Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 2 of 163
Found at i:298067 original size:26 final size:25
Alignment explanation
Indices: 298007--298069 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
297997 TTCTAAAATC
* *
298007 GTAACAAAATTTACAATAAAAGAAGA
1 GTAACAAAA-TAACAACAAAAGAAGA
* * *
298033 GTTATAAAATAACAACAAAATAAGTA
1 GTAACAAAATAACAACAAAAGAAG-A
298059 GTAACAAAATA
1 GTAACAAAATA
298070 GTGAAAAACA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
25 12 0.41
26 17 0.59
ACGTcount: A:0.62, C:0.08, G:0.10, T:0.21
Consensus pattern (25 bp):
GTAACAAAATAACAACAAAAGAAGA
Found at i:305572 original size:129 final size:129
Alignment explanation
Indices: 305337--305580 Score: 328
Period size: 129 Copynumber: 1.9 Consensus size: 129
305327 TCAACAAAGA
* *
305337 TGAGTCTCATTGATCCTAACTTCAAAGTTTGCATTGCTACTTCTTCCTTTAAGTCCGATACACAA
1 TGAGCCTCATTGATCCTAACTTCAAAGTTTGCATTGCTACTTCTTCCTCTAAGTCCGATACACAA
* * **
305402 TTCACCTTTTCCTTAGATGGAAGCTTCGTCAACGACTCAACAAGCTCCGTAGCTTTCCTAGAAT
66 CTCACCTCTTCCTTAGATGGAAGCCCCGTCAACGACTCAACAAGCTCCGTAGCTTTCCTAGAAT
* * * * * *
305466 TGAGCCTCATTGGTCTTAGCTTCAATGTTTGCATTGCTACTTCTTCCTCTAAGTTCGATGCACAA
1 TGAGCCTCATTGATCCTAACTTCAAAGTTTGCATTGCTACTTCTTCCTCTAAGTCCGATACACAA
* ** *
305531 CTCACCTCTTCCTTA-AGTGGAAGCCCCTTTGATGACTCAACAAGCTCCGT
66 CTCACCTCTTCCTTAGA-TGGAAGCCCCGTCAACGACTCAACAAGCTCCGT
305581 CGTTGCCTTT
Statistics
Matches: 98, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
128 1 0.01
129 97 0.99
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.34
Consensus pattern (129 bp):
TGAGCCTCATTGATCCTAACTTCAAAGTTTGCATTGCTACTTCTTCCTCTAAGTCCGATACACAA
CTCACCTCTTCCTTAGATGGAAGCCCCGTCAACGACTCAACAAGCTCCGTAGCTTTCCTAGAAT
Found at i:308489 original size:84 final size:84
Alignment explanation
Indices: 308341--308500 Score: 295
Period size: 84 Copynumber: 1.9 Consensus size: 84
308331 TTTGATGCTC
308341 GCTTTTCTCAATCTCAATGGAGTTTTGTTTAAGGATCAAATTTGTTGCTTGATTCAAAAGTGCTT
1 GCTTTTCTCAATCTCAATGGAGTTTTGTTTAAGGATCAAATTTGTTGCTTGATTCAAAAGTGCTT
308406 TGAAGGTGACCTAATTCCT
66 TGAAGGTGACCTAATTCCT
*
308425 GCTTTTGTCAATCTCAATGGAGTTTTGTTTAAGGATCAAATTTGTTGCTTGATTCCAAAA-TGCT
1 GCTTTTCTCAATCTCAATGGAGTTTTGTTTAAGGATCAAATTTGTTGCTTGATT-CAAAAGTGCT
308489 TTGAAGGTGACC
65 TTGAAGGTGACC
308501 CAAATATTCC
Statistics
Matches: 74, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
84 69 0.93
85 5 0.07
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (84 bp):
GCTTTTCTCAATCTCAATGGAGTTTTGTTTAAGGATCAAATTTGTTGCTTGATTCAAAAGTGCTT
TGAAGGTGACCTAATTCCT
Found at i:309806 original size:34 final size:35
Alignment explanation
Indices: 309742--309809 Score: 86
Period size: 34 Copynumber: 1.9 Consensus size: 35
309732 TATTGTCGAC
*
309742 TTTTTTTTAAAAAAAAAAGTTGATGGTCAAATTTGA
1 TTTTTTTT-AAAAAAAAAGTTGATGATCAAATTTGA
*
309778 TTTTTTTT-AAAAAAAATTTGA-GAATCAAATTT
1 TTTTTTTTAAAAAAAAAGTTGATG-ATCAAATTT
309810 AGCTCAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 1 0.03
34 20 0.69
36 8 0.28
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (35 bp):
TTTTTTTTAAAAAAAAAGTTGATGATCAAATTTGA
Found at i:312340 original size:210 final size:210
Alignment explanation
Indices: 311952--312358 Score: 573
Period size: 210 Copynumber: 1.9 Consensus size: 210
311942 AAGACTGCTC
* * * * * * * **
311952 AGATTTCCGATTGAAATATGTAGCTCTTTAATGCCCGTCCCATCTAAATAAAGCTCTAGCAGGCA
1 AGATTTCCGATCGAAATAGGTAACTCTTTAATGCCCGTCCCATCAAAACAAAGCTCCAACAAACA
* *
312017 TTCCATTTTGCCATCAATCTCTGGAAAGCTTTTAAGATTGGAGCAACCTGAAAGAATTAACTTTT
66 TTCCATTTTCCCATCAATCTCTGGAAAGCTTTCAAGATTGGAGCAACCTGAAAGAATTAACTTTT
* * * *
312082 CAAGAGATCCCATTCCAATTTTGATTGGAAGACTCCTAAGACTTTTGCAGTCTTTTAAATTCAAA
131 CAAGAGATCCCATACCAACTTTGATTGGAAAACTCCTAAGACTTTTGCAGCCTTTTAAATTCAAA
312147 AGTTCAAGTCTTCTG
196 AGTTCAAGTCTTCTG
***
312162 AGATTTCCGATCGAAGA-AGGTAACTCTTTAATGTTTGTCCCATCAAAACAAAGCTCCAACAAAC
1 AGATTTCCGATCGAA-ATAGGTAACTCTTTAATGCCCGTCCCATCAAAACAAAGCTCCAACAAAC
* *
312226 ATTCCATTTTCCCATCAATCTCTGGAAAGCTTTCAAGTTTTGAGCAACCTGAAAGAATTAACTTT
65 ATTCCATTTTCCCATCAATCTCTGGAAAGCTTTCAAGATTGGAGCAACCTGAAAGAATTAACTTT
* * * * *
312291 TCAAGAGATTCCATACCAACTTTGGTTGGAAAACTCCTCATATTTTTGCAGCCTTTTAAATTCAA
130 TCAAGAGATCCCATACCAACTTTGATTGGAAAACTCCTAAGACTTTTGCAGCCTTTTAAATTCAA
312356 AAG
195 AAG
312359 CTTAAGCCTT
Statistics
Matches: 171, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
210 170 0.99
211 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (210 bp):
AGATTTCCGATCGAAATAGGTAACTCTTTAATGCCCGTCCCATCAAAACAAAGCTCCAACAAACA
TTCCATTTTCCCATCAATCTCTGGAAAGCTTTCAAGATTGGAGCAACCTGAAAGAATTAACTTTT
CAAGAGATCCCATACCAACTTTGATTGGAAAACTCCTAAGACTTTTGCAGCCTTTTAAATTCAAA
AGTTCAAGTCTTCTG
Found at i:317026 original size:24 final size:25
Alignment explanation
Indices: 316987--317036 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
316977 CAGGCAAGCA
*
316987 CCCAAAAATAGAAAAATTTTTATTT
1 CCCAAAAATAGAAAAATTTTCATTT
317012 CCCAAAAATAGAAAAATTTTCATTT
1 CCCAAAAATAGAAAAATTTTCATTT
317037 AGATCCATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.48, C:0.14, G:0.04, T:0.34
Consensus pattern (25 bp):
CCCAAAAATAGAAAAATTTTCATTT
Found at i:318031 original size:41 final size:41
Alignment explanation
Indices: 317970--318194 Score: 362
Period size: 41 Copynumber: 5.5 Consensus size: 41
317960 TGACTTTTCG
* * *
317970 TGGGCTTTAGCGGCGATTTTATGGAAGTGCCGCTAATGTTC
1 TGGGCTTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTC
*
318011 TGTGCTTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTC
1 TGGGCTTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTC
318052 TGGGCTTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTC
1 TGGGCTTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTC
* *
318093 TGGGATTTAGCGGCGTTTTTATTTAAGCGCCGCTAATGTTC
1 TGGGCTTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTC
* *
318134 TGGGATTTAGTGGCGTTTTTA-GTAAAGCGCCGCTAATGTTC
1 TGGGCTTTAGCGGCGTTTTTATGT-AAGCGCCGCTAATGTTC
318175 TGGGCTTTAGCGGCGTTTTT
1 TGGGCTTTAGCGGCGTTTTT
318195 GTTGATGCGC
Statistics
Matches: 172, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 1 0.01
41 171 0.99
ACGTcount: A:0.16, C:0.17, G:0.29, T:0.38
Consensus pattern (41 bp):
TGGGCTTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTC
Found at i:321065 original size:12 final size:12
Alignment explanation
Indices: 321048--321072 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
321038 AACTAGAGGC
321048 ATTCGTATGTCT
1 ATTCGTATGTCT
321060 ATTCGTATGTCT
1 ATTCGTATGTCT
321072 A
1 A
321073 AGTATATCAT
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:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (12 bp):
ATTCGTATGTCT
Found at i:322280 original size:29 final size:29
Alignment explanation
Indices: 322238--322295 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
322228 TAAATCTTCT
*
322238 TCCATTTGTCAACTATTTCATTTCTAAAA
1 TCCATTTGTCAACTATTTCATTTCCAAAA
322267 TCCATTTGTCAACTATTTCATTTCCAAAA
1 TCCATTTGTCAACTATTTCATTTCCAAAA
322296 ATATATTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.43
Consensus pattern (29 bp):
TCCATTTGTCAACTATTTCATTTCCAAAA
Found at i:322456 original size:9 final size:9
Alignment explanation
Indices: 322425--322481 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 9
322415 TTAAAGTTCA
322425 AATTT-CAT
1 AATTTACAT
* *
322433 AACTTACGT
1 AATTTACAT
*
322442 ATTTTACAT
1 AATTTACAT
322451 AATTTACAT
1 AATTTACAT
322460 AA-TT-CAT
1 AATTTACAT
*
322467 AATTTACAA
1 AATTTACAT
322476 AATTTA
1 AATTTA
322482 AATATATAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
7 5 0.13
8 8 0.21
9 26 0.67
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (9 bp):
AATTTACAT
Found at i:322469 original size:16 final size:16
Alignment explanation
Indices: 322448--322479 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
322438 ACGTATTTTA
*
322448 CATAATTTACATAATT
1 CATAATTTACAAAATT
322464 CATAATTTACAAAATT
1 CATAATTTACAAAATT
322480 TAAATATATA
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:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (16 bp):
CATAATTTACAAAATT
Found at i:322606 original size:12 final size:12
Alignment explanation
Indices: 322574--322643 Score: 72
Period size: 12 Copynumber: 6.0 Consensus size: 12
322564 CATAATATCC
*
322574 TAACTTACATAG
1 TAACTTACATAA
* *
322586 TATCGTACATAA
1 TAACTTACATAA
322598 TAACTTACA-AA
1 TAACTTACATAA
322609 -AACTTACATAA
1 TAACTTACATAA
*
322620 TAACCTACATAA
1 TAACTTACATAA
* *
322632 TACCTTATATAA
1 TAACTTACATAA
322644 CAATACATAA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
10 8 0.17
11 4 0.09
12 35 0.74
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (12 bp):
TAACTTACATAA
Found at i:322783 original size:64 final size:64
Alignment explanation
Indices: 322697--323866 Score: 2245
Period size: 64 Copynumber: 18.3 Consensus size: 64
322687 CACAAAAACA
* * * * * * *
322697 ATAACTTACATAACTTAAATAACTTACATAACTTATA-TAAACTTGCATAAATTAAAT-AACTTG
1 ATAAATTAAATAACTTACATAACTTACATAAATTA-AGT-AACTTACATAACTTACATAAACTTG
322760 C
64 C
322761 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
1 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
322825 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
1 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
322889 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
1 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
322953 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
1 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
323017 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
1 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
323081 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
1 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
323145 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
1 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
323209 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
1 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
323273 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
1 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
323337 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
1 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
323401 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
1 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
323465 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
1 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
323529 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
1 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
323593 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
1 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
323657 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
1 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
323721 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
1 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
323785 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
1 ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
323849 ATAAATTAAATAACTTAC
1 ATAAATTAAATAACTTAC
323867 NNNNNNNNNN
Statistics
Matches: 1097, Mismatches: 7, Indels: 4
0.99 0.01 0.00
Matches are distributed among these distances:
63 16 0.01
64 1081 0.99
ACGTcount: A:0.48, C:0.16, G:0.03, T:0.33
Consensus pattern (64 bp):
ATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAAACTTGC
Found at i:328321 original size:43 final size:43
Alignment explanation
Indices: 328267--328388 Score: 174
Period size: 43 Copynumber: 2.8 Consensus size: 43
328257 GCGTTTTTTA
*
328267 AAAAAGCGCCGCTAAAGAACAT-TAGCTTTAGCGGCGTTTGTGT
1 AAAAAGCGCCGCTAAAGAACATGT-GCTTCAGCGGCGTTTGTGT
* * * *
328310 TAGAAGTGCCGCTAAAGAACATGTTCTTCAGCGGCGTTTGTGT
1 AAAAAGCGCCGCTAAAGAACATGTGCTTCAGCGGCGTTTGTGT
*
328353 AAAAAGCGCCGCTAAAGAACATGTTCTTCAGCGGCG
1 AAAAAGCGCCGCTAAAGAACATGTGCTTCAGCGGCG
328389 CTTTTAAAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
43 69 0.99
44 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (43 bp):
AAAAAGCGCCGCTAAAGAACATGTGCTTCAGCGGCGTTTGTGT
Found at i:329164 original size:16 final size:16
Alignment explanation
Indices: 329143--329173 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
329133 ATCATCATCA
*
329143 TTATTTTGCTTCGTAT
1 TTATTTTACTTCGTAT
329159 TTATTTTACTTCGTA
1 TTATTTTACTTCGTA
329174 GCCCTCGCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.13, G:0.10, T:0.61
Consensus pattern (16 bp):
TTATTTTACTTCGTAT
Found at i:331077 original size:41 final size:41
Alignment explanation
Indices: 331020--331184 Score: 330
Period size: 41 Copynumber: 4.0 Consensus size: 41
331010 AATGAACTCA
331020 AACCAAAAAACAAAGGCAACATCAAAGCCATAGAATTTGTC
1 AACCAAAAAACAAAGGCAACATCAAAGCCATAGAATTTGTC
331061 AACCAAAAAACAAAGGCAACATCAAAGCCATAGAATTTGTC
1 AACCAAAAAACAAAGGCAACATCAAAGCCATAGAATTTGTC
331102 AACCAAAAAACAAAGGCAACATCAAAGCCATAGAATTTGTC
1 AACCAAAAAACAAAGGCAACATCAAAGCCATAGAATTTGTC
331143 AACCAAAAAACAAAGGCAACATCAAAGCCATAGAATTTGTC
1 AACCAAAAAACAAAGGCAACATCAAAGCCATAGAATTTGTC
331184 A
1 A
331185 TTCCTCTTTG
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 124 1.00
ACGTcount: A:0.52, C:0.22, G:0.12, T:0.15
Consensus pattern (41 bp):
AACCAAAAAACAAAGGCAACATCAAAGCCATAGAATTTGTC
Found at i:332129 original size:34 final size:36
Alignment explanation
Indices: 332065--332132 Score: 97
Period size: 34 Copynumber: 1.9 Consensus size: 36
332055 TCATGTCGAC
*
332065 TTTTTTTTAAAAAAAAAAGTTGATGGTCAAATTTGA
1 TTTTTTTTAAAAAAAAAAGTTGATGATCAAATTTGA
332101 TTTTTTTT-AAAAAAAAA-TTGA-GAATCAAATTT
1 TTTTTTTTAAAAAAAAAAGTTGATG-ATCAAATTT
332133 AGCTCAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 1 0.03
34 12 0.40
35 9 0.30
36 8 0.27
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (36 bp):
TTTTTTTTAAAAAAAAAAGTTGATGATCAAATTTGA
Found at i:343768 original size:18 final size:18
Alignment explanation
Indices: 343745--343786 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
343735 TTAATTACAG
*
343745 TAATTAATAAAATAAATA
1 TAATTAATAAAATAAAAA
*
343763 TAATTAATGAAATAAAAA
1 TAATTAATAAAATAAAAA
343781 TAATTA
1 TAATTA
343787 GATGTACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
TAATTAATAAAATAAAAA
Found at i:349597 original size:210 final size:210
Alignment explanation
Indices: 349235--349634 Score: 570
Period size: 210 Copynumber: 1.9 Consensus size: 210
349225 AAGACTGCTC
* * * * * **
349235 AGATTTCCGATTGAAATATGTAGCTCTTTAATGCCCGTCCCATCTAAATAAAGCTCTAGCAGGCA
1 AGATTTCCGATCGAAATAGGTAGCTCTTTAATGCCCGTCCCATCTAAACAAAGCTCCAACAAACA
* *
349300 TTCCATTTTGCCATCAATCTCTGGAAAGCTTTTAAGATTGGAGCAACCTGAAAGAATTAACTTTT
66 TTCCATTTTCCCATCAATCTCTGGAAAGCTTTGAAGATTGGAGCAACCTGAAAGAATTAACTTTT
* * * *
349365 CAAGAGATTCCATTCCAATTTTGATTGGAAGACTCCTAAGACTTTTGCAGTCTTTTAAATTCAAT
131 CAAGAGATTCCATACCAATTTTGATTGGAAAACTCCTAAGACTTTTGCAGCCTCTTAAATTCAAT
349430 AGTTCAAGTCTTCTG
196 AGTTCAAGTCTTCTG
***
349445 AGATTTCCGATCGAAGA-AGGTAGCTCTTTAATGTTTGTCCCATC-AAGACAAAGCTCCAACAAA
1 AGATTTCCGATCGAA-ATAGGTAGCTCTTTAATGCCCGTCCCATCTAA-ACAAAGCTCCAACAAA
* *
349508 CATTCCATTTTCCCATCAATCTCTGGAAAGCTTTGAAGTTTTGAGCAACCTGAAAGAATTAACTT
64 CATTCCATTTTCCCATCAATCTCTGGAAAGCTTTGAAGATTGGAGCAACCTGAAAGAATTAACTT
* * * *
349573 TTCAAGAGGTTCCATACCAATTTTGGTTGGAAAACTCCTCAGATTTTTGCAGCCTCTTAAAT
129 TTCAAGAGATTCCATACCAATTTTGATTGGAAAACTCCTAAGACTTTTGCAGCCTCTTAAAT
349635 CCAAAAGCTT
Statistics
Matches: 166, Mismatches: 22, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
209 2 0.01
210 163 0.98
211 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (210 bp):
AGATTTCCGATCGAAATAGGTAGCTCTTTAATGCCCGTCCCATCTAAACAAAGCTCCAACAAACA
TTCCATTTTCCCATCAATCTCTGGAAAGCTTTGAAGATTGGAGCAACCTGAAAGAATTAACTTTT
CAAGAGATTCCATACCAATTTTGATTGGAAAACTCCTAAGACTTTTGCAGCCTCTTAAATTCAAT
AGTTCAAGTCTTCTG
Found at i:360953 original size:8 final size:8
Alignment explanation
Indices: 360926--360969 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
360916 AATATATGTG
*
360926 TATAAAAA
1 TATATAAA
360934 T-TATAGAA
1 TATATA-AA
360942 TATATAAA
1 TATATAAA
360950 TATATAAA
1 TATATAAA
*
360958 TATATATA
1 TATATAAA
360966 TATA
1 TATA
360970 CACGCTTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 3 0.09
8 25 0.78
9 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (8 bp):
TATATAAA
Found at i:363874 original size:210 final size:210
Alignment explanation
Indices: 363486--363874 Score: 564
Period size: 210 Copynumber: 1.9 Consensus size: 210
363476 CAATTGAAAT
* * * * ** *
363486 AGGTAGCTCTTTAATGCCCGTCCCATCTAAATAAAGCTCTAGCAGGCATTCCATTTTGCCATCAA
1 AGGTAGCTCTTTAATGCCCGTCCCATCAAAACAAAGCTCCAACAAACATTCCATTTTCCCATCAA
*
363551 TCTCTGGAAAGCTTTCAAGATTTGAGCAACCTGAAAGAATTAACTTTTCAAGAGATTCCATTCCA
66 TCTCTGGAAAGCTTTCAAGATTTGAGCAACCTGAAAGAATTAACCTTTCAAGAGATTCCATTCCA
* * * * **
363616 ATTTTGATTGGAAGACCTTTAAGACTTTTGCAGTCTTTTAAATTCAAAACTTTAAGTCTTTTGAG
131 ATTCTGATTGGAAAACCTCTAAGACTTTTGCAGCCTCCTAAATTCAAAACTTTAAGTCTTTTGAG
363681 ACTTCCGATCAAAGA
196 ACTTCCGATCAAAGA
***
363696 AGGTAGCTCTTTAATGTTTGTCCCATCAAAACAAAGCTCCAACAAACATTCCATTTTCCCATCAA
1 AGGTAGCTCTTTAATGCCCGTCCCATCAAAACAAAGCTCCAACAAACATTCCATTTTCCCATCAA
* *
363761 TCTCTGGAAAGCTTTCAAGTTTTGAGCAACCTGAAAGAGTTAACCTTTCAAGAGATTCCATTCCA
66 TCTCTGGAAAGCTTTCAAGATTTGAGCAACCTGAAAGAATTAACCTTTCAAGAGATTCCATTCCA
* * *
363826 ATTCTGGTTGGAAAA-CTCCTCAGACTTTTGCAGCCTCCTAACTTCAAAA
131 ATTCTGATTGGAAAACCT-CTAAGACTTTTGCAGCCTCCTAAATTCAAAA
363875 GCTTAAGCCT
Statistics
Matches: 156, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
209 2 0.01
210 154 0.99
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (210 bp):
AGGTAGCTCTTTAATGCCCGTCCCATCAAAACAAAGCTCCAACAAACATTCCATTTTCCCATCAA
TCTCTGGAAAGCTTTCAAGATTTGAGCAACCTGAAAGAATTAACCTTTCAAGAGATTCCATTCCA
ATTCTGATTGGAAAACCTCTAAGACTTTTGCAGCCTCCTAAATTCAAAACTTTAAGTCTTTTGAG
ACTTCCGATCAAAGA
Found at i:364921 original size:42 final size:42
Alignment explanation
Indices: 364874--365000 Score: 254
Period size: 42 Copynumber: 3.0 Consensus size: 42
364864 AAAAAAAAAA
364874 CAACAACATTAAAATTATATATAGATATATATGTCATCTTAC
1 CAACAACATTAAAATTATATATAGATATATATGTCATCTTAC
364916 CAACAACATTAAAATTATATATAGATATATATGTCATCTTAC
1 CAACAACATTAAAATTATATATAGATATATATGTCATCTTAC
364958 CAACAACATTAAAATTATATATAGATATATATGTCATCTTAC
1 CAACAACATTAAAATTATATATAGATATATATGTCATCTTAC
365000 C
1 C
365001 TTTTATTGTC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 85 1.00
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (42 bp):
CAACAACATTAAAATTATATATAGATATATATGTCATCTTAC
Found at i:379599 original size:2 final size:2
Alignment explanation
Indices: 379594--379620 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
379584 CGTTTTTTCC
379594 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
379621 AGAGACATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:380886 original size:91 final size:90
Alignment explanation
Indices: 380750--380947 Score: 242
Period size: 91 Copynumber: 2.2 Consensus size: 90
380740 CTTAATTTTT
* * * * * *
380750 TTTTAAAAAAAGTAATTAA-ACACCT-CTAT-TTTTTTTCCACTCAATTGAGCATTTGAACTTTC
1 TTTTAAAAAAAGCAATTAAGTC-CCTGCTTTCTTTTTTTCCACTCAATTGAGAACTTGAAATTTC
* * *
380812 AAAATGCATCAAAAAGGCTCTCAAAC
65 AAAATGCATCAAAAAGACCCTCAAAA
*
380838 TTCTTCAAAAAAAGCAATTAAGTCCCTGCTTTCTTTTTTT-CACTCAATTGGGAACTTGAAATTT
1 TT-TT-AAAAAAAGCAATTAAGTCCCTGCTTTCTTTTTTTCCACTCAATTGAGAACTTGAAATTT
380902 CAAAATGCATCAAAAAGACCCTCAAAA
64 CAAAATGCATCAAAAAGACCCTCAAAA
*
380929 TTTTAAAAAAATCAATTAA
1 TTTTAAAAAAAGCAATTAA
380948 ACCCTTGCTC
Statistics
Matches: 94, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
88 2 0.02
89 16 0.17
90 19 0.20
91 50 0.53
92 7 0.07
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (90 bp):
TTTTAAAAAAAGCAATTAAGTCCCTGCTTTCTTTTTTTCCACTCAATTGAGAACTTGAAATTTCA
AAATGCATCAAAAAGACCCTCAAAA
Found at i:382819 original size:17 final size:16
Alignment explanation
Indices: 382789--382831 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
382779 TATATTTTTC
382789 TTATAAAAATATAAAA
1 TTATAAAAATATAAAA
*
382805 TTATAAAATTCATAAAA
1 TTATAAAAAT-ATAAAA
*
382822 ATATACAAAA
1 TTATA-AAAA
382832 ACTTAACATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 9 0.41
17 10 0.45
18 3 0.14
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (16 bp):
TTATAAAAATATAAAA
Found at i:383998 original size:26 final size:24
Alignment explanation
Indices: 383969--384033 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 24
383959 TAAAATACAT
383969 ATATATATTATAAAGA-ATGCATAAAC
1 ATATATATTATAAA-ATATG-A-AAAC
* * *
383995 ATATAGACTATAAAATATGAAAAT
1 ATATATATTATAAAATATGAAAAC
*
384019 ATAAATATTATAAAA
1 ATATATATTATAAAA
384034 ATATAAATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
24 15 0.47
25 2 0.06
26 15 0.47
ACGTcount: A:0.58, C:0.05, G:0.06, T:0.31
Consensus pattern (24 bp):
ATATATATTATAAAATATGAAAAC
Found at i:384019 original size:8 final size:7
Alignment explanation
Indices: 383989--384084 Score: 52
Period size: 8 Copynumber: 12.4 Consensus size: 7
383979 TAAAGAATGC
383989 ATAAACAT
1 ATAAA-AT
* *
383997 ATAGACT
1 ATAAAAT
384004 ATAAAAT
1 ATAAAAT
384011 ATGAAAAT
1 AT-AAAAT
384019 ATAAATATT
1 ATAAA-A-T
384028 ATAAAAAT
1 AT-AAAAT
384036 ATAAATGTAT
1 ATAAA---AT
384046 ATAAAAT
1 ATAAAAT
384053 ATAAAAACT
1 AT-AAAA-T
*
384062 ATGAAA-
1 ATAAAAT
384068 ATAAAAT
1 ATAAAAT
384075 A-AAATAT
1 ATAAA-AT
384082 ATA
1 ATA
384085 CATACTATGT
Statistics
Matches: 70, Mismatches: 6, Indels: 24
0.70 0.06 0.24
Matches are distributed among these distances:
6 8 0.11
7 22 0.31
8 23 0.33
9 7 0.10
10 10 0.14
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (7 bp):
ATAAAAT
Found at i:384036 original size:17 final size:17
Alignment explanation
Indices: 384014--384075 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 17
384004 ATAAAATATG
*
384014 AAAATATAAATATTATA
1 AAAATATAAATACTATA
*
384031 AAAATATAAAT-GTATA
1 AAAATATAAATACTATA
* *
384047 TAAAATATAAAAACTATG
1 -AAAATATAAATACTATA
384065 AAAATA-AAATA
1 AAAATATAAATA
384076 AAATATATAC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.21
17 27 0.71
18 3 0.08
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (17 bp):
AAAATATAAATACTATA
Found at i:384082 original size:34 final size:35
Alignment explanation
Indices: 384004--384082 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 35
383994 CATATAGACT
* *
384004 ATAAAATATGAAAATATAAATATTATAAAAATATAA
1 ATAAAATAT-AAAATATAAAAACTATAAAAATATAA
** *
384040 AT-GTATATAAAATATAAAAACTATGAAAATA-AA
1 ATAAAATATAAAATATAAAAACTATAAAAATATAA
384073 ATAAAATATA
1 ATAAAATATA
384083 TACATACTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
33 4 0.11
34 25 0.71
35 4 0.11
36 2 0.06
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (35 bp):
ATAAAATATAAAATATAAAAACTATAAAAATATAA
Found at i:385632 original size:18 final size:17
Alignment explanation
Indices: 385602--385636 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
385592 AACACACACT
385602 TTTCCCTCCCCTTTTCC
1 TTTCCCTCCCCTTTTCC
*
385619 TTTCCCTTCTCCTTTTCC
1 TTTCCC-TCCCCTTTTCC
385637 ACCATCCACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTCCCTCCCCTTTTCC
Found at i:386058 original size:18 final size:18
Alignment explanation
Indices: 386037--386093 Score: 86
Period size: 18 Copynumber: 3.4 Consensus size: 18
386027 ACATTATCAT
386037 TTATTTTTATTAAACTTA
1 TTATTTTTATTAAACTTA
386055 TTATTTTTA-T---CTTA
1 TTATTTTTATTAAACTTA
386069 TTATTTTTATTAAACTTA
1 TTATTTTTATTAAACTTA
386087 TTATTTT
1 TTATTTT
386094 CACTGCCCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
14 13 0.37
15 1 0.03
17 1 0.03
18 20 0.57
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATTTTTATTAAACTTA
Found at i:386070 original size:14 final size:14
Alignment explanation
Indices: 386051--386078 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
386041 TTTTATTAAA
386051 CTTATTATTTTTAT
1 CTTATTATTTTTAT
386065 CTTATTATTTTTAT
1 CTTATTATTTTTAT
386079 TAAACTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (14 bp):
CTTATTATTTTTAT
Found at i:389241 original size:47 final size:47
Alignment explanation
Indices: 389172--389265 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
389162 TCAGCAAAGT
*
389172 CATGTCAAGCATATCCGATTGTCCATCATGATGAGTTAGTTGGAATC
1 CATGTCAAACATATCCGATTGTCCATCATGATGAGTTAGTTGGAATC
389219 CATGTCAAACATATCCGATTGTCCATCATGATGAGTTAGTTGGAATC
1 CATGTCAAACATATCCGATTGTCCATCATGATGAGTTAGTTGGAATC
389266 AGTCTATGCT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (47 bp):
CATGTCAAACATATCCGATTGTCCATCATGATGAGTTAGTTGGAATC
Found at i:391929 original size:209 final size:207
Alignment explanation
Indices: 391558--392167 Score: 799
Period size: 209 Copynumber: 2.9 Consensus size: 207
391548 TGCGAGGCTT
* * * * * *
391558 AAGTTGTTGAATTTAAGAGGCTGCAAAAGTCTGAGGAGTTTTCCAACCAGAATTGGAATAGAATC
1 AAGTT-TTGAATTTAAAAGACTGCAAAAGTCT-AGGAGTCTTCCAATCAAAATTGGAATGGAATC
* * * *
391623 TCTTGAAAAGTTGACTCTTTCAGGTTGCTCAAAACTTCAAAGCGTTCCAGAGATTGATGGGAAAA
64 TCTTGAAAAGTT-A-TCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGCAAAA
** * * * *
391688 TGGAATGTTTGTTGGAGCTTTGTTTTGATGGGACAAACATTAAAGAGCTACCTTCTTCAATCGGA
127 TGGAATGCCTGCTAGAGCTTTATTTAGATGGGACAAACATTAAAGAGCTACCTTCTTCAATCGGA
391753 AATCTCAGAA-ACTTA
192 AATCTCAGAAGACTTA
* *
391768 AAGTTTTGAATTTAAAAGACTGCAAAAGTCGTAGGAGTCATCCAATCAAAATTGGAATGGGATCT
1 AAGTTTTGAATTTAAAAGACTGCAAAAGTC-TAGGAGTCTTCCAATCAAAATTGGAATGGAATCT
391833 CTTGAAAAGTTAATTCTTTCAGGTTGCTTC-AATCTTAAAAGCTTTCCAGAGATTGATGGCAAAA
65 CTTGAAAAGTT-A-TCTTTCAGGTTGC-TCAAATCTTAAAAGCTTTCCAGAGATTGATGGCAAAA
* * *
391897 TGGAATGCCTGCTAGTGCTTTATTTAGATGGGATAAACATTAAAGAGCTACCCTCTTCAATCGGA
127 TGGAATGCCTGCTAGAGCTTTATTTAGATGGGACAAACATTAAAGAGCTACCTTCTTCAATCGGA
391962 AATCTCAGAAGACTTA
192 AATCTCAGAAGACTTA
*
391978 AAGTTTTGAATTTAAAGGACTGCAAAAGTCTTAGGAGTCTTCCAATCAAAATTGGAATGGAATCT
1 AAGTTTTGAATTTAAAAGACTGCAAAAGTC-TAGGAGTCTTCCAATCAAAATTGGAATGGAATCT
*
392043 CTTGAAAAG-------TCAGGTTGCTCAAATCTTAAAAGGTTTCCAGAGATTGATGGCAAAATGG
65 CTTGAAAAGTTATCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGCAAAATGG
* * ** * *
392101 AATGCCTGCAAGAGCTTTCTTTAGATGGGACAGGCATTAAAGAGCTGCCTAT-TTCAATTGGAAA
130 AATGCCTGCTAGAGCTTTATTTAGATGGGACAAACATTAAAGAGCTACCT-TCTTCAATCGGAAA
392165 TCT
194 TCT
392168 GAGCAGTCTT
Statistics
Matches: 358, Mismatches: 37, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
200 2 0.01
201 101 0.28
202 1 0.00
209 171 0.48
210 83 0.23
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (207 bp):
AAGTTTTGAATTTAAAAGACTGCAAAAGTCTAGGAGTCTTCCAATCAAAATTGGAATGGAATCTC
TTGAAAAGTTATCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGCAAAATGGA
ATGCCTGCTAGAGCTTTATTTAGATGGGACAAACATTAAAGAGCTACCTTCTTCAATCGGAAATC
TCAGAAGACTTA
Found at i:392979 original size:24 final size:25
Alignment explanation
Indices: 392933--392994 Score: 90
Period size: 24 Copynumber: 2.5 Consensus size: 25
392923 TATTATATCT
*
392933 ATAAAGTGTTTATTTTTTTAAAAATA
1 ATAAAGTGTTTA-TTTTTTAAAAAAA
392959 ATAAAGTGTTTA-TTTTTAAAAAAA
1 ATAAAGTGTTTATTTTTTAAAAAAA
*
392983 ATAAAATGTTTA
1 ATAAAGTGTTTA
392995 ATTTAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 22 0.65
26 12 0.35
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (25 bp):
ATAAAGTGTTTATTTTTTAAAAAAA
Found at i:392999 original size:23 final size:24
Alignment explanation
Indices: 392949--393001 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
392939 TGTTTATTTT
* * *
392949 TTTAAAAATAATAAAGTGTTTATT
1 TTTAAAAAAAATAAAATGTTTATA
392973 TTTAAAAAAAATAAAATGTTTA-A
1 TTTAAAAAAAATAAAATGTTTATA
392996 TTTAAA
1 TTTAAA
393002 TATTGATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (24 bp):
TTTAAAAAAAATAAAATGTTTATA
Found at i:397131 original size:3 final size:3
Alignment explanation
Indices: 397123--397157 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
397113 ATTGAGAAGT
397123 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
397158 GAAGTCGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:399287 original size:28 final size:28
Alignment explanation
Indices: 399248--399313 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
399238 CTATCAAATT
* *
399248 AAAAATTATATTTTCATTTCATCATCCATA
1 AAAAATTAT-TTCT-ATTCCATCATCCATA
* *
399278 AAAAATTATTTCTATTCCATCATCTATT
1 AAAAATTATTTCTATTCCATCATCCATA
399306 AAAAATTA
1 AAAAATTA
399314 ATCATATACT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 20 0.62
29 3 0.09
30 9 0.28
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (28 bp):
AAAAATTATTTCTATTCCATCATCCATA
Found at i:399610 original size:9 final size:10
Alignment explanation
Indices: 399587--399612 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
399577 AAAGACCCTA
399587 AAAAATTTTC
1 AAAAATTTTC
399597 AAAAATTTTC
1 AAAAATTTTC
399607 AAAAAT
1 AAAAAT
399613 GCAATTAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAAATTTTC
Found at i:399714 original size:106 final size:107
Alignment explanation
Indices: 399591--399804 Score: 421
Period size: 106 Copynumber: 2.0 Consensus size: 107
399581 ACCCTAAAAA
399591 ATTTTCAAAAATTTTCAAAAATGCAATTAAGCCTTTGCTCTTTAACAAAAAAATTATAAAAAATA
1 ATTTTCAAAAATTTTCAAAAATGCAATTAAGCCTTTGCTCTTTAACAAAAAAATTATAAAAAATA
399656 AAAAAAAATGTAAAATTTTATAAAAATCAT-AAAAGAATTAT
66 AAAAAAAATGTAAAATTTTATAAAAATCATAAAAAGAATTAT
399697 ATTTTCAAAAATTTTCAAAAATGCAATTAAGCCTTTGCTCTTTAACAAAAAAATTATAAAAAATA
1 ATTTTCAAAAATTTTCAAAAATGCAATTAAGCCTTTGCTCTTTAACAAAAAAATTATAAAAAATA
399762 AAAAAAAATGTAAAATTTTATAAAAATCATAAAAAGAATTAT
66 AAAAAAAATGTAAAATTTTATAAAAATCATAAAAAGAATTAT
399804 A
1 A
399805 AAATGCATCA
Statistics
Matches: 107, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
106 95 0.89
107 12 0.11
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (107 bp):
ATTTTCAAAAATTTTCAAAAATGCAATTAAGCCTTTGCTCTTTAACAAAAAAATTATAAAAAATA
AAAAAAAATGTAAAATTTTATAAAAATCATAAAAAGAATTAT
Found at i:399807 original size:31 final size:29
Alignment explanation
Indices: 399750--399808 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
399740 AACAAAAAAA
*
399750 TTATAAAAAATAAAAAAAAATGTAAAATT
1 TTATAAAAAATAAAAAAAAATATAAAATT
* *
399779 TTATAAAAATCATAAAAAGAATTATAAAAT
1 TTATAAAAA--ATAAAAAAAAATATAAAAT
399809 GCATCAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.36
31 16 0.64
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (29 bp):
TTATAAAAAATAAAAAAAAATATAAAATT
Found at i:400113 original size:21 final size:19
Alignment explanation
Indices: 400089--400137 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 19
400079 TATTTTTCTC
400089 ATAAAAAAATACATAAAAATT
1 ATAAAAAAAT-CATAAAAA-T
*
400110 ATAAAAATATCATAAAAAT
1 ATAAAAAAATCATAAAAAT
400129 ATACAAAAA
1 ATA-AAAAA
400138 CTTAACATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 12 0.48
21 9 0.36
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
ATAAAAAAATCATAAAAAT
Found at i:400124 original size:11 final size:11
Alignment explanation
Indices: 400087--400130 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
400077 TATATTTTTC
*
400087 TCATAAAAAAA
1 TCATAAAAATA
400098 TACATAAAAAT-
1 T-CATAAAAATA
400109 T-ATAAAAATA
1 TCATAAAAATA
400119 TCATAAAAATA
1 TCATAAAAATA
400130 T
1 T
400131 ACAAAAACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
9 8 0.28
10 1 0.03
11 12 0.41
12 8 0.28
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (11 bp):
TCATAAAAATA
Found at i:401452 original size:3 final size:3
Alignment explanation
Indices: 401444--401524 Score: 92
Period size: 3 Copynumber: 26.3 Consensus size: 3
401434 NNNNNNNNNN
401444 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
* * * *
401489 TAT TACT TAG TAT TAT AAT TGT TAAT TAT TGT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT T-AT TAT TAT TAT T
401525 CCAATTTTAG
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.03
3 56 0.85
4 8 0.12
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:419687 original size:18 final size:17
Alignment explanation
Indices: 419664--419697 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
419654 CCGAAGATAG
419664 CTTTCTTCTACTTTTTCC
1 CTTTCTT-TACTTTTTCC
*
419682 CTTTCTTTTCTTTTTC
1 CTTTCTTTACTTTTTC
419698 TTATGATAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (17 bp):
CTTTCTTTACTTTTTCC
Found at i:426118 original size:40 final size:40
Alignment explanation
Indices: 426074--426164 Score: 112
Period size: 40 Copynumber: 2.3 Consensus size: 40
426064 ACTTTTTAAC
* *
426074 AAACGCCGCAATAGATCGAGAATTAGTGGTGCTTTCTAGG-
1 AAACGCCGCAATAGATCAAGAATTAGCGGTGCTTT-TAGGA
* * * *
426114 AAACGCTGCTATAGATCAAGTATTAGCGGTGCTTTTCGGA
1 AAACGCCGCAATAGATCAAGAATTAGCGGTGCTTTTAGGA
426154 AAACGCCGCAA
1 AAACGCCGCAA
426165 AAAGATGAGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
39 3 0.07
40 39 0.93
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (40 bp):
AAACGCCGCAATAGATCAAGAATTAGCGGTGCTTTTAGGA
Found at i:426467 original size:21 final size:21
Alignment explanation
Indices: 426423--426538 Score: 96
Period size: 21 Copynumber: 5.6 Consensus size: 21
426413 AATATCTATA
* *
426423 TTTAGGGTTTAGGGTGT-ATG
1 TTTAGGGTTTAGGGTTTAAGG
*
426443 TTTATGGTTT-GAGGTTTAAGG
1 TTTAGGGTTTAG-GGTTTAAGG
426464 TTTAGGGTTTAGGGTTTAAGG
1 TTTAGGGTTTAGGGTTTAAGG
*
426485 TTTTAGGGTTTAGAGTTT-AGTG
1 -TTTAGGGTTTAGGGTTTAAG-G
* * * **
426507 TTTACGGTGTA-TGTTTGTGG
1 TTTAGGGTTTAGGGTTTAAGG
426527 TTTAGGGTTTAG
1 TTTAGGGTTTAG
426539 TATTTAAGAT
Statistics
Matches: 78, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
19 1 0.01
20 27 0.35
21 32 0.41
22 18 0.23
ACGTcount: A:0.16, C:0.01, G:0.35, T:0.47
Consensus pattern (21 bp):
TTTAGGGTTTAGGGTTTAAGG
Found at i:426494 original size:8 final size:7
Alignment explanation
Indices: 426423--426538 Score: 87
Period size: 7 Copynumber: 16.7 Consensus size: 7
426413 AATATCTATA
426423 TTTAGGG
1 TTTAGGG
426430 TTTAGGG
1 TTTAGGG
* *
426437 TGTA-TG
1 TTTAGGG
*
426443 TTTATGG
1 TTTAGGG
426450 TTT-GAGG
1 TTTAG-GG
*
426457 TTTAAGG
1 TTTAGGG
426464 TTTAGGG
1 TTTAGGG
426471 TTTAGGG
1 TTTAGGG
*
426478 TTTAAGGT
1 TTT-AGGG
426486 TTTAGGG
1 TTTAGGG
*
426493 TTTAGAG
1 TTTAGGG
*
426500 TTTAGTG
1 TTTAGGG
*
426507 TTTACGG
1 TTTAGGG
* *
426514 TGTA-TG
1 TTTAGGG
426520 TTT-GTGG
1 TTTAG-GG
426527 TTTAGGG
1 TTTAGGG
426534 TTTAG
1 TTTAG
426539 TATTTAAGAT
Statistics
Matches: 85, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
6 7 0.08
7 71 0.84
8 7 0.08
ACGTcount: A:0.16, C:0.01, G:0.35, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:426598 original size:7 final size:7
Alignment explanation
Indices: 426586--426768 Score: 74
Period size: 7 Copynumber: 26.0 Consensus size: 7
426576 AATATCTATA
426586 TTTAGGG
1 TTTAGGG
426593 TTTAGGG
1 TTTAGGG
* *
426600 TGTA-TG
1 TTTAGGG
*
426606 TTTACGG
1 TTTAGGG
426613 TTT-GAGG
1 TTTAG-GG
*
426620 TTTAAGG
1 TTTAGGG
*
426627 TTTAAGG
1 TTTAGGG
426634 TTTAGGG
1 TTTAGGG
*
426641 TTTTAAGG
1 -TTTAGGG
*
426649 TTTAGAG
1 TTTAGGG
*
426656 TTTAGTG
1 TTTAGGG
426663 TTTAGGG
1 TTTAGGG
* *
426670 TGTA-TG
1 TTTAGGG
426676 TTT-GTGG
1 TTTAG-GG
426683 TTT-GGG
1 TTTAGGG
426689 TCTT-GGG
1 T-TTAGGG
426696 TTTAGGG
1 TTTAGGG
* **
426703 ATTAATG
1 TTTAGGG
*
426710 TTTAGAAG
1 TTTAG-GG
*
426718 TATAGAGG
1 TTTAG-GG
426726 -TTAGGG
1 TTTAGGG
**
426732 TTTAAAG
1 TTTAGGG
* *
426739 TTTATGA
1 TTTAGGG
426746 TTTAAGGG
1 TTT-AGGG
426754 TTTTAGGG
1 -TTTAGGG
426762 TTTAGGG
1 TTTAGGG
426769 GGTTTTTGGT
Statistics
Matches: 132, Mismatches: 32, Indels: 24
0.70 0.17 0.13
Matches are distributed among these distances:
6 14 0.11
7 96 0.73
8 19 0.14
9 3 0.02
ACGTcount: A:0.20, C:0.01, G:0.34, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:426648 original size:22 final size:22
Alignment explanation
Indices: 426620--426665 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
426610 CGGTTTGAGG
426620 TTTAAGGTTTA-AGGTTTAGGGT
1 TTTAAGGTTTAGA-GTTTAGGGT
*
426642 TTTAAGGTTTAGAGTTTAGTGT
1 TTTAAGGTTTAGAGTTTAGGGT
426664 TT
1 TT
426666 AGGGTGTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (22 bp):
TTTAAGGTTTAGAGTTTAGGGT
Found at i:426672 original size:156 final size:158
Alignment explanation
Indices: 426356--426689 Score: 548
Period size: 163 Copynumber: 2.1 Consensus size: 158
426346 AATGTTTAGA
*
426356 GTTTGGGGTTTAGGGTTTAGTATTTAAGATTCTTTTTTAATTAATTTTGTCCCCTATAATATCTA
1 GTTTGTGGTTTAGGGTTTAGTATTTAAGATTCTTTTTTAATTAATTTTGTCCCCTATAATATCTA
*
426421 TATTTAGGGTTTAGGGTGTATGTTTATGGTTTGAGGTTTAAGGTTTAGGGTTTAGGGTTTAAGGT
66 TATTTAGGGTTTAGGGTGTATGTTTACGGTTTGAGGTTTAAGGTTTA--G---AGGGTTTAAGGT
*
426486 TTTAGGGTTTAGAGTTTAGTGTTTACGGTGTAT
126 TTTAAGGTTTAGAGTTTAGTGTTTACGGTGTAT
*
426519 GTTTGTGGTTTAGGGTTTAGTATTTAAGATTCTTTTTTAATTACTTTTGTCCCCTATAATATCTA
1 GTTTGTGGTTTAGGGTTTAGTATTTAAGATTCTTTTTTAATTAATTTTGTCCCCTATAATATCTA
*
426584 TATTTAGGGTTTAGGGTGTATGTTTACGGTTTGAGGTTTAAGGTTTA-A-GGTTTAGGGTTTTAA
66 TATTTAGGGTTTAGGGTGTATGTTTACGGTTTGAGGTTTAAGGTTTAGAGGGTTTAAGGTTTTAA
*
426647 GGTTTAGAGTTTAGTGTTTAGGGTGTAT
131 GGTTTAGAGTTTAGTGTTTACGGTGTAT
426675 GTTTGTGGTTT-GGGT
1 GTTTGTGGTTTAGGGT
426690 CTTGGGTTTA
Statistics
Matches: 165, Mismatches: 6, Indels: 8
0.92 0.03 0.04
Matches are distributed among these distances:
155 4 0.02
156 51 0.31
157 1 0.01
163 109 0.66
ACGTcount: A:0.19, C:0.04, G:0.27, T:0.49
Consensus pattern (158 bp):
GTTTGTGGTTTAGGGTTTAGTATTTAAGATTCTTTTTTAATTAATTTTGTCCCCTATAATATCTA
TATTTAGGGTTTAGGGTGTATGTTTACGGTTTGAGGTTTAAGGTTTAGAGGGTTTAAGGTTTTAA
GGTTTAGAGTTTAGTGTTTACGGTGTAT
Found at i:427223 original size:39 final size:40
Alignment explanation
Indices: 427167--427244 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 40
427157 CATTATATTC
*
427167 AATTTTAAAATTGAACAA-T-AAAATAATGTCATATTAAA
1 AATTTTAAAATTGAACAATTAAAAAAAATGTCATATTAAA
*
427205 AATTTTAAAAATTTAACAATTAAAAAAAATGTCATATTAA
1 AATTTT-AAAATTGAACAATTAAAAAAAATGTCATATTAA
427245 TGTATCAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
38 6 0.17
39 11 0.31
40 1 0.03
41 17 0.49
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (40 bp):
AATTTTAAAATTGAACAATTAAAAAAAATGTCATATTAAA
Found at i:427651 original size:125 final size:124
Alignment explanation
Indices: 427341--427739 Score: 480
Period size: 125 Copynumber: 3.2 Consensus size: 124
427331 ATCTTTAGCA
* * * * *
427341 GCGTTTTTCAT-AGAAACGCCACAAAAGGTAAACAATAGTGGCGTTTGGACTAAAAATGCCGCAA
1 GCGTTTTTC-TCAAAAACGCCGCAAAAGGTAAGCAATAGTGGCGTTTTGTCTAAAAATGCCGCAA
* * * ** *
427405 CAATGTATTAAAAATTATACAAAACGGCGCCGTTTGGTTATTGGAATTTGATTTTTAGTG
65 CAATGTATTAAAAACTGTACAAAACGGCGCCATTTGGTTACAGGAATTTAATTTTTAGTG
* * * *
427465 GCGTTTTTCTCCAAAACGCCGCAAAAGGTATGTAATAGTGGCG-TTTGTTCTAAAAACGCCGCAA
1 GCGTTTTTCTCAAAAACGCCGCAAAAGGTAAGCAATAGTGGCGTTTTG-TCTAAAAATGCCGCAA
* * *
427529 CAATGTATTAAAAAGTGTACAAAATGACGCCATTTGGTTACAGGAATTTAACTTTTTAGTG
65 CAATGTATTAAAAACTGTACAAAACGGCGCCATTTGGTTACAGGAATTTAA-TTTTTAGTG
* * ** *
427590 GCATTTTTCTCAAAAACGCCGCAAAAGGTAAGCATTAGCAGTGTTTTGTCTAAAAATGCCGCAAC
1 GCGTTTTTCTCAAAAACGCCGCAAAAGGTAAGCAATAGTGGCGTTTTGTCTAAAAATGCCGCAAC
* * *
427655 AATGTATTAAAAACTGTACAAAACGGCGCCATTTTGTTTCAGGAAATTAATTTTGTAGTG
66 AATGTATTAAAAACTGTACAAAACGGCGCCATTTGGTTACAGGAATTTAATTTT-TAGTG
* *
427715 TCGTTTTTGCT-GAAAACGCCGCAAA
1 GCGTTTTT-CTCAAAAACGCCGCAAA
427740 TATTTCAATA
Statistics
Matches: 234, Mismatches: 35, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
123 4 0.02
124 96 0.41
125 128 0.55
126 6 0.03
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (124 bp):
GCGTTTTTCTCAAAAACGCCGCAAAAGGTAAGCAATAGTGGCGTTTTGTCTAAAAATGCCGCAAC
AATGTATTAAAAACTGTACAAAACGGCGCCATTTGGTTACAGGAATTTAATTTTTAGTG
Found at i:430295 original size:5 final size:5
Alignment explanation
Indices: 430285--430309 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
430275 AATAAGAACG
430285 ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA
430310 CCATTTGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:432062 original size:27 final size:27
Alignment explanation
Indices: 432032--432083 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
432022 AAGGAAAGCC
432032 TTTTAGAACGTCCTAGATTTTATAAAA
1 TTTTAGAACGTCCTAGATTTTATAAAA
432059 TTTTAGAACGTCCTAGATTTTATAA
1 TTTTAGAACGTCCTAGATTTTATAA
432084 TATTCAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (27 bp):
TTTTAGAACGTCCTAGATTTTATAAAA
Found at i:438623 original size:142 final size:143
Alignment explanation
Indices: 438466--438748 Score: 559
Period size: 143 Copynumber: 2.0 Consensus size: 143
438456 TAATTTAACC
438466 AGATTTATTACGCTTTTTATTTTCTTTAACTAGATTTTTGTAAGAAAACCTTCAAATTTTGAT-A
1 AGATTTATTACGCTTTTTATTTTCTTTAACTAGATTTTTGTAAGAAAACCTTCAAATTTTGATAA
438530 AAAAAATCATATCATTTAAAATTTATAAAATTCAAAGGTATCCATAAAATTTTTAAAATACCTTT
66 AAAAAATCATATCATTTAAAATTTATAAAATTCAAAGGTATCCATAAAATTTTTAAAATACCTTT
438595 AATAGAAAATTTA
131 AATAGAAAATTTA
438608 AGATTTATTACGCTTTTTATTTTCTTTAACTAGATTTTTGTAAGAAAACCTTCAAATTTTGATAA
1 AGATTTATTACGCTTTTTATTTTCTTTAACTAGATTTTTGTAAGAAAACCTTCAAATTTTGATAA
438673 AAAAAATCATATCATTTAAAATTTATAAAATTCAAAGGTATCCATAAAATTTTTAAAATACCTTT
66 AAAAAATCATATCATTTAAAATTTATAAAATTCAAAGGTATCCATAAAATTTTTAAAATACCTTT
438738 AATAGAAAATT
131 AATAGAAAATT
438749 ATTTAAGATT
Statistics
Matches: 140, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
142 63 0.45
143 77 0.55
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.41
Consensus pattern (143 bp):
AGATTTATTACGCTTTTTATTTTCTTTAACTAGATTTTTGTAAGAAAACCTTCAAATTTTGATAA
AAAAAATCATATCATTTAAAATTTATAAAATTCAAAGGTATCCATAAAATTTTTAAAATACCTTT
AATAGAAAATTTA
Found at i:439727 original size:24 final size:24
Alignment explanation
Indices: 439699--439783 Score: 71
Period size: 24 Copynumber: 3.3 Consensus size: 24
439689 AAAAATTAAA
*
439699 TTAGGGTATTATGTTTTTAATTGT
1 TTAGGGTATTAGGTTTTTAATTGT
* * **
439723 TTAGGGTTTTAAGGTTTATGAAAAATTAAA
1 TTAGGGTATT-AGGTTT-T---TAATT-GT
439753 TTAGGGTATTAGGTTTTTAATTGT
1 TTAGGGTATTAGGTTTTTAATTGT
439777 TTAGGGT
1 TTAGGGT
439784 TTCTGGGCTT
Statistics
Matches: 46, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
24 16 0.35
25 9 0.20
26 1 0.02
28 1 0.02
29 10 0.22
30 9 0.20
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (24 bp):
TTAGGGTATTAGGTTTTTAATTGT
Found at i:439742 original size:54 final size:54
Alignment explanation
Indices: 439683--439851 Score: 203
Period size: 54 Copynumber: 2.9 Consensus size: 54
439673 TTGATTAGGT
*
439683 TTTATGAAAAATTAAATTAGGGTATTATGTTTTTAATTGTTTAGGGTTTTAAGG
1 TTTATGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAGGGTTTTAAGG
439737 TTTATGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAGGGTTTCTGGGCTTGATTAGGG
1 TTTATGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAGGG--T-T----TT-A--A-GG
* * *
439802 TTTAAGAAAAATTAAATCAAGGTATTAGGTTTTTAATTGTTTAGGGTTTT
1 TTTATGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAGGGTTTT
439852 GGGGTTTGAT
Statistics
Matches: 100, Mismatches: 4, Indels: 18
0.82 0.03 0.15
Matches are distributed among these distances:
54 45 0.45
56 1 0.01
57 1 0.01
58 2 0.02
61 2 0.02
62 2 0.02
63 1 0.01
64 1 0.01
65 45 0.45
ACGTcount: A:0.30, C:0.02, G:0.22, T:0.46
Consensus pattern (54 bp):
TTTATGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAGGGTTTTAAGG
Found at i:439811 original size:65 final size:65
Alignment explanation
Indices: 439731--439903 Score: 258
Period size: 65 Copynumber: 2.7 Consensus size: 65
439721 GTTTAGGGTT
*
439731 TTAAGGTTTATGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAGGGTTTCT-GGGCTTG
1 TTAAGGTTTAAGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAGGGTTT-TGGGGCTTG
439795 A
65 A
* * * *
439796 TTAGGGTTTAAGAAAAATTAAATCAAGGTATTAGGTTTTTAATTGTTTAGGGTTTTGGGGTTTGA
1 TTAAGGTTTAAGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAGGGTTTTGGGGCTTGA
* * *
439861 TTAAGGTTTAGGAAAATTTAAATTAGGGTATTAAGTTTTTAAT
1 TTAAGGTTTAAGAAAAATTAAATTAGGGTATTAGGTTTTTAAT
439904 AGGACTGAAG
Statistics
Matches: 96, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
64 1 0.01
65 95 0.99
ACGTcount: A:0.31, C:0.02, G:0.24, T:0.44
Consensus pattern (65 bp):
TTAAGGTTTAAGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAGGGTTTTGGGGCTTGA
Found at i:442954 original size:18 final size:17
Alignment explanation
Indices: 442931--442964 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
442921 CCGAATATAG
442931 CTTTCTTCTACTTTTTCC
1 CTTTCTT-TACTTTTTCC
*
442949 CTTTCTTTTCTTTTTC
1 CTTTCTTTACTTTTTC
442965 TTATGATAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (17 bp):
CTTTCTTTACTTTTTCC
Found at i:458343 original size:51 final size:51
Alignment explanation
Indices: 458283--458385 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
458273 AGACAATAAC
458283 AGGCTGTTTTGTATCTTGCTTGAATAGCAAGCCTCGAGCCTTGGTGAAGAA
1 AGGCTGTTTTGTATCTTGCTTGAATAGCAAGCCTCGAGCCTTGGTGAAGAA
*
458334 AGGCTGTTTTGTATCTTGCTTGAATAGCAAGCCTCGAGCCTTGTTGAAGAA
1 AGGCTGTTTTGTATCTTGCTTGAATAGCAAGCCTCGAGCCTTGGTGAAGAA
458385 A
1 A
458386 CAAACTCAGA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.32
Consensus pattern (51 bp):
AGGCTGTTTTGTATCTTGCTTGAATAGCAAGCCTCGAGCCTTGGTGAAGAA
Found at i:469499 original size:17 final size:18
Alignment explanation
Indices: 469479--469512 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
469469 ACATTTTTAA
469479 TATATATTTTT-AAAATC
1 TATATATTTTTCAAAATC
*
469496 TATATTTTTTTCAAAAT
1 TATATATTTTTCAAAAT
469513 TTATCAATCA
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:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATTTTTCAAAATC
Found at i:469646 original size:9 final size:9
Alignment explanation
Indices: 469627--469700 Score: 85
Period size: 9 Copynumber: 8.2 Consensus size: 9
469617 CTTATATATA
*
469627 AACTTGCAT
1 AACTTACAT
*
469636 AACTTATAT
1 AACTTACAT
*
469645 AAATTACAT
1 AACTTACAT
469654 AACTTACAT
1 AACTTACAT
* *
469663 AAATTATAT
1 AACTTACAT
469672 AACTTACAT
1 AACTTACAT
* *
469681 AAATTAAAT
1 AACTTACAT
469690 AACTTACAT
1 AACTTACAT
469699 AA
1 AA
469701 NNNNNNNNNN
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 52 1.00
ACGTcount: A:0.50, C:0.14, G:0.01, T:0.35
Consensus pattern (9 bp):
AACTTACAT
Found at i:469656 original size:18 final size:18
Alignment explanation
Indices: 469633--469700 Score: 109
Period size: 18 Copynumber: 3.8 Consensus size: 18
469623 TATAAACTTG
*
469633 CATAACTTATATAAATTA
1 CATAACTTACATAAATTA
469651 CATAACTTACATAAATTA
1 CATAACTTACATAAATTA
*
469669 TATAACTTACATAAATTA
1 CATAACTTACATAAATTA
*
469687 AATAACTTACATAA
1 CATAACTTACATAA
469701 NNNNNNNNNN
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.35
Consensus pattern (18 bp):
CATAACTTACATAAATTA
Found at i:469663 original size:27 final size:27
Alignment explanation
Indices: 469627--469700 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
469617 CTTATATATA
*
469627 AACTTGCATAACTTATATAAATTACAT
1 AACTTACATAACTTATATAAATTACAT
* *
469654 AACTTACATAAATTATATAACTTACAT
1 AACTTACATAACTTATATAAATTACAT
* * *
469681 AAATTAAATAACTTACATAA
1 AACTTACATAACTTATATAA
469701 NNNNNNNNNN
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.50, C:0.14, G:0.01, T:0.35
Consensus pattern (27 bp):
AACTTACATAACTTATATAAATTACAT
Found at i:471204 original size:17 final size:17
Alignment explanation
Indices: 471182--471244 Score: 63
Period size: 17 Copynumber: 3.4 Consensus size: 17
471172 CCTTTAAACA
471182 AAAACAATTTCAAATAC
1 AAAACAATTTCAAATAC
*
471199 AAAACAAGGTTTACAAATGC
1 AAAACAA--TTT-CAAATAC
*
471219 TGCAAACAATTTCAAATAC
1 --AAAACAATTTCAAATAC
471238 AAAACAA
1 AAAACAA
471245 GGTTTACAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
17 13 0.35
19 9 0.24
20 9 0.24
22 6 0.16
ACGTcount: A:0.56, C:0.17, G:0.06, T:0.21
Consensus pattern (17 bp):
AAAACAATTTCAAATAC
Found at i:471226 original size:39 final size:40
Alignment explanation
Indices: 471183--471264 Score: 157
Period size: 39 Copynumber: 2.1 Consensus size: 40
471173 CTTTAAACAA
471183 AAACAATTTCAAATACAAAACAAGGTTTACAA-ATGCTGC
1 AAACAATTTCAAATACAAAACAAGGTTTACAATATGCTGC
471222 AAACAATTTCAAATACAAAACAAGGTTTACAATATGCTGC
1 AAACAATTTCAAATACAAAACAAGGTTTACAATATGCTGC
471262 AAA
1 AAA
471265 ATCATTTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 32 0.76
40 10 0.24
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.23
Consensus pattern (40 bp):
AAACAATTTCAAATACAAAACAAGGTTTACAATATGCTGC
Found at i:472735 original size:28 final size:28
Alignment explanation
Indices: 472704--472758 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
472694 ACCACAACCC
*
472704 CTATCCCCTAAACCCTAAACCGTAAACT
1 CTATCCCCTAAACCCTAAACCCTAAACT
* * * *
472732 CTATTCCTTAGACCTTAAACCCTAAAC
1 CTATCCCCTAAACCCTAAACCCTAAAC
472759 CGGTTTAGGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.35, C:0.36, G:0.04, T:0.25
Consensus pattern (28 bp):
CTATCCCCTAAACCCTAAACCCTAAACT
Found at i:473115 original size:14 final size:15
Alignment explanation
Indices: 473091--473126 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
473081 AATCATAGAA
473091 CATATAAACCCTAAAT
1 CATA-AAACCCTAAAT
473107 C-TAAAACCCTAAAT
1 CATAAAACCCTAAAT
473121 CATAAA
1 CATAAA
473127 CATATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 12 0.63
15 6 0.32
16 1 0.05
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (15 bp):
CATAAAACCCTAAAT
Found at i:504955 original size:5 final size:5
Alignment explanation
Indices: 504945--504988 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
504935 AAGAACGATT
504945 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAAT
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAAT
504989 GTACCATTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:506372 original size:226 final size:226
Alignment explanation
Indices: 505978--506430 Score: 784
Period size: 226 Copynumber: 2.0 Consensus size: 226
505968 AAACCAATAA
* * *
505978 TTTATGGATAACAGATTGCTTAGATCAAGAATGCGATCAACTTGAATTGTCTTTCACTGGTCCCT
1 TTTATGGATAACAGATTGCTTAGATCAAGAAAGCAATCAACTTGAATTGTCTTTCACCGGTCCCT
*
506043 ACAGTGTTAACGCGAAGAAGTGTGGAGTTAGAATAGTGTATAAGAGAGATCTGGAAGAGATGGAA
66 ACAGTGTTAACGCGAAGAAGTGTGGAGTTAGAATAGTGTACAAGAGAGATCTGGAAGAGATGGAA
*
506108 CAAATAAAAGAGCTGCATAGTAGTCAGTGTTGTGCGAATTTTGAAGATATCCAGCAACACTCTGC
131 CAAATAAAAGAGCTGCATAGTAGTCAATGTTGTGCGAATTTTGAAGATATCCAGCAACACTCTGC
506173 TGATGATGGATCAATAGGTAACTGTTCCCTT
196 TGATGATGGATCAATAGGTAACTGTTCCCTT
* *
506204 TTTATGGATAACAGATTGCTTAGATCAAGAAAAG-AATGCGA-TTGAATTGTCTTTCACCGGTCG
1 TTTATGGATAACAGATTGCTTAGATCAAG-AAAGCAAT-CAACTTGAATTGTCTTTCACCGGTCC
* * *
506267 CTACAGTGTTAACGCGAAGAATTGTGGCGTTAGAATAGTGTACAAGTGAGATCTGGAAGAGATGG
64 CTACAGTGTTAACGCGAAGAAGTGTGGAGTTAGAATAGTGTACAAGAGAGATCTGGAAGAGATGG
506332 AACAAATAAAAGAGCTGCATAGTAGTCAATGTTGTGCGAATTTTGAAGATATCCAGCAACACTCT
129 AACAAATAAAAGAGCTGCATAGTAGTCAATGTTGTGCGAATTTTGAAGATATCCAGCAACACTCT
506397 GCTGATGATGGATCAATAGGTAACTGTTCCCTT
194 GCTGATGATGGATCAATAGGTAACTGTTCCCTT
506430 T
1 T
506431 AACATATTTA
Statistics
Matches: 215, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
226 210 0.98
227 5 0.02
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (226 bp):
TTTATGGATAACAGATTGCTTAGATCAAGAAAGCAATCAACTTGAATTGTCTTTCACCGGTCCCT
ACAGTGTTAACGCGAAGAAGTGTGGAGTTAGAATAGTGTACAAGAGAGATCTGGAAGAGATGGAA
CAAATAAAAGAGCTGCATAGTAGTCAATGTTGTGCGAATTTTGAAGATATCCAGCAACACTCTGC
TGATGATGGATCAATAGGTAACTGTTCCCTT
Found at i:524473 original size:5 final size:5
Alignment explanation
Indices: 524463--524487 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
524453 AATAAGAACG
524463 ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA
524488 CCATTTGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:526415 original size:5 final size:5
Alignment explanation
Indices: 526407--526442 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
526397 ATANNNNNNN
526407 AATAT AATAT AATAT AATAT AATAT AATAT AATAT A
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT A
526443 CCATTGGATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:527327 original size:29 final size:31
Alignment explanation
Indices: 527295--527360 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 31
527285 GTCTAAATTT
*
527295 AATTTTAAGAAATTTAGAGGTC-AAA-ATAA
1 AATTTTAAAAAATTTAGAGGTCAAAATATAA
* *
527324 AATTTCAAAAAATTTGGAGGTCAAAATATAA
1 AATTTTAAAAAATTTAGAGGTCAAAATATAA
527355 AATTTT
1 AATTTT
527361 TTTTAAACAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 19 0.61
30 3 0.10
31 9 0.29
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.33
Consensus pattern (31 bp):
AATTTTAAAAAATTTAGAGGTCAAAATATAA
Found at i:527334 original size:87 final size:88
Alignment explanation
Indices: 527193--527354 Score: 215
Period size: 87 Copynumber: 1.9 Consensus size: 88
527183 GAAAAAAAAT
*
527193 TAGGGGTCAAAATGTAATTTTAGAAAATTTTAAGGTTCAAAATAAAATTTAAAAAATAAGG-GGT
1 TAGGAGTCAAAATGTAATTTTAGAAAATTTTAAGGTTCAAAATAAAATTTAAAAAATAAGGAGGT
*
527257 TAAAATATAATTTCATTAAAGTA
66 CAAAATATAATTTCATTAAAGTA
* * **
527280 TAGGAGTCTAAATTTAATTTTA-AGAAA-TTTAGAGG-TCAAAATAAAATTTCAAAAAATTTGGA
1 TAGGAGTCAAAATGTAATTTTAGA-AAATTTTA-AGGTTCAAAATAAAATTT-AAAAAATAAGGA
527342 GGTCAAAATATAA
63 GGTCAAAATATAA
527355 AATTTTTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
86 19 0.29
87 34 0.52
88 12 0.18
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (88 bp):
TAGGAGTCAAAATGTAATTTTAGAAAATTTTAAGGTTCAAAATAAAATTTAAAAAATAAGGAGGT
CAAAATATAATTTCATTAAAGTA
Found at i:527359 original size:31 final size:29
Alignment explanation
Indices: 527185--527351 Score: 99
Period size: 29 Copynumber: 5.8 Consensus size: 29
527175 GTAATTTTGA
* * ** *
527185 AAAAAAATTAGGGGTCAAAATGTAATTTT
1 AAAAAATTTAGAGGTCAAAATAAAATTTC
*
527214 AGAAAATTTTA-AGGTTCAAAATAAAATTT-
1 A-AAAAATTTAGAGG-TCAAAATAAAATTTC
* * * *
527243 AAAAAA-TAAGGGGTTAAAATATAATTTC
1 AAAAAATTTAGAGGTCAAAATAAAATTTC
* * * * ** *
527271 ATTAAAGTATAG-GAGTCTAAATTTAATTTT
1 A-AAAAATTTAGAG-GTCAAAATAAAATTTC
*
527301 AAGAAATTTAGAGGTCAAAATAAAATTTC
1 AAAAAATTTAGAGGTCAAAATAAAATTTC
*
527330 AAAAAATTTGGAGGTCAAAATA
1 AAAAAATTTAGAGGTCAAAATA
527352 TAAAATTTTT
Statistics
Matches: 102, Mismatches: 28, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
27 14 0.14
28 7 0.07
29 46 0.45
30 35 0.34
ACGTcount: A:0.50, C:0.04, G:0.14, T:0.32
Consensus pattern (29 bp):
AAAAAATTTAGAGGTCAAAATAAAATTTC
Found at i:541871 original size:114 final size:112
Alignment explanation
Indices: 541667--541953 Score: 439
Period size: 114 Copynumber: 2.5 Consensus size: 112
541657 CTTTCAGAAA
* * * * *
541667 TTTAGCGGCGTTTTTGAGAATGCGCCACAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTG
* * *
541732 TCGGGGATTTAGTGGTGTTTTTAGGTAAGCGCCGCTAATGCTCAGGGC
66 TCGGGGATTTAGTGGCGCTTCTAGGTAAGCGCCGCTAATGCTCA-GGC
* * * *
541780 TTTAGCTGTGTTTTTGGGAAAGCGTCGCAAAAATACCTAAGACCAACGACGCCGTTTTTTGAGCT
1 TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAA-ACCTAAGCCCAACGACGCCGTTTTCTGAGCT
541845 GTCGGGGATTTAGTGGCGCTTCTAGGTAAGCGCCGCTAATGCTCAGGC
65 GTCGGGGATTTAGTGGCGCTTCTAGGTAAGCGCCGCTAATGCTCAGGC
*
541893 TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAACCTTAGCCCAACGACGCCGTTTTCTGA
1 TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGA
541954 TCTTTCAGAT
Statistics
Matches: 156, Mismatches: 17, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
112 25 0.16
113 61 0.39
114 70 0.45
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (112 bp):
TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTG
TCGGGGATTTAGTGGCGCTTCTAGGTAAGCGCCGCTAATGCTCAGGC
Found at i:541989 original size:113 final size:113
Alignment explanation
Indices: 541667--542002 Score: 467
Period size: 113 Copynumber: 3.0 Consensus size: 113
541657 CTTTCAGAAA
* * * *
541667 TTTAGCGGCGTTTTTGAGAATGCGCCACAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
*
541732 TCGGGGATTTAGTGGTGTTTTTAGGTAAGCGCCGCTAATGCTCAGGGC
66 TCGGGGATTTAGTGGCGTTTTTAGGTAAGCGCCGCTAATGCTCAGGGC
* * * *
541780 TTTAGCTGTGTTTTTGGGAAAGCGTCGCAAAAATACCTAAGACCAACGACGCCGTTTTTTGAGCT
1 TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAA-ACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * *
541845 GTCGGGGATTTAGTGGCGCTTCTAGGTAAGCGCCGCTAATGCTCA-GGC
65 TTCGGGGATTTAGTGGCGTTTTTAGGTAAGCGCCGCTAATGCTCAGGGC
* *
541893 TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAACCTTAGCCCAACGACGCCGTTTTCTGATCTT
1 TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
** * * * *
541958 TCAGATGATTTAGCGGCGTTTTTCGGAAAGCGTCGCTAATGCTCA
66 TC-GGGGATTTAGTGGCGTTTTTAGGTAAGCGCCGCTAATGCTCA
542003 AGGATTTAAA
Statistics
Matches: 194, Mismatches: 27, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
112 29 0.15
113 95 0.49
114 70 0.36
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (113 bp):
TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
TCGGGGATTTAGTGGCGTTTTTAGGTAAGCGCCGCTAATGCTCAGGGC
Found at i:542309 original size:30 final size:31
Alignment explanation
Indices: 542266--542327 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
542256 TATGCTTTAA
542266 GGGTTAGTGGATTTAGGGGTAAGGGGTTAGG
1 GGGTTAGTGGATTTAGGGGTAAGGGGTTAGG
* * *
542297 GGGTTA-TGGATTTAGGGTTTAGGGTTTAGG
1 GGGTTAGTGGATTTAGGGGTAAGGGGTTAGG
542327 G
1 G
542328 TTTCAACGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 22 0.79
31 6 0.21
ACGTcount: A:0.18, C:0.00, G:0.48, T:0.34
Consensus pattern (31 bp):
GGGTTAGTGGATTTAGGGGTAAGGGGTTAGG
Found at i:544764 original size:22 final size:21
Alignment explanation
Indices: 544736--544851 Score: 79
Period size: 18 Copynumber: 5.6 Consensus size: 21
544726 ATTAGATTAC
544736 TTACATTACTTACTAAAATATA
1 TTACATTACTTA-TAAAATATA
544758 TTACATTAC-T-T-AAATATA
1 TTACATTACTTATAAAATATA
*
544776 TTAC-TTAC-TA-AAATTTATAA
1 TTACATTACTTATAAA-ATAT-A
544796 CTTACATTAC-T-T-AAATATA
1 -TTACATTACTTATAAAATATA
*
544815 TTACATTACTTAAAATTTATATATA
1 TTACATTACTTATAA---A-ATATA
544840 TTACATTACTTA
1 TTACATTACTTA
544852 AATAAAAATT
Statistics
Matches: 77, Mismatches: 3, Indels: 25
0.73 0.03 0.24
Matches are distributed among these distances:
17 5 0.06
18 22 0.29
19 6 0.08
20 4 0.05
21 8 0.10
22 14 0.18
24 1 0.01
25 17 0.22
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (21 bp):
TTACATTACTTATAAAATATA
Found at i:544772 original size:18 final size:18
Alignment explanation
Indices: 544740--544828 Score: 110
Period size: 18 Copynumber: 4.8 Consensus size: 18
544730 GATTACTTAC
*
544740 ATTAC-TTACTAAAATAT
1 ATTACATTACTTAAATAT
544757 ATTACATTACTTAAATAT
1 ATTACATTACTTAAATAT
*
544775 ATTAC-TTACTAAAATTTAT
1 ATTACATTACTTAAA--TAT
544794 AACTTACATTACTTAAATAT
1 -A-TTACATTACTTAAATAT
544814 ATTACATTACTTAAA
1 ATTACATTACTTAAA
544829 ATTTATATAT
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
17 13 0.21
18 30 0.48
19 4 0.06
20 4 0.06
21 4 0.06
22 8 0.13
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTACATTACTTAAATAT
Found at i:544784 original size:39 final size:39
Alignment explanation
Indices: 544736--544855 Score: 138
Period size: 39 Copynumber: 2.9 Consensus size: 39
544726 ATTAGATTAC
544736 TTACATTACTTACTAAA-ATATATTACATTACTTAAATATA
1 TTACATTACTTA--AAATATATATTACATTACTTAAATATA
*
544776 TTAC-TTAC-TAAAATTTATAACTTACATTACTTAAATATA
1 TTACATTACTTAAAATATAT-A-TTACATTACTTAAATATA
544815 TTACATTACTTAAAATTTATATATATTACATTACTTAAATA
1 TTACATTACTT-AAA---ATATATATTACATTACTTAAATA
544856 AAAATTAGCT
Statistics
Matches: 69, Mismatches: 2, Indels: 15
0.80 0.02 0.17
Matches are distributed among these distances:
36 3 0.04
37 3 0.04
38 3 0.04
39 26 0.38
40 8 0.12
41 1 0.01
42 3 0.04
43 16 0.23
44 1 0.01
45 5 0.07
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (39 bp):
TTACATTACTTAAAATATATATTACATTACTTAAATATA
Found at i:545183 original size:9 final size:9
Alignment explanation
Indices: 545169--545374 Score: 86
Period size: 9 Copynumber: 23.3 Consensus size: 9
545159 ATTAATATTA
545169 TACATAACT
1 TACATAACT
545178 TACATAA--
1 TACATAACT
545185 TACATAA--
1 TACATAACT
545192 TACATAACT
1 TACATAACT
*
545201 TACATAAAT
1 TACATAACT
545210 TACATAA--
1 TACATAACT
545217 TACATAACT
1 TACATAACT
545226 TACATAA--
1 TACATAACT
*
545233 TACACAACT
1 TACATAACT
*
545242 TA-ATTAATATT
1 TACA-T-A-ACT
545253 ATACATAACT
1 -TACATAACT
*
545263 TA-ATTACAAGTT
1 TACA-T--AA-CT
545275 ATACATAACT
1 -TACATAACT
545285 TACATAA--
1 TACATAACT
*
545292 TACACAACT
1 TACATAACT
545301 TACATAA--
1 TACATAACT
*
545308 TACACAACT
1 TACATAACT
*
545317 TA-ATTAATATT
1 TACA-T-A-ACT
*
545328 ATACATAACA
1 -TACATAACT
*
545338 TGCATAA--
1 TACATAACT
545345 TACATAACT
1 TACATAACT
545354 TACATAACT
1 TACATAACT
*
545363 TACATAATT
1 TACATAACT
545372 TAC
1 TAC
545375 CTAATACATA
Statistics
Matches: 152, Mismatches: 17, Indels: 56
0.68 0.08 0.25
Matches are distributed among these distances:
7 45 0.30
8 3 0.02
9 75 0.49
10 6 0.04
11 10 0.07
12 7 0.05
13 5 0.03
14 1 0.01
ACGTcount: A:0.49, C:0.17, G:0.01, T:0.33
Consensus pattern (9 bp):
TACATAACT
Found at i:545189 original size:16 final size:16
Alignment explanation
Indices: 545168--545385 Score: 150
Period size: 16 Copynumber: 13.5 Consensus size: 16
545158 AATTAATATT
545168 ATACATAACTTACATA
1 ATACATAACTTACATA
545184 ATACATAA--TACATA
1 ATACATAACTTACATA
*
545198 ACTTACATAAATTACATA
1 A--TACATAACTTACATA
545216 ATACATAACTTACATA
1 ATACATAACTTACATA
*
545232 ATACACAACTTA-AT-
1 ATACATAACTTACATA
*
545246 -TA-AT-ATTATACAT-
1 ATACATAACT-TACATA
* *
545259 A-ACTTAA-TTACAAGTT
1 ATACATAACTTAC-A-TA
545275 ATACATAACTTACATA
1 ATACATAACTTACATA
*
545291 ATACACAACTTACATA
1 ATACATAACTTACATA
* *
545307 ATACACAACTTAATTAATA
1 ATACATAACTT-A--CATA
* *
545326 TTATACATAACATGCATA
1 --ATACATAACTTACATA
545344 ATACATAACTTACATA
1 ATACATAACTTACATA
* *
545360 ACTTACATAATTTACCTA
1 A--TACATAACTTACATA
545378 ATACATAA
1 ATACATAA
545386 ATATATATCA
Statistics
Matches: 164, Mismatches: 17, Indels: 42
0.74 0.08 0.19
Matches are distributed among these distances:
11 2 0.01
12 3 0.02
13 8 0.05
14 10 0.06
15 4 0.02
16 90 0.55
17 7 0.04
18 28 0.17
19 3 0.02
21 9 0.05
ACGTcount: A:0.49, C:0.17, G:0.01, T:0.33
Consensus pattern (16 bp):
ATACATAACTTACATA
Found at i:545219 original size:25 final size:24
Alignment explanation
Indices: 545130--545236 Score: 118
Period size: 23 Copynumber: 4.7 Consensus size: 24
545120 TAATAAATAA
* * *
545130 AACTTGCAT-AATTCATAATACAC
1 AACTTACATAAATACATAATACAT
* *
545153 AACTTA-ATTAAT--ATTATACAT
1 AACTTACATAAATACATAATACAT
545174 AACTTACAT-AATACATAATACAT
1 AACTTACATAAATACATAATACAT
545197 AACTTACATAAATTACATAATACAT
1 AACTTACATAAA-TACATAATACAT
545222 AACTTACAT-AATACA
1 AACTTACATAAATACA
545237 CAACTTAATT
Statistics
Matches: 74, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
21 16 0.22
22 4 0.05
23 29 0.39
24 4 0.05
25 21 0.28
ACGTcount: A:0.50, C:0.17, G:0.01, T:0.33
Consensus pattern (24 bp):
AACTTACATAAATACATAATACAT
Found at i:545279 original size:22 final size:21
Alignment explanation
Indices: 545147--545286 Score: 98
Period size: 21 Copynumber: 6.6 Consensus size: 21
545137 ATAATTCATA
*
545147 ATACACAACTTAATTAATATT
1 ATACATAACTTAATTAATATT
*
545168 ATACATAACTTACA-TAATACATA
1 ATACATAACTTA-ATTAAT--ATT
545191 ATACATAACTTACA-TAA-A-T
1 ATACATAACTTA-ATTAATATT
*
545210 -TACATAATACATAACTTACATA--
1 ATACAT-A-ACTTAA-TTA-ATATT
*
545232 ATACACAACTTAATTAATATT
1 ATACATAACTTAATTAATATT
545253 ATACATAACTTAATTACA-AGTT
1 ATACATAACTTAATTA-ATA-TT
545275 ATACATAACTTA
1 ATACATAACTTA
545287 CATAATACAC
Statistics
Matches: 98, Mismatches: 7, Indels: 27
0.74 0.05 0.20
Matches are distributed among these distances:
18 5 0.05
19 5 0.05
20 8 0.08
21 38 0.39
22 18 0.18
23 24 0.24
ACGTcount: A:0.49, C:0.16, G:0.01, T:0.34
Consensus pattern (21 bp):
ATACATAACTTAATTAATATT
Found at i:550515 original size:21 final size:22
Alignment explanation
Indices: 550491--550539 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
550481 CTACAACTTA
550491 AAGCAGAAG-CGGCAGCGAGGG
1 AAGCAGAAGACGGCAGCGAGGG
* *
550512 AAGCA-ACGACTGCAGCGAGGG
1 AAGCAGAAGACGGCAGCGAGGG
550533 AAGCAGA
1 AAGCAGA
550540 GGCTACAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 21 0.88
22 1 0.04
ACGTcount: A:0.37, C:0.20, G:0.41, T:0.02
Consensus pattern (22 bp):
AAGCAGAAGACGGCAGCGAGGG
Found at i:550927 original size:42 final size:42
Alignment explanation
Indices: 550880--551077 Score: 299
Period size: 42 Copynumber: 4.7 Consensus size: 42
550870 TTTTGTATAA
550880 AAATGCCGCTAAAGACCATGTTCTTTAGCGGCACTTAGAAAG
1 AAATGCCGCTAAAGACCATGTTCTTTAGCGGCACTTAGAAAG
* *
550922 AAATGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGAAA-
1 AAATGCCGCTAAAGACCATGTTCTTTAGCGGCACTTAGAAAG
*
550963 AAATGCCGTTAAAGACCATGTTCTTTAGCGGCACTTAGAAAG
1 AAATGCCGCTAAAGACCATGTTCTTTAGCGGCACTTAGAAAG
* ** * * *
551005 AAACGCTACTAAAGACCATGTTCTTTAGCTGCGCTTAGAAAA
1 AAATGCCGCTAAAGACCATGTTCTTTAGCGGCACTTAGAAAG
*
551047 AAACGCCGCTAAAGACCATGTTCTTTAGCGG
1 AAATGCCGCTAAAGACCATGTTCTTTAGCGG
551078 AGTTTTTTTC
Statistics
Matches: 140, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
41 38 0.27
42 102 0.73
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (42 bp):
AAATGCCGCTAAAGACCATGTTCTTTAGCGGCACTTAGAAAG
Found at i:551017 original size:83 final size:84
Alignment explanation
Indices: 550878--551077 Score: 348
Period size: 83 Copynumber: 2.4 Consensus size: 84
550868 ATTTTTGTAT
*
550878 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCACTTAGAAAGAAATGCCACTAAAGACCATGT
1 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCACTTAGAAAGAAACGCCACTAAAGACCATGT
550943 TCTTTAGCGGCGCTTAG-A
66 TCTTTAGCGGCGCTTAGAA
* *
550961 AAAAATGCCGTTAAAGACCATGTTCTTTAGCGGCACTTAGAAAGAAACGCTACTAAAGACCATGT
1 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCACTTAGAAAGAAACGCCACTAAAGACCATGT
*
551026 TCTTTAGCTGCGCTTAGAA
66 TCTTTAGCGGCGCTTAGAA
*
551045 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGG
1 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGG
551078 AGTTTTTTTC
Statistics
Matches: 110, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
83 78 0.71
84 32 0.29
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (84 bp):
AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCACTTAGAAAGAAACGCCACTAAAGACCATGT
TCTTTAGCGGCGCTTAGAA
Found at i:557772 original size:111 final size:110
Alignment explanation
Indices: 557522--557928 Score: 525
Period size: 110 Copynumber: 3.7 Consensus size: 110
557512 GAAATTCAAG
* * * * *
557522 AGGATATTTGGCTATTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGGTACG-TTCCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGAAACCCAGCACCTTAGGGCACGTTTTCTC
* * ***
557584 AAATTTTCAAACGCAAAACATTGCCTTATTTTGAAAAAAAAAATTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTG---AAAATTTTTAAA
* * * *
557632 AGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGTACCTTAGGGCATGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGAAACCCAGCACCTTAGGGCACGTTTTCTC
*
557697 GAATTTCCCAAACGCAAAGCATTGCCTTATTTTGAAAATTTTTAAA
66 GAATTT-CCAAACGCAAAACATTGCCTTATTTTGAAAATTTTTAAA
* * *
557743 AGGATATTAAGCCATTTTGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGAAACCCAGCACCTTAGGGCACGTTTTCTC
557808 GAATTTCCAAACGCAAAACATTGCCTTATTTT-AAAATTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATTTTTAAA
* * * * * *
557852 AGGATATTTAGCTATTTGGTTGAACGAGAAGAGATCGAAACCCAACACATTAGGACACATTTTCT
1 AGGATATTTAGCCATTTGGTTGAACGAGAA-AAATCGAAACCCAGCACCTTAGGGCACGTTTTCT
557917 CGAATTTCCAAA
65 CGAATTTCCAAA
557929 TGGTAAATAT
Statistics
Matches: 262, Mismatches: 30, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
109 39 0.15
110 89 0.34
111 75 0.29
112 24 0.09
113 10 0.04
114 25 0.10
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (110 bp):
AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGAAACCCAGCACCTTAGGGCACGTTTTCTC
GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATTTTTAAA
Found at i:558283 original size:16 final size:16
Alignment explanation
Indices: 558264--558300 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
558254 ATACTTTTTT
*
558264 ATATATATATATGTAA
1 ATATATATATATATAA
*
558280 ATATATGTATATATAA
1 ATATATATATATATAA
558296 ATATA
1 ATATA
558301 AAAAGAACAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (16 bp):
ATATATATATATATAA
Found at i:559221 original size:88 final size:88
Alignment explanation
Indices: 558984--560100 Score: 1654
Period size: 88 Copynumber: 12.7 Consensus size: 88
558974 TCAGGGGGTG
*
558984 AGGTTTGTATCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAG
1 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAG
* *
559049 CTCCACTACGATCGAGAGAGGCA
66 CTCCACTACAACCGAGAGAGGCA
* *
559072 ATGTTTGTG--TT----CTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTGTTGTCTTCAACCAG
1 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAG
559131 CTCCACTACAACCGAGAGAGGCA
66 CTCCACTACAACCGAGAGAGGCA
* * *
559154 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTATTATCTTCAACCAG
1 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAG
*
559219 CTCCACCACAACCGAGAGAGGCA
66 CTCCACTACAACCGAGAGAGGCA
* * * * *
559242 ATGTTTGTGTCTTCGATCTGCTACGCTGTCAATGCAGGAAGGCAAGATCTATTATCTTCAACCAG
1 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAG
559307 CTCCACTACAACCGAGAGAGGCA
66 CTCCACTACAACCGAGAGAGGCA
** * *
559330 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATATAGGAAGGCAAGATCTATTATCTTCAACCAG
1 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAG
* *
559395 CTCTACCACAACCGAGAGAGGCA
66 CTCCACTACAACCGAGAGAGGCA
** * * *
559418 AGGTTTGTGTCTTTAATCTGCTTCGCTATCAATGCAGGAAGACAAGATCTGTTGTCTTCAACCAG
1 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAG
559483 CTCCACTACAACCGAGAGAGGCA
66 CTCCACTACAACCGAGAGAGGCA
* *
559506 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTATTGTCTTCAACCAG
1 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAG
*
559571 CTCCACCACAACCGAGAGAGGCA
66 CTCCACTACAACCGAGAGAGGCA
* **
559594 AGGTTTGTGTCTTTGACCTGCTTCGCTGTCAATNNNNNNNNNAGGAAGGCAAGATCTGTTGTCTT
1 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAAT-------GCAGGAAGGCAAGATCTGTTGTCTT
559659 CAACCAGCTCCACTACAACCGAGAGAGGCA
59 CAACCAGCTCCACTACAACCGAGAGAGGCA
* * * *
559689 AGGTTTGTATATTCGACCTGCTTCGCTGTCAATGCAGGAAAGAAAGATCTGTTGTCTTCAACCAG
1 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAG
559754 CTCCACTACAACCGAGAGAGGCA
66 CTCCACTACAACCGAGAGAGGCA
* *
559777 AGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAAGAAGGCAAGATCTGTTGTCTTCAACCAG
1 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAG
559842 CTCCACTACAACCGAGAGAGGCA
66 CTCCACTACAACCGAGAGAGGCA
* * * *
559865 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGGAAGGAAAGATCTATTGTCTTTAACCAG
1 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAG
* * *
559930 ATCCACTACAACGGAGGGAGGCA
66 CTCCACTACAACCGAGAGAGGCA
* * *
559953 AGGCTTGTGTCTTCGATCC-GCTTCGCTGTCGATTCAGGAAGGCAAGATCTGTTGTCTTCAACCA
1 AGGTTTGTGTCTTCGA-CCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCA
* *
560017 GCTCCACTACAACGGAGGGAGGCA
65 GCTCCACTACAACCGAGAGAGGCA
* *
560041 AGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGTTGTCTTCA
1 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCA
560101 TTAATCTATT
Statistics
Matches: 934, Mismatches: 80, Indels: 30
0.89 0.08 0.03
Matches are distributed among these distances:
82 76 0.08
84 2 0.00
86 2 0.00
87 1 0.00
88 770 0.82
89 2 0.00
95 81 0.09
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.26
Consensus pattern (88 bp):
AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAG
CTCCACTACAACCGAGAGAGGCA
Found at i:561337 original size:7 final size:7
Alignment explanation
Indices: 561325--561374 Score: 86
Period size: 7 Copynumber: 7.4 Consensus size: 7
561315 TGGCCTCTCC
561325 TTTTTCT
1 TTTTTCT
561332 TTTTTCT
1 TTTTTCT
561339 TTTTTCT
1 TTTTTCT
561346 TTTTTC-
1 TTTTTCT
561352 TTTTTCT
1 TTTTTCT
561359 TTTTTCT
1 TTTTTCT
561366 TTTTT-T
1 TTTTTCT
561372 TTT
1 TTT
561375 GAAATATTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
6 10 0.24
7 32 0.76
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:561342 original size:13 final size:13
Alignment explanation
Indices: 561324--561374 Score: 86
Period size: 13 Copynumber: 3.9 Consensus size: 13
561314 TTGGCCTCTC
561324 CTTTTTCTTTTTT
1 CTTTTTCTTTTTT
561337 CTTTTTTCTTTTTT
1 C-TTTTTCTTTTTT
561351 CTTTTTCTTTTTT
1 CTTTTTCTTTTTT
561364 CTTTTT-TTTTT
1 CTTTTTCTTTTT
561375 GAAATATTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
12 5 0.14
13 19 0.51
14 13 0.35
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
CTTTTTCTTTTTT
Found at i:561347 original size:20 final size:20
Alignment explanation
Indices: 561325--561374 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
561315 TGGCCTCTCC
561325 TTTTTCTTTTTTCTTTTTTCT
1 TTTTTC-TTTTTCTTTTTTCT
561346 TTTTTCTTTTTCTTTTTTCT
1 TTTTTCTTTTTCTTTTTTCT
561366 TTTTT-TTTT
1 TTTTTCTTTT
561375 GAAATATTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 4 0.14
20 19 0.66
21 6 0.21
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (20 bp):
TTTTTCTTTTTCTTTTTTCT
Found at i:564389 original size:110 final size:109
Alignment explanation
Indices: 564196--564598 Score: 538
Period size: 110 Copynumber: 3.7 Consensus size: 109
564186 GTTAAACGAG
* * * *
564196 AAATCGAAACCCAGCACCTTAGGGTACG-TTCCTCAAATTTCCAAATGCAAAACATTGCCTTATT
1 AAATCGAAACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
** *
564260 TTGAATTTTTTTTAAAAGGATATTTAGCCATTTGATTGAATGAGAA
66 TTGAA--AATTTTAAAAGGATATTTAGCCATTTGGTTGAATGAGAA
* *
564306 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCCAAACGCAAAACATTGCCTTAT
1 AAATCGAAACCCAGCACCTTAGGGCACGTTTTCTCGAATTT-CCAAACGCAAAACATTGCCTTAT
*
564371 TTTGAAAATTTTAAAAGGATATTAAGCCATTTGGTTGAATGAGAA
65 TTTGAAAATTTTAAAAGGATATTTAGCCATTTGGTTGAATGAGAA
* *
564416 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCCAAACGCAAAACATTGCCTTAT
1 AAATCGAAACCCAGCACCTTAGGGCACGTTTTCTCGAATTT-CCAAACGCAAAACATTGCCTTAT
* * *
564481 TTTGAAATTTTTAAAAGGATATTTAGCTATTTGGTTGAACGAGAA
65 TTTGAAAATTTTAAAAGGATATTTAGCCATTTGGTTGAATGAGAA
* * * * * * * *
564526 GAGATCGAAACCCAACACATTAGGACACGTTTTCTCGAATTTCCAAATGCTAAATATTGCCTCAT
1 -AAATCGAAACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTAT
*
564591 TTAGAAAA
65 TTTGAAAA
564599 AAATTCCTCT
Statistics
Matches: 264, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
110 191 0.72
111 45 0.17
112 28 0.11
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.31
Consensus pattern (109 bp):
AAATCGAAACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
TTGAAAATTTTAAAAGGATATTTAGCCATTTGGTTGAATGAGAA
Found at i:564685 original size:18 final size:19
Alignment explanation
Indices: 564662--564697 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
564652 TGATAATATG
*
564662 AATG-AAAATAATATAAAA
1 AATGAAAAATAAGATAAAA
564680 AATGAAAAATAAGATAAA
1 AATGAAAAATAAGATAAA
564698 TCAATCATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (19 bp):
AATGAAAAATAAGATAAAA
Found at i:564901 original size:28 final size:28
Alignment explanation
Indices: 564869--564929 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
564859 ATATGTATGT
*
564869 ATATACATA-AAATTATGAAAATATGAAA
1 ATATACATATAAATTAT-AAAATATAAAA
* * *
564897 ATATATATATGAATTATAAGATATAAAA
1 ATATACATATAAATTATAAAATATAAAA
564925 ATATA
1 ATATA
564930 AGTACTTACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 22 0.79
29 6 0.21
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (28 bp):
ATATACATATAAATTATAAAATATAAAA
Found at i:570759 original size:17 final size:17
Alignment explanation
Indices: 570737--570770 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
570727 ATGATCCATA
570737 GAAATTATATATATTGT
1 GAAATTATATATATTGT
570754 GAAATTATATATATTGT
1 GAAATTATATATATTGT
570771 CTGATTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (17 bp):
GAAATTATATATATTGT
Found at i:571445 original size:3 final size:3
Alignment explanation
Indices: 571437--571465 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
571427 GTCAAGCATA
571437 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
571466 TTGTTACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:577138 original size:22 final size:20
Alignment explanation
Indices: 577095--577133 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
577085 TAATTTAAAA
577095 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
577115 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
577134 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:577256 original size:20 final size:20
Alignment explanation
Indices: 577231--577270 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
577221 AAATATTTTC
*
577231 AGTAAATTATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
*
577251 AGTAAATCATTTTTCAGAAA
1 AGTAAATCATTTTCCAGAAA
577271 TCATTTTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (20 bp):
AGTAAATCATTTTCCAGAAA
Found at i:588747 original size:81 final size:80
Alignment explanation
Indices: 588649--588807 Score: 264
Period size: 81 Copynumber: 2.0 Consensus size: 80
588639 GTCAAAGGAT
* * *
588649 TTGTTATGGCCAAGGAAATTTTGCTAGTCAAAATAGGCATATTGATGGTCAAAATTGGTGTGCTG
1 TTGTTATGGCCAAGGAAATTTTGCCAGTCAAAATAGGCATAGTCATGGTCAAAATTGGTGTGCTG
588714 GCTTAAACAATGAAA
66 GCTTAAACAATGAAA
* *
588729 TTGTTGATGGCCAAGGAAATTTTTCCAGTCAAAATAGGCATGGTCATGGTCAAAATTGGTGTGCT
1 TTGTT-ATGGCCAAGGAAATTTTGCCAGTCAAAATAGGCATAGTCATGGTCAAAATTGGTGTGCT
588794 GGCTTAAACAATGA
65 GGCTTAAACAATGA
588808 TCAATTGGCG
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
80 5 0.07
81 68 0.93
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.31
Consensus pattern (80 bp):
TTGTTATGGCCAAGGAAATTTTGCCAGTCAAAATAGGCATAGTCATGGTCAAAATTGGTGTGCTG
GCTTAAACAATGAAA
Found at i:625672 original size:4 final size:4
Alignment explanation
Indices: 625663--625721 Score: 52
Period size: 4 Copynumber: 14.5 Consensus size: 4
625653 CAACCTAATT
*
625663 TTTA TTTA TTTA TTTA -TTC TTTA CTTTA TTTA -TTA CTTTA TTTTA TTT-
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA -TTTA -TTTA TTTA
625711 TATTA TTTA TT
1 T-TTA TTTA TT
625722 ACTTATTTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
3 6 0.13
4 28 0.61
5 12 0.26
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:625680 original size:12 final size:13
Alignment explanation
Indices: 625663--625729 Score: 58
Period size: 12 Copynumber: 5.5 Consensus size: 13
625653 CAACCTAATT
625663 TTTATTTATTTA-
1 TTTATTTATTTAC
*
625675 TTTA-TTCTTTAC
1 TTTATTTATTTAC
625687 TTTATTTA-TTAC
1 TTTATTTATTTAC
625699 TTTATTTTATTT--
1 TTTA-TTTATTTAC
625711 TATTATTTA-TTAC
1 T-TTATTTATTTAC
625724 -TTATTT
1 TTTATTT
625730 GGATATTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
11 14 0.30
12 21 0.46
13 9 0.20
14 2 0.04
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTTATTTAC
Found at i:625692 original size:16 final size:16
Alignment explanation
Indices: 625667--625721 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 16
625657 CTAATTTTTA
625667 TTTATTTATTTATT-C
1 TTTATTTATTTATTAC
625682 TTTACTTTATTTATTAC
1 TTTA-TTTATTTATTAC
625699 TTTATTTTATTTTATTA-
1 TTTA-TTTA-TTTATTAC
625716 TTTATT
1 TTTATT
625722 ACTTATTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
15 4 0.11
16 12 0.33
17 13 0.36
18 7 0.19
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTATTTATTTATTAC
Found at i:636582 original size:18 final size:19
Alignment explanation
Indices: 636559--636594 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
636549 GAATTATTTT
636559 AGTTTACTTTT-TTTATTG
1 AGTTTACTTTTGTTTATTG
636577 AGTTTACTTTTGTTTATT
1 AGTTTACTTTTGTTTATT
636595 AATTTTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.17, C:0.06, G:0.11, T:0.67
Consensus pattern (19 bp):
AGTTTACTTTTGTTTATTG
Found at i:636601 original size:19 final size:18
Alignment explanation
Indices: 636559--636601 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
636549 GAATTATTTT
*
636559 AGTTTACTTTTTTTATTG
1 AGTTTACTTTTTTTATTA
636577 AGTTTACTTTTGTTTATTA
1 AGTTTACTTTT-TTTATTA
*
636596 ATTTTA
1 AGTTTA
636602 ATCAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.21, C:0.05, G:0.09, T:0.65
Consensus pattern (18 bp):
AGTTTACTTTTTTTATTA
Found at i:638914 original size:4 final size:4
Alignment explanation
Indices: 638907--638935 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
638897 TGAGATATTA
638907 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
638936 TTTGAAGGTG
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:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:641936 original size:6 final size:6
Alignment explanation
Indices: 641925--641957 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
641915 CACGTTACCT
641925 TTAGGA TTAGGA TTAGGA TTAGGA TTAGGA TTA
1 TTAGGA TTAGGA TTAGGA TTAGGA TTAGGA TTA
641958 TATATTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.36
Consensus pattern (6 bp):
TTAGGA
Found at i:646510 original size:21 final size:21
Alignment explanation
Indices: 646484--646526 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
646474 TGATTTGATT
646484 TTTTTTCCGAATCGAGTCGAG
1 TTTTTTCCGAATCGAGTCGAG
* *
646505 TTTTTTCCGAATCTAGTTGAG
1 TTTTTTCCGAATCGAGTCGAG
646526 T
1 T
646527 GAAATGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (21 bp):
TTTTTTCCGAATCGAGTCGAG
Found at i:646858 original size:9 final size:9
Alignment explanation
Indices: 646844--646873 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
646834 AAAATATAAA
646844 TTTTTTAAT
1 TTTTTTAAT
646853 TTTTTTAAT
1 TTTTTTAAT
646862 TTTTTTAAT
1 TTTTTTAAT
646871 TTT
1 TTT
646874 AAAATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:649609 original size:41 final size:39
Alignment explanation
Indices: 649546--649718 Score: 150
Period size: 41 Copynumber: 4.2 Consensus size: 39
649536 GAGGGCTTTC
* * *
649546 GTGGCGTTTTTAAACAAACGCCGCTAATGTTATGGTTTTTA
1 GTGGCGTTTTT-TATAAGCGCCGCTAATGTTA-GGTTTTTA
* * *
649587 GTGGCGTTTTTTCCTAAGCGCCGCTAATTTTAGGGCTTTTA
1 GTGGCGTTTTTT-ATAAGCGCCGCTAATGTTA-GGTTTTTA
* * *
649628 GCGGCGTTTTTGATAATGCGCCGCTAAAGTTGAGGTTTTTA
1 GTGGCGTTTTTTATAA-GCGCCGCTAATGTT-AGGTTTTTA
* *
649669 GTGGCGTTTGTTTATAAAGCGCCACTAATGTT-GGAGTTTTA
1 GTGGCGTTT-TTTAT-AAGCGCCGCTAATGTTAGG-TTTTTA
*
649710 GCGGCGTTT
1 GTGGCGTTT
649719 CGATGGAAAC
Statistics
Matches: 107, Mismatches: 19, Indels: 12
0.78 0.14 0.09
Matches are distributed among these distances:
40 5 0.05
41 83 0.78
42 17 0.16
43 2 0.02
ACGTcount: A:0.19, C:0.16, G:0.27, T:0.39
Consensus pattern (39 bp):
GTGGCGTTTTTTATAAGCGCCGCTAATGTTAGGTTTTTA
Found at i:649653 original size:82 final size:82
Alignment explanation
Indices: 649564--649718 Score: 210
Period size: 82 Copynumber: 1.9 Consensus size: 82
649554 TTTAAACAAA
* * * *
649564 CGCCGCTAATGTT-ATGGTTTTTAGTGGCGTTT-TTTCCT-AAGCGCCGCTAATTTTAGG-GCTT
1 CGCCGCTAAAGTTGA-GGTTTTTAGTGGCGTTTGTTT-ATAAAGCGCCACTAATGTT-GGAG-TT
649625 TTAGCGGCGTTTTTGATAATG
62 TTAGCGGCGTTTTTGATAATG
649646 CGCCGCTAAAGTTGAGGTTTTTAGTGGCGTTTGTTTATAAAGCGCCACTAATGTTGGAGTTTTAG
1 CGCCGCTAAAGTTGAGGTTTTTAGTGGCGTTTGTTTATAAAGCGCCACTAATGTTGGAGTTTTAG
649711 CGGCGTTT
66 CGGCGTTT
649719 CGATGGAAAC
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
82 46 0.71
83 19 0.29
ACGTcount: A:0.17, C:0.16, G:0.27, T:0.39
Consensus pattern (82 bp):
CGCCGCTAAAGTTGAGGTTTTTAGTGGCGTTTGTTTATAAAGCGCCACTAATGTTGGAGTTTTAG
CGGCGTTTTTGATAATG
Found at i:649732 original size:82 final size:81
Alignment explanation
Indices: 649561--649733 Score: 194
Period size: 82 Copynumber: 2.1 Consensus size: 81
649551 GTTTTTAAAC
* * * *
649561 AAACGCCGCTAATGTTATGGTTTTTAGTGGCGTTTTTTCCTAAGCGCCGCTAATTTTAGGGCTTT
1 AAACGCCGCTAAAGTTATGGTTTTTAGTGGCGTTTTTTCATAAGCGCCACTAATGTTAGGGCTTT
*
649626 TAGCGGCGTTTTTGAT
66 TAGCGGCGTTTTCGAT
*
649642 AATGCGCCGCTAAAGTTGA-GGTTTTTAGTGGCGTTTGTTT-ATAAAGCGCCACTAATGTT-GGA
1 AA-ACGCCGCTAAAGTT-ATGGTTTTTAGTGGCGTTT-TTTCAT-AAGCGCCACTAATGTTAGG-
649704 G-TTTTAGCGGCG-TTTCGAT
61 GCTTTTAGCGGCGTTTTCGAT
649723 GGAAACGCCGC
1 --AAACGCCGC
649734 AAAATACATT
Statistics
Matches: 78, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
81 8 0.10
82 49 0.63
83 21 0.27
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.36
Consensus pattern (81 bp):
AAACGCCGCTAAAGTTATGGTTTTTAGTGGCGTTTTTTCATAAGCGCCACTAATGTTAGGGCTTT
TAGCGGCGTTTTCGAT
Found at i:650361 original size:7 final size:7
Alignment explanation
Indices: 650349--650423 Score: 51
Period size: 7 Copynumber: 9.9 Consensus size: 7
650339 GGTTAGGAAT
650349 TTAGGGG
1 TTAGGGG
650356 TTAGGGG
1 TTAGGGG
**
650363 TTAGTGAT
1 TTAG-GGG
*
650371 TTGGGGGG
1 TT-AGGGG
650379 TTAGGGAG
1 TTAGGG-G
*
650387 ATTTAAGGG
1 --TTAGGGG
650396 TTAGGGG
1 TTAGGGG
*
650403 TTAGGGAT
1 TTAGGG-G
650411 TTAGGGG
1 TTAGGGG
650418 TTAGGG
1 TTAGGG
650424 TGTCAAGGGT
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
7 32 0.62
8 13 0.25
9 2 0.04
10 5 0.10
ACGTcount: A:0.19, C:0.00, G:0.49, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:650366 original size:22 final size:21
Alignment explanation
Indices: 650327--650423 Score: 96
Period size: 22 Copynumber: 4.7 Consensus size: 21
650317 GGGATTAAGG
*
650327 TTTAGGGG-TATGGGTTAGGAA
1 TTTAGGGGTTAGGGGTTAGG-A
650348 TTTAGGGGTTAGGGGTTAGTGA
1 TTTAGGGGTTAGGGGTTAG-GA
*
650370 TTTGGGGGGTTA-GGG--A-GA
1 TTT-AGGGGTTAGGGGTTAGGA
*
650388 TTTAAGGGTTAGGGGTTAGGGA
1 TTTAGGGGTTAGGGGTTA-GGA
650410 TTTAGGGGTTAGGG
1 TTTAGGGGTTAGGG
650424 TGTCAAGGGT
Statistics
Matches: 63, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
17 6 0.10
18 8 0.13
20 2 0.03
21 8 0.13
22 31 0.49
23 8 0.13
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (21 bp):
TTTAGGGGTTAGGGGTTAGGA
Found at i:650397 original size:40 final size:38
Alignment explanation
Indices: 650338--650423 Score: 120
Period size: 40 Copynumber: 2.2 Consensus size: 38
650328 TTAGGGGTAT
* * *
650338 GGGTTA-GGAATTTAGGGGTTAGGGGTTAGTGATTTGGG
1 GGGTTAGGGAATTTAAGGGTTAGGGGTTAGGGATTT-AG
650376 GGGTTAGGGAGATTTAAGGGTTAGGGGTTAGGGATTTAG
1 GGGTTAGGGA-ATTTAAGGGTTAGGGGTTAGGGATTTAG
650415 GGGTTAGGG
1 GGGTTAGGG
650424 TGTCAAGGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 6 0.14
39 13 0.30
40 24 0.56
ACGTcount: A:0.20, C:0.00, G:0.49, T:0.31
Consensus pattern (38 bp):
GGGTTAGGGAATTTAAGGGTTAGGGGTTAGGGATTTAG
Found at i:651879 original size:24 final size:22
Alignment explanation
Indices: 651850--651895 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
651840 ATCAGTTTTC
651850 TCCCCAAAAATTCCCCCCAAATTT
1 TCCCCAAAAA-T-CCCCCAAATTT
651874 TCCCCAAAAATCCCCCAAATTT
1 TCCCCAAAAATCCCCCAAATTT
651896 AGAACCCTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 11 0.50
23 1 0.05
24 10 0.45
ACGTcount: A:0.35, C:0.41, G:0.00, T:0.24
Consensus pattern (22 bp):
TCCCCAAAAATCCCCCAAATTT
Found at i:652918 original size:31 final size:32
Alignment explanation
Indices: 652883--652942 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
652873 TTTTAGCTAG
* *
652883 ATTTGGTCATTAACCTTTT-AAAAAGAGTCGA
1 ATTTGATCATCAACCTTTTAAAAAAGAGTCGA
*
652914 ATTTGATTATCAACCTTTTAAAAAAGAGT
1 ATTTGATCATCAACCTTTTAAAAAAGAGT
652943 TGAAGTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (32 bp):
ATTTGATCATCAACCTTTTAAAAAAGAGTCGA
Done.