Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold107
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: 2327068
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 15 of 15
Found at i:2239448 original size:157 final size:158
Alignment explanation
Indices: 2238966--2239454 Score: 542
Period size: 157 Copynumber: 3.1 Consensus size: 158
2238956 AATATAAAAG
* * * * *
2238966 ATTAAAA-TTATCTCAGAAATATTAATTCAGTTCAATTTTATTTTTTTTTAAAAATACCATTTTT
1 ATTAAAATTTATC-CCGAAATATTAATTCAATTTAATTTTATTTATTTTTAAAAATACCATTTTA
* * *
2239030 TACCCTAATGGAAGCCCGAAAGAAAACAAAAAGTTTTTTTTTGAAATCTTTTATACCCTTACGGA
65 TACCCTAATGGAAGCCCGAAAGGATACAAAAA---TCTTTTTGAAATCTTTTATACCC-TACGGA
* *
2239095 TGCCCATAGGAATATAAAAGCTTAGAAAAAATAGA
126 TGCCTATAGGAATATAAAAGATTAGAAAAAAT--A
* ** * * *
2239130 CATTAGAATTTATCCCGATAATACCAATTTAATTTAATTTAATTTATTTTTAAAAATACCATTTC
1 -ATTAAAATTTATCCCGA-AATATTAATTCAATTTAATTTTATTTATTTTTAAAAATACCATTTT
* * *
2239195 ATACCCTAATAGAAGCCCGAAAGGATACAAAAATGTTTTTGAAATCTTTTATACCTCCACGGATG
64 ATACCCTAATGGAAGCCCGAAAGGATACAAAAATCTTTTTGAAATCTTTTATACC-CTACGGATG
* *
2239260 CCTATAGGAATATAAAATAATAG--AAAA-A
128 CCTATAGGAATATAAAAGATTAGAAAAAATA
* ** *
2239288 ATTAAAATTTAAT-CTGAAAGTATTAATTCAATTTAATTTTATTTATTTTCGAAAATACTATTTT
1 ATTAAAATTT-ATCCCGAAA-TATTAATTCAATTTAATTTTATTTATTTTTAAAAATACCATTTT
* * * * *
2239352 GTACCTTAATGGAAGCTCGAAAGGATACGAAAA-CATTTTGAAATCTTTTATACCCTACGG-TGC
64 ATACCCTAATGGAAGCCCGAAAGGATACAAAAATCTTTTTGAAATCTTTTATACCCTACGGATGC
*
2239415 CTATAGGAATGTAAAAGATTAGAAAAAATA
129 CTATAGGAATATAAAAGATTAGAAAAAATA
2239445 ATTAAAATTT
1 ATTAAAATTT
2239455 GATTTCATCA
Statistics
Matches: 275, Mismatches: 41, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
154 22 0.08
155 5 0.02
156 25 0.09
157 87 0.32
158 3 0.01
161 4 0.01
163 47 0.17
164 1 0.00
165 9 0.03
166 72 0.26
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.36
Consensus pattern (158 bp):
ATTAAAATTTATCCCGAAATATTAATTCAATTTAATTTTATTTATTTTTAAAAATACCATTTTAT
ACCCTAATGGAAGCCCGAAAGGATACAAAAATCTTTTTGAAATCTTTTATACCCTACGGATGCCT
ATAGGAATATAAAAGATTAGAAAAAATA
Found at i:2241193 original size:20 final size:20
Alignment explanation
Indices: 2241162--2241218 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
2241152 GTCAAAACCC
*
2241162 TGAAAAGTATCGATACACAT
1 TGAAATGTATCGATACACAT
* *
2241182 TTAAATGTATCGATACAGAT
1 TGAAATGTATCGATACACAT
* *
2241202 TGCATTGTATCGATACA
1 TGAAATGTATCGATACA
2241219 TTGTATCGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
TGAAATGTATCGATACACAT
Found at i:2241222 original size:13 final size:13
Alignment explanation
Indices: 2241204--2241232 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2241194 ATACAGATTG
2241204 CATTGTATCGATA
1 CATTGTATCGATA
2241217 CATTGTATCGATA
1 CATTGTATCGATA
2241230 CAT
1 CAT
2241233 GACCAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:2241264 original size:21 final size:20
Alignment explanation
Indices: 2241220--2241272 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2241210 ATCGATACAT
**
2241220 TGTATCGATACATGACCAAA
1 TGTATCGATACATGAAAAAA
*
2241240 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAA-AA
*
2241261 TGTATCGGTACA
1 TGTATCGATACA
2241273 AGTCATTGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Found at i:2241342 original size:13 final size:13
Alignment explanation
Indices: 2241324--2241349 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2241314 ACACACAGTA
2241324 TGTATCGATACAT
1 TGTATCGATACAT
2241337 TGTATCGATACAT
1 TGTATCGATACAT
2241350 CATAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2241365 original size:33 final size:32
Alignment explanation
Indices: 2241304--2241371 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
2241294 GTAGCTAAAC
**
2241304 TTGTATCGATACACACAGTATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
2241336 TTGTATCGATACATCATAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
2241369 TTG
1 TTG
2241372 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:2242972 original size:9 final size:9
Alignment explanation
Indices: 2242958--2242989 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
2242948 TATCAAGGAC
2242958 GATGAAGAT
1 GATGAAGAT
2242967 GATGAAGAT
1 GATGAAGAT
*
2242976 GATGACGAT
1 GATGAAGAT
2242985 GATGA
1 GATGA
2242990 TGACTCAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.41, C:0.03, G:0.34, T:0.22
Consensus pattern (9 bp):
GATGAAGAT
Found at i:2248021 original size:21 final size:20
Alignment explanation
Indices: 2247972--2248010 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2247962 CTCCTAGGCA
*
2247972 GCACCCACCAGGTCGCGACCG
1 GCACCC-CCAGGTCGCAACCG
2247993 GCACCCCCAGGTCGCAAC
1 GCACCCCCAGGTCGCAAC
2248011 AGGGCAGCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.21, C:0.49, G:0.26, T:0.05
Consensus pattern (20 bp):
GCACCCCCAGGTCGCAACCG
Found at i:2248401 original size:158 final size:159
Alignment explanation
Indices: 2248034--2248429 Score: 459
Period size: 164 Copynumber: 2.5 Consensus size: 159
2248024 CACTCTGTAT
* * * *
2248034 TTTAGAAAATTAAAAAACAAGAAAAATCCTTCCGAAATAATTTACGAAGTA-AAAAC-TCTGTAT
1 TTTA-AAAATTAAAAAACAAGAAAAATCCCTCCAAAAAAATTTACGGAGTAGAAAACTTC-GTAT
* * * *
2248097 TT--TAGAAAAAAATTTCAAGGAAAAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAAAC
64 TTAAAAAAAAAAAATTTCAAGGAAAAAAA-T-AAAATTTATGAAAATGAATGAATCTTTGAAAAC
2248160 TGAATTAAGATGAAATAAATAATAATATTTGATAA
127 TGAATTAAGATGAAATAAATAATAATATTTG--AA
* * **
2248195 CTTTTAAAAATTAAAAATCAAGAAAAATTCCTTTAAAAAAA-TTACGGAGTAGAAAACTTCGTAT
1 --TTTAAAAATTAAAAAACAAGAAAAATCCCTCCAAAAAAATTTACGGAGTAGAAAACTTCGTAT
*
2248259 TTCAAAAAAAAGAAAATTTCAAGGAAAAATAA-AAAATTTATGAAAATGAATGAATCTTTGAGAA
64 TT-AAAAAAAA-AAAATTTCAAGGAAAAA-AATAAAATTTATGAAAATGAATGAATCTTTGAAAA
* *
2248323 CTGATTTAATATGAAATAAATAATAATATTTG-A
126 CTGAATTAAGATGAAATAAATAATAATATTTGAA
* *
2248356 -TTAAAAATTAAAAAACAAG-AAAATCCCTCCAAAAAAATTTACGGAGTAGAAAACTCCATATTT
1 TTTAAAAATTAAAAAACAAGAAAAATCCCTCCAAAAAAATTTACGGAGTAGAAAACTTCGTATTT
**
2248419 TGAAAAAAAAA
66 AAAAAAAAAAA
2248430 GGAAAAAATA
Statistics
Matches: 202, Mismatches: 23, Indels: 23
0.81 0.09 0.09
Matches are distributed among these distances:
156 3 0.01
157 21 0.10
158 41 0.20
161 10 0.05
162 39 0.19
163 6 0.03
164 59 0.29
165 4 0.02
166 17 0.08
167 2 0.01
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.28
Consensus pattern (159 bp):
TTTAAAAATTAAAAAACAAGAAAAATCCCTCCAAAAAAATTTACGGAGTAGAAAACTTCGTATTT
AAAAAAAAAAAATTTCAAGGAAAAAAATAAAATTTATGAAAATGAATGAATCTTTGAAAACTGAA
TTAAGATGAAATAAATAATAATATTTGAA
Found at i:2250041 original size:84 final size:83
Alignment explanation
Indices: 2249897--2250342 Score: 399
Period size: 84 Copynumber: 5.3 Consensus size: 83
2249887 TATTAGGGAT
* * ** * *
2249897 TGAGCTGATAGGTAAACAAGGGATGAGGGGTTGATTAGGGACTAAGCCAACAGGTTACCAAGGGA
1 TGAGCTGACAGGTAAACAAGGGATGAAGGGTTGATCGGGGACTAAGCCAATAGGTCACCAAGGGA
*
2249962 TAAGGGTTTACCAAGGAT
66 TAAGGGTTTACCAAGGAC
* * * * * *
2249980 TGAGCCGACAGGTAAATAAAGAGATGAAGGGTTGACCGGGGACTAAGCTAATAGGTCACCAAGGA
1 TGAGCTGACAGGTAAA-CAAGGGATGAAGGGTTGATCGGGGACTAAGCCAATAGGTCACCAAGGG
* * *
2250045 AAAAGAGGTTTATCGAGGAC
65 ATAAG-GGTTTACCAAGGAC
* * * * ** *
2250065 TGAGTTGACAGGTAAACAAAGGATGAAGGGTTGATCGGGGACTAAGCCGACAGCCCACCATGGGA
1 TGAGCTGACAGGTAAACAAGGGATGAAGGGTTGATCGGGGACTAAGCCAATAGGTCACCAAGGGA
*
2250130 TAAGGGTTTACCATGGAC
66 TAAGGGTTTACCAAGGAC
* ** * * * * * * * * * *
2250148 TAAGCCAATATGTAAACAAGGGATGGAGAGTTTAACTAGAGACTGAGCTAATAGGTCACCATA-G
1 TGAGCTGACAGGTAAACAAGGGATGAAGGGTTGATC-GGGGACTAAGCCAATAGGTCACCA-AGG
* * * *
2250212 GATATGGGTTTATCGAGGAT
64 GATAAGGGTTTACCAAGGAC
* * * *
2250232 TGAGCTGATAGGTAAACAAGGGATAAAGGGTTAATCGGGGACTAAGCCAATAGGTCACCCAGGGA
1 TGAGCTGACAGGTAAACAAGGGATGAAGGGTTGATCGGGGACTAAGCCAATAGGTCACCAAGGGA
* * *
2250297 TAAAGGTTTACTAGGGAC
66 TAAGGGTTTACCAAGGAC
* *
2250315 TAAGCTGACAGGTAAATAAGGGATGAAG
1 TGAGCTGACAGGTAAACAAGGGATGAAG
2250343 AGTTTGGAGT
Statistics
Matches: 275, Mismatches: 83, Indels: 10
0.75 0.23 0.03
Matches are distributed among these distances:
82 1 0.00
83 107 0.39
84 142 0.52
85 25 0.09
ACGTcount: A:0.35, C:0.14, G:0.31, T:0.20
Consensus pattern (83 bp):
TGAGCTGACAGGTAAACAAGGGATGAAGGGTTGATCGGGGACTAAGCCAATAGGTCACCAAGGGA
TAAGGGTTTACCAAGGAC
Found at i:2250098 original size:168 final size:167
Alignment explanation
Indices: 2249897--2250344 Score: 522
Period size: 167 Copynumber: 2.7 Consensus size: 167
2249887 TATTAGGGAT
* ** *
2249897 TGAGCTGATAGGTAAACAAGGGATGAGGGGTTGATTAGGGACTAAGCCAACAGGTTACCAAGGGA
1 TGAGCTGATAGGTAAACAAGGGATGAAGGGTTGATCGGGGACTAAGCCAACAGGTCACCAAGGGA
* * * * * *
2249962 TAAGGGTTTACCAAGGATTGAGCCGACAGGTAAATAAAGAGATGAAG-GGTTGACCGGGGACTAA
66 TAAGGGTTTACCAAGGACTAAGCCGACAGGTAAAT-AAGGGATGAAGAGGTTAACCAGAGACTAA
2250026 GCTAATAGGTCACCA-AGGAAAAAGAGGTTTATCGAGGAC
130 GCTAATAGGTCACCATAGG-AAAAG-GGTTTATCGAGGAC
* * * * ** *
2250065 TGAGTTGACAGGTAAACAAAGGATGAAGGGTTGATCGGGGACTAAGCCGACAGCCCACCATGGGA
1 TGAGCTGATAGGTAAACAAGGGATGAAGGGTTGATCGGGGACTAAGCCAACAGGTCACCAAGGGA
* * * * * * * * *
2250130 TAAGGGTTTACCATGGACTAAGCCAATATGTAAACAAGGGATGGAGAGTTTAACTAGAGACTGAG
66 TAAGGGTTTACCAAGGACTAAGCCGACAGGTAAATAAGGGATGAAGAGGTTAACCAGAGACTAAG
* * *
2250195 CTAATAGGTCACCATAGGATATGGGTTTATCGAGGAT
131 CTAATAGGTCACCATAGGAAAAGGGTTTATCGAGGAC
* * * *
2250232 TGAGCTGATAGGTAAACAAGGGATAAAGGGTTAATCGGGGACTAAGCCAATAGGTCACCCAGGGA
1 TGAGCTGATAGGTAAACAAGGGATGAAGGGTTGATCGGGGACTAAGCCAACAGGTCACCAAGGGA
* * * *
2250297 TAAAGGTTTACTAGGGACTAAGCTGACAGGTAAATAAGGGATGAAGAG
66 TAAGGGTTTACCAAGGACTAAGCCGACAGGTAAATAAGGGATGAAGAG
2250345 TTTGGAGTGA
Statistics
Matches: 229, Mismatches: 49, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
167 115 0.50
168 111 0.48
169 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.31, T:0.20
Consensus pattern (167 bp):
TGAGCTGATAGGTAAACAAGGGATGAAGGGTTGATCGGGGACTAAGCCAACAGGTCACCAAGGGA
TAAGGGTTTACCAAGGACTAAGCCGACAGGTAAATAAGGGATGAAGAGGTTAACCAGAGACTAAG
CTAATAGGTCACCATAGGAAAAGGGTTTATCGAGGAC
Found at i:2250117 original size:42 final size:42
Alignment explanation
Indices: 2249809--2250117 Score: 146
Period size: 41 Copynumber: 7.4 Consensus size: 42
2249799 TGGGTTTACT
* *
2249809 AGGGACTAAGCCGACAGGTAAACAATA-GATGAA-AGTTGACC
1 AGGGACTAAGCCGACAGGTAAACAA-AGGATGAAGGGTTGATC
* * * * * * * * *
2249850 CGAGACTGAA-CTGACAGGTCAATAAATGATCAA-GGTTTATT
1 AGGGACT-AAGCCGACAGGTAAACAAAGGATGAAGGGTTGATC
* * * * * * *
2249891 AGGGATTGAGCTGATAGGTAAACAAGGGATGAGGGGTTGATT
1 AGGGACTAAGCCGACAGGTAAACAAAGGATGAAGGGTTGATC
* * * * * *
2249933 AGGGACTAAGCCAACAGGTTACCAAGGGAT-AAGGGTTTACC
1 AGGGACTAAGCCGACAGGTAAACAAAGGATGAAGGGTTGATC
* * * * *
2249974 AAGGATTGAGCCGACAGGTAAATAAAGAGATGAAGGGTTGACC
1 AGGGACTAAGCCGACAGGTAAACAAAG-GATGAAGGGTTGATC
* ** * * * ** *
2250017 GGGGACTAAGCTAATAGGT-CACCAAGGAAAAAGAGGTTTATC
1 AGGGACTAAGCCGACAGGTAAACAAAGGATGAAG-GGTTGATC
* **
2250059 -GAGGACTGAGTTGACAGGTAAACAAAGGATGAAGGGTTGATC
1 AG-GGACTAAGCCGACAGGTAAACAAAGGATGAAGGGTTGATC
*
2250101 GGGGACTAAGCCGACAG
1 AGGGACTAAGCCGACAG
2250118 CCCACCATGG
Statistics
Matches: 190, Mismatches: 68, Indels: 19
0.69 0.25 0.07
Matches are distributed among these distances:
40 2 0.01
41 78 0.41
42 77 0.41
43 33 0.17
ACGTcount: A:0.36, C:0.14, G:0.31, T:0.19
Consensus pattern (42 bp):
AGGGACTAAGCCGACAGGTAAACAAAGGATGAAGGGTTGATC
Found at i:2250278 original size:167 final size:167
Alignment explanation
Indices: 2249639--2250347 Score: 521
Period size: 167 Copynumber: 4.2 Consensus size: 167
2249629 AAAAAGTTCT
* * * * ** * * *
2249639 CCAAGGACTGAGCCGACTGATAAACAATAGATGAAG-GTTTGACCAGGGACTAAG-TCGATAGGT
1 CCAAGGACTAAGCCGACAGGTAAAAAAGGGATGAAGAGTTTAACCAGAGACTAAGCT-AATAGGT
* * * * *
2249702 CACCAAGAAAGAAAG-GGTTTATCGGGGATTGAGCTGACAGGTAAACAATGGATGGA-GGTTGA-
65 CACCAAGGAA-AAAGAGGTTTATCGAGGATTGAGCTGATAGGTAAACAAGGGATGAAGGGTTGAT
* * * * ** * *
2249764 CTAGAGATTGAGCTGATAGATCACCATAAGGG-TAATGGGTTTA
129 C-GGGGACTAAGCCAACAGGTCACC---AGGGATAA-GGGTTTA
* * * ** * * * *
2249807 CTAGGGACTAAGCCGACAGGTAAACAATAGATGAA-AG-TTGACCCGAGACTGAA-CTGACAGGT
1 CCAAGGACTAAGCCGACAGGTAAAAAAGGGATGAAGAGTTTAACCAGAGACT-AAGCTAATAGGT
** * ** * *
2249869 CAATAAATG-ATCA-AGGTTTAT-TAGGGATTGAGCTGATAGGTAAACAAGGGATGAGGGGTTGA
65 C-ACCAAGGAAAAAGAGGTTTATCGA-GGATTGAGCTGATAGGTAAACAAGGGATGAAGGGTTGA
** *
2249931 TTAGGGACTAAGCCAACAGGTTACCAAGGGATAAGGGTTTA
128 TCGGGGACTAAGCCAACAGGTCACC-AGGGATAAGGGTTTA
* * * * * * *
2249972 CCAAGGATTGAGCCGACAGGTAAATAAAGAGATGAAG-GGTTGACCGGGGACTAAGCTAATAGGT
1 CCAAGGACTAAGCCGACAGGTAAA-AAAGGGATGAAGAGTTTAACCAGAGACTAAGCTAATAGGT
* * * *
2250036 CACCAAGGAAAAAGAGGTTTATCGAGGACTGAGTTGACAGGTAAACAAAGGATGAAGGGTTGATC
65 CACCAAGGAAAAAGAGGTTTATCGAGGATTGAGCTGATAGGTAAACAAGGGATGAAGGGTTGATC
* **
2250101 GGGGACTAAGCCGACAGCCCACCATGGGATAAGGGTTTA
130 GGGGACTAAGCCAACAGGTCACCA-GGGATAAGGGTTTA
* * * * * * * *
2250140 CCATGGACTAAGCCAATATGTAAACAAGGGATGGAGAGTTTAACTAGAGACTGAGCTAATAGGTC
1 CCAAGGACTAAGCCGACAGGTAAAAAAGGGATGAAGAGTTTAACCAGAGACTAAGCTAATAGGTC
* * * *
2250205 ACCATAGG-ATATG-GGTTTATCGAGGATTGAGCTGATAGGTAAACAAGGGATAAAGGGTTAATC
66 ACCA-AGGAAAAAGAGGTTTATCGAGGATTGAGCTGATAGGTAAACAAGGGATGAAGGGTTGATC
* *
2250268 GGGGACTAAGCCAATAGGTCACCCAGGGATAAAGGTTTA
130 GGGGACTAAGCCAACAGGTCA-CCAGGGATAAGGGTTTA
* * * *
2250307 CTAGGGACTAAGCTGACAGGTAAATAAGGGATGAAGAGTTT
1 CCAAGGACTAAGCCGACAGGTAAAAAAGGGATGAAGAGTTT
2250348 GGAGTGAGGC
Statistics
Matches: 429, Mismatches: 92, Indels: 41
0.76 0.16 0.07
Matches are distributed among these distances:
165 32 0.07
166 54 0.13
167 178 0.41
168 161 0.38
169 4 0.01
ACGTcount: A:0.35, C:0.14, G:0.30, T:0.21
Consensus pattern (167 bp):
CCAAGGACTAAGCCGACAGGTAAAAAAGGGATGAAGAGTTTAACCAGAGACTAAGCTAATAGGTC
ACCAAGGAAAAAGAGGTTTATCGAGGATTGAGCTGATAGGTAAACAAGGGATGAAGGGTTGATCG
GGGACTAAGCCAACAGGTCACCAGGGATAAGGGTTTA
Found at i:2251664 original size:55 final size:54
Alignment explanation
Indices: 2251585--2251749 Score: 219
Period size: 55 Copynumber: 3.1 Consensus size: 54
2251575 TTTCATTCAA
* * * *
2251585 TTTTTTCTCTTTTTTGTGACTTGAATGCCCTTTCGGGTTTTCATCTAAGCTTTTT
1 TTTTTTCT-TTTTTTGTGACTTGAACGCCCTTTCAGGTTTTTATCCAAGCTTTTT
* *
2251640 TTTCTTTCTTTTTTTGTGACTTGAAGGCCCTTGCAGGTTTTTATCCAAGC-TTTT
1 TTT-TTTCTTTTTTTGTGACTTGAACGCCCTTTCAGGTTTTTATCCAAGCTTTTT
* *
2251694 TTTTTTC-TTTTTT-TGACTTGAACGCCGTTTCAGGTTTTTATCCAAGCTTCTT
1 TTTTTTCTTTTTTTGTGACTTGAACGCCCTTTCAGGTTTTTATCCAAGCTTTTT
2251746 TTTT
1 TTTT
2251750 ATGCATAGTA
Statistics
Matches: 99, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
51 31 0.31
52 13 0.13
53 4 0.04
54 7 0.07
55 39 0.39
56 5 0.05
ACGTcount: A:0.12, C:0.18, G:0.15, T:0.55
Consensus pattern (54 bp):
TTTTTTCTTTTTTTGTGACTTGAACGCCCTTTCAGGTTTTTATCCAAGCTTTTT
Found at i:2251728 original size:51 final size:52
Alignment explanation
Indices: 2251585--2251749 Score: 215
Period size: 51 Copynumber: 3.1 Consensus size: 52
2251575 TTTCATTCAA
* * * * *
2251585 TTTTTTCTCTTTTTTGTGACTTGAATGCCCTTTCGGGTTTTCATCTAAGCTTT
1 TTTTTTTTCTTTTTTGTGACTTGAACGCCCTTTCAGGTTTTTATCCAAGC-TT
* *
2251638 TTTTTCTTTCTTTTTTTGTGACTTGAAGGCCCTTGCAGGTTTTTATCCAAGCTT
1 TTTTT-TTTC-TTTTTTGTGACTTGAACGCCCTTTCAGGTTTTTATCCAAGCTT
*
2251692 TTTTTTTTCTTTTTT-TGACTTGAACGCCGTTTCAGGTTTTTATCCAAGCTT
1 TTTTTTTTCTTTTTTGTGACTTGAACGCCCTTTCAGGTTTTTATCCAAGCTT
*
2251743 CTTTTTT
1 TTTTTTT
2251750 ATGCATAGTA
Statistics
Matches: 100, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
51 39 0.39
52 6 0.06
53 9 0.09
54 10 0.10
55 36 0.36
ACGTcount: A:0.12, C:0.18, G:0.15, T:0.55
Consensus pattern (52 bp):
TTTTTTTTCTTTTTTGTGACTTGAACGCCCTTTCAGGTTTTTATCCAAGCTT
Found at i:2254474 original size:97 final size:96
Alignment explanation
Indices: 2254321--2254547 Score: 296
Period size: 97 Copynumber: 2.3 Consensus size: 96
2254311 AACAGGGTTA
* ** *
2254321 GAGTATCCCCTCGGAGGAATGGGGTTGGAG-CGTCTCCGACGATGATAATTTAAGCAAACTAAGA
1 GAGTATCCCCT-TGAGGAAT-GGGTTGGAGTATTCTCCGACGATGATAATTTAAGCAAAATAAGA
*
2254385 TTCAGATCTTGACATGTTTTAAAAACGAGATTG
64 TTCAGATCTTGACAAGTTTTAAAAACGAGATTG
*
2254418 GAGTATCCCCTTAGAGGAATGTGGTTGGAGTATTCT-TGACGATGATAATTTAAGCAAAATAAGA
1 GAGTATCCCCTT-GAGGAATG-GGTTGGAGTATTCTCCGACGATGATAATTTAAGCAAAATAAGA
* * * *
2254482 TTTAGATCTTGACAAGTTTTAAAAAGGGGGTTG
64 TTCAGATCTTGACAAGTTTTAAAAACGAGATTG
2254515 GAGTATCCCCTTGAAGGAATGGAGTTGGAGTAT
1 GAGTATCCCCTTG-AGGAATGG-GTTGGAGTAT
2254548 CCCTAATAAA
Statistics
Matches: 115, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
96 3 0.03
97 109 0.95
98 3 0.03
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (96 bp):
GAGTATCCCCTTGAGGAATGGGTTGGAGTATTCTCCGACGATGATAATTTAAGCAAAATAAGATT
CAGATCTTGACAAGTTTTAAAAACGAGATTG
Found at i:2261103 original size:18 final size:17
Alignment explanation
Indices: 2261072--2261105 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2261062 CACTAAACTT
*
2261072 AAAGATGATGAAGATGA
1 AAAGATGATAAAGATGA
2261089 AAAGAGTGATAAAGATG
1 AAAGA-TGATAAAGATG
2261106 CCAATATGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.00, G:0.29, T:0.18
Consensus pattern (17 bp):
AAAGATGATAAAGATGA
Found at i:2261177 original size:61 final size:60
Alignment explanation
Indices: 2261082--2261269 Score: 211
Period size: 61 Copynumber: 3.1 Consensus size: 60
2261072 AAAGATGATG
*
2261082 AAGATGAA-AAGAGTGATAAAGATGCCAATATGCTGATTCAGAGCTAACGATATTGGGTTCA
1 AAGAT-AAGAAGAATGATAAAGATGCCAATATGCTGATTCAGAGCTAACGATATTGGGTT-A
* * * * *
2261143 AAGATAAGAAGAATGATAAATATGCCAATATGCTGACTTAAG-GCCAATGATATTGAGCTTA
1 AAGATAAGAAGAATGATAAAGATGCCAATATGCTGA-TTCAGAGCTAACGATATTG-GGTTA
* * * *
2261204 AAGATAAGACGAATGATAAAGGTGCCAATATGCTAATTCA-AGGCTAGCGATATTGGGCTTA
1 AAGATAAGAAGAATGATAAAGATGCCAATATGCTGATTCAGA-GCTAACGATATTGGG-TTA
2261265 AAGAT
1 AAGAT
2261270 GATCTTCCAC
Statistics
Matches: 106, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
60 6 0.06
61 93 0.88
62 7 0.07
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (60 bp):
AAGATAAGAAGAATGATAAAGATGCCAATATGCTGATTCAGAGCTAACGATATTGGGTTA
Found at i:2262251 original size:24 final size:24
Alignment explanation
Indices: 2262219--2262267 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2262209 TAACAAGTTT
2262219 TCATAACTTATATTTCTTTAAAAC
1 TCATAACTTATATTTCTTTAAAAC
2262243 TCATAACTTATATTTCTTTAAAAC
1 TCATAACTTATATTTCTTTAAAAC
2262267 T
1 T
2262268 ATGTGTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (24 bp):
TCATAACTTATATTTCTTTAAAAC
Found at i:2262496 original size:13 final size:13
Alignment explanation
Indices: 2262478--2262502 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2262468 ATATTACTTA
2262478 GTATCGATACATT
1 GTATCGATACATT
2262491 GTATCGATACAT
1 GTATCGATACAT
2262503 GTTCTTTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:2262657 original size:52 final size:53
Alignment explanation
Indices: 2262567--2262676 Score: 150
Period size: 52 Copynumber: 2.1 Consensus size: 53
2262557 TACCCTAAGT
*
2262567 GAATTGTATCGATACATGGTAAAATTGTATCAATACATTAAGCCCAACGGCTA
1 GAATTGTATCGATACATGATAAAATTGTATCAATACATTAAGCCCAACGGCTA
* * * * * *
2262620 TAATTGTATCGATATATTATGAAA-TGTATCGATACATTGAGCCCAACGGCTA
1 GAATTGTATCGATACATGATAAAATTGTATCAATACATTAAGCCCAACGGCTA
2262672 GAATT
1 GAATT
2262677 TCAAATGATT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
52 30 0.61
53 19 0.39
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (53 bp):
GAATTGTATCGATACATGATAAAATTGTATCAATACATTAAGCCCAACGGCTA
Found at i:2263112 original size:35 final size:34
Alignment explanation
Indices: 2263066--2263132 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 34
2263056 CAAAGTGGTT
*
2263066 AAGAGATTCTATGTTAGCCTTTGTAAAAGATAGGG
1 AAGAGATTCTATCTTAGCCTTTG-AAAAGATAGGG
*
2263101 AAGAGGTTCTATCTTAGCCTTTGAAAAGATAG
1 AAGAGATTCTATCTTAGCCTTTGAAAAGATAG
2263133 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 9 0.30
35 21 0.70
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.31
Consensus pattern (34 bp):
AAGAGATTCTATCTTAGCCTTTGAAAAGATAGGG
Found at i:2264221 original size:3 final size:3
Alignment explanation
Indices: 2264213--2264266 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
2264203 AGTCAACCAT
* *
2264213 TGA TGA TGA TGAA T-A TGA TGA TGA TGG TGA TGA TGA TGA TAA TGA
1 TGA TGA TGA TG-A TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
2264258 TGA TGA TGA
1 TGA TGA TGA
2264267 GGTTGACTCG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.04
3 41 0.91
4 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:2267312 original size:22 final size:22
Alignment explanation
Indices: 2267282--2267325 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2267272 GCTTTCAAAG
2267282 TTTTCAATTGAAAAAAGTTTTA
1 TTTTCAATTGAAAAAAGTTTTA
* *
2267304 TTTTTAATTGAAAAATGTTTTA
1 TTTTCAATTGAAAAAAGTTTTA
2267326 ATAGAGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (22 bp):
TTTTCAATTGAAAAAAGTTTTA
Found at i:2268114 original size:33 final size:32
Alignment explanation
Indices: 2268069--2268133 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
2268059 TACACACCCA
*
2268069 AATGTATCGATACAT-TATGCTTTGTATCGATAC
1 AATGTATCGATACATGT-T-CATTGTATCGATAC
*
2268102 AATGTATTGATACATGTTCATTGTATCGATAC
1 AATGTATCGATACATGTTCATTGTATCGATAC
2268134 GTGGACAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 13 0.45
33 15 0.52
34 1 0.03
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (32 bp):
AATGTATCGATACATGTTCATTGTATCGATAC
Found at i:2268132 original size:19 final size:20
Alignment explanation
Indices: 2268100--2268156 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
2268090 TTGTATCGAT
* *
2268100 ACAA-TGTATTGATACATGT
1 ACAATTGTATCGATACATGG
* *
2268119 TC-ATTGTATCGATACGTGG
1 ACAATTGTATCGATACATGG
2268138 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
2268157 AAACTGGCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 1 0.03
19 14 0.47
20 15 0.50
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:2269858 original size:18 final size:18
Alignment explanation
Indices: 2269835--2269869 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2269825 AGTCACCCAT
2269835 TAATGATGATGAAGATGA
1 TAATGATGATGAAGATGA
*
2269853 TAATGATGATGATGATG
1 TAATGATGATGAAGATG
2269870 GTGATTCGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.31
Consensus pattern (18 bp):
TAATGATGATGAAGATGA
Found at i:2271766 original size:33 final size:34
Alignment explanation
Indices: 2271724--2271788 Score: 105
Period size: 33 Copynumber: 1.9 Consensus size: 34
2271714 CGAAGTGGTT
* *
2271724 AAGAGGTTCTATCTTAG-CTTTTATAAGATAGGG
1 AAGAGGTTCTATCTTAGCCTTTGAAAAGATAGGG
2271757 AAGAGGTTCTATCTTAGCCTTTGAAAAGATAG
1 AAGAGGTTCTATCTTAGCCTTTGAAAAGATAG
2271789 TAGTATAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 17 0.59
34 12 0.41
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (34 bp):
AAGAGGTTCTATCTTAGCCTTTGAAAAGATAGGG
Found at i:2286248 original size:19 final size:22
Alignment explanation
Indices: 2286224--2286270 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
2286214 ATGTTTTCGT
*
2286224 TAAAAAAT-AATTT-AA-TTAA
1 TAAAAAATGAATTTCAAGTCAA
2286243 TAAAAAATGAATTTCAAGTCAA
1 TAAAAAATGAATTTCAAGTCAA
2286265 TAAAAA
1 TAAAAA
2286271 TATCATTCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 5 0.21
21 2 0.08
22 9 0.38
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (22 bp):
TAAAAAATGAATTTCAAGTCAA
Found at i:2287002 original size:21 final size:22
Alignment explanation
Indices: 2286971--2287011 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2286961 ATTTAATTAA
*
2286971 ATTTATATTATTTTAATAATTT
1 ATTTATATTATTTAAATAATTT
2286993 ATTT-TATTATTTAAATAAT
1 ATTTATATTATTTAAATAAT
2287012 ATTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTATATTATTTAAATAATTT
Found at i:2287052 original size:22 final size:22
Alignment explanation
Indices: 2287026--2287098 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
2287016 AAATTTTAAA
2287026 AAATTTATTATTATATAAATAT
1 AAATTTATTATTATATAAATAT
* * **
2287048 AAATTTATAATTAAATTTATAT
1 AAATTTATTATTATATAAATAT
*
2287070 AAAATTTTTTATTAT-TAAATA-
1 -AAATTTATTATTATATAAATAT
2287091 ATAATTTA
1 A-AATTTA
2287099 AATCAAACAA
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
20 1 0.03
21 5 0.13
22 22 0.56
23 11 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATTTATTATTATATAAATAT
Found at i:2287174 original size:16 final size:17
Alignment explanation
Indices: 2287153--2287205 Score: 67
Period size: 16 Copynumber: 3.3 Consensus size: 17
2287143 TTTATAAAAA
2287153 ATAAAT-TATTTAATTT
1 ATAAATATATTTAATTT
*
2287169 ATAAATAAATTTAA-TT
1 ATAAATATATTTAATTT
*
2287185 ATAAATATATTAAATTT
1 ATAAATATATTTAATTT
2287202 -TAAA
1 ATAAA
2287206 ATTTTTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 24 0.75
17 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAAATATATTTAATTT
Found at i:2287614 original size:13 final size:14
Alignment explanation
Indices: 2287584--2287618 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
2287574 GAAGAAATTA
2287584 AAATATATAAAAAT
1 AAATATATAAAAAT
*
2287598 AAATATAT-AATAT
1 AAATATATAAAAAT
2287611 AAATATAT
1 AAATATAT
2287619 TTAAATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATATATAAAAAT
Found at i:2287688 original size:32 final size:32
Alignment explanation
Indices: 2287596--2287688 Score: 100
Period size: 32 Copynumber: 2.9 Consensus size: 32
2287586 ATATATAAAA
* *
2287596 ATAAATATATAATATAAATATATTTAAATTTAT
1 ATAAATATATAA-ATAAAAATATTAAAATTTAT
* *
2287629 TTAAA-ATA-AATTAATAAATTATTAAAATTTAT
1 ATAAATATATAAATAA-AAA-TATTAAAATTTAT
*
2287661 ATAAATATATAAATAAAAATATAAAAAT
1 ATAAATATATAAATAAAAATATTAAAAT
2287689 AATTTTTTTG
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
30 3 0.06
31 4 0.08
32 27 0.55
33 10 0.20
34 5 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (32 bp):
ATAAATATATAAATAAAAATATTAAAATTTAT
Found at i:2287778 original size:15 final size:15
Alignment explanation
Indices: 2287754--2287897 Score: 57
Period size: 15 Copynumber: 9.4 Consensus size: 15
2287744 AAATATTTAA
*
2287754 AATATAATATTATAT
1 AATATTATATTATAT
*
2287769 TATATTATATTATAT
1 AATATTATATTATAT
* *
2287784 AA-ATATATATTTTAA
1 AATAT-TATATTATAT
*
2287799 AAT-TTATATAATAT
1 AATATTATATTATAT
*
2287813 AA-ATTAATAATATATT
1 AATATT-ATATTATA-T
* *
2287829 AAAATTTATATAAATAT
1 AATA-TTATAT-TATAT
2287846 AATTATTA-ATTATGAT
1 AA-TATTATATTAT-AT
* *
2287862 -ATAATA-AATATAT
1 AATATTATATTATAT
* *
2287875 AAATATATAGATTATCT
1 -AATAT-TATATTATAT
2287892 AATATT
1 AATATT
2287898 TTTTAAGCAG
Statistics
Matches: 96, Mismatches: 19, Indels: 28
0.67 0.13 0.20
Matches are distributed among these distances:
13 2 0.02
14 21 0.22
15 38 0.40
16 14 0.15
17 15 0.16
18 6 0.06
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (15 bp):
AATATTATATTATAT
Found at i:2287806 original size:16 final size:16
Alignment explanation
Indices: 2287787--2287840 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
2287777 ATTATATAAA
2287787 TATATATTTTAAAATT
1 TATATATTTTAAAATT
* *
2287803 TATATAATAT-AAATT
1 TATATATTTTAAAATT
* *
2287818 AATAATATATTAAAATT
1 TAT-ATATTTTAAAATT
2287835 TATATA
1 TATATA
2287841 AATATAATTA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
15 7 0.24
16 15 0.52
17 7 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATATATTTTAAAATT
Found at i:2287827 original size:49 final size:45
Alignment explanation
Indices: 2287726--2287829 Score: 111
Period size: 45 Copynumber: 2.2 Consensus size: 45
2287716 AATAATATCA
*
2287726 AATATAATTATATAAATAAAATATTTAAAATATAATATTATATTAT
1 AATAT-ATTATATAAATAAAATATTTAAAATATAATATTAAATTAT
* * *
2287772 ATTATATTATATAAAT-ATATATTTTAAAATTTATATAATATAAATTAAT
1 AATATATTATATAAATAAAATA-TTTAAAATATA-AT-AT-TAAATT-AT
2287821 AATATATTA
1 AATATATTA
2287830 AAATTTATAT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
44 4 0.08
45 21 0.44
46 6 0.12
47 2 0.04
48 5 0.10
49 10 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (45 bp):
AATATATTATATAAATAAAATATTTAAAATATAATATTAAATTAT
Found at i:2287836 original size:32 final size:32
Alignment explanation
Indices: 2287773--2287855 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 32
2287763 TTATATTATA
* *
2287773 TTATATTATATAAA-T-AT-ATATTTTAAAAT
1 TTATATAATATAAATTAATAATATATTAAAAT
2287802 TTATATAATATAAATTAATAATATATTAAAAT
1 TTATATAATATAAATTAATAATATATTAAAAT
*
2287834 TTATATAA-ATATAATTATTAAT
1 TTATATAATATA-AATTAATAAT
2287856 TATGATATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
29 13 0.28
30 1 0.02
31 5 0.11
32 28 0.60
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
TTATATAATATAAATTAATAATATATTAAAAT
Found at i:2287846 original size:87 final size:92
Alignment explanation
Indices: 2287711--2287883 Score: 220
Period size: 87 Copynumber: 1.9 Consensus size: 92
2287701 GTTGATATTT
*
2287711 AATTTAATAATATCAAATATAATTATATAAATAAAATATTTAAAATATAA-TATTATATTAT-AT
1 AATTTAATAATATCAAATATAATAATATAAATAAAATATTTAAAATATAATTATTA-ATTATGAT
*
2287774 -T-AT-ATTATATAAATATATATTTTAA
65 ATAATAAATATATAAATATATATTTTAA
*
2287799 AATTTATATAATAT-AAAT-TAATAATAT-ATTAAAAT-TTATATAAATATAATTATTAATTATG
1 AATTTA-ATAATATCAAATATAATAATATAAATAAAATATT-TA-AAATATAATTATTAATTATG
2287860 ATATAATAAATATATAAATATATA
63 ATATAATAAATATATAAATATATA
2287884 GATTATCTAA
Statistics
Matches: 74, Mismatches: 3, Indels: 13
0.82 0.03 0.14
Matches are distributed among these distances:
85 2 0.03
86 9 0.12
87 21 0.28
88 17 0.23
89 8 0.11
90 2 0.03
91 15 0.20
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.45
Consensus pattern (92 bp):
AATTTAATAATATCAAATATAATAATATAAATAAAATATTTAAAATATAATTATTAATTATGATA
TAATAAATATATAAATATATATTTTAA
Found at i:2287864 original size:56 final size:53
Alignment explanation
Indices: 2287754--2287882 Score: 133
Period size: 56 Copynumber: 2.4 Consensus size: 53
2287744 AAATATTTAA
* *
2287754 AATATAATATTATATTATATTATATTATATAAATATATATTTTAAAATTTATAT
1 AATATAATATTATAATATATTAAATTATATAAATATATATTTT-AAATTTATAT
2287808 AATATAA-ATTAATAATATATTAAAATTTATATAAATATA-ATTATT-AATTATGATAT
1 AATATAATATT-ATAATATATT-AAA-TTATATAAATATATATT-TTAAATT-T-ATAT
2287864 AATA-AATA-TATAAATATAT
1 AATATAATATTAT-AATATAT
2287883 AGATTATCTA
Statistics
Matches: 65, Mismatches: 2, Indels: 15
0.79 0.02 0.18
Matches are distributed among these distances:
53 3 0.05
54 22 0.34
55 16 0.25
56 24 0.37
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.47
Consensus pattern (53 bp):
AATATAATATTATAATATATTAAATTATATAAATATATATTTTAAATTTATAT
Found at i:2288449 original size:16 final size:16
Alignment explanation
Indices: 2288430--2288461 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2288420 ATATATTACA
2288430 ATATGTATATATATAT
1 ATATGTATATATATAT
*
2288446 ATATGTATGTATATAT
1 ATATGTATATATATAT
2288462 GTCAATGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (16 bp):
ATATGTATATATATAT
Found at i:2290488 original size:22 final size:22
Alignment explanation
Indices: 2290463--2290512 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
2290453 ATATTAAAAA
*
2290463 TAAAATATTTTTATAGT-ATTT
1 TAAAATATTTTTATACTAATTT
* *
2290484 TTAAATTTTTTTATACTAATTT
1 TAAAATATTTTTATACTAATTT
*
2290506 AAAAATA
1 TAAAATA
2290513 AATTATTTAG
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
TAAAATATTTTTATACTAATTT
Found at i:2291503 original size:18 final size:19
Alignment explanation
Indices: 2291468--2291509 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
2291458 GTTGAATCAC
2291468 TATTTATAAAATAATAAAA
1 TATTTATAAAATAATAAAA
2291487 TATTT-TAAAA-AATTAAAA
1 TATTTATAAAATAA-TAAAA
2291505 T-TTTA
1 TATTTA
2291510 ATATTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.24
18 11 0.52
19 5 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TATTTATAAAATAATAAAA
Found at i:2291978 original size:8 final size:8
Alignment explanation
Indices: 2291965--2292008 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
2291955 TAGAAATAAA
2291965 AAATATTT
1 AAATATTT
2291973 AAATATTT
1 AAATATTT
2291981 --ATATTT
1 AAATATTT
2291987 AAAT-TTT
1 AAATATTT
2291994 AAATATATT
1 AAATAT-TT
2292003 AAATAT
1 AAATAT
2292009 CATAACTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 6 0.19
7 7 0.22
8 11 0.34
9 8 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
AAATATTT
Found at i:2291986 original size:14 final size:15
Alignment explanation
Indices: 2291966--2292008 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
2291956 AGAAATAAAA
2291966 AATATTTAAATATTT
1 AATATTTAAATATTT
2291981 -ATATTTAAAT-TTT
1 AATATTTAAATATTT
2291994 AAATATATTAAATAT
1 -AATAT-TTAAATAT
2292009 CATAACTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 3 0.12
14 10 0.42
15 4 0.17
16 6 0.25
17 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATATTTAAATATTT
Found at i:2292427 original size:3 final size:3
Alignment explanation
Indices: 2292421--2292448 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2292411 GAAAAAAATT
2292421 TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA T
2292449 AATAATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:2295223 original size:24 final size:25
Alignment explanation
Indices: 2295171--2295226 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 25
2295161 AAAGTTAGTT
2295171 AATAA-TTT-TATTAAATGTATAAA
1 AATAATTTTGTATTAAATGTATAAA
2295194 AATAATTTTGTATTAAATGTA-AAA
1 AATAATTTTGTATTAAATGTATAAA
*
2295218 ATTAATTTT
1 AATAATTTT
2295227 TTTATTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 5 0.17
24 14 0.47
25 11 0.37
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.46
Consensus pattern (25 bp):
AATAATTTTGTATTAAATGTATAAA
Found at i:2295232 original size:25 final size:25
Alignment explanation
Indices: 2295176--2295228 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
2295166 TAGTTAATAA
2295176 TTTTATTAAATGTATAAAAATAATT
1 TTTTATTAAATGTATAAAAATAATT
* *
2295201 TTGTATTAAATGTA-AAAATTAATT
1 TTTTATTAAATGTATAAAAATAATT
2295225 TTTT
1 TTTT
2295229 TATTTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (25 bp):
TTTTATTAAATGTATAAAAATAATT
Found at i:2296471 original size:28 final size:27
Alignment explanation
Indices: 2296431--2296501 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
2296421 AAACAAGCCT
* *
2296431 CCATATTTAACAAATACAAAGGA-AACCA
1 CCATTTTTAACAAACACAAA--ATAACCA
*
2296459 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTAACAAACACAAAATAACCA
*
2296486 CCATTTTTTACAAACA
1 CCATTTTTAACAAACA
2296502 AATGGGTGGC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 17 0.45
ACGTcount: A:0.48, C:0.24, G:0.04, T:0.24
Consensus pattern (27 bp):
CCATTTTTAACAAACACAAAATAACCA
Found at i:2301056 original size:27 final size:28
Alignment explanation
Indices: 2300996--2301066 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 28
2300986 AAACAAGCCT
* * *
2300996 CCATATTTGACAAATACAAAAAAAACTA
1 CCATTTTTGACAAACACAAAAAAAACCA
*
2301024 CCATTTTTGACAAACAC-AAAATAACCA
1 CCATTTTTGACAAACACAAAAAAAACCA
*
2301051 CTATTTTTGACAAACA
1 CCATTTTTGACAAACA
2301067 AATGTGTGGC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.49, C:0.21, G:0.04, T:0.25
Consensus pattern (28 bp):
CCATTTTTGACAAACACAAAAAAAACCA
Found at i:2301300 original size:14 final size:14
Alignment explanation
Indices: 2301283--2301339 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
2301273 TTATTATTTT
2301283 TATAAAAAATTAAA
1 TATAAAAAATTAAA
2301297 TATATAAAAA-TAAA
1 TATA-AAAAATTAAA
* **
2301311 -AT-AATAATTTTA
1 TATAAAAAATTAAA
2301323 TATAAAAAATTAAA
1 TATAAAAAATTAAA
2301337 TAT
1 TAT
2301340 TTAAAGATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
11 4 0.12
12 2 0.06
13 4 0.12
14 18 0.55
15 5 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TATAAAAAATTAAA
Found at i:2301324 original size:22 final size:22
Alignment explanation
Indices: 2301299--2301362 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 22
2301289 AAATTAAATA
2301299 TATAAAAATAAAATAATAATTT
1 TATAAAAATAAAATAATAATTT
* * *
2301321 TAT-ATAA-AAAATTA-AATAT
1 TATAAAAATAAAATAATAATTT
*
2301340 T-TAAAGATAAAATAATAATTT
1 TATAAAAATAAAATAATAATTT
2301361 TA
1 TA
2301363 AATTGCGAGA
Statistics
Matches: 31, Mismatches: 7, Indels: 8
0.67 0.15 0.17
Matches are distributed among these distances:
18 1 0.03
19 7 0.23
20 12 0.39
21 8 0.26
22 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
TATAAAAATAAAATAATAATTT
Found at i:2301333 original size:40 final size:40
Alignment explanation
Indices: 2301278--2301362 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 40
2301268 TTATTTTATT
2301278 ATTTT-TATAAAAAATTAAATATATAAAAATAAAATAATA
1 ATTTTATATAAAAAATTAAATATATAAAAATAAAATAATA
* *
2301317 ATTTTATATAAAAAATTAAATATTTAAAGATAAAATAATA
1 ATTTTATATAAAAAATTAAATATATAAAAATAAAATAATA
2301357 ATTTTA
1 ATTTTA
2301363 AATTGCGAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
39 5 0.12
40 38 0.88
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (40 bp):
ATTTTATATAAAAAATTAAATATATAAAAATAAAATAATA
Found at i:2304107 original size:3 final size:3
Alignment explanation
Indices: 2304099--2304147 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
2304089 ATTTTAATAG
2304099 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2304147 T
1 T
2304148 CTTGAGGTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2307520 original size:16 final size:16
Alignment explanation
Indices: 2307495--2307531 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2307485 TTTTTCTTAT
2307495 TAAA-TTAAAT-TAAA
1 TAAATTTAAATCTAAA
2307509 TCAAATTTAAATCTAAA
1 T-AAATTTAAATCTAAA
2307526 TAAATT
1 TAAATT
2307532 AATTAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.05
15 3 0.15
16 11 0.55
17 5 0.25
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATTTAAATCTAAA
Found at i:2307542 original size:26 final size:28
Alignment explanation
Indices: 2307495--2307547 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
2307485 TTTTTCTTAT
2307495 TAAATTAAATTAAATCAAA-TTTAAATC
1 TAAATTAAATTAAATCAAATTTTAAATC
*
2307522 TAAA-TAAATT-AATTAATATTTTAAAT
1 TAAATTAAATTAAATCAA-ATTTTAAAT
2307548 TTAAGTCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 5 0.22
26 7 0.30
27 11 0.48
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (28 bp):
TAAATTAAATTAAATCAAATTTTAAATC
Found at i:2308396 original size:2 final size:2
Alignment explanation
Indices: 2308389--2308431 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
2308379 TAAGTGAATG
* * * *
2308389 TA TA TA TA CA AA TG TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2308431 T
1 T
2308432 GTTGGAGCAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2314314 original size:39 final size:39
Alignment explanation
Indices: 2314268--2314345 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
2314258 CAAATTAATC
2314268 AATAAAGTTAGAATAGAATATTTATCTCAAATTAAAAAT
1 AATAAAGTTAGAATAGAATATTTATCTCAAATTAAAAAT
2314307 AATAAAGTTAGAATAGAATATTTATCTCAAATTAAAAAT
1 AATAAAGTTAGAATAGAATATTTATCTCAAATTAAAAAT
2314346 CAAACTTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (39 bp):
AATAAAGTTAGAATAGAATATTTATCTCAAATTAAAAAT
Found at i:2316070 original size:15 final size:16
Alignment explanation
Indices: 2316041--2316084 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
2316031 CATATTTTTA
* *
2316041 TAATTTTTATATAATT
1 TAATATTTATTTAATT
2316057 T-ATATTTATTTAATT
1 TAATATTTATTTAATT
2316072 TAATATTATATTT
1 TAATATT-TATTT
2316085 TTATATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 13 0.54
16 6 0.25
17 5 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TAATATTTATTTAATT
Found at i:2316289 original size:9 final size:9
Alignment explanation
Indices: 2316275--2316299 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2316265 TAAATTAAAC
2316275 ATATAAATT
1 ATATAAATT
2316284 ATATAAATT
1 ATATAAATT
2316293 ATATAAA
1 ATATAAA
2316300 AAATATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
ATATAAATT
Found at i:2316318 original size:11 final size:10
Alignment explanation
Indices: 2316275--2316320 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
2316265 TAAATTAAAC
2316275 ATAT-AAATT
1 ATATAAAATT
2316284 ATAT-AAATT
1 ATATAAAATT
*
2316293 ATATAAAAAAT
1 ATAT-AAAATT
2316304 ATATAAAATT
1 ATATAAAATT
2316314 AATATAA
1 -ATATAA
2316321 TTTTACAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 13 0.41
10 5 0.16
11 14 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATATAAAATT
Found at i:2316346 original size:2 final size:2
Alignment explanation
Indices: 2316339--2316372 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2316329 ATATAAGTGA
2316339 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2316373 GTTGAAGCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2316914 original size:18 final size:18
Alignment explanation
Indices: 2316893--2316941 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
2316883 AATTTTAAAA
2316893 TATATATTTATATTTTAT
1 TATATATTTATATTTTAT
*
2316911 TATA-AATTATTATTTTAT
1 TATATATTTA-TATTTTAT
*
2316929 T-TAT-TTAATATTT
1 TATATATTTATATTT
2316942 GTATAAGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
16 5 0.19
17 8 0.31
18 13 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TATATATTTATATTTTAT
Found at i:2316915 original size:32 final size:30
Alignment explanation
Indices: 2316831--2316918 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 30
2316821 GAATTATTCC
*
2316831 ATATAT-TTTATATTTATATAAATTTTAAT
1 ATATATATTTATATTTATATAAATTTTAAA
* *
2316860 GTATTAATAAATTATA-TTATATAAATTTTAAA
1 ATA-T-AT-ATTTATATTTATATAAATTTTAAA
2316892 ATATATATTTATATTTTATTATAAATT
1 ATATATATTTATA-TTTA-TATAAATT
2316919 ATTATTTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
29 8 0.17
30 3 0.06
31 6 0.13
32 25 0.53
33 5 0.11
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (30 bp):
ATATATATTTATATTTATATAAATTTTAAA
Found at i:2316917 original size:24 final size:23
Alignment explanation
Indices: 2316861--2316930 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 23
2316851 AATTTTAATG
**
2316861 TATTAATAAATTATATTATATAAAT
1 TATT-ATAAATTATATT-TATATTT
2316886 T-TTA-AAATATATATTTATATTT
1 TATTATAAAT-TATATTTATATTT
2316908 TATTATAAATTATTATTT-TATTT
1 TATTATAAATTA-TATTTATATTT
2316931 ATTTAATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
22 10 0.26
23 17 0.44
24 11 0.28
25 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTATAAATTATATTTATATTT
Found at i:2317583 original size:12 final size:12
Alignment explanation
Indices: 2317564--2317596 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2317554 AAATTTAATT
2317564 TAAT-ATTTTTA
1 TAATAATTTTTA
2317575 TAATAATTTTTA
1 TAATAATTTTTA
*
2317587 TTATAATTTT
1 TAATAATTTT
2317597 ACCATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TAATAATTTTTA
Found at i:2318979 original size:27 final size:27
Alignment explanation
Indices: 2318923--2318992 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
2318913 AACTTATAAA
2318923 AATATAAAT-TATTAATATATTAAAATT
1 AATATAAATATA-TAATATATTAAAATT
* *
2318950 AATATAAATATAAAATAT-TTTAAATAT
1 AATATAAATATATAATATATTAAAAT-T
*
2318977 AAT-TAATTATATAATA
1 AATATAAATATATAATA
2318993 CATATATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 17 0.46
27 18 0.49
28 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
AATATAAATATATAATATATTAAAATT
Found at i:2318992 original size:26 final size:27
Alignment explanation
Indices: 2318923--2318992 Score: 74
Period size: 26 Copynumber: 2.6 Consensus size: 27
2318913 AACTTATAAA
2318923 AATATAAATTAT-TAATATATTAAAATT
1 AATAT-AATTATATAATATATTAAAATT
* * *
2318950 AATATAAATATAAAATAT-TTTAAATAT
1 AATATAATTATATAATATATTAAAAT-T
2318977 AAT-TAATTATATAATA
1 AATATAATTATATAATA
2318993 CATATATATA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
26 22 0.61
27 14 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
AATATAATTATATAATATATTAAAATT
Found at i:2319380 original size:15 final size:15
Alignment explanation
Indices: 2319360--2319393 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2319350 TCTTTCTCTT
2319360 CTCCTTCTCCTCCTC
1 CTCCTTCTCCTCCTC
*
2319375 CTCCTTGTCCTCCTC
1 CTCCTTCTCCTCCTC
2319390 CTCC
1 CTCC
2319394 CCATTTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.59, G:0.03, T:0.38
Consensus pattern (15 bp):
CTCCTTCTCCTCCTC
Found at i:2320401 original size:39 final size:36
Alignment explanation
Indices: 2320324--2320417 Score: 91
Period size: 39 Copynumber: 2.4 Consensus size: 36
2320314 GTGTTAAAGT
*
2320324 AAATTTATAAAAAATATATATAATGTATTTTTAATA
1 AAATTTATAAAAAATATATATAATATATTTTTAATA
*
2320360 AAATTTAATAAAAATTATATATTTAATATAATTTTTTTAA-A
1 AAATTT-ATAAAAA--ATATATATAATAT-A--TTTTTAATA
*
2320401 AAAGTTATAATAAAATA
1 AAATTTATAA-AAAATA
2320418 ATTTTTAATG
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
36 6 0.12
37 7 0.15
39 14 0.29
40 5 0.10
41 9 0.19
42 7 0.15
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (36 bp):
AAATTTATAAAAAATATATATAATATATTTTTAATA
Found at i:2323745 original size:15 final size:17
Alignment explanation
Indices: 2323719--2323750 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2323709 GGCATTGTGA
2323719 GAAAAAGCCAAG-GCTT
1 GAAAAAGCCAAGCGCTT
2323735 GAAAAAG-CAAGCGCTT
1 GAAAAAGCCAAGCGCTT
2323751 TTTTCATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (17 bp):
GAAAAAGCCAAGCGCTT
Found at i:2325119 original size:20 final size:20
Alignment explanation
Indices: 2325094--2325131 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2325084 TATTTTTAAA
2325094 TTATCATT-ATAAATATTTTT
1 TTATCATTAAT-AATATTTTT
2325114 TTATCATTAATAATATTT
1 TTATCATTAATAATATTT
2325132 ATCTAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATCATTAATAATATTTTT
Found at i:2326075 original size:45 final size:47
Alignment explanation
Indices: 2325973--2326077 Score: 135
Period size: 45 Copynumber: 2.3 Consensus size: 47
2325963 AATTAACTAG
** ** *
2325973 ATGTATCGATACA-TTGAAAAATGTATCGATGTGAGTAAAAAATAGA
1 ATGTATCGATACATTTGAAAAATAAATCGATGACAGTAAAAAACAGA
*
2326019 ATGTATTGATACATTTGAAAAATAAATCGAT-ACA-TAAAAAACAGA
1 ATGTATCGATACATTTGAAAAATAAATCGATGACAGTAAAAAACAGA
2326064 ATGTATCGATACAT
1 ATGTATCGATACAT
2326078 GTACGTTCAT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
45 23 0.45
46 13 0.25
47 15 0.29
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.29
Consensus pattern (47 bp):
ATGTATCGATACATTTGAAAAATAAATCGATGACAGTAAAAAACAGA
Found at i:2326092 original size:20 final size:21
Alignment explanation
Indices: 2326067--2326117 Score: 95
Period size: 20 Copynumber: 2.5 Consensus size: 21
2326057 AAACAGAATG
2326067 TATCGATACATGTAC-GTTCA
1 TATCGATACATGTACTGTTCA
2326087 TATCGATACATGTACTGTTCA
1 TATCGATACATGTACTGTTCA
2326108 TATCGATACA
1 TATCGATACA
2326118 AATTGTGGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (21 bp):
TATCGATACATGTACTGTTCA
Found at i:2326964 original size:17 final size:18
Alignment explanation
Indices: 2326942--2326975 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2326932 ATATATTTTA
2326942 AAAATAAATA-AACTAAT
1 AAAATAAATATAACTAAT
*
2326959 AAAATATATATAACTAA
1 AAAATAAATATAACTAA
2326976 AATTTACATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATAAATATAACTAAT
Done.