Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008029.1 Hibiscus syriacus cultivar Beakdansim tig00110505_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: 3983240
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 18
Found at i:1246295 original size:20 final size:20
Alignment explanation
Indices: 1246270--1246307 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1246260 TTCCCCTTGA
1246270 AGTGCATCAATGCATTCTAC
1 AGTGCATCAATGCATTCTAC
*
1246290 AGTGCATCGATGCATTCT
1 AGTGCATCAATGCATTCT
1246308 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCAATGCATTCTAC
Found at i:1246438 original size:64 final size:63
Alignment explanation
Indices: 1246315--1246455 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 63
1246305 TCTTTAACAT
* * * * *
1246315 GTGCATTGATGCACTACC-CATGCATCGATACACAAATTACCTTCGATGTTTTCATTTTAAGGG
1 GTGCATCGATGCACT-CCTTATGCATCGATACACAAATTACATTCGATGTTTTCATTTTAAAGA
* * * * *
1246378 GATGGATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATG-TTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTTATGCATCGATACACAAATTACATTCGATGTTTTCAT-TTTAAAGA
1246442 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1246456 ATTGAATGTG
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
63 20 0.31
64 44 0.69
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTTATGCATCGATACACAAATTACATTCGATGTTTTCATTTTAAAGA
Found at i:1249319 original size:18 final size:18
Alignment explanation
Indices: 1249296--1249437 Score: 203
Period size: 18 Copynumber: 7.9 Consensus size: 18
1249286 GCGTAGAATT
*
1249296 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
1249314 TGTCCCTAAGGACCACTG
1 TGTCCCGAAGGACCACTA
** *
1249332 TGTCCCGAAAAACCATTA
1 TGTCCCGAAGGACCACTA
1249350 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1249368 TATCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
1249386 TGTCCCGAAAGACCATTA
1 TGTCCCGAAGGACCACTA
1249404 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1249422 TGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
1249438 GTTGACCCTC
Statistics
Matches: 107, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 107 1.00
ACGTcount: A:0.29, C:0.32, G:0.20, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1249362 original size:54 final size:54
Alignment explanation
Indices: 1249296--1249437 Score: 239
Period size: 54 Copynumber: 2.6 Consensus size: 54
1249286 GCGTAGAATT
* * *
1249296 TGTCCCGTAGGACCACTATGTCCCTAAGGACCACTGTGTCCCGAAAAACCATTA
1 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTATGTCCCGAAAAACCATTA
* *
1249350 TGTCCCGAAGGACCACTATATCCCGAAGGACCACTATGTCCCGAAAGACCATTA
1 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTATGTCCCGAAAAACCATTA
1249404 TGTCCCGAAGGACCACTATGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCACTATGTCCCGAAGGACCAC
1249438 GTTGACCCTC
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 82 1.00
ACGTcount: A:0.29, C:0.32, G:0.20, T:0.19
Consensus pattern (54 bp):
TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTATGTCCCGAAAAACCATTA
Found at i:1259174 original size:18 final size:16
Alignment explanation
Indices: 1259147--1259184 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 16
1259137 AATATACTAA
1259147 TTTTTTTTTTGTAATTT
1 TTTTTTTTTTGT-ATTT
1259164 TTTTATTTTTTGTATTT
1 TTTT-TTTTTTGTATTT
1259181 TTTT
1 TTTT
1259185 CTGATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.11, C:0.00, G:0.05, T:0.84
Consensus pattern (16 bp):
TTTTTTTTTTGTATTT
Found at i:1259288 original size:19 final size:20
Alignment explanation
Indices: 1259264--1259309 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
1259254 ACATACTAAT
1259264 TTTTTTTGTAATTTTTCT-A
1 TTTTTTTGTAATTTTTCTGA
1259283 TTTTTTTGTAATTTTTCTGA
1 TTTTTTTGTAATTTTTCTGA
1259303 TTTTTTT
1 TTTTTTT
1259310 TAAATTCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.13, C:0.04, G:0.07, T:0.76
Consensus pattern (20 bp):
TTTTTTTGTAATTTTTCTGA
Found at i:1259380 original size:114 final size:115
Alignment explanation
Indices: 1259071--1259607 Score: 768
Period size: 114 Copynumber: 4.7 Consensus size: 115
1259061 TATAATTTCG
* * * *
1259071 TTTTTTTAAAAATTAAATTAGATTAAATTACAAGATAGATAAAAATACATTGAAATTAGATAAAT
1 TTTTTTT-TAAATTCAAGTAGATTAAATTGCAAGATAGATAAAAATACATTGAAATTAGATAAAT
* * *
1259136 AAATATACTAATTTTTTTTTTGTAATTTTT-TTATTTTTTGTATTTTTTTCTGA
65 AAACATACTAA--TTTTTTTTGTAATTTTTCTGATTTTTTGTA-ATTTTTCTGA
* * * * *
1259189 -TTTTTTTAAATTCAAATAGACTAATTTGCAAGATAGATAAAATTACATTAAAATTAGATAAATA
1 TTTTTTTTAAATTCAAGTAGATTAAATTGCAAGATAGATAAAAATACATTGAAATTAGATAAATA
1259253 AACATACTAATTTTTTTTGTAATTTTTCT-ATTTTTTTGTAATTTTTCTGA
66 AACATACTAATTTTTTTTGTAATTTTTCTGA-TTTTTTGTAATTTTTCTGA
* *
1259303 TTTTTTTTAAATTCAAGTAGATTAAATTACAAAATAGATAAAAATACATTGAAATTAGATAAATA
1 TTTTTTTTAAATTCAAGTAGATTAAATTGCAAGATAGATAAAAATACATTGAAATTAGATAAATA
* * * *
1259368 AACATACT-ATTTTTTTTATAATTTTTCTGATTTTTTAT-TTTTTTTTGA
66 AACATACTAATTTTTTTTGTAATTTTTCTGATTTTTTGTAATTTTTCTGA
1259416 --TTTTTT-AATTCAAGTAGATTAAATTGCAAGATAGATAAAAATACATTGAAATTAGATAAATA
1 TTTTTTTTAAATTCAAGTAGATTAAATTGCAAGATAGATAAAAATACATTGAAATTAGATAAATA
* * *
1259478 AAAATACTAATTTTTTTTGCAATTTTTCTGATTTTTTGTAATTTGTCTG-
66 AACATACTAATTTTTTTTGTAATTTTTCTGATTTTTTGTAATTTTTCTGA
*
1259527 TTTTTTTTTAATTCAAGTAGATTAAATTGCAAGATAGATAAAAATACATTGAAATTAGATAAATA
1 TTTTTTTTAAATTCAAGTAGATTAAATTGCAAGATAGATAAAAATACATTGAAATTAGATAAATA
1259592 AACATACTAATTTTTT
66 AACATACTAATTTTTT
1259608 GAAACATAAA
Statistics
Matches: 379, Mismatches: 31, Indels: 22
0.88 0.07 0.05
Matches are distributed among these distances:
110 61 0.16
111 33 0.09
112 6 0.02
113 14 0.04
114 124 0.33
115 76 0.20
116 59 0.16
117 6 0.02
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (115 bp):
TTTTTTTTAAATTCAAGTAGATTAAATTGCAAGATAGATAAAAATACATTGAAATTAGATAAATA
AACATACTAATTTTTTTTGTAATTTTTCTGATTTTTTGTAATTTTTCTGA
Found at i:1259410 original size:18 final size:19
Alignment explanation
Indices: 1259379--1259422 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
1259369 ACATACTATT
1259379 TTTTTTATAATTTTTCTGA
1 TTTTTTATAATTTTTCTGA
* *
1259398 TTTTTTAT-TTTTTTTTGA
1 TTTTTTATAATTTTTCTGA
1259416 TTTTTTA
1 TTTTTTA
1259423 ATTCAAGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (19 bp):
TTTTTTATAATTTTTCTGA
Found at i:1259496 original size:225 final size:227
Alignment explanation
Indices: 1259070--1259607 Score: 807
Period size: 225 Copynumber: 2.4 Consensus size: 227
1259060 CTATAATTTC
* * *
1259070 GTTTTTTTAAAAATTAAATTAGATTAAATTACAAGATAGATAAAAATACATTGAAATTAGATAAA
1 GTTTTTTT-TAAATTCAAGTAGATTAAATTACAAGATAGATAAAAATACATTGAAATTAGATAAA
* * *
1259135 TAAATATACTAATTTTTTTTTTGTAATTTTTTTATTTTTTGTATTTTTTTCTGATTTTTTTAAAT
65 TAAACATACT-A--TTTTTTTTATAATTTTTTGATTTTTTGTATTTTTTTCTGATTTTTTTAAAT
* * *
1259200 TCAAATAGACTAATTTGCAAGATAGATAAAATTACATTAAAATTAGATAAATAAACATACTAATT
127 TCAAATAGACTAAATTGCAAGATAGATAAAAATACATTAAAATTAGATAAATAAAAATACTAATT
* *
1259265 TTTTTTGTAATTTTTCT-ATTTTTTTGTAATTTTTCT
192 TTTTTTGCAATTTTTCTGA-TTTTTTGTAATTTGTCT
*
1259301 GATTTTTTTTAAATTCAAGTAGATTAAATTACAAAATAGATAAAAATACATTGAAATTAGATAAA
1 G-TTTTTTTTAAATTCAAGTAGATTAAATTACAAGATAGATAAAAATACATTGAAATTAGATAAA
*
1259366 TAAACATACTATTTTTTTTATAATTTTTCTGA-TTTTT-TATTTTTTTTTGA-TTTTTT-AATTC
65 TAAACATACTATTTTTTTTATAATTTTT-TGATTTTTTGTATTTTTTTCTGATTTTTTTAAATTC
* * *
1259427 AAGTAGATTAAATTGCAAGATAGATAAAAATACATTGAAATTAGATAAATAAAAATACTAATTTT
129 AAATAGACTAAATTGCAAGATAGATAAAAATACATTAAAATTAGATAAATAAAAATACTAATTTT
1259492 TTTTGCAATTTTTCTGATTTTTTGTAATTTGTCT
194 TTTTGCAATTTTTCTGATTTTTTGTAATTTGTCT
* *
1259526 GTTTTTTTTTAATTCAAGTAGATTAAATTGCAAGATAGATAAAAATACATTGAAATTAGATAAAT
1 GTTTTTTTTAAATTCAAGTAGATTAAATTACAAGATAGATAAAAATACATTGAAATTAGATAAAT
*
1259591 AAACATACTAATTTTTT
66 AAACATACTATTTTTTT
1259608 GAAACATAAA
Statistics
Matches: 284, Mismatches: 20, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
224 77 0.27
225 95 0.33
226 7 0.02
227 12 0.04
228 21 0.07
229 2 0.01
230 1 0.00
231 62 0.22
232 7 0.02
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (227 bp):
GTTTTTTTTAAATTCAAGTAGATTAAATTACAAGATAGATAAAAATACATTGAAATTAGATAAAT
AAACATACTATTTTTTTTATAATTTTTTGATTTTTTGTATTTTTTTCTGATTTTTTTAAATTCAA
ATAGACTAAATTGCAAGATAGATAAAAATACATTAAAATTAGATAAATAAAAATACTAATTTTTT
TTGCAATTTTTCTGATTTTTTGTAATTTGTCT
Found at i:1259533 original size:19 final size:19
Alignment explanation
Indices: 1259489--1259539 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
1259479 AAATACTAAT
* *
1259489 TTTTTTTGCAATTTTTCTG
1 TTTTTTTGTAATTTGTCTG
*
1259508 ATTTTTTGTAATTTGTCTG
1 TTTTTTTGTAATTTGTCTG
*
1259527 TTTTTTTTTAATT
1 TTTTTTTGTAATT
1259540 CAAGTAGATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.14, C:0.06, G:0.10, T:0.71
Consensus pattern (19 bp):
TTTTTTTGTAATTTGTCTG
Found at i:1287423 original size:13 final size:14
Alignment explanation
Indices: 1287391--1287428 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1287381 CTAATGGGCA
1287391 AAGTTTGAAAAACT
1 AAGTTTGAAAAACT
*
1287405 ATGTTTGAAAAAC-
1 AAGTTTGAAAAACT
1287418 AAGTTTTGAAA
1 AAG-TTTGAAA
1287429 TTAATATGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 2 0.10
14 19 0.90
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.32
Consensus pattern (14 bp):
AAGTTTGAAAAACT
Found at i:1287916 original size:21 final size:21
Alignment explanation
Indices: 1287891--1287975 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
1287881 ACCAGAACCC
1287891 TCAGGGGGTATCGATTCCCCT
1 TCAGGGGGTATCGATTCCCCT
* * *
1287912 ACAGGGGGAATCGGTTCCCCT
1 TCAGGGGGTATCGATTCCCCT
* * **
1287933 TCAAAGGGGTAATCGGTTATCCT
1 TC-AGGGGGT-ATCGATTCCCCT
1287956 TCAGGAGGGTATCGATTCCC
1 TCAGG-GGGTATCGATTCCC
1287976 TCTGCACCAA
Statistics
Matches: 49, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
21 19 0.39
22 14 0.29
23 16 0.33
ACGTcount: A:0.20, C:0.25, G:0.29, T:0.26
Consensus pattern (21 bp):
TCAGGGGGTATCGATTCCCCT
Found at i:1287956 original size:23 final size:23
Alignment explanation
Indices: 1287914--1287958 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1287904 ATTCCCCTAC
*
1287914 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTACCCTTCAA
* *
1287937 AGGGGTAATCGGTTATCCTTCA
1 AGGGGGAATCGGTTACCCTTCA
1287959 GGAGGGTATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (23 bp):
AGGGGGAATCGGTTACCCTTCAA
Found at i:1291779 original size:22 final size:21
Alignment explanation
Indices: 1291737--1291776 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1291727 GAGATTATTT
*
1291737 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
1291758 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1291777 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:1299085 original size:301 final size:302
Alignment explanation
Indices: 1298543--1299111 Score: 971
Period size: 301 Copynumber: 1.9 Consensus size: 302
1298533 TAAATAGTGA
* *
1298543 TATGGTAAATGCTATGAGTAAATGTTCTACGTGAGATGTTTTATGTGAATAAATACTATGTGAAT
1 TATGGTAAATGCTATGAGTAAATGTTCTACGTGAGATGTTCTATATGAATAAATACTATGTGAAT
*
1298608 ATGTGCCAAGAGACCTTAGTTTATGTTGAATTATTATAAGCGAAATGTGATCTATATGAATAAAA
66 ATGTGCCAAGAGACCTTAGTTTATGTGGAATTATTATAAGCGAAATGTGATCTATATGAATAAAA
* * *
1298673 TACCTCTTGAATAATAAATGTGACCTAATTATATGGAATAAGCTCAAAGTATATTTTATGAGAAT
131 TACCTCTTAAATAATAAATGTGACCTAATTATATGGAATAAGCCCAAAGAATATTTTATGAGAAT
*
1298738 TAGGCGTATAGTTGGCATGCCAAGAGTCGAGGGTTCTATGTGGTCCTTCAGAACAAA-CTATGTG
196 TAGGCGTATAGTTGGCATGCCAAGAGTCGAGGGTTCTATGTGGTCCTTCAGAACAAACCTAAGTG
*
1298802 GTCCTTCGGGATATATATGGCTCTTCGGTATAAATTATGTGC
261 GTCATTCGGGATATATATGGCTCTTCGGTATAAATTATGTGC
* *
1298844 TATGGTAAATGTTATGAGTAAATGTTCTACGTGAGATGTTCTATATGAATAAATGCTATGTGAAT
1 TATGGTAAATGCTATGAGTAAATGTTCTACGTGAGATGTTCTATATGAATAAATACTATGTGAAT
* * * *
1298909 ATGTGCCAAGAGACCTTAGTTTATGTGGATTTATTGTACGTGAAATGTGATCTATATGAATAAAA
66 ATGTGCCAAGAGACCTTAGTTTATGTGGAATTATTATAAGCGAAATGTGATCTATATGAATAAAA
1298974 TACCTCTTAAATAATAAATGTGACCTAATTATATGGAATAAGCCCAAAGAATATTTTATGAGAAT
131 TACCTCTTAAATAATAAATGTGACCTAATTATATGGAATAAGCCCAAAGAATATTTTATGAGAAT
* *
1299039 TAGG-GTTATAGTTGGCATGCCAAGAGTCGAGGGTTCTATGTGGTCCTTCGGGACAAACCTAAGT
196 TAGGCG-TATAGTTGGCATGCCAAGAGTCGAGGGTTCTATGTGGTCCTTCAGAACAAACCTAAGT
1299103 GGTCATTCG
260 GGTCATTCG
1299112 AGACAAACCT
Statistics
Matches: 250, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
300 1 0.00
301 236 0.94
302 13 0.05
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.34
Consensus pattern (302 bp):
TATGGTAAATGCTATGAGTAAATGTTCTACGTGAGATGTTCTATATGAATAAATACTATGTGAAT
ATGTGCCAAGAGACCTTAGTTTATGTGGAATTATTATAAGCGAAATGTGATCTATATGAATAAAA
TACCTCTTAAATAATAAATGTGACCTAATTATATGGAATAAGCCCAAAGAATATTTTATGAGAAT
TAGGCGTATAGTTGGCATGCCAAGAGTCGAGGGTTCTATGTGGTCCTTCAGAACAAACCTAAGTG
GTCATTCGGGATATATATGGCTCTTCGGTATAAATTATGTGC
Found at i:1299111 original size:23 final size:23
Alignment explanation
Indices: 1299078--1299122 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1299068 AGGGTTCTAT
* *
1299078 GTGGTCCTTCGGGACAAACCTAA
1 GTGGTCATTCGAGACAAACCTAA
1299101 GTGGTCATTCGAGACAAACCTA
1 GTGGTCATTCGAGACAAACCTA
1299123 TATGATCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.22
Consensus pattern (23 bp):
GTGGTCATTCGAGACAAACCTAA
Found at i:1299138 original size:23 final size:23
Alignment explanation
Indices: 1299090--1299141 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1299080 GGTCCTTCGG
* *
1299090 GACAAACCTAAGTGGTCATTCGA
1 GACAAACCTAAGTGATCATTCAA
*
1299113 GACAAACCTATA-TGATCTTTCAA
1 GACAAACCTA-AGTGATCATTCAA
1299136 GACAAA
1 GACAAA
1299142 TATGTGGCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.23
Consensus pattern (23 bp):
GACAAACCTAAGTGATCATTCAA
Found at i:1300580 original size:38 final size:37
Alignment explanation
Indices: 1300488--1300581 Score: 152
Period size: 38 Copynumber: 2.5 Consensus size: 37
1300478 TTTATTTTGT
1300488 TCGAGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGG
1 TCGAGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGG
1300525 TCGAGTCGGGTCGGGGTTTTTTAAGTGTGATATTCGGG
1 TCGAGTCGGGTC-GGGTTTTTTAAGTGTGATATTCGGG
* *
1300563 TTGGGTCGGGTTCGGGTTT
1 TCGAGTCGGG-TCGGGTTT
1300582 AGGGTGAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
37 12 0.23
38 39 0.74
39 2 0.04
ACGTcount: A:0.11, C:0.11, G:0.40, T:0.38
Consensus pattern (37 bp):
TCGAGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGG
Found at i:1300783 original size:258 final size:254
Alignment explanation
Indices: 1300271--1301134 Score: 1207
Period size: 249 Copynumber: 3.4 Consensus size: 254
1300261 ACTTTATTTT
* * *
1300271 GGTCGGGTCGGATCAGGTTTTTTTAAGTGTGATATTCGGGTCAGGTTCGGGTTTAGGGTGAAAAA
1 GGTCGAGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTGAAAAA
*
1300336 AATCGGACCGACCCGAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAA
66 AATCGGACCGACCCGAAAATATATATAATTCGGGTCGGGTCGGATTAAGTCACTGTTTTTATTAA
*
1300401 ATAAAAAT-ATTTTTTATTATTTCGGGTCGGGTC-GGTTGGATTTCTAATTCATATATTCGGGTC
131 ATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTC
* * *
1300464 GGGTCGGATGAAACTTTATTTTGTTCGAGTCGGGTCGGGTTTTTTAAGTGTGATATTCG
196 GGGTCGGATGAAACTTTATTTTGTTTGGGTCGGGTCAGGTTTTTTAAGTGTGATATTCG
* *
1300523 GGTCGAGTCGGGTCGGGGTTTTTTAAGTGTGATATTCGGGTTGGGTCGGGTTCGGGTTTAGGGTG
1 GGTCGAGTCGGATCGGGTTTTTTTAAGTGTGATATTC-----GGGTCGGGTTCGGGTTTAGGGTG
* * *
1300588 AAAAAACT-TGACTGACCCGAAAATATATATAATTCGGGTCGGGTCGGATTAAGTCACTGTTTTT
61 AAAAAAATCGGACCGACCCGAAAATATATATAATTCGGGTCGGGTCGGATTAAGTCACTGTTTTT
1300652 ATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTCGGATTTCTAATTCATATATTC
126 ATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTCGGATTTCTAATTCATATATTC
* * *
1300717 AGGGT-GGGTCGAATGAAATTTTATTTTGTTTGGGTCAGGTCAGGTTTTTTAAGTGTGATATTCG
191 -GGGTCGGGTCGGATGAAACTTTATTTTGTTTGGGTCGGGTCAGGTTTTTTAAGTGTGATATTCG
* * * * *
1300781 GGTTGAGTCGGGTCGGGTTTTTTTAAGTATGATATTCGGGTCGGGTTTGAGTTTAGGGTGAAAAA
1 GGTCGAGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTGAAAAA
* * *
1300846 AACCGAACCGACCCGAAAATATATATAATTCGGGTTGGGTCGAGTCGGATTAAGTCACTGTTTTT
66 AATCGGACCGACCCGAAAATATATATAATTC-----GGGTCGGGTCGGATTAAGTCACTGTTTTT
1300911 ATTAAATAAAAATAATTTTTTATTA--T----T----TCGGGTCGGATTTCTAATTCATATATTC
126 ATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTCGGATTTCTAATTCATATATTC
*
1300966 GGGTCGGGTCGGATGAAACTTTATTTTGTTTGGGTCGGGTCAGGTTTTTTAAGTATGATATTCG
191 GGGTCGGGTCGGATGAAACTTTATTTTGTTTGGGTCGGGTCAGGTTTTTTAAGTGTGATATTCG
1301030 GGTCGAGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGGTCGGGTTCGGGTTTA
1 GGTCGAGTCGGATCGGGTTTTTTTAAGTGTGATA------T----TCGGGTCGGGTTCGGGTTTA
*
1301095 GGGTGAAAAAAATCGGACCGACCCGAAAAAATATATAATT
56 GGGTGAAAAAAATCGGACCGACCCGAAAATATATATAATT
1301135 TTACCTTATA
Statistics
Matches: 548, Mismatches: 39, Indels: 43
0.87 0.06 0.07
Matches are distributed among these distances:
248 4 0.01
249 114 0.21
252 33 0.06
253 28 0.05
254 24 0.04
255 1 0.00
256 66 0.12
257 55 0.10
258 111 0.20
259 112 0.20
ACGTcount: A:0.24, C:0.11, G:0.28, T:0.37
Consensus pattern (254 bp):
GGTCGAGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTGAAAAA
AATCGGACCGACCCGAAAATATATATAATTCGGGTCGGGTCGGATTAAGTCACTGTTTTTATTAA
ATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTC
GGGTCGGATGAAACTTTATTTTGTTTGGGTCGGGTCAGGTTTTTTAAGTGTGATATTCG
Found at i:1301049 original size:37 final size:37
Alignment explanation
Indices: 1300998--1301086 Score: 126
Period size: 38 Copynumber: 2.4 Consensus size: 37
1300988 ATTTTGTTTG
*
1300998 GGTCGGGTCAGGTTTTTTAAGTATGATATTCGGGTC-
1 GGTCGGGTCGGGTTTTTTAAGTATGATATTCGGGTCA
* *
1301034 GAGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCA
1 G-GTCGGGTCGGG-TTTTTTAAGTATGATATTCGGGTCA
1301073 GGTCGGGTCGGGTT
1 GGTCGGGTCGGGTT
1301087 CGGGTTTAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
36 1 0.02
37 11 0.24
38 33 0.72
39 1 0.02
ACGTcount: A:0.15, C:0.11, G:0.37, T:0.37
Consensus pattern (37 bp):
GGTCGGGTCGGGTTTTTTAAGTATGATATTCGGGTCA
Found at i:1301690 original size:17 final size:16
Alignment explanation
Indices: 1301651--1301695 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
1301641 TATGAAATTG
1301651 GATTCCAATTCCTACA
1 GATTCCAATTCCTACA
* *
1301667 TATTCCAATTCTTCACA
1 GATTCCAATTCCT-ACA
1301684 GATTCCAATTCC
1 GATTCCAATTCC
1301696 CTCATAAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.29, C:0.31, G:0.04, T:0.36
Consensus pattern (16 bp):
GATTCCAATTCCTACA
Found at i:1306579 original size:23 final size:23
Alignment explanation
Indices: 1306549--1306648 Score: 143
Period size: 23 Copynumber: 4.4 Consensus size: 23
1306539 AGTCGCGGGT
1306549 TCTATGTGGTCCTTCGGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
**
1306572 TCTATGTGGTATTTCGGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
*
1306595 TCTATGTGGTTCTTCGGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
1306618 -CGTATGTGGTCCTTCGGGACAAA
1 TC-TATGTGGTCCTTCGGGACAAA
1306641 --TATGTGGT
1 TCTATGTGGT
1306649 ACATCGGTGC
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
21 8 0.11
22 1 0.01
23 62 0.87
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (23 bp):
TCTATGTGGTCCTTCGGGACAAA
Found at i:1323186 original size:18 final size:16
Alignment explanation
Indices: 1323160--1323198 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
1323150 ATTTTACTTT
*
1323160 TAAATTATTAAATACATC
1 TAAAATATTAAAT-CA-C
1323178 TAAAATATTAAATCAC
1 TAAAATATTAAATCAC
1323194 TAAAA
1 TAAAA
1323199 CTGTTACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 2 0.10
18 12 0.60
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAATATTAAATCAC
Found at i:1326686 original size:2 final size:2
Alignment explanation
Indices: 1326631--1326677 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1326621 TTACATGATT
*
1326631 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1326673 TA TA T
1 TA TA T
1326678 GCATATATAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1326876 original size:24 final size:24
Alignment explanation
Indices: 1326829--1326877 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
1326819 ATGTAATCTA
1326829 ATATAATATACACTTACATAAAAAT
1 ATATAATATACAC-TACATAAAAAT
1326854 ATATGAATATACA-TACATGAAAAA
1 ATAT-AATATACACTACAT-AAAAA
1326878 ATAAGAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.23
25 9 0.41
26 8 0.36
ACGTcount: A:0.57, C:0.10, G:0.04, T:0.29
Consensus pattern (24 bp):
ATATAATATACACTACATAAAAAT
Found at i:1327205 original size:27 final size:29
Alignment explanation
Indices: 1327123--1327211 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 29
1327113 TGACATAGCT
**
1327123 AAAATAGAAGTTTAAAGGA-CTAAAATGACA
1 AAAATAGAAAATTAAAGGAGCTAAAAT-A-A
*
1327153 AAAATAGAAAATTAAAGGATCT-AAATAA
1 AAAATAGAAAATTAAAGGAGCTAAAATAA
*
1327181 AAAATAGAAAATT-TAGG-GCTAAAATAA
1 AAAATAGAAAATTAAAGGAGCTAAAATAA
1327208 AAAA
1 AAAA
1327212 CAAAAACATC
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
26 2 0.04
27 13 0.25
28 14 0.26
29 1 0.02
30 21 0.40
31 2 0.04
ACGTcount: A:0.62, C:0.04, G:0.13, T:0.20
Consensus pattern (29 bp):
AAAATAGAAAATTAAAGGAGCTAAAATAA
Found at i:1327780 original size:10 final size:10
Alignment explanation
Indices: 1327765--1327796 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1327755 GGCGGAGCTC
1327765 GCGGTGGCGA
1 GCGGTGGCGA
1327775 GCGGTGGCGA
1 GCGGTGGCGA
*
1327785 GCGGCGGCGA
1 GCGGTGGCGA
1327795 GC
1 GC
1327797 AGCGGCGCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.09, C:0.25, G:0.59, T:0.06
Consensus pattern (10 bp):
GCGGTGGCGA
Found at i:1327801 original size:10 final size:10
Alignment explanation
Indices: 1327765--1327803 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1327755 GGCGGAGCTC
*
1327765 GCGGTGGCGA
1 GCGGCGGCGA
*
1327775 GCGGTGGCGA
1 GCGGCGGCGA
1327785 GCGGCGGCGA
1 GCGGCGGCGA
*
1327795 GCAGCGGCG
1 GCGGCGGCG
1327804 CCGGTGACCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.10, C:0.26, G:0.59, T:0.05
Consensus pattern (10 bp):
GCGGCGGCGA
Found at i:1328560 original size:3 final size:3
Alignment explanation
Indices: 1328539--1328581 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
1328529 TAATTACTAT
* *
1328539 TAA TAA AAA TAA CAA TAA TAA TAA TAA TAA TAA -AA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1328582 AAAAGACCCG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (3 bp):
TAA
Found at i:1328844 original size:40 final size:40
Alignment explanation
Indices: 1328731--1328846 Score: 110
Period size: 40 Copynumber: 2.8 Consensus size: 40
1328721 TGTTGGGAAC
* * *
1328731 GACATTGCTCATACGCGATGAAGAGTTCGGGTCGTCTAAGGGT
1 GACACTGCTCATACGTGATGAAGAGTTCTGGTCG--T-AGGGT
* * **
1328774 GACACAGCTTC-TACGTGATGAGGAAATCTGGTCG-AGGGAT
1 GACACTGC-TCATACGTGATGAAGAGTTCTGGTCGTAGGG-T
1328814 GACACTGCTCATACGTGATGAAGAGTTCTGGTC
1 GACACTGCTCATACGTGATGAAGAGTTCTGGTC
1328847 ATCTTTAAGA
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
39 6 0.10
40 27 0.46
43 24 0.41
44 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (40 bp):
GACACTGCTCATACGTGATGAAGAGTTCTGGTCGTAGGGT
Found at i:1328984 original size:134 final size:134
Alignment explanation
Indices: 1328765--1329201 Score: 628
Period size: 134 Copynumber: 3.3 Consensus size: 134
1328755 GTTCGGGTCG
* * * ** * * *
1328765 TCTAAGGGTGACACAGCTTCTACGTGATGAGGAAATCTGGTCGAG-GGATGACACTGCTCATACG
1 TCTAAGGGTGACACGGCTCCTATGTGATGAGGAGGTCTGTTCG-GTGGATGACACGGCTCATACT
* *
1328829 TGATGAAGAGTTCTGGTCATCTTTAAGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGCT
65 TGATGAAGAGTTCTGGCCATCTTTAAGAAGGGTGATAACACGGTTCCTACGCGATGAGGACGGCT
1328894 GGTTA
130 GGTTA
* *
1328899 TCTAAGGGTGACACGGCTCCTATGCGATGAAGAGGTCTGTTCGGTGGATGACACGGCTCATACTT
1 TCTAAGGGTGACACGGCTCCTATGTGATGAGGAGGTCTGTTCGGTGGATGACACGGCTCATACTT
*
1328964 GATGAAGAGTTCTGGCCATCTTT-AGGAGAGGTGATAACACGGTTCCTACGCGATGAGGACGGCT
66 GATGAAGAGTTCTGGCCATCTTTAAGAAG-GGTGATAACACGGTTCCTACGCGATGAGGACGGCT
1329028 GGTTA
130 GGTTA
* * *
1329033 TCTAAGGGTGAAACGGCTCCTATATGATGAGGAGGTCTGTTCGGTGGATGACACGACTCATACTT
1 TCTAAGGGTGACACGGCTCCTATGTGATGAGGAGGTCTGTTCGGTGGATGACACGGCTCATACTT
* * * *
1329098 GATGTAGAGTTCTAGCCATCTTTAGGATA-GGTGATAACACGGTTCCTACGTGATGAGGACGGCT
66 GATGAAGAGTTCTGGCCATCTTTAAGA-AGGGTGATAACACGGTTCCTACGCGATGAGGACGGCT
1329162 GGTTA
130 GGTTA
**
1329167 TCTAAGGGTGACACGGCTCCTACATGATGAGGAGG
1 TCTAAGGGTGACACGGCTCCTATGTGATGAGGAGG
1329202 ACTGGTCATC
Statistics
Matches: 274, Mismatches: 25, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
133 5 0.02
134 267 0.97
135 1 0.00
136 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.26
Consensus pattern (134 bp):
TCTAAGGGTGACACGGCTCCTATGTGATGAGGAGGTCTGTTCGGTGGATGACACGGCTCATACTT
GATGAAGAGTTCTGGCCATCTTTAAGAAGGGTGATAACACGGTTCCTACGCGATGAGGACGGCTG
GTTA
Found at i:1329195 original size:43 final size:43
Alignment explanation
Indices: 1329134--1329293 Score: 160
Period size: 43 Copynumber: 3.5 Consensus size: 43
1329124 ATAGGTGATA
* *
1329134 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGTG
1 ACACGGCTCCTACATGATGAGGACGGCTGGTTATCTAAGGGTG
*
1329177 ACACGGCTCCTACATGATGAGGA-GGACTGGTCATCTTTAGGAGAGGTG
1 ACACGGCTCCTACATGATGAGGACGG-CTGGTTATC--TA--AG-GGTG
* * ** *
1329225 ATAACATGGTTCCTACGCGATGAGGACGGCTGGTTATCTAAGGGTA
1 ---ACACGGCTCCTACATGATGAGGACGGCTGGTTATCTAAGGGTG
1329271 ACACGGCTCCTACATGATGAGGA
1 ACACGGCTCCTACATGATGAGGA
1329294 GGATTGGTCA
Statistics
Matches: 94, Mismatches: 13, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
42 2 0.02
43 48 0.51
45 2 0.02
46 3 0.03
47 4 0.04
48 4 0.04
49 2 0.02
51 27 0.29
52 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (43 bp):
ACACGGCTCCTACATGATGAGGACGGCTGGTTATCTAAGGGTG
Found at i:1329212 original size:94 final size:94
Alignment explanation
Indices: 1329114--1329310 Score: 349
Period size: 94 Copynumber: 2.1 Consensus size: 94
1329104 GAGTTCTAGC
* * *
1329114 CATCTTTAGGATAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGTGAC
1 CATCTTTAGGAGAGGTGATAACACGGTTCCTACGCGATGAGGACGGCTGGTTATCTAAGGGTAAC
1329179 ACGGCTCCTACATGATGAGGAGGACTGGT
66 ACGGCTCCTACATGATGAGGAGGACTGGT
*
1329208 CATCTTTAGGAGAGGTGATAACATGGTTCCTACGCGATGAGGACGGCTGGTTATCTAAGGGTAAC
1 CATCTTTAGGAGAGGTGATAACACGGTTCCTACGCGATGAGGACGGCTGGTTATCTAAGGGTAAC
*
1329273 ACGGCTCCTACATGATGAGGAGGATTGGT
66 ACGGCTCCTACATGATGAGGAGGACTGGT
1329302 CATCTTTAG
1 CATCTTTAG
1329311 TGATTATGGT
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 98 1.00
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (94 bp):
CATCTTTAGGAGAGGTGATAACACGGTTCCTACGCGATGAGGACGGCTGGTTATCTAAGGGTAAC
ACGGCTCCTACATGATGAGGAGGACTGGT
Found at i:1329240 original size:51 final size:47
Alignment explanation
Indices: 1329114--1329310 Score: 144
Period size: 43 Copynumber: 4.2 Consensus size: 47
1329104 GAGTTCTAGC
* *
1329114 CATCTTTAGGATAGGTGATAACACGGTTCCTACGTGATGAGGACGG-CTGGT
1 CATCTTTA-GA-AGG-G-TAACACGGCTCCTACATGATGAGGA-GGACTGGT
* *
1329165 TATC--T--AAGGGTGACACGGCTCCTACATGATGAGGAGGACTGGT
1 CATCTTTAGAAGGGTAACACGGCTCCTACATGATGAGGAGGACTGGT
* * **
1329208 CATCTTTAGGAGAGGTGATAACATGGTTCCTACGCGATGAGGACGG-CTGGT
1 CATCTTTA-GA-AGG-G-TAACACGGCTCCTACATGATGAGGA-GGACTGGT
* *
1329259 TATC--T--AAGGGTAACACGGCTCCTACATGATGAGGAGGATTGGT
1 CATCTTTAGAAGGGTAACACGGCTCCTACATGATGAGGAGGACTGGT
1329302 CATCTTTAG
1 CATCTTTAG
1329311 TGATTATGGT
Statistics
Matches: 114, Mismatches: 17, Indels: 34
0.69 0.10 0.21
Matches are distributed among these distances:
42 4 0.04
43 58 0.51
44 2 0.02
45 8 0.07
46 2 0.02
48 1 0.01
49 5 0.04
50 1 0.01
51 31 0.27
52 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (47 bp):
CATCTTTAGAAGGGTAACACGGCTCCTACATGATGAGGAGGACTGGT
Found at i:1329554 original size:32 final size:33
Alignment explanation
Indices: 1329507--1329639 Score: 126
Period size: 36 Copynumber: 3.8 Consensus size: 33
1329497 CAAAGATCGG
*
1329507 TGTTTCGAGAGAAACAAACTCAAAGATGT-TTT
1 TGTTTCAAGAGAAACAAACTCAAAGATGTATTT
* * *
1329539 TGTTTCAAGAAAAACATACTCAAAGATTTTGTTTGTTT
1 TGTTTCAAGAGAAACAAACTCAAAGA---TG--TATTT
*
1329577 TGTTTCAAGGGAAACAAACTCAAAGATGGTAAATTT
1 TGTTTCAAGAGAAACAAACTCAAAGAT-GT--ATTT
1329613 TGTTTCCAA-AGAAACAAACTCAAAGAT
1 TGTTT-CAAGAGAAACAAACTCAAAGAT
1329640 TTTTTTTTCT
Statistics
Matches: 83, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
32 23 0.28
34 1 0.01
35 3 0.04
36 26 0.31
37 4 0.05
38 26 0.31
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.32
Consensus pattern (33 bp):
TGTTTCAAGAGAAACAAACTCAAAGATGTATTT
Found at i:1329594 original size:70 final size:72
Alignment explanation
Indices: 1329507--1329642 Score: 188
Period size: 74 Copynumber: 1.9 Consensus size: 72
1329497 CAAAGATCGG
* *
1329507 TGTTTCGAGAGAAACAAACTCAAAGAT-GT-TTTTGTTT-CAAGAAAAACATACTCAAAGATTTT
1 TGTTTCAAGAGAAACAAACTCAAAGATGGTATTTTGTTTCCAA-AAAAACAAACTCAAAGATTTT
1329569 GTTTGTTT
65 GTTTGTTT
* *
1329577 TGTTTCAAGGGAAACAAACTCAAAGATGGTAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTT
1 TGTTTCAAGAGAAACAAACTCAAAGATGGT--ATTTTGTTTCCAAAAAAACAAACTCAAAGATTT
1329642 T
64 T
1329643 TTTTTCTCAA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
70 25 0.44
71 2 0.04
74 27 0.47
75 3 0.05
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (72 bp):
TGTTTCAAGAGAAACAAACTCAAAGATGGTATTTTGTTTCCAAAAAAACAAACTCAAAGATTTTG
TTTGTTT
Found at i:1329844 original size:30 final size:31
Alignment explanation
Indices: 1329798--1329857 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
1329788 GAGAGACAAA
* * *
1329798 ATTTGTTTTAATAGAAATAGACTCAAAGATG
1 ATTTGTTTTAAAAGAAACAAACTCAAAGATG
1329829 ATTT-TTTTAAAAGAAACAAACTCAAAGAT
1 ATTTGTTTTAAAAGAAACAAACTCAAAGAT
1329858 TTTTTTACGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (31 bp):
ATTTGTTTTAAAAGAAACAAACTCAAAGATG
Found at i:1330628 original size:106 final size:104
Alignment explanation
Indices: 1330412--1330630 Score: 242
Period size: 106 Copynumber: 2.1 Consensus size: 104
1330402 TGAGCTTACT
* * *
1330412 TTTGTCTCAAGTGAATCAAATTCGAAATTTGTATATCAAAGGAAAAAATGTCTCAAACGAGACGA
1 TTTGTTTCAAGTGAATCAAATTCAAAATTTGTATATCAAAGAAAAAAATGTCTCAAACGAGACGA
* * * ** *
1330477 AATTTGTTTTGAAAGAAATAACAATCTCAAGTGAGATTAAT
66 AATTTATTTTGAAAGAAAT-A-AATCTCAAGCGAAAAAAAA
** * *
1330518 TTTGTTTCAAGTGAATTGAATTCAAAATTTGTATCTCAAAGAAAAAAAATGTCTCAAGCGAGACG
1 TTTGTTTCAAGTGAATCAAATTCAAAATTTGTATATCAAAG-AAAAAAATGTCTCAAACGAGACG
* * *
1330583 AAGTTTATTTTTAAGAGAAAT-TATCTCAAGCGAAACAAAAA
65 AAATTTATTTTGAA-AGAAATAAATCTCAAGCGAAA-AAAAA
1330624 TTTGTTT
1 TTTGTTT
1330631 TAAAACTCTC
Statistics
Matches: 94, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
105 11 0.12
106 45 0.48
107 32 0.34
108 6 0.06
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (104 bp):
TTTGTTTCAAGTGAATCAAATTCAAAATTTGTATATCAAAGAAAAAAATGTCTCAAACGAGACGA
AATTTATTTTGAAAGAAATAAATCTCAAGCGAAAAAAAA
Found at i:1330998 original size:10 final size:10
Alignment explanation
Indices: 1330976--1331032 Score: 87
Period size: 10 Copynumber: 5.6 Consensus size: 10
1330966 ATGCAAAATT
1330976 TATGTATCGTG
1 TATGTA-CGTG
1330987 TATGTACGTG
1 TATGTACGTG
*
1330997 TATGTACGTA
1 TATGTACGTG
1331007 TATGTACGTG
1 TATGTACGTG
*
1331017 TATGTACATG
1 TATGTACGTG
1331027 TATGTA
1 TATGTA
1331033 TATATATCTA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
10 37 0.86
11 6 0.14
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.42
Consensus pattern (10 bp):
TATGTACGTG
Found at i:1331002 original size:4 final size:4
Alignment explanation
Indices: 1330985--1331082 Score: 51
Period size: 4 Copynumber: 23.5 Consensus size: 4
1330975 TTATGTATCG
*
1330985 TGTA TGTA CGTGTA TGTA CGTA --TA TGTA CGTGTA TGTACA TGTA TGTA
1 TGTA TGTA --TGTA TGTA TGTA TGTA TGTA --TGTA TGT--A TGTA TGTA
* * * *
1331033 --TA TATA TCTA TGTA TGTA TGTA TATACA TGCA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGT--A TGTA TGTA TGTA TGTA TGTA
1331081 TG
1 TG
1331083 CTTTTCTCGA
Statistics
Matches: 75, Mismatches: 7, Indels: 24
0.71 0.07 0.23
Matches are distributed among these distances:
2 4 0.05
4 57 0.76
6 14 0.19
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.44
Consensus pattern (4 bp):
TGTA
Found at i:1331012 original size:14 final size:14
Alignment explanation
Indices: 1330985--1331051 Score: 62
Period size: 14 Copynumber: 4.6 Consensus size: 14
1330975 TTATGTATCG
**
1330985 TGTATGTACGTGTA
1 TGTATGTATATGTA
*
1330999 TGTACGTATATGTA
1 TGTATGTATATGTA
*
1331013 CGTGTATGTACATGTA
1 --TGTATGTATATGTA
* *
1331029 TGTATATATATCTA
1 TGTATGTATATGTA
1331043 TGTATGTAT
1 TGTATGTAT
1331052 GTATATACAT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
14 30 0.71
16 12 0.29
ACGTcount: A:0.27, C:0.07, G:0.21, T:0.45
Consensus pattern (14 bp):
TGTATGTATATGTA
Found at i:1331039 original size:30 final size:31
Alignment explanation
Indices: 1330976--1331039 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
1330966 ATGCAAAATT
* *
1330976 TATGTATCGTGTATGTACGTGTATGTACGTA
1 TATGTATCGTGTATGTACATGTATGTACATA
*
1331007 TATGTA-CGTGTATGTACATGTATGTATATA
1 TATGTATCGTGTATGTACATGTATGTACATA
1331037 TAT
1 TAT
1331040 CTATGTATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 24 0.80
31 6 0.20
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.44
Consensus pattern (31 bp):
TATGTATCGTGTATGTACATGTATGTACATA
Found at i:1331049 original size:22 final size:22
Alignment explanation
Indices: 1331024--1331077 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1331014 GTGTATGTAC
*
1331024 ATGTATGTATATATAT-CTATGT
1 ATGTATGTATATACATGC-ATGT
1331046 ATGTATGTATATACATGCATGT
1 ATGTATGTATATACATGCATGT
1331068 ATGTATGTAT
1 ATGTATGTAT
1331078 GTATGCTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (22 bp):
ATGTATGTATATACATGCATGT
Found at i:1331067 original size:18 final size:18
Alignment explanation
Indices: 1331015--1331073 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
1331005 TATATGTACG
*
1331015 TGTATGTACATGTATGTA
1 TGTATATACATGTATGTA
*
1331033 TATATAT-CTATGTATGTA
1 TGTATATAC-ATGTATGTA
*
1331051 TGTATATACATGCATGTA
1 TGTATATACATGTATGTA
1331069 TGTAT
1 TGTAT
1331074 GTATGTATGC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
17 1 0.03
18 33 0.94
19 1 0.03
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.46
Consensus pattern (18 bp):
TGTATATACATGTATGTA
Found at i:1332292 original size:11 final size:11
Alignment explanation
Indices: 1332264--1332318 Score: 56
Period size: 11 Copynumber: 4.7 Consensus size: 11
1332254 GTCTTTGTGC
*
1332264 TTTTCTCTTCT
1 TTTTCTTTTCT
1332275 TTTTCTTTTCT
1 TTTTCTTTTCT
1332286 TTTTCTTTTGCTAT
1 TTTTCTTTT-C--T
**
1332300 TTTTCTTTGAT
1 TTTTCTTTTCT
1332311 TTTTCTTT
1 TTTTCTTT
1332319 GTACTCTGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
11 28 0.74
12 1 0.03
14 9 0.24
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:1332934 original size:20 final size:20
Alignment explanation
Indices: 1332896--1332934 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1332886 GGATAAATGC
*
1332896 AATGTTTCAATGTCACAAAG
1 AATGTTTCAAGGTCACAAAG
*
1332916 AATGTTTCAAGGTCTCAAA
1 AATGTTTCAAGGTCACAAA
1332935 AAGAGGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
AATGTTTCAAGGTCACAAAG
Found at i:1333982 original size:64 final size:64
Alignment explanation
Indices: 1333909--1334092 Score: 185
Period size: 64 Copynumber: 2.9 Consensus size: 64
1333899 TGTTTGAATA
* ** **
1333909 TGCACCGATGCATTGGTAATGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAATTC
1 TGCATCGATGCATAAGTAATGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAA-TC
1333972 -G
63 GG
* * *
1333973 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAAACATCGAATGCAATCGG
1 TGCATCGATGCATAAGTAATGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATCGG
* * * ** **
1334037 TGCATCGATGCATAAGGAGTGCATCGATGTATCCCAGCAATAATACTACATCGAAT
1 TGCATCGATGCATAAGTAATGCATCGATGCATCCCATTAATAATAAAACATCGAAT
1334093 ACCTTTTATG
Statistics
Matches: 101, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
63 2 0.02
64 94 0.93
65 5 0.05
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (64 bp):
TGCATCGATGCATAAGTAATGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATCGG
Found at i:1334399 original size:26 final size:26
Alignment explanation
Indices: 1334370--1334429 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
1334360 TGTTGATTTT
1334370 TATA-ATACAGTAGTTGTGA-ACATGCA
1 TATAGATA-AGTA-TTGTGATACATGCA
*
1334396 TATATGATAATTATTGTGATACATGCA
1 TATA-GATAAGTATTGTGATACATGCA
1334423 TA-AGATA
1 TATAGATA
1334430 TATATATGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
25 4 0.13
26 11 0.37
27 12 0.40
28 3 0.10
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (26 bp):
TATAGATAAGTATTGTGATACATGCA
Found at i:1334458 original size:12 final size:12
Alignment explanation
Indices: 1334440--1334475 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1334430 TATATATGTT
1334440 CATGTGATATGA
1 CATGTGATATGA
*
1334452 TATGTGATATGA
1 CATGTGATATGA
*
1334464 CCTGTGATATGA
1 CATGTGATATGA
1334476 GAACATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:1334682 original size:15 final size:15
Alignment explanation
Indices: 1334620--1334674 Score: 101
Period size: 15 Copynumber: 3.7 Consensus size: 15
1334610 GAGGGTATAA
*
1334620 TAGTCCTTCGGGACG
1 TAGTCCTTCGAGACG
1334635 TAGTCCTTCGAGACG
1 TAGTCCTTCGAGACG
1334650 TAGTCCTTCGAGACG
1 TAGTCCTTCGAGACG
1334665 TAGTCCTTCG
1 TAGTCCTTCG
1334675 GGATGTAGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.29
Consensus pattern (15 bp):
TAGTCCTTCGAGACG
Found at i:1340916 original size:64 final size:64
Alignment explanation
Indices: 1340848--1341024 Score: 214
Period size: 64 Copynumber: 2.8 Consensus size: 64
1340838 TAAAATAAAG
** *
1340848 ACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGA-A
1 ACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAAT-ACA
* * *
1340912 ACATCGAATGCAA-TCGGTGCATCGATGCATAAGGAGTGCATCGATGCATCCCAGCAATAATACT
1 ACATCGAATGCAATTC-ATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATACA
* ** * * *
1340976 ACATCGAATACCTTTTATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 ACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCAT
1341025 ACCTTCATTA
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
63 3 0.03
64 92 0.96
65 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (64 bp):
ACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATACA
Found at i:1341349 original size:12 final size:12
Alignment explanation
Indices: 1341331--1341366 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1341321 TATATATGTT
1341331 CATGTGATATGA
1 CATGTGATATGA
*
1341343 TATGTGATATGA
1 CATGTGATATGA
*
1341355 CCTGTGATATGA
1 CATGTGATATGA
1341367 GAACATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:1342639 original size:21 final size:20
Alignment explanation
Indices: 1342614--1342653 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1342604 TAAAAATGAA
*
1342614 ATGCATATACCAAATGCAAAG
1 ATGCAAATA-CAAATGCAAAG
*
1342635 ATGCAAATACAGATGCAAA
1 ATGCAAATACAAATGCAAA
1342654 AATGTTGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.17
Consensus pattern (20 bp):
ATGCAAATACAAATGCAAAG
Found at i:1345236 original size:24 final size:24
Alignment explanation
Indices: 1345189--1345237 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
1345179 ATGTAATCTA
1345189 ATATAATATACACTTACATAAAAAT
1 ATATAATATACAC-TACATAAAAAT
1345214 ATATGAATATACA-TACATGAAAAA
1 ATAT-AATATACACTACAT-AAAAA
1345238 ATAAGAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.23
25 9 0.41
26 8 0.36
ACGTcount: A:0.57, C:0.10, G:0.04, T:0.29
Consensus pattern (24 bp):
ATATAATATACACTACATAAAAAT
Found at i:1347622 original size:12 final size:12
Alignment explanation
Indices: 1347605--1347629 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1347595 GAAAATGACC
1347605 AACAAATTCGCA
1 AACAAATTCGCA
1347617 AACAAATTCGCA
1 AACAAATTCGCA
1347629 A
1 A
1347630 CGCGATCTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.24, G:0.08, T:0.16
Consensus pattern (12 bp):
AACAAATTCGCA
Found at i:1347679 original size:20 final size:20
Alignment explanation
Indices: 1347656--1347697 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1347646 CAACGCAAAC
*
1347656 TCCAATTTCGCAACACAGTT
1 TCCAAATTCGCAACACAGTT
*
1347676 TCCAAATTCGCAACTCAGTT
1 TCCAAATTCGCAACACAGTT
1347696 TC
1 TC
1347698 TGCAATCGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.31
Consensus pattern (20 bp):
TCCAAATTCGCAACACAGTT
Found at i:1347763 original size:20 final size:21
Alignment explanation
Indices: 1347723--1347820 Score: 78
Period size: 20 Copynumber: 4.7 Consensus size: 21
1347713 AATTTCTTTC
*
1347723 TCGCAACGCGATTTTCCAAAT
1 TCGCAACGCGATTTCCCAAAT
1347744 TCGCAACGCGA-TTCCCAAAT
1 TCGCAACGCGATTTCCCAAAT
** *
1347764 TCGCAAAACGAAATTT--TAAAT
1 TCGC--AACGCGATTTCCCAAAT
* **
1347785 TCGCAACTCGATTT-CTGAAT
1 TCGCAACGCGATTTCCCAAAT
1347805 TCGCAACGCGAATTTC
1 TCGCAACGCG-ATTTC
1347821 TTTTTCGCAA
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
19 7 0.11
20 25 0.40
21 23 0.37
22 5 0.08
23 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.28
Consensus pattern (21 bp):
TCGCAACGCGATTTCCCAAAT
Found at i:1347768 original size:41 final size:40
Alignment explanation
Indices: 1347723--1347820 Score: 99
Period size: 41 Copynumber: 2.4 Consensus size: 40
1347713 AATTTCTTTC
1347723 TCGCAACGCGATTTTCCAAATTCGCAACGCGATTCCCAAAT
1 TCGCAACGCGATTTT-CAAATTCGCAACGCGATTCCCAAAT
** * * **
1347764 TCGCAAAACGAAATTTT-AAATTCGCAACTCGATTTCTGAAT
1 TCGC--AACGCGATTTTCAAATTCGCAACGCGATTCCCAAAT
*
1347805 TCGCAACGCGAATTTC
1 TCGCAACGCGATTTTC
1347821 TTTTTCGCAA
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
39 8 0.18
41 28 0.62
43 9 0.20
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.28
Consensus pattern (40 bp):
TCGCAACGCGATTTTCAAATTCGCAACGCGATTCCCAAAT
Found at i:1347840 original size:20 final size:20
Alignment explanation
Indices: 1347804--1347919 Score: 67
Period size: 20 Copynumber: 5.8 Consensus size: 20
1347794 GATTTCTGAA
* *
1347804 TTCGCAACGCGAATTTCTTT
1 TTCGCAACACGAATTTCCTT
1347824 TTCGCAACAC-AAGTTTCCTT
1 TTCGCAACACGAA-TTTCCTT
* * * *
1347844 TTCACAACAAG-ATTTTCTAA
1 TTCGCAACACGAATTTCCT-T
* *
1347864 ATCGCAACACGAAATTT-GTT
1 TTCGCAACACG-AATTTCCTT
* * ***
1347884 TTCGCAACTCGATTTTCGAA
1 TTCGCAACACGAATTTCCTT
1347904 TTCGCAACACGAATTT
1 TTCGCAACACGAATTT
1347920 TAATTTTGCA
Statistics
Matches: 72, Mismatches: 18, Indels: 12
0.71 0.18 0.12
Matches are distributed among these distances:
19 11 0.15
20 56 0.78
21 1 0.01
22 4 0.06
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.34
Consensus pattern (20 bp):
TTCGCAACACGAATTTCCTT
Found at i:1347869 original size:40 final size:40
Alignment explanation
Indices: 1347825--1347916 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 40
1347815 AATTTCTTTT
* *
1347825 TCGCAACAC-AAGTTTCCTTTTCACAACAAGATTTTCTAAA
1 TCGCAACACGAAATTT-CTTTTCACAACAAGATTTTCGAAA
* * ** *
1347865 TCGCAACACGAAATTTGTTTTCGCAACTCGATTTTCGAAT
1 TCGCAACACGAAATTTCTTTTCACAACAAGATTTTCGAAA
1347905 TCGCAACACGAA
1 TCGCAACACGAA
1347917 TTTTAATTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 39 0.89
41 5 0.11
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (40 bp):
TCGCAACACGAAATTTCTTTTCACAACAAGATTTTCGAAA
Found at i:1347931 original size:40 final size:40
Alignment explanation
Indices: 1347854--1347931 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
1347844 TTCACAACAA
* *
1347854 GATTTTCTAAATCGCAACACGAAATTTGTTTTCGCAACTC
1 GATTTTCGAAATCGCAACACGAAATTTATTTTCGCAACTC
* *
1347894 GATTTTCGAATTCGCAACACGAATTTTAATTTT-GCAAC
1 GATTTTCGAAATCGCAACACGAAATTT-ATTTTCGCAAC
1347932 AGCTTTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 29 0.88
41 4 0.12
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (40 bp):
GATTTTCGAAATCGCAACACGAAATTTATTTTCGCAACTC
Found at i:1348933 original size:24 final size:24
Alignment explanation
Indices: 1348875--1348921 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1348865 AGTCAGTATT
* *
1348875 CGAAATTTGATTTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
1348899 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
1348922 TCGGATTTTG
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:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:1351210 original size:6 final size:6
Alignment explanation
Indices: 1351201--1351242 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
1351191 AAGCAAAAAA
**
1351201 AAAATC AAAATC AAAATC AAAATC GCAATC AAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
1351243 CCAATCACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.62, C:0.19, G:0.02, T:0.17
Consensus pattern (6 bp):
AAAATC
Found at i:1351247 original size:18 final size:18
Alignment explanation
Indices: 1351209--1351249 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1351199 AAAAAATCAA
*
1351209 AATCAAAATCAAAATCGC
1 AATCAAAATCAAAATCCC
1351227 AATCAAAATCAAAATCCC
1 AATCAAAATCAAAATCCC
1351245 AATCA
1 AATCA
1351250 CAACCGGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.56, C:0.24, G:0.02, T:0.17
Consensus pattern (18 bp):
AATCAAAATCAAAATCCC
Found at i:1351504 original size:29 final size:29
Alignment explanation
Indices: 1351462--1351535 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 29
1351452 AATTCGCAAC
* * **
1351462 GCGAATGTCAAATTCATGTTGTGATTGTT
1 GCGAAAGTCAAATTCATATTGCAATTGTT
* *
1351491 GCGAAAGTTAAATTCGTATTGCAATTGTT
1 GCGAAAGTCAAATTCATATTGCAATTGTT
*
1351520 GCGAAAGACAAATTCA
1 GCGAAAGTCAAATTCA
1351536 CAACACGAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (29 bp):
GCGAAAGTCAAATTCATATTGCAATTGTT
Found at i:1351599 original size:20 final size:20
Alignment explanation
Indices: 1351574--1351618 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1351564 AAATCGCAAC
1351574 GCGAATTTGACTTCCGCGTT
1 GCGAATTTGACTTCCGCGTT
* *
1351594 GCGAATTTGATTTTCGCGTT
1 GCGAATTTGACTTCCGCGTT
1351614 GCGAA
1 GCGAA
1351619 AGTGTACCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.36
Consensus pattern (20 bp):
GCGAATTTGACTTCCGCGTT
Found at i:1353010 original size:21 final size:21
Alignment explanation
Indices: 1352972--1353048 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
1352962 GTTAATTGGG
* *
1352972 CTCTTGAACGGT-ATGAGGGAC
1 CTCTTGAACGATGA-GAGGGGC
*
1352993 CTCTTGAACGATGAGAGGGGT
1 CTCTTGAACGATGAGAGGGGC
* * * *
1353014 TTCTTGAAAGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
1353035 CTCTTGAATGATGA
1 CTCTTGAACGATGA
1353049 TAGGTGAATC
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
21 42 0.98
22 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.36, T:0.26
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:1354161 original size:20 final size:20
Alignment explanation
Indices: 1354124--1354162 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1354114 CTAAAATCAT
* *
1354124 GTTGCGAATTTCATTTTCAC
1 GTTGCGAATTTAAGTTTCAC
1354144 GTTGCGAATTTAAGTTTCA
1 GTTGCGAATTTAAGTTTCA
1354163 AAAACTATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (20 bp):
GTTGCGAATTTAAGTTTCAC
Found at i:1354671 original size:19 final size:20
Alignment explanation
Indices: 1354649--1354687 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1354639 TAATATTGTG
1354649 TTTCGAATT-CGAAAATAAA
1 TTTCGAATTGCGAAAATAAA
**
1354668 TTTCGCGTTGCGAAAATAAA
1 TTTCGAATTGCGAAAATAAA
1354688 CGCGCTTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (20 bp):
TTTCGAATTGCGAAAATAAA
Found at i:1355441 original size:24 final size:24
Alignment explanation
Indices: 1355413--1355459 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1355403 AACTCAAAAA
*
1355413 AAAAATAGAAGCTTGATTGAAGTCT
1 AAAATTAG-AGCTTGATTGAAGTCT
*
1355438 AAAATTCGAGCTTGATTGAAGT
1 AAAATTAGAGCTTGATTGAAGT
1355460 GAAAGAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (24 bp):
AAAATTAGAGCTTGATTGAAGTCT
Found at i:1355587 original size:36 final size:36
Alignment explanation
Indices: 1355547--1355658 Score: 96
Period size: 36 Copynumber: 3.2 Consensus size: 36
1355537 TTAGTTGGGA
1355547 TGTTCTTCTATGTTTCTTAGCCATATGAGATTGTTT
1 TGTTCTTCTATGTTTCTTAGCCATATGAGATTGTTT
* *
1355583 TGTTC-TC-ATATTT-TTA-CTC-T-TTAGACTT-TTGT
1 TGTTCTTCTATGTTTCTTAGC-CATATGAGA-TTGTT-T
1355615 GATGCTT-TTCTATGTTTCTTAGCCATATGAGATTGTTT
1 --TG-TTCTTCTATGTTTCTTAGCCATATGAGATTGTTT
1355653 TGTTCT
1 TGTTCT
1355659 CATAATTTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 28
0.64 0.04 0.31
Matches are distributed among these distances:
31 6 0.10
32 5 0.09
33 4 0.07
34 7 0.12
35 8 0.14
36 13 0.22
37 4 0.07
38 5 0.09
39 6 0.10
ACGTcount: A:0.16, C:0.14, G:0.15, T:0.54
Consensus pattern (36 bp):
TGTTCTTCTATGTTTCTTAGCCATATGAGATTGTTT
Found at i:1355668 original size:70 final size:70
Alignment explanation
Indices: 1355541--1355722 Score: 305
Period size: 70 Copynumber: 2.6 Consensus size: 70
1355531 TAGAAGTTAG
*
1355541 TTGGGATG-TTCTTCTATGTTTCTTAGCCATATGAGATTGTTTTGTTCTCATATTTTTACTCTTT
1 TTGGGATGCTT-TTCTATGTTTCTTAGCCATATGAGATTGTTTTGTTCTCATAATTTTACTCTTT
1355605 AGACTT
65 AGACTT
*
1355611 TTGTGATGCTTTTCTATGTTTCTTAGCCATATGAGATTGTTTTGTTCTCATAATTTTACTCTTTA
1 TTGGGATGCTTTTCTATGTTTCTTAGCCATATGAGATTGTTTTGTTCTCATAATTTTACTCTTTA
1355676 GACTT
66 GACTT
* *
1355681 TTGGGATGCTTTTCTATGTTT-TTACCCATGTGAGATTGTTTT
1 TTGGGATGCTTTTCTATGTTTCTTAGCCATATGAGATTGTTTT
1355723 TAAAAAAAAT
Statistics
Matches: 106, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
69 19 0.18
70 85 0.80
71 2 0.02
ACGTcount: A:0.17, C:0.14, G:0.16, T:0.53
Consensus pattern (70 bp):
TTGGGATGCTTTTCTATGTTTCTTAGCCATATGAGATTGTTTTGTTCTCATAATTTTACTCTTTA
GACTT
Found at i:1358479 original size:20 final size:20
Alignment explanation
Indices: 1358438--1358477 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1358428 TCCCTAATTA
**
1358438 ATAAAAAATATTTTATATTT
1 ATAAAAAATATAATATATTT
1358458 ATAAAAAATATAAATATATT
1 ATAAAAAATAT-AATATATT
1358478 ATCTAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAAAAAATATAATATATTT
Found at i:1359416 original size:63 final size:66
Alignment explanation
Indices: 1359342--1359519 Score: 204
Period size: 63 Copynumber: 2.7 Consensus size: 66
1359332 TATTAATCGA
1359342 ATTTTTTTCTTTAACCATTAATCGAACCGAAATTTATTTGACCGTTAAT-A-GAA-TAAAATAAA
1 ATTTTTTTCTTTAA-CATTAATCGAACCGAAATTTATTTGACCGTTAATAACGAACTAAAATAAA
**
1359404 TT
65 CG
** *** * *
1359406 A-TTTTTTCTTTAATTGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACTAAATTAA
1 ATTTTTTTCTTTAA-CATTAATCGAACCGAAATTTATTTGACCGTTAATAA-CGAACTAAAATAA
1359470 ACG
64 ACG
*
1359473 ATTTTTTTCTTTAACATTAATCGAACCGAAA-TTATTTTACCGTTAAT
1 ATTTTTTTCTTTAACATTAATCGAACCGAAATTTATTTGACCGTTAAT
1359520 CGAACCAAAA
Statistics
Matches: 92, Mismatches: 17, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
63 40 0.43
64 2 0.02
66 14 0.15
67 24 0.26
68 12 0.13
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (66 bp):
ATTTTTTTCTTTAACATTAATCGAACCGAAATTTATTTGACCGTTAATAACGAACTAAAATAAAC
G
Found at i:1359710 original size:26 final size:27
Alignment explanation
Indices: 1359679--1359729 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
1359669 TTCTTTACGT
1359679 ATTAATCAAACCGAAA-TTATTTGATC
1 ATTAATCAAACCGAAATTTATTTGATC
* *
1359705 ATTAATCGAATCGAAATTTATTTGA
1 ATTAATCAAACCGAAATTTATTTGA
1359730 AATTTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (27 bp):
ATTAATCAAACCGAAATTTATTTGATC
Found at i:1359730 original size:95 final size:93
Alignment explanation
Indices: 1359421--1359744 Score: 461
Period size: 96 Copynumber: 3.4 Consensus size: 93
1359411 TTCTTTAATT
* *
1359421 GTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACTAAATTAAACGATTTTTTTCTTTA
1 GTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTTCTTTA
* *
1359486 ACATTAATCGAACCGAAATTATTTTACC
66 ACATTAATCAAACCGAAATTATTTGACC
* * *
1359514 GTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACGAAATTAACTGAATTTTTTTCTTT
1 GTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCG-ATTTTTTTCTTT
*
1359579 AACCATTAATCGAAACTGAAATTATTTGACC
65 AA-CATTAATC-AAACCGAAATTATTTGACC
* *
1359610 GTTAATCGAACTGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGATTTTTTTTCTTT
1 GTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGA-TTTTTTTCTTT
*
1359675 -ACGTATTAATCAAACCGAAATTATTTGATC
65 AAC--ATTAATCAAACCGAAATTATTTGACC
* * *
1359705 ATTAATCGAATCGAAATTTATTTGAAATTTATTAACCGAA
1 GTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAA
1359745 TTAACTGAAT
Statistics
Matches: 207, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
93 48 0.23
94 15 0.07
95 63 0.30
96 81 0.39
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (93 bp):
GTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTTCTTTA
ACATTAATCAAACCGAAATTATTTGACC
Found at i:1368361 original size:41 final size:41
Alignment explanation
Indices: 1368313--1368403 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
1368303 TGTAAAAATG
* * * *
1368313 GTATCGATACCGAAAAAGAGTATCGGTACCATAATGTAGTAA
1 GTATCGATACCAAAAAAAAGTATCGATACCATAATATAG-AA
* *
1368355 -TATCGATACTAAAAAAAAGTATCGATACCATAGTATAGAA
1 GTATCGATACCAAAAAAAAGTATCGATACCATAATATAGAA
1368395 GTATCGATA
1 GTATCGATA
1368404 ACATGGTAGG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
40 2 0.05
41 40 0.95
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.25
Consensus pattern (41 bp):
GTATCGATACCAAAAAAAAGTATCGATACCATAATATAGAA
Found at i:1369129 original size:81 final size:81
Alignment explanation
Indices: 1368941--1369527 Score: 855
Period size: 81 Copynumber: 7.3 Consensus size: 81
1368931 AATTTTGCCA
1368941 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAA-AGTGTCAATTA
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGA-TGTCAATTA
1369005 TG-CAGTTAGATGAAAG
65 TGCCAGTTAGATGAAAG
* *
1369021 GTTAAATACCTTTGAGTAAAAGATTAATGACCTAGTTGTGCATTTCGCAGAAAGATGTCAATTAT
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGATGTCAATTAT
*
1369086 GCCACTTAGATGAAAG
66 GCCAGTTAGATGAAAG
* * * *
1369102 GTTAAATACTTTTGAGTAAAAGATTAATGGCCTAGCTATGCATTTGTCAGAAATG-TGTCAATTA
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAA-GATGTCAATTA
1369166 TGCCAGTTAGATGAAAG
65 TGCCAGTTAGATGAAAG
* *
1369183 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGT--ATTAT
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGATGTCAATTAT
1369246 GCCAGTTAGATGAAAG
66 GCCAGTTAGATGAAAG
* * *
1369262 GTTAAATACCTTTGAGTAAAAGATTAATGGCTTAGCTATGCATTTGGCAGAAATG-TGTCAATTA
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAA-GATGTCAATTA
* *
1369326 TGCAAGTTAGATGAAGG
65 TGCCAGTTAGATGAAAG
* * * *
1369343 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTATGCATTTGGTAGAAAGGTGTCAATTAT
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGATGTCAATTAT
*
1369408 GCCAATTAGATGAAAG
66 GCCAGTTAGATGAAAG
* **
1369424 GTTAAATACCTTTGAGTAAAAGAGTAATGGCCTAGTTGTGCATTTGGCA-AGAAGATGTCAAACA
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGA-AAGATGTCAATTA
*
1369488 TGCAAGTTAGATGAAAG
65 TGCCAGTTAGATGAAAG
* * *
1369505 GCTAAATGCCTTTGGGTAAAAGA
1 GTTAAATACCTTTGAGTAAAAGA
1369528 CTAAATGCTT
Statistics
Matches: 461, Mismatches: 37, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
79 73 0.16
80 66 0.14
81 321 0.70
82 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (81 bp):
GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGATGTCAATTAT
GCCAGTTAGATGAAAG
Found at i:1369306 original size:241 final size:242
Alignment explanation
Indices: 1368941--1369527 Score: 905
Period size: 241 Copynumber: 2.4 Consensus size: 242
1368931 AATTTTGCCA
*
1368941 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAAGTGTCAATTAT
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGT-AATTAT
* *
1369006 G-CAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGACCTAGTTGTGCATTTCGCA
65 GCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGACCTAGCTATGCATTTCGCA
* *
1369070 GAAA-GATGTCAATTATGCCACTTAGATGAAAGGTTAAATACTTTTGAGTAAAAGATTAATGGCC
130 GAAATG-TGTCAATTATGCAACTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCC
* *
1369134 TAGCTATGCATTT-GTCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
194 TAGCTATGCATTTGGT-AGAAAGGTGTCAATTATGCCAATTAGATGAAAG
*
1369183 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGT-ATTATG
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTAATTATG
* * *
1369247 CCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCTTAGCTATGCATTTGGCAG
66 CCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGACCTAGCTATGCATTTCGCAG
* *
1369312 AAATGTGTCAATTATGCAAGTTAGATGAAGGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTA
131 AAATGTGTCAATTATGCAACTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTA
1369377 GCTATGCATTTGGTAGAAAGGTGTCAATTATGCCAATTAGATGAAAG
196 GCTATGCATTTGGTAGAAAGGTGTCAATTATGCCAATTAGATGAAAG
* * **
1369424 GTTAAATACCTTTGAGTAAAAGAGTAATGGCCTAGTTGTGCATTTGGCA-AGAAGATGTCAAACA
1 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGA-AAGGTGT-AATTA
* * * *
1369488 TGCAAGTTAGATGAAAGGCTAAATGCCTTTGGGTAAAAGA
64 TGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGA
1369528 CTAAATGCTT
Statistics
Matches: 317, Mismatches: 22, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
240 7 0.02
241 213 0.67
242 59 0.19
243 38 0.12
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (242 bp):
GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTAATTATG
CCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGACCTAGCTATGCATTTCGCAG
AAATGTGTCAATTATGCAACTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTA
GCTATGCATTTGGTAGAAAGGTGTCAATTATGCCAATTAGATGAAAG
Found at i:1369645 original size:46 final size:46
Alignment explanation
Indices: 1369587--1369703 Score: 189
Period size: 46 Copynumber: 2.5 Consensus size: 46
1369577 TGACAAAAAA
*
1369587 GCATAAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTAAAG
1 GCATAAAAGGATGCCATAAATGAAAATGCATAACAGTGCATTAAAG
*
1369633 GCATTAAAGGATGCCATAAATGAAAATGCATAACAGTGCATTAAAG
1 GCATAAAAGGATGCCATAAATGAAAATGCATAACAGTGCATTAAAG
* * *
1369679 GTATGAACGGATGCCATAAATGAAA
1 GCATAAAAGGATGCCATAAATGAAA
1369704 TTAATGAATA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 66 1.00
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (46 bp):
GCATAAAAGGATGCCATAAATGAAAATGCATAACAGTGCATTAAAG
Found at i:1370048 original size:4 final size:4
Alignment explanation
Indices: 1370039--1370067 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1370029 TATTAGAAAC
1370039 AATA AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA A
1370068 CAATGGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:1370274 original size:29 final size:29
Alignment explanation
Indices: 1370203--1370275 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
1370193 AATAATAATG
* *
1370203 GTTAAAGTGCAATAAAATAAAAGTCAGTA
1 GTTAAAATGAAATAAAATAAAAGTCAGTA
* *
1370232 GTTAATATGCAATAAAATAAAAG-CTAGTA
1 GTTAAAATGAAATAAAATAAAAGTC-AGTA
1370261 GTTAGAAAT-AAATAA
1 GTTA-AAATGAAATAA
1370276 CATAGCAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 34 0.89
30 3 0.08
ACGTcount: A:0.53, C:0.05, G:0.15, T:0.26
Consensus pattern (29 bp):
GTTAAAATGAAATAAAATAAAAGTCAGTA
Found at i:1370861 original size:3 final size:3
Alignment explanation
Indices: 1370846--1370883 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1370836 AACGAGACTA
*
1370846 AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1370884 AGAAAACAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1371732 original size:134 final size:133
Alignment explanation
Indices: 1371492--1371970 Score: 602
Period size: 134 Copynumber: 3.6 Consensus size: 133
1371482 GGTGTGCTCC
* * * * * **
1371492 TCCTACGTGATGAGGAGGTCTGCTCGGTGGATGACA-CAGTTCCTATGTGATGAGGATGGCTGAT
1 TCCTACGTGATGACGAGATCTGGTCGGTGGATGACATGA-TTCCTATGTGATGAGGACGGCTGGC
* * * * *
1371556 CATCTTAAGGGATGATAATAGCACGATTACTACGTGATGAGGATGAATGGTTATCTAAGGTTGAT
65 CATCTTTAGGGATGATGATAACACG-TTCCTACGTGATGAGGATGACTGGTTATCTAAGGTTGAT
1371621 GCGGG
129 GCGGG
* *
1371626 TCCTACGTGATGACGAGATCTGGTCGGTAGATGACATGATTCCTATGTGATGAGGACGGTTGGCC
1 TCCTACGTGATGACGAGATCTGGTCGGTGGATGACATGATTCCTATGTGATGAGGACGGCTGGCC
* *
1371691 ATCTTTAGGGATGATGATAACACAGTTCCTACGTAATGAGGATGACTAGTTATCTAAGGTTGATG
66 ATCTTTAGGGATGATGATAACAC-GTTCCTACGTGATGAGGATGACTGGTTATCTAAGGTTGATG
1371756 CGGG
130 CGGG
** * * * * *
1371760 TTATATGTGATGACGAGATCTGGTCGGTGGATGACACGATTCCTACGTTATGAGGACGGTTGGCC
1 TCCTACGTGATGACGAGATCTGGTCGGTGGATGACATGATTCCTATGTGATGAGGACGGCTGGCC
* * * *
1371825 ATCTTTAGGGATGATGATAACATGGTTCCTACGTGATGGGGATGGCTGGTTATCTAAGGTTGACG
66 ATCTTTAGGGATGATGATAACA-CGTTCCTACGTGATGAGGATGACTGGTTATCTAAGGTTGATG
*
1371890 CGGC
130 CGGG
** * * *
1371894 TATTACGTGATGAGGATATCTGGTCGGTGGATGACATAGATT-CTATGTGATGAGGACGACTGGC
1 TCCTACGTGATGACGAGATCTGGTCGGTGGATGACAT-GATTCCTATGTGATGAGGACGGCTGGC
1371958 CATCTTTAGGGAT
65 CATCTTTAGGGAT
1371971 AATGGTTTCA
Statistics
Matches: 301, Mismatches: 40, Indels: 8
0.86 0.11 0.02
Matches are distributed among these distances:
134 295 0.98
135 6 0.02
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.29
Consensus pattern (133 bp):
TCCTACGTGATGACGAGATCTGGTCGGTGGATGACATGATTCCTATGTGATGAGGACGGCTGGCC
ATCTTTAGGGATGATGATAACACGTTCCTACGTGATGAGGATGACTGGTTATCTAAGGTTGATGC
GGG
Found at i:1372104 original size:67 final size:67
Alignment explanation
Indices: 1371975--1372348 Score: 599
Period size: 67 Copynumber: 5.6 Consensus size: 67
1371965 AGGGATAATG
** * * *
1371975 GTTTCAAGAGAAACCATCTCAATTA-AGACAAAA-TTTGTTTCAAAGGAAACATACTCAAAGATT
1 GTTTCAAGAGAAACTGTCTCAA-GAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAAGATT
1372038 TTT
65 TTT
* *
1372041 GTTTCAAGAGAAACTCTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAAGATTT
1372106 TT
66 TT
*
1372108 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAATAGACTCAAAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAAGATTT
1372173 TT
66 TT
* * *
1372175 GTTTCAAGAGAAACTGTCTTAAGAGAGACAAAAATTTGTTTCAAGGGAAACATACTCAAAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAAGATTT
1372240 TT
66 TT
*
1372242 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAAGATTT
1372307 TT
66 TT
* *
1372309 GTTTCAATAGAAACTGTCTCAAGAGAGAGAAAACTTTGTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTT
1372349 CCAAATGAAA
Statistics
Matches: 287, Mismatches: 19, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
65 1 0.00
66 28 0.10
67 258 0.90
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (67 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAAGATTT
TT
Found at i:1375622 original size:42 final size:42
Alignment explanation
Indices: 1375567--1375652 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
1375557 ATTGGGGATC
*
1375567 ATTAATGAAGTTTTTGGATCCGTTTAAGTGTGAAAACAATTA
1 ATTAATGAAGTTTTTGGAGCCGTTTAAGTGTGAAAACAATTA
1375609 ATTAATGAAGTTTTTGGAGCCGTTTAAGTGTGAAAACAATTA
1 ATTAATGAAGTTTTTGGAGCCGTTTAAGTGTGAAAACAATTA
1375651 AT
1 AT
1375653 ATTTCTGCTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.37
Consensus pattern (42 bp):
ATTAATGAAGTTTTTGGAGCCGTTTAAGTGTGAAAACAATTA
Found at i:1378478 original size:20 final size:20
Alignment explanation
Indices: 1378455--1378532 Score: 70
Period size: 19 Copynumber: 3.8 Consensus size: 20
1378445 AGAATCCCAG
*
1378455 GGGGGTATCGATTCCCCT-A
1 GGGGGAATCGATTCCCCTCA
*
1378474 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCC-TC--A
*
1378497 GGGGGAATCGGTT-CCCTCA
1 GGGGGAATCGATTCCCCTCA
*
1378516 TGGGGGTATCGATTCCC
1 -GGGGGAATCGATTCCC
1378533 TCTACACCAG
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
19 16 0.33
20 12 0.24
21 4 0.08
22 3 0.06
23 14 0.29
ACGTcount: A:0.17, C:0.26, G:0.33, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTCA
Found at i:1378533 original size:20 final size:20
Alignment explanation
Indices: 1378455--1378534 Score: 65
Period size: 20 Copynumber: 3.9 Consensus size: 20
1378445 AGAATCCCAG
*
1378455 GGGGGTATCGATTCCC-C-T
1 GGGGGAATCGATTCCCTCAT
* *
1378473 AGGGGGAATCGGTTCCCCTTCAAA
1 -GGGGGAATCGATT-CCC-TC-AT
*
1378497 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
1378517 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
1378535 TACACCAGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
19 11 0.22
20 20 0.40
21 2 0.04
22 4 0.08
23 13 0.26
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:1388855 original size:19 final size:19
Alignment explanation
Indices: 1388822--1388900 Score: 151
Period size: 19 Copynumber: 4.2 Consensus size: 19
1388812 AAATCGAGTG
1388822 GTTACTGTT-GTTGGAACT
1 GTTACTGTTGGTTGGAACT
1388840 GTTACTGTTGGTTGGAACT
1 GTTACTGTTGGTTGGAACT
1388859 GTTACTGTTGGTTGGAACT
1 GTTACTGTTGGTTGGAACT
1388878 GTTACTGTTGGTTGGAACT
1 GTTACTGTTGGTTGGAACT
1388897 GTTA
1 GTTA
1388901 TCGGCGCCTC
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
18 9 0.15
19 51 0.85
ACGTcount: A:0.16, C:0.10, G:0.30, T:0.43
Consensus pattern (19 bp):
GTTACTGTTGGTTGGAACT
Found at i:1400584 original size:15 final size:15
Alignment explanation
Indices: 1400564--1400600 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1400554 CGCAAAGTGA
*
1400564 TCATCAGCAGAGATG
1 TCATCAACAGAGATG
1400579 TCATCAACAGAGATG
1 TCATCAACAGAGATG
*
1400594 TTATCAA
1 TCATCAA
1400601 GCATCGAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (15 bp):
TCATCAACAGAGATG
Found at i:1403097 original size:20 final size:21
Alignment explanation
Indices: 1403074--1403114 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1403064 TGAGAAATTG
1403074 TGTTT-AAAATAT-AAAAATGA
1 TGTTTCAAAAT-TGAAAAATGA
1403094 TGTTTCAAAATTGAAAAATGA
1 TGTTTCAAAATTGAAAAATGA
1403115 AAATAAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.34
Consensus pattern (21 bp):
TGTTTCAAAATTGAAAAATGA
Found at i:1406952 original size:22 final size:23
Alignment explanation
Indices: 1406922--1406975 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
1406912 CAGAGGGAAT
*
1406922 CGATACCCCC-TTGAAGGGAAAC
1 CGATTCCCCCTTTGAAGGGAAAC
*
1406944 CGATTCCCCCTTTGAAGGGGAAC
1 CGATTCCCCCTTTGAAGGGAAAC
1406967 CGATTCCCC
1 CGATTCCCC
1406976 TCACAGGGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 9 0.31
23 20 0.69
ACGTcount: A:0.24, C:0.35, G:0.22, T:0.19
Consensus pattern (23 bp):
CGATTCCCCCTTTGAAGGGAAAC
Found at i:1406976 original size:22 final size:22
Alignment explanation
Indices: 1406916--1406976 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
1406906 TTGGTGCAGA
* * *
1406916 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCTTTGAAG
*
1406938 GGAAACCGATTCCCCCTTTGAAG
1 GGGAACCGATT-CCCCTTTGAAG
1406961 GGGAACCGATTCCCCT
1 GGGAACCGATTCCCCT
1406977 CACAGGGGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 13 0.39
23 20 0.61
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.20
Consensus pattern (22 bp):
GGGAACCGATTCCCCTTTGAAG
Found at i:1406997 original size:22 final size:22
Alignment explanation
Indices: 1406916--1406998 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
1406906 TTGGTGCAGA
*
1406916 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
* *
1406938 GGAAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
* *
1406961 GGGAACCGAT-TCCCC-TCACAG
1 GGGAACCGATACCCCCTTGA-AG
*
1406982 GGGAATCGATACCCCCT
1 GGGAACCGATACCCCCT
1406999 AAGGGTTCTG
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
20 2 0.04
21 11 0.22
22 21 0.43
23 15 0.31
ACGTcount: A:0.25, C:0.33, G:0.24, T:0.18
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:1409215 original size:15 final size:15
Alignment explanation
Indices: 1409191--1409220 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1409181 ACAAAAAGGG
1409191 GAGAAATGTTAAAGT
1 GAGAAATGTTAAAGT
*
1409206 GAGAAGTGTTAAAGT
1 GAGAAATGTTAAAGT
1409221 AAGGGGGAGT
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:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (15 bp):
GAGAAATGTTAAAGT
Found at i:1409253 original size:16 final size:16
Alignment explanation
Indices: 1409232--1409263 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1409222 AGGGGGAGTA
1409232 ATTTCAAACTTGATTT
1 ATTTCAAACTTGATTT
1409248 ATTTCAAACTTGATTT
1 ATTTCAAACTTGATTT
1409264 TAAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (16 bp):
ATTTCAAACTTGATTT
Found at i:1411805 original size:51 final size:54
Alignment explanation
Indices: 1411739--1411867 Score: 192
Period size: 55 Copynumber: 2.4 Consensus size: 54
1411729 ATCGAATAAT
*
1411739 AAAAGCAGCAACGTTTAGCAAAATTT-AAG-AAAAACTAACAATTA-TTTTGTA
1 AAAAGCAGCAGCGTTTAGCAAAATTTAAAGAAAAAACTAACAATTATTTTTGTA
1411790 AAAAGCAGCAGCGTTTAGCAAAATTTAAAAGAAAAAACTAACAATTATTTTTGTA
1 AAAAGCAGCAGCGTTTAGCAAAATTT-AAAGAAAAAACTAACAATTATTTTTGTA
* * *
1411845 AAAAACAGAAGCGTTTAACAAAA
1 AAAAGCAGCAGCGTTTAGCAAAA
1411868 AATCAGAAAT
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
51 25 0.36
53 3 0.04
54 15 0.21
55 27 0.39
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (54 bp):
AAAAGCAGCAGCGTTTAGCAAAATTTAAAGAAAAAACTAACAATTATTTTTGTA
Found at i:1412155 original size:7 final size:7
Alignment explanation
Indices: 1412145--1412171 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1412135 TTTTTATAAT
1412145 TATTAAA
1 TATTAAA
1412152 TATTAAA
1 TATTAAA
1412159 TATTAAA
1 TATTAAA
1412166 TATTAA
1 TATTAA
1412172 TTTGGTGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TATTAAA
Found at i:1413604 original size:10 final size:10
Alignment explanation
Indices: 1413589--1413628 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
1413579 AAAACAAAAA
1413589 TCCCGGTTTT
1 TCCCGGTTTT
1413599 TCCCGGTTTT
1 TCCCGGTTTT
* *
1413609 TTCTGGTTTT
1 TCCCGGTTTT
*
1413619 TTCCGGTTTT
1 TCCCGGTTTT
1413629 CAACCGGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.00, C:0.23, G:0.20, T:0.57
Consensus pattern (10 bp):
TCCCGGTTTT
Found at i:1417484 original size:31 final size:31
Alignment explanation
Indices: 1417446--1417515 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
1417436 GGAGATTGTT
* *
1417446 GAAAGTTGATGTGAATGCACCGAATTCCACC
1 GAAAGTTGATATAAATGCACCGAATTCCACC
*
1417477 GAAAGTTGGTATAAATGCACCGAATTCCACC
1 GAAAGTTGATATAAATGCACCGAATTCCACC
*
1417508 AAAAGTTG
1 GAAAGTTG
1417516 CAGCTTGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (31 bp):
GAAAGTTGATATAAATGCACCGAATTCCACC
Found at i:1422311 original size:42 final size:42
Alignment explanation
Indices: 1422247--1422330 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
1422237 TGGAGAAGAC
*
1422247 CGGTGATGCAAAATAACAACCGTGACATCGTGTTTAAACTTT
1 CGGTGATGCAAAATAAAAACCGTGACATCGTGTTTAAACTTT
* *
1422289 CGGTTATGCAAAATAAAAACCGTGACATCTTGTTTAAACTTT
1 CGGTGATGCAAAATAAAAACCGTGACATCGTGTTTAAACTTT
1422331 ATATTTTACT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (42 bp):
CGGTGATGCAAAATAAAAACCGTGACATCGTGTTTAAACTTT
Found at i:1424700 original size:39 final size:39
Alignment explanation
Indices: 1424656--1424751 Score: 113
Period size: 39 Copynumber: 2.4 Consensus size: 39
1424646 TGCCATAATA
*
1424656 CCTAATTCCCCATTTTCATTT-TCCTCTCGCCCCTCAATC
1 CCTAATTCCCCATTTTCATTTCTCCT-TCGCACCTCAATC
* * *
1424695 CCTAATTCCCCTTTTTCATTTCTCCTTCGCATCTCACTC
1 CCTAATTCCCCATTTTCATTTCTCCTTCGCACCTCAATC
* *
1424734 CCTACTTCACCATCTTTC
1 CCTAATTCCCCAT-TTTC
1424752 TCTTCGTTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
39 40 0.83
40 8 0.17
ACGTcount: A:0.15, C:0.43, G:0.02, T:0.41
Consensus pattern (39 bp):
CCTAATTCCCCATTTTCATTTCTCCTTCGCACCTCAATC
Found at i:1429947 original size:39 final size:39
Alignment explanation
Indices: 1429867--1429957 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 39
1429857 TGCCATAATT
*
1429867 CCTAATTCCCCATTTTTATTTTCCTCTCGCCCCTCAATC
1 CCTAATTCCCCATTTTTATTTTCCTCTCGCACCTCAATC
* *
1429906 CCTAATTCCCC-TTTTTCATTTCTCCT-TCGCATCTCACTC
1 CCTAATTCCCCATTTTT-ATTT-TCCTCTCGCACCTCAATC
* *
1429945 CCTACTTCACCAT
1 CCTAATTCCCCAT
1429958 CTTCCTCTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
38 5 0.11
39 34 0.77
40 5 0.11
ACGTcount: A:0.15, C:0.42, G:0.02, T:0.41
Consensus pattern (39 bp):
CCTAATTCCCCATTTTTATTTTCCTCTCGCACCTCAATC
Found at i:1430702 original size:2 final size:2
Alignment explanation
Indices: 1430691--1430731 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1430681 TAATATTTTT
*
1430691 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1430732 TAATTTATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1430796 original size:28 final size:30
Alignment explanation
Indices: 1430764--1430831 Score: 113
Period size: 28 Copynumber: 2.3 Consensus size: 30
1430754 CCTAAATGGT
1430764 ATACTAAACTTATTTAATTT-T-ATTAAGG
1 ATACTAAACTTATTTAATTTCTAATTAAGG
1430792 ATACTAAACTTATTTAATTTCTAATTAAGG
1 ATACTAAACTTATTTAATTTCTAATTAAGG
*
1430822 AAACTAAACT
1 ATACTAAACT
1430832 AAGGCTTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
28 20 0.54
29 1 0.03
30 16 0.43
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (30 bp):
ATACTAAACTTATTTAATTTCTAATTAAGG
Found at i:1430893 original size:18 final size:18
Alignment explanation
Indices: 1430857--1430896 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1430847 AATTAAACAC
*
1430857 TTAAAATCTAAGGCTTAA
1 TTAAAATCTAAGACTTAA
1430875 TTAAAATCTAAAGAC-TAA
1 TTAAAATCT-AAGACTTAA
1430893 TTAA
1 TTAA
1430897 TATTTAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (18 bp):
TTAAAATCTAAGACTTAA
Found at i:1432926 original size:16 final size:16
Alignment explanation
Indices: 1432905--1432940 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1432895 TATGTTTGGC
1432905 TTGAAAGTTGGCAAAA
1 TTGAAAGTTGGCAAAA
*
1432921 TTGAAAGTTGGCAAAG
1 TTGAAAGTTGGCAAAA
1432937 TTGA
1 TTGA
1432941 CATCTTTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.06, G:0.28, T:0.28
Consensus pattern (16 bp):
TTGAAAGTTGGCAAAA
Found at i:1432985 original size:37 final size:37
Alignment explanation
Indices: 1432943--1433014 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
1432933 AAAGTTGACA
*
1432943 TCTTTGGT-TGGTGGCTAAATTGTACACATTGGAAAAT
1 TCTTTGGTAT-GTGGCCAAATTGTACACATTGGAAAAT
* *
1432980 TCTTTGGTATGTGGCCAACTTGTCCACATTGGAAA
1 TCTTTGGTATGTGGCCAAATTGTACACATTGGAAA
1433015 TTCATATTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 30 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (37 bp):
TCTTTGGTATGTGGCCAAATTGTACACATTGGAAAAT
Found at i:1437628 original size:9 final size:9
Alignment explanation
Indices: 1437616--1437662 Score: 50
Period size: 7 Copynumber: 5.8 Consensus size: 9
1437606 GTTTGGCTTG
1437616 AAAGTTGGC
1 AAAGTTGGC
1437625 AAAGTT-G-
1 AAAGTTGGC
1437632 AAAGTTGGC
1 AAAGTTGGC
*
1437641 AAAATT-G-
1 AAAGTTGGC
1437648 AAAGTTGGC
1 AAAGTTGGC
1437657 -AAGTTG
1 AAAGTTG
1437663 ACATCTTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
7 11 0.34
8 10 0.31
9 11 0.34
ACGTcount: A:0.38, C:0.06, G:0.30, T:0.26
Consensus pattern (9 bp):
AAAGTTGGC
Found at i:1437634 original size:16 final size:16
Alignment explanation
Indices: 1437613--1437663 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
1437603 TTTGTTTGGC
1437613 TTGAAAGTTGGCAAAG
1 TTGAAAGTTGGCAAAG
*
1437629 TTGAAAGTTGGCAAAA
1 TTGAAAGTTGGCAAAG
1437645 TTGAAAGTTGGC-AAG
1 TTGAAAGTTGGCAAAG
1437660 TTGA
1 TTGA
1437664 CATCTTTGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
15 6 0.18
16 27 0.82
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.27
Consensus pattern (16 bp):
TTGAAAGTTGGCAAAG
Found at i:1443504 original size:18 final size:20
Alignment explanation
Indices: 1443466--1443507 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
1443456 TGCAATCTAG
*
1443466 TTATTCAAACTAAATTAAAT
1 TTATTCAAAATAAATTAAAT
1443486 TTATT-AAAATAAA-TAAAT
1 TTATTCAAAATAAATTAAAT
1443504 TTAT
1 TTAT
1443508 ATGGATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 7 0.33
20 5 0.24
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (20 bp):
TTATTCAAAATAAATTAAAT
Found at i:1447172 original size:22 final size:21
Alignment explanation
Indices: 1447131--1447191 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
1447121 AGCAAATGCT
*
1447131 TTTTAAGATTTTTTTCGAAATAC
1 TTTTAGGA-TTTTTT-GAAATAC
1447154 TTTTAGGGATTTTTTGAAATAC
1 TTTTA-GGATTTTTTGAAATAC
*
1447176 TTTTAGGTTTTTTTGA
1 TTTTAGGATTTTTTGA
1447192 TGAAAACACT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.29
22 12 0.34
23 11 0.31
24 2 0.06
ACGTcount: A:0.25, C:0.05, G:0.15, T:0.56
Consensus pattern (21 bp):
TTTTAGGATTTTTTGAAATAC
Found at i:1447189 original size:21 final size:22
Alignment explanation
Indices: 1447139--1447191 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
1447129 CTTTTTAAGA
1447139 TTTTTTTCGAAATACTTTTAGGG
1 TTTTTTT-GAAATACTTTTAGGG
*
1447162 ATTTTTTGAAATACTTTTA-GG
1 TTTTTTTGAAATACTTTTAGGG
1447183 TTTTTTTGA
1 TTTTTTTGA
1447192 TGAAAACACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 10 0.36
22 12 0.43
23 6 0.21
ACGTcount: A:0.23, C:0.06, G:0.15, T:0.57
Consensus pattern (22 bp):
TTTTTTTGAAATACTTTTAGGG
Found at i:1454017 original size:18 final size:19
Alignment explanation
Indices: 1453994--1454052 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 19
1453984 TTTTGGTGCA
*
1453994 GAGGGAATCGA-TCCCCCT
1 GAGGGAACCGATTCCCCCT
1454012 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC--T
1454033 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
1454053 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
18 10 0.29
19 6 0.17
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.22, C:0.34, G:0.27, T:0.17
Consensus pattern (19 bp):
GAGGGAACCGATTCCCCCT
Found at i:1460309 original size:15 final size:15
Alignment explanation
Indices: 1460291--1460338 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
1460281 AAGGCTGCAA
1460291 CATCACAAACACCAT
1 CATCACAAACACCAT
* ** *
1460306 CATCACAAGCTGCAA
1 CATCACAAACACCAT
*
1460321 CATCACAACCACCAT
1 CATCACAAACACCAT
1460336 CAT
1 CAT
1460339 TATCACAAGC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.42, C:0.40, G:0.04, T:0.15
Consensus pattern (15 bp):
CATCACAAACACCAT
Found at i:1460350 original size:33 final size:30
Alignment explanation
Indices: 1460269--1460338 Score: 115
Period size: 30 Copynumber: 2.3 Consensus size: 30
1460259 AACAAGGATT
1460269 ACACCATCATCA-AAGGCTGCAACATCACAA
1 ACACCATCATCACAA-GCTGCAACATCACAA
1460299 ACACCATCATCACAAGCTGCAACATCACAA
1 ACACCATCATCACAAGCTGCAACATCACAA
*
1460329 CCACCATCAT
1 ACACCATCAT
1460339 TATCACAAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
30 36 0.95
31 2 0.05
ACGTcount: A:0.41, C:0.37, G:0.07, T:0.14
Consensus pattern (30 bp):
ACACCATCATCACAAGCTGCAACATCACAA
Found at i:1461394 original size:10 final size:10
Alignment explanation
Indices: 1461379--1461405 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1461369 CACCGGTGAA
1461379 CTTCTTCTTC
1 CTTCTTCTTC
1461389 CTTCTTCTTC
1 CTTCTTCTTC
1461399 CTTCTTC
1 CTTCTTC
1461406 CTATTTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (10 bp):
CTTCTTCTTC
Found at i:1462711 original size:21 final size:22
Alignment explanation
Indices: 1462679--1462720 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
1462669 ACTTTTATAT
1462679 AAATTAACATA-TAAAGTATTA
1 AAATTAACATATTAAAGTATTA
*
1462700 AAATTATA-ATATTAAATTATT
1 AAATTA-ACATATTAAAGTATT
1462721 TTAATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATTAACATATTAAAGTATTA
Found at i:1469097 original size:15 final size:15
Alignment explanation
Indices: 1469073--1469143 Score: 72
Period size: 15 Copynumber: 4.8 Consensus size: 15
1469063 GGTTTTTTGA
1469073 AAAATGAATTACTGG
1 AAAATGAATTACTGG
** * *
1469088 AATTTGAATTATTGA
1 AAAATGAATTACTGG
* *
1469103 AAAATGAATTATTAG
1 AAAATGAATTACTGG
*
1469118 AATATGAATT-CTGG
1 AAAATGAATTACTGG
1469132 AAAATGAATTAC
1 AAAATGAATTAC
1469144 ATTTCTGGAA
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
14 11 0.26
15 32 0.74
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.34
Consensus pattern (15 bp):
AAAATGAATTACTGG
Found at i:1469103 original size:30 final size:29
Alignment explanation
Indices: 1469067--1469143 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 29
1469057 GTAATTGGTT
* *
1469067 TTTTGAAAAATGAATTACTGGAATTTGAA
1 TTTTGAAAAATGAATTACTAGAATATGAA
*
1469096 TTATTGAAAAATGAATTATTAGAATATGAA
1 TT-TTGAAAAATGAATTACTAGAATATGAA
* *
1469126 TTCTGGAAAATGAATTAC
1 TTTTGAAAAATGAATTAC
1469144 ATTTCTGGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 15 0.37
30 26 0.63
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (29 bp):
TTTTGAAAAATGAATTACTAGAATATGAA
Done.