Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 105 of 196
Found at i:31652929 original size:44 final size:45
Alignment explanation
Indices: 31652830--31653094 Score: 133
Period size: 44 Copynumber: 6.1 Consensus size: 45
31652820 AGGTCTTACC
* * * *
31652830 CCCTGAAGTTGCAGTGGGGCAGATCGAAGATGATCAATCTTATCT
1 CCCTGAAGTTACAGTGGAGCAGATCGAAGACGATCAATCCTATCT
* * *
31652875 CCCTGAAGTTACAGTGGATCAGATTGAAGCCGAT-AATCCTATCT
1 CCCTGAAGTTACAGTGGAGCAGATCGAAGACGATCAATCCTATCT
* * * ** *
31652919 CCCTGAAGTTATAGTGCAGCGGATTAAAGTA--AT-AGATCTTATCT
1 CCCTGAAGTTACAGTGGAGCAGATCGAAG-ACGATCA-ATCCTATCT
* * * * * * *
31652963 CTCTGAAGTTGCAGT--AG-AG-TGGATTG-C-ATCGAGTCTTATCC
1 CCCTGAAGTTACAGTGGAGCAGATCGA-AGACGATC-AATCCTATCT
* * * *
31653004 CCCTGAAGTTGCAGTGGGGCAGATCGAAGA-TA-CAAATCATATCT
1 CCCTGAAGTTACAGTGGAGCAGATCGAAGACGATC-AATCCTATCT
* * * * *
31653048 CCCTGAGGTTGCAGTGGAGCAGATTGAAGTCAAT-AATCCTATCT
1 CCCTGAAGTTACAGTGGAGCAGATCGAAGACGATCAATCCTATCT
31653092 CCC
1 CCC
31653095 CAACGTTGCG
Statistics
Matches: 169, Mismatches: 37, Indels: 29
0.72 0.16 0.12
Matches are distributed among these distances:
40 4 0.02
41 23 0.14
42 3 0.02
43 4 0.02
44 102 0.60
45 33 0.20
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (45 bp):
CCCTGAAGTTACAGTGGAGCAGATCGAAGACGATCAATCCTATCT
Found at i:31653059 original size:85 final size:87
Alignment explanation
Indices: 31652822--31653076 Score: 227
Period size: 85 Copynumber: 2.9 Consensus size: 87
31652812 AAGTAAGCAG
31652822 GTCTTA-CCCCCTGAAGTTGCAGTGGGGCAGATCGAAGATGATC-AATCTTATCTCCCTGAAGTT
1 GTCTTATCCCCCTGAAGTTGCAGTGGGGCAGATCGAAGAT-A-CAAATCTTATCTCCCTGAAGTT
* *
31652885 ACAGTGGATCAGATTGAAGCCGATA
64 GCAGTAGATCAGATTGAAGCCGA-A
* * * ** ** * ** *
31652910 ATCCTATCTCCCTGAAGTTATAGTGCAGCGGATTAAAG-TA-ATAGATCTTATCTCTCTGAAGTT
1 GTCTTATCCCCCTGAAGTTGCAGTGGGGCAGATCGAAGATACA-A-ATCTTATCTCCCTGAAGTT
* * *
31652973 GCAGTAGAGT-GGATTGCA-TCG-A
64 GCAGTAGA-TCAGATTGAAGCCGAA
* *
31652995 GTCTTATCCCCCTGAAGTTGCAGTGGGGCAGATCGAAGATACAAATCATATCTCCCTGAGGTTGC
1 GTCTTATCCCCCTGAAGTTGCAGTGGGGCAGATCGAAGATACAAATCTTATCTCCCTGAAGTTGC
* *
31653060 AGTGGAGCAGATTGAAG
66 AGTAGATCAGATTGAAG
31653077 TCAATAATCC
Statistics
Matches: 125, Mismatches: 33, Indels: 20
0.70 0.19 0.11
Matches are distributed among these distances:
85 58 0.46
86 3 0.02
87 5 0.04
88 35 0.28
89 24 0.19
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (87 bp):
GTCTTATCCCCCTGAAGTTGCAGTGGGGCAGATCGAAGATACAAATCTTATCTCCCTGAAGTTGC
AGTAGATCAGATTGAAGCCGAA
Found at i:31653103 original size:44 final size:44
Alignment explanation
Indices: 31653011--31653109 Score: 103
Period size: 44 Copynumber: 2.2 Consensus size: 44
31653001 TCCCCCTGAA
* ** *
31653011 GTTGCAGTGGGGCAGATCGAAGATACAAATCATATCTCCCTGAG
1 GTTGCAGTGGAGCAGATCGAAGATACAAATCATATCTCCCCAAC
* *
31653055 GTTGCAGTGGAGCAGATTGAAG-T-CAATAATCCTATCTCCCCAAC
1 GTTGCAGTGGAGCAGATCGAAGATAC-A-AATCATATCTCCCCAAC
*
31653099 GTTGCGGTGGA
1 GTTGCAGTGGA
31653110 AAGGATCGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
42 1 0.02
43 2 0.04
44 43 0.93
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.24
Consensus pattern (44 bp):
GTTGCAGTGGAGCAGATCGAAGATACAAATCATATCTCCCCAAC
Found at i:31653142 original size:173 final size:173
Alignment explanation
Indices: 31652822--31653152 Score: 402
Period size: 173 Copynumber: 1.9 Consensus size: 173
31652812 AAGTAAGCAG
*
31652822 GTCTTACCCCCTGAAGTTGCAGTGGGGCAGATCGAAGATGATCAATCTTATCTCCCTGAAGTTAC
1 GTCTTACCCCCTGAAGTTGCAGTGGGGCAGATCGAAGATGATCAATCATATCTCCCTGAAGTTAC
* * * * ** * * *
31652887 AGTGGATCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTATAGTGCAGCGGATTAAAGTAAT
66 AGTGGAGCAGATTGAAGCCAATAATCCTATCTCCCTCAAGTTACAGTGCAAAGGATCAAAGCAAC
* *
31652952 AGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATTGCATCGA
131 AGATCCTATCTCTCTGAAGATGCAGTAGAGTGGATTGCATCGA
*
31652995 GTCTTATCCCCCTGAAGTTGCAGTGGGGCAGATCGAAGAT-A-CAAATCATATCTCCCTGAGGTT
1 GTCTTA-CCCCCTGAAGTTGCAGTGGGGCAGATCGAAGATGATC-AATCATATCTCCCTGAAGTT
* * * * * *
31653058 GCAGTGGAGCAGATTGAAGTCAATAATCCTATCTCCC-CAACGTTGCGGTGGAAAGGATCGAAGC
64 ACAGTGGAGCAGATTGAAGCCAATAATCCTATCTCCCTCAA-GTTACAGTGCAAAGGATCAAAGC
*
31653122 ACCA-ATTCCTATAC-CTCTGAAGATGCAGTAG
128 AACAGA-TCCTAT-CTCTCTGAAGATGCAGTAG
31653153 GATGGAATGA
Statistics
Matches: 133, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
172 4 0.03
173 95 0.71
174 34 0.26
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (173 bp):
GTCTTACCCCCTGAAGTTGCAGTGGGGCAGATCGAAGATGATCAATCATATCTCCCTGAAGTTAC
AGTGGAGCAGATTGAAGCCAATAATCCTATCTCCCTCAAGTTACAGTGCAAAGGATCAAAGCAAC
AGATCCTATCTCTCTGAAGATGCAGTAGAGTGGATTGCATCGA
Found at i:31662904 original size:230 final size:235
Alignment explanation
Indices: 31662498--31663194 Score: 821
Period size: 230 Copynumber: 3.0 Consensus size: 235
31662488 GTAACACGTA
* * * * *
31662498 ATATATTAATCATTATCATATATTATCATTTATTATTCTA--G-TTGAAATATGCTTTGAGTCCT
1 ATATATTAATTATTATCATATA-TATTATTTATTATTATACTGATTGAAATATGCTTTAAGTCCC
* * *
31662560 TATACTTTTCCTACATGTGAAAGTTAACCCTCCTACTATAATATATAATGTTATATCATATCATA
65 TATAATTTTCATACATTTGAAAGTTAACCCT--TACTAT-ATATATAATGTTATATCATATCATA
* * *
31662625 TAGTGTATAATATATTAATATTTATATGTATGCATCAATGATTAAACATTATAATATCATGTAAT
127 TAGTATATAATATATTAATAGTTATATATATGCATCAATGATTAAACATTATAATATCATGTAAT
*
31662690 ACTATATCTTTTATTATATTCTATAATATAATAGTAGT-GCAT-T
192 ACTATATCTTTTATTATAATCTATAATATAATA-TAGTAGCATAT
* *
31662733 ATATATTAATTATTATCATATATATTTTTTATTATTATACTGATTGAAATATGCTCTAAGTCCCT
1 ATATATTAATTATTATCATATATATTATTTATTATTATACTGATTGAAATATGCTTTAAGTCCCT
* * * *
31662798 ATAATTTTCGTACATTTGAAAGTT-AGCCTT-C-GTAT-TATAATGTTAGATCATATCAT-TAGT
66 ATAATTTTCATACATTTGAAAGTTAACCCTTACTATATATATAATGTTATATCATATCATATAGT
* *
31662858 ATATAATATATTAATAGCTTATATATATGCATCAATGATCAAACATTATAATATCATCTAATACT
131 ATATAATATATTAATAG-TTATATATATGCATCAATGATTAAACATTATAATATCATGTAATACT
* *
31662923 ATATCTTTTATTATAGTCTATAATATATATAATAGTAGTATAGT
195 ATATCTTTTATTATAATCTATAATATA-AT-ATAGTAGCATA-T
* * * * *
31662967 ATATATTATTTACTAT-ATAT-TATTGTTTATTATTATACT-AGTTGAAATATGTTTTAAGTCTC
1 ATATATTAATTATTATCATATATATTATTTATTATTATACTGA-TTGAAATATGCTTTAAGTCCC
* * * *
31663029 TATACATTTT-ATACATTTTAAAGTTAATCATCTTCCTATATTATATAATGCTATATCATATCAT
65 TATA-ATTTTCATACATTTGAAAGTTAA-C-CCTTACTATA-TATATAATGTTATATCATATCAT
* * * * * *
31663093 GTAATATGTAATATATTAATAGTT-TATATTTGCATCAATAATTAAACATTATAATACCATGTAA
126 ATAGTATATAATATATTAATAGTTATATATATGCATCAATGATTAAACATTATAATATCATGTAA
*
31663157 TACTATATATTTTATTATAATCTATAATATAATATAGT
191 TACTATATCTTTTATTATAATCTATAATATAATATAGT
31663195 TATATATAAT
Statistics
Matches: 401, Mismatches: 42, Indels: 37
0.84 0.09 0.08
Matches are distributed among these distances:
229 19 0.05
230 90 0.22
231 9 0.02
232 58 0.14
233 11 0.03
234 30 0.07
235 24 0.06
236 11 0.03
237 44 0.11
238 65 0.16
239 21 0.05
240 19 0.05
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.45
Consensus pattern (235 bp):
ATATATTAATTATTATCATATATATTATTTATTATTATACTGATTGAAATATGCTTTAAGTCCCT
ATAATTTTCATACATTTGAAAGTTAACCCTTACTATATATATAATGTTATATCATATCATATAGT
ATATAATATATTAATAGTTATATATATGCATCAATGATTAAACATTATAATATCATGTAATACTA
TATCTTTTATTATAATCTATAATATAATATAGTAGCATAT
Found at i:31667504 original size:50 final size:50
Alignment explanation
Indices: 31667401--31667579 Score: 251
Period size: 50 Copynumber: 3.7 Consensus size: 50
31667391 TCTCGAGCCA
* * * *
31667401 ATGCCATGTCCCAGACATCGTCTTACA----C-CTTCTCTGTCCGTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCGGTCTGTGCCG
* * *
31667446 ATGCCATGTCCCAAACATGGTCTTACACTAGCACTCCTCGGTTTGTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCGGTCTGTGCCG
*
31667496 ATGTCATGTCCCAGACATGGTCTTACACTGGCACTCCTCGGTCTGTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCGGTCTGTGCCG
31667546 ATGCCATGTCCCAGACATGGTCTTACACTGGCAC
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCAC
31667580 ACTTACTACC
Statistics
Matches: 118, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
45 25 0.21
49 1 0.01
50 92 0.78
ACGTcount: A:0.18, C:0.34, G:0.21, T:0.27
Consensus pattern (50 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCGGTCTGTGCCG
Found at i:31667654 original size:44 final size:44
Alignment explanation
Indices: 31667600--31667694 Score: 172
Period size: 44 Copynumber: 2.2 Consensus size: 44
31667590 ATGGTCCAAC
* *
31667600 CATGGTCTTTTCCGTCAATTCTTTCTTAATTGCCATGTTATAAA
1 CATGGACTTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAA
31667644 CATGGACTTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAA
1 CATGGACTTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAA
31667688 CATGGAC
1 CATGGAC
31667695 CTTGAGATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (44 bp):
CATGGACTTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAA
Found at i:31669305 original size:18 final size:17
Alignment explanation
Indices: 31669275--31669328 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 17
31669265 TGCATCAATG
31669275 ATTAAACATTATAATATT
1 ATTAAA-ATTATAATATT
*
31669293 ATGTAAAATTATATATTTT
1 AT-TAAAATTATA-ATATT
*
31669312 ATTATAATTGATAATAT
1 ATTAAAATT-ATAATAT
31669329 AATAATAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 17 0.57
19 13 0.43
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (17 bp):
ATTAAAATTATAATATT
Found at i:31669657 original size:226 final size:227
Alignment explanation
Indices: 31669234--31669699 Score: 652
Period size: 226 Copynumber: 2.1 Consensus size: 227
31669224 ATGTCATATC
* * * *
31669234 ATATATATAATATATTAATAGCTTATATTTATGCATCAATGATTAAACATTATAATATTATGTAA
1 ATATATATAATATATTAATAGCTTATATATATGCATAAATAATTAAACATTATAATATCATGTAA
* *
31669299 AATTATATATTTTATTATAATTGATAATATAATAATAGTTATATATAATAGTAGTACATTATATA
66 AACTATATATTTTATTATAATTGATAATATAATAATAATTATATATAATAGTAGTACATTATATA
* *
31669364 TTACATATTATTATATATAACTGTTTATTAGTATACTAGTTGAAATATGCTCTAAGTCCCTATAC
131 TTACATATTATTATATATAACTATTTATTAGTATACTAGTTGAAATATGCTCAAAGTCCCTATAC
*
31669429 TTTTCGTACATTTGAAAA-TTAGCTTTCTTGCT
196 TTTTCATACATTT-AAAAGTTAGCTTTCTTGCT
*
31669461 ATATCATATCATATATTAATAG-TT-TATATATGCATAAATAATTAAACATTATAATATCATGTA
1 ATAT-ATATAATATATTAATAGCTTATATATATGCATAAATAATTAAACATTATAATATCATGTA
* * * *
31669524 ATACTATATCTTTTATTATAATCT-ATATTATAATAATAATTATATATAATTGTAGTACATTATA
65 AAACTATATATTTTATTATAAT-TGATAATATAATAATAATTATATATAATAGTAGTACATTATA
* * * * * * *
31669588 TATTGCTTATTGTTATATATTATTATTTATTATTATACTAGTTGAAATATGCTCAAAGTCTCTAT
129 TATTACATATTATTATATATAACTATTTATTAGTATACTAGTTGAAATATGCTCAAAGTCCCTAT
* * *
31669653 ACTTTTCATACATTTAAAAGTTAGCTCTCCTACT
194 ACTTTTCATACATTTAAAAGTTAGCTTTCTTGCT
31669687 ATATTATATAATA
1 ATA-TATATAATA
31669700 CTATCGTATT
Statistics
Matches: 210, Mismatches: 25, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
225 4 0.02
226 182 0.87
227 8 0.04
228 16 0.08
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (227 bp):
ATATATATAATATATTAATAGCTTATATATATGCATAAATAATTAAACATTATAATATCATGTAA
AACTATATATTTTATTATAATTGATAATATAATAATAATTATATATAATAGTAGTACATTATATA
TTACATATTATTATATATAACTATTTATTAGTATACTAGTTGAAATATGCTCAAAGTCCCTATAC
TTTTCATACATTTAAAAGTTAGCTTTCTTGCT
Found at i:31669847 original size:2 final size:2
Alignment explanation
Indices: 31669840--31669894 Score: 52
Period size: 2 Copynumber: 30.5 Consensus size: 2
31669830 TAGTAATAGT
31669840 TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA T- TA TA T- TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31669877 TA -A TA GTA TA TA T- TA TA T
1 TA TA TA -TA TA TA TA TA TA T
31669895 TTTTATTTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
1 7 0.16
2 36 0.80
3 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (2 bp):
TA
Found at i:31669855 original size:10 final size:10
Alignment explanation
Indices: 31669840--31669894 Score: 52
Period size: 9 Copynumber: 6.1 Consensus size: 10
31669830 TAGTAATAGT
31669840 TATATATATA
1 TATATATATA
31669850 TATATATAT-
1 TATATATATA
31669859 TATAT-TATA
1 TATATATATA
31669868 T-TATAT-TA
1 TATATATATA
31669876 T-TA-ATAGTA
1 TATATATA-TA
31669885 TATAT-TATA
1 TATATATATA
31669894 T
1 T
31669895 TTTTATTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
7 2 0.05
8 11 0.28
9 13 0.33
10 13 0.33
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (10 bp):
TATATATATA
Found at i:31669864 original size:5 final size:5
Alignment explanation
Indices: 31669839--31669895 Score: 57
Period size: 5 Copynumber: 11.4 Consensus size: 5
31669829 TTAGTAATAG
*
31669839 TTATA -TATA -TATA TATATA TTATA TTATA TTATA TTAT- TAATA GTATATA
1 TTATA TTATA TTATA T-TATA TTATA TTATA TTATA TTATA TTATA -T-TATA
31669889 TTATA TT
1 TTATA TT
31669896 TTTATTTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 11 0.24
5 24 0.53
6 7 0.16
7 3 0.07
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (5 bp):
TTATA
Found at i:31669900 original size:24 final size:23
Alignment explanation
Indices: 31669818--31669901 Score: 77
Period size: 26 Copynumber: 3.7 Consensus size: 23
31669808 GTTATATATG
*
31669818 TATTAATATTTTTAGTAATAGTTA
1 TATT-ATATTTTTATTAATAGTTA
* *
31669842 TA-TATATATATA-T-ATA-TTA
1 TATTATATTTTTATTAATAGTTA
31669861 TATTATATTATATTATTAATAGTATA
1 TATTATATT-T-TTATTAATAGT-TA
31669887 TATTATATTTTTATT
1 TATTATATTTTTATT
31669902 TTATGTATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
19 5 0.10
20 8 0.16
21 2 0.04
22 9 0.18
23 2 0.04
24 10 0.20
25 2 0.04
26 11 0.22
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (23 bp):
TATTATATTTTTATTAATAGTTA
Found at i:31672158 original size:21 final size:22
Alignment explanation
Indices: 31672129--31672185 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
31672119 TGTTAAAGAA
31672129 AAACC-CATAAGGGTTGAAC-G
1 AAACCTCATAAGGGTTGAACGG
* * *
31672149 AAAGCTCATAAGAGCTGAACGG
1 AAACCTCATAAGGGTTGAACGG
31672171 AAACCT-ATAAGGGTT
1 AAACCTCATAAGGGTT
31672186 AAATTGAAGC
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 4 0.14
21 19 0.66
22 6 0.21
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.18
Consensus pattern (22 bp):
AAACCTCATAAGGGTTGAACGG
Found at i:31672181 original size:42 final size:41
Alignment explanation
Indices: 31672129--31672232 Score: 127
Period size: 42 Copynumber: 2.5 Consensus size: 41
31672119 TGTTAAAGAA
* *
31672129 AAACCCATAAGGGTTGAACGAAAGCTCATAAGAGCTGAACGG
1 AAACCCATAAGGGTTAAACG-AAGCTCAAAAGAGCTGAACGG
* * * *
31672171 AAACCTATAAGGGTTAAATTGAAGCTCAAAATAGCTGAACTG
1 AAACCCATAAGGGTTAAA-CGAAGCTCAAAAGAGCTGAACGG
*
31672213 AAACCCATTAGGGTTAAACG
1 AAACCCATAAGGGTTAAACG
31672233 GAAACTTATA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.02
42 50 0.96
43 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.19
Consensus pattern (41 bp):
AAACCCATAAGGGTTAAACGAAGCTCAAAAGAGCTGAACGG
Found at i:31673214 original size:20 final size:16
Alignment explanation
Indices: 31673168--31673204 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
31673158 CCTAGAAATC
*
31673168 TTTAGAATTCAATTTA
1 TTTAAAATTCAATTTA
31673184 TTTAAAATTCAATTTA
1 TTTAAAATTCAATTTA
31673200 TTTAA
1 TTTAA
31673205 GTTAATTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (16 bp):
TTTAAAATTCAATTTA
Found at i:31680167 original size:21 final size:21
Alignment explanation
Indices: 31680141--31680182 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
31680131 ATCCAGAAAG
*
31680141 TCTAGTACCAGTCAAAATTAA
1 TCTAGTACCAGCCAAAATTAA
31680162 TCTAGTACCAGCCAAAATTAA
1 TCTAGTACCAGCCAAAATTAA
31680183 CTTTTCAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (21 bp):
TCTAGTACCAGCCAAAATTAA
Found at i:31682275 original size:31 final size:31
Alignment explanation
Indices: 31682234--31682298 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
31682224 GAAACAAGGA
* *
31682234 CAAGTTAGAAGGAATTGAAACTTCATTATTC
1 CAAGTCAGAAGAAATTGAAACTTCATTATTC
*
31682265 CAAGTCAGAAGAAATTGAAACTTCATTTTTC
1 CAAGTCAGAAGAAATTGAAACTTCATTATTC
31682296 CAA
1 CAA
31682299 AAATAGAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (31 bp):
CAAGTCAGAAGAAATTGAAACTTCATTATTC
Found at i:31683610 original size:14 final size:15
Alignment explanation
Indices: 31683587--31683615 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
31683577 TTGTTTTTTG
31683587 GTTTCTTTTTTCTTT
1 GTTTCTTTTTTCTTT
31683602 GTTTC-TTTTTCTTT
1 GTTTCTTTTTTCTTT
31683616 TTTGAGCGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (15 bp):
GTTTCTTTTTTCTTT
Found at i:31687830 original size:45 final size:45
Alignment explanation
Indices: 31687762--31687865 Score: 156
Period size: 45 Copynumber: 2.3 Consensus size: 45
31687752 ATTACTACAT
*
31687762 CTGCGTCACATCCTACTACAACACCTAG-TCCTTCACAAGCAACAC
1 CTGCGTCACATCCTACCACAACACCTAGCT-CTTCACAAGCAACAC
* * *
31687807 CTGTGTCACATCCTACCACAACACCTAGCTCTTCACATGTAACAC
1 CTGCGTCACATCCTACCACAACACCTAGCTCTTCACAAGCAACAC
31687852 CTGCGTCACATCCT
1 CTGCGTCACATCCT
31687866 GATCGCCACA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
45 52 0.98
46 1 0.02
ACGTcount: A:0.28, C:0.39, G:0.10, T:0.23
Consensus pattern (45 bp):
CTGCGTCACATCCTACCACAACACCTAGCTCTTCACAAGCAACAC
Found at i:31696247 original size:24 final size:23
Alignment explanation
Indices: 31696192--31696253 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 23
31696182 TTGTTTGTGG
*
31696192 TTAAATGACTGATTTGTCTGTGT
1 TTAAATGACTGATTTGTCTATGT
**
31696215 TTGGTATGACTGATTTGTCTATGAT
1 TT-AAATGACTGATTTGTCTATG-T
31696240 TTAAATGACTGATT
1 TTAAATGACTGATT
31696254 CTGAGCATGA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
23 2 0.06
24 27 0.84
25 3 0.09
ACGTcount: A:0.24, C:0.08, G:0.21, T:0.47
Consensus pattern (23 bp):
TTAAATGACTGATTTGTCTATGT
Found at i:31696360 original size:27 final size:27
Alignment explanation
Indices: 31696322--31696381 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 27
31696312 GGAAATACTG
*
31696322 TACTGGTGGCTTTGCCACA-ATCACTTT
1 TACTGGTGGCTTGGCCACATAT-ACTTT
31696349 TACTGGTGGCTTGGCCACATATACTTT
1 TACTGGTGGCTTGGCCACATATACTTT
31696376 TACTGG
1 TACTGG
31696382 CAGCTTAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 29 0.94
28 2 0.06
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (27 bp):
TACTGGTGGCTTGGCCACATATACTTT
Found at i:31696387 original size:27 final size:27
Alignment explanation
Indices: 31696330--31696387 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
31696320 TGTACTGGTG
* **
31696330 GCTTTGCCACAATCACTTTTACTGGTG
1 GCTTGGCCACAATCACTTTTACTGGCA
31696357 GCTTGGCCACATAT-ACTTTTACTGGCA
1 GCTTGGCCACA-ATCACTTTTACTGGCA
31696384 GCTT
1 GCTT
31696388 AGTTGCGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 25 0.93
28 2 0.07
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (27 bp):
GCTTGGCCACAATCACTTTTACTGGCA
Found at i:31696407 original size:26 final size:26
Alignment explanation
Indices: 31696369--31696434 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
31696359 TTGGCCACAT
* * *
31696369 ATACTTTTACTGGCAGCTTAGTTGCG
1 ATACTATTGCTGGCAGCTTAGATGCG
*
31696395 ATACTATTGCTGGCAGCTTTGATGCG
1 ATACTATTGCTGGCAGCTTAGATGCG
* *
31696421 ATGCTATTGATGGC
1 ATACTATTGCTGGC
31696435 TTTGTGCCGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (26 bp):
ATACTATTGCTGGCAGCTTAGATGCG
Found at i:31696464 original size:32 final size:32
Alignment explanation
Indices: 31696428--31696627 Score: 242
Period size: 32 Copynumber: 6.3 Consensus size: 32
31696418 GCGATGCTAT
*
31696428 TGATGGCTTTGTGCCGATCATATTACTATTAC
1 TGATGGCTTTGTGCCAATCATATTACTATTAC
* * * *
31696460 TGATGGCTATGTGCCGATCATATTACCATTAT
1 TGATGGCTTTGTGCCAATCATATTACTATTAC
* * *
31696492 TGATGG-TTGTGTACCGATCATATTACTACTAC
1 TGATGGCTT-TGTGCCAATCATATTACTATTAC
* *
31696524 TAATGGCTTTGTGCCAATCATACTACTATTAC
1 TGATGGCTTTGTGCCAATCATATTACTATTAC
* * *
31696556 TGATGGCTCTGTGCCAATTATATTACTACTAC
1 TGATGGCTTTGTGCCAATCATATTACTATTAC
*
31696588 TGATGGCTTTGTGCCAATCATATTACT-GTAC
1 TGATGGCTTTGTGCCAATCATATTACTATTAC
*
31696619 TTATGGCTT
1 TGATGGCTT
31696628 GTAGCCATTC
Statistics
Matches: 144, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
31 12 0.08
32 130 0.90
33 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (32 bp):
TGATGGCTTTGTGCCAATCATATTACTATTAC
Found at i:31696644 original size:22 final size:21
Alignment explanation
Indices: 31696619--31696692 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 21
31696609 ATTACTGTAC
31696619 TTATGGCTTGTAGCCATTCTGT
1 TTATGGCTT-TAGCCATTCTGT
* *
31696641 TTATAGCTTATAGCCATCCTGT
1 TTATGGCTT-TAGCCATTCTGT
* * *
31696663 TTACGGCTCTTAGTCATTCTGG
1 TTATGGCT-TTAGCCATTCTGT
31696685 TTACTGGC
1 TTA-TGGC
31696693 AGCTTTGCTA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
22 37 0.90
23 4 0.10
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (21 bp):
TTATGGCTTTAGCCATTCTGT
Found at i:31703181 original size:26 final size:26
Alignment explanation
Indices: 31703145--31703197 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
31703135 TTGGATAAAA
31703145 AGGGGTCGCTAAGTGT-AGATTCCCTG
1 AGGGGTCGCTAAGT-TCAGATTCCCTG
* *
31703171 AGGGGTTGCTAAGTTCTGATTCCCTG
1 AGGGGTCGCTAAGTTCAGATTCCCTG
31703197 A
1 A
31703198 ATTATTGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (26 bp):
AGGGGTCGCTAAGTTCAGATTCCCTG
Found at i:31703313 original size:41 final size:43
Alignment explanation
Indices: 31703174--31703321 Score: 130
Period size: 43 Copynumber: 3.5 Consensus size: 43
31703164 TTCCCTGAGG
* * * *
31703174 GGTTGCTAAGTTCTGATTCC-CTGAATTAT-TGATTCTAAAGGT
1 GGTTGCTAAGTGCTGATTCCACAGTA-TATCTGATTGTAAAGGT
* * *
31703216 GGTTTCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCACAGTATATCTGATTGT-AAAGGT
*
31703259 GGTTGCTATGTGCTGATTCCA-AGTATCA-CTGAATT-T-AAGGT
1 GGTTGCTAAGTGCTGATTCCACAGTAT-ATCTG-ATTGTAAAGGT
*
31703300 GGTTGCTAAGTGCTGAATCCAC
1 GGTTGCTAAGTGCTGATTCCAC
31703322 CGAGTAACGG
Statistics
Matches: 88, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
40 4 0.05
41 19 0.22
42 28 0.32
43 32 0.36
44 5 0.06
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (43 bp):
GGTTGCTAAGTGCTGATTCCACAGTATATCTGATTGTAAAGGT
Found at i:31705411 original size:38 final size:37
Alignment explanation
Indices: 31705359--31705465 Score: 166
Period size: 37 Copynumber: 2.9 Consensus size: 37
31705349 ACCAAAAATT
31705359 TATTTTAAAA-AAAAAATAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATAAAAAATAAAAAAAGTATTTTAAAAA
31705395 TATTTTAAAATTAAAAAAT-AAAAAAGTATTTTAAAAA
1 TATTTTAAAA-TAAAAAATAAAAAAAGTATTTTAAAAA
31705432 TATTTTAAAATAAAAAAATAAAAAAA-TATGTTTA
1 TATTTTAAAAT-AAAAAATAAAAAAAGTAT-TTTA
31705466 TTATATTCGG
Statistics
Matches: 66, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
36 11 0.17
37 38 0.58
38 17 0.26
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (37 bp):
TATTTTAAAATAAAAAATAAAAAAAGTATTTTAAAAA
Found at i:31706581 original size:14 final size:14
Alignment explanation
Indices: 31706562--31706639 Score: 50
Period size: 14 Copynumber: 5.1 Consensus size: 14
31706552 TTGATTGCCA
31706562 GTAAAATATTTTCT
1 GTAAAATATTTTCT
31706576 GTAAAATGA-TTTCT
1 GTAAAAT-ATTTTCT
*
31706590 GGAAAATGTTTTACTTTTCT
1 GTAAAA-----TA-TTTTCT
*
31706610 GTAAAATGATTTACT
1 GTAAAAT-ATTTTCT
*
31706625 GGAAAATATTTTCT
1 GTAAAATATTTTCT
31706639 G
1 G
31706640 GTGTTTGATT
Statistics
Matches: 50, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
14 24 0.48
15 13 0.26
16 1 0.02
18 1 0.02
19 1 0.02
20 10 0.20
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (14 bp):
GTAAAATATTTTCT
Found at i:31706610 original size:20 final size:20
Alignment explanation
Indices: 31706585--31706624 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
31706575 TGTAAAATGA
*
31706585 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
31706605 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
31706625 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:31706613 original size:34 final size:35
Alignment explanation
Indices: 31706570--31706636 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
31706560 CAGTAAAATA
*
31706570 TTTTCTGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCTGTAAAATGATTTACTGGAAAATATTTTAC
31706604 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
31706637 CTGGTGTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 18 0.58
35 13 0.42
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.48
Consensus pattern (35 bp):
TTTTCTGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:31707930 original size:14 final size:13
Alignment explanation
Indices: 31707901--31707927 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31707891 AGAAGGTAAG
31707901 ACAGATACTTAAA
1 ACAGATACTTAAA
31707914 ACAGATACTTAAA
1 ACAGATACTTAAA
31707927 A
1 A
31707928 ACATCAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (13 bp):
ACAGATACTTAAA
Found at i:31708980 original size:12 final size:12
Alignment explanation
Indices: 31708963--31708988 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31708953 ATCAAGAGAA
31708963 AACGAAAGGGAG
1 AACGAAAGGGAG
31708975 AACGAAAGGGAG
1 AACGAAAGGGAG
31708987 AA
1 AA
31708989 GGGAGAACGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.08, G:0.38, T:0.00
Consensus pattern (12 bp):
AACGAAAGGGAG
Found at i:31708992 original size:19 final size:19
Alignment explanation
Indices: 31708968--31709007 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
31708958 GAGAAAACGA
31708968 AAGGGAGAACGAAAGGGAG
1 AAGGGAGAACGAAAGGGAG
*
31708987 AAGGGAGAACGAACGGGAG
1 AAGGGAGAACGAAAGGGAG
31709006 AA
1 AA
31709008 CAAAACCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.47, C:0.07, G:0.45, T:0.00
Consensus pattern (19 bp):
AAGGGAGAACGAAAGGGAG
Found at i:31710294 original size:40 final size:40
Alignment explanation
Indices: 31710249--31710339 Score: 101
Period size: 40 Copynumber: 2.3 Consensus size: 40
31710239 ATTCGTTAAT
** * *
31710249 ATAAAAATTTACAGTTTAATAATTTATAAGTAAAAAATTA
1 ATAAAAATCAACAATTTAATAATTTATAAGCAAAAAATTA
* * * *
31710289 ATAAAAATCAATAATTTAATAATTTATATGCAACAAGTTA
1 ATAAAAATCAACAATTTAATAATTTATAAGCAAAAAATTA
*
31710329 ATAAAATTCAA
1 ATAAAAATCAA
31710340 TATGCTTTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.35
Consensus pattern (40 bp):
ATAAAAATCAACAATTTAATAATTTATAAGCAAAAAATTA
Found at i:31710340 original size:40 final size:40
Alignment explanation
Indices: 31710263--31710341 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
31710253 AAATTTACAG
*
31710263 TTTAATAATTTATAAGTAAAAAATTAATAAAAATCAATAA
1 TTTAATAATTTATAAGCAAAAAATTAATAAAAATCAATAA
* * * *
31710303 TTTAATAATTTATATGCAACAAGTTAATAAAATTCAATA
1 TTTAATAATTTATAAGCAAAAAATTAATAAAAATCAATA
31710342 TGCTTTAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (40 bp):
TTTAATAATTTATAAGCAAAAAATTAATAAAAATCAATAA
Found at i:31715698 original size:21 final size:22
Alignment explanation
Indices: 31715655--31715699 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
31715645 TTAAAATTTG
31715655 TGTTATGTATAGATTAAAATGAT
1 TGTTATGTATAGATT-AAATGAT
31715678 TGTTATGTGATA-ATT-AATGAT
1 TGTTATGT-ATAGATTAAATGAT
31715699 T
1 T
31715700 TGGATTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 7 0.33
23 11 0.52
24 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.47
Consensus pattern (22 bp):
TGTTATGTATAGATTAAATGAT
Found at i:31716173 original size:21 final size:21
Alignment explanation
Indices: 31716133--31716173 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31716123 ATATGGATTC
*
31716133 TTGAAATGAAAATGTGTGATG
1 TTGAAATGAAAATGTATGATG
31716154 TTGAAA-GAAAATGATATGAT
1 TTGAAATGAAAATG-TATGAT
31716174 TGAGTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (21 bp):
TTGAAATGAAAATGTATGATG
Found at i:31718407 original size:19 final size:19
Alignment explanation
Indices: 31718371--31718407 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
31718361 ATCTCAATTC
31718371 AAATTTATTTTTATCATAA
1 AAATTTATTTTTATCATAA
31718390 AAATATTATTTTTA-CATA
1 AAAT-TTATTTTTATCATA
31718408 TGAAAGCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATTTATTTTTATCATAA
Found at i:31719297 original size:15 final size:17
Alignment explanation
Indices: 31719279--31719319 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
31719269 ATATTATATT
31719279 TTTATAACATT-TAA-A
1 TTTATAACATTCTAATA
*
31719294 TTTATTA-ATTCTAATA
1 TTTATAACATTCTAATA
31719310 TTTATAACAT
1 TTTATAACAT
31719320 ATATATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 3 0.14
15 9 0.43
16 7 0.33
17 2 0.10
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTATAACATTCTAATA
Found at i:31719829 original size:23 final size:24
Alignment explanation
Indices: 31719785--31719830 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
31719775 CCACACACTT
*
31719785 TTTATCATCTTTTTAGGGTTTTAG
1 TTTATCAGCTTTTTAGGGTTTTAG
* *
31719809 TTTATCAGGTTTTT-GGTTTTTA
1 TTTATCAGCTTTTTAGGGTTTTA
31719831 CCTGTTAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.15, C:0.07, G:0.17, T:0.61
Consensus pattern (24 bp):
TTTATCAGCTTTTTAGGGTTTTAG
Found at i:31722845 original size:25 final size:25
Alignment explanation
Indices: 31722817--31722913 Score: 95
Period size: 25 Copynumber: 3.9 Consensus size: 25
31722807 AGTAATTGAA
*
31722817 AAGCTCTTTTGAGCCATATAACGGG
1 AAGCTCTTGTGAGCCATATAACGGG
* *
31722842 AAGCTCATGTGAGCCATGTAACGGG
1 AAGCTCTTGTGAGCCATATAACGGG
* * * * *
31722867 AAGTTCTTGCGAGCCAGATATCAGG
1 AAGCTCTTGTGAGCCATATAACGGG
** *
31722892 AAGCTAGTGAGAGCCATATAAC
1 AAGCTCTTGTGAGCCATATAAC
31722914 AGGATGGTCA
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.23
Consensus pattern (25 bp):
AAGCTCTTGTGAGCCATATAACGGG
Found at i:31724366 original size:30 final size:30
Alignment explanation
Indices: 31724330--31724388 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
31724320 AAAACCCTCA
*
31724330 TAGTATAGAATTAGTTTTAGTTTACTTTCG
1 TAGTATAGAATTAGTTTCAGTTTACTTTCG
31724360 TAGTATAGAATTAGTTTCAGTTTACTTTC
1 TAGTATAGAATTAGTTTCAGTTTACTTTC
31724389 TTTTTGGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.49
Consensus pattern (30 bp):
TAGTATAGAATTAGTTTCAGTTTACTTTCG
Found at i:31733174 original size:195 final size:195
Alignment explanation
Indices: 31732842--31733234 Score: 750
Period size: 195 Copynumber: 2.0 Consensus size: 195
31732832 CATTCAGATC
*
31732842 ATCTGACTCAATCTGGATAATCTCATTATTTCAACATCTCAACTCGATCGTCTTTCGTTTGCAAT
1 ATCTGACTCAATCCGGATAATCTCATTATTTCAACATCTCAACTCGATCGTCTTTCGTTTGCAAT
31732907 TTACAATAGTATGGTGCAGTGTTAACCAATCCATACCCAGGATTATATCAAACTCATCAAATGGT
66 TTACAATAGTATGGTGCAGTGTTAACCAATCCATACCCAGGATTATATCAAACTCATCAAATGGT
* *
31732972 AACAACATCAAATCGGTCGGAAAACAGAAATCTCGAATCATCAACGGGAAGTTCTTGCACACTTT
131 AACAACATCAAATCGGTCAGAAAACAGAAATCTCAAATCATCAACGGGAAGTTCTTGCACACTTT
*
31733037 ATCTGACTCAATCCGGATAATCTCATTATTTCAACATCTCAACTCGATCGTCTTTCGTTTGCAGT
1 ATCTGACTCAATCCGGATAATCTCATTATTTCAACATCTCAACTCGATCGTCTTTCGTTTGCAAT
31733102 TTACAATAGTATGGTGCAGTGTTAACCAATCCATACCCAGGATTATATCAAACTCATCAAATGGT
66 TTACAATAGTATGGTGCAGTGTTAACCAATCCATACCCAGGATTATATCAAACTCATCAAATGGT
31733167 AACAACATCAAATCGGTCAGAAAACAGAAATCTCAAATCATCAACGGGAAGTTCTTGCACACTTT
131 AACAACATCAAATCGGTCAGAAAACAGAAATCTCAAATCATCAACGGGAAGTTCTTGCACACTTT
31733232 ATC
1 ATC
31733235 AACCAAAACA
Statistics
Matches: 194, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
195 194 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (195 bp):
ATCTGACTCAATCCGGATAATCTCATTATTTCAACATCTCAACTCGATCGTCTTTCGTTTGCAAT
TTACAATAGTATGGTGCAGTGTTAACCAATCCATACCCAGGATTATATCAAACTCATCAAATGGT
AACAACATCAAATCGGTCAGAAAACAGAAATCTCAAATCATCAACGGGAAGTTCTTGCACACTTT
Found at i:31743894 original size:58 final size:60
Alignment explanation
Indices: 31743830--31744029 Score: 172
Period size: 68 Copynumber: 3.2 Consensus size: 60
31743820 ATCACTTTAA
* * *
31743830 TATTAAAATCATATAATACTTA-T-CAAGATAAATATTATATTAAATTTAATATTAAATC
1 TATTAAAATAATAGAATACTTACTACAAGATAAATATTAAATTAAATTTAATATTAAATC
* *
31743888 TATTAAATTAATAGAATACTTATCTACAAGATAAATATTAAATTATATTTAATATTAAGATAGTC
1 TATTAAAATAATAGAATACTTA-CTACAAGATAAATATTAAATTAAATTTAATATT-A-A-A-TC
* * * ** * * *
31743953 ATTTTAATATTAA-ATTAATAAAATACTATCATGATAAGTATTAAATTAAATTTAATATTAAAAC
1 -TATTAA-AATAATA-GAAT-ACTTACTA-CAAGATAAATATTAAATTAAATTTAATATTAAATC
31744017 TATTAAAATAATA
1 TATTAAAATAATA
31744030 TTTTTGGAAT
Statistics
Matches: 114, Mismatches: 15, Indels: 21
0.76 0.10 0.14
Matches are distributed among these distances:
58 19 0.17
60 1 0.01
61 28 0.25
62 5 0.04
63 7 0.06
64 2 0.02
65 3 0.03
66 7 0.06
67 12 0.11
68 30 0.26
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.41
Consensus pattern (60 bp):
TATTAAAATAATAGAATACTTACTACAAGATAAATATTAAATTAAATTTAATATTAAATC
Found at i:31744319 original size:19 final size:19
Alignment explanation
Indices: 31744295--31744336 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
31744285 TTCGACCAAT
* *
31744295 TTTTGGGTCTCGATCTCAG
1 TTTTGGGTCTCGAGCCCAG
*
31744314 TTTTGGTTCTCGAGCCCAG
1 TTTTGGGTCTCGAGCCCAG
31744333 TTTT
1 TTTT
31744337 TTTTATCTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.21, G:0.24, T:0.45
Consensus pattern (19 bp):
TTTTGGGTCTCGAGCCCAG
Found at i:31758898 original size:22 final size:21
Alignment explanation
Indices: 31758849--31758898 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
31758839 AAACATCGAC
* *
31758849 GTCATGACTTTGTTTTTTAAT
1 GTCATGACATTGTTTCTTAAT
* *
31758870 GCCATGACATTGTTCTCTTCAT
1 GTCATGACATTGTT-TCTTAAT
31758892 GTCATGA
1 GTCATGA
31758899 TGTTGCCAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.46
Consensus pattern (21 bp):
GTCATGACATTGTTTCTTAAT
Found at i:31766411 original size:81 final size:81
Alignment explanation
Indices: 31766276--31766432 Score: 314
Period size: 81 Copynumber: 1.9 Consensus size: 81
31766266 TTTTTTGCAG
31766276 AAATCACACCACTTAAGACTTTTGTCCTTGCTGCCTCAGCTGGGCTTTATTGGCATCAGAAGTCA
1 AAATCACACCACTTAAGACTTTTGTCCTTGCTGCCTCAGCTGGGCTTTATTGGCATCAGAAGTCA
31766341 TTAGGGCTGAAGCAAA
66 TTAGGGCTGAAGCAAA
31766357 AAATCACACCACTTAAGACTTTTGTCCTTGCTGCCTCAGCTGGGCTTTATTGGCATCAGAAGTCA
1 AAATCACACCACTTAAGACTTTTGTCCTTGCTGCCTCAGCTGGGCTTTATTGGCATCAGAAGTCA
31766422 TTAGGGCTGAA
66 TTAGGGCTGAA
31766433 TTCTCAAGTG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 76 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (81 bp):
AAATCACACCACTTAAGACTTTTGTCCTTGCTGCCTCAGCTGGGCTTTATTGGCATCAGAAGTCA
TTAGGGCTGAAGCAAA
Found at i:31773234 original size:22 final size:22
Alignment explanation
Indices: 31773209--31773261 Score: 81
Period size: 21 Copynumber: 2.4 Consensus size: 22
31773199 AATAAATACC
31773209 AAAAATTTATTTTAAAAATTAAA
1 AAAAATTTATTTT-AAAATTAAA
*
31773232 AAAAA-GTATTTTAAAATTAAA
1 AAAAATTTATTTTAAAATTAAA
31773253 AAAAATTTA
1 AAAAATTTA
31773262 AAAAGTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 14 0.52
22 8 0.30
23 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAAATTTATTTTAAAATTAAA
Found at i:31773247 original size:21 final size:22
Alignment explanation
Indices: 31773216--31773310 Score: 78
Period size: 22 Copynumber: 4.5 Consensus size: 22
31773206 ACCAAAAATT
31773216 TATTTTAAAAATTAAAAAAAAG
1 TATTTTAAAAATTAAAAAAAAG
31773238 TATTTT-AAAATT-AAAAAAA-
1 TATTTTAAAAATTAAAAAAAAG
***
31773257 -A-TTTAAAAAGTATTTTAAAAA-
1 TATTTTAAAAA-T-TAAAAAAAAG
* *
31773278 TA-TTTAAAATTTTAAAAAAAG
1 TATTTTAAAAATTAAAAAAAAG
31773299 TATTTTAAAAAT
1 TATTTTAAAAAT
31773311 ATTTTAAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
17 3 0.05
18 5 0.08
19 1 0.02
20 15 0.25
21 14 0.23
22 22 0.37
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (22 bp):
TATTTTAAAAATTAAAAAAAAG
Found at i:31773264 original size:29 final size:31
Alignment explanation
Indices: 31773222--31773339 Score: 111
Period size: 32 Copynumber: 3.9 Consensus size: 31
31773212 AATTTATTTT
* *
31773222 AAAAATTAAAAAAAAGTATTTTAAAATTA-AA
1 AAAAATT-TAAAAAAGTATTTTAAAAATATAA
**
31773253 AAAAATTT-AAAAAGTATTTTAAAAATATTT
1 AAAAATTTAAAAAAGTATTTTAAAAATATAA
* **
31773283 AAAATTTTAAAAAAAGTATTTTAAAAATATTT
1 AAAAATTT-AAAAAAGTATTTTAAAAATATAA
*
31773315 TAAAA-TTAAAAAA--ATTTTAAAAATA
1 AAAAATTTAAAAAAGTATTTTAAAAATA
31773340 AATATATTTA
Statistics
Matches: 77, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
28 12 0.16
29 18 0.23
30 13 0.17
31 9 0.12
32 25 0.32
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (31 bp):
AAAAATTTAAAAAAGTATTTTAAAAATATAA
Found at i:31773324 original size:61 final size:60
Alignment explanation
Indices: 31773219--31773339 Score: 154
Period size: 61 Copynumber: 2.0 Consensus size: 60
31773209 AAAAATTTAT
* *
31773219 TTTAAAAATTAAAAAAAAGTATTTTAAAATTAAAAAAAATTTAAAAAGTATTTTAAAAATA
1 TTTAAAAATTAAAAAAAAGTATTTTAAAAATAAAAAAAATTTAAAAA-AATTTTAAAAATA
* * ***
31773280 TTTAAAATTTTAAAAAAAGTATTTTAAAAATATTTTAAAA-TTAAAAAAATTTTAAAAATA
1 TTTAAAAATTAAAAAAAAGTATTTTAAAAATA-AAAAAAATTTAAAAAAATTTTAAAAATA
31773340 AATATATTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
60 12 0.23
61 36 0.69
62 4 0.08
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (60 bp):
TTTAAAAATTAAAAAAAAGTATTTTAAAAATAAAAAAAATTTAAAAAAATTTTAAAAATA
Found at i:31773325 original size:17 final size:17
Alignment explanation
Indices: 31773303--31773348 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
31773293 AAAAAGTATT
31773303 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
*
31773320 TTAAAAAAATTTTAAAA
1 TTAAAAATATTTTAAAA
* *
31773337 ATAAATATATTT
1 TTAAAAATATTT
31773349 ATTATATCGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:31777197 original size:42 final size:42
Alignment explanation
Indices: 31777132--31777287 Score: 169
Period size: 42 Copynumber: 3.7 Consensus size: 42
31777122 AAATCGGACA
*
31777132 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGAAATCAATATCG
*
31777174 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAATCAAATAT-G
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGAAATC-AATATCG
* * *
31777216 ATGCCGATGTCCCAGACATGGTCTTATACAT-AAATCTCAA-ATCG
1 ATGCCAACGTCCCAGACGTGGTC-T-TACATGAAA--TCAATATCG
31777260 ATGCCAACGTCCCAGACGTGGTCTTACA
1 ATGCCAACGTCCCAGACGTGGTCTTACA
31777288 CGATAACATA
Statistics
Matches: 96, Mismatches: 8, Indels: 20
0.77 0.06 0.16
Matches are distributed among these distances:
41 2 0.02
42 51 0.53
43 14 0.15
44 27 0.28
45 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGAAATCAATATCG
Found at i:31784521 original size:42 final size:42
Alignment explanation
Indices: 31784456--31784611 Score: 169
Period size: 42 Copynumber: 3.7 Consensus size: 42
31784446 AAATCGGACA
*
31784456 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGAAATCAATATCG
*
31784498 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAATCAAATAT-G
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGAAATC-AATATCG
* * *
31784540 ATGCCGATGTCCCAGACATGGTCTTATACAT-AAATCTCAA-ATCG
1 ATGCCAACGTCCCAGACGTGGTC-T-TACATGAAA--TCAATATCG
31784584 ATGCCAACGTCCCAGACGTGGTCTTACA
1 ATGCCAACGTCCCAGACGTGGTCTTACA
31784612 CGATAACATA
Statistics
Matches: 96, Mismatches: 8, Indels: 20
0.77 0.06 0.16
Matches are distributed among these distances:
41 2 0.02
42 51 0.53
43 14 0.15
44 27 0.28
45 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGAAATCAATATCG
Found at i:31786088 original size:24 final size:24
Alignment explanation
Indices: 31786061--31786201 Score: 85
Period size: 24 Copynumber: 5.8 Consensus size: 24
31786051 TATAACGGGG
31786061 AGCTCATAAGAGCCATAATCAGGA
1 AGCTCATAAGAGCCATAATCAGGA
** * *
31786085 AGCTCATGCGAGCCAATAA-CGGGT
1 AGCTCATAAGAGCC-ATAATCAGGA
*
31786109 AGCTC-TGAAAAGCCATTAATC-GGTA
1 AGCTCAT-AAGAGCCA-TAATCAGG-A
* *
31786134 AGTTCA-AGCGAGCCAT-ATCAGGA
1 AGCTCATA-AGAGCCATAATCAGGA
* *
31786157 AGCTCATAAAGAGCCTTTAATCGGGA
1 AGCTCAT-AAGAGCC-ATAATCAGGA
*
31786183 AGCTCACGAAGAGCCATAA
1 AGCTCA-TAAGAGCCATAA
31786202 AATGGGACGC
Statistics
Matches: 87, Mismatches: 17, Indels: 25
0.67 0.13 0.19
Matches are distributed among these distances:
23 11 0.13
24 38 0.44
25 19 0.22
26 19 0.22
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.18
Consensus pattern (24 bp):
AGCTCATAAGAGCCATAATCAGGA
Found at i:31786107 original size:48 final size:47
Alignment explanation
Indices: 31786052--31786188 Score: 127
Period size: 49 Copynumber: 2.8 Consensus size: 47
31786042 TACAGGCTGT
* *
31786052 ATAACGGGGAGCTCAT-AAGAGCCATAATCAGGAAGCTCATGCGAGCC
1 ATAACGGGAAGCTCATAAAGAGCCATAATC-GGAAGCTCAAGCGAGCC
* *
31786099 AATAACGGGTAGCTC-TGAAA-AGCCATTAATCGGTAAGTTCAAGCGAGCC
1 -ATAACGGGAAGCTCAT-AAAGAGCCA-TAATCGG-AAGCTCAAGCGAGCC
* * *
31786148 ATATCAGGAAGCTCATAAAGAGCCTTTAATCGGGAAGCTCA
1 ATAACGGGAAGCTCATAAAGAGCC-ATAATC-GGAAGCTCA
31786189 CGAAGAGCCA
Statistics
Matches: 73, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
47 1 0.01
48 34 0.47
49 36 0.49
50 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (47 bp):
ATAACGGGAAGCTCATAAAGAGCCATAATCGGAAGCTCAAGCGAGCC
Found at i:31788754 original size:27 final size:27
Alignment explanation
Indices: 31788724--31788775 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
31788714 ATGAGTAATT
31788724 AAAAACATGAATTAAAAATAAAAAATA
1 AAAAACATGAATTAAAAATAAAAAATA
*
31788751 AAAAACATGTATTAAAAATAAAAAA
1 AAAAACATGAATTAAAAATAAAAAA
31788776 AATGCTCGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (27 bp):
AAAAACATGAATTAAAAATAAAAAATA
Found at i:31789336 original size:20 final size:20
Alignment explanation
Indices: 31789308--31789353 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
31789298 CAATCGATCC
* *
31789308 CTATATTTTTTTGTTTCAAG
1 CTATTTTTTTTTCTTTCAAG
* *
31789328 CTATTTTTTTTTCTTTTATG
1 CTATTTTTTTTTCTTTCAAG
31789348 CTATTT
1 CTATTT
31789354 GAACTTTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.15, C:0.11, G:0.07, T:0.67
Consensus pattern (20 bp):
CTATTTTTTTTTCTTTCAAG
Found at i:31790184 original size:48 final size:48
Alignment explanation
Indices: 31790102--31790195 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
31790092 TTTCTTGGCT
* * *
31790102 TAAAAATGCCTAAGTCAGCCTAACTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
31790150 TAAAAACGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
31790196 AGAATTCCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
47 4 0.10
48 37 0.90
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:31792696 original size:48 final size:48
Alignment explanation
Indices: 31792614--31792707 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
31792604 TTTCTTGGCT
* *
31792614 TAAAAACGCCTAAGTCAGCCTAACTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
31792662 TAAAAACGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
31792708 AGAATTCCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 4 0.10
48 38 0.90
ACGTcount: A:0.40, C:0.28, G:0.13, T:0.19
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:31795210 original size:48 final size:48
Alignment explanation
Indices: 31795128--31795221 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
31795118 TTTCTTGGCT
* *
31795128 TAAAAACGCCTAAGTCAGCCTAACTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
31795176 TAAAAACGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
31795222 AGAATTCCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 4 0.10
48 38 0.90
ACGTcount: A:0.40, C:0.28, G:0.13, T:0.19
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:31797722 original size:48 final size:48
Alignment explanation
Indices: 31797640--31797733 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
31797630 TTTCTTGGCT
* * *
31797640 TAAAAATGCCTAAGTCAGCCTAACTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
31797688 TAAAAACGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
31797734 AGAATTCCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
47 4 0.10
48 37 0.90
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:31798722 original size:22 final size:20
Alignment explanation
Indices: 31798694--31798747 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
31798684 TCAATTGTTT
31798694 AATTAGGGTTTAGCATTTATTA
1 AATTAGGGTTTAG--TTTATTA
*
31798716 AATTAGGGTTATTGTTTATTA
1 AATTAGGGTT-TAGTTTATTA
*
31798737 AATTAAGGTTT
1 AATTAGGGTTT
31798748 TAGTGTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 1 0.03
21 16 0.55
22 10 0.34
23 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (20 bp):
AATTAGGGTTTAGTTTATTA
Found at i:31798777 original size:20 final size:19
Alignment explanation
Indices: 31798745--31798783 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
31798735 TAAATTAAGG
31798745 TTTTAGTGTTTTATTTAATT
1 TTTTAGTGTTTTA-TTAATT
31798765 TTTTAAGTG-TTTATTAATT
1 TTTT-AGTGTTTTATTAATT
31798784 AGTGTTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 8 0.44
21 4 0.22
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (19 bp):
TTTTAGTGTTTTATTAATT
Found at i:31798828 original size:21 final size:21
Alignment explanation
Indices: 31798803--31798845 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
31798793 GGAAAAATGA
31798803 TTATTATTAGGGTTTTGGGTT
1 TTATTATTAGGGTTTTGGGTT
31798824 TTATTATTAGGGTTTTGGGTT
1 TTATTATTAGGGTTTTGGGTT
31798845 T
1 T
31798846 GTTTAGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.28, T:0.58
Consensus pattern (21 bp):
TTATTATTAGGGTTTTGGGTT
Found at i:31804684 original size:180 final size:180
Alignment explanation
Indices: 31804382--31804744 Score: 566
Period size: 180 Copynumber: 2.0 Consensus size: 180
31804372 GAATAGTTAA
*
31804382 TTCTAAATCAAATTATCTGGTAGAGTCCCAATAGGAGTATAACTCTTTCACTACTCAATCAACAA
1 TTCTAAATCAAATTATCTGGTAGAGTCCCAATAGGAGTATAACTCTTCCACTACTCAATCAACAA
* * *
31804447 TGACCAATTGTCACCGGCCACTGGGACACCACCGTCGCAGCCACTAGCATCGCCGTGTCCGGTGA
66 TGACCAATCGTCACCGACCACTAGGACACCACCGTCGCAGCCACTAGCATCGCCGTGTCCGGTGA
* * *
31804512 TGCAGGGGCGACACCCTTACAGCACCCTGAGCCGGTTCGATTGCTACTAG
131 TGCAGGGGAGACACACTTACAGCACCCAGAGCCGGTTCGATTGCTACTAG
* * *
31804562 TTCTAAATCAAATTCTCTGGTAGAGTCCCAATATGAGTATAACTCTTCCACTGCTCAATCAACAA
1 TTCTAAATCAAATTATCTGGTAGAGTCCCAATAGGAGTATAACTCTTCCACTACTCAATCAACAA
* * *
31804627 TGACCAATCG-CTGCCGACCATTAGGACACCACCGTCGCAGCCACTGGCATCGCCGTGTCCGGTG
66 TGACCAATCGTC-ACCGACCACTAGGACACCACCGTCGCAGCCACTAGCATCGCCGTGTCCGGTG
* * *
31804691 ATGCAGGTGAGACACACTTACAGCACTCAGAGCCGGTTCGATTGCTGCTAG
130 ATGCAGGGGAGACACACTTACAGCACCCAGAGCCGGTTCGATTGCTACTAG
31804742 TTC
1 TTC
31804745 GGTCTGAGTA
Statistics
Matches: 166, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
179 1 0.01
180 165 0.99
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (180 bp):
TTCTAAATCAAATTATCTGGTAGAGTCCCAATAGGAGTATAACTCTTCCACTACTCAATCAACAA
TGACCAATCGTCACCGACCACTAGGACACCACCGTCGCAGCCACTAGCATCGCCGTGTCCGGTGA
TGCAGGGGAGACACACTTACAGCACCCAGAGCCGGTTCGATTGCTACTAG
Found at i:31805313 original size:43 final size:42
Alignment explanation
Indices: 31805216--31805414 Score: 166
Period size: 43 Copynumber: 4.6 Consensus size: 42
31805206 TTATTTGAAA
* * ** *
31805216 AAACGCCGCTATAGAACATGGCCTTTAGTGGCGCTTTTA-TAAA
1 AAACG-CGCTAAAGAACATGACCTTTAGTGGCGC-TTTACCCAC
* *
31805259 AAACGCTGCTAAAGAACATGGCCTTTAGTGGAGCTTTACCCAC
1 AAACGC-GCTAAAGAACATGACCTTTAGTGGCGCTTTACCCAC
* **
31805302 AAATGTCGCTAAAGAACATGACCTTTAGCAGCGCTTTACCCAC
1 AAACG-CGCTAAAGAACATGACCTTTAGTGGCGCTTTACCCAC
* *** ***
31805345 AAACGCCGCTAAAGAGCATGACCTTTAGCAACGCTTTTTTCAC
1 AAACG-CGCTAAAGAACATGACCTTTAGTGGCGCTTTACCCAC
* *
31805388 AAACGTCGCTAAAAAAAATGACCTTTA
1 AAACG-CGCTAAAGAACATGACCTTTA
31805415 ACGACACTTT
Statistics
Matches: 132, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
42 5 0.04
43 126 0.95
44 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (42 bp):
AAACGCGCTAAAGAACATGACCTTTAGTGGCGCTTTACCCAC
Found at i:31805425 original size:43 final size:43
Alignment explanation
Indices: 31805342--31805445 Score: 136
Period size: 43 Copynumber: 2.4 Consensus size: 43
31805332 GCGCTTTACC
* ** * * *
31805342 CACAAACGCCGCTAAAGAGCATGACCTTTAGCAACGCTTTTTT
1 CACAAACGCCGCTAAAAAAAATGACCTTTAACAACACTTTTAT
* *
31805385 CACAAACGTCGCTAAAAAAAATGACCTTTAACGACACTTTTAT
1 CACAAACGCCGCTAAAAAAAATGACCTTTAACAACACTTTTAT
31805428 CACAAACGCCGCTAAAAA
1 CACAAACGCCGCTAAAAA
31805446 TACCGTTTCT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.22
Consensus pattern (43 bp):
CACAAACGCCGCTAAAAAAAATGACCTTTAACAACACTTTTAT
Found at i:31811868 original size:41 final size:41
Alignment explanation
Indices: 31811805--31811985 Score: 240
Period size: 41 Copynumber: 4.4 Consensus size: 41
31811795 TTACCTTTCG
*
31811805 GGGCTTTAGCGGTGTTTCTT-GAAAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTT-TTGGAAAAGCGCCGCTAATGCTCA
* *
31811846 GGGATTTAGCGGCGTTTTTTGAAAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCA
* * **
31811887 TGGCTTTAGCGGCGTTTTCGGATTAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCA
* * *
31811928 GGGTTTTAGCGGCGTTTTTGGGAAAGCGCTGCTAATGCTC-
1 GGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCA
*
31811968 GGGCTTTAGCGGCATTTT
1 GGGCTTTAGCGGCGTTTT
31811986 CAAAAAAGCG
Statistics
Matches: 122, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
40 18 0.15
41 104 0.85
ACGTcount: A:0.17, C:0.20, G:0.31, T:0.31
Consensus pattern (41 bp):
GGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCA
Found at i:31812348 original size:14 final size:14
Alignment explanation
Indices: 31812331--31812367 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
31812321 GGGTTTAATA
*
31812331 TATATTGTTTAGGG
1 TATATGGTTTAGGG
31812345 TATATGGTTTAGGG
1 TATATGGTTTAGGG
31812359 TATATGGTT
1 TATATGGTT
31812368 AATTTAGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.49
Consensus pattern (14 bp):
TATATGGTTTAGGG
Found at i:31814775 original size:21 final size:21
Alignment explanation
Indices: 31814751--31814796 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
31814741 GTATATATAT
31814751 GTTTAGCTTAGTATTGATCTG
1 GTTTAGCTTAGTATTGATCTG
31814772 GTTTAGCTTAGTATTGATCTG
1 GTTTAGCTTAGTATTGATCTG
31814793 GTTT
1 GTTT
31814797 TTTTATATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.09, G:0.24, T:0.50
Consensus pattern (21 bp):
GTTTAGCTTAGTATTGATCTG
Found at i:31816693 original size:43 final size:43
Alignment explanation
Indices: 31816646--31816785 Score: 183
Period size: 43 Copynumber: 3.3 Consensus size: 43
31816636 GCGATATTTT
* *
31816646 TAGCGGGGTTTGTGAGAAAAGCGCCGCTAAAAGCCATGATCTA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCATGATCTA
*
31816689 TAGCGGCGTTTGTGAGAAAAGCGCTGCTAAAAGTCATGATCTA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCATGATCTA
* * * * * *
31816732 TAGCGACGTTT-TAGGGGAAAGCGCCGTTAAAAGTCTTTATCTA
1 TAGCGGCGTTTGT-GAGAAAAGCGCCGCTAAAAGTCATGATCTA
31816775 TAGCGGCGTTT
1 TAGCGGCGTTT
31816786 TTTTAGAAGC
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 1 0.01
43 84 0.99
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCATGATCTA
Found at i:31817393 original size:14 final size:14
Alignment explanation
Indices: 31817362--31817431 Score: 56
Period size: 14 Copynumber: 4.9 Consensus size: 14
31817352 CCCTAATATA
*
31817362 TAACCCCTAAACCCC
1 TAACACCTAAA-CCC
31817377 TAACACCTAAACCC
1 TAACACCTAAACCC
31817391 TAA-ACCTTAAATCCC
1 TAACACC-TAAA-CCC
*
31817406 -AAC-CCTTAAACCA
1 TAACACC-TAAACCC
*
31817419 TAATACCTAAACC
1 TAACACCTAAACC
31817432 ATAATCCCTA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
13 5 0.11
14 27 0.57
15 15 0.32
ACGTcount: A:0.41, C:0.40, G:0.00, T:0.19
Consensus pattern (14 bp):
TAACACCTAAACCC
Found at i:31817444 original size:42 final size:43
Alignment explanation
Indices: 31817363--31817460 Score: 110
Period size: 42 Copynumber: 2.3 Consensus size: 43
31817353 CCTAATATAT
* * *
31817363 AACCCCTAAACCCCTAACACCTAAACCCTAAACCTTAAATCCC
1 AACCCCTAAACCCATAACACCTAAACCATAAACCCTAAATCCC
* * *
31817406 AACCCTTAAA-CCATAATACCTAAACCATAATCCCTAAAT-CC
1 AACCCCTAAACCCATAACACCTAAACCATAAACCCTAAATCCC
31817447 ATACTCCCTAAACC
1 A-AC-CCCTAAACC
31817461 TTAAAATAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
41 3 0.07
42 26 0.58
43 15 0.33
44 1 0.02
ACGTcount: A:0.41, C:0.40, G:0.00, T:0.19
Consensus pattern (43 bp):
AACCCCTAAACCCATAACACCTAAACCATAAACCCTAAATCCC
Found at i:31817454 original size:15 final size:14
Alignment explanation
Indices: 31817412--31817460 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
31817402 TCCCAACCCT
*
31817412 TAAACCATAATACC
1 TAAACCATAATCCC
31817426 TAAACCATAATCCC
1 TAAACCATAATCCC
*
31817440 TAAATCCATACTCCC
1 TAAA-CCATAATCCC
31817455 TAAACC
1 TAAACC
31817461 TTAAAATAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 19 0.59
15 13 0.41
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCATAATCCC
Found at i:31817867 original size:41 final size:41
Alignment explanation
Indices: 31817807--31818245 Score: 425
Period size: 41 Copynumber: 10.8 Consensus size: 41
31817797 TAAAAAAATT
* * *
31817807 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCCAGCA
1 TTAGCGGTGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
** * * * *
31817848 TTAGCAATGCTTTTCCAAAAACACCGCTAAAGCCCCCAGCA
1 TTAGCGGTGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* * * *
31817889 TTAGCGGTGCTTTTCCAAAAACGCAGCTAAAGCCCTC-AACA
1 TTAGCGGTGCTTTTTCAAAAACGCCGCTAAAACCC-CGAGCA
* * * *
31817930 TTAGAGGTGCTTTTTCAGAAACGCCACTAAAACCTCGAGCA
1 TTAGCGGTGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* *
31817971 TTAGCGGCGC-TTTTAAAAAACGCCGCTAAAACCCCGAGCA
1 TTAGCGGTGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* ** * *
31818011 TTAGCAGCACTTTTTCAAAAACGCCGCT-AAAGCCCTAGCA
1 TTAGCGGTGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* ** *
31818051 TTAGTGACGCTTTTTCAAAAACGCCGCTAAAACCTCGAGCA
1 TTAGCGGTGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* * ** **
31818092 TTAGCGGCGCTTTTTAAAAAACATCGCTAAAACATCGAGCA
1 TTAGCGGTGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* * * *
31818133 TTAGTGTTGCTTTTTCAAAAACGCAGCTAAAACCTCGAGCA
1 TTAGCGGTGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* * *
31818174 TTAGCGGTGCATTTTCAAAAACACCGCTAAAGCCCCGAGCA
1 TTAGCGGTGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* ** * **
31818215 TTGGCGACGTTTTTTTGAAAACGCCGCTAAA
1 TTAGCGGTGCTTTTTCAAAAACGCCGCTAAA
31818246 GCTCCGAAAG
Statistics
Matches: 329, Mismatches: 65, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
40 69 0.21
41 259 0.79
42 1 0.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.23
Consensus pattern (41 bp):
TTAGCGGTGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
Found at i:31821648 original size:116 final size:113
Alignment explanation
Indices: 31821371--31821929 Score: 511
Period size: 115 Copynumber: 4.9 Consensus size: 113
31821361 TATGTTACAG
* * * * * *
31821371 TTAGTGGCGTTTAAGGGAAAACGCCGCTATAGCATAATATTAGCGGCGTTTTGTGAGAAGCGCCG
1 TTAGTGGCGTATATGAGAAAACGCCGCTAAAGCATACTATTAGCGGCGCTTT-TGAGAAGCGCCG
* *
31821436 CAAAATATCTTAACCAAAACGCAGAG-TTTGGTCTTGAGGTATACAAGAA
65 CAAAATATGTTAACCAAAACGCAGAGTTTTTGTCTTGAGGTATAC-AGAA
* * * * *
31821485 TTAGTGGCGCA-AAGGGAACACGCCGCT-AAGTCATACTATTAGCGGCGCTTTCGAAGAAGCGCC
1 TTAGTGGCGTATATGAGAAAACGCCGCTAAAG-CATACTATTAGCGGCGCTTTTG-AGAAGCGCC
* * * * * *
31821548 GCAATATTTGGTAACCAAAACGCAGTGTTTTTTGTCTTGATGTATACAGTTA
64 GCAAAATATGTTAACCAAAACGCAGAG-TTTTTGTCTTGAGGTATACAG-AA
* * * * * * *
31821600 TTAGTGGCGTATATTAAAAAACGCCGCTAAATCATAGTATTAGCGGCGC-TTGGAAAAAAGCACC
1 TTAGTGGCGTATATGAGAAAACGCCGCTAAAGCATACTATTAGCGGCGCTTTTG--AGAAGCGCC
* * *
31821664 GCAAAATATGCTCACCAAAACGCAGAGTTTTT-TCTTGAGGTATATTAGAA
64 GCAAAATATGTTAACCAAAACGCAGAGTTTTTGTCTTGAGGTATA-CAGAA
* * * *
31821714 TTAGTTGCGCT-TATGGGAGAACGCCGCTAAAGCATACTATTAGCGGCACTTTTTGAGAAGCGCC
1 TTAGTGGCG-TATATGAGAAAACGCCGCTAAAGCATACTATTAGCGGCGC-TTTTGAGAAGCGCC
* * ** * *
31821778 GCAAAATATATTAACAAAAACGCA-ACGTTTAAGTCTTGATGTATACTGGAA
64 GCAAAATATGTTAACCAAAACGCAGA-GTTTTTGTCTTGAGGTATAC-AGAA
** * * * *
31821829 TTAGTGGCGTCCACGAGAAATCGCCGCTAAAGCATAGTATTAGTGGCGCTTTTTGAGAAGCGCCG
1 TTAGTGGCGTATATGAGAAAACGCCGCTAAAGCATACTATTAGCGGCGC-TTTTGAGAAGCGCCG
* * *
31821894 AAAAATATTTTAACCAAAACGCAGAGTTTTGGTCTT
65 CAAAATATGTTAACCAAAACGCAGAGTTTTTGTCTT
31821930 AATTAACCAT
Statistics
Matches: 360, Mismatches: 68, Indels: 33
0.78 0.15 0.07
Matches are distributed among these distances:
112 3 0.01
113 65 0.18
114 94 0.26
115 135 0.38
116 61 0.17
117 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (113 bp):
TTAGTGGCGTATATGAGAAAACGCCGCTAAAGCATACTATTAGCGGCGCTTTTGAGAAGCGCCGC
AAAATATGTTAACCAAAACGCAGAGTTTTTGTCTTGAGGTATACAGAA
Found at i:31821816 original size:229 final size:229
Alignment explanation
Indices: 31821388--31821929 Score: 581
Period size: 229 Copynumber: 2.4 Consensus size: 229
31821378 CGTTTAAGGG
* * * * ** * *
31821388 AAAACGCCGCTATAGCATAATATTAGCGGCGTTTTGTGAGAAGCGCCGCAAAATATCTTAACCAA
1 AAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTGGAAAAAAGCACCGCAAAATATCTTAACCAA
31821453 AACGCAGAGTTTGGTCTTGAGGTATACAAGAATTAGTGGCGCAAAGGGAACACGCCGCTAAGTCA
66 AACGCAGAGTTTGGTCTTGAGGTATACAAGAATTAGTGGCGCAAAGGGAACACGCCGCTAAGTCA
* * * * * ** **
31821518 TACTATTAGCGGCGCTTTCGAAGAAGCGCCGCAATATTTGGTAACCAAAACGCAGTGTTTTTTGT
131 TACTATTAGCGGCACTTTCGAAGAAGCGCCGCAAAATATAGTAACAAAAACGCAACGTTTTAAGT
** * **
31821583 CTTGATGTATACAGTTATTAGTGGCGTATATTAA
196 CTTGATGTATACAGGAATTAGTGGCGTACACGAA
* *
31821617 AAAACGCCGCTAAATCATAGTATTAGCGGCGCTTGGAAAAAAGCACCGCAAAATATGC-TCACCA
1 AAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTGGAAAAAAGCACCGCAAAATAT-CTTAACCA
** ** * * *
31821681 AAACGCAGAGTTTTTTCTTGAGGTATATTAGAATTAGTTGCGCTTATGGGAGA-ACGCCGCTAAA
65 AAACGCAGAGTTTGGTCTTGAGGTATACAAGAATTAGTGGCGC-AAAGGGA-ACACGCCGCT-AA
* *
31821745 G-CATACTATTAGCGGCACTTTTTG-AGAAGCGCCGCAAAATATATTAACAAAAACGCAACG-TT
127 GTCATACTATTAGCGGCAC-TTTCGAAGAAGCGCCGCAAAATATAGTAACAAAAACGCAACGTTT
* * *
31821807 TAAGTCTTGATGTATACTGGAATTAGTGGCGTCCACGAG
191 TAAGTCTTGATGTATACAGGAATTAGTGGCGTACACGAA
* * **** * * * *
31821846 AAATCGCCGCTAAAGCATAGTATTAGTGGCGCTTTTTGAGAAGCGCCGAAAAATATTTTAACCAA
1 AAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTGGAAAAAAGCACCGCAAAATATCTTAACCAA
31821911 AACGCAGAGTTTTGGTCTT
66 AACGCAGAG-TTTGGTCTT
31821930 AATTAACCAT
Statistics
Matches: 256, Mismatches: 50, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
229 182 0.71
230 66 0.26
231 8 0.03
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (229 bp):
AAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTGGAAAAAAGCACCGCAAAATATCTTAACCAA
AACGCAGAGTTTGGTCTTGAGGTATACAAGAATTAGTGGCGCAAAGGGAACACGCCGCTAAGTCA
TACTATTAGCGGCACTTTCGAAGAAGCGCCGCAAAATATAGTAACAAAAACGCAACGTTTTAAGT
CTTGATGTATACAGGAATTAGTGGCGTACACGAA
Found at i:31823853 original size:43 final size:43
Alignment explanation
Indices: 31823795--31824130 Score: 415
Period size: 43 Copynumber: 7.8 Consensus size: 43
31823785 AGAAAAAAAT
* * * *
31823795 GCCGCTAAAGATCATGTCCTTTAGCGGCGCTTTTTCTAAAAAC
1 GCCGCTAAAGACCTTGTCCTTTAGCGGCGCTTTTTCCACAAAC
** * *
31823838 GCCGCTAAAGGTCATGTCCTTTAGCGGCGCTTTTAT-C-CAAGC
1 GCCGCTAAAGACCTTGTCCTTTAGCGGCGCTTTT-TCCACAAAC
*
31823880 GCCGCTAAAGACCTTGTCCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTAAAGACCTTGTCCTTTAGCGGCGCTTTTTCCACAAAC
* * ** *
31823923 GCCGCGAAAGACCATGTTATTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTAAAGACCTTGTCCTTTAGCGGCGCTTTTTCCACAAAC
* *
31823966 ACTGCTAAAGACCTTGTCCTTTAGCGGCGCTTTTTCCACAAAC
1 GCCGCTAAAGACCTTGTCCTTTAGCGGCGCTTTTTCCACAAAC
* * *
31824009 GCTGCTAAAGACCTTGACCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTAAAGACCTTGTCCTTTAGCGGCGCTTTTTCCACAAAC
*
31824052 GCCGCTAAAGACCTTTGTCCTTTAGCGGCGCTTTTTTCACAAAC
1 GCCGCTAAAGACC-TTGTCCTTTAGCGGCGCTTTTTCCACAAAC
* * ** *
31824096 ACCGCTAAAGACCCTAACCTTTAGCGGCACTTTTT
1 GCCGCTAAAGACCTTGTCCTTTAGCGGCGCTTTTT
31824131 TAAAAAACGC
Statistics
Matches: 257, Mismatches: 32, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
42 35 0.14
43 182 0.71
44 40 0.16
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (43 bp):
GCCGCTAAAGACCTTGTCCTTTAGCGGCGCTTTTTCCACAAAC
Found at i:31824352 original size:19 final size:19
Alignment explanation
Indices: 31824324--31824380 Score: 96
Period size: 19 Copynumber: 3.0 Consensus size: 19
31824314 ACAAAAATGT
*
31824324 TAAAATTTAAAATGATAAA
1 TAAAAGTTAAAATGATAAA
*
31824343 TAAAAGTTAAAATGATAAT
1 TAAAAGTTAAAATGATAAA
31824362 TAAAAGTTAAAATGATAAA
1 TAAAAGTTAAAATGATAAA
31824381 AATATTTACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (19 bp):
TAAAAGTTAAAATGATAAA
Found at i:31824511 original size:21 final size:21
Alignment explanation
Indices: 31824483--31824531 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
31824473 TCTACGCTGG
*
31824483 TCTGCTTCCCTTGCTGCAGCC
1 TCTGCTTCCCTCGCTGCAGCC
* * *
31824504 TTTGCTTCTCTCGCTGCCGCC
1 TCTGCTTCCCTCGCTGCAGCC
31824525 TCTGCTT
1 TCTGCTT
31824532 TAAGCTGCAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.02, C:0.41, G:0.18, T:0.39
Consensus pattern (21 bp):
TCTGCTTCCCTCGCTGCAGCC
Found at i:31824999 original size:13 final size:14
Alignment explanation
Indices: 31824970--31825002 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
31824960 ACAATAGATG
*
31824970 AAATAAACCATTAA
1 AAATAAACCACTAA
31824984 AAATAAA-CACTAA
1 AAATAAACCACTAA
31824997 AAATAA
1 AAATAA
31825003 TTAAAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (14 bp):
AAATAAACCACTAA
Found at i:31830102 original size:9 final size:9
Alignment explanation
Indices: 31830085--31830428 Score: 244
Period size: 9 Copynumber: 39.8 Consensus size: 9
31830075 TATGTATTTA
*
31830085 GTAAATTAT
1 GTAAGTTAT
31830094 GTAAGTTAT
1 GTAAGTTAT
*
31830103 GTACGTGTA-
1 GTAAGT-TAT
31830112 -TAAGTTAT
1 GTAAGTTAT
31830120 GTAAGTTAT
1 GTAAGTTAT
*
31830129 GT-A-TTAA
1 GTAAGTTAT
*
31830136 GTAAGCTAT
1 GTAAGTTAT
*
31830145 GTAAGTTTT
1 GTAAGTTAT
31830154 GT-A-TTAT
1 GTAAGTTAT
*
31830161 GTAACTTAT
1 GTAAGTTAT
31830170 GTAAGTTAT
1 GTAAGTTAT
** *
31830179 CAAAGTAAT
1 GTAAGTTAT
*
31830188 GTATGTTAT
1 GTAAGTTAT
31830197 GTAAG-T-T
1 GTAAGTTAT
31830204 GTAAGTTAT
1 GTAAGTTAT
31830213 GT-A-TTAT
1 GTAAGTTAT
* *
31830220 GTAACTTGT
1 GTAAGTTAT
31830229 GTAAGTTAT
1 GTAAGTTAT
* *
31830238 -CAAATTAAT
1 GTAAGTT-AT
*
31830247 GTATGTTAT
1 GTAAGTTAT
31830256 GTAAG-T-T
1 GTAAGTTAT
31830263 GTAAGTTAT
1 GTAAGTTAT
*
31830272 -TATGTATTAT
1 GTAAG--TTAT
31830282 GTAAGTTAT
1 GTAAGTTAT
31830291 GTAAGTTAT
1 GTAAGTTAT
*
31830300 ATAAGTTAT
1 GTAAGTTAT
31830309 GT-A-TTAT
1 GTAAGTTAT
*
31830316 GTAGGTTAT
1 GTAAGTTAT
*
31830325 GTAAGTTGT
1 GTAAGTTAT
*
31830334 GTAAGATAT
1 GTAAGTTAT
*
31830343 TTAAGTTAT
1 GTAAGTTAT
*
31830352 GTAAGTTTT
1 GTAAGTTAT
31830361 GT-A-TTAT
1 GTAAGTTAT
31830368 GTAAGTTAT
1 GTAAGTTAT
* *
31830377 GTATGCTAT
1 GTAAGTTAT
31830386 GT-A-TTAT
1 GTAAGTTAT
31830393 GTAAGTTGTTAT
1 GTAA---GTTAT
*
31830405 GTTA-TTAT
1 GTAAGTTAT
31830413 GTAAGTTAT
1 GTAAGTTAT
*
31830422 GCAAGTT
1 GTAAGTT
31830429 TAAATATAAG
Statistics
Matches: 259, Mismatches: 48, Indels: 56
0.71 0.13 0.15
Matches are distributed among these distances:
7 46 0.18
8 32 0.12
9 162 0.63
10 9 0.03
11 3 0.01
12 7 0.03
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:31830190 original size:59 final size:58
Alignment explanation
Indices: 31830112--31830336 Score: 240
Period size: 59 Copynumber: 3.8 Consensus size: 58
31830102 TGTACGTGTA
** * *
31830112 TAAGTTATGTAAGTTATGTA-TTAAGTAAGCTATGTAAGTTTTGTATTATGTAACTTATG
1 TAAGTTATCAAAGTAATGTAGTTATGTAAG-T-TGTAAGTTTTGTATTATGTAACTTATG
* *
31830171 TAAGTTATCAAAGTAATGTATGTTATGTAAGTTGTAAGTTATGTATTATGTAACTTGTG
1 TAAGTTATCAAAGTAATGTA-GTTATGTAAGTTGTAAGTTTTGTATTATGTAACTTATG
* *
31830230 TAAGTTATCAAATTAATGTATGTTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTATG
1 TAAGTTATCAAAGTAATGTA-GTTATGTAAGTTGTAAG-T-TT-TGTATTATGTAACTTATG
* * *
31830292 TAAGTTAT-ATAAGTTATGTA-TTATGTAGGTTATGTAAGTTGTGTA
1 TAAGTTATCA-AAGTAATGTAGTTATGTAAG-T-TGTAAGTTTTGTA
31830337 AGATATTTAA
Statistics
Matches: 144, Mismatches: 14, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
59 83 0.58
60 11 0.08
61 12 0.08
62 38 0.26
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (58 bp):
TAAGTTATCAAAGTAATGTAGTTATGTAAGTTGTAAGTTTTGTATTATGTAACTTATG
Found at i:31830276 original size:19 final size:19
Alignment explanation
Indices: 31830252--31830290 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
31830242 TTAATGTATG
31830252 TTATGTAAGT-TGTAAGTTA
1 TTATGT-AGTATGTAAGTTA
*
31830271 TTATGTATTATGTAAGTTA
1 TTATGTAGTATGTAAGTTA
31830290 T
1 T
31830291 GTAAGTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (19 bp):
TTATGTAGTATGTAAGTTA
Found at i:31830337 original size:43 final size:41
Alignment explanation
Indices: 31830269--31830379 Score: 150
Period size: 43 Copynumber: 2.6 Consensus size: 41
31830259 AGTTGTAAGT
*
31830269 TATTATGTATTATGTAAGTTATGTAAGTTATATAAGTTATG
1 TATTATGTATTATGTAAGTTATGTAAGATATATAAGTTATG
* *
31830310 TATTATGTAGGTTATGTAAGTTGTGTAAGATATTTAAGTTATG
1 TATTATGTA--TTATGTAAGTTATGTAAGATATATAAGTTATG
*
31830353 TAAGTTTTGTATTATGTAAGTTATGTA
1 T-A-TTATGTATTATGTAAGTTATGTA
31830380 TGCTATGTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
41 9 0.15
43 45 0.74
44 1 0.02
45 6 0.10
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.49
Consensus pattern (41 bp):
TATTATGTATTATGTAAGTTATGTAAGATATATAAGTTATG
Found at i:31830350 original size:52 final size:52
Alignment explanation
Indices: 31830136--31830379 Score: 162
Period size: 52 Copynumber: 4.7 Consensus size: 52
31830126 TATGTATTAA
* * * * * **
31830136 GTAAGCTATGTAAGTTTTGTATTATGTAACTTATGTAAGTTATCAAAG-TAAT
1 GTAAGTTATATAAGTTATGTATTATGTAAGTTATGTAAGTTGTGTAAGAT-AT
* * * *
31830188 GTATGTTATGTAAG-T-TGTAAGTTATGT-A-TTATGTAACTTGTGTAAGTTAT
1 GTAAGTTATATAAGTTATGT-A-TTATGTAAGTTATGTAAGTTGTGTAAGATAT
* * * * * * * *
31830238 -CAAATTAATGTATGTTATGTAAGT-TGTAAGTTAT-TATGTATTATGTAAGTTAT
1 GTAAGTT-ATATAAGTTATGT-ATTATGTAAGTTATGTAAG--TTGTGTAAGATAT
*
31830291 GTAAGTTATATAAGTTATGTATTATGTAGGTTATGTAAGTTGTGTAAGATAT
1 GTAAGTTATATAAGTTATGTATTATGTAAGTTATGTAAGTTGTGTAAGATAT
* * *
31830343 TTAAGTTATGTAAGTTTTGTATTATGTAAGTTATGTA
1 GTAAGTTATATAAGTTATGTATTATGTAAGTTATGTA
31830380 TGCTATGTAT
Statistics
Matches: 152, Mismatches: 27, Indels: 26
0.74 0.13 0.13
Matches are distributed among these distances:
49 3 0.02
50 28 0.18
51 9 0.06
52 73 0.48
53 32 0.21
54 7 0.05
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (52 bp):
GTAAGTTATATAAGTTATGTATTATGTAAGTTATGTAAGTTGTGTAAGATAT
Found at i:31830387 original size:34 final size:34
Alignment explanation
Indices: 31830085--31830581 Score: 197
Period size: 34 Copynumber: 14.5 Consensus size: 34
31830075 TATGTATTTA
* * * *
31830085 GTAAATTATGTAAGTTATGTACGTGTATAAGTTAT
1 GTAAGTTATGTAAGTTATGTA-TTATGTAAGTTAT
* * *
31830120 GTAAGTTATGT-A-TTAAGTAAGCTATGTAAGTTTT
1 GTAAGTTATGTAAGTTATGT-A-TTATGTAAGTTAT
* ** *
31830154 GT-A-TTATGTAACTTATGTAAGTTATCAAAGTAAT
1 GTAAGTTATGTAAGTTATGT-A-TTATGTAAGTTAT
*
31830188 GTATGTTATGTAAG-T-TGTAAGTTATGT-A-TTAT
1 GTAAGTTATGTAAGTTATGT-A-TTATGTAAGTTAT
* * ** *
31830220 GTAACTTGTGTAAGTTATCAAATTAATGTATGTTAT
1 GTAAGTTATGTAAGTTAT-GTATT-ATGTAAGTTAT
31830256 GTAAG-T-TGTAAGTTATTATGTATTATGTAAGTTAT
1 GTAAGTTATGTAAG---TTATGTATTATGTAAGTTAT
* *
31830291 GTAAGTTATATAAGTTATGTATTATGTAGGTTAT
1 GTAAGTTATGTAAGTTATGTATTATGTAAGTTAT
* * * *
31830325 GTAAGTTGTGTAAGATATTTAAGTTATGTAAGTTTT
1 GTAAGTTATGTAAGTTATGT-A-TTATGTAAGTTAT
31830361 GT-A-TTATGTAAGTTATGTATGCTATGT-A-TTAT
1 GTAAGTTATGTAAGTTATGTAT--TATGTAAGTTAT
31830393 GTAAG---T-T--GTTATGTTATTATGTAAGTTAT
1 GTAAGTTATGTAAGTTATG-TATTATGTAAGTTAT
* * * * *
31830422 GCAAGTTTAAATATAAGCT-TGTA-GA--TAACTTAT
1 GTAAG-TT--ATGTAAGTTATGTATTATGTAAGTTAT
*
31830455 GTAAGTTAATATGTAAGTAATGTATTATGTAAGTTTAT
1 GTAAG-T--TATGTAAGTTATGTATTATGTAAG-TTAT
* * * *
31830493 ATAAAAATTTTATATAAGTTATGTATTATGTAAGGTAACAT
1 GT---AA-GTTATGTAAGTTATGTATTATGTAA-GT--TAT
*
31830534 ATAAGTTTATGTAAGTTATG-A--ATGTAAGTTAT
1 GTAAG-TTATGTAAGTTATGTATTATGTAAGTTAT
31830566 GT-A-TTATGTAAGTTAT
1 GTAAGTTATGTAAGTTAT
31830582 TTAAATTATT
Statistics
Matches: 354, Mismatches: 59, Indels: 104
0.68 0.11 0.20
Matches are distributed among these distances:
27 5 0.01
28 7 0.02
29 24 0.07
30 1 0.00
31 2 0.01
32 29 0.08
33 33 0.09
34 111 0.31
35 39 0.11
36 36 0.10
37 15 0.04
38 22 0.06
39 22 0.06
40 1 0.00
41 7 0.02
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45
Consensus pattern (34 bp):
GTAAGTTATGTAAGTTATGTATTATGTAAGTTAT
Found at i:31830399 original size:25 final size:25
Alignment explanation
Indices: 31830074--31830395 Score: 158
Period size: 25 Copynumber: 12.3 Consensus size: 25
31830064 GTTACATAAT
*
31830074 TTATGTATT-TAGTAAATTATGTAAG
1 TTATGTATTAT-GTAAGTTATGTAAG
* * *
31830099 TTATGTACGTGTATAAGTTATGTAAG
1 TTATGTA-TTATGTAAGTTATGTAAG
* *
31830125 TTATGTATTAAGTAAGCTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
* *
31830150 TTTTGTATTATGTAACTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
* *
31830175 TTATCAAAGTAATGTATGTTATGTAAGTTGTAAG
1 TTAT----GT-AT-TATG-TAAGTTA--TGTAAG
* *
31830209 TTATGTATTATGTAACTTGTGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
** *
31830234 TTATCAAATTAATGTATGTTATGTAAG
1 TTAT-GTATT-ATGTAAGTTATGTAAG
*
31830261 TTGTAAGTTATTATGT-A-TTATGTAAG
1 -T-TATG-TATTATGTAAGTTATGTAAG
*
31830287 TTATGTAAGTTATATAAGTTATGT-A-
1 TTATGT-A-TTATGTAAGTTATGTAAG
*
31830312 TTATGTAGGTTATGTAAGTTGTGTAAG
1 TTATGTA--TTATGTAAGTTATGTAAG
* * *
31830339 ATATTTAAGTTATGTAAGTTTTGT-A-
1 TTATGT-A-TTATGTAAGTTATGTAAG
* *
31830364 TTATGTAAGTTATGTATGCTATGT-A-
1 TTATGT-A-TTATGTAAGTTATGTAAG
31830389 TTATGTA
1 TTATGTA
31830396 AGTTGTTATG
Statistics
Matches: 232, Mismatches: 41, Indels: 49
0.72 0.13 0.15
Matches are distributed among these distances:
23 1 0.00
24 6 0.03
25 106 0.46
26 36 0.16
27 42 0.18
28 10 0.04
29 9 0.04
30 4 0.02
31 4 0.02
32 4 0.02
34 10 0.04
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.47
Consensus pattern (25 bp):
TTATGTATTATGTAAGTTATGTAAG
Found at i:31830560 original size:13 final size:15
Alignment explanation
Indices: 31830541--31830581 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
31830531 CATATAAGTT
31830541 TATGTAAGTTATG-A
1 TATGTAAGTTATGTA
31830555 -ATGTAAGTTATGTA
1 TATGTAAGTTATGTA
31830569 TTATGTAAGTTAT
1 -TATGTAAGTTAT
31830582 TTAAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
16 11 0.46
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (15 bp):
TATGTAAGTTATGTA
Found at i:31830567 original size:9 final size:9
Alignment explanation
Indices: 31830555--31830695 Score: 50
Period size: 9 Copynumber: 16.2 Consensus size: 9
31830545 TAAGTTATGA
31830555 ATGTAAGTT
1 ATGTAAGTT
31830564 ATGT-A-TT
1 ATGTAAGTT
31830571 ATGTAAGTT
1 ATGTAAGTT
* *
31830580 ATTTAAATT
1 ATGTAAGTT
* *
31830589 ATTTAAATT
1 ATGTAAGTT
*
31830598 GTGT-A-TT
1 ATGTAAGTT
*
31830605 ATGTAAGTC
1 ATGTAAGTT
* *
31830614 ATGTAGGCT
1 ATGTAAGTT
31830623 ATGT--GTT
1 ATGTAAGTT
*
31830630 TTGTAAGTT
1 ATGTAAGTT
31830639 AT-T-A--T
1 ATGTAAGTT
*
31830644 AAGTAAGTT
1 ATGTAAGTT
*
31830653 ATGAAAGTTAT
1 ATGTAAG-T-T
*
31830664 ATATAAGTTTAT
1 ATGTAAG--T-T
*
31830676 ATATAAGTT
1 ATGTAAGTT
31830685 ATGTAAGTT
1 ATGTAAGTT
31830694 AT
1 AT
31830696 TGTGTAAGTT
Statistics
Matches: 101, Mismatches: 18, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
5 2 0.02
6 1 0.01
7 18 0.18
8 5 0.05
9 56 0.55
10 2 0.02
11 6 0.06
12 11 0.11
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.47
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:31830678 original size:10 final size:11
Alignment explanation
Indices: 31830657--31830788 Score: 74
Period size: 12 Copynumber: 11.6 Consensus size: 11
31830647 TAAGTTATGA
31830657 AAGTTATATAT
1 AAGTTATATAT
31830668 AAGTTTATATAT
1 AAG-TTATATAT
*
31830680 AAG-T-TATGT
1 AAGTTATATAT
* *
31830689 AAGTTATTGTGT
1 AAGTTA-TATAT
31830701 AAGTTTATATAT
1 AAG-TTATATAT
* * *
31830713 AAATTTTGATTT
1 AAGTTAT-ATAT
*
31830725 AAGTTATGTATGT
1 AAGTTA--TATAT
31830738 AAGTTATATAT
1 AAGTTATATAT
31830749 AAGTTTATATAT
1 AAG-TTATATAT
* *
31830761 AA-CT-TATGT
1 AAGTTATATAT
*
31830770 AAGTTATTATGT
1 AAGTTA-TATAT
31830782 AAGTTAT
1 AAGTTAT
31830789 GTGTTGTGTA
Statistics
Matches: 95, Mismatches: 14, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
9 13 0.14
10 4 0.04
11 14 0.15
12 51 0.54
13 12 0.13
14 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.14, T:0.48
Consensus pattern (11 bp):
AAGTTATATAT
Found at i:31830683 original size:32 final size:33
Alignment explanation
Indices: 31830647--31830753 Score: 110
Period size: 33 Copynumber: 3.2 Consensus size: 33
31830637 TTATTATAAG
31830647 TAAGTTATGAAAGTTA-TATATAAGTTTATATA
1 TAAGTTATGAAAGTTATTATATAAGTTTATATA
* * *
31830679 TAAGTTATGTAAGTTATTGTGTAAGTTTATATA
1 TAAGTTATGAAAGTTATTATATAAGTTTATATA
* * *
31830712 TAAATTTTGATTTAAGTTATGTATGTAAG-TTATATA
1 TAAGTTATGA---AAGTTAT-TATATAAGTTTATATA
31830748 TAAGTT
1 TAAGTT
31830754 TATATATAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
32 15 0.24
33 21 0.34
36 19 0.31
37 7 0.11
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (33 bp):
TAAGTTATGAAAGTTATTATATAAGTTTATATA
Found at i:31830709 original size:45 final size:44
Alignment explanation
Indices: 31830660--31830786 Score: 137
Period size: 45 Copynumber: 3.0 Consensus size: 44
31830650 GTTATGAAAG
31830660 TTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGTAAGT
1 TTATATATAAGTTTATATATAAGTTATGTAAGTTATT-TGTAAGT
* *
31830705 TTATATATAAATTT-TGATTTAAGTTA--T--G-TA--TGTAAG-
1 TTATATATAAGTTTAT-ATATAAGTTATGTAAGTTATTTGTAAGT
*
31830741 TTATATATAAGTTTATATATAACTTATGTAAGTTATTATGTAAGT
1 TTATATATAAGTTTATATATAAGTTATGTAAGTTATT-TGTAAGT
31830786 T
1 T
31830787 ATGTGTTGTG
Statistics
Matches: 66, Mismatches: 5, Indels: 22
0.71 0.05 0.24
Matches are distributed among these distances:
36 21 0.32
37 7 0.11
38 1 0.02
40 3 0.05
41 3 0.05
43 1 0.02
44 7 0.11
45 23 0.35
ACGTcount: A:0.36, C:0.01, G:0.13, T:0.50
Consensus pattern (44 bp):
TTATATATAAGTTTATATATAAGTTATGTAAGTTATTTGTAAGT
Found at i:31830779 original size:12 final size:12
Alignment explanation
Indices: 31830631--31830788 Score: 65
Period size: 12 Copynumber: 13.8 Consensus size: 12
31830621 CTATGTGTTT
31830631 TGTAAGTTATTA
1 TGTAAGTTATTA
*
31830643 --TAAGTAAGTTA
1 TGTAAGTTA-TTA
*
31830654 TGAAAGTTA-TA
1 TGTAAGTTATTA
*
31830665 TATAAGTT-TATA
1 TGTAAGTTAT-TA
*
31830677 TATAAG---TTA
1 TGTAAGTTATTA
*
31830686 TGTAAGTTATTG
1 TGTAAGTTATTA
31830698 TGTAAGTT-TATA
1 TGTAAGTTAT-TA
* *
31830710 TATAAATT-TTGA
1 TGTAAGTTATT-A
*
31830722 TTTAAGTTATGTA
1 TGTAAGTTAT-TA
31830735 TGTAAGTTA-TA
1 TGTAAGTTATTA
*
31830746 TATAAGTT-TATA
1 TGTAAGTTAT-TA
* *
31830758 TATAA---CTTA
1 TGTAAGTTATTA
31830767 TGTAAGTTATTA
1 TGTAAGTTATTA
31830779 TGTAAGTTAT
1 TGTAAGTTAT
31830789 GTGTTGTGTA
Statistics
Matches: 112, Mismatches: 16, Indels: 36
0.68 0.10 0.22
Matches are distributed among these distances:
9 13 0.12
10 8 0.07
11 22 0.20
12 53 0.47
13 15 0.13
14 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.15, T:0.47
Consensus pattern (12 bp):
TGTAAGTTATTA
Found at i:31830788 original size:21 final size:22
Alignment explanation
Indices: 31830631--31830790 Score: 71
Period size: 23 Copynumber: 7.1 Consensus size: 22
31830621 CTATGTGTTT
*
31830631 TGTAAGTTATTATAAGTAAGTTA
1 TGTAAGTTA-TATATGTAAGTTA
*
31830654 TGAAAGTTATATA--TAAGTTTATA
1 TGTAAGTTATATATGTAAG--T-TA
* * * * *
31830677 TATAAGTTATGTAAGTTA-TTG
1 TGTAAGTTATATATGTAAGTTA
* *
31830698 TGTAAGTTTATATAT-AAATTTTGA
1 TGTAAG-TTATATATGTAA-GTT-A
* *
31830722 TTTAAGTTATGTATGTAAGTTATA
1 TGTAAGTTATATATGTAAG-T-TA
* * *
31830746 TATAAGTT-TATATATAACTTA
1 TGTAAGTTATATATGTAAGTTA
31830767 TGTAAGTTAT-TATGTAAGTTA
1 TGTAAGTTATATATGTAAGTTA
31830788 TGT
1 TGT
31830791 GTTGTGTAAG
Statistics
Matches: 101, Mismatches: 23, Indels: 28
0.66 0.15 0.18
Matches are distributed among these distances:
20 4 0.04
21 28 0.28
22 14 0.14
23 36 0.36
24 16 0.16
25 3 0.03
ACGTcount: A:0.37, C:0.01, G:0.15, T:0.47
Consensus pattern (22 bp):
TGTAAGTTATATATGTAAGTTA
Found at i:31830887 original size:19 final size:19
Alignment explanation
Indices: 31830850--31830911 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
31830840 AATATGATTG
*
31830850 ATAAAATTTTCAA-ATATAT
1 ATAAAATTTT-AATAAATAT
31830869 ATAAAATTTTAATAAATAT
1 ATAAAATTTTAATAAATAT
* *
31830888 ATTAAAACTGTATATAAATAT
1 A-TAAAATTTTA-ATAAATAT
31830909 ATA
1 ATA
31830912 TATCAAAGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.05
19 16 0.43
20 10 0.27
21 9 0.24
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (19 bp):
ATAAAATTTTAATAAATAT
Found at i:31830887 original size:21 final size:22
Alignment explanation
Indices: 31830861--31830913 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
31830851 TAAAATTTTC
* *
31830861 AAATATATATAAAATTTTA-AT
1 AAATATATATAAAACTGTATAT
31830882 AAATATAT-TAAAACTGTATAT
1 AAATATATATAAAACTGTATAT
31830903 AAATATATATA
1 AAATATATATA
31830914 TCAAAGATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 8 0.29
21 18 0.64
22 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATATATATAAAACTGTATAT
Found at i:31833268 original size:27 final size:27
Alignment explanation
Indices: 31833220--31833271 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
31833210 TCTTACATTT
* *
31833220 AAATAATTAATTACCAATTTATTTAAC
1 AAATAAATAATTACCAACTTATTTAAC
**
31833247 AAATAAATAATTACTTACTTATTTA
1 AAATAAATAATTACCAACTTATTTA
31833272 TTTGTTTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (27 bp):
AAATAAATAATTACCAACTTATTTAAC
Found at i:31833354 original size:10 final size:10
Alignment explanation
Indices: 31833339--31833367 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
31833329 TAATAACTAT
31833339 ATATATATCC
1 ATATATATCC
31833349 ATATATATCC
1 ATATATATCC
31833359 ATATATATC
1 ATATATATC
31833368 AAAAAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATATATCC
Found at i:31836130 original size:41 final size:41
Alignment explanation
Indices: 31836061--31836323 Score: 271
Period size: 41 Copynumber: 6.4 Consensus size: 41
31836051 GCGCTTCGGC
* * *
31836061 AAAAACGCCGCTAAAGG-TAAATGCATTAGCGGCGCTTAGCT
1 AAAAACGCCGCTAAAGGCTAGA-GCATTAGCGGCGCTCAGAT
** * * *
31836102 GTAAACGCCGCTAAAGGCTAGAGAATTAGTGGCACTCAGAT
1 AAAAACGCCGCTAAAGGCTAGAGCATTAGCGGCGCTCAGAT
* * * * *
31836143 AAAAATGCCACTAAA-GATCCGAGCATTAGCGGCGCTTAGAT
1 AAAAACGCCGCTAAAGGCT-AGAGCATTAGCGGCGCTCAGAT
* * *
31836184 AAAAACGCCGCTAAAGGCCAGAGGATTAGCGACGCTCAGAT
1 AAAAACGCCGCTAAAGGCTAGAGCATTAGCGGCGCTCAGAT
** * * *
31836225 AAAAACGCCATTAAA-GATCCGAGCATTAGCGGCGCTTAGAT
1 AAAAACGCCGCTAAAGGCT-AGAGCATTAGCGGCGCTCAGAT
* *
31836266 AAAAACGCCGCTAAAGGCCAGAGGATTAGCGGCGCTCAGAT
1 AAAAACGCCGCTAAAGGCTAGAGCATTAGCGGCGCTCAGAT
31836307 AAAAACGCCGCTAAAGG
1 AAAAACGCCGCTAAAGG
31836324 TTTAAAAAAT
Statistics
Matches: 176, Mismatches: 41, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
40 3 0.02
41 168 0.95
42 5 0.03
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.16
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGGCTAGAGCATTAGCGGCGCTCAGAT
Found at i:31836181 original size:82 final size:82
Alignment explanation
Indices: 31836083--31836322 Score: 381
Period size: 82 Copynumber: 2.9 Consensus size: 82
31836073 AAAGGTAAAT
* ** * * * *
31836083 GCATTAGCGGCGCTTAGCTGTAAACGCCGCTAAAGGCTAGAGAATTAGTGGCACTCAGATAAAAA
1 GCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGGATTAGCGGCGCTCAGATAAAAA
*
31836148 TGCCACTAAAGATCCGA
66 CGCCACTAAAGATCCGA
*
31836165 GCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGGATTAGCGACGCTCAGATAAAAA
1 GCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGGATTAGCGGCGCTCAGATAAAAA
*
31836230 CGCCATTAAAGATCCGA
66 CGCCACTAAAGATCCGA
31836247 GCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGGATTAGCGGCGCTCAGATAAAAA
1 GCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGGATTAGCGGCGCTCAGATAAAAA
*
31836312 CGCCGCTAAAG
66 CGCCACTAAAG
31836323 GTTTAAAAAA
Statistics
Matches: 145, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 145 1.00
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.17
Consensus pattern (82 bp):
GCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGGATTAGCGGCGCTCAGATAAAAA
CGCCACTAAAGATCCGA
Found at i:31836492 original size:40 final size:38
Alignment explanation
Indices: 31836380--31836495 Score: 115
Period size: 40 Copynumber: 2.9 Consensus size: 38
31836370 GCGCTTTATA
* * *
31836380 TAAAACGCCGCTAATTCCTATTTTTAGCGGCGCTTCTGG
1 TAAATCGCCGCTAATGCTTATTTTTAGCGGCGCTT-TGG
* * **
31836419 GAAATCGCCGCTGATGCTCTACCTTTAGCGGCGCTTTGG
1 TAAATCGCCGCTAATGCT-TATTTTTAGCGGCGCTTTGG
* *
31836458 CTAAATCGCCGCTAATGCTTGATTTTTTGTGGCGCTTT
1 -TAAATCGCCGCTAATGCTT-ATTTTTAGCGGCGCTTT
31836496 TGTTCCAAAC
Statistics
Matches: 61, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
39 17 0.28
40 44 0.72
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.34
Consensus pattern (38 bp):
TAAATCGCCGCTAATGCTTATTTTTAGCGGCGCTTTGG
Found at i:31839504 original size:9 final size:9
Alignment explanation
Indices: 31839478--31840248 Score: 678
Period size: 9 Copynumber: 87.7 Consensus size: 9
31839468 CACAAATTAA
31839478 ATAACTTAC
1 ATAACTTAC
31839487 ATTAA-TTAC
1 A-TAACTTAC
31839496 ATAACTTAC
1 ATAACTTAC
* * *
31839505 AAAAATTAA
1 ATAACTTAC
31839514 ATAACTTAC
1 ATAACTTAC
31839523 ATAACTTAC
1 ATAACTTAC
*
31839532 ATAAATTA-
1 ATAACTTAC
31839540 AGTAACTTAC
1 A-TAACTTAC
31839550 ATAACGTCTTAC
1 ATAA---CTTAC
* * *
31839562 AAAAATTAA
1 ATAACTTAC
31839571 ATAACTTAC
1 ATAACTTAC
31839580 ATAACTTAC
1 ATAACTTAC
31839589 ATAACTTAC
1 ATAACTTAC
*
31839598 ATAAAC-TAA
1 AT-AACTTAC
*
31839607 ATATCTTAC
1 ATAACTTAC
31839616 ATAACTTAC
1 ATAACTTAC
* *
31839625 ATAAATTAA
1 ATAACTTAC
31839634 ATAACTTAC
1 ATAACTTAC
31839643 ATAACTTAC
1 ATAACTTAC
* *
31839652 ATAAATTAA
1 ATAACTTAC
31839661 ATAACTTAC
1 ATAACTTAC
31839670 ATAACTTAC
1 ATAACTTAC
31839679 ATAACTTAC
1 ATAACTTAC
*
31839688 ATAAAC-TAA
1 AT-AACTTAC
31839697 ATAACTTAC
1 ATAACTTAC
31839706 ATAACTTAC
1 ATAACTTAC
*
31839715 ATAAATT-C
1 ATAACTTAC
31839723 AATAACTTAC
1 -ATAACTTAC
* *
31839733 ATAAATTAA
1 ATAACTTAC
31839742 ATAACTTAC
1 ATAACTTAC
31839751 ATAACTTAC
1 ATAACTTAC
*
31839760 ATAAATT--
1 ATAACTTAC
31839767 AT--CTTAC
1 ATAACTTAC
31839774 ATAACTTAC
1 ATAACTTAC
*
31839783 ATAAATTA-
1 ATAACTTAC
31839791 AGTAACTTAC
1 A-TAACTTAC
31839801 ATAACTTAC
1 ATAACTTAC
31839810 ATAACTTAC
1 ATAACTTAC
*
31839819 ATAAATTA-
1 ATAACTTAC
31839827 AGTAACTTAC
1 A-TAACTTAC
31839837 ATAACTTAC
1 ATAACTTAC
* *
31839846 ATAAATTAA
1 ATAACTTAC
31839855 ATAACTTAC
1 ATAACTTAC
31839864 ATAACTTAC
1 ATAACTTAC
* *
31839873 ATAAATTAA
1 ATAACTTAC
*
31839882 ATATCTTAC
1 ATAACTTAC
31839891 ATAACTTAC
1 ATAACTTAC
*
31839900 ATAAATTA-
1 ATAACTTAC
31839908 AGTAACTTAC
1 A-TAACTTAC
*
31839918 ATAACTTAA
1 ATAACTTAC
31839927 ATAACTTAC
1 ATAACTTAC
* *
31839936 ATAAATTAA
1 ATAACTTAC
31839945 ATAACTTAC
1 ATAACTTAC
*
31839954 ATAAATTA-
1 ATAACTTAC
31839962 AGTAACTTAC
1 A-TAACTTAC
*
31839972 ATAAATTA-
1 ATAACTTAC
31839980 AGTAACTTAC
1 A-TAACTTAC
31839990 ATAACTTAC
1 ATAACTTAC
*
31839999 ATAAATTA-
1 ATAACTTAC
31840007 AGTAACTTAC
1 A-TAACTTAC
31840017 ATAACTTAC
1 ATAACTTAC
31840026 ATAACTTAC
1 ATAACTTAC
* *
31840035 ATAAATTAA
1 ATAACTTAC
**
31840044 ATAACTGGC
1 ATAACTTAC
31840053 ATAACTTAC
1 ATAACTTAC
*
31840062 ATTA--TAC
1 ATAACTTAC
31840069 ATAACCTT-C
1 ATAA-CTTAC
*
31840078 TTAACTTAC
1 ATAACTTAC
*
31840087 ATTA--TAC
1 ATAACTTAC
* *
31840094 ACAACTCAC
1 ATAACTTAC
* *
31840103 ATAA-TGAT
1 ATAACTTAC
* *
31840111 GT-A-GTAC
1 ATAACTTAC
*
31840118 ACAACTTAC
1 ATAACTTAC
31840127 ATAA--TAC
1 ATAACTTAC
*
31840134 ATTACTTAC
1 ATAACTTAC
*
31840143 ATAGCTTAC
1 ATAACTTAC
*
31840152 ATTACTTAC
1 ATAACTTAC
31840161 AGT-ACTTAC
1 A-TAACTTAC
31840170 ATAA--TAC
1 ATAACTTAC
31840177 ATAA--TAC
1 ATAACTTAC
31840184 ATAACTTAC
1 ATAACTTAC
31840193 ATAACTTAC
1 ATAACTTAC
*
31840202 ATTACTTAC
1 ATAACTTAC
31840211 AGT-ACTTAC
1 A-TAACTTAC
31840220 AGT-ACTTAC
1 A-TAACTTAC
31840229 ATAA--TAC
1 ATAACTTAC
31840236 ATAA--TAC
1 ATAACTTAC
31840243 ATAACT
1 ATAACT
31840249 GGCGTTTTAA
Statistics
Matches: 618, Mismatches: 97, Indels: 94
0.76 0.12 0.12
Matches are distributed among these distances:
5 2 0.00
7 51 0.08
8 25 0.04
9 512 0.83
10 20 0.03
12 8 0.01
ACGTcount: A:0.47, C:0.17, G:0.02, T:0.33
Consensus pattern (9 bp):
ATAACTTAC
Found at i:31840180 original size:50 final size:52
Alignment explanation
Indices: 31840124--31840248 Score: 195
Period size: 50 Copynumber: 2.5 Consensus size: 52
31840114 GTACACAACT
* *
31840124 TACATAATACATTACTTACATAGCTTACATTACTTACAGTACTTACA-TA-A
1 TACATAATACATAACTTACATAACTTACATTACTTACAGTACTTACAGTACA
*
31840174 TACATAATACATAACTTACATAACTTACATTACTTACAGTACTTACAGTACT
1 TACATAATACATAACTTACATAACTTACATTACTTACAGTACTTACAGTACA
31840226 TACATAATACATAA--TACATAACT
1 TACATAATACATAACTTACATAACT
31840249 GGCGTTTTAA
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
50 54 0.77
51 2 0.03
52 14 0.20
ACGTcount: A:0.42, C:0.20, G:0.03, T:0.34
Consensus pattern (52 bp):
TACATAATACATAACTTACATAACTTACATTACTTACAGTACTTACAGTACA
Found at i:31845730 original size:21 final size:21
Alignment explanation
Indices: 31845695--31845745 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
31845685 CTACAACTTA
* ** *
31845695 AAGCAGACGCGGCAGTGAGGG
1 AAGCAGAGGCGGCAGCCAGAG
*
31845716 AAGCAGAGGCTGCAGCCAGAG
1 AAGCAGAGGCGGCAGCCAGAG
31845737 AAGCAGAGG
1 AAGCAGAGG
31845746 TTCAAAAGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.43, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCCAGAG
Found at i:31846225 original size:43 final size:43
Alignment explanation
Indices: 31846123--31846235 Score: 111
Period size: 43 Copynumber: 2.6 Consensus size: 43
31846113 AAATAGTGGC
* * * *
31846123 GTTTTTATACAAAAGTGCCGCTAAAGACCATGTTCTGTAGCGGT
1 GTTTTTATAC-AAAGCGCCGCTAAAGACCATGCTCTCTAGCAGT
* * * **
31846167 GTTTGTA-AAAGAAGCGCTGCTAAAGATTATGCTCTCTAGCAGT
1 GTTTTTATACA-AAGCGCCGCTAAAGACCATGCTCTCTAGCAGT
*
31846210 GTTTTTATACAAAGCGCCGTTAAAGA
1 GTTTTTATACAAAGCGCCGCTAAAGA
31846236 ACATATTCTT
Statistics
Matches: 54, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
42 1 0.02
43 45 0.83
44 8 0.15
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (43 bp):
GTTTTTATACAAAGCGCCGCTAAAGACCATGCTCTCTAGCAGT
Found at i:31846277 original size:42 final size:42
Alignment explanation
Indices: 31846230--31846337 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
31846220 AAAGCGCCGT
* *
31846230 TAAAGAACATATTCTTTAGTGGCGCTTAAT-AAAAAATGCCAC
1 TAAAGAACATATTCTTTAGCGGCGCTT-ATGAAAAAACGCCAC
* * * *
31846272 TAAAGATCATGTTCTTTCGCGGCGCTTATGAAAAAACGCCGC
1 TAAAGAACATATTCTTTAGCGGCGCTTATGAAAAAACGCCAC
*
31846314 TAAAGAACATGA-TCTTTAACGGCG
1 TAAAGAACAT-ATTCTTTAGCGGCG
31846338 TTTTTGGTTG
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.96
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (42 bp):
TAAAGAACATATTCTTTAGCGGCGCTTATGAAAAAACGCCAC
Found at i:31849016 original size:26 final size:26
Alignment explanation
Indices: 31848987--31849065 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 26
31848977 TAATCACTTA
31848987 AATATTAAATTAATATAATATTTATC
1 AATATTAAATTAATATAATATTTATC
* * *
31849013 AATATTAGATTAATTTTAATATTAAAT-
1 AATATTAAATTAA-TATAATATT-TATC
* * *
31849040 ATTATTAAAATAATAGAATATTTATC
1 AATATTAAATTAATATAATATTTATC
31849066 TTGTAGATAA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
25 2 0.05
26 19 0.46
27 18 0.44
28 2 0.05
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (26 bp):
AATATTAAATTAATATAATATTTATC
Found at i:31851297 original size:18 final size:18
Alignment explanation
Indices: 31851274--31851315 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
31851264 TGAAAATATT
31851274 AATAGAAAATTA-ATAATA
1 AATAGAAAATTAGATAA-A
*
31851292 AATAG-AATTTAGATAAA
1 AATAGAAAATTAGATAAA
31851309 AATAGAA
1 AATAGAA
31851316 TTTAGGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (18 bp):
AATAGAAAATTAGATAAA
Found at i:31851313 original size:17 final size:18
Alignment explanation
Indices: 31851286--31851320 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
31851276 TAGAAAATTA
31851286 ATAATAAATAGAATTTAG
1 ATAATAAATAGAATTTAG
31851304 ATAA-AAATAGAATTTAG
1 ATAATAAATAGAATTTAG
31851321 GAAAAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.31
Consensus pattern (18 bp):
ATAATAAATAGAATTTAG
Found at i:31851329 original size:18 final size:17
Alignment explanation
Indices: 31851291--31851329 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
31851281 AATTAATAAT
*
31851291 AAATAGAATTTAGATAA
1 AAATAGAATTTAGAAAA
31851308 AAATAGAATTTAGGAAAA
1 AAATAGAATTTA-GAAAA
31851326 AAAT
1 AAAT
31851330 CTAAGAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.26
Consensus pattern (17 bp):
AAATAGAATTTAGAAAA
Found at i:31852811 original size:16 final size:15
Alignment explanation
Indices: 31852790--31852820 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
31852780 ATAATTTAGC
31852790 AAAAAAAGAAAAGAAA
1 AAAAAAAG-AAAGAAA
31852806 AAAAAAAGAAAGAAA
1 AAAAAAAGAAAGAAA
31852821 TAGACAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAGAAA
Found at i:31853320 original size:31 final size:30
Alignment explanation
Indices: 31853285--31853359 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 30
31853275 TAAATATATT
31853285 TAAAATTTATTAAAAAT-TAGAAAAAAAATGA
1 TAAAATTTA-TAAAAATATAG-AAAAAAATGA
* * *
31853316 TAAAATATATAGAAATATAGAAAAAAATTA
1 TAAAATTTATAAAAATATAGAAAAAAATGA
31853346 TAAAATTTTATAAA
1 TAAAA-TTTATAAA
31853360 GTCGTAAGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 20 0.54
31 17 0.46
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (30 bp):
TAAAATTTATAAAAATATAGAAAAAAATGA
Found at i:31853407 original size:10 final size:9
Alignment explanation
Indices: 31853368--31853411 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
31853358 AAGTCGTAAG
31853368 AAAATTATA
1 AAAATTATA
*
31853377 AAAAATATA
1 AAAATTATA
*
31853386 AAAAATAT-
1 AAAATTATA
31853394 AAAATTCATA
1 AAAATT-ATA
31853404 AAAATTAT
1 AAAATTAT
31853412 CGTACAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 5 0.16
9 20 0.65
10 6 0.19
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAATTATA
Found at i:31853612 original size:10 final size:10
Alignment explanation
Indices: 31853594--31853666 Score: 53
Period size: 10 Copynumber: 7.6 Consensus size: 10
31853584 TTGATGCATC
31853594 TTATAATTTT
1 TTATAATTTT
*
31853604 TTATGA--TT
1 TTATAATTTT
**
31853612 TTATAACATT
1 TTATAATTTT
**
31853622 TTACCATTTT
1 TTATAATTTT
31853632 TTATAA-TTT
1 TTATAATTTT
*
31853641 TTACAATTTT
1 TTATAATTTT
*
31853651 GTATAATTTT
1 TTATAATTTT
*
31853661 TAATAA
1 TTATAA
31853667 AATTTAAATA
Statistics
Matches: 47, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
8 7 0.15
9 8 0.17
10 32 0.68
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (10 bp):
TTATAATTTT
Found at i:31853632 original size:19 final size:19
Alignment explanation
Indices: 31853610--31853662 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
31853600 TTTTTTATGA
*
31853610 TTTTATAACATTTTACCATT
1 TTTTATAA-ATTTTACAATT
*
31853630 TTTTATAATTTTTACAATT
1 TTTTATAAATTTTACAATT
* *
31853649 TTGTATAATTTTTA
1 TTTTATAAATTTTA
31853663 ATAAAATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 22 0.73
20 8 0.27
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTATAAATTTTACAATT
Found at i:31853641 original size:9 final size:9
Alignment explanation
Indices: 31853629--31853662 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
31853619 ATTTTACCAT
31853629 TTTTTATAA
1 TTTTTATAA
*
31853638 TTTTTACAA
1 TTTTTATAA
31853647 TTTTGTATAA
1 TTTT-TATAA
31853657 TTTTTA
1 TTTTTA
31853663 ATAAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Done.