Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold173
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: 2040036
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 5 of 16
Found at i:573438 original size:28 final size:28
Alignment explanation
Indices: 573408--573466 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
573398 AAAATATTAT
* *
573408 TTTTTTA-ATATATTTAATAATTAAA-A
1 TTTTTTATATATAATAAATAATTAAATA
*
573434 TTTTTTATATCTAATAAATAATTAAATA
1 TTTTTTATATATAATAAATAATTAAATA
573462 TTTTT
1 TTTTT
573467 AATTTACTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 7 0.25
27 15 0.54
28 6 0.21
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTTTTATATATAATAAATAATTAAATA
Found at i:573526 original size:13 final size:13
Alignment explanation
Indices: 573504--573535 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
573494 TCTATATCAA
573504 TAAA-AATTGAAT
1 TAAATAATTGAAT
573516 TAAATAATTGAAT
1 TAAATAATTGAAT
573529 TAAATAA
1 TAAATAA
573536 ATATAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (13 bp):
TAAATAATTGAAT
Found at i:574236 original size:18 final size:16
Alignment explanation
Indices: 574193--574253 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
574183 TTATCATAAC
*
574193 AATAAAAT-AAAATAA
1 AATAAAATAAAAAAAA
* *
574208 ATTAAATTAAACGAAAAA
1 AATAAAATAAA--AAAAA
574226 AATAAAATAAAAAAAA
1 AATAAAATAAAAAAAA
*
574242 AAGAAAA-AAAAA
1 AATAAAATAAAAA
574254 GAAAGAGGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
15 11 0.30
16 13 0.35
18 13 0.35
ACGTcount: A:0.80, C:0.02, G:0.03, T:0.15
Consensus pattern (16 bp):
AATAAAATAAAAAAAA
Found at i:574433 original size:19 final size:19
Alignment explanation
Indices: 574409--574480 Score: 57
Period size: 19 Copynumber: 4.1 Consensus size: 19
574399 ATTATGTTTA
574409 AAATATTATATATTTATAT
1 AAATATTATATATTTATAT
*
574428 AAATATTAT-TATGTATA-
1 AAATATTATATATTTATAT
* *
574445 ATA-ATT-TA-AGTTATAT
1 AAATATTATATATTTATAT
*
574461 AAATTTTGATATA-TTATAT
1 AAATATT-ATATATTTATAT
574480 A
1 A
574481 TTCATTTTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
15 6 0.15
16 5 0.12
17 4 0.10
18 7 0.17
19 18 0.44
20 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (19 bp):
AAATATTATATATTTATAT
Found at i:575376 original size:132 final size:129
Alignment explanation
Indices: 575240--575503 Score: 332
Period size: 132 Copynumber: 2.0 Consensus size: 129
575230 TTTTACAATC
* * * * * *
575240 TTATAAATTATGTGGCATAATTTTAAAAAATTAGTTAGACTTAAAATCTTAATCTAAAAAATAAT
1 TTATAAATCATGTGGCATAATTTTAAAAAATTAGTCAAAATTAAAATATTAATCT-AAAAAGAAT
* * ***
575305 CTATAATTCTAGTTTAAAAAATTA-TTAAAAACATAAATATTCCATACTATAAAAGAAAAAGATA
65 ATAT-ATTATA-ACAAAAAAATTATTTAAAAACATAAATATT-CATACTATAAAAGAAAAAGATA
575369 AGA
127 AGA
* * *
575372 TTATAAATCATGTGGCATATTTTTAAAAAGTTAGTCAAAATTAAAATATTAATGTAAAAAGAATA
1 TTATAAATCATGTGGCATAATTTTAAAAAATTAGTCAAAATTAAAATATTAATCTAAAAAGAATA
* * *
575437 TCTATTATAACAAAAAAATTATTTAAAAACATAAATATTTATATTATAAAAGAAAAAGATAAGA
66 TATATTATAACAAAAAAATTATTTAAAAACATAAATATTCATACTATAAAAGAAAAAGATAAGA
575501 TTA
1 TTA
575504 CACACATTTA
Statistics
Matches: 114, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
129 35 0.31
130 22 0.19
131 10 0.09
132 47 0.41
ACGTcount: A:0.53, C:0.06, G:0.07, T:0.34
Consensus pattern (129 bp):
TTATAAATCATGTGGCATAATTTTAAAAAATTAGTCAAAATTAAAATATTAATCTAAAAAGAATA
TATATTATAACAAAAAAATTATTTAAAAACATAAATATTCATACTATAAAAGAAAAAGATAAGA
Found at i:576443 original size:3 final size:3
Alignment explanation
Indices: 576435--576473 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
576425 GTACTCATAA
*
576435 ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
576474 TCCCTTTTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:577000 original size:2 final size:2
Alignment explanation
Indices: 576993--577050 Score: 89
Period size: 2 Copynumber: 29.0 Consensus size: 2
576983 TGCCATTACT
576993 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * *
577035 AG GG GG AG GG AG AG AG
1 AG AG AG AG AG AG AG AG
577051 GGAGGGAGTG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
AG
Found at i:577211 original size:20 final size:18
Alignment explanation
Indices: 577181--577235 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 18
577171 GCTTCTTTTT
* *
577181 CTTTTTTTTTTTTTTTGCT
1 CTTTGTTTTTTTTTTT-CG
577200 CTTTGATTTTTTTTCTTTCG
1 CTTTG-TTTTTTTT-TTTCG
577220 CTTTGTTTTTTTTTTT
1 CTTTGTTTTTTTTTTT
577236 TTTTGATCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 3 0.09
19 12 0.38
20 14 0.44
21 3 0.09
ACGTcount: A:0.02, C:0.11, G:0.07, T:0.80
Consensus pattern (18 bp):
CTTTGTTTTTTTTTTTCG
Found at i:582096 original size:21 final size:22
Alignment explanation
Indices: 582045--582104 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
582035 AAAAAAATAT
582045 CGAGAAAA-GGAGAAGGAAAGA
1 CGAGAAAATGGAGAAGGAAAGA
* * *
582066 CGGGAGAATGGA-AAGGAGAGA
1 CGAGAAAATGGAGAAGGAAAGA
* *
582087 GGAGAAAATGGAGGAGGA
1 CGAGAAAATGGAGAAGGA
582105 GAAAGGTGGT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
21 23 0.77
22 7 0.23
ACGTcount: A:0.48, C:0.03, G:0.45, T:0.03
Consensus pattern (22 bp):
CGAGAAAATGGAGAAGGAAAGA
Found at i:583298 original size:20 final size:20
Alignment explanation
Indices: 583273--583449 Score: 111
Period size: 20 Copynumber: 8.8 Consensus size: 20
583263 TTTTCACAAT
583273 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
*
583293 TTGTATCGATACATCGTTCA
1 TTGTATCGATACATTGTTCA
583313 TTGTATCGATACATTCTGGGTTTACCCA
1 TTGTATCGATACA-T-T--G-TT---CA
* *
583341 GATGTATCGATACATT-TTGTA
1 -TTGTATCGATACATTGTT-CA
* *
583362 TTGTATCGATACATGGCTCA
1 TTGTATCGATACATTGTTCA
583382 TTGTATCGAT--A----T-A
1 TTGTATCGATACATTGTTCA
* *
583395 TTGTATCGATACATAGCTCA
1 TTGTATCGATACATTGTTCA
*
583415 TTGTATCGATATATT-TTACA
1 TTGTATCGATACATTGTT-CA
*
583435 ATGTATCGATACATT
1 TTGTATCGATACATT
583450 CAGGCATTTT
Statistics
Matches: 125, Mismatches: 14, Indels: 36
0.71 0.08 0.21
Matches are distributed among these distances:
13 11 0.09
14 1 0.01
15 1 0.01
18 1 0.01
19 2 0.02
20 85 0.68
21 3 0.02
23 2 0.02
24 1 0.01
25 2 0.02
27 1 0.01
28 3 0.02
29 12 0.10
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:583399 original size:13 final size:13
Alignment explanation
Indices: 583381--583405 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
583371 TACATGGCTC
583381 ATTGTATCGATAT
1 ATTGTATCGATAT
583394 ATTGTATCGATA
1 ATTGTATCGATA
583406 CATAGCTCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGTATCGATAT
Found at i:583402 original size:33 final size:33
Alignment explanation
Indices: 583360--583429 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
583350 ATACATTTTG
*
583360 TATTGTATCGATACATGGCTCATTGTATCGATA
1 TATTGTATCGATACATAGCTCATTGTATCGATA
583393 TATTGTATCGATACATAGCTCATTGTATCGATA
1 TATTGTATCGATACATAGCTCATTGTATCGATA
583426 TATT
1 TATT
583430 TTACAATGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (33 bp):
TATTGTATCGATACATAGCTCATTGTATCGATA
Found at i:585876 original size:79 final size:79
Alignment explanation
Indices: 585744--585956 Score: 313
Period size: 79 Copynumber: 2.7 Consensus size: 79
585734 TCATCTCGGA
* * *
585744 GATACTCCAACCCCGGTTTTATTT-TCAAAATATTAATTTCTCATAATCGGGGATACTCCAAACC
1 GATACTCCAACCCCGGTTTTATTTCT-AAAACATCAATTTTTCATAATCGGGGATACTCCAAACC
585808 C-TTCATTTCCGAGGG
65 CGTT-ATTTCCGAGGG
** *
585823 GATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATTTGGGATACTCCAACCCC
1 GATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAACCC
585888 GTTATTTCCGAGGG
66 GTTATTTCCGAGGG
* * *
585902 GATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTTCACAATCGGGGATA
1 GATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATA
585957 TTCTAACTCC
Statistics
Matches: 121, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
79 118 0.98
80 3 0.02
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (79 bp):
GATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAACCC
GTTATTTCCGAGGG
Found at i:585976 original size:51 final size:51
Alignment explanation
Indices: 585899--586018 Score: 159
Period size: 51 Copynumber: 2.4 Consensus size: 51
585889 TTATTTCCGA
* *
585899 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTTCACAATC
* * * * * *
585950 GGGGATATTCTAACTCCGATTTTATTTCCAAAACACTAATTTTTTACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTTCACAATC
*
586001 GGGGATACTCCAATCCCG
1 GGGGATACTCCAACCCCG
586019 TTATTTCATC
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTTCACAATC
Found at i:586038 original size:28 final size:28
Alignment explanation
Indices: 585998--586072 Score: 100
Period size: 28 Copynumber: 2.7 Consensus size: 28
585988 ATTTTTTACA
*
585998 ATCGGGGATACTCCAATCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
586026 ATCGGGGATACTCTAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
586054 --CGAGAGGATACTCCAACCC
1 ATCG-G-GGATACTCCAACCC
586073 TGGCTTTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 2 0.05
27 1 0.02
28 39 0.93
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:586104 original size:158 final size:158
Alignment explanation
Indices: 585872--586199 Score: 392
Period size: 158 Copynumber: 2.1 Consensus size: 158
585862 TTCATAATTT
* *
585872 GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCA
1 GGGATACTCCAACCCCGTTATTTCCGAGAGGATACTCCAACCCCGGCTTTATTTCTAAAACACCA
* * ** * *
585937 ATTCTTCACAATCGGGGATA-TTCTAACTCCGATTTTATTTCCAAAACACTAATTTTTTACAATC
66 ATTCTTCACAATCAGGGATACTTC-AACCCCGACCTTATTTCCAAAACACTAATTTCTCACAATC
* *
586001 GGGGATACTCCAATCCCGTTA-TTTCATCG
130 GGGGATACTCCAACCCCATTATTTTCA-CG
* * * ***
586030 GGGATACTCTAACCCCGTTATTTCCGAGAGGATACTCCAACCCTGGCTTTATTTCTAAAATATTG
1 GGGATACTCCAACCCCGTTATTTCCGAGAGGATACTCCAACCCCGGCTTTATTTCTAAAACACCA
* * * * * * *
586095 ATT-TCTCACAATCATGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCATAATT
66 ATTCT-TCACAATCAGGGATACTTCAACCCCGACCTTATTTCCAAAACACTAATTTCTCACAATC
586159 GGGGATACTCCAACCCCATTATTTTCACG
130 GGGGATACTCCAACCCCATTATTTTCACG
*
586188 AGGATACTCCAA
1 GGGATACTCCAA
586200 TCCTGATTTT
Statistics
Matches: 142, Mismatches: 25, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
157 1 0.01
158 133 0.94
159 8 0.06
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (158 bp):
GGGATACTCCAACCCCGTTATTTCCGAGAGGATACTCCAACCCCGGCTTTATTTCTAAAACACCA
ATTCTTCACAATCAGGGATACTTCAACCCCGACCTTATTTCCAAAACACTAATTTCTCACAATCG
GGGATACTCCAACCCCATTATTTTCACG
Found at i:586165 original size:51 final size:51
Alignment explanation
Indices: 586059--586175 Score: 162
Period size: 51 Copynumber: 2.3 Consensus size: 51
586049 ATTTCCGAGA
* * * *
586059 GGATACTCCAACCCTGGCTTTATTTCTAAAATATTGATTTCTCACAATCAT
1 GGATACTCCAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATCAG
* * **
586110 GGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCATAATTGG
1 GGATACTCCAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATCAG
586161 GGATACTCCAACCCC
1 GGATACTCCAACCCC
586176 ATTATTTTCA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (51 bp):
GGATACTCCAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATCAG
Found at i:586167 original size:130 final size:130
Alignment explanation
Indices: 586026--586332 Score: 340
Period size: 130 Copynumber: 2.4 Consensus size: 130
586016 CCGTTATTTC
* * * *
586026 ATCGGGGATACTCTAACCCCGTTATTTCCGAGAGGATACTCCAACCCTGGCTTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGAGGATACTCCAACCCTGACTTTATTTCTAAAAC
* *
586091 AT-TGA-TTTCTCACAATCAT-G-GATACTTCAACCC-CGACCTTATTTCTAAAAT-ATTGATTT
66 ATCT-ATTTTCT-ACAAT--TGGAGACACTTCAACCCTCG-CCTTATTTCT-AAATCATCGATTT
*
586150 CTCATA
125 CTCACA
* * * * * *
586156 ATTGGGGATACTCCAACCCCATTATTTTC-ACGAGGATACTCCAATCCTGATTTTATTTTTGAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGA-GAGGATACTCCAACCCTGACTTTATTTCTAAAA
* * * *
586220 CATCTATTTTCTATAATTGGAGACACTTCAACCCTTGCTTTATTTCTAAATCATCGATTTTTCAC
65 CATCTATTTTCTACAATTGGAGACACTTCAACCCTCGCCTTATTTCTAAATCATCGATTTCTCAC
586285 A
130 A
*
586286 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCC
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGAGGATACTCCAACCC
586333 CGTTATTATC
Statistics
Matches: 148, Mismatches: 21, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
128 1 0.01
129 6 0.04
130 133 0.90
131 8 0.05
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAGAGGATACTCCAACCCTGACTTTATTTCTAAAAC
ATCTATTTTCTACAATTGGAGACACTTCAACCCTCGCCTTATTTCTAAATCATCGATTTCTCACA
Found at i:588238 original size:3 final size:3
Alignment explanation
Indices: 588232--588268 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
588222 AAAAATGAAT
588232 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
588269 TGATTTATCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:588597 original size:24 final size:24
Alignment explanation
Indices: 588565--588613 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
588555 CCACGGCTTC
588565 TTTCAATTTACTAAAGTATTAATA
1 TTTCAATTTACTAAAGTATTAATA
588589 TTTCAATTTACTAAAGTATTAATA
1 TTTCAATTTACTAAAGTATTAATA
588613 T
1 T
588614 CCGATATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (24 bp):
TTTCAATTTACTAAAGTATTAATA
Found at i:589874 original size:2 final size:2
Alignment explanation
Indices: 589867--589893 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
589857 GTACTTAGAA
589867 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
589894 ACCCAAATCA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:590103 original size:14 final size:14
Alignment explanation
Indices: 590084--590113 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
590074 TCCAAGTAAC
*
590084 ATAGGAATTAAGTG
1 ATAGGAATTAAATG
590098 ATAGGAATTAAATG
1 ATAGGAATTAAATG
590112 AT
1 AT
590114 TTACGTGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (14 bp):
ATAGGAATTAAATG
Found at i:592660 original size:3 final size:3
Alignment explanation
Indices: 592652--592678 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
592642 TTGTGGCGGC
592652 TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT
592679 AAATTAGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TGT
Found at i:592704 original size:6 final size:6
Alignment explanation
Indices: 592693--592737 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
592683 TAGGAGTGGA
* * *
592693 ATTAGG ATTAGG ATTAGG GTTCGG ATTAGG ATTAGG GTTAGG ATT
1 ATTAGG ATTAGG ATTAGG ATTAGG ATTAGG ATTAGG ATTAGG ATT
592738 GGGGGTAGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.27, C:0.02, G:0.36, T:0.36
Consensus pattern (6 bp):
ATTAGG
Found at i:592718 original size:18 final size:18
Alignment explanation
Indices: 592694--592737 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
592684 AGGAGTGGAA
592694 TTAGGATTAGGATTAGGG
1 TTAGGATTAGGATTAGGG
*
592712 TTCGGATTAGGATTAGGG
1 TTAGGATTAGGATTAGGG
592730 TTAGGATT
1 TTAGGATT
592738 GGGGGTAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.25, C:0.02, G:0.36, T:0.36
Consensus pattern (18 bp):
TTAGGATTAGGATTAGGG
Found at i:592928 original size:3 final size:3
Alignment explanation
Indices: 592922--592956 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
592912 TTGTTGTTGA
* *
592922 TGC TGC TGC TGC TGC TGC TGT TGT TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
592957 TTTCTGTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.26, G:0.34, T:0.40
Consensus pattern (3 bp):
TGC
Found at i:593271 original size:24 final size:25
Alignment explanation
Indices: 593228--593303 Score: 79
Period size: 24 Copynumber: 3.1 Consensus size: 25
593218 AGATTTCTTC
*
593228 AAAAATT--ATATTTAACTTTATTT
1 AAAAATTAAATATTTAATTTTATTT
593251 AAAAATTAAATATTT-ATTTTATTT
1 AAAAATTAAATATTTAATTTTATTT
* *
593275 TAAATTTAAAT-TTATAATTTTTATTT
1 AAAAATTAAATATT-TAA-TTTTATTT
593301 AAA
1 AAA
593304 TTGATTCGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
23 9 0.20
24 18 0.41
25 7 0.16
26 10 0.23
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (25 bp):
AAAAATTAAATATTTAATTTTATTT
Found at i:593426 original size:19 final size:19
Alignment explanation
Indices: 593394--593431 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
593384 TTAAAAAATA
*
593394 ATTTTTTAAGTATTTTATT
1 ATTTTTTAAGTATTATATT
593413 ATTTTTTATA-TATTATATT
1 ATTTTTTA-AGTATTATATT
593432 CGATTGCTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
ATTTTTTAAGTATTATATT
Found at i:593988 original size:18 final size:20
Alignment explanation
Indices: 593965--594003 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
593955 ACCCATAAAT
593965 AATTTTT-TATTT-TTTATA
1 AATTTTTATATTTATTTATA
593983 AATTTTTAATATTTATTTATA
1 AATTTTT-ATATTTATTTATA
594004 CTACTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
AATTTTTATATTTATTTATA
Found at i:594226 original size:18 final size:18
Alignment explanation
Indices: 594203--594238 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
594193 AAATATGATT
*
594203 TTTTAAAAAATTATTAAA
1 TTTTAAAAAATTACTAAA
594221 TTTTAAAAAATTACTAAA
1 TTTTAAAAAATTACTAAA
594239 ATACTATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTTAAAAAATTACTAAA
Found at i:595372 original size:64 final size:65
Alignment explanation
Indices: 595250--595375 Score: 184
Period size: 64 Copynumber: 2.0 Consensus size: 65
595240 TTTAAATTTG
* * *
595250 TTTAATTTTATGATTAATAAAATAAATTAAAGCCTAGAAATAAAGCAATTCATTATAAATTTTTA
1 TTTAATTTTATGATTAATAAAATAAATTAAAACCTAAAAATAAAGCAATTCATCATAAATTTTTA
* *
595315 TTTACTTTTATGATTAAT-AAA-AAATTAAAACTTTAAAAATAAAGCAATTCATCATAAATTT
1 TTTAATTTTATGATTAATAAAATAAATTAAAAC-CTAAAAATAAAGCAATTCATCATAAATTT
595376 AAATATTTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
63 9 0.16
64 29 0.53
65 17 0.31
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (65 bp):
TTTAATTTTATGATTAATAAAATAAATTAAAACCTAAAAATAAAGCAATTCATCATAAATTTTTA
Found at i:595561 original size:16 final size:16
Alignment explanation
Indices: 595540--595574 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
595530 AATTAAATAT
595540 TATATA-TAATAATTTA
1 TATATACTAATAA-TTA
595556 TATATACTAATAATTA
1 TATATACTAATAATTA
595572 TAT
1 TAT
595575 TACATACGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
TATATACTAATAATTA
Found at i:596672 original size:12 final size:11
Alignment explanation
Indices: 596652--596694 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
596642 ACATATAAAT
596652 AAAAAATTATA
1 AAAAAATTATA
596663 AAAAATATTATA
1 AAAAA-ATTATA
**
596675 AAGTAATTATA
1 AAAAAATTATA
*
596686 AATAAATTA
1 AAAAAATTA
596695 CGGATGTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
AAAAAATTATA
Found at i:600270 original size:10 final size:10
Alignment explanation
Indices: 600252--600281 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
600242 CAATCAAAAA
*
600252 ATTGACATAT
1 ATTGGCATAT
600262 ATTGGCATAT
1 ATTGGCATAT
600272 ATTGGCATAT
1 ATTGGCATAT
600282 TAAGAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (10 bp):
ATTGGCATAT
Found at i:600606 original size:26 final size:25
Alignment explanation
Indices: 600575--600627 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
600565 AGACATGATA
*
600575 AAAACACAACATAAATAAA-AATAATT
1 AAAACACAACACAAA-AAATAAT-ATT
600601 AAAACACAACACAAAAAATAATATT
1 AAAACACAACACAAAAAATAATATT
600626 AA
1 AA
600628 CACGACATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (25 bp):
AAAACACAACACAAAAAATAATATT
Found at i:600754 original size:10 final size:11
Alignment explanation
Indices: 600711--600829 Score: 79
Period size: 11 Copynumber: 10.5 Consensus size: 11
600701 TTAATACTTT
600711 AAAT-ATATAA
1 AAATAATATAA
600721 GAAATAATATAA
1 -AAATAATATAA
*
600733 AAATGATATAA
1 AAATAATATAA
600744 AAATAAT-TAA
1 AAATAATATAA
600754 AACATAATA-AA
1 AA-ATAATATAA
600765 AAATAAATATAA
1 AAAT-AATATAA
*
600777 CACA-AATATAA
1 -AAATAATATAA
600788 TTAAA-ACATAATAA
1 --AAATA-AT-ATAA
600802 AAATAAATATAA
1 AAAT-AATATAA
*
600814 CACA-AATATAA
1 -AAATAATATAA
600825 AAATA
1 AAATA
600830 TAAAATATAT
Statistics
Matches: 88, Mismatches: 7, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
10 9 0.10
11 48 0.55
12 18 0.20
13 8 0.09
14 5 0.06
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (11 bp):
AAATAATATAA
Found at i:600813 original size:37 final size:38
Alignment explanation
Indices: 600746--600824 Score: 151
Period size: 37 Copynumber: 2.1 Consensus size: 38
600736 TGATATAAAA
600746 ATAATTAAAACATAATAAAAAATAAATATAACACAAAT
1 ATAATTAAAACATAATAAAAAATAAATATAACACAAAT
600784 ATAATTAAAACATAAT-AAAAATAAATATAACACAAAT
1 ATAATTAAAACATAATAAAAAATAAATATAACACAAAT
600821 ATAA
1 ATAA
600825 AAATATAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 25 0.61
38 16 0.39
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (38 bp):
ATAATTAAAACATAATAAAAAATAAATATAACACAAAT
Found at i:600893 original size:12 final size:12
Alignment explanation
Indices: 600878--600902 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
600868 TAAATAATAA
600878 AAAAATATAAAT
1 AAAAATATAAAT
600890 AAAAATATAAAT
1 AAAAATATAAAT
600902 A
1 A
600903 CATAAAATTT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAATATAAAT
Found at i:601599 original size:16 final size:16
Alignment explanation
Indices: 601559--601605 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
601549 AATATATTTT
601559 TATTAAATATT-TTT-A
1 TATTAAA-ATTATTTAA
601574 TA-TAATAATTATTTAA
1 TATTAA-AATTATTTAA
601590 TATTAAAATTATTTAA
1 TATTAAAATTATTTAA
601606 AAAAATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
14 6 0.21
15 6 0.21
16 13 0.46
17 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTAAAATTATTTAA
Found at i:601612 original size:13 final size:15
Alignment explanation
Indices: 601573--601613 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
601563 AAATATTTTT
601573 ATATAATAATTATTTA
1 ATATAA-AATTATTTA
601589 ATATTAAAATTATTTA
1 ATA-TAAAATTATTTA
601605 A-A-AAAATTA
1 ATATAAAATTA
601614 AAATTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.29
15 1 0.04
16 13 0.54
17 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATATAAAATTATTTA
Found at i:601624 original size:21 final size:19
Alignment explanation
Indices: 601591--601636 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 19
601581 ATTATTTAAT
601591 ATTAAAATTATTTAAAAAA
1 ATTAAAATTATTTAAAAAA
*
601610 ATTAAAATTTTATTTAAATAA
1 ATTAAAA--TTATTTAAAAAA
601631 ATTAAA
1 ATTAAA
601637 TAATTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.29
21 17 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTAAAATTATTTAAAAAA
Found at i:607697 original size:20 final size:20
Alignment explanation
Indices: 607672--607728 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
607662 TATATTATTA
*
607672 AATTAAAATTTTATTAAATT
1 AATTAAAATTTAATTAAATT
**
607692 AATTAAAAAATAATTAAATT
1 AATTAAAATTTAATTAAATT
*
607712 GA-TAAAATTTAATTAAA
1 AATTAAAATTTAATTAAA
607729 AAAAAAAACT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
AATTAAAATTTAATTAAATT
Found at i:608418 original size:21 final size:21
Alignment explanation
Indices: 608401--608447 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
608391 ATCATATCAT
608401 TTAATTAAATATATATATATA
1 TTAATTAAATATATATATATA
* *
608422 TTTATTAAATATTTAT-TATAA
1 TTAATTAAATATATATATAT-A
608443 TTAAT
1 TTAAT
608448 ACTCATTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAATTAAATATATATATATA
Found at i:611058 original size:6 final size:6
Alignment explanation
Indices: 611047--611080 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
611037 TATCACCGAG
* *
611047 AGCAGA AGCAGA AGCAGA AGCAGT AGCAGT AGCA
1 AGCAGA AGCAGA AGCAGA AGCAGA AGCAGA AGCA
611081 AAATCAGACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.44, C:0.18, G:0.32, T:0.06
Consensus pattern (6 bp):
AGCAGA
Found at i:612557 original size:247 final size:247
Alignment explanation
Indices: 611861--613572 Score: 2160
Period size: 247 Copynumber: 6.9 Consensus size: 247
611851 TACATAAAGT
* * *
611861 AATTAAAAAGCCGATTTCCAGTTTATGGTGAATTAAAACATATAGAGAACAACAGTTTGGCAAAA
1 AATTAAAAAACCAATTTCCAGTTTATGGTGAATTAAAACATATAGAGAATAACAGTTTGGCAAAA
* * * * * *
611926 CAATCTGTACAGATGAAGGA--AAAAAATTCAAACAGATTACAGAATAATTGATGCATT-AAGCG
66 CAATCTGTAC-G--GACGGATTAAAAAATCCGAACAGATTACAGAACAATAGATGC-TTCAACCG
* * * * *
611988 GTTGATCATCAAAATAAGGTATAATCTTAAAATCAATAGAAACATGAAACAGTTTAAATAAAAGA
127 GTTAATCATCAATATAAGGTATAATCTTAAAATCAATAAAAACACGAAACAGTTCAAATAAAAGA
* * ** *
612053 TTATCCCATGCAAAACAGTCCATCACTCCCATCAAATAATGATCTGAACAATGTTG
192 TTACCCCATCCAAAATGGTCCATCACTCCCATCAAATAATGATCTGAACAATGGTG
* * *
612109 AATTAAAAAACCAATTTCCAGTTAATGGTGAATTAAAACATATAGAGAATAACAGTTTTGCAAGA
1 AATTAAAAAACCAATTTCCAGTTTATGGTGAATTAAAACATATAGAGAATAACAGTTTGGCAAAA
* * ** * * *
612174 CAATCTGTACAGATAGAGAAAAAAAAAAATCCGAACAGATTACAGAACAATTGATGCATCAACCA
66 CAATCTGTACGGA-CG-G--ATTAAAAAATCCGAACAGATTACAGAACAATAGATGCTTCAACCG
* * *
612239 GTTGATCATCGATATAAGGTATAATCTTAAAATCAATAAAAACATGAAACAGTTCAAATAAAAGA
127 GTTAATCATCAATATAAGGTATAATCTTAAAATCAATAAAAACACGAAACAGTTCAAATAAAAGA
** ** * * *
612304 TTACCCCAAACGGAATGGTGCATCACTCCCACCAAACAATGATCTGAACAATGGTG
192 TTACCCCATCCAAAATGGTCCATCACTCCCATCAAATAATGATCTGAACAATGGTG
** * * * *
612360 AATTAGGAAACCAATTTCCAGTTTATGGTGAATTAAAATATCTAGAGAATAACGGCTTGGCAAAA
1 AATTAAAAAACCAATTTCCAGTTTATGGTGAATTAAAACATATAGAGAATAACAGTTTGGCAAAA
* * *
612425 CAATCTGTACGGACGGATTAAAAAATCCGAATAGATTACAGAACAATTGATGCATCAACCGGTTA
66 CAATCTGTACGGACGGATTAAAAAATCCGAACAGATTACAGAACAATAGATGCTTCAACCGGTTA
* * *
612490 ATCATCAATATAAGGTATAATCTTAAAATCAATAAAAGCACGAAACAGTTCCAGTAAAAGATTAC
131 ATCATCAATATAAGGTATAATCTTAAAATCAATAAAAACACGAAACAGTTCAAATAAAAGATTAC
* * ***
612555 CCCATCCGAAATTGTCCATCACTCCCATCAAATAATGATCTGAACAACATTG
196 CCCATCCAAAATGGTCCATCACTCCCATCAAATAATGATCTGAACAATGGTG
* * *
612607 AATTAAAAAACCGATTTCCAGTTTATGGAGAATTAAAACATATAGAGAATAACAGTTTGGCAAGA
1 AATTAAAAAACCAATTTCCAGTTTATGGTGAATTAAAACATATAGAGAATAACAGTTTGGCAAAA
** * *
612672 CAATCTGTACGGACGGAGAAAAAAAAATCCGAACAGATTACAGAACAAAAGATTCTTCAACCGGT
66 CAATCTGTACGGAC-G-GATTAAAAAATCCGAACAGATTACAGAACAATAGATGCTTCAACCGGT
* * *
612737 TAATCATCAATATAAGGTATAATCTTAAAATTAATAAAAACACGAAACAGTTCAAAGAGAAGATT
129 TAATCATCAATATAAGGTATAATCTTAAAATCAATAAAAACACGAAACAGTTCAAATAAAAGATT
* * ** * * *
612802 ACCCCATACGAAACAGTGCATCACTCCCATCAAATTATGATATGAACAATGGTG
194 ACCCCATCCAAAATGGTCCATCACTCCCATCAAATAATGATCTGAACAATGGTG
* ** * * *
612856 AGTTAAAAAACCAATTAGCAGTTTATGGTGAATTAAAATATAGAGAGAATAACAGCTTGTG-AAA
1 AATTAAAAAACCAATTTCCAGTTTATGGTGAATTAAAACATATAGAGAATAACAGTTTG-GCAAA
* * *
612920 ACAATCTGTTCGGACGGATTAAAAAAATCCGAACAGATTACAGAATAATAAATGCTTCAACCGGT
65 ACAATCTGTACGGACGGATT-AAAAAATCCGAACAGATTACAGAACAATAGATGCTTCAACCGGT
* *
612985 TAACCATCAATATAAGGTATAATCTT--AA--AAT-----CACGAAACAGTTCAAATAAAAGAGT
129 TAATCATCAATATAAGGTATAATCTTAAAATCAATAAAAACACGAAACAGTTCAAATAAAAGATT
* *
613041 AACCCATCCAAAATGGTCCATCACTCCCATCAAATAATGTTCTGAACAATGGTG
194 ACCCCATCCAAAATGGTCCATCACTCCCATCAAATAATGATCTGAACAATGGTG
* * * * *
613095 AATTAAAAAAACGATTTCCAGTTTATGATGAATTAAAACATATAAAGAATAACAGTTTGGCAAGA
1 AATTAAAAAACCAATTTCCAGTTTATGGTGAATTAAAACATATAGAGAATAACAGTTTGGCAAAA
* * * *
613160 CAATCTGTACGGATGGATTAAAAAATCCGAACAGATTACAGAGCAATAGATTCTTCAACTGGTTA
66 CAATCTGTACGGACGGATTAAAAAATCCGAACAGATTACAGAACAATAGATGCTTCAACCGGTTA
*
613225 ATCATCAATATAAGGTATAATCTTAAAATTAATAAAAACACGAAACAGTTCAAATAAAAGATTAC
131 ATCATCAATATAAGGTATAATCTTAAAATCAATAAAAACACGAAACAGTTCAAATAAAAGATTAC
* *
613290 CCCATCCAAAATGGTCCATCACTCCCATCAAATAATGATCTGGACGATGGTG
196 CCCATCCAAAATGGTCCATCACTCCCATCAAATAATGATCTGAACAATGGTG
* * *
613342 AATTAAAAAATCAATTTCCAGTTTATGGTGAATTAAAACACAGAGAGAATAACAGTTTGGCAAAA
1 AATTAAAAAACCAATTTCCAGTTTATGGTGAATTAAAACATATAGAGAATAACAGTTTGGCAAAA
* * * * * *
613407 CAATCTGTACGGACAGA--CAAAAATCCAAACAGATTACAGAACAATAAATACTTCAACTGGTTA
66 CAATCTGTACGGACGGATTAAAAAATCCGAACAGATTACAGAACAATAGATGCTTCAACCGGTTA
* * *
613470 ATCATCAATA-CAGAGTATAATCTTAGAATCAACAAAAACACGAAACAGTTCAAATAAAAGATTA
131 ATCATCAATATAAG-GTATAATCTTAAAATCAATAAAAACACGAAACAGTTCAAATAAAAGATTA
* ** * *
613534 CCCCATCCGAAACAGTCCATCACTTCCATCACATAATGA
195 CCCCATCCAAAATGGTCCATCACTCCCATCAAATAATGA
613573 CCCAAACAAC
Statistics
Matches: 1276, Mismatches: 166, Indels: 47
0.86 0.11 0.03
Matches are distributed among these distances:
238 65 0.05
239 136 0.11
240 2 0.00
242 3 0.00
244 5 0.00
245 134 0.11
246 4 0.00
247 366 0.29
248 136 0.11
249 214 0.17
250 3 0.00
251 208 0.16
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (247 bp):
AATTAAAAAACCAATTTCCAGTTTATGGTGAATTAAAACATATAGAGAATAACAGTTTGGCAAAA
CAATCTGTACGGACGGATTAAAAAATCCGAACAGATTACAGAACAATAGATGCTTCAACCGGTTA
ATCATCAATATAAGGTATAATCTTAAAATCAATAAAAACACGAAACAGTTCAAATAAAAGATTAC
CCCATCCAAAATGGTCCATCACTCCCATCAAATAATGATCTGAACAATGGTG
Found at i:613285 original size:735 final size:737
Alignment explanation
Indices: 611861--613572 Score: 2301
Period size: 735 Copynumber: 2.3 Consensus size: 737
611851 TACATAAAGT
* *
611861 AATTAAAAAGCCGATTTCCAGTTTATGGTGAATTAAAACATATAGAGAACAACAGTTTGGCAAAA
1 AATTAAAAAACCGATTTCCAGTTTATGGTGAATTAAAACATATAGAGAATAACAGTTTGGCAAAA
* * * * ** * *
611926 CAATCTGTACAGATGAAGGAAAAAAATTCAAACAGATTACAGAATAATTGATGCATT-AAGCGGT
66 CAATCTGTACGGACG-A-GAAAAAAATCCAAACAGATTACAGAACAAAAGATAC-TTCAACCGGT
* * * * *
611990 TGATCATCAAAATAAGGTATAATCTTAAAATCAATAGAAACATGAAACAGTTTAAATAAAAGATT
128 TAATCATCAATATAAGGTATAATCTTAAAATCAATAAAAACACGAAACAGTTCAAATAAAAGATT
* * * * *
612055 ATCCCATGCAAAACAGTCCATCACTCCCATCAAATAATGATCTGAACAATGTTGAATTAAAAAAC
193 ACCCCATACGAAACAGTCCATCACTCCCATCAAATAATGATATGAACAATGGTGAATTAAAAAAC
* * * *
612120 CAATTTCCAGTTAATGGTGAATTAAAACATATAGAGAATAACAGTTTTGCAAGACAATCTGTACA
258 CAATTACCAGTTAATGGTGAATTAAAACATAGAGAGAATAACAGTTGTGCAAAACAATCTGTACA
** * * *
612185 GATAGAGAAAAAAAAAAATCCGAACAGATTACAGAACAATTGATGCATCAACCAGTTGATCATCG
323 GATAGAGAAAAAAAAAAATCCGAACAGATTACAGAACAATAAATGCATCAACCAGTTAACCATCA
* *
612250 ATATAAGGTATAATCTTAAAATCAATAAAAACATGAAACAGTTCAAATAAAAGATTACCCCAAAC
388 ATATAAGGTATAATCTTAAAATC------AACA-GAAACAGTTCAAATAAAAGAGTAACCCAAAC
** * ** *
612315 GGAATGGTGCATCACTCCCACCAAACAATGATCTGAACAATGGTGAATTAGGAAACCAATTTCCA
446 AAAATGGTCCATCACTCCCACCAAACAATGATCTGAACAATGGTGAATTAAAAAAACAATTTCCA
* * * * *
612380 GTTTATGGTGAATTAAAATATCTAGAGAATAACGGCTTGGCAAAACAATCTGTACGGACGGATTA
511 GTTTATGATGAATTAAAACATATAAAGAATAACAGCTTGGCAAAACAATCTGTACGGACGGATTA
* *
612445 AAAAATCCGAATAGATTACAGAACAATTGATGCATCAACCGGTTAATCATCAATATAAGGTATAA
576 AAAAATCCGAACAGATTACAGAACAATAGATGCATCAACCGGTTAATCATCAATATAAGGTATAA
* * * * *
612510 TCTTAAAATCAATAAAAGCACGAAACAGTTCCAGTAAAAGATTACCCCATCCGAAATTGTCCATC
641 TCTTAAAATCAATAAAAACACGAAACAGTTCAAATAAAAGATTACCCCATCCAAAATGGTCCATC
*
612575 ACTCCCATCAAATAATGATCTGAACAACATTG
706 ACTCCCATCAAATAATGATCTGAACAACAGTG
* *
612607 AATTAAAAAACCGATTTCCAGTTTATGGAGAATTAAAACATATAGAGAATAACAGTTTGGCAAGA
1 AATTAAAAAACCGATTTCCAGTTTATGGTGAATTAAAACATATAGAGAATAACAGTTTGGCAAAA
* *
612672 CAATCTGTACGGACGGAGAAAAAAAAATCCGAACAGATTACAGAACAAAAGATTCTTCAACCGGT
66 CAATCTGTACGGAC-GAG--AAAAAAATCCAAACAGATTACAGAACAAAAGATACTTCAACCGGT
* * *
612737 TAATCATCAATATAAGGTATAATCTTAAAATTAATAAAAACACGAAACAGTTCAAAGAGAAGATT
128 TAATCATCAATATAAGGTATAATCTTAAAATCAATAAAAACACGAAACAGTTCAAATAAAAGATT
* * *
612802 ACCCCATACGAAACAGTGCATCACTCCCATCAAATTATGATATGAACAATGGTGAGTTAAAAAAC
193 ACCCCATACGAAACAGTCCATCACTCCCATCAAATAATGATATGAACAATGGTGAATTAAAAAAC
* * * *
612867 CAATTAGCAGTTTATGGTGAATTAAAATATAGAGAGAATAACAGCTTGTG-AAAACAATCTGTTC
258 CAATTACCAGTTAATGGTGAATTAAAACATAGAGAGAATAACAG-TTGTGCAAAACAATCTGTAC
* * ** * * *
612931 GGA-CG-G-ATTAAAAAAATCCGAACAGATTACAGAATAATAAATGCTTCAACCGGTTAACCATC
322 AGATAGAGAAAAAAAAAAATCCGAACAGATTACAGAACAATAAATGCATCAACCAGTTAACCATC
**
612993 AATATAAGGTATAATCTTAAAATC-AC-GAAACAGTTCAAATAAAAGAGTAACCCATCCAAAATG
387 AATATAAGGTATAATCTTAAAATCAACAGAAACAGTTCAAATAAAAGAGTAACCCAAACAAAATG
* * * *
613056 GTCCATCACTCCCATCAAATAATGTTCTGAACAATGGTGAATTAAAAAAACGATTTCCAGTTTAT
452 GTCCATCACTCCCACCAAACAATGATCTGAACAATGGTGAATTAAAAAAACAATTTCCAGTTTAT
* * *
613121 GATGAATTAAAACATATAAAGAATAACAGTTTGGCAAGACAATCTGTACGGATGGATTAAAAAAT
517 GATGAATTAAAACATATAAAGAATAACAGCTTGGCAAAACAATCTGTACGGACGGATTAAAAAAT
* * * *
613186 CCGAACAGATTACAGAGCAATAGATTCTTCAACTGGTTAATCATCAATATAAGGTATAATCTTAA
582 CCGAACAGATTACAGAACAATAGATGCATCAACCGGTTAATCATCAATATAAGGTATAATCTTAA
*
613251 AATTAATAAAAACACGAAACAGTTCAAATAAAAGATTACCCCATCCAAAATGGTCCATCACTCCC
647 AATCAATAAAAACACGAAACAGTTCAAATAAAAGATTACCCCATCCAAAATGGTCCATCACTCCC
* * **
613316 ATCAAATAATGATCTGGACGATGGTG
712 ATCAAATAATGATCTGAACAACAGTG
* * * *
613342 AATTAAAAAATCAATTTCCAGTTTATGGTGAATTAAAACACAGAGAGAATAACAGTTTGGCAAAA
1 AATTAAAAAACCGATTTCCAGTTTATGGTGAATTAAAACATATAGAGAATAACAGTTTGGCAAAA
* *
613407 CAATCTGTACGGAC-AGACAAAAATCCAAACAGATTACAGAACAATAA-ATACTTCAACTGGTTA
66 CAATCTGTACGGACGAGAAAAAAATCCAAACAGATTACAGAACAA-AAGATACTTCAACCGGTTA
* * *
613470 ATCATCAATA-CAGAGTATAATCTTAGAATCAACAAAAACACGAAACAGTTCAAATAAAAGATTA
130 ATCATCAATATAAG-GTATAATCTTAAAATCAATAAAAACACGAAACAGTTCAAATAAAAGATTA
* * *
613534 CCCCATCCGAAACAGTCCATCACTTCCATCACATAATGA
194 CCCCATACGAAACAGTCCATCACTCCCATCAAATAATGA
613573 CCCAAACAAC
Statistics
Matches: 850, Mismatches: 109, Indels: 29
0.86 0.11 0.03
Matches are distributed among these distances:
730 2 0.00
731 129 0.15
732 2 0.00
733 2 0.00
735 357 0.42
737 2 0.00
744 70 0.08
745 2 0.00
746 77 0.09
747 203 0.24
748 4 0.00
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (737 bp):
AATTAAAAAACCGATTTCCAGTTTATGGTGAATTAAAACATATAGAGAATAACAGTTTGGCAAAA
CAATCTGTACGGACGAGAAAAAAATCCAAACAGATTACAGAACAAAAGATACTTCAACCGGTTAA
TCATCAATATAAGGTATAATCTTAAAATCAATAAAAACACGAAACAGTTCAAATAAAAGATTACC
CCATACGAAACAGTCCATCACTCCCATCAAATAATGATATGAACAATGGTGAATTAAAAAACCAA
TTACCAGTTAATGGTGAATTAAAACATAGAGAGAATAACAGTTGTGCAAAACAATCTGTACAGAT
AGAGAAAAAAAAAAATCCGAACAGATTACAGAACAATAAATGCATCAACCAGTTAACCATCAATA
TAAGGTATAATCTTAAAATCAACAGAAACAGTTCAAATAAAAGAGTAACCCAAACAAAATGGTCC
ATCACTCCCACCAAACAATGATCTGAACAATGGTGAATTAAAAAAACAATTTCCAGTTTATGATG
AATTAAAACATATAAAGAATAACAGCTTGGCAAAACAATCTGTACGGACGGATTAAAAAATCCGA
ACAGATTACAGAACAATAGATGCATCAACCGGTTAATCATCAATATAAGGTATAATCTTAAAATC
AATAAAAACACGAAACAGTTCAAATAAAAGATTACCCCATCCAAAATGGTCCATCACTCCCATCA
AATAATGATCTGAACAACAGTG
Found at i:614834 original size:18 final size:19
Alignment explanation
Indices: 614811--614848 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
614801 AATTTTTTAT
614811 TTTTTTAAAGT-ATATTAA
1 TTTTTTAAAGTAATATTAA
*
614829 TTTTTTAAATTAATATTAA
1 TTTTTTAAAGTAATATTAA
614848 T
1 T
614849 AATTAAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (19 bp):
TTTTTTAAAGTAATATTAA
Found at i:615159 original size:17 final size:19
Alignment explanation
Indices: 615123--615159 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
615113 AATATCTAAT
*
615123 TAAAAATTAATCTGAAATA
1 TAAAAATTAATATGAAATA
615142 TAAAAATTAA-AT-AAATA
1 TAAAAATTAATATGAAATA
615159 T
1 T
615160 TTTACCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 1 0.06
19 10 0.59
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (19 bp):
TAAAAATTAATATGAAATA
Found at i:615402 original size:17 final size:16
Alignment explanation
Indices: 615380--615421 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
615370 ATTAATATCT
615380 TATTTAATTTATATTTA
1 TATTTAATTTAT-TTTA
*
615397 TATTTATTATTATTTTA
1 TATTTAAT-TTATTTTA
615414 T-TTTAATT
1 TATTTAATT
615422 CTCAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.05
16 5 0.23
17 12 0.55
18 4 0.18
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTTAATTTATTTTA
Found at i:615611 original size:30 final size:27
Alignment explanation
Indices: 615561--615638 Score: 93
Period size: 27 Copynumber: 2.7 Consensus size: 27
615551 AAATAATATA
615561 AAATATTAATGATGTATTAAAATTTATTTAAT
1 AAATATTAAT-A--TATTAAAATTTA-TT-AT
615593 AAATTATTAATATATTAAAATTTATTAT
1 AAA-TATTAATATATTAAAATTTATTAT
*
615621 AAATATTAATATTTTAAA
1 AAATATTAATATATTAAA
615639 TATAATTATA
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
27 14 0.32
28 5 0.11
29 2 0.05
30 12 0.27
32 4 0.09
33 7 0.16
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (27 bp):
AAATATTAATATATTAAAATTTATTAT
Found at i:615646 original size:27 final size:28
Alignment explanation
Indices: 615543--615649 Score: 82
Period size: 27 Copynumber: 3.8 Consensus size: 28
615533 TAATTAAATA
*
615543 TAATATA-T-AAA-TAA-TATAAAATAT
1 TAATATATTAAAATTAATTATAAATTAT
*
615567 TAATGATGTATTAAAATTTATTTAATAAATTAT
1 TAAT-A--TATTAAAA-TTAATT-ATAAATTAT
*
615600 TAATATATTAAAATTTATTATAAA-TAT
1 TAATATATTAAAATTAATTATAAATTAT
*
615627 TAATAT-TTTAAATATAATTATAA
1 TAATATATTAAAAT-TAATTATAA
615650 TTAAAAAGAC
Statistics
Matches: 67, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
24 4 0.06
25 1 0.01
26 6 0.09
27 19 0.28
28 6 0.09
29 7 0.10
30 8 0.12
31 2 0.03
32 2 0.03
33 12 0.18
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
TAATATATTAAAATTAATTATAAATTAT
Found at i:616676 original size:15 final size:14
Alignment explanation
Indices: 616637--616677 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
616627 AATTCAATAA
616637 TTTAATTA-ATTTT
1 TTTAATTATATTTT
616650 TTTAATATATATTTT
1 TTTAAT-TATATTTT
616665 TTTAATTGATATT
1 TTTAATT-ATATT
616678 AAAAAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.24
14 3 0.12
15 16 0.64
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TTTAATTATATTTT
Found at i:619446 original size:27 final size:26
Alignment explanation
Indices: 619416--619478 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
619406 TATATAGATT
619416 TCATATATTTATATTTATGTATTCATA
1 TCATATATTTATATTTATGTATT-ATA
*
619443 TCATA-ATTATATATTTTTGTATTATA
1 TCATATATT-TATATTTATGTATTATA
*
619469 TTATAT-TTTA
1 TCATATATTTA
619479 ATTATTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 2 0.06
26 12 0.38
27 18 0.56
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (26 bp):
TCATATATTTATATTTATGTATTATA
Found at i:619697 original size:22 final size:24
Alignment explanation
Indices: 619651--619700 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
619641 TACGGATATG
* *
619651 ATAAAAAAATAATTAAAATATAAT
1 ATAAAAAAATAAGTAAAATAGAAT
619675 ATAAAAAAA-AAGTAAAAT-GAAT
1 ATAAAAAAATAAGTAAAATAGAAT
619697 ATAA
1 ATAA
619701 TATGAATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.29
23 8 0.33
24 9 0.38
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (24 bp):
ATAAAAAAATAAGTAAAATAGAAT
Found at i:622714 original size:25 final size:26
Alignment explanation
Indices: 622684--622732 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
622674 AATAGATTCG
*
622684 ATTTA-TCTAATTTAATAATAAAAAA
1 ATTTATTCTAAATTAATAATAAAAAA
* *
622709 ATTTATTTTAAATTAATTATAAAA
1 ATTTATTCTAAATTAATAATAAAA
622733 TATATAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 5 0.25
26 15 0.75
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
ATTTATTCTAAATTAATAATAAAAAA
Found at i:622773 original size:28 final size:29
Alignment explanation
Indices: 622741--622798 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
622731 AATATATAAA
*
622741 TATTAATATAAAAATAAT-TTTTAATTTT
1 TATTAATATAAAAATAATAATTTAATTTT
* *
622769 TATTAATTTATAAATAATAATTTAATTTT
1 TATTAATATAAAAATAATAATTTAATTTT
622798 T
1 T
622799 TGAATTAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
TATTAATATAAAAATAATAATTTAATTTT
Found at i:622804 original size:28 final size:29
Alignment explanation
Indices: 622747--622804 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
622737 TAAATATTAA
*
622747 TATAAAAATAATTTTTAATTTTTATTAATT
1 TATAAAAATAA-TTTTAATTTTTATGAATT
622777 TATAAATAATAA-TTTAATTTTT-TGAATT
1 TATAAA-AATAATTTTAATTTTTATGAATT
622805 AATCATTAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 5 0.19
29 10 0.38
30 6 0.23
31 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (29 bp):
TATAAAAATAATTTTAATTTTTATGAATT
Found at i:623521 original size:15 final size:15
Alignment explanation
Indices: 623487--623544 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 15
623477 CTTCCTTTCG
623487 AATT-TATATTATAT
1 AATTATATATTATAT
**
623501 TTTTATATATTATAT
1 AATTATATATTATAT
*
623516 AATTATAT-TTAAAT
1 AATTATATATTATAT
*
623530 -ATTATATATTTTAT
1 AATTATATATTATAT
623544 A
1 A
623545 TATAATTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
13 7 0.21
14 11 0.32
15 16 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTATATATTATAT
Found at i:623629 original size:29 final size:26
Alignment explanation
Indices: 623592--623673 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 26
623582 TTTGATATGA
623592 TTATATATTTATATATTCATATTATTTT
1 TTATATATTTATATATT-A-ATTATTTT
623620 TTATATTATTTATATATTAATTATTTT
1 TTATA-TATTTATATATTAATTATTTT
* *
623647 GATAGTGTATTTATATTATATAATTAT
1 -TTA-TATATTTATA-TAT-TAATTAT
623674 ATTACATATA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
27 8 0.17
28 16 0.34
29 16 0.34
30 7 0.15
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (26 bp):
TTATATATTTATATATTAATTATTTT
Found at i:623646 original size:26 final size:26
Alignment explanation
Indices: 623592--623673 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 26
623582 TTTGATATGA
623592 TTATA-TATTTATATATTCATATTATTTT
1 TTATATTATTTATATATT-A-ATTA-TTT
623620 TTATATTATTTATATATTAATTATTT
1 TTATATTATTTATATATTAATTATTT
*
623646 TGATAGTGTATTTATATTATATAATTAT
1 TTATA-T-TATTTATA-TAT-TAATTAT
623674 ATTACATATA
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
26 7 0.15
27 5 0.10
28 14 0.29
29 15 0.31
30 7 0.15
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (26 bp):
TTATATTATTTATATATTAATTATTT
Found at i:624706 original size:23 final size:23
Alignment explanation
Indices: 624680--624723 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
624670 TATATTTATT
624680 TTTAAAAAATAATATTTAATAAA
1 TTTAAAAAATAATATTTAATAAA
***
624703 TTTAAATTTTAATATTTAATA
1 TTTAAAAAATAATATTTAATA
624724 TTTATAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTAAAAAATAATATTTAATAAA
Found at i:624731 original size:16 final size:16
Alignment explanation
Indices: 624689--624745 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
624679 TTTTAAAAAA
624689 TAATATTTAATAA-ATT
1 TAATATTT-ATAATATT
624705 TAA-ATTT-TAATATT
1 TAATATTTATAATATT
*
624719 TAATATTTATAATTTT
1 TAATATTTATAATATT
*
624735 TTATATCTTAT
1 TAATAT-TTAT
624746 GACAATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
13 3 0.09
14 6 0.17
15 8 0.23
16 14 0.40
17 4 0.11
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATATTTATAATATT
Found at i:624740 original size:23 final size:22
Alignment explanation
Indices: 624689--624734 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
624679 TTTTAAAAAA
624689 TAATATTTAATAAATTTAAATTT
1 TAATATTTAAT-AATTTAAATTT
624712 TAATATTTAAT-ATTTATAATTT
1 TAATATTTAATAATTTA-AATTT
624734 T
1 T
624735 TTATATCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TAATATTTAATAATTTAAATTT
Found at i:625580 original size:20 final size:20
Alignment explanation
Indices: 625555--625597 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
625545 ACTATATTAC
625555 TTATAT-TTTA-ATATTAATAT
1 TTATATATTTATA-ATTAA-AT
625575 TTATATATTTATAATTAAAT
1 TTATATATTTATAATTAAAT
625595 TTA
1 TTA
625598 AATAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 11 0.52
21 9 0.43
22 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATATATTTATAATTAAAT
Found at i:627501 original size:59 final size:58
Alignment explanation
Indices: 627404--627523 Score: 170
Period size: 59 Copynumber: 2.1 Consensus size: 58
627394 AGATGGTGAA
* * *
627404 AATATAATTTTTTTTTATAAAATGTAATATAATTGAATC-AGTTAGATTTTCAATTCTT
1 AATATAATTTTTTTTTATAAAATGTAATACAATCGAATCGA-TTAAATTTTCAATTCTT
* *
627462 AATATAATATTTTTTTTATAAAATGTAATACAATCGAATCGATTAAATTTTCAGTTTTT
1 AATATAAT-TTTTTTTTATAAAATGTAATACAATCGAATCGATTAAATTTTCAATTCTT
627521 AAT
1 AAT
627524 TAAATTAGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
58 8 0.15
59 46 0.84
60 1 0.02
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (58 bp):
AATATAATTTTTTTTTATAAAATGTAATACAATCGAATCGATTAAATTTTCAATTCTT
Found at i:632180 original size:18 final size:17
Alignment explanation
Indices: 632150--632183 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
632140 TTCTCATTCT
632150 CCTTCTCAAATTCAGCA
1 CCTTCTCAAATTCAGCA
*
632167 CCTTCCTCATATTCAGC
1 CCTT-CTCAAATTCAGC
632184 GGAAGGATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.38, G:0.06, T:0.32
Consensus pattern (17 bp):
CCTTCTCAAATTCAGCA
Found at i:634731 original size:2 final size:2
Alignment explanation
Indices: 634724--634751 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
634714 TGCTCAAAAC
634724 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
634752 TTATTTATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:635135 original size:2 final size:2
Alignment explanation
Indices: 635128--635152 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
635118 TTCTATAGCA
635128 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
635153 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:635957 original size:81 final size:81
Alignment explanation
Indices: 635822--635985 Score: 328
Period size: 81 Copynumber: 2.0 Consensus size: 81
635812 CGTTTGCAAA
635822 TAAAGGATGAGTAGCAATCACCATCTTTCTTCTTCTTTGCCTTCTTGATCTTGTTTTCAATTGCG
1 TAAAGGATGAGTAGCAATCACCATCTTTCTTCTTCTTTGCCTTCTTGATCTTGTTTTCAATTGCG
635887 ATTATAAACATGTTTT
66 ATTATAAACATGTTTT
635903 TAAAGGATGAGTAGCAATCACCATCTTTCTTCTTCTTTGCCTTCTTGATCTTGTTTTCAATTGCG
1 TAAAGGATGAGTAGCAATCACCATCTTTCTTCTTCTTTGCCTTCTTGATCTTGTTTTCAATTGCG
635968 ATTATAAACATGTTTT
66 ATTATAAACATGTTTT
635984 TA
1 TA
635986 GTTGTGTTAT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.45
Consensus pattern (81 bp):
TAAAGGATGAGTAGCAATCACCATCTTTCTTCTTCTTTGCCTTCTTGATCTTGTTTTCAATTGCG
ATTATAAACATGTTTT
Found at i:640374 original size:10 final size:10
Alignment explanation
Indices: 640351--640383 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
640341 TAACTTGAGA
640351 TTTCTTTC-T
1 TTTCTTTCTT
640360 TTTCTTTCTT
1 TTTCTTTCTT
640370 TTTCTTTCATT
1 TTTCTTTC-TT
640381 TTT
1 TTT
640384 TAAACATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 8 0.36
10 9 0.41
11 5 0.23
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:640438 original size:2 final size:2
Alignment explanation
Indices: 640431--640457 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
640421 TTGACCACAA
640431 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
640458 TTACTTACTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:640712 original size:2 final size:2
Alignment explanation
Indices: 640705--640736 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
640695 ATTTTCATCA
*
640705 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
640737 CAAATTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:642255 original size:29 final size:28
Alignment explanation
Indices: 642190--642273 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 28
642180 TTTACCAATT
**
642190 AAAATAATAATATTTTAATAATTTATTTT
1 AAAATAA-AATATTTTAATAATTTATTAA
*
642219 AAATTAAAATTATTTT-ATAATTTATTAAA
1 AAAATAAAA-TATTTTAATAATTTATT-AA
*
642248 AAAATAAAAGTATTTTGATAAATTTA
1 AAAATAAAA-TATTTTAAT-AATTTA
642274 CTATTTGTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
28 12 0.26
29 26 0.57
30 2 0.04
31 6 0.13
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
AAAATAAAATATTTTAATAATTTATTAA
Found at i:643329 original size:14 final size:15
Alignment explanation
Indices: 643306--643344 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
643296 CTGTATAAGT
*
643306 TAAATTTAAA-TTTA
1 TAAATGTAAACTTTA
643320 TAAATGTAAACTTTA
1 TAAATGTAAACTTTA
*
643335 TTAATGTAAA
1 TAAATGTAAA
643345 ATTAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (15 bp):
TAAATGTAAACTTTA
Found at i:644571 original size:6 final size:6
Alignment explanation
Indices: 644560--644590 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
644550 CGCTGCTGAC
644560 AACAGA AACAGA AACAGA AACAGA AACAGA A
1 AACAGA AACAGA AACAGA AACAGA AACAGA A
644591 GCCAGAGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.16, G:0.16, T:0.00
Consensus pattern (6 bp):
AACAGA
Found at i:646806 original size:51 final size:51
Alignment explanation
Indices: 646747--646848 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
646737 AAATCTCTTA
646747 GAATCTCTACTAGAGGAAGGCAAAAAGTTCCTAAAACTTTCAATAATTAGT
1 GAATCTCTACTAGAGGAAGGCAAAAAGTTCCTAAAACTTTCAATAATTAGT
646798 GAATCTCTACTAGAGGAAGGCAAAAAGTTCCTAAAACTTTCAATAATTAGT
1 GAATCTCTACTAGAGGAAGGCAAAAAGTTCCTAAAACTTTCAATAATTAGT
646849 TTCATATTGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (51 bp):
GAATCTCTACTAGAGGAAGGCAAAAAGTTCCTAAAACTTTCAATAATTAGT
Found at i:648019 original size:126 final size:126
Alignment explanation
Indices: 647794--648044 Score: 430
Period size: 126 Copynumber: 2.0 Consensus size: 126
647784 AGTGTATACT
* * *
647794 GAATAAATGCATAAAAGCAGCATGACAAATAAGGAAATACCAGCATGTGACAGTGAACTAAAAAG
1 GAATAAATGCACAAAAGCAGCATCACAAATAAGGAAATACCAGCATGTAACAGTGAACTAAAAAG
* *
647859 GATAAAAAGAAGGCTGATAAACTACATGACAAACATCGGTATACTAAAGAAATGTCTCCAA
66 GATAAAAAGAAGGCTAATAAACTACATGACAAACATCAGTATACTAAAGAAATGTCTCCAA
* * *
647920 GAATAAATGCACAAAATCAGCATCATAAATAAGGAAATACCAGTATGTAACAGTGAACTAAAAAG
1 GAATAAATGCACAAAAGCAGCATCACAAATAAGGAAATACCAGCATGTAACAGTGAACTAAAAAG
647985 GATAAAAAGAAGGCTAATAAACTACATGACAAACATCAGTATACTAAAGAAATGTCTCCA
66 GATAAAAAGAAGGCTAATAAACTACATGACAAACATCAGTATACTAAAGAAATGTCTCCA
648045 CGCTTAAGGC
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 117 1.00
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.18
Consensus pattern (126 bp):
GAATAAATGCACAAAAGCAGCATCACAAATAAGGAAATACCAGCATGTAACAGTGAACTAAAAAG
GATAAAAAGAAGGCTAATAAACTACATGACAAACATCAGTATACTAAAGAAATGTCTCCAA
Found at i:650941 original size:43 final size:43
Alignment explanation
Indices: 650880--650965 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
650870 GTAGGAAGGA
*
650880 TTCTAAAATTCTAAAGATGGGACACACATTATCATGCAAAATT
1 TTCTAAAATTCTAAAGATGGGACACAAATTATCATGCAAAATT
*
650923 TTCTAAAATTCTAAAGATGGGACACAAATTGTCATGCAAAATT
1 TTCTAAAATTCTAAAGATGGGACACAAATTATCATGCAAAATT
650966 CTAAACTTCC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (43 bp):
TTCTAAAATTCTAAAGATGGGACACAAATTATCATGCAAAATT
Found at i:657969 original size:5 final size:5
Alignment explanation
Indices: 657961--658023 Score: 54
Period size: 5 Copynumber: 11.8 Consensus size: 5
657951 ATATTTCCCT
* * *
657961 TTTTA TTTTA TTTTA TTTTA TTTTTAA TTAATTA TTTAA TTATA TTATA
1 TTTTA TTTTA TTTTA TTTTA -TTTT-A TT--TTA TTTTA TTTTA TTTTA
*
658010 TATTA TTTTA TTTT
1 TTTTA TTTTA TTTT
658024 TTATAAATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
5 36 0.75
6 6 0.12
7 4 0.08
8 2 0.04
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (5 bp):
TTTTA
Found at i:658000 original size:12 final size:13
Alignment explanation
Indices: 657963--658022 Score: 54
Period size: 12 Copynumber: 4.8 Consensus size: 13
657953 ATTTCCCTTT
* *
657963 TTATTTTATTTTA
1 TTATATTATTTAA
*
657976 TTTTATT-TTTAA
1 TTATATTATTTAA
657988 TTA-ATTATTTAA
1 TTATATTATTTAA
*
658000 TTATATTATAT-A
1 TTATATTATTTAA
*
658012 TTATTTTATTT
1 TTATATTATTT
658023 TTTATAAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
11 3 0.08
12 24 0.63
13 11 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATATTATTTAA
Found at i:658805 original size:21 final size:22
Alignment explanation
Indices: 658777--658827 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
658767 TAAATTTATT
* *
658777 TAAA-AATTATTTTAA-TTAAA
1 TAAATAATTATTTAAACTGAAA
*
658797 TAAATAATTATTTAAACTGAAC
1 TAAATAATTATTTAAACTGAAA
658819 TAAATAATT
1 TAAATAATT
658828 CAACGTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 4 0.15
21 10 0.38
22 12 0.46
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (22 bp):
TAAATAATTATTTAAACTGAAA
Found at i:659165 original size:21 final size:20
Alignment explanation
Indices: 659131--659176 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
659121 TATTAGATAA
*
659131 AAATTAAAGTTAAAAAAATT
1 AAATTAAAATTAAAAAAATT
**
659151 AAATTGAAAATTAAATTAATT
1 AAATT-AAAATTAAAAAAATT
659172 AAATT
1 AAATT
659177 TTTTATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (20 bp):
AAATTAAAATTAAAAAAATT
Found at i:659234 original size:20 final size:20
Alignment explanation
Indices: 659209--659269 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 20
659199 TAGATTGATT
659209 TATTTAAATAAAATTTTAAA
1 TATTTAAATAAAATTTTAAA
*
659229 TATTTAAAATATAATTTT-AA
1 TATTT-AAATAAAATTTTAAA
*
659249 TA-TTAAAT-AAATATTAAA
1 TATTTAAATAAAATTTTAAA
659267 TAT
1 TAT
659270 AATAAATATG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
17 5 0.14
18 8 0.23
19 2 0.06
20 9 0.26
21 11 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATTTAAATAAAATTTTAAA
Found at i:659805 original size:6 final size:5
Alignment explanation
Indices: 659762--659801 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
659752 ATTTTTATTT
*
659762 ATTAA ATTATA ATTTAA ATTAA ATTAA ATTAA TTTAA ATT
1 ATTAA ATTA-A A-TTAA ATTAA ATTAA ATTAA ATTAA ATT
659802 TAAAATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 24 0.77
6 4 0.13
7 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (5 bp):
ATTAA
Found at i:659819 original size:41 final size:42
Alignment explanation
Indices: 659716--659821 Score: 99
Period size: 41 Copynumber: 2.5 Consensus size: 42
659706 TAAAAAATAT
* * **
659716 TTTAATATATTTTATAATTAAATATAAATAAAAATAATTTTTA
1 TTTAAAATATTTTAT-TTTAAATATAAATAAAAATAATTTAAA
* * * * *
659759 TTTATTAA-ATTATAATTTAAAT-TAAATTAAATTAATTTAAA
1 TTTA-AAATATTTTATTTTAAATATAAATAAAAATAATTTAAA
659800 TTTAAAATATTTTATTTTAAAT
1 TTTAAAATATTTTATTTTAAAT
659822 CTAATCAAAT
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
40 2 0.04
41 31 0.63
42 6 0.12
43 9 0.18
44 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (42 bp):
TTTAAAATATTTTATTTTAAATATAAATAAAAATAATTTAAA
Found at i:660347 original size:12 final size:12
Alignment explanation
Indices: 660302--660361 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 12
660292 AAAAATTTAA
660302 AATTTAAATT-T
1 AATTTAAATTAT
660313 AAGTTTAAA-TAT
1 AA-TTTAAATTAT
660325 AATTT-AATTAT
1 AATTTAAATTAT
*
660336 GATTTAAATTAT
1 AATTTAAATTAT
* *
660348 TA-TTAAAATAT
1 AATTTAAATTAT
660359 AAT
1 AAT
660362 AAATAATGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
10 2 0.05
11 22 0.55
12 16 0.40
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (12 bp):
AATTTAAATTAT
Found at i:661541 original size:16 final size:17
Alignment explanation
Indices: 661500--661541 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
661490 TGAAATATAA
661500 ATATTTT-AATTATTTT
1 ATATTTTAAATTATTTT
*
661516 AAATTTTAAATT-TTTT
1 ATATTTTAAATTATTTT
661532 ATATTTTAAA
1 ATATTTTAAA
661542 AATTATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATTTTAAATTATTTT
Found at i:661601 original size:25 final size:26
Alignment explanation
Indices: 661573--661630 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
661563 ATATATTATA
*
661573 TTTAAATATAT-AAAAATCTAAAT-AT
1 TTTAAATAAATAAAAAAT-TAAATCAT
*
661598 TTTAAAAAAATAAAAAATTAAATCAT
1 TTTAAATAAATAAAAAATTAAATCAT
*
661624 TATAAAT
1 TTTAAAT
661631 TGAGATTAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (26 bp):
TTTAAATAAATAAAAAATTAAATCAT
Found at i:661820 original size:11 final size:13
Alignment explanation
Indices: 661788--661831 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
661778 CAACAATATA
*
661788 TAAATATTAATAT
1 TAAATATTAATTT
*
661801 AAAATA-TATATTT
1 TAAATATTA-ATTT
661814 TAAATATTAATTT
1 TAAATATTAATTT
661827 TAAAT
1 TAAAT
661832 TAAAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 2 0.08
13 22 0.85
14 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAATATTAATTT
Found at i:662066 original size:16 final size:15
Alignment explanation
Indices: 662032--662081 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
662022 TTTATTATAT
662032 ATTTAATTATTTAAA
1 ATTTAATTATTTAAA
662047 ATTTAATTTAATTTAAA
1 ATTTAA-TT-ATTTAAA
* * *
662064 TTTTAAATATTTTAA
1 ATTTAATTATTTAAA
662079 ATT
1 ATT
662082 CAAACATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 14 0.48
16 3 0.10
17 12 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTAATTATTTAAA
Found at i:662762 original size:35 final size:35
Alignment explanation
Indices: 662716--662787 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
662706 TACATATATA
662716 TATATATACATAAAAACTGTAGAAATGAAAATAAT
1 TATATATACATAAAAACTGTAGAAATGAAAATAAT
662751 TATATATACATAAAAACTGTAGAAATGAAAATAAT
1 TATATATACATAAAAACTGTAGAAATGAAAATAAT
662786 TA
1 TA
662788 AATGCTATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.57, C:0.06, G:0.08, T:0.29
Consensus pattern (35 bp):
TATATATACATAAAAACTGTAGAAATGAAAATAAT
Found at i:664225 original size:2 final size:2
Alignment explanation
Indices: 664218--664244 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
664208 TGCCTTTTAC
664218 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
664245 ATGTGACATA
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:665400 original size:10 final size:9
Alignment explanation
Indices: 665375--665399 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
665365 TTTAACATAG
665375 TTTTTTTAA
1 TTTTTTTAA
665384 TTTTTTTAA
1 TTTTTTTAA
665393 TTTTTTT
1 TTTTTTT
665400 TGGAGAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:665670 original size:13 final size:13
Alignment explanation
Indices: 665661--665694 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
665651 TAGATTTTTT
665661 TTTAATATTTATA
1 TTTAATATTTATA
665674 TTTAATATTTATA
1 TTTAATATTTATA
*
665687 TTTGATAT
1 TTTAATAT
665695 ATTTTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (13 bp):
TTTAATATTTATA
Found at i:667764 original size:18 final size:18
Alignment explanation
Indices: 667741--667804 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
667731 ATTTACTAAG
667741 ATATCTTGCATTGTCAGC
1 ATATCTTGCATTGTCAGC
*
667759 ATATCTTTG-ATTGTAATCAAC
1 ATATC-TTGCATTG---TCAGC
*
667780 ATGTCTTGCATTGTCAGC
1 ATATCTTGCATTGTCAGC
667798 ATATCTT
1 ATATCTT
667805 TAATTATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
18 19 0.51
19 3 0.08
20 3 0.08
21 12 0.32
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (18 bp):
ATATCTTGCATTGTCAGC
Found at i:668301 original size:23 final size:24
Alignment explanation
Indices: 668263--668309 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
668253 CGTCAATTGC
668263 CACATCATCAACCATGACAGCATA
1 CACATCATCAACCATGACAGCATA
* *
668287 CACATCCTC-ACCATGTCAGCATA
1 CACATCATCAACCATGACAGCATA
668310 ACAGACACGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.36, C:0.36, G:0.09, T:0.19
Consensus pattern (24 bp):
CACATCATCAACCATGACAGCATA
Found at i:672519 original size:19 final size:19
Alignment explanation
Indices: 672495--672532 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
672485 TACGATGAAT
672495 ATCTTGCATTGTCAACATA
1 ATCTTGCATTGTCAACATA
672514 ATCTTGCATTGTCAACATA
1 ATCTTGCATTGTCAACATA
672533 TTGTCAGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (19 bp):
ATCTTGCATTGTCAACATA
Found at i:672553 original size:29 final size:29
Alignment explanation
Indices: 672502--672601 Score: 88
Period size: 29 Copynumber: 3.6 Consensus size: 29
672492 AATATCTTGC
*
672502 ATTGTCAACATAATCTTGCATTGTCAACAT
1 ATTGTCAGCAT-ATCTTGCATTGTCAACAT
*
672532 ATTGTCAGCATATCTTTG-ATTGT-AATCACC
1 ATTGTCAGCATATC-TTGCATTGTCAA-CA-T
*
672562 A-TG--A--ATATCTTGCATTGTCAGCAT
1 ATTGTCAGCATATCTTGCATTGTCAACAT
672586 ATTGTCAGCATATCTT
1 ATTGTCAGCATATCTT
672602 TGATGGTAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 21
0.69 0.05 0.26
Matches are distributed among these distances:
24 4 0.07
25 14 0.25
26 1 0.02
27 2 0.04
28 2 0.04
29 19 0.34
30 14 0.25
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (29 bp):
ATTGTCAGCATATCTTGCATTGTCAACAT
Found at i:672578 original size:54 final size:54
Alignment explanation
Indices: 672514--672617 Score: 190
Period size: 54 Copynumber: 1.9 Consensus size: 54
672504 TGTCAACATA
*
672514 ATCTTGCATTGTCAACATATTGTCAGCATATCTTTGATTGTAATCACCATGAAT
1 ATCTTGCATTGTCAACATATTGTCAGCATATCTTTGATGGTAATCACCATGAAT
*
672568 ATCTTGCATTGTCAGCATATTGTCAGCATATCTTTGATGGTAATCACCAT
1 ATCTTGCATTGTCAACATATTGTCAGCATATCTTTGATGGTAATCACCAT
672618 CATTATTAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (54 bp):
ATCTTGCATTGTCAACATATTGTCAGCATATCTTTGATGGTAATCACCATGAAT
Found at i:674061 original size:19 final size:19
Alignment explanation
Indices: 674030--674067 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
674020 TGATTCAACC
*
674030 AATTAATTCAATTCATTAA
1 AATTAATTCAATTAATTAA
674049 AATT-ATTCAAATTAATTAA
1 AATTAATTC-AATTAATTAA
674068 TTAAGACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTAATTCAATTAATTAA
Found at i:674577 original size:3 final size:3
Alignment explanation
Indices: 674516--674560 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
674506 GTGGAAAAAC
674516 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
674561 AAGGAGAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:676813 original size:103 final size:99
Alignment explanation
Indices: 676673--676876 Score: 275
Period size: 103 Copynumber: 2.0 Consensus size: 99
676663 CTCAAGAATA
*
676673 ATTAGAAGACTTGAGTATTTATTATTTATTTTGTTTTTAAATAATGTTACATATACATGCATGCA
1 ATTAAAAGACTTGAGTATTTATTATTTATTTTGTTTTTAAATAATGTTACATATACATGCATG--
*
676738 TACATACATATACGTATATACATGATTGCTAGATTCCT
64 --CATACATATACATATATACATGATTGCTAGATTCCT
* * * * *
676776 ATTAAAAGATTTGAGTATTTATTCTTTCCTTTT-TTTTTAGATAATGTTACATTTACATGCATGC
1 ATTAAAAGACTTGAGTATTTATTATTT-ATTTTGTTTTTAAATAATGTTACATATACATGCATGC
* *
676840 ATACATATGCATATATACATGATTGCTATATTCCT
65 ATACATATACATATATACATGATTGCTAGATTCCT
676875 AT
1 AT
676877 CGACTTGACT
Statistics
Matches: 91, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
99 35 0.38
103 52 0.57
104 4 0.04
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (99 bp):
ATTAAAAGACTTGAGTATTTATTATTTATTTTGTTTTTAAATAATGTTACATATACATGCATGCA
TACATATACATATATACATGATTGCTAGATTCCT
Found at i:677609 original size:22 final size:22
Alignment explanation
Indices: 677584--677631 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
677574 ATATATGATG
*
677584 AAATAATAAT-TTATTAAAAAGT
1 AAATAAT-ATCTTATCAAAAAGT
*
677606 AAATTATATCTTATCAAAAAGT
1 AAATAATATCTTATCAAAAAGT
677628 AAAT
1 AAAT
677632 TATCTCATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (22 bp):
AAATAATATCTTATCAAAAAGT
Found at i:678516 original size:65 final size:62
Alignment explanation
Indices: 678436--678565 Score: 147
Period size: 62 Copynumber: 2.0 Consensus size: 62
678426 AAAATGTATC
* * * *
678436 AATTATTTTAAATATC-AATATAATTAATTTGTAATATATAATATTATAATAATAGATAT-TTAA
1 AATTATTTTAAATATCAAAT-TAATT-ATATATAA-ATAT-ATATTATAATAAAAAATATATTAA
678499 A
62 A
* *
678500 AATTAATTTTATATATCAAATTAATTATATATAAATATATGTTATAATAAAAAATATATTAAA
1 AATT-ATTTTAAATATCAAATTAATTATATATAAATATATATTATAATAAAAAATATATTAAA
678563 AAT
1 AAT
678566 AACATATTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
62 16 0.28
63 12 0.21
64 10 0.18
65 16 0.28
66 3 0.05
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (62 bp):
AATTATTTTAAATATCAAATTAATTATATATAAATATATATTATAATAAAAAATATATTAAA
Found at i:678882 original size:16 final size:16
Alignment explanation
Indices: 678861--678896 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
678851 TTGAAAGAAC
*
678861 TCGAACCTAAAATAAT
1 TCGAACATAAAATAAT
*
678877 TCGAACATAAAATGAT
1 TCGAACATAAAATAAT
678893 TCGA
1 TCGA
678897 TTTGAACTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.25
Consensus pattern (16 bp):
TCGAACATAAAATAAT
Found at i:680086 original size:20 final size:20
Alignment explanation
Indices: 680061--680128 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
680051 TACCCAGATG
680061 TATCGATACATTTTTCAATA
1 TATCGATACATTTTTCAATA
* * * *
680081 TATCGATACATGTATGAATG
1 TATCGATACATTTTTCAATA
* *
680101 TATCGATATATTCTTCAATA
1 TATCGATACATTTTTCAATA
*
680121 TATTGATA
1 TATCGATA
680129 TATTATGTCT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (20 bp):
TATCGATACATTTTTCAATA
Found at i:687240 original size:38 final size:39
Alignment explanation
Indices: 687157--687240 Score: 102
Period size: 39 Copynumber: 2.2 Consensus size: 39
687147 CTTCAAAATG
*
687157 ACAAAAAAAAGGTGAAAAGCAAAATCACAAAAAATGAAA
1 ACAAAAAAAAGGTGAAAAGCAAAATCACAAAAAAGGAAA
* *
687196 AGAAAAAAAA-GTGCAAAAGCAAAAT-A-AAAAAGGGAACA
1 ACAAAAAAAAGGTG-AAAAGCAAAATCACAAAAAAGGAA-A
687234 ACAAAAA
1 ACAAAAA
687241 TAAAAAACGA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
37 8 0.21
38 11 0.28
39 20 0.51
ACGTcount: A:0.70, C:0.10, G:0.14, T:0.06
Consensus pattern (39 bp):
ACAAAAAAAAGGTGAAAAGCAAAATCACAAAAAAGGAAA
Found at i:688602 original size:27 final size:27
Alignment explanation
Indices: 688561--689139 Score: 583
Period size: 27 Copynumber: 21.1 Consensus size: 27
688551 TGGCATTTCT
*
688561 TTTTAAAGTCCACAACTCTGTGGCATCC
1 TTTT-AAGTCCACAACTCCGTGGCATCC
* *
688589 TTTTAAGTCCACAACTTCGTGGCATAC
1 TTTTAAGTCCACAACTCCGTGGCATCC
*
688616 TTTTAAAGTCCACAACTCCGTGACATCC
1 TTTT-AAGTCCACAACTCCGTGGCATCC
*
688644 TTTTAAGTCCACAACTCTGTGGCATCCC
1 TTTTAAGTCCACAACTCCGTGGCAT-CC
* * *
688672 TTTAAAGTCCATAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCATCC
* *
688699 TTTTAAAGTCTACAACTCCGTGG-AACC
1 TTTT-AAGTCCACAACTCCGTGGCATCC
**
688726 TTTTTAAAGTCCACAACTCCGTGGCATTA
1 -TTTT-AAGTCCACAACTCCGTGGCATCC
* * * *
688755 TTTTAAGTCCATAACTCCATGGTACCC
1 TTTTAAGTCCACAACTCCGTGGCATCC
* * ** * * *
688782 TTTAAAATCCGTAACTCTGTAGCACCC
1 TTTTAAGTCCACAACTCCGTGGCATCC
* *
688809 TTTTAAAGTCCAAAACTCCGTGGCATCA
1 TTTT-AAGTCCACAACTCCGTGGCATCC
**
688837 TTTTAAGTCCACAACTGTGTGGCA-CC
1 TTTTAAGTCCACAACTCCGTGGCATCC
* * *
688863 ATTTAAAGTCCACAACTCCGTGACACCC
1 -TTTTAAGTCCACAACTCCGTGGCATCC
* *
688891 TTTTAAAGTCCACAACTCTGTGGCATCG
1 TTTT-AAGTCCACAACTCCGTGGCATCC
**
688919 TTTTAAGTCCACAACTGTGTGGCA-CC
1 TTTTAAGTCCACAACTCCGTGGCATCC
* *
688945 ATTTAAAGTCCACAACT-CGTGGCACCC
1 -TTTTAAGTCCACAACTCCGTGGCATCC
* *
688972 TTTTAAAGTCCACAACTTCGTGGCATCG
1 TTTT-AAGTCCACAACTCCGTGGCATCC
689000 TTTTAAGTCCACAACTCCGTGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCATCC
* *
689027 TTTAAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCATCC
* *
689054 TTTTAAAGTCCATAACTCCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCATCC
* *
689082 TTTTAAGTTCACAACTTCGTGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCATCC
* * *
689109 TTTTTAAGCCCACAAGTCAGTGGCA-CC
1 -TTTTAAGTCCACAACTCCGTGGCATCC
689136 TTTT
1 TTTT
689140 TAAAGCCCAC
Statistics
Matches: 460, Mismatches: 76, Indels: 32
0.81 0.13 0.06
Matches are distributed among these distances:
26 15 0.03
27 249 0.54
28 195 0.42
29 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.30
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCGTGGCATCC
Found at i:688629 original size:55 final size:55
Alignment explanation
Indices: 688561--689139 Score: 634
Period size: 55 Copynumber: 10.6 Consensus size: 55
688551 TGGCATTTCT
* * *
688561 TTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTTCGTGGCATAC
1 TTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCC
* *
688616 TTTTAAAGTCCACAACTCCGTGACATCCTTTTAAGTCCACAACTCTGTGGCATCC
1 TTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCC
* * * * *
688671 CTTTAAAGTCCATAACTCCGTGGCACCCTTTTAAAGTCTACAACTCCGTGG-AACC
1 TTTTAAAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTCCGTGGCATCC
** * * *
688726 TTTTTAAAGTCCACAACTCCGTGGCATTATTTTAAGTCCATAACTCCATGGTA-CC
1 -TTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCC
* * ** * * * * *
688781 CTTTAAAATCCGTAACTCTGTAGCACCCTTTTAAAGTCCAAAACTCCGTGGCATCA
1 TTTTAAAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTCCGTGGCATCC
** * * *
688837 TTTT-AAGTCCACAACTGTGTGGCA-CCATTTAAAGTCCACAACTCCGTGACACCC
1 TTTTAAAGTCCACAACTCCGTGGCATCC-TTTTAAGTCCACAACTCCGTGGCATCC
* * **
688891 TTTTAAAGTCCACAACTCTGTGGCATCGTTTTAAGTCCACAACTGTGTGGCA-CC
1 TTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCC
* * * *
688945 ATTTAAAGTCCACAACT-CGTGGCACCCTTTTAAAGTCCACAACTTCGTGGCATCG
1 TTTTAAAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTCCGTGGCATCC
* *
689000 TTTT-AAGTCCACAACTCCGTGGCATCCTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCC
* * * *
689054 TTTTAAAGTCCATAACTCCGTGGCACCCTTTTAAGTTCACAACTTCGTGGCATCC
1 TTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCC
* * * *
689109 TTTTTAAGCCCACAAGTCAGTGGCA-CCTTTT
1 TTTTAAAGTCCACAACTCCGTGGCATCCTTTT
689140 TAAAGCCCAC
Statistics
Matches: 438, Mismatches: 74, Indels: 25
0.82 0.14 0.05
Matches are distributed among these distances:
53 11 0.03
54 126 0.29
55 252 0.58
56 49 0.11
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.30
Consensus pattern (55 bp):
TTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCC
Found at i:688728 original size:82 final size:82
Alignment explanation
Indices: 688561--689150 Score: 631
Period size: 82 Copynumber: 7.2 Consensus size: 82
688551 TGGCATTTCT
* *
688561 TTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTTCGTGGCATACTTTTAAAGTC
1 TTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAAGTC
688626 CACAACTCCGT-GACATCC
66 CACAACTCCGTGGA-A-CC
* * *
688644 TTTT-AAGTCCACAACTCTGTGGCATCCCTTTAAAGTCCATAACTCCGTGGCACCCTTTTAAAGT
1 TTTTAAAGTCCACAACTCTGTGGCAT-CCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAAGT
*
688708 CTACAACTCCGTGGAACC
65 CCACAACTCCGTGGAACC
* ** * * * * *
688726 TTTTTAAAGTCCACAACTCCGTGGCATTATTTTAAGTCCATAACTCCATGGTA-CCCTTTAAAAT
1 -TTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAAGT
** * * *
688790 CCGTAACTCTGTAGCACCC
65 CCACAACTCCGT-GGAACC
* * * ** *
688809 TTTTAAAGTCCAAAACTCCGTGGCATCATTTTAAGTCCACAACTGTGTGGCA-CCATTTAAAGTC
1 TTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAAGTC
688873 CACAACTCCGT-GACACCC
66 CACAACTCCGTGGA-A-CC
* ** *
688891 TTTTAAAGTCCACAACTCTGTGGCATCGTTTTAAGTCCACAACTGTGTGGCA-CCATTTAAAGTC
1 TTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAAGTC
*
688955 CACAACT-CGTGGCACCC
66 CACAACTCCGTGG-AACC
*
688972 TTTTAAAGTCCACAACT-TCGTGGCATCGTTTTAAGTCCACAACTCCGTGGCATCC-TTTAAAGT
1 TTTTAAAGTCCACAACTCT-GTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAAGT
*
689035 CCACAACTCCGTGGCACCC
65 CCACAACTCCGTGG-AACC
* * * * * * *
689054 TTTTAAAGTCCATAACTCCGTGGCACCCTTTTAAGTTCACAACTTCGTGGCATCCTTTTTAAGCC
1 TTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAAGTC
* * *
689119 CACAAGTCAGTGGCACC
66 CACAACTCCGTGGAACC
*
689136 TTTTTAAAGCCCACA
1 -TTTTAAAGTCCACA
689151 CAAGTCGGTG
Statistics
Matches: 438, Mismatches: 54, Indels: 30
0.84 0.10 0.06
Matches are distributed among these distances:
80 2 0.00
81 69 0.16
82 236 0.54
83 109 0.25
84 22 0.05
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.30
Consensus pattern (82 bp):
TTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAAGTC
CACAACTCCGTGGAACC
Found at i:689316 original size:28 final size:28
Alignment explanation
Indices: 688561--690023 Score: 903
Period size: 28 Copynumber: 51.1 Consensus size: 28
688551 TGGCATTTCT
* * * *
688561 TTTTAAAGTCCACAACTCTGTGGCATCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* * **
688589 TTTT-AAGTCCACAACTTC-GTGGCATAC
1 TTTTAAAGCCCACAA-GTCAGTGGCACCC
* * * * *
688616 TTTTAAAGTCCACAACTCCGTGACATCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* * *
688644 TTTT-AAGTCCACAACTCTGTGGCATCCC
1 TTTTAAAGCCCACAAGTCAGTGGCA-CCC
* * * *
688672 -TTTAAAGTCCATAACTCCGTGGCACCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* * * * * *
688699 TTTTAAAGTCTACAACTCCGTGGAACCT
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* * * ***
688727 TTTTAAAGTCCACAACTCCGTGGCATTA
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* * * *
688755 TTTT-AAGTCCATAACTCCA-TGGTACCC
1 TTTTAAAGCCCACAAGT-CAGTGGCACCC
** ** * * *
688782 -TTTAAAATCCGTAACTCTGTAGCACCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* * * * * *
688809 TTTTAAAGTCCAAAACTCCGTGGCATCA
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* * **
688837 TTTT-AAGTCCACAACTGTGTGGCA-CC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* * * * *
688863 ATTTAAAGTCCACAACTCCGTGACACCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* * * * *
688891 TTTTAAAGTCCACAACTCTGTGGCATCG
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* * **
688919 TTTT-AAGTCCACAACTGTGTGGCA-CC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* * *
688945 ATTTAAAGTCCACAACTC-GTGGCACCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* * * *
688972 TTTTAAAGTCCACAACTTC-GTGGCATCG
1 TTTTAAAGCCCACAA-GTCAGTGGCACCC
* * * *
689000 TTTT-AAGTCCACAACTCCGTGGCATCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* * *
689027 -TTTAAAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* * * *
689054 TTTTAAAGTCCATAACTCCGTGGCACCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
** * *
689082 TTTT-AAGTTCACAACTTC-GTGGCATCC
1 TTTTAAAGCCCACAA-GTCAGTGGCACCC
* *
689109 TTTTTAAGCCCACAAGTCAGTGGCACCT
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* *
689137 TTTTAAAGCCCACACAAGTCGGTGGCAACC
1 TTTTAAAG-CC-CACAAGTCAGTGGCACCC
* *
689167 TATTTCAAAGCCCACACAAATCGGTGGCAACCC
1 T-TTT-AAAG-CC-CACAAGTCAGTGGC-ACCC
* *
689200 ATTTGAAAGCCCACACAAGTCGGTGGCAACCC
1 -TTTTAAAG-CC-CACAAGTCAGTGGC-ACCC
* * *
689232 ATTTCAAAGGCCACAAATCAGTGGCACCC
1 -TTTTAAAGCCCACAAGTCAGTGGCACCC
* *
689261 TTTCAAA-CCCATAAGTCAGTGGCACCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* *
689288 TTTTAAAGCTCACAAATCAGTGGCACCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* *
689316 TTTCAAAGCCCACAAGTCAGTGGCACTC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* **
689344 TTTTCAAAGCTCACACGAGTTGGTGGCAACCC
1 TTTT-AAAGC-C-CACAAGTCAGTGGC-ACCC
* * *
689376 TTTTCAAAGCCCACAAGTTAGTGGAATCC
1 TTTT-AAAGCCCACAAGTCAGTGGCACCC
* * * *
689405 TTTCAAAGCCCACGAGTCGGTGGCAACAC
1 TTTTAAAGCCCACAAGTCAGTGGC-ACCC
* * *
689434 TCTTCAAAGCCCACAAATCAGTGGCA-TC
1 T-TTTAAAGCCCACAAGTCAGTGGCACCC
689462 TTTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTT-AAAGCCCACAAGTCAGTGGCACCC
* *
689491 TTTCAAAGCCCACAAGTCAGTGGCACTC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* *
689519 TTTTCAAAGCCCACACGAGTCGGTGGCAATCC
1 TTTT-AAAGCCCACA--AGTCAGTGGC-ACCC
*
689551 TTTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTT-AAAGCCCACAAGTCAGTGGCACCC
* * * *
689580 TTTCAAAGCCCACGAGTCGGTGGCAACAC
1 TTTTAAAGCCCACAAGTCAGTGGC-ACCC
*
689609 TTTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTT-AAAGCCCACAAGTCAGTGGCACCC
* * *
689638 TTTCAAAGCCCACAAGTTAATGGCACCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* **
689666 TTTCAAAGCCCACAAGTCAGTGGCACTT
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* *
689694 TTTTCAAAGCCCATACGAGTCGGTGGCAACCC
1 TTTT-AAAGCCC--ACAAGTCAGTGGC-ACCC
* *
689726 TTTTCAAAGCCCACAAGTCAGTGACATCC
1 TTTT-AAAGCCCACAAGTCAGTGGCACCC
* * ** *
689755 TTTCAAAGCCCACGAGTTGGTGGCAACAC
1 TTTTAAAGCCCACAAGTCAGTGGC-ACCC
*
689784 TTTTCAAAGCCCATAAGTCAGTGGCACCC
1 TTTT-AAAGCCCACAAGTCAGTGGCACCC
* *
689813 TTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* *
689841 TTTCAAAGCCCACACGAGTCGGTGGCAACCC
1 TTTTAAAGCCCACA--AGTCAGTGGC-ACCC
689872 TTTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTT-AAAGCCCACAAGTCAGTGGCACCC
* * * *
689901 TTTCAAAGCCTACAAGTAAGTGGCACTC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* *
689929 TTTCAAAGCCCACAAGTCAGTGGCACTC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
** *
689957 TTTTCAAAGCCCACATGAGTTGGTGGCAACTC
1 TTTT-AAAGCCCACA--AGTCAGTGGC-ACCC
* *
689989 TTTTCAAAGCTCACACAAGTTAGTGGCACCA
1 TTTT-AAAGC-C-CACAAGTCAGTGGCACCC
690020 TTTT
1 TTTT
690024 TTTAAAAAAA
Statistics
Matches: 1194, Mismatches: 183, Indels: 113
0.80 0.12 0.08
Matches are distributed among these distances:
26 23 0.02
27 247 0.21
28 501 0.42
29 93 0.08
30 131 0.11
31 56 0.05
32 132 0.11
33 6 0.01
34 5 0.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (28 bp):
TTTTAAAGCCCACAAGTCAGTGGCACCC
Found at i:689441 original size:58 final size:58
Alignment explanation
Indices: 689100--689971 Score: 774
Period size: 58 Copynumber: 14.9 Consensus size: 58
689090 TCACAACTTC
* ** * * * *
689100 GTGGCATCCTTTTTAAGCCCACAAGTCAGTGGC-A-CCTTTTTAAAGCCCACACAAGTCG
1 GTGGAATCCTTTCAAAGCCCACGAGTCGGTGGCAACCCTTTTCAAAG-CC-CACAAGTCA
* * * * *
689158 GTGGCAA-CCTATTTCAAAGCCCACACAAATCGGTGGCAACCCATTTGAAAGCCCACACAAGTCG
1 GTGG-AATCC--TTTCAAAG-CC-CACGAGTCGGTGGCAACCCTTTTCAAAG-CC-CACAAGTCA
* * * * * *
689222 GTGGCAACCCATTTCAAAGGCCACAAATCAGTGGC-ACCC-TTTCAAA-CCCATAAGTCA
1 GTGG-AATCC-TTTCAAAGCCCACGAGTCGGTGGCAACCCTTTTCAAAGCCCACAAGTCA
* * * * * * *
689279 GTGGCACCCTTTTAAAGCTCACAAATCAGTGGC-ACCC-TTTCAAAGCCCACAAGTCA
1 GTGGAATCCTTTCAAAGCCCACGAGTCGGTGGCAACCCTTTTCAAAGCCCACAAGTCA
* * * *
689335 GTGGCACTCTTTTCAAAGCTCACACGAGTTGGTGGCAACCCTTTTCAAAGCCCACAAGTTA
1 GTGG-AATCCTTTCAAAGC-C-CACGAGTCGGTGGCAACCCTTTTCAAAGCCCACAAGTCA
* * *
689396 GTGGAATCCTTTCAAAGCCCACGAGTCGGTGGCAACACTCTTCAAAGCCCACAAATCA
1 GTGGAATCCTTTCAAAGCCCACGAGTCGGTGGCAACCCTTTTCAAAGCCCACAAGTCA
* * * *
689454 GTGGCATCTTTTCAAAGCCCACAAGTCAGTGGC-ACCC-TTTCAAAGCCCACAAGTCA
1 GTGGAATCCTTTCAAAGCCCACGAGTCGGTGGCAACCCTTTTCAAAGCCCACAAGTCA
* * *
689510 GTGGCACTCTTTTCAAAGCCCACACGAGTCGGTGGCAATCCTTTTCAAAGCCCACAAGTCA
1 GTGG-AATCCTTTCAAAG-CC-CACGAGTCGGTGGCAACCCTTTTCAAAGCCCACAAGTCA
* *
689571 GTGGCATCCTTTCAAAGCCCACGAGTCGGTGGCAACACTTTTCAAAGCCCACAAGTCA
1 GTGGAATCCTTTCAAAGCCCACGAGTCGGTGGCAACCCTTTTCAAAGCCCACAAGTCA
* * ***
689629 GTGGCATCCTTTCAAAGCCCACAAGTTAATGGC-ACCC-TTTCAAAGCCCACAAGTCA
1 GTGGAATCCTTTCAAAGCCCACGAGTCGGTGGCAACCCTTTTCAAAGCCCACAAGTCA
* **
689685 GTGGCACTTTTTTCAAAGCCCATACGAGTCGGTGGCAACCCTTTTCAAAGCCCACAAGTCA
1 GTGG-AATCCTTTCAAAGCCC--ACGAGTCGGTGGCAACCCTTTTCAAAGCCCACAAGTCA
* * *
689746 GT-GACATCCTTTCAAAGCCCACGAGTTGGTGGCAACACTTTTCAAAGCCCATAAGTCA
1 GTGGA-ATCCTTTCAAAGCCCACGAGTCGGTGGCAACCCTTTTCAAAGCCCACAAGTCA
* * * * * *
689804 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC-ATCC-TTTCAAAGCCCACACGAGTCG
1 GTGGAATCCTTTCAAAGCCCACGAGTCGGTGGCAACCCTTTTCAAAGCCCACA--AGTCA
* * * * *
689862 GTGGCAACCCTTTTCAAAGCCCACAAGTCAGTGGC-ACCC-TTTCAAAGCCTACAAGTAA
1 GTGG-AATCC-TTTCAAAGCCCACGAGTCGGTGGCAACCCTTTTCAAAGCCCACAAGTCA
* * * *
689920 GTGGCA-CTCTTTCAAAGCCCACAAGTCAGTGGC-ACTCTTTTCAAAGCCCACA
1 GTGGAATC-CTTTCAAAGCCCACGAGTCGGTGGCAACCCTTTTCAAAGCCCACA
689972 TGAGTTGGTG
Statistics
Matches: 694, Mismatches: 88, Indels: 65
0.82 0.10 0.08
Matches are distributed among these distances:
55 32 0.05
56 103 0.15
57 66 0.10
58 215 0.31
59 41 0.06
60 98 0.14
61 72 0.10
62 25 0.04
63 2 0.00
64 38 0.05
65 2 0.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (58 bp):
GTGGAATCCTTTCAAAGCCCACGAGTCGGTGGCAACCCTTTTCAAAGCCCACAAGTCA
Found at i:689499 original size:175 final size:175
Alignment explanation
Indices: 689100--690018 Score: 1126
Period size: 175 Copynumber: 5.2 Consensus size: 175
689090 TCACAACTTC
* * * *
689100 GTGGCATCCTTTT-TAAGCCCACAAGTCAGTGGCACCTTTTTAAAGCCCACACAAGTCGGTGGCA
1 GTGGCAT-CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGC-
* * * * *
689164 AC-CTATTTCAAAGCCCACACAAATCGGTGGCAACCCATTTGAAAGCCCACACAAGTCGGTGGCA
62 ACTCT-TTTCAAAGCCCACACGAGTCGGTGGCAACCCTTTTCAAAG-CC-CACAAGTCAGTGG-A
* * * * * * *
689228 ACCCATTTCAAAGGCCACAAATCAGTGGC-AC-CCTTTCAAA-CCCATAAGTCA
123 ATCC-TTTCAAAGCCCACGAGTCGGTGGCAACACTTTTCAAAGCCCACAAGTCA
* * *
689279 GTGGCACCCTTTT-AAAGCTCACAAATCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
1 GTGGCA-TCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
689343 CTTTTCAAAGCTCACACGAGTTGGTGGCAACCCTTTTCAAAGCCCACAAGTTAGTGGAATCCTTT
65 CTTTTCAAAGCCCACACGAGTCGGTGGCAACCCTTTTCAAAGCCCACAAGTCAGTGGAATCCTTT
* *
689408 CAAAGCCCACGAGTCGGTGGCAACACTCTTCAAAGCCCACAAATCA
130 CAAAGCCCACGAGTCGGTGGCAACACTTTTCAAAGCCCACAAGTCA
689454 GTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTC
1 GTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTC
* *
689519 TTTTCAAAGCCCACACGAGTCGGTGGCAATCCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC
66 TTTTCAAAGCCCACACGAGTCGGTGGCAACCCTTTTCAAAGCCCACAAGTCAGTGGAATCCTTTC
689584 AAAGCCCACGAGTCGGTGGCAACACTTTTCAAAGCCCACAAGTCA
131 AAAGCCCACGAGTCGGTGGCAACACTTTTCAAAGCCCACAAGTCA
* * * *
689629 GTGGCATCCTTTCAAAGCCCACAAGTTAATGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTT
1 GTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTC
*
689694 TTTTCAAAGCCCATACGAGTCGGTGGCAACCCTTTTCAAAGCCCACAAGTCAGT-GACATCCTTT
66 TTTTCAAAGCCCACACGAGTCGGTGGCAACCCTTTTCAAAGCCCACAAGTCAGTGGA-ATCCTTT
* *
689758 CAAAGCCCACGAGTTGGTGGCAACACTTTTCAAAGCCCATAAGTCA
130 CAAAGCCCACGAGTCGGTGGCAACACTTTTCAAAGCCCACAAGTCA
* * * *
689804 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACACGAGTCGGTGGCAA
1 GTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACA--AGTCAGTGGC-A
* * * * *
689869 CCCTTTTCAAAGCCCACA--AGTCAGTGGC-ACCC-TTTCAAAGCCTACAAGTAAGTGGCA-CTC
63 CTCTTTTCAAAGCCCACACGAGTCGGTGGCAACCCTTTTCAAAGCCCACAAGTCAGTGGAATC-C
* * * **
689929 TTTCAAAGCCCACAAGTCAGTGGC-ACTCTTTTCAAAGCCCACATGAGTTG
127 TTTCAAAGCCCACGAGTCGGTGGCAACACTTTTCAAAGCCCACA--AGTCA
*
689979 GTGGCAACTCTTTTCAAAGCTCACACAAGTTAGTGGCACC
1 GTGGC-A-TCTTTTCAAAGC-C-CACAAGTCAGTGGCACC
690019 ATTTTTTTAA
Statistics
Matches: 656, Mismatches: 66, Indels: 36
0.87 0.09 0.05
Matches are distributed among these distances:
172 20 0.03
173 24 0.04
174 66 0.10
175 394 0.60
176 46 0.07
177 34 0.05
178 19 0.03
179 53 0.08
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.22
Consensus pattern (175 bp):
GTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTC
TTTTCAAAGCCCACACGAGTCGGTGGCAACCCTTTTCAAAGCCCACAAGTCAGTGGAATCCTTTC
AAAGCCCACGAGTCGGTGGCAACACTTTTCAAAGCCCACAAGTCA
Found at i:690471 original size:20 final size:20
Alignment explanation
Indices: 690443--690516 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 20
690433 TTTTACCTAG
690443 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
690463 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
690483 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
690503 ATGTATCGATACAT
1 ATGTATCGATACAT
690517 CTAGTTAAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:691413 original size:23 final size:23
Alignment explanation
Indices: 691377--691432 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
691367 AGCCTTTGAC
691377 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
691399 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
691422 CATGCATTTTT
1 CATGCATTTTT
691433 AACATGTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 6 0.18
23 27 0.82
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:691439 original size:20 final size:21
Alignment explanation
Indices: 691377--691439 Score: 56
Period size: 23 Copynumber: 2.9 Consensus size: 21
691367 AGCCTTTGAC
**
691377 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
**
691399 CATGCATTTTTTTTATTATGTTT
1 CATGCA--TTTTTTAACATGTTT
691422 CATGCA-TTTTTAACATGT
1 CATGCATTTTTTAACATGT
691440 CCAGCATCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.26
22 6 0.16
23 22 0.58
ACGTcount: A:0.21, C:0.11, G:0.10, T:0.59
Consensus pattern (21 bp):
CATGCATTTTTTAACATGTTT
Found at i:694105 original size:65 final size:62
Alignment explanation
Indices: 694025--694154 Score: 147
Period size: 62 Copynumber: 2.0 Consensus size: 62
694015 AAAATGTATC
* * * *
694025 AATTATTTTAAATATC-AATATAATTAATTTGTAATATATAATATTATAATAATAGATAT-TTAA
1 AATTATTTTAAATATCAAAT-TAATT-ATATATAA-ATAT-ATATTATAATAAAAAATATATTAA
694088 A
62 A
* *
694089 AATTAATTTTATATATCAAATTAATTATATATAAATATATGTTATAATAAAAAATATATTAAA
1 AATT-ATTTTAAATATCAAATTAATTATATATAAATATATATTATAATAAAAAATATATTAAA
694152 AAT
1 AAT
694155 AACATATTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
62 16 0.28
63 12 0.21
64 10 0.18
65 16 0.28
66 3 0.05
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (62 bp):
AATTATTTTAAATATCAAATTAATTATATATAAATATATATTATAATAAAAAATATATTAAA
Found at i:694476 original size:16 final size:16
Alignment explanation
Indices: 694451--694485 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
694441 TGAAAGAACC
*
694451 CGAACCTAAAATAATT
1 CGAACATAAAATAATT
*
694467 CGAACATAAAATGATT
1 CGAACATAAAATAATT
694483 CGA
1 CGA
694486 TTTGAACTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.17, G:0.11, T:0.23
Consensus pattern (16 bp):
CGAACATAAAATAATT
Found at i:695710 original size:20 final size:19
Alignment explanation
Indices: 695648--695718 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
695638 TTTTACCCAG
695648 ATGTATCGATACATTTTTCA
1 ATGTATCGATACA-TTTTCA
* * *
695668 ATATATCGATACATGTATGA
1 ATGTATCGATACAT-TTTCA
*
695688 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATT-TTCA
*
695708 ATGTATTGATA
1 ATGTATCGATA
695719 TATTATGTCT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 2 0.05
20 39 0.95
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (19 bp):
ATGTATCGATACATTTTCA
Found at i:702836 original size:38 final size:39
Alignment explanation
Indices: 702755--702836 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 39
702745 CAAAATGACA
* *
702755 AAAAAAAAGGTCAAAAGCAAAATCACAAAAAATGAAAAG
1 AAAAAAAAGGTCAAAAGCAAAATCACAAAAAAGGAAAAC
*
702794 AAAAAAAA-GTGCAAAAGCAAAAT-A-AAAAAGGGAACAAC
1 AAAAAAAAGGT-CAAAAGCAAAATCACAAAAAAGGAA-AAC
702832 AAAAA
1 AAAAA
702837 TAAAAAACGA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
37 8 0.21
38 10 0.26
39 20 0.53
ACGTcount: A:0.71, C:0.10, G:0.13, T:0.06
Consensus pattern (39 bp):
AAAAAAAAGGTCAAAAGCAAAATCACAAAAAAGGAAAAC
Done.