Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008421.1 Hibiscus syriacus cultivar Beakdansim tig00111201_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1159951
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:232061 original size:45 final size:45
Alignment explanation
Indices: 231988--232096 Score: 121
Period size: 45 Copynumber: 2.4 Consensus size: 45
231978 TCAAAAAGCT
* * ** *
231988 CCCGAAGGCTTTTTGAAAACATTCTGCACTGCATGGCTTATGGATGG
1 CCCGAAGG--TTTTGAAAACATTCTGCACTGAAGGGCTTACAGATGA
*
232035 CCCGAAGGTTTTGAAAGCA-TCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATTC-TGCACTGAAGGGCTTACAGATGA
*
232080 CCCGAAGGCTTTGAAAA
1 CCCGAAGGTTTTGAAAA
232097 TATCAAAAAG
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
44 2 0.04
45 43 0.81
47 8 0.15
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATTCTGCACTGAAGGGCTTACAGATGA
Found at i:232182 original size:45 final size:45
Alignment explanation
Indices: 232119--232222 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 45
232109 CCTGAAGGCT
* * * **
232119 TTTTGAAAACATCCTGCACTGCATGGCTTACGGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGG
* *
232164 TTTTGAAAGCATCATGCACTGAAGGGCTTACAAATGACTCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGG
* *
232209 CTTTGAAAATATCA
1 TTTTGAAAACATCA
232223 AAAAGCTCCC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGG
Found at i:233462 original size:54 final size:53
Alignment explanation
Indices: 233332--233479 Score: 185
Period size: 54 Copynumber: 2.7 Consensus size: 53
233322 CACTGGTTCA
* **
233332 TAAAACATTTGACAACACATTCATCTAGT-TGTGTATTCTGCACAGATGTTTCG
1 TAAAACATTTGACAACACATTCATCT-TTCTGTGGCTTCTGCACAGATGTTTCG
233385 TAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGC-CAAGATGTTT-G
1 TAAAACATTTGACAACACATTCATC-TTT-CTGTGGCTTCTGCAC-AGATGTTTCG
*
233439 TAAAACATTTGACAATACATTCATCCTTTCATGTGGCTTCT
1 TAAAACATTTGACAACACATTCAT-CTTTC-TGTGGCTTCT
233480 TCTGATCTTG
Statistics
Matches: 85, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
53 27 0.32
54 39 0.46
55 19 0.22
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (53 bp):
TAAAACATTTGACAACACATTCATCTTTCTGTGGCTTCTGCACAGATGTTTCG
Found at i:234691 original size:192 final size:190
Alignment explanation
Indices: 234349--234700 Score: 417
Period size: 192 Copynumber: 1.8 Consensus size: 190
234339 TTATTGACGT
* * * * * *
234349 AAACATTCAAAATGCGTCAATGTTCCTGATTATGATTGAAATGAGTTTTCAGCATACCCCAGCAT
1 AAACATTCAAAATACATCAATATTCCTGATTATGATTGAAAGGAGCTTTCAGCATACCCCAACAT
* * * * *
234414 TTGCTTCTTGTTGATGTGAGCTTTCAAAATGCCCAAATATTCATACTGACGTGGGACCTCAAAAT
66 TTGCTTCTTGTTAATCTGAGCCTTCAAAATGCCCAAATATGCATACTGACGTGGAACCTCAAAAT
234479 GCCCCACATGAATCATTTCT-GTCTGAAATGGGCTTTCAATATGCCCCAACATTTGCTAATAC
131 GCCCCACAT--ATCATTTCTGGT-TGAAATGGGCTTTCAATATGCCCCAACATTTGCTAATAC
* * * * *
234541 AAACGTTCAAAATACATCAATATTCCTGATTCTGATTGAAAGGGGCTTTCAGCATGCCCCAATAT
1 AAACATTCAAAATACATCAATATTCCTGATTATGATTGAAAGGAGCTTTCAGCATACCCCAACAT
* * *
234606 TTGCTTCTTGTTAATCTGAGCCTTCAAAATGCCC-CATATGGAT-CTGTC-TGAAGTAACCTTCA
66 TTGCTTCTTGTTAATCTGAGCCTTCAAAATGCCCAAATATGCATACTGACGTG--G-AACC-TCA
234668 AAATGCCCCAACAT-TCTATTTCTGGTTGAAATG
127 AAATGCCCC-ACATATC-ATTTCTGGTTGAAATG
234701 AGCCTCCAAG
Statistics
Matches: 134, Mismatches: 19, Indels: 14
0.80 0.11 0.08
Matches are distributed among these distances:
189 2 0.01
190 4 0.03
191 9 0.07
192 101 0.75
193 14 0.10
194 4 0.03
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (190 bp):
AAACATTCAAAATACATCAATATTCCTGATTATGATTGAAAGGAGCTTTCAGCATACCCCAACAT
TTGCTTCTTGTTAATCTGAGCCTTCAAAATGCCCAAATATGCATACTGACGTGGAACCTCAAAAT
GCCCCACATATCATTTCTGGTTGAAATGGGCTTTCAATATGCCCCAACATTTGCTAATAC
Found at i:237501 original size:32 final size:32
Alignment explanation
Indices: 237460--237522 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
237450 TGAAGAAATG
* *
237460 ATTGTTATGCTCATCTTGTAGAGATACTTCTC
1 ATTGTTATGCACATCTCGTAGAGATACTTCTC
237492 ATTGTTATGCACATCTCGTAGAGATACTTCT
1 ATTGTTATGCACATCTCGTAGAGATACTTCT
237523 TATTTCCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (32 bp):
ATTGTTATGCACATCTCGTAGAGATACTTCTC
Found at i:244230 original size:2 final size:2
Alignment explanation
Indices: 244223--244264 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
244213 TTTTTATTTA
* *
244223 AT AT AT AT AT AT AT AT A- AT AT TT AT -T AT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
244263 AT
1 AT
244265 GACTACATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:244234 original size:24 final size:24
Alignment explanation
Indices: 244217--244263 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
244207 ATATAATTTT
244217 TATTTAATATATATATATATATAA
1 TATTTAATATATATATATATATAA
* *
244241 TATTTATTATATATATATTTATA
1 TATTTAATATATATATATATATA
244264 TGACTACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TATTTAATATATATATATATATAA
Found at i:244239 original size:28 final size:26
Alignment explanation
Indices: 244202--244264 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 26
244192 AAATTAAATT
* *
244202 TATAAATATAATTTTTATTTAATATATA
1 TATATATATAATATTTA-TT-ATATATA
244230 TATATATATAATATTTATTATATATA
1 TATATATATAATATTTATTATATATA
*
244256 TATTTATAT
1 TATATATAT
244265 GACTACATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 15 0.47
27 2 0.06
28 15 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TATATATATAATATTTATTATATATA
Found at i:244339 original size:23 final size:23
Alignment explanation
Indices: 244286--244339 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 23
244276 AATAATAACA
244286 ATAATAATAATTAAATATATAAAC
1 ATAATAA-AATTAAATATATAAAC
*
244310 AT-ATAAAATTAAA-ATATAAAT
1 ATAATAAAATTAAATATATAAAC
244331 ATAAATAAA
1 AT-AATAAA
244340 CAATGACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 9 0.33
22 7 0.26
23 9 0.33
24 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (23 bp):
ATAATAAAATTAAATATATAAAC
Found at i:245766 original size:3 final size:3
Alignment explanation
Indices: 245758--245818 Score: 59
Period size: 3 Copynumber: 19.7 Consensus size: 3
245748 ATTTTTTATT
** * *
245758 TAA TAA TAA TAA TAA TAA TAA TATA TTT TATT TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TA-A TAA TAA TAA TAA TAA
*
245805 TAA TAA AAA TAA TA
1 TAA TAA TAA TAA TA
245819 GAATGAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
3 43 0.90
4 5 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:247415 original size:252 final size:253
Alignment explanation
Indices: 246897--247416 Score: 684
Period size: 254 Copynumber: 2.1 Consensus size: 253
246887 CTGTAACGAC
* **
246897 ATTTATTGGAAAAATGCAACTATGGATGAACATATTGTAGAGTTTTTAGATACAAACACCACTAA
1 ATTTATTGG-AAAACGCAACTATGGATGAACATATTACAGAGTTTTTAGATACAAACACCACTAA
* *
246962 AGAATAGTTGAAATAATTTTAGGGATCAGACAGGAGAAAAGGATAGAACATATATTTATCCTTTG
65 AGAAAAGTTGAAATAATTTTAAGGATCAGACAGGAGAAAAGGATAGAACA-ATATTTATCCTTTG
* * * **
247027 GCAGCATTTTAAAAAAAGCCACTATAGCACATGTTTTTGCGGCGGTTTTATAACAAATGCCACTA
129 GCAGCATTTTAAAAAAAACCACTATAGCACATGTTTTTACGGCAGTTTTATAACAAACACCACTA
* *
247092 TTGATGAACCTTATTATGGCATTTATCTAAAAATGCCGCTAAAGTACTCTTTATCACGGC
194 TTGATGAACCCTATTATGGCATTTATCTAAAAATGCCGCTAAAGTACTCTTTATCACGGA
* * * * * * * *
247152 ATTTGTTGGAAAACGCCACTATGGATGAACCTATTACGGTGTTTTTGGATATAAATACCACTAAA
1 ATTTATTGGAAAACGCAACTATGGATGAACATATTACAGAGTTTTTAGATACAAACACCACTAAA
* ** * * *
247217 GAAAAGTTGAAATGATTTTAAGGATCAGTGAGGAGAAAAGGGTGGAGC-ATATTTATCCTTTGGC
66 GAAAAGTTGAAATAATTTTAAGGATCAGACAGGAGAAAAGGATAGAACAATATTTATCCTTTGGC
* * * *
247281 GGCGTTTTTAAAAAAAACCACTATAGCACATGTTTTTACGGTATTTTTATAACAAACACCACTAT
131 AGC-ATTTTAAAAAAAACCACTATAGCACATGTTTTTACGGCAGTTTTATAACAAACACCACTAT
* * * * *
247346 TGAT-AACCCTATTATGGCATTTGTTTAAAAATGTCGTTAAAGTACTCTTTATCGCGGA
195 TGATGAACCCTATTATGGCATTTATCTAAAAATGCCGCTAAAGTACTCTTTATCACGGA
247404 ATTTATTGGAAAA
1 ATTTATTGGAAAA
247417 ATGTCACTAT
Statistics
Matches: 228, Mismatches: 36, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
252 77 0.34
253 57 0.25
254 86 0.38
255 8 0.04
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (253 bp):
ATTTATTGGAAAACGCAACTATGGATGAACATATTACAGAGTTTTTAGATACAAACACCACTAAA
GAAAAGTTGAAATAATTTTAAGGATCAGACAGGAGAAAAGGATAGAACAATATTTATCCTTTGGC
AGCATTTTAAAAAAAACCACTATAGCACATGTTTTTACGGCAGTTTTATAACAAACACCACTATT
GATGAACCCTATTATGGCATTTATCTAAAAATGCCGCTAAAGTACTCTTTATCACGGA
Found at i:247467 original size:253 final size:253
Alignment explanation
Indices: 246945--247469 Score: 660
Period size: 253 Copynumber: 2.1 Consensus size: 253
246935 AGAGTTTTTA
* *
246945 GATACAAACACCACTAAAGAATAGTTGAAATAATTTTAGGGATCAGACAGGAGAAAAGGATAGAA
1 GATACAAACACCACTAAAGAAAAGTTGAAATAATTTTAAGGATCAGACAGGAGAAAAGGATAGAA
* * *
247010 CATATATTTATCCTTTGGCAGCATTTTAAAAAAAGCCACTATAGCACATGTTTTTGCGGCGGTTT
66 CA-ATATTTATCCTTTGGCAGCATTTTAAAAAAAACCACTATAGCACATGTTTTTACGGCAGTTT
** *
247075 TATAACAAATGCCACTATTGATGAACCTTATTATGGCATTTATCTAAAAATGCCGCTAAAGTACT
130 TATAACAAACACCACTATTGATGAACCCTATTATGGCATTTATCTAAAAATGCCGCTAAAGTACT
* * ** * ** * *
247140 CTTTATCACGGCATTTGTTGGAAAACGCCACTATGGATGAACCTATTACGGTGTTTTTG
195 CTTTATCACGGAATTTATTGGAAAACGCCACTATAAACGAACCTATTACCATATTTATG
* * * ** * * *
247199 GATATAAATACCACTAAAGAAAAGTTGAAATGATTTTAAGGATCAGTGAGGAGAAAAGGGTGGAG
1 GATACAAACACCACTAAAGAAAAGTTGAAATAATTTTAAGGATCAGACAGGAGAAAAGGATAGAA
* * * *
247264 C-ATATTTATCCTTTGGCGGCGTTTTTAAAAAAAACCACTATAGCACATGTTTTTACGGTATTTT
66 CAATATTTATCCTTTGGCAGC-ATTTTAAAAAAAACCACTATAGCACATGTTTTTACGGCAGTTT
* * * *
247328 TATAACAAACACCACTATTGAT-AACCCTATTATGGCATTTGTTTAAAAATGTCGTTAAAGTACT
130 TATAACAAACACCACTATTGATGAACCCTATTATGGCATTTATCTAAAAATGCCGCTAAAGTACT
* * *
247392 CTTTATCGCGGAATTTATTGGAAAAATGTCACTATAAACGAACCCTATTACCATATTTAT-
195 CTTTATCACGGAATTTATTGG-AAAACGCCACTATAAACGAA-CCTATTACCATATTTATG
*
247452 GCTACAAACACCACTAAA
1 GATACAAACACCACTAAA
247470 TTACTACTCT
Statistics
Matches: 229, Mismatches: 39, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
252 73 0.32
253 87 0.38
254 69 0.30
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (253 bp):
GATACAAACACCACTAAAGAAAAGTTGAAATAATTTTAAGGATCAGACAGGAGAAAAGGATAGAA
CAATATTTATCCTTTGGCAGCATTTTAAAAAAAACCACTATAGCACATGTTTTTACGGCAGTTTT
ATAACAAACACCACTATTGATGAACCCTATTATGGCATTTATCTAAAAATGCCGCTAAAGTACTC
TTTATCACGGAATTTATTGGAAAACGCCACTATAAACGAACCTATTACCATATTTATG
Found at i:265681 original size:21 final size:22
Alignment explanation
Indices: 265659--265698 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
265649 TCTATTTAAT
265659 TTTA-TTCATTTT-AATTTTCA
1 TTTATTTCATTTTGAATTTTCA
*
265679 TTTATTTGATTTTGAATTTT
1 TTTATTTCATTTTGAATTTT
265699 ATTCAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 7 0.41
22 6 0.35
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTATTTCATTTTGAATTTTCA
Found at i:265711 original size:21 final size:21
Alignment explanation
Indices: 265666--265711 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
265656 AATTTTATTC
*
265666 ATTTTAATTTTCATTTATTTG
1 ATTTTAATTTTCATTAATTTG
265687 ATTTTGAATTTT-ATTCAATTT-
1 ATTTT-AATTTTCATT-AATTTG
265708 ATTT
1 ATTT
265712 CATATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (21 bp):
ATTTTAATTTTCATTAATTTG
Found at i:265719 original size:37 final size:36
Alignment explanation
Indices: 265656--265727 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 36
265646 CATTCTATTT
*
265656 AATTTTATTCATTTTAATTTTCATTTATTTGATTTTG
1 AATTTTATTCAATTTAATTTTCATTTATTT-ATTTTG
265693 AATTTTATTCAATTT-A-TTTCATATTTATTTATTTT
1 AATTTTATTCAATTTAATTTTC--ATTTATTTATTTT
265728 TGTTTTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
35 4 0.12
36 6 0.19
37 22 0.69
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (36 bp):
AATTTTATTCAATTTAATTTTCATTTATTTATTTTG
Found at i:267408 original size:29 final size:30
Alignment explanation
Indices: 267372--267442 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
267362 CAAATTTCAG
* * *
267372 TTAGTGGCTAAAATAT-AGGTTTTAAAAGT
1 TTAGTGGCCAAAATATAAAGTTATAAAAGT
*
267401 TTAGTGGCCAAAGTATAAAGTTATAAAAGT
1 TTAGTGGCCAAAATATAAAGTTATAAAAGT
*
267431 TTAG-GACCAAAA
1 TTAGTGGCCAAAA
267443 ATGTAATTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (30 bp):
TTAGTGGCCAAAATATAAAGTTATAAAAGT
Found at i:267830 original size:15 final size:15
Alignment explanation
Indices: 267810--267839 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
267800 TTGACCATAG
*
267810 GATGTTTTGATGGAA
1 GATGTTTTAATGGAA
267825 GATGTTTTAATGGAA
1 GATGTTTTAATGGAA
267840 AATGGTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.40
Consensus pattern (15 bp):
GATGTTTTAATGGAA
Found at i:269071 original size:14 final size:13
Alignment explanation
Indices: 269052--269081 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
269042 GTCCAGTCAC
269052 TGAGTCAACTCTGT
1 TGAGTCAACTC-GT
269066 TGAGTCAACTCGT
1 TGAGTCAACTCGT
269079 TGA
1 TGA
269082 CTTTGACCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (13 bp):
TGAGTCAACTCGT
Found at i:269149 original size:22 final size:23
Alignment explanation
Indices: 269098--269157 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
269088 CCTTGTCAAC
* *
269098 CCATTGACTGTTGATCGGTCTGA
1 CCATTGACTGTTGACCGATCTGA
*
269121 CCGTTGACT-TTGACCGATCAT-A
1 CCATTGACTGTTGACCGATC-TGA
*
269143 CCATTGACCGTTGAC
1 CCATTGACTGTTGAC
269158 TTTGACTTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 16 0.53
23 14 0.47
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (23 bp):
CCATTGACTGTTGACCGATCTGA
Found at i:277141 original size:17 final size:18
Alignment explanation
Indices: 277121--277154 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
277111 TTTATAAGGT
277121 ATATTTTATTA-TATTTA
1 ATATTTTATTAGTATTTA
*
277138 ATATTTTGTTAGTATTT
1 ATATTTTATTAGTATTT
277155 TATTTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTTATTAGTATTTA
Found at i:277186 original size:13 final size:13
Alignment explanation
Indices: 277152--277201 Score: 73
Period size: 13 Copynumber: 3.6 Consensus size: 13
277142 TTTGTTAGTA
277152 TTTTATTTAATTAT
1 TTTTATTTAATT-T
277166 TGTATTATTTAATTT
1 T-T-TTATTTAATTT
277181 TTTTATTTAATTT
1 TTTTATTTAATTT
277194 TTTTATTT
1 TTTTATTT
277202 TTTTGCAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
13 19 0.56
14 2 0.06
15 3 0.09
16 10 0.29
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTTATTTAATTT
Found at i:278199 original size:22 final size:22
Alignment explanation
Indices: 278169--278212 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
278159 GCAGTGATTT
*
278169 CATACCACAACATGATTAATTC
1 CATAACACAACATGATTAATTC
278191 CATAACACAACATGATTAATTC
1 CATAACACAACATGATTAATTC
278213 TTTGTTGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.25, G:0.05, T:0.27
Consensus pattern (22 bp):
CATAACACAACATGATTAATTC
Found at i:281628 original size:27 final size:27
Alignment explanation
Indices: 281597--281668 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 27
281587 TACTCCAACT
281597 GATATGTTAGATGCTACTTCAGAAAA-
1 GATATGTTAGATGCTACTTCAGAAAAC
* *
281623 GCATAT-TCTCGA-GCTTCTTCAGAAAAC
1 G-ATATGT-TAGATGCTACTTCAGAAAAC
281650 TGATATGTTAGATGCTACT
1 -GATATGTTAGATGCTACT
281669 CCAACTCCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
26 15 0.42
27 14 0.39
28 7 0.19
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (27 bp):
GATATGTTAGATGCTACTTCAGAAAAC
Found at i:287525 original size:22 final size:21
Alignment explanation
Indices: 287498--287563 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
287488 AATCATTTAG
287498 TTTTATGATATATTTTTTCTAT
1 TTTTATGATAT-TTTTTTCTAT
* *
287520 TTTTATGAGACTCTCTTTT-TAT
1 TTTTATGATA-T-TTTTTTCTAT
287542 TTTTATGATATTTTCTTTCTAT
1 TTTTATGATATTTT-TTTCTAT
287564 GTGATATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
20 2 0.06
21 4 0.11
22 24 0.67
23 6 0.17
ACGTcount: A:0.20, C:0.09, G:0.06, T:0.65
Consensus pattern (21 bp):
TTTTATGATATTTTTTTCTAT
Found at i:287570 original size:18 final size:18
Alignment explanation
Indices: 287547--287581 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
287537 TTTATTTTTA
287547 TGATATTTTCTTTCTATG
1 TGATATTTTCTTTCTATG
287565 TGATATTTTCTTTCTAT
1 TGATATTTTCTTTCTAT
287582 ATTCCAGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.11, G:0.09, T:0.63
Consensus pattern (18 bp):
TGATATTTTCTTTCTATG
Found at i:287820 original size:11 final size:11
Alignment explanation
Indices: 287804--287842 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
287794 TAATTATTTA
287804 AAAAATTAAAT
1 AAAAATTAAAT
287815 AAAAATATAAAT
1 AAAAAT-TAAAT
* *
287827 AAACATTTAAT
1 AAAAATTAAAT
287838 AAAAA
1 AAAAA
287843 AACAGTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAAATTAAAT
Found at i:290031 original size:22 final size:22
Alignment explanation
Indices: 289981--290031 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
289971 CATTCAAAAT
* *
289981 TTTTAATTTTTTAATTATTTTA
1 TTTTAATTTTTAAATTATTTCA
*
290003 TTCTAATATTTTAAATTA-TTCA
1 TTTTAAT-TTTTAAATTATTTCA
290025 TTTTAAT
1 TTTTAAT
290032 CTCAAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTAATTTTTAAATTATTTCA
Found at i:293564 original size:12 final size:12
Alignment explanation
Indices: 293545--293574 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
293535 TTTAAATAAT
293545 TATATTTATCTA
1 TATATTTATCTA
*
293557 TCTATTTATCTA
1 TATATTTATCTA
293569 TATATT
1 TATATT
293575 ATTGATTAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATTTATCTA
Found at i:294899 original size:19 final size:19
Alignment explanation
Indices: 294875--294930 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
294865 ATGACCAACA
*
294875 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
294894 AAATCGCAACGCGATCTCT
1 AAATCGCAACGCGATCTCT
294913 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
294931 CAGTATCGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.21
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:294979 original size:20 final size:20
Alignment explanation
Indices: 294956--295125 Score: 182
Period size: 20 Copynumber: 8.4 Consensus size: 20
294946 GTTTCCAGAT
*
294956 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTCTGACTA
* * *
294976 TCGCAACGCGAATATGTA-AA
1 TCGCAACGCGATTCTG-ACTA
**
294996 TCGCAACATGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
295016 TCGCAACGTGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
* **
295036 TCGTAACGCGATAAT-ACATAA
1 TCGCAACGCGATTCTGAC-T-A
*
295057 TCGCAACTCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
295077 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
* *
295097 ACGCAACGCGATTCTGACTG
1 TCGCAACGCGATTCTGACTA
295117 TCGCAACGC
1 TCGCAACGC
295126 TGAATTTCAA
Statistics
Matches: 124, Mismatches: 21, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 3 0.02
20 105 0.85
21 14 0.11
22 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:295072 original size:41 final size:41
Alignment explanation
Indices: 295010--295125 Score: 141
Period size: 41 Copynumber: 2.9 Consensus size: 41
295000 AACATGATTC
*
295010 TGACT-ATCGCAACGT-GATTCTGACTATCGTAACGCGATAA
1 TGACTAATCGCAAC-TCGATTCTGACTATCGCAACGCGATAA
**
295050 T-ACATAATCGCAACTCGATTCTGACTATCGCAACGCGATTC
1 TGAC-TAATCGCAACTCGATTCTGACTATCGCAACGCGATAA
* *
295091 TGACTAA-CGCAACGCGATTCTGACTGTCGCAACGC
1 TGACTAATCGCAACTCGATTCTGACTATCGCAACGC
295126 TGAATTTCAA
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
39 2 0.03
40 29 0.43
41 34 0.51
42 2 0.03
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (41 bp):
TGACTAATCGCAACTCGATTCTGACTATCGCAACGCGATAA
Found at i:295080 original size:61 final size:62
Alignment explanation
Indices: 294956--295108 Score: 215
Period size: 61 Copynumber: 2.5 Consensus size: 62
294946 GTTTCCAGAT
* **
294956 TCGCAACGCGATTTTGACTATCGCAACGCG--AATATGTAAATCGCAACATGATTCTGACTA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAAATCGCAACATGATTCTGACTA
* *
295016 TCGCAACGTGATTCTGACTATCGTAACGCGATAATACAT-AATCGCAAC-TCGATTCTGACTA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAAATCGCAACAT-GATTCTGACTA
*
295077 TCGCAACGCGATTCTGACTAACGCAACGCGAT
1 TCGCAACGCGATTCTGACTATCGCAACGCGAT
295109 TCTGACTGTC
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
60 28 0.34
61 49 0.60
62 5 0.06
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (62 bp):
TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAAATCGCAACATGATTCTGACTA
Found at i:296216 original size:14 final size:14
Alignment explanation
Indices: 296187--296223 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
296177 AGAAAAAGAA
296187 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
296202 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
296216 GAAGAAAA
1 GAAGAAAA
296224 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:298283 original size:18 final size:18
Alignment explanation
Indices: 298260--298294 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
298250 AGAAAAAGAC
*
298260 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
298278 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
298295 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:298604 original size:140 final size:140
Alignment explanation
Indices: 298352--298774 Score: 765
Period size: 140 Copynumber: 3.0 Consensus size: 140
298342 GCAAACGTTG
*
298352 TATTATGTGTATTTTATGTGTAAACTTTGAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* *
298417 TTAAACATTGTTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCACAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCACAACG
*
298482 CGAATTTGAC
131 CAAATTTGAC
*
298492 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTTAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* *
298557 TTGAACATTGCTATGATCTATTCAGTTTTTATCACTTATTACACATTCATTTGAATATCACAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCACAACG
298622 CAAATTTGAC
131 CAAATTTGAC
298632 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* *
298697 TTGAACATTGCTATGATCTGTTCAGTTGTTATAACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCACAACG
298762 CAAATTTGAC
131 CAAATTTGAC
298772 TAT
1 TAT
298775 CTCAACGCGA
Statistics
Matches: 271, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 271 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCACAACG
CAAATTTGAC
Found at i:298770 original size:20 final size:20
Alignment explanation
Indices: 298745--298955 Score: 245
Period size: 20 Copynumber: 10.8 Consensus size: 20
298735 TTACACATTC
* *
298745 ATTTGAATATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
*
298765 ATTTGACTATCTCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
298785 ATTTGACTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
298804 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
298819 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
298839 ATATGACTATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
*
298859 ATTTGACTATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
* **
298879 ATTTGGCTATCGCAACATGA
1 ATTTGACTATCGCAACGCGA
* * *
298899 ATTTGATTATCACAACGGGA
1 ATTTGACTATCGCAACGCGA
*
298919 ATTTGACTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
298939 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
298956 AGAAAATCGC
Statistics
Matches: 161, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
14 9 0.06
15 3 0.02
19 3 0.02
20 146 0.91
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:299057 original size:20 final size:20
Alignment explanation
Indices: 298994--299071 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
298984 GCAATATGAA
*
298994 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCGATT
*
299014 TTGGCTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
299034 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
* * *
299054 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCATTGCGA
299072 AAGTGTACCT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.13, C:0.18, G:0.26, T:0.44
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:299207 original size:27 final size:26
Alignment explanation
Indices: 299175--299225 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
299165 ATAAGAATTA
*
299175 TTTACACATCAATTAAACAAATCAACT
1 TTTACAAATCAATTAAAC-AATCAACT
299202 TTTACAAATCAATTAAACAATCAA
1 TTTACAAATCAATTAAACAATCAA
299226 AAAAAGTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (26 bp):
TTTACAAATCAATTAAACAATCAACT
Found at i:300577 original size:42 final size:42
Alignment explanation
Indices: 300518--300640 Score: 151
Period size: 42 Copynumber: 2.9 Consensus size: 42
300508 GTGAATCGTG
* * *
300518 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
1 CTCTTGAACGATGGGAGGGACCTCTTGAACGATGACAGGGGC
** *
300560 CTCTTGAACGATGGGAGGAGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGATGGGAGG-GACCTCTTGAACGATGACAGGGGC
*
300602 CTCTTGAACGATAGGAGAGG-CCTCTTGAACGATGACAGG
1 CTCTTGAACGATGGGAG-GGACCTCTTGAACGATGACAGG
300641 TGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
42 65 0.96
43 3 0.04
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGATGGGAGGGACCTCTTGAACGATGACAGGGGC
Found at i:300584 original size:21 final size:21
Alignment explanation
Indices: 300518--300635 Score: 87
Period size: 21 Copynumber: 5.6 Consensus size: 21
300508 GTGAATCGTG
* *
300518 CTCTTGAATGGTGGGAGG-GAC
1 CTCTTGAACGATGGGAGGAG-C
* ** *
300539 CTCTTCAACGATGACAGGGGC
1 CTCTTGAACGATGGGAGGAGC
*
300560 CTCTTGAACGATGGGAGGAGA
1 CTCTTGAACGATGGGAGGAGC
** ** *
300581 CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGATGGGAGGAGC
*
300602 CTCTTGAACGATAGGA-GAGGC
1 CTCTTGAACGATGGGAGGA-GC
300623 CTCTTGAACGATG
1 CTCTTGAACGATG
300636 ACAGGTGAGT
Statistics
Matches: 72, Mismatches: 23, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
20 1 0.01
21 70 0.97
22 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGAGC
Found at i:301206 original size:19 final size:19
Alignment explanation
Indices: 301184--301248 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
301174 GCAATGGGAT
301184 AATCGCAATGCAAAATAAA
1 AATCGCAATGCAAAATAAA
*
301203 AATCGCAATGCAAAATAAC
1 AATCGCAATGCAAAATAAA
* * **
301222 AATCGCAACGCGAAACCAA
1 AATCGCAATGCAAAATAAA
301241 AATCGCAA
1 AATCGCAA
301249 CGCGAAACTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.52, C:0.23, G:0.12, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCAAAATAAA
Found at i:301329 original size:20 final size:21
Alignment explanation
Indices: 301299--301352 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
301289 GCGATTATCC
*
301299 CGTTGCAATAGTCAAATT-CG
1 CGTTGCGATAGTCAAATTCCG
* *
301319 TGTTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAAATTCCG
301339 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
301353 TTTTCGCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (21 bp):
CGTTGCGATAGTCAAATTCCG
Found at i:301353 original size:20 final size:20
Alignment explanation
Indices: 301320--301367 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
301310 TCAAATTCGT
301320 GTTGCGATAGTCATTTCCGC
1 GTTGCGATAGTCATTTCCGC
*
301340 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCATTTCCGC
*
301360 ATTGCGAT
1 GTTGCGAT
301368 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGC
Found at i:301365 original size:40 final size:35
Alignment explanation
Indices: 301264--301368 Score: 95
Period size: 40 Copynumber: 2.9 Consensus size: 35
301254 AACTAAATTT
**
301264 GCGTTGCGATTTTCATTTTCGCATTGCGATTATCC
1 GCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
* ** **
301299 -CGTTGCAATAGTCAAATTCGTGTTGCGATAGTCATTTCC
1 GCGTTGCGATAGTCATTTTCGCATTGCGAT--T-A--TCC
301338 GCGTTGCGATAGTCATTTTCGCATTGCGATT
1 GCGTTGCGATAGTCATTTTCGCATTGCGATT
301369 TTAAGTTTCG
Statistics
Matches: 52, Mismatches: 12, Indels: 9
0.71 0.16 0.12
Matches are distributed among these distances:
34 22 0.42
36 1 0.02
37 1 0.02
38 1 0.02
39 3 0.06
40 24 0.46
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.39
Consensus pattern (35 bp):
GCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
Found at i:301377 original size:20 final size:20
Alignment explanation
Indices: 301354--301397 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
301344 CGATAGTCAT
301354 TTTCGCATTGCGATTTTAAG
1 TTTCGCATTGCGATTTTAAG
**
301374 TTTCGTGTTGCGATTTTAAG
1 TTTCGCATTGCGATTTTAAG
301394 TTTC
1 TTTC
301398 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCATTGCGATTTTAAG
Found at i:303319 original size:20 final size:20
Alignment explanation
Indices: 303296--303382 Score: 95
Period size: 20 Copynumber: 4.4 Consensus size: 20
303286 TTTGAAACTT
303296 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
303316 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
* * **
303336 ACAATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** * *
303356 ACTATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
303375 AAAATCGC
1 AAAATCGC
303383 GTTGCGATTT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
19 6 0.10
20 52 0.90
ACGTcount: A:0.46, C:0.24, G:0.16, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:303786 original size:22 final size:22
Alignment explanation
Indices: 303761--303808 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
303751 GGAGATAGAA
*
303761 GGATTTCGTCGAAAATGGGGAC
1 GGATTTCGTCGAAAATGGGAAC
* *
303783 GGATTTCGTCGGAGATGGGAAC
1 GGATTTCGTCGAAAATGGGAAC
303805 GGAT
1 GGAT
303809 GTCATCGTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.25, C:0.12, G:0.40, T:0.23
Consensus pattern (22 bp):
GGATTTCGTCGAAAATGGGAAC
Found at i:304006 original size:20 final size:20
Alignment explanation
Indices: 303983--304065 Score: 60
Period size: 20 Copynumber: 4.1 Consensus size: 20
303973 TTATCGCAAC
* *
303983 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAAAATCGCATT
* * *
304003 GCGAT-TTACATATTCGCATT
1 GCGATAGT-CAAAATCGCATT
** *
304023 GCGATTTTCTAAAATCGCAAT
1 GCGATAGTC-AAAATCGCATT
*
304044 GCGATAGTCAAAATCGCGTT
1 GCGATAGTCAAAATCGCATT
304064 GC
1 GC
304066 AAATCTGGAA
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
19 1 0.02
20 31 0.63
21 17 0.35
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (20 bp):
GCGATAGTCAAAATCGCATT
Found at i:304105 original size:20 final size:19
Alignment explanation
Indices: 304082--304127 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
304072 GGAAACTGAT
* *
304082 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
304102 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
304121 TTGCGAT
1 TTGCGAT
304128 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:304117 original size:19 final size:19
Alignment explanation
Indices: 304093--304129 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
304083 TGCGATACTG
*
304093 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
304112 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
304130 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:305968 original size:20 final size:19
Alignment explanation
Indices: 305945--305995 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
305935 GAACTTTACT
*
305945 AAAATGAATGGTCAATTTGA
1 AAAATAAATGGTCAA-TTGA
*
305965 AAAATTAAATGGTTAATTGA
1 AAAA-TAAATGGTCAATTGA
305985 AAAATTAAATG
1 AAAA-TAAATG
305996 AGCAATTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.51, C:0.02, G:0.16, T:0.31
Consensus pattern (19 bp):
AAAATAAATGGTCAATTGA
Found at i:306002 original size:20 final size:21
Alignment explanation
Indices: 305951--306013 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
305941 TACTAAAATG
305951 AATGGTCAATTTGAAAAATTA
1 AATGGTCAATTTGAAAAATTA
*
305972 AATGGTTAA-TTGAAAAATTA
1 AATGGTCAATTTGAAAAATTA
*
305992 AATGAG-CAATTTGTAAAATTA
1 AATG-GTCAATTTGAAAAATTA
306013 A
1 A
306014 TGACCATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.49, C:0.03, G:0.14, T:0.33
Consensus pattern (21 bp):
AATGGTCAATTTGAAAAATTA
Found at i:306555 original size:16 final size:18
Alignment explanation
Indices: 306524--306556 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
306514 TCTATAAATA
306524 TTATGCAAATAATCCAAC
1 TTATGCAAATAATCCAAC
306542 TTAT-CAAA-AATCCAA
1 TTATGCAAATAATCCAA
306557 AACATATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.27
Consensus pattern (18 bp):
TTATGCAAATAATCCAAC
Found at i:307393 original size:19 final size:19
Alignment explanation
Indices: 307366--307421 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
307356 GTGCTGACCG
* *
307366 GCTGAACCGGTCTGGATCA
1 GCTGGACCGGTCTAGATCA
*
307385 GCTGGACCGGTCTAGACCA
1 GCTGGACCGGTCTAGATCA
307404 GCTGGACCGGTCTAGATC
1 GCTGGACCGGTCTAGATC
307422 GAGCCGAGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.20, C:0.29, G:0.32, T:0.20
Consensus pattern (19 bp):
GCTGGACCGGTCTAGATCA
Found at i:309338 original size:66 final size:66
Alignment explanation
Indices: 309247--309375 Score: 177
Period size: 66 Copynumber: 2.0 Consensus size: 66
309237 GTATGAAGAA
* *** *
309247 TCTGGCAGGTTCAATCGCTGTTGGTAATTCCTTGTATAGGTTTTGCACCGACTGGTAATTCCTAT
1 TCTGGCAGGTTCAATCGCTGCTGGTAATTCCTTGTATAGGTTCACCACCAACTGGTAATTCCTAT
309312 C
66 C
* * * *
309313 TCTGGTAGGTTCAGTCTCTGCTGGTAATTCCTTTTATAGGTTCACCACCAACTGGTAATTCCT
1 TCTGGCAGGTTCAATCGCTGCTGGTAATTCCTTGTATAGGTTCACCACCAACTGGTAATTCCT
309376 TATTGACCTA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (66 bp):
TCTGGCAGGTTCAATCGCTGCTGGTAATTCCTTGTATAGGTTCACCACCAACTGGTAATTCCTAT
C
Found at i:311402 original size:19 final size:19
Alignment explanation
Indices: 311375--311416 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
311365 GGAGGGTGTT
* *
311375 GACCGACTGAACCGGTCTG
1 GACCAACTGAACAGGTCTG
*
311394 GACCAACTGGACAGGTCTG
1 GACCAACTGAACAGGTCTG
311413 GACC
1 GACC
311417 GAGCCAAGTC
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:0.24, C:0.31, G:0.31, T:0.14
Consensus pattern (19 bp):
GACCAACTGAACAGGTCTG
Found at i:313189 original size:12 final size:12
Alignment explanation
Indices: 313171--313206 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
313161 TGGATGTTTT
313171 CTCTGATTTCTG
1 CTCTGATTTCTG
* *
313183 TTCTGATCTCTG
1 CTCTGATTTCTG
313195 CTCTGATTTCTG
1 CTCTGATTTCTG
313207 ATACCTCTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.08, C:0.25, G:0.17, T:0.50
Consensus pattern (12 bp):
CTCTGATTTCTG
Found at i:313374 original size:66 final size:66
Alignment explanation
Indices: 313268--313397 Score: 179
Period size: 66 Copynumber: 2.0 Consensus size: 66
313258 GGTATGAATC
* * * *
313268 CTCTGGCAAGTTCAGTCGTTGTGGGTAATTCCTTGTATAGGTTCTGCACTAACTTGTAATTCCTA
1 CTCTGGCAAGTTCAGTCGTTGTGGATAATTCCTTGTATAGGTTCAGCACCAACTGGTAATTCCTA
313333 T
66 T
* * * * *
313334 CTCTGGCAGGTTCATTCGTTGTTGATAATTCCTTTTATAGGTTCAGCACCGACTGGTAATTCCT
1 CTCTGGCAAGTTCAGTCGTTGTGGATAATTCCTTGTATAGGTTCAGCACCAACTGGTAATTCCT
313398 TATGGACCTA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (66 bp):
CTCTGGCAAGTTCAGTCGTTGTGGATAATTCCTTGTATAGGTTCAGCACCAACTGGTAATTCCTA
T
Found at i:316501 original size:44 final size:43
Alignment explanation
Indices: 316438--316523 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 43
316428 CTGTCTTTAT
* *
316438 CTATGTTGGAGCTATTACCAAT-TTTTCTAACTTATTCCCTAAAA
1 CTATGTTAGAGCTATTACC-ATCTTTTCCAACTTATT-CCTAAAA
* *
316482 CTATGTTAGAGTTGTTACCATCTTTTCCAACTTATTCCTAAA
1 CTATGTTAGAGCTATTACCATCTTTTCCAACTTATTCCTAAA
316524 TTTCAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 8 0.22
44 29 0.78
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (43 bp):
CTATGTTAGAGCTATTACCATCTTTTCCAACTTATTCCTAAAA
Found at i:317790 original size:24 final size:25
Alignment explanation
Indices: 317754--317842 Score: 89
Period size: 24 Copynumber: 3.7 Consensus size: 25
317744 AAACATAATT
317754 CAGGTC-AGATATCATAAT-AGAATC
1 CAGGTCAAG-TATCATAATCAGAATC
317778 CAGGTCAAGTATCAGT--TCAGAATC
1 CAGGTCAAGTATCA-TAATCAGAATC
* * *
317802 CAAGTCAAGTATCA-GATCAAAATC
1 CAGGTCAAGTATCATAATCAGAATC
*
317826 CAGGTCATGTATCATAA
1 CAGGTCAAGTATCATAA
317843 CAAAATTCAA
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
23 1 0.02
24 49 0.91
25 4 0.07
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (25 bp):
CAGGTCAAGTATCATAATCAGAATC
Found at i:317846 original size:24 final size:24
Alignment explanation
Indices: 317740--317848 Score: 87
Period size: 24 Copynumber: 4.5 Consensus size: 24
317730 TATATCAAAA
* * *
317740 ATCAAAACATAATTCAGGTC-AGAT
1 ATCATAACAAAATCCAGGTCAAG-T
* *
317764 ATCATAATAGAATCCAGGTCAAGT
1 ATCATAACAAAATCCAGGTCAAGT
* * *
317788 ATCAGT-TCAGAATCCAAGTCAAGT
1 ATCA-TAACAAAATCCAGGTCAAGT
* * *
317812 ATCAGATCAAAATCCAGGTCATGT
1 ATCATAACAAAATCCAGGTCAAGT
317836 ATCATAACAAAAT
1 ATCATAACAAAAT
317849 TCAAATAAGA
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
24 66 0.96
25 3 0.04
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (24 bp):
ATCATAACAAAATCCAGGTCAAGT
Found at i:320215 original size:30 final size:30
Alignment explanation
Indices: 320174--320245 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
320164 GACTTTTAGT
*
320174 TCAAAGTCAACGGTCAA-TGGTTTGACTCAG
1 TCAAAGTCAACGGTCAACAGG-TTGACTCAG
* *
320204 TCAAAGCCAACGGTCAACAGGTTGACTCGG
1 TCAAAGTCAACGGTCAACAGGTTGACTCAG
320234 TCAAAGTCAACG
1 TCAAAGTCAACG
320246 AGTTGACCCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 35 0.95
31 2 0.05
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.21
Consensus pattern (30 bp):
TCAAAGTCAACGGTCAACAGGTTGACTCAG
Found at i:320298 original size:15 final size:14
Alignment explanation
Indices: 320244--320298 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 14
320234 TCAAAGTCAA
*
320244 CGAGTTGACCCAG-
1 CGAGTTGACTCAGC
*
320257 TGAGTTGACTCAGC
1 CGAGTTGACTCAGC
*
320271 CGAGTTAACTCAG-
1 CGAGTTGACTCAGC
320284 CGCAGGTTGACTCAG
1 CG-A-GTTGACTCAG
320299 TTGGCTCGGC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
13 13 0.38
14 12 0.35
15 9 0.26
ACGTcount: A:0.24, C:0.25, G:0.29, T:0.22
Consensus pattern (14 bp):
CGAGTTGACTCAGC
Found at i:322346 original size:24 final size:24
Alignment explanation
Indices: 322328--322380 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
322318 TCAGGTTAGA
322328 TATCATAAT-AGAATCCAGGTCAAG
1 TATCA-AATCAGAATCCAGGTCAAG
*
322352 TATCAAATCAGAATCCAGGTCATG
1 TATCAAATCAGAATCCAGGTCAAG
322376 TATCA
1 TATCA
322381 TAACATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (24 bp):
TATCAAATCAGAATCCAGGTCAAG
Found at i:328272 original size:29 final size:27
Alignment explanation
Indices: 328240--328312 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
328230 TGTTGTTTTG
328240 TTTTCTACTTTTTTTTCGAACAACATCTTT
1 TTTTCT-CTTTTTTTTCGAACAAC-TC-TT
* * * *
328270 TTTTTTCTTTTCTTTCGAACTACTGTT
1 TTTTCTCTTTTTTTTCGAACAACTCTT
*
328297 TTTTCTTTTTTTTTTC
1 TTTTCTCTTTTTTTTC
328313 ATGGAGCATA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 15 0.42
28 1 0.03
29 15 0.42
30 5 0.14
ACGTcount: A:0.12, C:0.18, G:0.04, T:0.66
Consensus pattern (27 bp):
TTTTCTCTTTTTTTTCGAACAACTCTT
Found at i:346593 original size:26 final size:26
Alignment explanation
Indices: 346564--346617 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
346554 TATAGACAGT
*
346564 TAATAAAATCAATT-TCTCAAATCAGC
1 TAATAAAATCAATTGT-TCAAACCAGC
* *
346590 TAATCAAATCAGTTGTTCAAACCAGC
1 TAATAAAATCAATTGTTCAAACCAGC
346616 TA
1 TA
346618 CTGGAATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (26 bp):
TAATAAAATCAATTGTTCAAACCAGC
Found at i:347916 original size:22 final size:20
Alignment explanation
Indices: 347888--347933 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
347878 TTAAAATATT
347888 TTTATAAATTTT-TATTTAAATA
1 TTTAT-AATTTTATA-TTAAA-A
347910 TTTATAATTTTATATTAAAA
1 TTTATAATTTTATATTAAAA
347930 TTTA
1 TTTA
347934 ACTTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.22
21 11 0.48
22 7 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATAATTTTATATTAAAA
Found at i:356242 original size:22 final size:23
Alignment explanation
Indices: 356192--356242 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
356182 CGATTCCCCT
*
356192 AGGGAGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
*
356215 AGGGGGAATCTGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
356237 AGGGGG
1 AGGGGG
356243 CATCAATTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.22, C:0.24, G:0.33, T:0.22
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:356252 original size:22 final size:23
Alignment explanation
Indices: 356204--356253 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
356194 GGAGAATCGG
**
356204 TTCCCCTTCAAAGGGGGAATCTG
1 TTCCCCTTCAAAGGGGGAATCAA
*
356227 TTCCCCTTC-AAGGGGGCATCAA
1 TTCCCCTTCAAAGGGGGAATCAA
356249 TTCCC
1 TTCCC
356254 TCTGTCCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.20, C:0.32, G:0.22, T:0.26
Consensus pattern (23 bp):
TTCCCCTTCAAAGGGGGAATCAA
Found at i:363586 original size:43 final size:43
Alignment explanation
Indices: 363393--363596 Score: 139
Period size: 43 Copynumber: 4.8 Consensus size: 43
363383 CGCCACAATA
* * * *
363393 TGTTGATATTTAATGGCGTTTGTCAT-ACAAACGCCGCAATAGG
1 TGTTGAGATTTAACGGCGTTTTTC-TCACAAACGACGCAATAGG
* ** * * * *
363436 TGTTGAGGTTTAGTGGCATTTTT-TTATAAATG-CGACAATAGG
1 TGTTGAGATTTAACGGCGTTTTTCTCACAAACGACG-CAATAGG
* * * *
363478 TGTTAAGATTTAGA-TGCGTTTTTCTAACAAACGACGCAATAGA
1 TGTTGAGATTTA-ACGGCGTTTTTCTCACAAACGACGCAATAGG
* * ** *
363521 TTTTGAGATTTAGCGGTATTTTTCTCACAAA-TACCGCAATAGG
1 TGTTGAGATTTAACGGCGTTTTTCTCACAAACGA-CGCAATAGG
* *
363564 TGTTGAGATATAACGGCGTTTTTCCCACAAACG
1 TGTTGAGATTTAACGGCGTTTTTCTCACAAACG
363597 CCACTATATG
Statistics
Matches: 121, Mismatches: 32, Indels: 15
0.72 0.19 0.09
Matches are distributed among these distances:
41 3 0.02
42 30 0.25
43 86 0.71
44 2 0.02
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.35
Consensus pattern (43 bp):
TGTTGAGATTTAACGGCGTTTTTCTCACAAACGACGCAATAGG
Found at i:363595 original size:86 final size:85
Alignment explanation
Indices: 363419--363596 Score: 189
Period size: 86 Copynumber: 2.1 Consensus size: 85
363409 CGTTTGTCAT
* * * * * * *
363419 ACAAACGCCGCAATAGGTGTTGAGGTTTAGTGGCATTTTTTTATAAATGCGACAATAGGTGTTAA
1 ACAAACGACGCAATAGATGTTGAGATTTAGCGGCATTTTTTCACAAATCCGACAATAGGTGTTAA
* * *
363484 GATTTAGATGCGTTTTTCTA
66 GATATAGAGGCGTTTTTCCA
* *
363504 ACAAACGACGCAATAGATTTTGAGATTTAGCGGTATTTTTCTCACAAATACCG-CAATAGGTGTT
1 ACAAACGACGCAATAGATGTTGAGATTTAGCGGCATTTTT-TCACAAAT-CCGACAATAGGTGTT
* *
363568 GAGATATA-ACGGCGTTTTTCCC
64 AAGATATAGA-GGCGTTTTTCCA
363590 ACAAACG
1 ACAAACG
363597 CCACTATATG
Statistics
Matches: 76, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
85 35 0.46
86 39 0.51
87 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (85 bp):
ACAAACGACGCAATAGATGTTGAGATTTAGCGGCATTTTTTCACAAATCCGACAATAGGTGTTAA
GATATAGAGGCGTTTTTCCA
Found at i:364148 original size:23 final size:21
Alignment explanation
Indices: 364097--364154 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
364087 GTTGATTTGT
* *
364097 TGCTTCTCTCTGTGTTGTCAC
1 TGCTTCTCTCTGTGCTATCAC
*
364118 TGCTTCTCTCTGTGCTATCGC
1 TGCTTCTCTCTGTGCTATCAC
* *
364139 TGCTACTCTCTCTGCT
1 TGCTTCTCTCTGTGCT
364155 TCTTCTGCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.05, C:0.33, G:0.17, T:0.45
Consensus pattern (21 bp):
TGCTTCTCTCTGTGCTATCAC
Found at i:364162 original size:21 final size:21
Alignment explanation
Indices: 364138--364177 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
364128 TGTGCTATCG
364138 CTGCTACTCTCTCTGCTTCTT
1 CTGCTACTCTCTCTGCTTCTT
* *
364159 CTGCTGCTCTCTCTTCTTC
1 CTGCTACTCTCTCTGCTTC
364178 CGTTGGTGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.03, C:0.40, G:0.10, T:0.47
Consensus pattern (21 bp):
CTGCTACTCTCTCTGCTTCTT
Found at i:369083 original size:19 final size:19
Alignment explanation
Indices: 369055--369116 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
369045 TGTATTTTAG
*
369055 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
369074 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* *
369093 ATTATATTA-TTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
369113 TTTA
1 TTTA
369117 GTTTAAATAG
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
19 23 0.70
20 10 0.30
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:369766 original size:18 final size:18
Alignment explanation
Indices: 369743--369785 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
369733 CTTTAATTTG
* *
369743 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTGTAT
*
369761 TTTATTTAATTCTTGTAT
1 TTTATTTAATTATTGTAT
369779 TTTATTT
1 TTTATTT
369786 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTGTAT
Found at i:370970 original size:22 final size:22
Alignment explanation
Indices: 370938--370985 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
370928 GGTTCACGAG
370938 ATAAGTACATTTTCCCTTGAAA
1 ATAAGTACATTTTCCCTTGAAA
*
370960 ATAAGTTCATTTTCCCTTGAAA
1 ATAAGTACATTTTCCCTTGAAA
370982 ATAA
1 ATAA
370986 ATTAGATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (22 bp):
ATAAGTACATTTTCCCTTGAAA
Found at i:371559 original size:15 final size:15
Alignment explanation
Indices: 371541--371574 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
371531 CCAGCAGAAA
*
371541 AAGACGTACATCAGG
1 AAGACGCACATCAGG
371556 AAGACGCACATCAGG
1 AAGACGCACATCAGG
371571 AAGA
1 AAGA
371575 ACAAGAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.26, T:0.09
Consensus pattern (15 bp):
AAGACGCACATCAGG
Found at i:375499 original size:14 final size:14
Alignment explanation
Indices: 375477--375528 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
375467 ACCCATTTCA
* *
375477 TTATATTTTTGTTT
1 TTATTTTTTTATTT
375491 TTATTTTTTTATTT
1 TTATTTTTTTATTT
* *
375505 TCA-TTTTATATTT
1 TTATTTTTTTATTT
*
375518 TTATTTCTTTA
1 TTATTTTTTTA
375529 GCGAACTTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
13 11 0.37
14 19 0.63
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (14 bp):
TTATTTTTTTATTT
Found at i:375706 original size:16 final size:16
Alignment explanation
Indices: 375685--375716 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
375675 TCAAACAATG
*
375685 CAGTGCATAAAAAAAA
1 CAGTGCAGAAAAAAAA
375701 CAGTGCAGAAAAAAAA
1 CAGTGCAGAAAAAAAA
375717 ACAGATTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.62, C:0.12, G:0.16, T:0.09
Consensus pattern (16 bp):
CAGTGCAGAAAAAAAA
Found at i:377458 original size:65 final size:65
Alignment explanation
Indices: 377331--377466 Score: 163
Period size: 65 Copynumber: 2.1 Consensus size: 65
377321 CTTTATCTTT
* * *
377331 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTCAGAATATTATATTATTTTTTTAG
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTAAGAATATTATACTATGTTTTTAG
* * *
377396 GTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTAAG-ATGTTTTAGCT-TGTTTT
1 GTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGGA-TTAAGAATATTATA-CTATGTTTT
377458 TAG
63 TAG
377461 G-ATTTT
1 GTATTTT
377467 GAAGGCTATA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
64 10 0.16
65 47 0.76
66 5 0.08
ACGTcount: A:0.28, C:0.01, G:0.16, T:0.54
Consensus pattern (65 bp):
GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTAAGAATATTATACTATGTTTTTAG
Found at i:378054 original size:18 final size:18
Alignment explanation
Indices: 378031--378073 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
378021 CTTTAATTTG
* *
378031 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATAT
*
378049 TTTATTTAATTCTTATAT
1 TTTATTTAATTATTATAT
378067 TTTATTT
1 TTTATTT
378074 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATAT
Found at i:380904 original size:41 final size:41
Alignment explanation
Indices: 380818--380895 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
380808 TTTGTGTTAA
* *
380818 AAAAATGCCACTAACATATAACTCTTTAGCGGCGTTTTGAT
1 AAAAATGCCACAAACATATAACTATTTAGCGGCGTTTTGAT
* *
380859 AAAAATGCTACAAACGTATAACTATATT-GCGGCGTTT
1 AAAAATGCCACAAACATATAACTAT-TTAGCGGCGTTT
380896 GTTGAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 30 0.94
42 2 0.06
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (41 bp):
AAAAATGCCACAAACATATAACTATTTAGCGGCGTTTTGAT
Found at i:382125 original size:22 final size:23
Alignment explanation
Indices: 382095--382142 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
382085 TAAGGTTTTC
382095 AAAAGCTATTA-TTTTCCTATTCG
1 AAAAGCTATTACTTTT-CTATTCG
382118 AAAA-CTATTACTTTTCTATTCG
1 AAAAGCTATTACTTTTCTATTCG
382140 AAA
1 AAA
382143 GCAGAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (23 bp):
AAAAGCTATTACTTTTCTATTCG
Found at i:382652 original size:41 final size:40
Alignment explanation
Indices: 382593--382716 Score: 97
Period size: 41 Copynumber: 3.0 Consensus size: 40
382583 ACTCTATAGG
* * *
382593 GGCGTTTGATGTACAAACGCCACTATAAACAAGCCTTTTGC
1 GGCGTTTGTTGGA-AAACGCCACTATAAACAAGCCTATTGC
* * * * * *
382634 GGCGTTTGTTTGATAAACGCCAGTA-AGTTACTAGTCTATAGC
1 GGCGTTTGTTGGA-AAACGCCACTATA--AACAAGCCTATTGC
* * *
382676 GGCGTTTGTTGGAAAATGCCACTATAAACAACCCTGTTGC
1 GGCGTTTGTTGGAAAACGCCACTATAAACAAGCCTATTGC
382716 G
1 G
382717 ACATTTTTAT
Statistics
Matches: 61, Mismatches: 19, Indels: 7
0.70 0.22 0.08
Matches are distributed among these distances:
40 10 0.16
41 29 0.48
42 22 0.36
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (40 bp):
GGCGTTTGTTGGAAAACGCCACTATAAACAAGCCTATTGC
Found at i:382699 original size:82 final size:82
Alignment explanation
Indices: 382546--382716 Score: 229
Period size: 82 Copynumber: 2.1 Consensus size: 82
382536 TAGTACATGT
* *
382546 TTTTGCGGCGTTTGCCTATAAACGCCGCTAAGTTACTACTCTATAGGGGCGTTTGATGTACAAAC
1 TTTTGCGGCGTTTGCCTATAAACGCCGCTAAGTTACTACTCTATAGCGGCGTTTGATGGACAAAC
*
382611 GCCACTATAAACAAGCC
66 GCCACTATAAACAACCC
** * *
382628 TTTTGCGGCGTTTGTTTGATAAACGCCAG-TAAGTTACTAGTCTATAGCGGCGTTTGTTGGA-AA
1 TTTTGCGGCGTTTGCCT-ATAAACGCC-GCTAAGTTACTACTCTATAGCGGCGTTTGATGGACAA
*
382691 ATGCCACTATAAACAACCC
64 ACGCCACTATAAACAACCC
*
382710 TGTTGCG
1 TTTTGCG
382717 ACATTTTTAT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
82 40 0.51
83 37 0.47
84 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (82 bp):
TTTTGCGGCGTTTGCCTATAAACGCCGCTAAGTTACTACTCTATAGCGGCGTTTGATGGACAAAC
GCCACTATAAACAACCC
Found at i:383215 original size:72 final size:72
Alignment explanation
Indices: 383098--383247 Score: 248
Period size: 72 Copynumber: 2.1 Consensus size: 72
383088 ATAAAAATGA
*
383098 AAGTTATACCGTGACAAATGTTAGTAATAGAGGGCTTCTCGAACCTACCGGTGGGGATTTTCAAG
1 AAGTTATACCGTGACAAATGTTAGTAATAGAGGGCTTCTCGAACCTACAGGTGGGGATTTTCAAG
*
383163 CTATTAT
66 CTACTAT
*
383170 AAGTTATACCGTGACAAATGTTAGTACA-ATAGGGCTTCTCGAACCTACAGGTGGGGATTTTCAA
1 AAGTTATACCGTGACAAATGTTAGTA-ATAGAGGGCTTCTCGAACCTACAGGTGGGGATTTTCAA
*
383234 GCTACTCT
65 GCTACTAT
383242 AAGTTA
1 AAGTTA
383248 AGTAGTTTGT
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
72 72 0.99
73 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (72 bp):
AAGTTATACCGTGACAAATGTTAGTAATAGAGGGCTTCTCGAACCTACAGGTGGGGATTTTCAAG
CTACTAT
Found at i:388316 original size:16 final size:16
Alignment explanation
Indices: 388295--388329 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
388285 TTAAAAAAGA
388295 AAATAGTTGAGTGGTC
1 AAATAGTTGAGTGGTC
388311 AAATAGTTGAGTGGTC
1 AAATAGTTGAGTGGTC
388327 AAA
1 AAA
388330 ACATAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.29
Consensus pattern (16 bp):
AAATAGTTGAGTGGTC
Found at i:391371 original size:43 final size:43
Alignment explanation
Indices: 391309--391399 Score: 173
Period size: 43 Copynumber: 2.1 Consensus size: 43
391299 GAAAACTAAG
*
391309 GAACTCAAAGGGAGCAACAACTCATTTATTGACTATAAGACTA
1 GAACTCAAAGGGAGAAACAACTCATTTATTGACTATAAGACTA
391352 GAACTCAAAGGGAGAAACAACTCATTTATTGACTATAAGACTA
1 GAACTCAAAGGGAGAAACAACTCATTTATTGACTATAAGACTA
391395 GAACT
1 GAACT
391400 ACGGTGGTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (43 bp):
GAACTCAAAGGGAGAAACAACTCATTTATTGACTATAAGACTA
Found at i:399619 original size:26 final size:26
Alignment explanation
Indices: 399590--399641 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
399580 AAAACTGATG
* * *
399590 ACCAATCTTGAGAGGAATCGAAGATC
1 ACCAATCTTGAAAGGAACCAAAGATC
399616 ACCAATCTTGAAAGGAACCAAAGATC
1 ACCAATCTTGAAAGGAACCAAAGATC
399642 CTTAAGTAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.17
Consensus pattern (26 bp):
ACCAATCTTGAAAGGAACCAAAGATC
Found at i:402161 original size:14 final size:14
Alignment explanation
Indices: 402144--402173 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
402134 CAAATACTTA
*
402144 AAATGTATCCGATC
1 AAATGTATCCAATC
402158 AAATGTATCCAATC
1 AAATGTATCCAATC
402172 AA
1 AA
402174 CCAACCGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (14 bp):
AAATGTATCCAATC
Found at i:402307 original size:125 final size:126
Alignment explanation
Indices: 402160--402397 Score: 406
Period size: 126 Copynumber: 1.9 Consensus size: 126
402150 ATCCGATCAA
*
402160 ATGTATCCAATCAACCAACCGAAGCTTGATTTCAAGCTTGAAATTAAT-AAAAAATTATCTAATT
1 ATGTATCCAATCAACCAACCGAAGCTTCATTTCAAGCTTGAAATTAATCAAAAAATTATCTAATT
*
402224 TTAATATATAATTTTGAGATTATTTCAAAATTAATGTGTTTTTAATTTTGAGATACTTGAT
66 TTAATATATAATTTTGAGATTATTTCAAAAGTAATGTGTTTTTAATTTTGAGATACTTGAT
* ** * *
402285 ATGTATCCGATCAACCCGCCGAAGCTTCATTTCAAGCTTGAAATTAATCCAAAAATTATCTTATT
1 ATGTATCCAATCAACCAACCGAAGCTTCATTTCAAGCTTGAAATTAATCAAAAAATTATCTAATT
402350 TTAATATATAATTTTGAGATTATTTCAAAAGTAATGTGTTTTTAATTT
66 TTAATATATAATTTTGAGATTATTTCAAAAGTAATGTGTTTTTAATTT
402398 CAAGCTTGAA
Statistics
Matches: 105, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
125 44 0.42
126 61 0.58
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.41
Consensus pattern (126 bp):
ATGTATCCAATCAACCAACCGAAGCTTCATTTCAAGCTTGAAATTAATCAAAAAATTATCTAATT
TTAATATATAATTTTGAGATTATTTCAAAAGTAATGTGTTTTTAATTTTGAGATACTTGAT
Found at i:402545 original size:12 final size:12
Alignment explanation
Indices: 402524--402552 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
402514 AAAAACACAT
402524 TAAT-TTTGAAA
1 TAATCTTTGAAA
402535 TAATCTTTGAAA
1 TAATCTTTGAAA
402547 TAATCT
1 TAATCT
402553 CAAAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (12 bp):
TAATCTTTGAAA
Found at i:402720 original size:128 final size:133
Alignment explanation
Indices: 402403--402769 Score: 543
Period size: 128 Copynumber: 2.8 Consensus size: 133
402393 AATTTCAAGC
402403 TTGAAATAATCTCAAAATTATATATTAAAATCAGATAATTTTTGGATTAATTTCAAGCTTGAAAT
1 TTGAAATAATCTCAAAATTATATATTAAAATCAGATAATTTTTGGATTAATTTCAAGCTTGAAAT
* * *
402468 CAAGCTTCGACGAGTTGATAGGATACATTTCAAGTATCTTAAAATTAAAAACACATTAATTTTGA
66 CAAGCTTCGACGGGTTGATCGGATACATTTCAAGTATCTCAAAATTAAAAACACA-TAA---T-A
402533 AATAATCT
126 AATAATCT
*
402541 TTGAAATAATCTCAAAATTATATATTAAAATTAGATAATTGTTT--ATTAATTTCAAGCTTGAAA
1 TTGAAATAATCTCAAAATTATATATTAAAATCAGATAATT-TTTGGATTAATTTCAAGCTTGAAA
* *
402604 TCAAGCTTCGGCGGGTTGATCGGATACATTTCAAGTATCTCAAAATTAAAAA-A-A-AA-ACATT
65 TCAAGCTTCGACGGGTTGATCGGATACATTTCAAGTATCTCAAAATTAAAAACACATAATA-AAT
402665 AAT-T
129 AATCT
*
402669 TTGAAATAATCTC-AAATTATATATTAAAATCAGATAATTTTTGGATTAATTTCAAGTTTGAAAT
1 TTGAAATAATCTCAAAATTATATATTAAAATCAGATAATTTTTGGATTAATTTCAAGCTTGAAAT
*
402733 CAAGCTTCGACAGGTTGATCGGATACATTTCAAGTAT
66 CAAGCTTCGACGGGTTGATCGGATACATTTCAAGTAT
402770 ATGATTTTAA
Statistics
Matches: 215, Mismatches: 10, Indels: 18
0.88 0.04 0.07
Matches are distributed among these distances:
126 3 0.01
127 25 0.12
128 69 0.32
129 5 0.02
133 2 0.01
135 1 0.00
136 1 0.00
137 67 0.31
138 39 0.18
139 3 0.01
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (133 bp):
TTGAAATAATCTCAAAATTATATATTAAAATCAGATAATTTTTGGATTAATTTCAAGCTTGAAAT
CAAGCTTCGACGGGTTGATCGGATACATTTCAAGTATCTCAAAATTAAAAACACATAATAAATAA
TCT
Found at i:408969 original size:11 final size:11
Alignment explanation
Indices: 408953--408983 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
408943 AAGTAATCAT
408953 AAAAAATAATA
1 AAAAAATAATA
408964 AAAAAATAATA
1 AAAAAATAATA
408975 AAAAAATAA
1 AAAAAATAA
408984 CATCAACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAATAATA
Found at i:412727 original size:31 final size:31
Alignment explanation
Indices: 412682--412759 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
412672 AAAAAAAACA
*
412682 TAAGTTTTGATCACTTACATTATTATTTCAT
1 TAAGTTTTGGTCACTTACATTATTATTTCAT
* * *
412713 TAGGTTTTGGTCACTTACGTTATTATTTTAT
1 TAAGTTTTGGTCACTTACATTATTATTTCAT
412744 TAAGTTTTGGTCACTT
1 TAAGTTTTGGTCACTT
412760 GGACGTTGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.23, C:0.12, G:0.13, T:0.53
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACATTATTATTTCAT
Found at i:422186 original size:3 final size:3
Alignment explanation
Indices: 422180--422241 Score: 90
Period size: 3 Copynumber: 20.0 Consensus size: 3
422170 ACATTTGGTT
422180 TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
422227 TTA TTAA TT- TTA TTA
1 TTA TT-A TTA TTA TTA
422242 CAGACCCAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.04
3 44 0.80
4 9 0.16
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:423555 original size:3 final size:3
Alignment explanation
Indices: 423547--423573 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
423537 TTTACTTTTA
423547 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
423574 TAACCATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:423788 original size:20 final size:19
Alignment explanation
Indices: 423763--423804 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
423753 TTATTTTATA
423763 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
423783 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
423802 AAT
1 AAT
423805 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:423795 original size:120 final size:117
Alignment explanation
Indices: 423660--423895 Score: 278
Period size: 120 Copynumber: 2.0 Consensus size: 117
423650 TTTAATCCTA
* * * *
423660 TTTTAATATTTATTTATTTTCCAATAT-TAAG-AAAGTGCAGTCTTAAAATAACTAGATGTCCAT
1 TTTTAATATTTATTTATTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT-CAT
*
423723 TTTCTGATATTAAAAAAATAAATAAATATCTTATTTTATAAATTATATATTAATTG
65 TTTCTGATATT-AAAAAATAAATAAATATCTTA-TTTATAAA-TATATATAAATTG
** * ** *
423779 TTTTAATTATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCAT
1 TTTTAA-TATTTATTTATTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCAT
*** *
423844 TTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAATT
65 TTTCTGATATTAAAAAATAAATAAATATCTTATTTATAAATATATATAAATT
423896 AATATATATT
Statistics
Matches: 99, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
118 11 0.11
119 14 0.14
120 36 0.36
121 17 0.17
122 21 0.21
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (117 bp):
TTTTAATATTTATTTATTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCATT
TTCTGATATTAAAAAATAAATAAATATCTTATTTATAAATATATATAAATTG
Found at i:424445 original size:25 final size:24
Alignment explanation
Indices: 424398--424461 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 24
424388 AATTCTTTTC
* *
424398 TTTTAAATT-TTTTATTACGTATTAT
1 TTTTATATTATTTTATTACATA-T-T
424423 TTTTATATTATTTTATTA-ATATT
1 TTTTATATTATTTTATTACATATT
424446 TTTTAT-TTATTTTATT
1 TTTTATATTATTTTATT
424462 CAGGTATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
22 10 0.28
23 7 0.19
24 1 0.03
25 10 0.28
26 8 0.22
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTTATATTATTTTATTACATATT
Found at i:427746 original size:15 final size:15
Alignment explanation
Indices: 427726--427757 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
427716 GATCAATACC
427726 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
427741 TTTTGCATACATTCA
1 TTTTGCATACATGCA
427756 TT
1 TT
427758 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:435082 original size:11 final size:11
Alignment explanation
Indices: 435068--435139 Score: 64
Period size: 10 Copynumber: 6.8 Consensus size: 11
435058 AAATGAAAAG
435068 AAGAAAAGAAA
1 AAGAAAAGAAA
435079 AAGAAAA-AAA
1 AAGAAAAGAAA
* * *
435089 GAGAGGAAGAAG
1 AAGA-AAAGAAA
435101 AAGAAAA-AAA
1 AAGAAAAGAAA
435111 AA-AAAAGAAA
1 AAGAAAAGAAA
435121 AA-AAAAGAGAA
1 AAGAAAAGA-AA
435132 AA-AAAAGA
1 AAGAAAAGA
435140 GGGGGTCAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
9 4 0.08
10 21 0.41
11 21 0.41
12 5 0.10
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAGAAAAGAAA
Found at i:435083 original size:27 final size:27
Alignment explanation
Indices: 435052--435134 Score: 98
Period size: 27 Copynumber: 3.1 Consensus size: 27
435042 ATTATGCTTG
*
435052 AAGAAAAAATGAAAAGAAGAAAAGAAA
1 AAGAAAAAAAGAAAAGAAGAAAAGAAA
* *
435079 AAGAAAAAAAGAGAGGAAGAAGAAGAAA
1 AAGAAAAAAAGAAAAGAAGAA-AAGAAA
*
435107 AAAAAAAAAAGAAAA-AA-AAAGAGAAA
1 AAGAAAAAAAGAAAAGAAGAAA-AGAAA
435133 AA
1 AA
435135 AAAGAGGGGG
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
25 1 0.02
26 9 0.19
27 20 0.42
28 18 0.38
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (27 bp):
AAGAAAAAAAGAAAAGAAGAAAAGAAA
Found at i:436002 original size:114 final size:114
Alignment explanation
Indices: 435802--436017 Score: 333
Period size: 114 Copynumber: 1.9 Consensus size: 114
435792 CACCTTCTCG
* * *
435802 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGAAGACACAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* * * * *
435867 GGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATTTGCTCA
66 GGTAGGAACCACAAAACCAATCATTGGAATTAAAAGATGAATTTGCTCA
* *
435916 TAGTAGAAATAAGAAGACACAATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGAAGACACAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
*
435981 GGTAGGAACCACAGAACCAATCATTGGAATTAAAAGA
66 GGTAGGAACCACAAAACCAATCATTGGAATTAAAAGA
436018 AGAACTGCAC
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
114 91 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (114 bp):
TAGTAGAAATAAGAAGACACAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
GGTAGGAACCACAAAACCAATCATTGGAATTAAAAGATGAATTTGCTCA
Found at i:437040 original size:112 final size:112
Alignment explanation
Indices: 436719--437151 Score: 609
Period size: 113 Copynumber: 3.8 Consensus size: 112
436709 ATCCATCACA
436719 ATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGT
* * * *
436784 TCATAATGAGAAGAGCTTGTTCAATCTTTTGCTCAAATCCATCACTTG
65 TCATAATGAGAAGAGCTTGTTCAACCTTTTGTTTAAATTCATCACTTG
* * * * *
436832 ATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAATTTATCTGAAGAAGGAAAAAGAAGT
1 ATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGT
*
436897 TCATAATGAGAAGAGCTTGTTCAACCTTTTGTTTAAATTCATCATTTG
65 TCATAATGAGAAGAGCTTGTTCAACCTTTTGTTTAAATTCATCACTTG
* * **
436945 ATGGATCAACATTGCCA-AGTAGAGTTCATAATGAGAAGAACTCATCAT-CTGAAGAAGAAGAAG
1 ATGGATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATC-TGAAGAAGAAGAAGAAG
** * * *
437008 TTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATTCATCACTCG
64 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGTTTAAATTCATCACTTG
* * *
437057 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGAAGCT
1 ATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTT
*
437122 CATAATGAAAAGAGCTTGTTCAACCTTTTG
66 CATAATGAGAAGAGCTTGTTCAACCTTTTG
437152 CATAACTCTA
Statistics
Matches: 280, Mismatches: 36, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
111 1 0.00
112 133 0.47
113 145 0.52
114 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (112 bp):
ATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTT
CATAATGAGAAGAGCTTGTTCAACCTTTTGTTTAAATTCATCACTTG
Found at i:437501 original size:3 final size:3
Alignment explanation
Indices: 437495--437560 Score: 71
Period size: 3 Copynumber: 21.0 Consensus size: 3
437485 ACATTTGGTT
* *
437495 TTA TTA TTTA ATA TTA TTA TTTA TTA TTA TTA TTA TTA ATA TTA TTA
1 TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
437542 TTTA TTA TTAA TT- TTA TTA
1 -TTA TTA TT-A TTA TTA TTA
437561 CAGGCCTAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
2 2 0.04
3 40 0.74
4 12 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:437509 original size:7 final size:7
Alignment explanation
Indices: 437494--437550 Score: 66
Period size: 7 Copynumber: 8.3 Consensus size: 7
437484 TACATTTGGT
437494 TTTATTA
1 TTTATTA
*
437501 TTTAATA
1 TTTATTA
437508 -TTATTA
1 TTTATTA
437514 TTTATTA
1 TTTATTA
437521 -TTATTA
1 TTTATTA
437527 -TTATTAA
1 TTTATT-A
437534 TATTATTA
1 T-TTATTA
437542 TTTATTA
1 TTTATTA
437549 TT
1 TT
437551 AATTTTATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
6 16 0.36
7 21 0.48
8 2 0.05
9 5 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
TTTATTA
Found at i:437511 original size:13 final size:13
Alignment explanation
Indices: 437495--437551 Score: 78
Period size: 13 Copynumber: 4.2 Consensus size: 13
437485 ACATTTGGTT
437495 TTATTATTTAATA
1 TTATTATTTAATA
*
437508 TTATTATTTATTA
1 TTATTATTTAATA
437521 TTATTATTATTAATA
1 TTATTA-T-TTAATA
*
437536 TTATTATTTATTA
1 TTATTATTTAATA
437549 TTA
1 TTA
437552 ATTTTATTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
13 26 0.67
14 2 0.05
15 11 0.28
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTATTATTTAATA
Found at i:437541 original size:28 final size:29
Alignment explanation
Indices: 437495--437560 Score: 109
Period size: 28 Copynumber: 2.3 Consensus size: 29
437485 ACATTTGGTT
437495 TTATTATTTAATATTATTATTTATTATT-A
1 TTATTA-TTAATATTATTATTTATTATTAA
437524 TTATTATTAATATTATTATTTATTATTAA
1 TTATTATTAATATTATTATTTATTATTAA
437553 TT-TTATTA
1 TTATTATTA
437561 CAGGCCTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
28 27 0.75
29 9 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (29 bp):
TTATTATTAATATTATTATTTATTATTAA
Found at i:437558 original size:16 final size:17
Alignment explanation
Indices: 437495--437559 Score: 64
Period size: 16 Copynumber: 3.9 Consensus size: 17
437485 ACATTTGGTT
* *
437495 TTATTATTTAATA-TTA
1 TTATTAATTATTATTTA
*
437511 TTATTTATTATTA-TTA
1 TTATTAATTATTATTTA
437527 TTATTAATATTATTATTTA
1 TTATT-A-ATTATTATTTA
437546 TTATTAATT-TTATT
1 TTATTAATTATTATT
437560 ACAGGCCTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
16 23 0.55
17 3 0.07
18 8 0.19
19 8 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATTAATTATTATTTA
Found at i:439129 original size:20 final size:19
Alignment explanation
Indices: 439104--439145 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
439094 TTATTTTATA
439104 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
439124 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
439143 AAT
1 AAT
439146 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:443690 original size:64 final size:62
Alignment explanation
Indices: 443600--443762 Score: 177
Period size: 64 Copynumber: 2.6 Consensus size: 62
443590 CGGTGCACTA
* * * *
443600 AGAGTGCATCGATTCATGAAGTGCATTCGATGTTTGAA-AAAT-AGCCTGGTGCATTGATGCATG
1 AGAGTGCATCGATGCATGAAATGCATTCGATGTTT-AATAAATCAG---AGTGCATCGATGCATG
443663 G
62 G
** *
443664 ATTGTGCATCGATGCATCAAATGCATTCGATGTGTTAATTAAATCAGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGAAATGCATTCGATGT-TTAA-TAAATCAGAGTGCATCGATGCATGG
* *
443728 AGAGTGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGAGTGCATCGATGCATGAAATGCATTCGATGTTT
443763 CAACTTATTC
Statistics
Matches: 83, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
63 2 0.02
64 73 0.88
65 2 0.02
66 4 0.05
67 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.31
Consensus pattern (62 bp):
AGAGTGCATCGATGCATGAAATGCATTCGATGTTTAATAAATCAGAGTGCATCGATGCATGG
Found at i:443733 original size:19 final size:19
Alignment explanation
Indices: 443709--443759 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
443699 TAATTAAATC
443709 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
443728 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
443747 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
443760 TTTCAACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:444401 original size:2 final size:2
Alignment explanation
Indices: 444394--444419 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
444384 ACCAAACCAA
444394 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
444420 TAAGTTCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:445496 original size:24 final size:23
Alignment explanation
Indices: 445425--445504 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 23
445415 CATGGTCTTG
* *
445425 TGCATCGATGCACATTTAAGGCA
1 TGCATCGATGCACATTCAAGGGA
* *
445448 TGCATCGGTG--CA-TCATGCGGA
1 TGCATCGATGCACATTCAAG-GGA
445469 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
445493 TGCATCGATGCA
1 TGCATCGATGCA
445505 TTGTTAAGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 3 0.07
21 13 0.28
23 11 0.24
24 17 0.37
25 2 0.04
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.24
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:445517 original size:44 final size:42
Alignment explanation
Indices: 445402--445524 Score: 113
Period size: 44 Copynumber: 2.8 Consensus size: 42
445392 AAAACCCAAC
* * *
445402 GGATGCATCGATGCATGGTCTTGTGCATCGATGCACATTTAAG
1 GGATGCATCGATGCATTGT-TAGTGCATCGATGCACATTAAAG
* * **
445445 GCATGCATCGGTGCATCATG-CGGATGCATCGATGCACATTCAAAG
1 GGATGCATCGATGCAT--TGTTAG-TGCATCGATGCACATT-AAAG
*
445490 GGATGCATCGATGCATTGTTAAGTGCATCGGTGCA
1 GGATGCATCGATGCATTGTT-AGTGCATCGATGCA
445525 TTAAGCACAA
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
43 17 0.27
44 27 0.43
45 19 0.30
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (42 bp):
GGATGCATCGATGCATTGTTAGTGCATCGATGCACATTAAAG
Found at i:449223 original size:21 final size:20
Alignment explanation
Indices: 449181--449224 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
449171 TCAAAAGAAG
*
449181 TTTTAAGATCATCAATTTTC
1 TTTTAAGATCATCAATTATC
449201 TTTTAATGATCATC-ATTGATC
1 TTTTAA-GATCATCAATT-ATC
449222 TTT
1 TTT
449225 GAAAGTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.52
Consensus pattern (20 bp):
TTTTAAGATCATCAATTATC
Found at i:450212 original size:30 final size:30
Alignment explanation
Indices: 450176--450235 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
450166 ACCTCATCGG
450176 TACCTTCATGAGTGACTTGAAGTTTGTCCC
1 TACCTTCATGAGTGACTTGAAGTTTGTCCC
450206 TACCTTCATGAGTGACTTGAAGTTTGTCCC
1 TACCTTCATGAGTGACTTGAAGTTTGTCCC
450236 ATATTTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (30 bp):
TACCTTCATGAGTGACTTGAAGTTTGTCCC
Found at i:451426 original size:64 final size:62
Alignment explanation
Indices: 451346--451508 Score: 177
Period size: 64 Copynumber: 2.5 Consensus size: 62
451336 CGGTGCACTA
* *
451346 AGAGTACATCGATGCATGAAGTGCATTCGATGTTTGAA-AAAT-AGCCTGGTACATCGATGCATG
1 AGAGTGCATCGATGCATGAA-TGCATTCGATGTTTGAATAAATCAG---AGTACATCGATGCATG
451409 G
62 G
** * * *
451410 ATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCAT-GAATGCATTCGATGTTTGAA-TAAATCAGAGTACATCGATGCATGG
*
451474 AGAGTGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGAGTGCATCGATGCAT-GAATGCATTCGATGTTT
451509 CAACTTATTC
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
64 75 0.90
65 2 0.02
66 4 0.05
67 2 0.02
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (62 bp):
AGAGTGCATCGATGCATGAATGCATTCGATGTTTGAATAAATCAGAGTACATCGATGCATGG
Found at i:451479 original size:19 final size:19
Alignment explanation
Indices: 451455--451505 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
451445 TAATTAAATC
451455 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
451474 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
451493 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
451506 TTTCAACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Done.