT-TGCCATTGTGACTTCAATCTTTCCCTTCACATTTCTAGGGTG
** * * * **
18605999 CAAGATTTGCCATTACGGCTTCAATCTTTCTCTTCACGTCTCCAAGGTACAAGATTGGCCATTGT
129 CAAGATTTGCCATTACAACTTCAATCTTTCCCTTCACATCTCCAAGGTACAAGATTCGCCATTAC
18606064 GG
194 GG
* *
18606066 CTTCAATCTTCCCTTCATATCTCTAGGGTGCAAGATTCGTCATTGCGGCTTCGATCTTTCCCTTC
1 CTTCAATCTTCCCTTCACATCTCTAGGGTGCAAGATTCGTCATTGCGGCTTCAATCTTTCCCTTC
*
18606131 ACATCTCTAAGGTACAAGATTTGCCATTGTGGCTTCAATCTTTCCCTTCACATTTCTAGGGTGCA
66 ACATCTCTAAGGTACAAGATTTGCCATTGTGACTTCAATCTTTCCCTTCACATTTCTAGGGTGCA
* * * *
18606196 AGATTTTCCATTGCAACTTCAATCTTTCCCTTTACATCTCCAAGGTATAAGATTCGCCATTACGG
131 AGATTTGCCATTACAACTTCAATCTTTCCCTTCACATCTCCAAGGTACAAGATTCGCCATTACGG
* ** *
18606261 CTTCAATCTTCTCTTCACATCTCTAGGGAACAAGATTCTTC-TATGCGGCTTCAATCTTTCCCTT
1 CTTCAATCTTCCCTTCACATCTCTAGGGTGCAAGATTCGTCAT-TGCGGCTTCAATCTTTCCCTT
* * * *
18606325 CACATTTCTAAGGTGCAAGATTTGCCATAGCGACTTCAATCTTTCC
65 CACATCTCTAAGGTACAAGATTTGCCATTGTGACTTCAATCTTTCC
18606371 GTCTTTAGGG
Statistics
Matches: 266, Mismatches: 37, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
194 2 0.01
195 256 0.96
196 8 0.03
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.36
Consensus pattern (195 bp):
CTTCAATCTTCCCTTCACATCTCTAGGGTGCAAGATTCGTCATTGCGGCTTCAATCTTTCCCTTC
ACATCTCTAAGGTACAAGATTTGCCATTGTGACTTCAATCTTTCCCTTCACATTTCTAGGGTGCA
AGATTTGCCATTACAACTTCAATCTTTCCCTTCACATCTCCAAGGTACAAGATTCGCCATTACGG
Found at i:18606368 original size:146 final size:147
Alignment explanation
Indices: 18605814--18606370 Score: 600
Period size: 146 Copynumber: 3.8 Consensus size: 147
18605804 AGATTTGCCT
** * * ** * *
18605814 TTGCGGCTTCAATCTAGCCC-TCTACAATCTTTAGGGTATAAGATTCACCGTTGCGACTTCAATC
1 TTGCGGCTTCAATCTTTCCCTTC-AC-ATCTCTAGGGTACAAGATTTGCCATTGCGGCTTCAATC
* * * ** * * * * *
18605878 TTTACCTCCACATTTCTAGGGTGCAAGATCCGCCATTGCGGCTTTAATATTTTCCTCCATATCTC
64 TTTCCCTTCACATTTCTAAGGTGCAAGATTTGCCATTGCGACTTCAATCTTTCCCTTCATATCTC
*
18605943 TAGGGTACAAGATTCTTCA
129 TAGGGTACAAGATTCGTCA
* * * * *
18605962 TTGTGACTTCAATCTTTCCCTTCACATTTCTAGGGTGCAAGATTTGCCATTACGGCTTCAATCTT
1 TTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTACAAGATTTGCCATTGCGGCTTCAATCTT
* * * * * * * *
18606027 TCTCTTCACGTCTCCAAGGTACAAGATTGGCCATTGTGGCTTCAATC-TTCCCTTCATATCTCTA
66 TCCCTTCACATTTCTAAGGTGCAAGATTTGCCATTGCGACTTCAATCTTTCCCTTCATATCTCTA
*
18606091 GGGTGCAAGATTCGTCA
131 GGGTACAAGATTCGTCA
* * *
18606108 TTGCGGCTTCGATCTTTCCCTTCACATCTCTAAGGTACAAGATTTGCCATTGTGGCTTCAATCTT
1 TTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTACAAGATTTGCCATTGCGGCTTCAATCTT
* * * * * *
18606173 TCCCTTCACATTTCTAGGGTGCAAGATTTTCCATTGCAACTTCAATCTTTCCCTTTACATCTCCA
66 TCCCTTCACATTTCTAAGGTGCAAGATTTGCCATTGCGACTTCAATCTTTCCCTTCATATCTCTA
* * *
18606238 AGGTATAAGATTCGCCA
131 GGGTACAAGATTCGTCA
* * * * *
18606255 TTACGGCTTCAATC-TTCTCTTCACATCTCTAGGGAACAAGATTCTTCTA-TGCGGCTTCAATCT
1 TTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTACAAGATT-TGCCATTGCGGCTTCAATCT
*
18606318 TTCCCTTCACATTTCTAAGGTGCAAGATTTGCCATAGCGACTTCAATCTTTCC
65 TTCCCTTCACATTTCTAAGGTGCAAGATTTGCCATTGCGACTTCAATCTTTCC
18606371 GTCTTTAGGG
Statistics
Matches: 338, Mismatches: 68, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
146 211 0.62
147 107 0.32
148 18 0.05
149 2 0.01
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.36
Consensus pattern (147 bp):
TTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTACAAGATTTGCCATTGCGGCTTCAATCTT
TCCCTTCACATTTCTAAGGTGCAAGATTTGCCATTGCGACTTCAATCTTTCCCTTCATATCTCTA
GGGTACAAGATTCGTCA
Found at i:18619764 original size:33 final size:33
Alignment explanation
Indices: 18619722--18619790 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
18619712 GAGAACAAGT
* *
18619722 AAAAACTCAAGTTTGAGTGTGTGATGGTATTAC
1 AAAAACTCAAGTTTGAGGGTGTGATCGTATTAC
18619755 AAAAACTCAAGTTTGAGGGTGTGATCGTATTAC
1 AAAAACTCAAGTTTGAGGGTGTGATCGTATTAC
18619788 AAA
1 AAA
18619791 TAGCATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.30
Consensus pattern (33 bp):
AAAAACTCAAGTTTGAGGGTGTGATCGTATTAC
Found at i:18626352 original size:30 final size:30
Alignment explanation
Indices: 18626300--18626360 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
18626290 CAGTTTTTAG
* * *
18626300 GAGCTACACGGGCTGGATACATGGCCTTGT
1 GAGCCACACGGGCTGGACACATGGCCATGT
18626330 GAGCCACACGGGCTGCG-CACATGGCCATGT
1 GAGCCACACGGGCTG-GACACATGGCCATGT
18626360 G
1 G
18626361 CCAAATCGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.20, C:0.28, G:0.34, T:0.18
Consensus pattern (30 bp):
GAGCCACACGGGCTGGACACATGGCCATGT
Found at i:18627468 original size:20 final size:20
Alignment explanation
Indices: 18627452--18627493 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
18627442 TTATTTTTGT
*
18627452 TTTAATATTTGTATTTTTAA
1 TTTAATATTTATATTTTTAA
*
18627472 TTTAATTTTTATA-TTTTAA
1 TTTAATATTTATATTTTTAA
18627491 TTT
1 TTT
18627494 TTTTTCTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTAATATTTATATTTTTAA
Found at i:18627807 original size:11 final size:11
Alignment explanation
Indices: 18627793--18627818 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
18627783 TAAAAAAATG
18627793 AAAAAATTCAA
1 AAAAAATTCAA
18627804 AAAAAATTCAA
1 AAAAAATTCAA
18627815 AAAA
1 AAAA
18627819 TTAATACTTT
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:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAATTCAA
Found at i:18627876 original size:7 final size:7
Alignment explanation
Indices: 18627826--18627925 Score: 75
Period size: 7 Copynumber: 14.4 Consensus size: 7
18627816 AAATTAATAC
18627826 TTTTA-T
1 TTTTATT
18627832 TTTTATT
1 TTTTATT
18627839 TTCATTATT
1 TT--TTATT
18627848 ATTTTGA-T
1 -TTTT-ATT
*
18627856 TTTGA-T
1 TTTTATT
*
18627862 TTTGATT
1 TTTTATT
18627869 TTTTATT
1 TTTTATT
18627876 TTTTATT
1 TTTTATT
*
18627883 TTTCATT
1 TTTTATT
*
18627890 TTTCATT
1 TTTTATT
*
18627897 TTTCATT
1 TTTTATT
*
18627904 TTTCA-T
1 TTTTATT
18627910 TTTTA-T
1 TTTTATT
18627916 TTTTATT
1 TTTTATT
18627923 TTT
1 TTT
18627926 ATCATGCACT
Statistics
Matches: 83, Mismatches: 4, Indels: 13
0.83 0.04 0.13
Matches are distributed among these distances:
6 23 0.28
7 49 0.59
8 3 0.04
9 6 0.07
10 2 0.02
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (7 bp):
TTTTATT
Found at i:18627885 original size:21 final size:21
Alignment explanation
Indices: 18627861--18627925 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
18627851 TTGATTTTGA
*
18627861 TTTTGATTTTTTATTTTTTAT
1 TTTTCATTTTTTATTTTTTAT
* *
18627882 TTTTCATTTTTCATTTTTCAT
1 TTTTCATTTTTTATTTTTTAT
18627903 TTTTCA-TTTTTA-TTTTTAT
1 TTTTCATTTTTTATTTTTTAT
18627922 TTTT
1 TTTT
18627926 ATCATGCACT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 24 0.62
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (21 bp):
TTTTCATTTTTTATTTTTTAT
Found at i:18627944 original size:6 final size:6
Alignment explanation
Indices: 18627826--18627927 Score: 105
Period size: 6 Copynumber: 16.0 Consensus size: 6
18627816 AAATTAATAC
* * * * *
18627826 TTTTAT TTTTAT TTTCAT TATTAT TTTGAT TTTGAT TTTGATT TTTTATT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T TTTTA-T
18627876 TTTTAT TTTTCAT TTTTCAT TTTTCAT TTTTCAT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTT-AT TTTT-AT TTTT-AT TTTT-AT TTTTAT TTTTAT TTTTAT
18627928 CATGCACTAT
Statistics
Matches: 88, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
6 49 0.56
7 39 0.44
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (6 bp):
TTTTAT
Found at i:18635345 original size:40 final size:40
Alignment explanation
Indices: 18635285--18635523 Score: 248
Period size: 40 Copynumber: 6.0 Consensus size: 40
18635275 TACGTTGAAA
* ** * *
18635285 AGAAGTCAAGCTTCGGCTTAGTGGGCTACAAGCCAGTGAT
1 AGAATTCAAGCTTCGGCTTAGCAGGCTACGAGCCGGTGAT
*
18635325 AGAATTCAAGCTTCGACTTAGCAGGCTACGAGCCGGTGAT
1 AGAATTCAAGCTTCGGCTTAGCAGGCTACGAGCCGGTGAT
* *
18635365 AAAATTCAAGCTTCGGCTTAGCAGGCTACGAGTCGGTGAT
1 AGAATTCAAGCTTCGGCTTAGCAGGCTACGAGCCGGTGAT
* * * * *
18635405 AGAATTCAAGCTTTGGCTTAGCACGTTATGAGCCAGTGAAT
1 AGAATTCAAGCTTCGGCTTAGCAGGCTACGAGCCGGTG-AT
* * *** *
18635446 A-AATTCAAGCTACGGCTTAGCAGGCTACAAATTGGTGTT
1 AGAATTCAAGCTTCGGCTTAGCAGGCTACGAGCCGGTGAT
* * *
18635485 AAAATTCAAGCTAT-GGCTTAGTAGGCTATGAGCCGGTGA
1 AGAATTCAAGCT-TCGGCTTAGCAGGCTACGAGCCGGTGA
18635524 ATTGATTAGA
Statistics
Matches: 161, Mismatches: 35, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
39 2 0.01
40 156 0.97
41 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (40 bp):
AGAATTCAAGCTTCGGCTTAGCAGGCTACGAGCCGGTGAT
Found at i:18635425 original size:80 final size:80
Alignment explanation
Indices: 18635290--18635525 Score: 294
Period size: 80 Copynumber: 3.0 Consensus size: 80
18635280 TGAAAAGAAG
** * * * * *
18635290 TCAAGCTTCGGCTTAGTGGGCTACAAGCCAGTGATAGAATTCAAGCTTCGACTTAGCAGGCTACG
1 TCAAGCTTCGGCTTAGCAGGCTACAAGTCGGTGATAGAATTCAAGCTTTGGCTTAGCAGGCTATG
18635355 AGCCGGTG-ATAAAAT
66 AGCCGGTGAAT-AAAT
* * *
18635370 TCAAGCTTCGGCTTAGCAGGCTACGAGTCGGTGATAGAATTCAAGCTTTGGCTTAGCACGTTATG
1 TCAAGCTTCGGCTTAGCAGGCTACAAGTCGGTGATAGAATTCAAGCTTTGGCTTAGCAGGCTATG
*
18635435 AGCCAGTGAATAAAT
66 AGCCGGTGAATAAAT
* * * * * * *
18635450 TCAAGCTACGGCTTAGCAGGCTACAAATTGGTGTTAAAATTCAAGCTATGGCTTAGTAGGCTATG
1 TCAAGCTTCGGCTTAGCAGGCTACAAGTCGGTGATAGAATTCAAGCTTTGGCTTAGCAGGCTATG
18635515 AGCCGGTGAAT
66 AGCCGGTGAAT
18635526 TGATTAGAAA
Statistics
Matches: 133, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
80 131 0.98
81 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (80 bp):
TCAAGCTTCGGCTTAGCAGGCTACAAGTCGGTGATAGAATTCAAGCTTTGGCTTAGCAGGCTATG
AGCCGGTGAATAAAT
Found at i:18638083 original size:44 final size:43
Alignment explanation
Indices: 18637971--18638083 Score: 199
Period size: 43 Copynumber: 2.6 Consensus size: 43
18637961 TGGAACACCA
*
18637971 TTTCCTATTATTGAAAGTATGTGATTGATTGAGAGTAACATTG
1 TTTCCTATTATTGAAAGTATGTGATTGATTGAGAGGAACATTG
18638014 TTTCCTATTATTGAAAGTATGTGATTGATTGAGAGGAACATTG
1 TTTCCTATTATTGAAAGTATGTGATTGATTGAGAGGAACATTG
*
18638057 TTTCCCTATTATTGAAAGTATATGATT
1 TTT-CCTATTATTGAAAGTATGTGATT
18638084 TATTATGAGC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
43 45 0.67
44 22 0.33
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.42
Consensus pattern (43 bp):
TTTCCTATTATTGAAAGTATGTGATTGATTGAGAGGAACATTG
Found at i:18658746 original size:18 final size:18
Alignment explanation
Indices: 18658696--18658751 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 18
18658686 TCGTTTTAAT
18658696 TTATTTTTA-AGT-TTATA
1 TTATTTTTATA-TATTATA
*
18658713 ATA-TTTTATATA--ATA
1 TTATTTTTATATATTATA
18658728 TTATTTTTATATATTATA
1 TTATTTTTATATATTATA
*
18658746 TAATTT
1 TTATTT
18658752 AGAATATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
15 5 0.16
16 15 0.48
17 3 0.10
18 8 0.26
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TTATTTTTATATATTATA
Found at i:18658784 original size:24 final size:25
Alignment explanation
Indices: 18658757--18658813 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
18658747 AATTTAGAAT
18658757 ATATTAAAAAATT-TTTT-ATAGTAA
1 ATATTAAAAAATTATTTTAAT-GTAA
* *
18658781 ATA-TATAATATTATTTTAATGTAA
1 ATATTAAAAAATTATTTTAATGTAA
18658805 ATATTAAAA
1 ATATTAAAA
18658814 TAATGTTAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
23 7 0.26
24 14 0.52
25 6 0.22
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
ATATTAAAAAATTATTTTAATGTAA
Found at i:18662555 original size:21 final size:21
Alignment explanation
Indices: 18662522--18662575 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
18662512 GGTAAAAAAA
** *
18662522 GTCAACGGCCAACGATCAATG
1 GTCAACGATCAACGATCAACG
* * *
18662543 GTCATCGATCAACGGTTAACG
1 GTCAACGATCAACGATCAACG
18662564 GTCAACGATCAA
1 GTCAACGATCAA
18662576 TAGGTCGAGT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (21 bp):
GTCAACGATCAACGATCAACG
Found at i:18666066 original size:18 final size:16
Alignment explanation
Indices: 18666034--18666077 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
18666024 ATGGGTTGAG
18666034 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
18666050 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
18666064 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
18666078 ACCCTAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:18666149 original size:26 final size:27
Alignment explanation
Indices: 18666113--18666163 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
18666103 ATTCATCTCC
18666113 TCTCTT-TTTTTTTAATTTTCTTTTCG
1 TCTCTTCTTTTTTTAATTTTCTTTTCG
*
18666139 TCTCTTCTTTTTTTAGTTTTCTTTT
1 TCTCTTCTTTTTTTAATTTTCTTTT
18666164 TCTTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.06, C:0.16, G:0.04, T:0.75
Consensus pattern (27 bp):
TCTCTTCTTTTTTTAATTTTCTTTTCG
Found at i:18667590 original size:29 final size:29
Alignment explanation
Indices: 18667528--18667592 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
18667518 AAAGAGAATT
* *
18667528 AACACACAACAAAGTGTAGCACAGATAGA
1 AACACACAACAAAGTGTAGCACAAACAGA
*
18667557 AACACATAACAATA-TGTAGCACAAACAGA
1 AACACACAACAA-AGTGTAGCACAAACAGA
*
18667586 GACACAC
1 AACACAC
18667593 CTCAAGCGGC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.52, C:0.23, G:0.14, T:0.11
Consensus pattern (29 bp):
AACACACAACAAAGTGTAGCACAAACAGA
Found at i:18669669 original size:79 final size:78
Alignment explanation
Indices: 18669538--18669757 Score: 368
Period size: 79 Copynumber: 2.8 Consensus size: 78
18669528 CTGACGATTA
* * *
18669538 TGGCACCCAGTGCCTAGCCGATAAACCGCAAATGTGAGCCTAGCTTTAGTTGGATTAACCAACAA
1 TGGCACCCAGTGCCTAGCGGATAAACCGCAATTGTGAGCC-AGCTCTAGTTGGATTAACCAACAA
18669603 TATCAGTCAAATCC
65 TATCAGTCAAATCC
18669617 TGGCACCCAGTGCCTAGCGGATAAACCGCAATTGTGAGTCCAGCTCTAGTTGGATTAACCAACAA
1 TGGCACCCAGTGCCTAGCGGATAAACCGCAATTGTGAG-CCAGCTCTAGTTGGATTAACCAACAA
*
18669682 TATCCGTCAAATCC
65 TATCAGTCAAATCC
*
18669696 TGGCACCCAGTGCCTAGCGGATAAACCGCAATTGTGAGCCCAACTCTAGTTGGATTAACCAA
1 TGGCACCCAGTGCCTAGCGGATAAACCGCAATTGTGAG-CCAGCTCTAGTTGGATTAACCAA
18669758 TAATGCCAAT
Statistics
Matches: 134, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
79 132 0.99
80 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.22
Consensus pattern (78 bp):
TGGCACCCAGTGCCTAGCGGATAAACCGCAATTGTGAGCCAGCTCTAGTTGGATTAACCAACAAT
ATCAGTCAAATCC
Found at i:18674487 original size:138 final size:138
Alignment explanation
Indices: 18674236--18674932 Score: 1130
Period size: 138 Copynumber: 5.1 Consensus size: 138
18674226 GAGAACATAG
* ** *
18674236 ATATAATTAATATATGAAATTGATTCATACAAAATATTAATAATATATATTTTACCAAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* * *
18674301 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTTTTT
66 AATATAAACAGTTATATTAATTAATTTCGGTAAAAATATAAAAGACATGGAAATTAATATTCTTT
18674366 TGGAAAGA
131 TGGAAAGA
* *
18674374 ATATAATTAATATATAAATTTGATTCATACAAAATAGTAATTGTATATATTTTACCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
** * *
18674439 AATATAAGTAGTTATATTAATTAATTTCGGTTAAAATATAAAAAACATGGAAATTAATATTCTTT
66 AATATAAACAGTTATATTAATTAATTTCGGTAAAAATATAAAAGACATGGAAATTAATATTCTTT
18674504 TGGAAAGA
131 TGGAAAGA
18674512 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
*
18674577 AATAT-AACAGTTATATTAATTAAATTT-GGCAAAAATATAAAAGACATGGAAATTAATATTCTT
66 AATATAAACAGTTATATTAATT-AATTTCGGTAAAAATATAAAAGACATGGAAATTAATATTCTT
18674640 TTGGAAAGA
130 TTGGAAAGA
*
18674649 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTCATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* * *
18674714 TATATAAACTA-TTATATTAATTAATTTCGGTAAAAATATAAAACACATGAAAATTAATATTCTT
66 AATATAAAC-AGTTATATTAATTAATTTCGGTAAAAATATAAAAGACATGGAAATTAATATTCTT
*
18674778 TTGGAAAAA
130 TTGGAAAGA
*
18674787 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* * * *
18674852 AATATAAACATTTATATTAATTAATTTCAGTTAAAATATAAAAGACATGAAAATTAATATTCTTT
66 AATATAAACAGTTATATTAATTAATTTCGGTAAAAATATAAAAGACATGGAAATTAATATTCTTT
*
18674917 TGGAAAAA
131 TGGAAAGA
18674925 ATATAATT
1 ATATAATT
18674933 TCTTTTTCTA
Statistics
Matches: 523, Mismatches: 31, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
137 130 0.25
138 392 0.75
139 1 0.00
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
AATATAAACAGTTATATTAATTAATTTCGGTAAAAATATAAAAGACATGGAAATTAATATTCTTT
TGGAAAGA
Found at i:18674548 original size:71 final size:71
Alignment explanation
Indices: 18674471--18674685 Score: 157
Period size: 71 Copynumber: 3.1 Consensus size: 71
18674461 AATTTCGGTT
18674471 AAAATATAAAAAACATGGAAATTAATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGAT
1 AAAATATAAAAAACATGGAAATTAATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGAT
18674536 TCATAC
66 TCATAC
* **** ** ** * * *
18674542 AAAATATTAATTGTATATATTTTACCGA-ATT-TATT--AATATAACAGTTATATTAAT-TA--A
1 AAAATATAAAAAACATGGAAATTA---ATATTCTTTTGGAA-AGAATA--TA-ATTAATATATGA
*
18674600 ATTTG--GC--A-
59 ATTTGATTCATAC
*
18674608 AAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGAT
1 AAAATATAAAAAACATGGAAATTAATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGAT
18674673 TCATAC
66 TCATAC
18674679 AAAATAT
1 AAAATAT
18674686 TAATTGTATA
Statistics
Matches: 99, Mismatches: 26, Indels: 38
0.61 0.16 0.23
Matches are distributed among these distances:
63 7 0.07
64 7 0.07
65 3 0.03
66 25 0.25
67 3 0.03
68 1 0.01
69 1 0.01
70 3 0.03
71 32 0.32
72 3 0.03
73 7 0.07
74 7 0.07
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (71 bp):
AAAATATAAAAAACATGGAAATTAATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGAT
TCATAC
Found at i:18674731 original size:275 final size:275
Alignment explanation
Indices: 18674236--18674932 Score: 1139
Period size: 275 Copynumber: 2.5 Consensus size: 275
18674226 GAGAACATAG
* ** *
18674236 ATATAATTAATATATGAAATTGATTCATACAAAATATTAATAATATATATTTTACCAAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
*
18674301 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTTTTT
66 AATATAAACAATTATATTAATTAATTTCGG-CAAAATATAAAAGACATGGAAATTAATATTCTTT
18674366 TGGAAAGAATATAATTAATATATAAATTTGATTCATACAAAATAGTAATTGTATATATTTTACCG
130 TGGAAAGAATATAATTAATATATAAATTTGATTCATACAAAATAGTAATTGTATATATTTTACCG
* * * *
18674431 AATTTATTAATATAAGTAGTTATATTAATTAATTTCGGTTAAAATATAAAAAACATGGAAATTAA
195 AATTCATTAATATAACTAGTTATATTAATTAATTTCGGTAAAAATATAAAAAACATGAAAATTAA
*
18674496 TATTCTTTTGGAAAGA
260 TATTCTTTTGGAAAAA
18674512 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
*
18674577 AATAT-AACAGTTATATTAATTAAATTT-GGCAAAAATATAAAAGACATGGAAATTAATATTCTT
66 AATATAAACAATTATATTAATT-AATTTCGGC-AAAATATAAAAGACATGGAAATTAATATTCTT
* *
18674640 TTGGAAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACC
129 TTGGAAAGAATATAATTAATATATAAATTTGATTCATACAAAATAGTAATTGTATATATTTTACC
* *
18674705 GAATTCATTTATATAAACTA-TTATATTAATTAATTTCGGTAAAAATATAAAACACATGAAAATT
194 GAATTCATTAATAT-AACTAGTTATATTAATTAATTTCGGTAAAAATATAAAAAACATGAAAATT
18674769 AATATTCTTTTGGAAAAA
258 AATATTCTTTTGGAAAAA
*
18674787 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* ** *
18674852 AATATAAACATTTATATTAATTAATTTCAGTTAAAATATAAAAGACATGAAAATTAATATTCTTT
66 AATATAAACAATTATATTAATTAATTTC-GGCAAAATATAAAAGACATGGAAATTAATATTCTTT
*
18674917 TGGAAAAAATATAATT
130 TGGAAAGAATATAATT
18674933 TCTTTTTCTA
Statistics
Matches: 394, Mismatches: 21, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
274 1 0.00
275 255 0.65
276 137 0.35
277 1 0.00
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (275 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
AATATAAACAATTATATTAATTAATTTCGGCAAAATATAAAAGACATGGAAATTAATATTCTTTT
GGAAAGAATATAATTAATATATAAATTTGATTCATACAAAATAGTAATTGTATATATTTTACCGA
ATTCATTAATATAACTAGTTATATTAATTAATTTCGGTAAAAATATAAAAAACATGAAAATTAAT
ATTCTTTTGGAAAAA
Found at i:18675041 original size:80 final size:80
Alignment explanation
Indices: 18674908--18675056 Score: 262
Period size: 80 Copynumber: 1.9 Consensus size: 80
18674898 ATGAAAATTA
18674908 ATATTCTTTTGGAAAAAATATAATTTCTTTTTCTAACTTTCCATTTACCTTCTCTATTAATAAGG
1 ATATTCTTTTGGAAAAAATATAATTTCTTTTTCTAACTTTCCATTTACCTTCTCTATTAATAAGG
18674973 GAATTGAATAATCCT
66 GAATTGAATAATCCT
* * **
18674988 ATATTCTTTTGGAAAGAATATAATTTGTTTTTCTAACTTTCCATTTTTCTTCTCTATTAATAAGG
1 ATATTCTTTTGGAAAAAATATAATTTCTTTTTCTAACTTTCCATTTACCTTCTCTATTAATAAGG
18675053 GAAT
66 GAAT
18675057 CTTAGTGTGT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 65 1.00
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (80 bp):
ATATTCTTTTGGAAAAAATATAATTTCTTTTTCTAACTTTCCATTTACCTTCTCTATTAATAAGG
GAATTGAATAATCCT
Found at i:18678753 original size:41 final size:41
Alignment explanation
Indices: 18678687--18679121 Score: 509
Period size: 41 Copynumber: 10.6 Consensus size: 41
18678677 TATGCACTAT
* *
18678687 CGAGTCATAAGTCTTCCTTTAAATATAATCTCATGCTCATCC
1 CGAGACATGAGTCTTCCTTT-AATATAATCTCATGCTCATCC
* * *
18678729 CGAGTCACGAATCTTCCTTTAATATAATCTCATGCTCATCC
1 CGAGACATGAGTCTTCCTTTAATATAATCTCATGCTCATCC
* * *
18678770 CAAGACATGAGTCTT--TAGT-GTATAATCTCATGCTCATCC
1 CGAGACATGAGTCTTCCT-TTAATATAATCTCATGCTCATCC
* * * **
18678809 CGAGACATGAGTCTCCCTTTAATTTAATCTCATGTTCATTT
1 CGAGACATGAGTCTTCCTTTAATATAATCTCATGCTCATCC
* * * *
18678850 TGAGTCACGAGTCTTCCTTTAATATATTCTCATGCTCATCC
1 CGAGACATGAGTCTTCCTTTAATATAATCTCATGCTCATCC
*
18678891 TGAGACATGAGTCTTCCTTTAATATAATCTCATGCTCATCC
1 CGAGACATGAGTCTTCCTTTAATATAATCTCATGCTCATCC
* * **
18678932 CGAGATATGAGTCTTCCTTTAATTTAATCTCATGCTCATTT
1 CGAGACATGAGTCTTCCTTTAATATAATCTCATGCTCATCC
* * * *
18678973 TGAGTA-ACGAGTCTTCTTTTAATATAATCTCATGTTCATCC
1 CGAG-ACATGAGTCTTCCTTTAATATAATCTCATGCTCATCC
* **
18679014 CGAGACATGAGTCTTCCTTTAATTTAATCTCATGCTCATTT
1 CGAGACATGAGTCTTCCTTTAATATAATCTCATGCTCATCC
* * * *
18679055 TGAGTCACGAGTTTTCCTTTAATATAATCTCATGCTCATCC
1 CGAGACATGAGTCTTCCTTTAATATAATCTCATGCTCATCC
*
18679096 CGAGACATGAGTCTTTCTTTAATATA
1 CGAGACATGAGTCTTCCTTTAATATA
18679122 TTTAAAGTGA
Statistics
Matches: 327, Mismatches: 60, Indels: 13
0.82 0.15 0.03
Matches are distributed among these distances:
39 33 0.10
40 3 0.01
41 273 0.83
42 18 0.06
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (41 bp):
CGAGACATGAGTCTTCCTTTAATATAATCTCATGCTCATCC
Found at i:18690315 original size:3 final size:3
Alignment explanation
Indices: 18690307--18690331 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
18690297 GCTGCTTTGG
18690307 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
18690332 GTGGCACTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:18694824 original size:41 final size:41
Alignment explanation
Indices: 18694758--18695012 Score: 323
Period size: 41 Copynumber: 6.2 Consensus size: 41
18694748 TCGATTCATA
* * * *
18694758 AGTCTTCCTTAACCATATTCCCATTCTTATCTCGAGACATG
1 AGTCTTCCTTAATCATAATCTCATTCTCATCTCGAGACATG
*
18694799 AGTCTTCCTTAATCATAATCTCATTCTCATTTCGAGACATG
1 AGTCTTCCTTAATCATAATCTCATTCTCATCTCGAGACATG
* *
18694840 AGTCTTCCTTATTCATAATCTCATTCTCATCTCAAGACATG
1 AGTCTTCCTTAATCATAATCTCATTCTCATCTCGAGACATG
* *
18694881 ATTCTTCCTTATTCATAATCTCATTCTCATCTCGAGACATG
1 AGTCTTCCTTAATCATAATCTCATTCTCATCTCGAGACATG
* * * *
18694922 AGTCTTCCTTATTCATAATCTCATTTTCATTTCGAGAGATG
1 AGTCTTCCTTAATCATAATCTCATTCTCATCTCGAGACATG
* * * *
18694963 AGTCTTCCATTTATACA-ATTTCTCATGCTCAACTCGAGACATG
1 AGTCTTCC-TTAAT-CATA-ATCTCATTCTCATCTCGAGACATG
18695006 AGTCTTC
1 AGTCTTC
18695013 TTTTTTATAC
Statistics
Matches: 189, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
41 158 0.84
42 4 0.02
43 27 0.14
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.39
Consensus pattern (41 bp):
AGTCTTCCTTAATCATAATCTCATTCTCATCTCGAGACATG
Found at i:18695610 original size:38 final size:38
Alignment explanation
Indices: 18695561--18695636 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
18695551 TACAACATTT
18695561 GATAGATTCATAAATTAGTCATTGCATAAGCTAGATTA
1 GATAGATTCATAAATTAGTCATTGCATAAGCTAGATTA
*
18695599 GATAGATTCATAAATTAGTCCTTGCATAAGCTAGATTA
1 GATAGATTCATAAATTAGTCATTGCATAAGCTAGATTA
18695637 AGCTAATACG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (38 bp):
GATAGATTCATAAATTAGTCATTGCATAAGCTAGATTA
Found at i:18695880 original size:21 final size:22
Alignment explanation
Indices: 18695854--18695895 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
18695844 ACTTTCATAA
18695854 TTAAC-TTAATTAATCATATTT
1 TTAACTTTAATTAATCATATTT
*
18695875 TTAACTTTAATTAATCCTATT
1 TTAACTTTAATTAATCATATT
18695896 ATGAATCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAACTTTAATTAATCATATTT
Found at i:18703434 original size:41 final size:41
Alignment explanation
Indices: 18703377--18703599 Score: 266
Period size: 41 Copynumber: 5.4 Consensus size: 41
18703367 TTATACTCTA
* * * * * *
18703377 TCGAGTCATAAGTCTTCCTTAACCATATTATTATTCTCATC
1 TCGAGACATGAGTCTTCCTTAATCATAATCTCATTCTCATC
* *
18703418 TCGAGACATGAGTCTTCCTTAATCATAATCTTATTCTCATT
1 TCGAGACATGAGTCTTCCTTAATCATAATCTCATTCTCATC
* * *
18703459 TCGAGACATGACTCTTCCTTATTCTTAATCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTAATCATAATCTCATTCTCATC
* *
18703500 TCAAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTAATCATAATCTCATTCTCATC
* * * * * *
18703541 TCAAGACATGGGTCTTCCTTATTTATAATCCCATTCTCATT
1 TCGAGACATGAGTCTTCCTTAATCATAATCTCATTCTCATC
*
18703582 TCGAGACATAAGTCTTCC
1 TCGAGACATGAGTCTTCC
18703600 ATTTATACAT
Statistics
Matches: 161, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 161 1.00
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.40
Consensus pattern (41 bp):
TCGAGACATGAGTCTTCCTTAATCATAATCTCATTCTCATC
Found at i:18721608 original size:53 final size:53
Alignment explanation
Indices: 18721514--18721633 Score: 168
Period size: 53 Copynumber: 2.3 Consensus size: 53
18721504 TGATTCTGTA
* * * * * *
18721514 AGTATATAAATCCTATTACGGATTAACAAGTTTGATTATTACGTATCATCGTG
1 AGTATATGAATCCTATTACGAATTAACAAGTCTGATGATTACATATCATCATG
* *
18721567 AGTATATGAATCCTATTACGAATTAATAGGTCTGATGATTACATATCATCATG
1 AGTATATGAATCCTATTACGAATTAACAAGTCTGATGATTACATATCATCATG
18721620 AGTATATGAATCCT
1 AGTATATGAATCCT
18721634 CTCACGGATG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 59 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (53 bp):
AGTATATGAATCCTATTACGAATTAACAAGTCTGATGATTACATATCATCATG
Found at i:18728256 original size:53 final size:53
Alignment explanation
Indices: 18728105--18728256 Score: 225
Period size: 53 Copynumber: 2.9 Consensus size: 53
18728095 GGAATTTGTG
* * *
18728105 TCATCGTGAGTATATGAATCCTATTATGGATGAATAGGTCTGAAGATTCTGTA
1 TCATCGTGAGTATATGAATCCTATTACGGATTAATAGGTCTGATGATTCTGTA
* * *
18728158 TCATCGTGAGTATATAAATCGTATTACGGATTAATAGGTCCGATGATTAC-GTA
1 TCATCGTGAGTATATGAATCCTATTACGGATTAATAGGTCTGATGATT-CTGTA
*
18728211 TCATCGTGAGTATATGAATCCTATTACGGATTAAAAGGTCTGATGA
1 TCATCGTGAGTATATGAATCCTATTACGGATTAATAGGTCTGATGA
18728257 CTTTGTGTTA
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
53 87 0.99
54 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (53 bp):
TCATCGTGAGTATATGAATCCTATTACGGATTAATAGGTCTGATGATTCTGTA
Found at i:18736920 original size:17 final size:17
Alignment explanation
Indices: 18736898--18736934 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
18736888 ACCAAAATTA
18736898 ATTTTTTATAAT-TGTTT
1 ATTTTTTA-AATATGTTT
18736915 ATTTTTTAAATATGTTT
1 ATTTTTTAAATATGTTT
18736932 ATT
1 ATT
18736935 ATATTATGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (17 bp):
ATTTTTTAAATATGTTT
Found at i:18739017 original size:1 final size:1
Alignment explanation
Indices: 18739011--18739036 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
18739001 AGTGGGTTAA
18739011 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
18739037 CACGAGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:18743377 original size:15 final size:15
Alignment explanation
Indices: 18743341--18743394 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
18743331 TTTGTCCTTC
* *
18743341 ATCCTTGCTCGCATT
1 ATCCATGCTCGCACT
*
18743356 GTCCATGCTCGCACT
1 ATCCATGCTCGCACT
* *
18743371 ATTCATGCTTGCACT
1 ATCCATGCTCGCACT
18743386 ATCCATGCT
1 ATCCATGCT
18743395 TGCATCATCA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.17, C:0.33, G:0.15, T:0.35
Consensus pattern (15 bp):
ATCCATGCTCGCACT
Found at i:18743395 original size:15 final size:15
Alignment explanation
Indices: 18743357--18743398 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
18743347 GCTCGCATTG
*
18743357 TCCATGCTCGCACTA
1 TCCATGCTTGCACTA
*
18743372 TTCATGCTTGCACTA
1 TCCATGCTTGCACTA
18743387 TCCATGCTTGCA
1 TCCATGCTTGCA
18743399 TCATCATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.19, C:0.33, G:0.14, T:0.33
Consensus pattern (15 bp):
TCCATGCTTGCACTA
Found at i:18743636 original size:49 final size:50
Alignment explanation
Indices: 18743532--18743651 Score: 161
Period size: 50 Copynumber: 2.4 Consensus size: 50
18743522 ATAATACACC
* * * * *
18743532 AATAATGTGGACAAGTCACCAGATAAAGCAGTCAAGCTGCCCAGATACAG
1 AATATTGTGGTCAAGCCACCAGATAAAGCAGTCAAGATGCCCAGATACAA
* * *
18743582 AATATTGTGGTCAAGCCACCATATAATGCAGTTAAGATG-CCAGATACAA
1 AATATTGTGGTCAAGCCACCAGATAAAGCAGTCAAGATGCCCAGATACAA
18743631 AATATTGTGGTCAAGCCACCA
1 AATATTGTGGTCAAGCCACCA
18743652 AACTTTTAGA
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
49 30 0.48
50 32 0.52
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (50 bp):
AATATTGTGGTCAAGCCACCAGATAAAGCAGTCAAGATGCCCAGATACAA
Found at i:18745672 original size:10 final size:10
Alignment explanation
Indices: 18745657--18745697 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
18745647 AACTATCAAT
18745657 TTTTTTATTC
1 TTTTTTATTC
18745667 TTTTTTATTC
1 TTTTTTATTC
* *
18745677 TTTTCTA-TA
1 TTTTTTATTC
18745686 TTTTTT-TTC
1 TTTTTTATTC
18745695 TTT
1 TTT
18745698 AAGAATAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
9 10 0.38
10 16 0.62
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTATTC
Found at i:18746667 original size:17 final size:17
Alignment explanation
Indices: 18746628--18746685 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 17
18746618 TACAGTGCAT
* *
18746628 AATAAAATAAAATTAAA
1 AATAAAACAAAAATAAA
*
18746645 TA-AAAACAAAAATAAA
1 AATAAAACAAAAATAAA
18746661 AATAAAAC-AAAATGAAA
1 AATAAAACAAAAAT-AAA
*
18746678 TATAAAAC
1 AATAAAAC
18746686 TAAATGAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
16 18 0.53
17 16 0.47
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.17
Consensus pattern (17 bp):
AATAAAACAAAAATAAA
Found at i:18746690 original size:17 final size:17
Alignment explanation
Indices: 18746629--18746696 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 17
18746619 ACAGTGCATA
* *
18746629 ATAAAATAAAATTAAAT
1 ATAAAACAAAATGAAAT
*
18746646 A-AAAACAAAAAT-AAAA
1 ATAAAAC-AAAATGAAAT
18746662 ATAAAACAAAATGAAAT
1 ATAAAACAAAATGAAAT
*
18746679 ATAAAACTAAATGAAAT
1 ATAAAACAAAATGAAAT
18746696 A
1 A
18746697 ACTTTGATTG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
16 13 0.30
17 31 0.70
ACGTcount: A:0.74, C:0.04, G:0.03, T:0.19
Consensus pattern (17 bp):
ATAAAACAAAATGAAAT
Found at i:18747087 original size:41 final size:41
Alignment explanation
Indices: 18747038--18747246 Score: 181
Period size: 41 Copynumber: 5.1 Consensus size: 41
18747028 CCCATGCCGA
* * * *
18747038 TGTGTAAGGTCATGTCGGGCACACAATCTCACACATGCCTG
1 TGTGTAAGGTCGTGTCGGGCACACAGTCTCACACACGCCCG
**
18747079 TGTGTAAGGTCGTG-CGGGACACACAGTCTCACACACGCTTG
1 TGTGTAAGGTCGTGTCGGG-CACACAGTCTCACACACGCCCG
* * * * * * *
18747120 TATGCAAGGTCGTATGGGGCACACAGTATAACACATGCCCG
1 TGTGTAAGGTCGTGTCGGGCACACAGTCTCACACACGCCCG
* * *
18747161 TGTGTCCAAGG-CGTGTGGGGCATACAGTCTCACACACACCCG
1 TGTGT--AAGGTCGTGTCGGGCACACAGTCTCACACACGCCCG
* ** *
18747203 TGTGTGAGGTTATGT-GGGACAAACAGTCTCACACACGCCCG
1 TGTGTAAGGTCGTGTCGGG-CACACAGTCTCACACACGCCCG
18747244 TGT
1 TGT
18747247 ACCAAAGCTG
Statistics
Matches: 136, Mismatches: 26, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
40 10 0.07
41 89 0.65
42 33 0.24
43 4 0.03
ACGTcount: A:0.24, C:0.26, G:0.28, T:0.22
Consensus pattern (41 bp):
TGTGTAAGGTCGTGTCGGGCACACAGTCTCACACACGCCCG
Found at i:18747188 original size:42 final size:43
Alignment explanation
Indices: 18747124--18747207 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 43
18747114 CGCTTGTATG
**
18747124 CAAGGTCGTATGGGGCACACAGTATAACACATGCCCGTGTGTC
1 CAAGGTCGTATGGGGCACACAGTATAACACACACCCGTGTGTC
* * * *
18747167 CAAGG-CGTGTGGGGCATACAGTCTCACACACACCCGTGTGT
1 CAAGGTCGTATGGGGCACACAGTATAACACACACCCGTGTGT
18747208 GAGGTTATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
42 30 0.86
43 5 0.14
ACGTcount: A:0.24, C:0.27, G:0.29, T:0.20
Consensus pattern (43 bp):
CAAGGTCGTATGGGGCACACAGTATAACACACACCCGTGTGTC
Found at i:18747311 original size:21 final size:22
Alignment explanation
Indices: 18747269--18747312 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
18747259 TAGATCACTT
**
18747269 TTTTTTTCAAATTTTTTGGTAA
1 TTTTTTTCAAATTTTTAAGTAA
18747291 TTTTTTTC-AATTTTTAAGTAA
1 TTTTTTTCAAATTTTTAAGTAA
18747312 T
1 T
18747313 AAAAATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.64
Consensus pattern (22 bp):
TTTTTTTCAAATTTTTAAGTAA
Found at i:18747815 original size:21 final size:21
Alignment explanation
Indices: 18747763--18747822 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
18747753 CATAGTGCAG
*
18747763 ACTTCTACCGATATAAGTGAC
1 ACTTCTACCGATACAAGTGAC
** *
18747784 AGGTCTGCCGATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
* *
18747805 TCTTCTACCGAAACAAGT
1 ACTTCTACCGATACAAGT
18747823 ATTACCTTTA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAC
Found at i:18748671 original size:51 final size:52
Alignment explanation
Indices: 18748556--18748735 Score: 281
Period size: 52 Copynumber: 3.5 Consensus size: 52
18748546 AGAATCACGT
*
18748556 ACGATGACACGTAGTCATAGGACCTCATAATCCGTAAAGGATTCATATACTC
1 ACGATGACACGTAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTC
*
18748608 ACGATGATACGTAGTCATCGGACCTCATAATCCGT-AAGGATTCATATACTC
1 ACGATGACACGTAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTC
* * * *
18748659 ACGATGAAACGTAGTCATCAGACCTCATAATCTGTAAAAGATTCATATACTC
1 ACGATGACACGTAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTC
* *
18748711 ATGATGACACGTAGTCATTGGACCT
1 ACGATGACACGTAGTCATCGGACCT
18748736 TTTTCATTTA
Statistics
Matches: 117, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
51 48 0.41
52 69 0.59
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (52 bp):
ACGATGACACGTAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTC
Found at i:18752299 original size:35 final size:35
Alignment explanation
Indices: 18752238--18752304 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
18752228 ATCACAATGG
* **
18752238 CATGCTTAACATGCGGATCAGGATCAGAAATATGA
1 CATGCTTAACATGCGAATCAAAATCAGAAATATGA
*
18752273 CATGGTTAACATGCGAATCAAAATCAGAAATA
1 CATGCTTAACATGCGAATCAAAATCAGAAATA
18752305 ATATCATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.22
Consensus pattern (35 bp):
CATGCTTAACATGCGAATCAAAATCAGAAATATGA
Found at i:18765778 original size:12 final size:12
Alignment explanation
Indices: 18765761--18765795 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
18765751 TTTTGAGAGC
18765761 ATAAAATAAAAG
1 ATAAAATAAAAG
*
18765773 ATAAAATAAAAT
1 ATAAAATAAAAG
*
18765785 AAAAAATAAAA
1 ATAAAATAAAA
18765796 CCAAAAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:18765783 original size:17 final size:17
Alignment explanation
Indices: 18765761--18765795 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
18765751 TTTTGAGAGC
*
18765761 ATAAAATAAAAGATAAA
1 ATAAAATAAAAAATAAA
18765778 ATAAAATAAAAAATAAA
1 ATAAAATAAAAAATAAA
18765795 A
1 A
18765796 CCAAAAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (17 bp):
ATAAAATAAAAAATAAA
Found at i:18776947 original size:23 final size:21
Alignment explanation
Indices: 18776921--18776963 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
18776911 TTTTGTCACT
18776921 ATTCATATGTTTACTTACTCATG
1 ATTCATATGTTT-C-TACTCATG
* *
18776944 ATTCTTTTGTTTCTACTCAT
1 ATTCATATGTTTCTACTCAT
18776964 TTTTCTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.21, C:0.19, G:0.07, T:0.53
Consensus pattern (21 bp):
ATTCATATGTTTCTACTCATG
Found at i:18798641 original size:18 final size:18
Alignment explanation
Indices: 18798618--18798652 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18798608 CCCTCATCCC
* *
18798618 CTAAGGGGAAGCAGAAAG
1 CTAAGGGAAAGAAGAAAG
18798636 CTAAGGGAAAGAAGAAA
1 CTAAGGGAAAGAAGAAA
18798653 TCGACTAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.09, G:0.34, T:0.06
Consensus pattern (18 bp):
CTAAGGGAAAGAAGAAAG
Found at i:18802803 original size:21 final size:21
Alignment explanation
Indices: 18802752--18802803 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
18802742 AGAGTTTTTA
*
18802752 GTATCGGTAGAAGCATGACAT
1 GTATCAGTAGAAGCATGACAT
* *
18802773 GTTTCAGTAGAAGTCAT-ACTT
1 GTATCAGTAGAAG-CATGACAT
*
18802794 GTATCTGTAG
1 GTATCAGTAG
18802804 TATTGTCTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (21 bp):
GTATCAGTAGAAGCATGACAT
Found at i:18805098 original size:16 final size:17
Alignment explanation
Indices: 18805079--18805117 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
18805069 AATTAAATAC
*
18805079 AATTAATCTAA-ATGCA
1 AATTAACCTAAGATGCA
18805095 AATTAACCTAAGTATGCA
1 AATTAACCTAAG-ATGCA
18805113 AATTA
1 AATTA
18805118 TCGATATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 10 0.50
18 10 0.50
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.31
Consensus pattern (17 bp):
AATTAACCTAAGATGCA
Found at i:18806410 original size:12 final size:13
Alignment explanation
Indices: 18806377--18806425 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
18806367 GTGTTAAATT
*
18806377 AATTAAATTAACCC
1 AATTTAATTAA-CC
18806391 AA-TTAATTAA-C
1 AATTTAATTAACC
18806402 AATTTAATTAATCC
1 AATTTAATTAA-CC
18806416 AATTT-ATTAA
1 AATTTAATTAA
18806426 TGAAATAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 3 0.10
12 8 0.26
13 12 0.39
14 8 0.26
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
AATTTAATTAACC
Found at i:18806410 original size:25 final size:25
Alignment explanation
Indices: 18806377--18806425 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
18806367 GTGTTAAATT
18806377 AATTAAATTAACCCAATTAATTAAC
1 AATTAAATTAACCCAATTAATTAAC
* * *
18806402 AATTTAATTAATCCAATTTATTAA
1 AATTAAATTAACCCAATTAATTAA
18806426 TGAAATAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (25 bp):
AATTAAATTAACCCAATTAATTAAC
Found at i:18806450 original size:26 final size:25
Alignment explanation
Indices: 18806419--18806467 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
18806409 TTAATCCAAT
18806419 TTATTAATGAAATAA-TTTATGTTTAA
1 TTATTAA--AAATAATTTTATGTTTAA
*
18806445 TTATTAAATATAATTTTATGTTT
1 TTATTAAAAATAATTTTATGTTT
18806468 TAAAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 9 0.43
26 7 0.33
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (25 bp):
TTATTAAAAATAATTTTATGTTTAA
Found at i:18811747 original size:77 final size:77
Alignment explanation
Indices: 18811615--18811764 Score: 246
Period size: 77 Copynumber: 1.9 Consensus size: 77
18811605 GCATATTCTT
* * * * *
18811615 GACAGCTCGTGTGAGTAGCATCGTTAGGGAACAGTTATATGCACAGATACTGTATCGATGGTTGG
1 GACAGCTCGTGTGAGCAGCATCGTTAGGGAACAATTATATACACAGATACCGTATCGATGGCTGG
*
18811680 GGTACCGTCCTC
66 GATACCGTCCTC
18811692 GACAGCTCGTGTGAGCAGCATCGTTAGGGAACAATTATATACACAGATACCGTATCGATGGCTGG
1 GACAGCTCGTGTGAGCAGCATCGTTAGGGAACAATTATATACACAGATACCGTATCGATGGCTGG
18811757 GATACCGT
66 GATACCGT
18811765 ATATGTTGCG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 67 1.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (77 bp):
GACAGCTCGTGTGAGCAGCATCGTTAGGGAACAATTATATACACAGATACCGTATCGATGGCTGG
GATACCGTCCTC
Found at i:18816763 original size:13 final size:13
Alignment explanation
Indices: 18816745--18816788 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
18816735 AAATTAATAA
18816745 AATTAACTCAATT
1 AATTAACTCAATT
18816758 AATTAA--CAATTT
1 AATTAACTCAA-TT
18816770 AATTAACTCAATT
1 AATTAACTCAATT
*
18816783 TATTAA
1 AATTAA
18816789 TGAAATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 3 0.11
12 8 0.30
13 13 0.48
14 3 0.11
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (13 bp):
AATTAACTCAATT
Found at i:18816798 original size:25 final size:25
Alignment explanation
Indices: 18816740--18816788 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
18816730 AGGTTAAATT
*
18816740 AATAAAATTAACTCAATTAATTAAC
1 AATATAATTAACTCAATTAATTAAC
* *
18816765 AATTTAATTAACTCAATTTATTAA
1 AATATAATTAACTCAATTAATTAA
18816789 TGAAATAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (25 bp):
AATATAATTAACTCAATTAATTAAC
Found at i:18821695 original size:7 final size:7
Alignment explanation
Indices: 18821683--18821708 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18821673 AGTGATAAAT
18821683 ATGATCA
1 ATGATCA
18821690 ATGATCA
1 ATGATCA
18821697 ATGATCA
1 ATGATCA
18821704 ATGAT
1 ATGAT
18821709 ATATATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (7 bp):
ATGATCA
Found at i:18830630 original size:57 final size:57
Alignment explanation
Indices: 18830537--18830669 Score: 149
Period size: 57 Copynumber: 2.3 Consensus size: 57
18830527 TTATTTCTAC
* * * * ** * *
18830537 ATTTATGTTGTCTAAATATAATTTATAGTTGGTGTCAAAATGACTCTTAGTGTGCAT
1 ATTTATGTTGTCAAAATGTAATTTAAAGCTACTGTCAAAACGACTCTTAATGTGCAT
* * * **
18830594 ATTTATGCTGTCCAAATGTAATTTAAAGCTACTGTCATAACGTTTCTTAATGTGCAT
1 ATTTATGTTGTCAAAATGTAATTTAAAGCTACTGTCAAAACGACTCTTAATGTGCAT
18830651 ATTTATGTTGTCAAAATGT
1 ATTTATGTTGTCAAAATGT
18830670 GAGTAAAGGC
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (57 bp):
ATTTATGTTGTCAAAATGTAATTTAAAGCTACTGTCAAAACGACTCTTAATGTGCAT
Found at i:18832467 original size:20 final size:20
Alignment explanation
Indices: 18832437--18832575 Score: 120
Period size: 20 Copynumber: 7.0 Consensus size: 20
18832427 TAAATAAATA
* *
18832437 TGTACGCACTTTGGTGCCTC
1 TGTATGCACTTTGGTGCCCC
* *
18832457 TCTATGCACTTTGGTGCCAC
1 TGTATGCACTTTGGTGCCCC
* * **
18832477 TATAAGCACTTCAGTGCCCC
1 TGTATGCACTTTGGTGCCCC
* * *
18832497 TATATGCACTTCGGTG-CCT
1 TGTATGCACTTTGGTGCCCC
* *
18832516 TGGTATGCACTCTGGTGCCCA
1 T-GTATGCACTTTGGTGCCCC
*
18832537 TGTA-GACACTCTGGTGCCCC
1 TGTATG-CACTTTGGTGCCCC
18832557 TGTATGCACTTTGGTGCCC
1 TGTATGCACTTTGGTGCCC
18832576 TAGTCTAAAA
Statistics
Matches: 98, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
19 4 0.04
20 90 0.92
21 4 0.04
ACGTcount: A:0.15, C:0.30, G:0.23, T:0.32
Consensus pattern (20 bp):
TGTATGCACTTTGGTGCCCC
Found at i:18835397 original size:21 final size:19
Alignment explanation
Indices: 18835371--18835423 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
18835361 GGAGTTTTTG
*
18835371 GTATCGATAGATGCATCACTT
1 GTATCGGTAGAT-CAT-ACTT
18835392 GTATCGGTAGAAATCATACTT
1 GTATCGGTAG--ATCATACTT
18835413 GTATCGGTAGA
1 GTATCGGTAGA
18835424 GCTAGCACAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 1 0.03
21 23 0.79
22 3 0.10
23 2 0.07
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (19 bp):
GTATCGGTAGATCATACTT
Found at i:18838710 original size:29 final size:29
Alignment explanation
Indices: 18838677--18838748 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
18838667 CCTTTTATTA
* *
18838677 CCCACTTTTTACTCTTTTTATTGTGTAAT
1 CCCACTTTTTACTCTCTTTATTGTGTAAC
18838706 CCCACTTTTTACTCTCTTTATTGTGTAAC
1 CCCACTTTTTACTCTCTTTATTGTGTAAC
*
18838735 CCCAATTTTTACTC
1 CCCACTTTTTACTC
18838749 CAATTGACTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.18, C:0.26, G:0.06, T:0.50
Consensus pattern (29 bp):
CCCACTTTTTACTCTCTTTATTGTGTAAC
Found at i:18845101 original size:29 final size:28
Alignment explanation
Indices: 18845069--18845140 Score: 108
Period size: 28 Copynumber: 2.5 Consensus size: 28
18845059 CCTTTTATGG
18845069 CCCCTTTTTTACTCCCTTTATTGTGTAAT
1 CCCC-TTTTTACTCCCTTTATTGTGTAAT
* *
18845098 CCCCTTTTTACACTCTTTATTGTGTAAT
1 CCCCTTTTTACTCCCTTTATTGTGTAAT
18845126 CCCCATTTTTACTCC
1 CCCC-TTTTTACTCC
18845141 AATTGACTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 26 0.68
29 12 0.32
ACGTcount: A:0.15, C:0.31, G:0.06, T:0.49
Consensus pattern (28 bp):
CCCCTTTTTACTCCCTTTATTGTGTAAT
Found at i:18846159 original size:36 final size:36
Alignment explanation
Indices: 18846100--18846198 Score: 99
Period size: 36 Copynumber: 2.8 Consensus size: 36
18846090 ATATATGAGA
* * * *
18846100 TCTGATCCGCATGTTAAGCATGCCACTGTTTCTGAT
1 TCTGATTCACATGTTAAACATGCCACTGTTTCTAAT
* ** * *
18846136 TTTGATTCGTATGTTAAATATGCCATTGTTTCTAAT
1 TCTGATTCACATGTTAAACATGCCACTGTTTCTAAT
* *
18846172 TCTGATTCACATGTTAAGCATGTCACT
1 TCTGATTCACATGTTAAACATGCCACT
18846199 ATGATAAACC
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.41
Consensus pattern (36 bp):
TCTGATTCACATGTTAAACATGCCACTGTTTCTAAT
Found at i:18846253 original size:46 final size:47
Alignment explanation
Indices: 18846174--18846293 Score: 163
Period size: 46 Copynumber: 2.6 Consensus size: 47
18846164 TTTCTAATTC
* *
18846174 TGATTCACATGTTAAGCATGTCACT-ATGATAAACCATAATGAGATA
1 TGATTCACATGTTAAGCATGCCACTGATGATAAACCACAATGAGATA
* *
18846220 TGATTCACATGTTAAGCATGCCACTGA-GTTAAACCGCAATGAGATA
1 TGATTCACATGTTAAGCATGCCACTGATGATAAACCACAATGAGATA
* *
18846266 TGATTCGCATGTAAAGCATGCCTACTGA
1 TGATTCACATGTTAAGCATGCC-ACTGA
18846294 AAATTTGTTA
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
46 60 0.91
47 6 0.09
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (47 bp):
TGATTCACATGTTAAGCATGCCACTGATGATAAACCACAATGAGATA
Found at i:18856009 original size:12 final size:12
Alignment explanation
Indices: 18855992--18856054 Score: 51
Period size: 12 Copynumber: 5.1 Consensus size: 12
18855982 AATTAATCAC
18855992 TTTAATATTAAA
1 TTTAATATTAAA
18856004 TTTAATA-TAATA
1 TTTAATATTAA-A
*
18856016 TTT-ATCAAGATAAA
1 TTTAAT--A-TTAAA
18856030 TATT-ATATTAAA
1 T-TTAATATTAAA
18856042 TTTAATATTAAA
1 TTTAATATTAAA
18856054 T
1 T
18856055 CTTATTAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
11 7 0.16
12 25 0.58
13 2 0.05
14 2 0.05
15 7 0.16
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:18856076 original size:38 final size:38
Alignment explanation
Indices: 18855995--18856076 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 38
18855985 TAATCACTTT
* *
18855995 AATATTAAATTTAATATAATATTTATCAAGATAAATAT
1 AATATTAAATTTAATATAATATTTATCAAAATAAATAA
* *
18856033 TATATTAAATTTAATATTAA-ATCTTATTAAAAT-AATAA
1 AATATTAAATTTAATA-TAATAT-TTATCAAAATAAATAA
18856071 AATATT
1 AATATT
18856077 TTATCTACAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
38 26 0.70
39 11 0.30
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (38 bp):
AATATTAAATTTAATATAATATTTATCAAAATAAATAA
Found at i:18856146 original size:17 final size:17
Alignment explanation
Indices: 18856118--18856162 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
18856108 ATACTAGTAG
18856118 AATAATTATTAAA-TTAA
1 AATAA-TATTAAACTTAA
*
18856135 ATTTAATATTAAACTTAA
1 A-ATAATATTAAACTTAA
18856153 AATAATATTA
1 AATAATATTA
18856163 TTTTGGAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
AATAATATTAAACTTAA
Found at i:18858925 original size:15 final size:15
Alignment explanation
Indices: 18858888--18858926 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
18858878 CGTAGATGTC
*
18858888 AAGCTCGCAGGTACA
1 AAGCTCGCAGCTACA
*
18858903 AAGGTCGCAGCTACA
1 AAGCTCGCAGCTACA
*
18858918 GAGCTCGCA
1 AAGCTCGCA
18858927 ACTATGAATG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.28, G:0.28, T:0.13
Consensus pattern (15 bp):
AAGCTCGCAGCTACA
Found at i:18863930 original size:183 final size:181
Alignment explanation
Indices: 18863567--18863957 Score: 450
Period size: 183 Copynumber: 2.1 Consensus size: 181
18863557 TAGCTCACTT
* * * * * *
18863567 TTCACCATTTTCAATAAAAAATAATTTTAATCTCACATTGACTATAGAATACTTCCATAGCTCAA
1 TTCACTATTTTCATTAAAAATTAATTTTAATCCCACATTCACTAGAGAATACTTCCATAGCTCAA
* *
18863632 TTATTGAATATTTTGATAAAAAATAATTTAGACCCTTAAAAAAGTTAATTTTAATCTCAAATTCA
66 TTATTCAATATTTTCATAAAAAATAATTTAGACCCTTAAAAAAGTTAATTTTAATCTCAAATTCA
* *
18863697 CTAGAGAACACTCTCATACTCATACTTACCGTATAAATAAGTATCAATTTC
131 CTAGAGAACACTCCCATACTCACACTTACCGTATAAATAAGTATCAATTTC
* * *
18863748 TTCATTGTTTTCATTAAAAAGTTAATTTTAATCCCACATTCACTAGAGAATAC-TCTTATAGCTC
1 TTCACTATTTTCATTAAAAA-TTAATTTTAATCCCACATTCACTAGAGAATACTTC-CATAGCTC
* * * * * * *
18863812 ACTTCTTCACTATTTTCATTAAAAATAAATGTTGGTCCCTT-AAAACGTTAATTTTAAT-TCCAA
64 AATTATTCAATATTTTCATAAAAAAT-AAT-TTAGACCCTTAAAAAAGTTAATTTTAATCT-CAA
** * * *
18863875 ATTGGCTATAGAACACTCCCCTGCTCACACTTGACC-TATAAATAAGCTA-CAATTTC
126 ATTCACTAGAGAACACTCCCATACTCACACTT-ACCGTATAAATAAG-TATCAATTTC
*
18863931 TTCACTATTTTTATTAAAAATTAATTT
1 TTCACTATTTTCATTAAAAATTAATTT
18863958 AAATTTAAAT
Statistics
Matches: 175, Mismatches: 28, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
181 18 0.10
182 63 0.36
183 81 0.46
184 13 0.07
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (181 bp):
TTCACTATTTTCATTAAAAATTAATTTTAATCCCACATTCACTAGAGAATACTTCCATAGCTCAA
TTATTCAATATTTTCATAAAAAATAATTTAGACCCTTAAAAAAGTTAATTTTAATCTCAAATTCA
CTAGAGAACACTCCCATACTCACACTTACCGTATAAATAAGTATCAATTTC
Found at i:18865980 original size:23 final size:25
Alignment explanation
Indices: 18865954--18866003 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
18865944 TTTTGAGAAA
18865954 TTTAA-TTTTTTTCTTT-TATATTT
1 TTTAACTTTTTTTCTTTCTATATTT
*
18865977 TTTAACTTTTTTTCTTTCTTTATTT
1 TTTAACTTTTTTTCTTTCTATATTT
18866002 TT
1 TT
18866004 CATTTTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 5 0.21
24 11 0.46
25 8 0.33
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTAACTTTTTTTCTTTCTATATTT
Found at i:18866681 original size:3 final size:3
Alignment explanation
Indices: 18866673--18866706 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
18866663 TGCACCAGGT
*
18866673 TAA TAA TAA TAA TAA TAG TAA -AA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
18866707 GTTAATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:18868412 original size:14 final size:14
Alignment explanation
Indices: 18868393--18868426 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
18868383 GTAGTCTTGT
*
18868393 TTGTTCTTCATGAG
1 TTGTTCTCCATGAG
*
18868407 TTGTTCTCCATGTG
1 TTGTTCTCCATGAG
18868421 TTGTTC
1 TTGTTC
18868427 CATCACGGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.09, C:0.18, G:0.21, T:0.53
Consensus pattern (14 bp):
TTGTTCTCCATGAG
Found at i:18884267 original size:17 final size:15
Alignment explanation
Indices: 18884230--18884269 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 15
18884220 GGTAACCCAA
18884230 ATTT-ATTTTAATTT
1 ATTTAATTTTAATTT
18884244 ATTTAATTTTGAATTT
1 ATTTAATTTT-AATTT
18884260 AGTTTAATTT
1 A-TTTAATTT
18884270 ATGTTGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.17
15 5 0.22
16 6 0.26
17 8 0.35
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (15 bp):
ATTTAATTTTAATTT
Found at i:18888075 original size:28 final size:28
Alignment explanation
Indices: 18888026--18888113 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 28
18888016 CCAAGCGGAA
*
18888026 GGCTTGAATAGAGTA-ATGTTCTTATTTT
1 GGCTTGAATAGAG-AGATATTCTTATTTT
* *
18888054 GGCTTGAATAGAGAGATATTCTAATTCT
1 GGCTTGAATAGAGAGATATTCTTATTTT
* *
18888082 AGCTT-AGATAGAGCGATATTC-TATTTCT
1 GGCTTGA-ATAGAGAGATATTCTTATTT-T
18888110 GGCT
1 GGCT
18888114 GGGGTAGAGC
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
27 5 0.10
28 44 0.90
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (28 bp):
GGCTTGAATAGAGAGATATTCTTATTTT
Found at i:18888121 original size:28 final size:28
Alignment explanation
Indices: 18888062--18888281 Score: 101
Period size: 28 Copynumber: 7.9 Consensus size: 28
18888052 TTGGCTTGAA
* * * ** *
18888062 TAGAGAGATATTCTAATTCTAGCTTAGA
1 TAGAGCGATATTCTATTTCTGGCTCGGG
*
18888090 TAGAGCGATATTCTATTTCTGGCTGGGG
1 TAGAGCGATATTCTATTTCTGGCTCGGG
18888118 TAGAGC-ATTATTCTATTTCTGGCTCGGG
1 TAGAGCGA-TATTCTATTTCTGGCTCGGG
* * * *
18888146 TAGAGTGTTACTT-TGA-ATCTGGCTCGAG
1 TAGAGCGATA-TTCT-ATTTCTGGCTCGGG
* * *
18888174 TAAAGC-ATTATTCTATTTTTGGCTTGGG
1 TAGAGCGA-TATTCTATTTCTGGCTCGGG
* * * * * * *
18888202 TAAAACGTTACTCTGA-ATCTGACTTGGG
1 TAGAGCGATATTCT-ATTTCTGGCTCGGG
*
18888230 TAAAGC-ATTATTCTATTTCTGGCTCGGG
1 TAGAGCGA-TATTCTATTTCTGGCTCGGG
* * * * *
18888258 CAAAGCGTTATTTTGTTTCTGGCT
1 TAGAGCGATATTCTATTTCTGGCT
18888282 TGGAAAGAGC
Statistics
Matches: 146, Mismatches: 34, Indels: 24
0.72 0.17 0.12
Matches are distributed among these distances:
27 5 0.03
28 137 0.94
29 4 0.03
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.39
Consensus pattern (28 bp):
TAGAGCGATATTCTATTTCTGGCTCGGG
Found at i:18888284 original size:56 final size:56
Alignment explanation
Indices: 18888107--18888284 Score: 221
Period size: 56 Copynumber: 3.2 Consensus size: 56
18888097 ATATTCTATT
* * * *
18888107 TCTGGCTGGGGTAGAGCATTATTCTATTTCTGGCTCGGGTAGAGTGTTACTTTGAA
1 TCTGGCTTGGGTAAAGCATTATTCTATTTCTGGCTCGGGTAAAGCGTTACTTTGAA
* * * * * *
18888163 TCTGGCTCGAGTAAAGCATTATTCTATTTTTGGCTTGGGTAAAACGTTACTCTGAA
1 TCTGGCTTGGGTAAAGCATTATTCTATTTCTGGCTCGGGTAAAGCGTTACTTTGAA
* * * **
18888219 TCTGACTTGGGTAAAGCATTATTCTATTTCTGGCTCGGGCAAAGCGTTATTTTGTT
1 TCTGGCTTGGGTAAAGCATTATTCTATTTCTGGCTCGGGTAAAGCGTTACTTTGAA
18888275 TCTGGCTTGG
1 TCTGGCTTGG
18888285 AAAGAGCGTT
Statistics
Matches: 101, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
56 101 1.00
ACGTcount: A:0.20, C:0.16, G:0.26, T:0.39
Consensus pattern (56 bp):
TCTGGCTTGGGTAAAGCATTATTCTATTTCTGGCTCGGGTAAAGCGTTACTTTGAA
Found at i:18888315 original size:28 final size:28
Alignment explanation
Indices: 18888261--18888317 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
18888251 GCTCGGGCAA
* *
18888261 AGCGTTATTTTGTTTCTGGCTTGGAAAG
1 AGCGTTATTTTGTATCTGGCTTAGAAAG
18888289 AGCGTTATTTTGTATCTGAGC-TAGAAAG
1 AGCGTTATTTTGTATCTG-GCTTAGAAAG
18888317 A
1 A
18888318 ATTATATTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.25, C:0.11, G:0.26, T:0.39
Consensus pattern (28 bp):
AGCGTTATTTTGTATCTGGCTTAGAAAG
Found at i:18902007 original size:547 final size:547
Alignment explanation
Indices: 18900973--18902589 Score: 3155
Period size: 547 Copynumber: 3.0 Consensus size: 547
18900963 TCAAGAAAAG
*
18900973 GAGCAAACATACCAACTTAAACATGAGCCACAAAACATTACATCTTCCTTACATGTATGTCCTAC
1 GAGCAAACATACCAATTTAAACATGAGCCACAAAACATTACATCTTCCTTACATGTATGTCCTAC
*
18901038 TTGAAGCACTAAACATGCCAACCAATAACTGTAAATCATCCATTTAGGCTACTAGAAATTTACAA
66 TTGAAGCACTAAACATGCCAACCAATAACTGTAAATCATCCATTTAGGCTACTAGTAATTTACAA
18901103 CTCAACAAAATCATGTAATAAACTAACATCCTAGTACATGCCATATAATCAGGTGATGTAAAAAC
131 CTCAACAAAATCATGTAATAAACTAACATCCTAGTACATGCCATATAATCAGGTGATGTAAAAAC
*
18901168 TACCGAACAAGCTCTCGAGATAGTGTGATTTCTCCTTGATGATTCGATCTTCAGACAACAAAATG
196 TACCGAACAAGCTCCCGAGATAGTGTGATTTCTCCTTGATGATTCGATCTTCAGACAACAAAATG
18901233 AAATCTACAAAATAACATACAAAAACACGGGTAAGCTTACAATGCTTAGTAAGTTCGTAACACAT
261 AAATCTACAAAATAACATACAAAAACACGGGTAAGCTTACAATGCTTAGTAAGTTCGTAACACAT
18901298 TAAACTTACAGAATAACCAATTCGATTATAAAAAGGAGTAATGAAACAACTCCGTGATTTCGCGA
326 TAAACTTACAGAATAACCAATTCGATTATAAAAAGGAGTAATGAAACAACTCCGTGATTTCGCGA
18901363 ATAGAGTATCAGATTGATCTCTTTAGGTCTTTCAGAATTTTAGCTCATACGAGCACAAAAAGAGA
391 ATAGAGTATCAGATTGATCTCTTTAGGTCTTTCAGAATTTTAGCTCATACGAGCACAAAAAGAGA
18901428 TTAAATAGTATATGATGTGCTCACACAAGCTGTTAAGAAATTGCAACATATGTAGGGTCTTAGCC
456 TTAAATAGTATATGATGTGCTCACACAAGCTGTTAAGAAATTGCAACATATGTAGGGTCTTAGCC
18901493 ATCGGAGGGTCCATATTTGTTACTCAC
521 ATCGGAGGGTCCATATTTGTTACTCAC
18901520 GAGCAAACATACCAATTTAAACATGAGCCACAAAACATTACATCTTCCTTACATGTATGTCCTAC
1 GAGCAAACATACCAATTTAAACATGAGCCACAAAACATTACATCTTCCTTACATGTATGTCCTAC
18901585 TTGAAGCACTAAACATGCCAACCAATAACTGTAAATCATCCATTTAGGCTACTAGTAATTTACAA
66 TTGAAGCACTAAACATGCCAACCAATAACTGTAAATCATCCATTTAGGCTACTAGTAATTTACAA
18901650 CTCAACAAAATCATGTAATAAACTAACATCCTAGTACATGCCATATAATCAGGTGATGTAAAAAC
131 CTCAACAAAATCATGTAATAAACTAACATCCTAGTACATGCCATATAATCAGGTGATGTAAAAAC
18901715 TACCGAACAAGCTCCCGAGATAGTGTGATTTCTCCTTGATGATTCGATCTTCAGACAACAAAATG
196 TACCGAACAAGCTCCCGAGATAGTGTGATTTCTCCTTGATGATTCGATCTTCAGACAACAAAATG
18901780 AAATCTACAAAATAACATACAAAAACACGGGTAAGCTTACAATGCTTAGTAAGTTCGTAACACAT
261 AAATCTACAAAATAACATACAAAAACACGGGTAAGCTTACAATGCTTAGTAAGTTCGTAACACAT
18901845 TAAACTTACAGAATAACCAATTCGATTATAAAAAGGAGTAATGAAACAACTCCGTGATTTCGCGA
326 TAAACTTACAGAATAACCAATTCGATTATAAAAAGGAGTAATGAAACAACTCCGTGATTTCGCGA
18901910 ATAGAGTATCAGATTGATCTCTTTAGGTCTTTCAGAATTTTAGCTCATACGAGCACAAAAAGAGA
391 ATAGAGTATCAGATTGATCTCTTTAGGTCTTTCAGAATTTTAGCTCATACGAGCACAAAAAGAGA
*
18901975 TTAAATAGTATATGATGTGCTCACACAAGCTGTTAAGAAATTGCAACATATGCAGGGTCTTAGCC
456 TTAAATAGTATATGATGTGCTCACACAAGCTGTTAAGAAATTGCAACATATGTAGGGTCTTAGCC
18902040 ATCGGAGGGTCCATATTTGTTACTCAC
521 ATCGGAGGGTCCATATTTGTTACTCAC
18902067 GAGCAAACATACCAATTTAAACATGAGCCACAAAACATTACATCTTCCTTACATGTATGTCCTAC
1 GAGCAAACATACCAATTTAAACATGAGCCACAAAACATTACATCTTCCTTACATGTATGTCCTAC
18902132 TTGAAGCACTAAACATGCCAACCAATAACTGTAAATCATCCATTTAGGCTACTAGTAATTTACAA
66 TTGAAGCACTAAACATGCCAACCAATAACTGTAAATCATCCATTTAGGCTACTAGTAATTTACAA
18902197 CTCAACAAAATCATGTAATAAACTAACATCCTAGTACATGCCATATAATCAGGTGATGTAAAAAC
131 CTCAACAAAATCATGTAATAAACTAACATCCTAGTACATGCCATATAATCAGGTGATGTAAAAAC
18902262 TACCGAACAAGCTCCCGAGATAGTGTGATTTCTCCTTGATGATTCGATCTTCAGACAACAAAATG
196 TACCGAACAAGCTCCCGAGATAGTGTGATTTCTCCTTGATGATTCGATCTTCAGACAACAAAATG
18902327 AAATCTACAAAATAACATACAAAAACACGGGTAAGCTTACAATGCTTAGTAAGTTCGTAACACAT
261 AAATCTACAAAATAACATACAAAAACACGGGTAAGCTTACAATGCTTAGTAAGTTCGTAACACAT
18902392 TAAACTTACAGAATAACCAATTCGATTATAAAAAGGAGTAATGAAACAACTCCGTGATTTCGCGA
326 TAAACTTACAGAATAACCAATTCGATTATAAAAAGGAGTAATGAAACAACTCCGTGATTTCGCGA
18902457 ATAGAGTATCAGATTGATCTCTTTAGGTCTTTCAGAATTTTAGCTCATACGAGCACAAAAAGAGA
391 ATAGAGTATCAGATTGATCTCTTTAGGTCTTTCAGAATTTTAGCTCATACGAGCACAAAAAGAGA
* * *
18902522 TTAAATAGTATATGATGTGCTCACACAAGCTGTCAAGAAACTGCAACATATGCT-GGATCTTAGC
456 TTAAATAGTATATGATGTGCTCACACAAGCTGTTAAGAAATTGCAACATATG-TAGGGTCTTAGC
18902586 CATC
520 CATC
18902590 AAAGGGTCTT
Statistics
Matches: 1061, Mismatches: 8, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
547 1061 1.00
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.27
Consensus pattern (547 bp):
GAGCAAACATACCAATTTAAACATGAGCCACAAAACATTACATCTTCCTTACATGTATGTCCTAC
TTGAAGCACTAAACATGCCAACCAATAACTGTAAATCATCCATTTAGGCTACTAGTAATTTACAA
CTCAACAAAATCATGTAATAAACTAACATCCTAGTACATGCCATATAATCAGGTGATGTAAAAAC
TACCGAACAAGCTCCCGAGATAGTGTGATTTCTCCTTGATGATTCGATCTTCAGACAACAAAATG
AAATCTACAAAATAACATACAAAAACACGGGTAAGCTTACAATGCTTAGTAAGTTCGTAACACAT
TAAACTTACAGAATAACCAATTCGATTATAAAAAGGAGTAATGAAACAACTCCGTGATTTCGCGA
ATAGAGTATCAGATTGATCTCTTTAGGTCTTTCAGAATTTTAGCTCATACGAGCACAAAAAGAGA
TTAAATAGTATATGATGTGCTCACACAAGCTGTTAAGAAATTGCAACATATGTAGGGTCTTAGCC
ATCGGAGGGTCCATATTTGTTACTCAC
Found at i:18905207 original size:27 final size:27
Alignment explanation
Indices: 18905177--18905230 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
18905167 AAATATCTTG
18905177 CCTCAAGTCTAGATCATCAAGAACGCA
1 CCTCAAGTCTAGATCATCAAGAACGCA
18905204 CCTCAAGTCTAGATCATCAAGAACGCA
1 CCTCAAGTCTAGATCATCAAGAACGCA
18905231 TACTCTGTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.30, G:0.15, T:0.19
Consensus pattern (27 bp):
CCTCAAGTCTAGATCATCAAGAACGCA
Done.