Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002660.1 Hibiscus syriacus cultivar Beakdansim tig00005459_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2211860
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:273661 original size:9 final size:9
Alignment explanation
Indices: 273647--273695 Score: 62
Period size: 9 Copynumber: 5.2 Consensus size: 9
273637 CTAATTGGAG
273647 ATTAAATTT
1 ATTAAATTT
*
273656 ATTAAATTGA
1 ATTAAATT-T
273666 ATTAAATTT
1 ATTAAATTT
*
273675 ATTAAATTGA
1 ATTAAATT-T
273685 ATTAAATTT
1 ATTAAATTT
273694 AT
1 AT
273696 GACCAAATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 18 0.53
10 16 0.47
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (9 bp):
ATTAAATTT
Found at i:273671 original size:19 final size:19
Alignment explanation
Indices: 273647--273695 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
273637 CTAATTGGAG
273647 ATTAAATTTATTAAATTGA
1 ATTAAATTTATTAAATTGA
273666 ATTAAATTTATTAAATTGA
1 ATTAAATTTATTAAATTGA
273685 ATTAAATTTAT
1 ATTAAATTTAT
273696 GACCAAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (19 bp):
ATTAAATTTATTAAATTGA
Found at i:275830 original size:17 final size:18
Alignment explanation
Indices: 275808--275841 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
275798 TCAGCCGGTC
275808 CGGTTC-GAACGGTTCAG
1 CGGTTCTGAACGGTTCAG
*
275825 CGGTTCTGATCGGTTCA
1 CGGTTCTGAACGGTTCA
275842 CTAGTAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.24, G:0.32, T:0.29
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAG
Found at i:277217 original size:28 final size:28
Alignment explanation
Indices: 277177--277232 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
277167 TTTGTGGAGC
*
277177 AGTAGGTGTTAGGGATGAGTAAAACTTG
1 AGTAGGTGTTAGGGATAAGTAAAACTTG
*
277205 AGTAGTTGTTAGGGATAAGTAAAACTTG
1 AGTAGGTGTTAGGGATAAGTAAAACTTG
277233 GTTAGATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.34, C:0.04, G:0.32, T:0.30
Consensus pattern (28 bp):
AGTAGGTGTTAGGGATAAGTAAAACTTG
Found at i:280558 original size:23 final size:23
Alignment explanation
Indices: 280540--280599 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
280530 CTCGTATAAA
280540 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
280563 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
280586 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
280600 ATATAATGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:280848 original size:149 final size:149
Alignment explanation
Indices: 280578--280881 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
280568 CGAAGTGCCC
* *
280578 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTGTAAGAAT
280643 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACAGGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACAGGTTCCAAAGAATATA
280708 CATATGTCCCTAAGAACCG
131 CATATGTCCCTAAGAACCG
280727 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTGTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTGTAAGAAT
280792 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACAGGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACAGGTTCCAAAGAATATA
280857 CATATGTCCCTAAGAACCG
131 CATATGTCCCTAAGAACCG
280876 CGTAGA
1 CGTAGA
280882 CCCTCGACTC
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTGTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACAGGTTCCAAAGAATATA
CATATGTCCCTAAGAACCG
Found at i:282422 original size:21 final size:21
Alignment explanation
Indices: 282392--282436 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
282382 TCTTGTTTGT
* *
282392 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
282413 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
282434 TTG
1 TTG
282437 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:285638 original size:2 final size:2
Alignment explanation
Indices: 285631--285673 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
285621 ACCTAGAACA
285631 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
285673 A
1 A
285674 CAAAATAGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:288277 original size:15 final size:15
Alignment explanation
Indices: 288254--288286 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
288244 CGTAGGACTC
288254 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
288269 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
288284 CTA
1 CTA
288287 TTATACCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.21, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:288465 original size:12 final size:12
Alignment explanation
Indices: 288431--288465 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
288421 TATCATGTTC
**
288431 TCATATCACAGG
1 TCATATCACATA
288443 TCATATCACATA
1 TCATATCACATA
288455 TCATATCACAT
1 TCATATCACAT
288466 GAACATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (12 bp):
TCATATCACATA
Found at i:288906 original size:64 final size:65
Alignment explanation
Indices: 288838--288979 Score: 182
Period size: 64 Copynumber: 2.2 Consensus size: 65
288828 TATTGCTGGG
* * *
288838 ATGCATCGATGCACCG-ATTGCATTCGATGT-TTTACTATTAATGGGATGCATCGATGCACTACT
1 ATGCATCGATGCACCGAATTGCATTCGATGTCTTTACTATTAAAGAG-TGCATCGATGCACTACC
*
288901 T
65 A
* * *
288902 ATGCATCGATGCA-CGAATTGCATTCGATGTCTTTATTTTTAAAGAGTGCATCGATGCATTACCA
1 ATGCATCGATGCACCGAATTGCATTCGATGTCTTTACTATTAAAGAGTGCATCGATGCACTACCA
*
288966 ATGCATCGGTGCAC
1 ATGCATCGATGCAC
288980 ATTCAAACAA
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
63 2 0.03
64 54 0.81
65 11 0.16
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (65 bp):
ATGCATCGATGCACCGAATTGCATTCGATGTCTTTACTATTAAAGAGTGCATCGATGCACTACCA
Found at i:290096 original size:36 final size:36
Alignment explanation
Indices: 290029--290099 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
290019 CCTTAGGTTC
** *
290029 ATAAGGAATTAATAGCTTGATCGGTGTTGAACCTAT
1 ATAAGGAATTAATAGCTTGATCGAAGCTGAACCTAT
*
290065 ATAAGGAATT-ATCAGTTTGATCGAAGCTGAACCTA
1 ATAAGGAATTAAT-AGCTTGATCGAAGCTGAACCTA
290100 CAAAGACTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 2 0.07
36 28 0.93
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (36 bp):
ATAAGGAATTAATAGCTTGATCGAAGCTGAACCTAT
Found at i:290669 original size:5 final size:5
Alignment explanation
Indices: 290659--290704 Score: 56
Period size: 5 Copynumber: 9.2 Consensus size: 5
290649 CCTTTACCCT
* ** *
290659 TTAAA TTAAA TTAAA TTAAA TTAAA CTAAA TGCAA TTAAT TTAAA T
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA T
290705 CACTTAAATT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (5 bp):
TTAAA
Found at i:295530 original size:128 final size:127
Alignment explanation
Indices: 295294--295548 Score: 456
Period size: 128 Copynumber: 2.0 Consensus size: 127
295284 GCTACGGCAA
* *
295294 TTAGCATATATTCTATGGGTTCGAAAATGAAATAAAAGTTTCGAGCTATTCTAAGTTCTAATCAC
1 TTAGCATATATTCTATGGGTTCGAAAATGAAATAAAAGTTTAGAGCTATTCTAAGTTATAATCAC
*
295359 CAAAAGCAAAAACATAAAGCAAAACATAAGATTTCATGCAAAAAACCTGCTGAAACTTCTTT
66 CAAAAGCAAAAACATAAAGCAAAACATAAGATTTCATGCAAAAAACCTACTGAAACTTCTTT
*
295421 TTAGCATATATTCTATGCGGTTCGAAAATGAAATAAAAGTTTAGAGCTATTGTAAGTTATAATCA
1 TTAGCATATATTCTATG-GGTTCGAAAATGAAATAAAAGTTTAGAGCTATTCTAAGTTATAATCA
*
295486 CCAAAAGCAAAAACATAAAGCAAAACATAAGATTTTATGCAAAAAACCTACTGAAACTTCTTT
65 CCAAAAGCAAAAACATAAAGCAAAACATAAGATTTCATGCAAAAAACCTACTGAAACTTCTTT
295549 ACTACAAGTT
Statistics
Matches: 122, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
127 17 0.14
128 105 0.86
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.29
Consensus pattern (127 bp):
TTAGCATATATTCTATGGGTTCGAAAATGAAATAAAAGTTTAGAGCTATTCTAAGTTATAATCAC
CAAAAGCAAAAACATAAAGCAAAACATAAGATTTCATGCAAAAAACCTACTGAAACTTCTTT
Found at i:305154 original size:20 final size:20
Alignment explanation
Indices: 305129--305169 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
305119 AATAAAAAGA
305129 ATACACCATAAAAATATCGG
1 ATACACCATAAAAATATCGG
* *
305149 ATACACCATGAAAATGTCGG
1 ATACACCATAAAAATATCGG
305169 A
1 A
305170 AGCATGAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.20, G:0.15, T:0.20
Consensus pattern (20 bp):
ATACACCATAAAAATATCGG
Found at i:305400 original size:24 final size:24
Alignment explanation
Indices: 305355--305401 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
305345 GGCAATTTTG
* *
305355 ACCTAATATAGGACTAATTATTTA
1 ACCTAATATAGCACTAAATATTTA
305379 ACCTAATATAGCAC-AAGATATTT
1 ACCTAATATAGCACTAA-ATATTT
305402 TATTTTAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.34
Consensus pattern (24 bp):
ACCTAATATAGCACTAAATATTTA
Found at i:305957 original size:18 final size:18
Alignment explanation
Indices: 305927--305961 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
305917 TTAAATTTTG
305927 AATTAGAATAAATAAATA
1 AATTAGAATAAATAAATA
305945 AATTATGAA-AAATAAAT
1 AATTA-GAATAAATAAAT
305962 TTTACATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
AATTAGAATAAATAAATA
Found at i:306626 original size:19 final size:17
Alignment explanation
Indices: 306602--306636 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
306592 ATTACTAAAT
306602 ATAATATTCATTGTTATTA
1 ATAATATT-ATT-TTATTA
306621 ATAATATTATTTTATT
1 ATAATATTATTTTATT
306637 TAGATTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
ATAATATTATTTTATTA
Found at i:308058 original size:42 final size:41
Alignment explanation
Indices: 307895--308119 Score: 175
Period size: 41 Copynumber: 5.3 Consensus size: 41
307885 CAAACAATGA
* * *
307895 GCCTCAATTAT-AAAGATAAAAAGTAATATTAGAAAAATTAAGG
1 GCCTCAATTATAAAAG-TAAAAAATGAGATTA-AAAAATTAA-G
* * * * * *
307938 GCTTCAAATATAAAGGTAAAAAGTGAGATTAAAAAATCAGG
1 GCCTCAATTATAAAAGTAAAAAATGAGATTAAAAAATTAAG
* * * *
307979 GGCTAAATTCTAAAAGTAAAAAATGGGATTAAAAAATTAAG
1 GCCTCAATTATAAAAGTAAAAAATGAGATTAAAAAATTAAG
*
308020 GCCTCAATTATAAAAGTAAAAAATGAGATTGAAAAAATTATG
1 GCCTCAATTATAAAAGTAAAAAATGAGATT-AAAAAATTAAG
* ** * *
308062 AGCATCGGTTATAAAGGT-AAAAATTAGATTGAAAAAAATTAAG
1 -GCCTCAATTATAAAAGTAAAAAATGAGATT--AAAAAATTAAG
* *
308105 ATCCTTAATTATAAA
1 -GCCTCAATTATAAA
308120 TGCAAAAAGT
Statistics
Matches: 144, Mismatches: 34, Indels: 8
0.77 0.18 0.04
Matches are distributed among these distances:
41 58 0.40
42 28 0.19
43 55 0.38
44 3 0.02
ACGTcount: A:0.52, C:0.07, G:0.16, T:0.26
Consensus pattern (41 bp):
GCCTCAATTATAAAAGTAAAAAATGAGATTAAAAAATTAAG
Found at i:308117 original size:43 final size:43
Alignment explanation
Indices: 307893--308143 Score: 144
Period size: 43 Copynumber: 5.9 Consensus size: 43
307883 GTCAAACAAT
* * *
307893 GAGCCTCAATTAT-AAAGATAAAAAGTA-ATATTAGAAAAATTAA
1 GAGCCTCAATTATAAAAG-TAAAAATTAGAT-TGAAAAAAATTAA
* * * * * *
307936 GGGCTTCAAATATAAAGGTAAAAAGTGAGATT--AAAAAA-TCA
1 GAGCCTCAATTATAAAAGTAAAAA-TTAGATTGAAAAAAATTAA
* * * * **
307977 GGGGCTAAATTCTAAAAGTAAAAAATGGGATT--AAAAAATTAA
1 GAGCCTCAATTATAAAAGT-AAAAATTAGATTGAAAAAAATTAA
* *
308019 G-GCCTCAATTATAAAAGTAAAAAATGAGATTG-AAAAAATTAT
1 GAGCCTCAATTATAAAAGT-AAAAATTAGATTGAAAAAAATTAA
* ** *
308061 GAGCATCGGTTATAAAGGTAAAAATTAGATTGAAAAAAATTAA
1 GAGCCTCAATTATAAAAGTAAAAATTAGATTGAAAAAAATTAA
* * * *
308104 GATCCTTAATTATAAATGCAAAAAGTT-GAATTGAAAAAAA
1 GAGCCTCAATTATAAAAGTAAAAA-TTAG-ATTGAAAAAAA
308144 AATTAGAACC
Statistics
Matches: 164, Mismatches: 34, Indels: 19
0.76 0.16 0.09
Matches are distributed among these distances:
41 53 0.32
42 35 0.21
43 56 0.34
44 18 0.11
45 2 0.01
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (43 bp):
GAGCCTCAATTATAAAAGTAAAAATTAGATTGAAAAAAATTAA
Found at i:311937 original size:2 final size:2
Alignment explanation
Indices: 311930--311974 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
311920 ATTTTATTTA
311930 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
311972 AT A
1 AT A
311975 AAACATAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:323346 original size:3 final size:3
Alignment explanation
Indices: 323338--323366 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
323328 GTATTTGTTT
323338 ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
323367 CGGGTCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:325328 original size:30 final size:30
Alignment explanation
Indices: 325292--325362 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
325282 TACCTAAACT
325292 TTTAGTTTTTAAAAAAAATCATACCTAATG
1 TTTAGTTTTTAAAAAAAATCATACCTAATG
**
325322 TTTAGTTTTTTTAAAAAATCATACCTAATG
1 TTTAGTTTTTAAAAAAAATCATACCTAATG
325352 TTTAGTTTTTA
1 TTTAGTTTTTA
325363 TTTCATTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.37, C:0.08, G:0.07, T:0.48
Consensus pattern (30 bp):
TTTAGTTTTTAAAAAAAATCATACCTAATG
Found at i:326783 original size:26 final size:26
Alignment explanation
Indices: 326753--326804 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
326743 TTTTAAACAT
326753 TAATTCTTTCAACTTCAATTTAATAA
1 TAATTCTTTCAACTTCAATTTAATAA
326779 TAATTCTTTCAACTTCAATTTAATAA
1 TAATTCTTTCAACTTCAATTTAATAA
326805 ATTATAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (26 bp):
TAATTCTTTCAACTTCAATTTAATAA
Found at i:329141 original size:3 final size:3
Alignment explanation
Indices: 329133--329164 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
329123 ATGACACTGC
*
329133 TCT TCT TCT TCT TCT TCT TCT TCT TCA TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
329165 CTCTCTCTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:331328 original size:2 final size:2
Alignment explanation
Indices: 331321--331376 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
331311 CACGTTGGAT
331321 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
331363 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
331377 AATGTATGTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:333301 original size:2 final size:2
Alignment explanation
Indices: 333286--333326 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
333276 AGAAAATGAT
333286 AG AG AG A- AG A- 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
333326 A
1 A
333327 AGGACGTCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:335632 original size:16 final size:16
Alignment explanation
Indices: 335613--335644 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
335603 TTATTTTTTC
*
335613 TTTAAATTATATATAT
1 TTTAAAATATATATAT
335629 TTTAAAATATATATAT
1 TTTAAAATATATATAT
335645 ATATATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAAAATATATATAT
Found at i:335851 original size:39 final size:38
Alignment explanation
Indices: 335807--335908 Score: 143
Period size: 39 Copynumber: 2.6 Consensus size: 38
335797 TAAAATAACT
335807 TAGAATGTTAATGTGAAATAATTTAAGAAATTAAGAATC
1 TAGAATGTT-ATGTGAAATAATTTAAGAAATTAAGAATC
* *
335846 TAGAATGTTATGATGACAA-AATTTAAGAAATTAGGAATT
1 TAGAATGTTATG-TGA-AATAATTTAAGAAATTAAGAATC
335885 TAGAATGTTATAGTGAAATAATTT
1 TAGAATGTTAT-GTGAAATAATTT
335909 GAGAGTTGTG
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
38 5 0.09
39 49 0.86
40 3 0.05
ACGTcount: A:0.46, C:0.02, G:0.17, T:0.35
Consensus pattern (38 bp):
TAGAATGTTATGTGAAATAATTTAAGAAATTAAGAATC
Found at i:335951 original size:14 final size:15
Alignment explanation
Indices: 335934--335963 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
335924 AAATTTTAAT
335934 ATAAAATAA-AAATA
1 ATAAAATAATAAATA
335948 ATAAAATAATAAATA
1 ATAAAATAATAAATA
335963 A
1 A
335964 GGTATTGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
ATAAAATAATAAATA
Found at i:337165 original size:20 final size:20
Alignment explanation
Indices: 337091--337168 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
337081 TTTGGTGTAA
* * *
337091 GGAATGTAAGATTATCAGTA
1 GGAATATAAGATTACCAGTG
* *
337111 GGAATGTAAGATTATCAGTG
1 GGAATATAAGATTACCAGTG
*
337131 AGAATATAAGATTACCAGTG
1 GGAATATAAGATTACCAGTG
337151 GGAATATAAGATTACCAG
1 GGAATATAAGATTACCAG
337169 GGAATTAGAT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (20 bp):
GGAATATAAGATTACCAGTG
Found at i:337180 original size:16 final size:19
Alignment explanation
Indices: 337091--337181 Score: 80
Period size: 20 Copynumber: 4.8 Consensus size: 19
337081 TTTGGTGTAA
* * *
337091 GGAATGTAAGATTATCAGTA
1 GGAATATAAGATTACCAG-G
* *
337111 GGAATGTAAGATTATCAGTG
1 GGAATATAAGATTACCAG-G
*
337131 AGAATATAAGATTACCAGTG
1 GGAATATAAGATTACCAG-G
337151 GGAATATAAGATTACCA-G
1 GGAATATAAGATTACCAGG
337169 GGAAT-T-AGATTAC
1 GGAATATAAGATTAC
337182 TGAGAATGTT
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
16 7 0.11
17 1 0.02
18 6 0.09
20 52 0.79
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (19 bp):
GGAATATAAGATTACCAGG
Found at i:337393 original size:37 final size:37
Alignment explanation
Indices: 337320--337394 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
337310 GTTGGAAAAT
* *
337320 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
337357 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
337394 A
1 A
337395 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:339377 original size:42 final size:41
Alignment explanation
Indices: 339324--339411 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 41
339314 ACTATCGCAA
*
339324 TGCGA-TTTTCCAAATTCGTTGTGATAGTCCAAGTTCGCGT
1 TGCGATTTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
*
339364 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
339406 TGCGAT
1 TGCGAT
339412 AGTCGAAGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 5 0.11
41 2 0.05
42 37 0.84
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.36
Consensus pattern (41 bp):
TGCGATTTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
Found at i:339385 original size:21 final size:20
Alignment explanation
Indices: 339340--339502 Score: 116
Period size: 21 Copynumber: 7.8 Consensus size: 20
339330 TTTCCAAATT
*
339340 CGTTGTGATAGTCCAAGTTC
1 CGTTGCGATAGTCCAAGTTC
* *
339360 GCGTTGCGATTTATTCCAAATT-
1 -CGTTGCGA--TAGTCCAAGTTC
*
339382 CGTTGCGATAGTCGAAGTTC
1 CGTTGCGATAGTCCAAGTTC
*
339402 GCGTTGCGATAGTCGAAGTTC
1 -CGTTGCGATAGTCCAAGTTC
* *
339423 GCGTTGCGATTTATTCCAA-TTT
1 -CGTTGCGA--TAGTCCAAGTTC
*
339445 CGTTGCGATAGTCGAAGTTC
1 CGTTGCGATAGTCCAAGTTC
* * *
339465 GCGCTGCGATTTATTCCAAATT-
1 -CGTTGCGA--TAGTCCAAGTTC
339487 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
339503 AATCGCAACG
Statistics
Matches: 114, Mismatches: 18, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
19 21 0.18
20 2 0.02
21 66 0.58
22 2 0.02
23 23 0.20
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCCAAGTTC
Found at i:339414 original size:63 final size:63
Alignment explanation
Indices: 339340--339474 Score: 234
Period size: 63 Copynumber: 2.1 Consensus size: 63
339330 TTTCCAAATT
*
339340 CGTTGTGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCG
* *
339403 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAATTTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCG
*
339466 CGCTGCGAT
1 CGTTGCGAT
339475 TTATTCCAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.34
Consensus pattern (63 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCG
Found at i:339428 original size:42 final size:42
Alignment explanation
Indices: 339340--339499 Score: 134
Period size: 42 Copynumber: 3.8 Consensus size: 42
339330 TTTCCAAATT
* * * *
339340 CGTTGTGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT--
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGA--TAGTCGAAGTTCG
*
339382 CGTTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCG
* *
339424 CGTTGCGATTTATTCCAA-TT-TCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGA--TAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCG
* * *
339466 CGCTGCGATTTATTCCAAATT--CGTTGCGATAGTC
1 CGTTGCGA--TAGTCCAAGTTCGCGTTGCGATAGTC
339500 CAAAATCGCA
Statistics
Matches: 104, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
40 8 0.08
42 86 0.83
43 4 0.04
44 6 0.06
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (42 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCG
Found at i:339491 original size:63 final size:62
Alignment explanation
Indices: 339346--339495 Score: 203
Period size: 63 Copynumber: 2.4 Consensus size: 62
339336 AATTCGTTGT
* *
339346 GATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGC
1 GATAGTCCAAATTC-CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGCTGC
* * *
339409 GATAGTCGAAGTTCGCGTTGCGATTTATTCCAATTTCGTTGCGATAGTCGAAGTTCGCGCTGC
1 GATAGTCCAAATTC-CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGCTGC
*
339472 GATTTATTCCAAATT-CGTTGCGAT
1 GA--TAGTCCAAATTCCGTTGCGAT
339496 AGTCCAAAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
63 71 0.90
65 8 0.10
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.35
Consensus pattern (62 bp):
GATAGTCCAAATTCCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGCTGC
Found at i:340846 original size:64 final size:65
Alignment explanation
Indices: 340733--340879 Score: 176
Period size: 64 Copynumber: 2.3 Consensus size: 65
340723 CATTCATAAG
* *
340733 TGCATCGATGCATTCC-TTTAAAAGAAAGAACATCAAATGCCTTTGATGCA-TCGATGCA-TAGC
1 TGCATCGATGCA-TCCTTTTAAAAGAAAGAACATCAAATGCATTTGATGCACT-GATGCACAAG-
340795 TAA
63 TAA
* * * *
340798 TGCATCGATGCATCCTTTTAAAATAAA-AACATCGAATGCATTTTATGCACTGATGCACAAGTAG
1 TGCATCGATGCATCCTTTTAAAAGAAAGAACATCAAATGCATTTGATGCACTGATGCACAAGTAA
340862 TGCATCGATGCATACCTT
1 TGCATCGATGCAT-CCTT
340880 CATTGAAAGA
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
64 43 0.60
65 29 0.40
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.29
Consensus pattern (65 bp):
TGCATCGATGCATCCTTTTAAAAGAAAGAACATCAAATGCATTTGATGCACTGATGCACAAGTAA
Found at i:341628 original size:31 final size:31
Alignment explanation
Indices: 341534--341641 Score: 94
Period size: 31 Copynumber: 3.5 Consensus size: 31
341524 AGTCGAGGGT
* *
341534 TTTACCTATG-TCTTTCGAGACATATGGACAG
1 TTTACCTAGGTTCTTT-GGGACATATGGACAG
* * ** * *
341565 TATACCTATGTTCTAAGGAACATATGAACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
*
341596 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
* *
341627 -TTGCCGAGGTTCTTT
1 TTTACCTAGGTTCTTT
341642 ATGACCTCTG
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
30 13 0.21
31 45 0.74
32 3 0.05
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (31 bp):
TTTACCTAGGTTCTTTGGGACATATGGACAG
Found at i:350504 original size:21 final size:21
Alignment explanation
Indices: 350478--350517 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
350468 CCCCCTTTGA
*
350478 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
350499 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
350518 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:354643 original size:64 final size:65
Alignment explanation
Indices: 354508--354676 Score: 193
Period size: 64 Copynumber: 2.6 Consensus size: 65
354498 CTGGACAAGG
*
354508 TGCATCGATGCACATA-CATAAGTGCATCGATGCATTCC-TTTAAAAGAAAGAACATCGAATGCC
1 TGCATCGATG--CATAGC-TAA-TGCATCGATGCA-TCCTTTTAAAAGAAAGAACATCGAATGCA
354571 TTTGA
61 TTTGA
* *
354576 TGCATCGATGCATAGCTAATGCATCGATGCATCCTTTTAAAATAAA-AACATCGAATGCATTTTA
1 TGCATCGATGCATAGCTAATGCATCGATGCATCCTTTTAAAAGAAAGAACATCGAATGCATTTGA
* * *
354640 TGCACCGATGCACAAG-TAGTGCATCGATGCATACCTT
1 TGCATCGATGCA-TAGCTAATGCATCGATGCAT-CCTT
354677 CATTGAAAGA
Statistics
Matches: 91, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
64 45 0.49
65 28 0.31
66 7 0.08
67 1 0.01
68 10 0.11
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (65 bp):
TGCATCGATGCATAGCTAATGCATCGATGCATCCTTTTAAAAGAAAGAACATCGAATGCATTTGA
Found at i:355425 original size:31 final size:31
Alignment explanation
Indices: 355331--355438 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 31
355321 AGTCGAGGGT
* *
355331 TTTACCTATG-TCTTTCGAGACATATGGACAG
1 TTTACCTAGGTTCTTT-GGGACATATGGACAG
* * ** *
355362 TATACCTATGTTCTAAGGAACATATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
*
355393 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
* *
355424 -TTGCCGAGGTTCTTT
1 TTTACCTAGGTTCTTT
355439 ATGACCTCTG
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
30 13 0.21
31 47 0.75
32 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (31 bp):
TTTACCTAGGTTCTTTGGGACATATGGACAG
Found at i:355445 original size:30 final size:30
Alignment explanation
Indices: 355353--355459 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 30
355343 TTTCGAGACA
* * * *
355353 TATGGACAGTATACCTATGTTC-TAAGGAACA
1 TATGGACAGT-TACCGAGGTTCTTTAGG-ACC
* *
355384 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTAGGACC
* *
355415 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
* *
355445 TCTGGATAGTTACCG
1 TATGGACAGTTACCG
355460 GGGTCTGTGT
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
30 29 0.46
31 30 0.48
32 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTAGGACC
Found at i:356557 original size:21 final size:21
Alignment explanation
Indices: 356533--356587 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
356523 TTTGTAATAA
356533 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
356554 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
356575 ATCGCAATGCGAA
1 ATCGCAACGCGAA
356588 TATGTAAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:390639 original size:91 final size:92
Alignment explanation
Indices: 390468--390650 Score: 332
Period size: 91 Copynumber: 2.0 Consensus size: 92
390458 TCTATCCCCG
*
390468 TAACCAGTAATTCTCTTTTTCCAAATTCGGACACATTTATTTCATAGTAAAAATATAAACCTGTA
1 TAACCAGTAATTCTCTTTTTCCAAATTCAGACACATTTATTTCATAGTAAAAATATAAACCTGTA
* *
390533 AATCGAATCGGTTCTGTTGTGTAGTAC
66 AATCAAATCGGTTCTGCTGTGTAGTAC
390560 TAACCAGTAATTCTCTTTTTCCAAATTCAGACACATTTA-TTCATAGTAAAAATATAAACCTGTA
1 TAACCAGTAATTCTCTTTTTCCAAATTCAGACACATTTATTTCATAGTAAAAATATAAACCTGTA
390624 AATCAAATCGGTTCTGCTGTGTAGTAC
66 AATCAAATCGGTTCTGCTGTGTAGTAC
390651 ATTGCAAGCT
Statistics
Matches: 88, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
91 50 0.57
92 38 0.43
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (92 bp):
TAACCAGTAATTCTCTTTTTCCAAATTCAGACACATTTATTTCATAGTAAAAATATAAACCTGTA
AATCAAATCGGTTCTGCTGTGTAGTAC
Found at i:398729 original size:25 final size:25
Alignment explanation
Indices: 398679--398734 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
398669 TCTTCATCAT
**
398679 AAAAACAAAGAGAAAAAATTTTAAA
1 AAAAACAAAGAGAAAAAATTAAAAA
* *
398704 AAAAATAAAGGGAAAAAATTAAAAA
1 AAAAACAAAGAGAAAAAATTAAAAA
398729 ATAAAA
1 A-AAAA
398735 ATTAATTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.14
Consensus pattern (25 bp):
AAAAACAAAGAGAAAAAATTAAAAA
Found at i:402169 original size:2 final size:2
Alignment explanation
Indices: 402122--402149 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
402112 AGAAAATTCC
402122 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
402150 AAAGAATCAA
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):
TA
Found at i:404559 original size:20 final size:20
Alignment explanation
Indices: 404534--404578 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
404524 TATTTTAGGA
404534 TAAATTACATA-TTTAGTACC
1 TAAATTA-ATAGTTTAGTACC
*
404554 TAAATTATTAGTTTTAGTACC
1 TAAATTAATAG-TTTAGTACC
404575 TAAA
1 TAAA
404579 CTTTCAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 2 0.09
20 7 0.32
21 13 0.59
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (20 bp):
TAAATTAATAGTTTAGTACC
Found at i:404589 original size:21 final size:21
Alignment explanation
Indices: 404545--404589 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
404535 AAATTACATA
* *
404545 TTTAGTACCTAAATTATTAGT
1 TTTAGTACCTAAATTATCAAT
404566 TTTAGTACCTAAACTT-TCAAT
1 TTTAGTACCTAAA-TTATCAAT
404587 TTT
1 TTT
404590 TTCAAAACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.31, C:0.13, G:0.07, T:0.49
Consensus pattern (21 bp):
TTTAGTACCTAAATTATCAAT
Found at i:406025 original size:21 final size:22
Alignment explanation
Indices: 406001--406059 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
405991 CGGGATGGAA
406001 CAGTGGAAGGA-GCAATTACAG
1 CAGTGGAAGGATGCAATTACAG
* * *
406022 CAGTTGAA-GATTCAATTAGAG
1 CAGTGGAAGGATGCAATTACAG
*
406043 CAGTGGAA-GATTCAATT
1 CAGTGGAAGGATGCAATT
406060 GGAGCCGTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 2 0.06
21 31 0.94
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (22 bp):
CAGTGGAAGGATGCAATTACAG
Found at i:406064 original size:21 final size:21
Alignment explanation
Indices: 406020--406090 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
406010 GAGCAATTAC
* *
406020 AGCAGTTGAAGATTCAATTAG
1 AGCAGTGGAAGATTCAATTGG
406041 AGCAGTGGAAGATTCAATTGG
1 AGCAGTGGAAGATTCAATTGG
* * *
406062 AGCCGTGGAAGAATCAAGTGG
1 AGCAGTGGAAGATTCAATTGG
406083 AGCAGTGG
1 AGCAGTGG
406091 TTGCATCCAG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.34, T:0.21
Consensus pattern (21 bp):
AGCAGTGGAAGATTCAATTGG
Found at i:432332 original size:19 final size:20
Alignment explanation
Indices: 432310--432348 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
432300 AATATTTTTA
*
432310 TTATATTTATG-TTTTAAAT
1 TTATAGTTATGTTTTTAAAT
*
432329 TTATGGTTATGTTTTTAAAT
1 TTATAGTTATGTTTTTAAAT
432349 AATGTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (20 bp):
TTATAGTTATGTTTTTAAAT
Found at i:433143 original size:26 final size:25
Alignment explanation
Indices: 433114--433164 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
433104 TTTTATTCCT
** *
433114 TTAAAATTTTATAAATTTACTCTTTC
1 TTAAAATTAAATAAATTCAC-CTTTC
433140 TTAAAATTAAATAAATTCACCTTTC
1 TTAAAATTAAATAAATTCACCTTTC
433165 ATAATGTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (25 bp):
TTAAAATTAAATAAATTCACCTTTC
Found at i:449043 original size:3 final size:3
Alignment explanation
Indices: 449030--449069 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
449020 ATAAATATAT
*
449030 TTA TATA TTA TTA TTA TT- CTA TTA TTA TTA TTA TTA TTA T
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
449070 AGAAAATGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 29 0.88
4 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:458747 original size:16 final size:16
Alignment explanation
Indices: 458717--458750 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
458707 TTACATTCAG
458717 ATTTTTTTAATAAAAT
1 ATTTTTTTAATAAAAT
458733 ATTTTATTTAA-AAAAT
1 ATTTT-TTTAATAAAAT
458749 AT
1 AT
458751 AAACATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTTTTTAATAAAAT
Found at i:460863 original size:26 final size:26
Alignment explanation
Indices: 460834--460886 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
460824 TGGTTGCCGA
460834 TTAT-TGGAATTCTTTATTGTCTTTTT
1 TTATATGGAA-TCTTTATTGTCTTTTT
* * *
460860 TTATATTGTATCTTTATTTTCTTTTT
1 TTATATGGAATCTTTATTGTCTTTTT
460886 T
1 T
460887 CCCTCAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.70
Consensus pattern (26 bp):
TTATATGGAATCTTTATTGTCTTTTT
Found at i:460964 original size:23 final size:23
Alignment explanation
Indices: 460914--460963 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
460904 TGTGTTTTAC
460914 GTTTTCATATGCCTTTATGACAT
1 GTTTTCATATGCCTTTATGACAT
* * *
460937 GTTTTCTTATG-CTTTTTGGCAT
1 GTTTTCATATGCCTTTATGACAT
460959 GTTTT
1 GTTTT
460964 TTTTTTGTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.14, C:0.14, G:0.16, T:0.56
Consensus pattern (23 bp):
GTTTTCATATGCCTTTATGACAT
Found at i:465800 original size:38 final size:38
Alignment explanation
Indices: 465749--465854 Score: 142
Period size: 38 Copynumber: 2.8 Consensus size: 38
465739 TAAGAGTTGC
*
465749 ATTGTTATGTTTCTAACTTTTTATTCAGTTTAACTTCG
1 ATTGTTATGTTTCTAATTTTTTATTCAGTTTAACTTCG
** *
465787 ATTGTTATGTTTCTAATTTTTTATTCAGTTTCTCTTTG
1 ATTGTTATGTTTCTAATTTTTTATTCAGTTTAACTTCG
** *
465825 ATCATTATGTTTCT-ATTTTTTTTTCAGTTT
1 ATTGTTATGTTTCTAATTTTTTATTCAGTTT
465855 TCCCTTTGAT
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
37 15 0.25
38 46 0.75
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.61
Consensus pattern (38 bp):
ATTGTTATGTTTCTAATTTTTTATTCAGTTTAACTTCG
Found at i:468918 original size:21 final size:22
Alignment explanation
Indices: 468880--468924 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
468870 AATATGTAAG
468880 AATTTAAAAATATTAAAAAATT
1 AATTTAAAAATATTAAAAAATT
468902 AATTT-AAAAT-TTCAAAAAATT
1 AATTTAAAAATATT-AAAAAATT
468923 AA
1 AA
468925 CAAAAAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 2 0.09
21 15 0.68
22 5 0.23
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
AATTTAAAAATATTAAAAAATT
Found at i:468931 original size:21 final size:21
Alignment explanation
Indices: 468885--468933 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
468875 GTAAGAATTT
**
468885 AAAAATATTAAAAAATTAATT
1 AAAAATATTAAAAAATTAACA
*
468906 TAAAAT-TTCAAAAAATTAACA
1 AAAAATATT-AAAAAATTAACA
468927 AAAAATA
1 AAAAATA
468934 CATATTGACT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAATATTAAAAAATTAACA
Found at i:470928 original size:3 final size:3
Alignment explanation
Indices: 470920--470976 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
470910 GGTGTTCCAT
470920 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
470968 TTA TT- TTA T
1 TTA TTA TTA T
470977 CCCTGTTGAG
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:479948 original size:17 final size:17
Alignment explanation
Indices: 479894--479938 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 17
479884 TCAATTTAAC
479894 TATAATAAAAATATAA-
1 TATAATAAAAATATAAT
479910 -A-AAT-AAAATATAAT
1 TATAATAAAAATATAAT
479924 TATAATAAAAATATA
1 TATAATAAAAATATA
479939 TTTTATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
13 9 0.36
14 3 0.12
15 2 0.08
16 3 0.12
17 8 0.32
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TATAATAAAAATATAAT
Found at i:482204 original size:22 final size:21
Alignment explanation
Indices: 482177--482234 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 21
482167 TAAATTTTTC
*
482177 AAAATTTTATTTAAAAAAATTT
1 AAAATTTTATTTAAAAAAA-TA
* *
482199 AAAATTATATTGAAAAAAATA
1 AAAATTTTATTTAAAAAAATA
*
482220 AAAATATT-TTTAAAA
1 AAAATTTTATTTAAAA
482235 TCTTAAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 6 0.20
21 7 0.23
22 17 0.57
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAATTTTATTTAAAAAAATA
Found at i:482234 original size:20 final size:21
Alignment explanation
Indices: 482184--482234 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
482174 TTCAAAATTT
*
482184 TATTTAAAAAAATTTAAAATTA
1 TATTTAAAAAAA-TTAAAAATA
*
482206 TATTGAAAAAAA-TAAAAATA
1 TATTTAAAAAAATTAAAAATA
*
482226 TTTTTAAAA
1 TATTTAAAA
482235 TCTTAAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 14 0.56
22 11 0.44
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
TATTTAAAAAAATTAAAAATA
Found at i:482245 original size:17 final size:18
Alignment explanation
Indices: 482225--482258 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
482215 AAATAAAAAT
*
482225 ATTTTTAAAAT-CTTAAA
1 ATTTTCAAAATCCTTAAA
482242 ATTTTCAAAATCCTTAA
1 ATTTTCAAAATCCTTAA
482259 TCTCAAAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTTCAAAATCCTTAAA
Found at i:482750 original size:2 final size:2
Alignment explanation
Indices: 482743--482793 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
482733 AATTTAGATT
482743 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
482785 TA TA TA TA T
1 TA TA TA TA T
482794 TTAATCACTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:490736 original size:31 final size:29
Alignment explanation
Indices: 490670--490740 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 29
490660 AAAATGTATA
490670 AAATAAA-TTT-ATAAAATTTTAAAGAAT
1 AAATAAATTTTAATAAAATTTTAAAGAAT
**
490697 AAATAAATTATTAATAAAATATTTAAATTAT
1 AAATAAATT-TTAATAAAAT-TTTAAAGAAT
490728 ATAA-AAATTTTAA
1 A-AATAAATTTTAA
490741 AATTTACATA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
27 7 0.19
28 1 0.03
29 2 0.05
30 11 0.30
31 14 0.38
32 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (29 bp):
AAATAAATTTTAATAAAATTTTAAAGAAT
Found at i:493897 original size:15 final size:15
Alignment explanation
Indices: 493877--493913 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
493867 GTATAATGTT
*
493877 TATATTGCAATATTA
1 TATATTACAATATTA
*
493892 TATATTATAATATTA
1 TATATTACAATATTA
493907 TATATTA
1 TATATTA
493914 TTATAGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (15 bp):
TATATTACAATATTA
Found at i:493914 original size:15 final size:15
Alignment explanation
Indices: 493885--493914 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
493875 TTTATATTGC
493885 AATATTATATATTAT
1 AATATTATATATTAT
493900 AATATTATATATTAT
1 AATATTATATATTAT
493915 TATAGGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATATTATATATTAT
Found at i:496773 original size:30 final size:29
Alignment explanation
Indices: 496724--496801 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
496714 TTATTTGGCG
* *
496724 ATTTTTCCGATATATCACCGGTGAACAGTAT
1 ATTTTT-CGATCTAACACCGGT-AACAGTAT
* * *
496755 ATTTCTT-GATCTAACACCGGTCAGATTAT
1 ATTT-TTCGATCTAACACCGGTAACAGTAT
496784 ATTTTTCGATCTAACACC
1 ATTTTTCGATCTAACACC
496802 CTTAGCAGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.05
29 20 0.50
30 12 0.30
31 4 0.10
32 2 0.05
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (29 bp):
ATTTTTCGATCTAACACCGGTAACAGTAT
Found at i:496936 original size:51 final size:52
Alignment explanation
Indices: 496813--496941 Score: 208
Period size: 52 Copynumber: 2.5 Consensus size: 52
496803 TTAGCAGTAA
*
496813 AGCGCGCCTCCTGCACCGCGCTATACGGTGATCTGGCATACACGTGGGGTAT
1 AGCGCGCCTCCTGCACCGCGCTATACGGTGATCTGACATACACGTGGGGTAT
*
496865 AGCGCGCCTCCTGCATCGCGCTATACGGTGATCTGACATACACGT-GGGTAT
1 AGCGCGCCTCCTGCACCGCGCTATACGGTGATCTGACATACACGTGGGGTAT
*
496916 AGCGCGGCC-CCTGCAGCGCGCTATAC
1 AGCGC-GCCTCCTGCACCGCGCTATAC
496942 CTGGATATTT
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
51 27 0.37
52 46 0.63
ACGTcount: A:0.18, C:0.33, G:0.29, T:0.20
Consensus pattern (52 bp):
AGCGCGCCTCCTGCACCGCGCTATACGGTGATCTGACATACACGTGGGGTAT
Found at i:497104 original size:12 final size:10
Alignment explanation
Indices: 497063--497103 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
497053 TTTATCACAC
497063 CAAATTCTCT
1 CAAATTCTCT
497073 CAAATTCTCT
1 CAAATTCTCT
497083 -AAATTTCTCT
1 CAAA-TTCTCT
*
497093 CAAATACTCT
1 CAAATTCTCT
497103 C
1 C
497104 TTTTAAGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:508117 original size:118 final size:120
Alignment explanation
Indices: 507906--508132 Score: 271
Period size: 118 Copynumber: 1.9 Consensus size: 120
507896 GTCAATCATA
* * * *
507906 TATAGAATGATAGAACCTTTTATTCTAAGATAGAAATAACTAATGCACTATGATATTTGTTGAGA
1 TATAGAATGATAGAACCTTTTATTCTAAGATAGAAATAACTAATGCAATATGATATCTGTTAAAA
* * * * *
507971 GTTTGAATTGAAGGAACATGCTATAAGTAGAATCTTATGTTTGACGTTAAACATG
66 GTTTGAAGTGAAGGAACATGCTAAAAGTAAAATCTCATGCTTGACGTTAAACATG
* * * * * *
508026 TATAGAATGATAGTA-CTTTTATTCT-TGGTAGAATTTAA-TAATGCAATTTGGTATCTGTTAAA
1 TATAGAATGATAGAACCTTTTATTCTAAGATAGAA-ATAACTAATGCAATATGATATCTGTTAAA
* *
508088 AGTTTGGAGTGTAGGAACATGCTAAAAGTAAAATCTCATGCTTGA
65 AGTTTGAAGTGAAGGAACATGCTAAAAGTAAAATCTCATGCTTGA
508133 AATGTTGTTA
Statistics
Matches: 89, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
118 62 0.70
119 13 0.15
120 14 0.16
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (120 bp):
TATAGAATGATAGAACCTTTTATTCTAAGATAGAAATAACTAATGCAATATGATATCTGTTAAAA
GTTTGAAGTGAAGGAACATGCTAAAAGTAAAATCTCATGCTTGACGTTAAACATG
Found at i:528480 original size:21 final size:21
Alignment explanation
Indices: 528447--528487 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
528437 TCTGGGCAAG
* *
528447 GGGAATCGGTACCCATTCAAT
1 GGGAACCGATACCCATTCAAT
*
528468 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
528488 ACGACAGAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAT
Found at i:529201 original size:31 final size:31
Alignment explanation
Indices: 529163--529316 Score: 274
Period size: 31 Copynumber: 5.0 Consensus size: 31
529153 GGGTCGAGGG
529163 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
529194 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
529225 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
529256 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
529287 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
529317 GTCCTTCGGG
Statistics
Matches: 120, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
31 119 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:533020 original size:21 final size:21
Alignment explanation
Indices: 532994--533038 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
532984 GATTTCTGGG
* *
532994 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
533015 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
533036 CAA
1 CAA
533039 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:533752 original size:31 final size:31
Alignment explanation
Indices: 533714--533867 Score: 274
Period size: 31 Copynumber: 5.0 Consensus size: 31
533704 GGGTCGAGGG
533714 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
533745 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
533776 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
533807 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
533838 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
533868 GTCCTTCGGG
Statistics
Matches: 120, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
31 119 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:539455 original size:13 final size:13
Alignment explanation
Indices: 539437--539480 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
539427 ATACTATGGT
539437 TTTTCAAACATTA
1 TTTTCAAACATTA
* *
539450 TTTTC-AATAGT-
1 TTTTCAAACATTA
539461 TTTTCAAACATTA
1 TTTTCAAACATTA
539474 TTTTCAA
1 TTTTCAA
539481 TAGTTTTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 5 0.20
12 8 0.32
13 12 0.48
ACGTcount: A:0.34, C:0.14, G:0.02, T:0.50
Consensus pattern (13 bp):
TTTTCAAACATTA
Found at i:539462 original size:24 final size:24
Alignment explanation
Indices: 539435--539492 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
539425 ACATACTATG
539435 GTTTTTCAAACATTATTTTCAATA
1 GTTTTTCAAACATTATTTTCAATA
539459 GTTTTTCAAACATTATTTTCAATA
1 GTTTTTCAAACATTATTTTCAATA
539483 GTTTTTCAAA
1 GTTTTTCAAA
539493 ACTTTGCCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (24 bp):
GTTTTTCAAACATTATTTTCAATA
Found at i:555346 original size:12 final size:12
Alignment explanation
Indices: 555329--555360 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
555319 TTTTTATTTA
555329 ATAAATTTAAAT
1 ATAAATTTAAAT
555341 ATAAATTTAAAT
1 ATAAATTTAAAT
555353 ATATAATT
1 ATA-AATT
555361 ATATAATCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
ATAAATTTAAAT
Found at i:557663 original size:3 final size:3
Alignment explanation
Indices: 557655--557695 Score: 64
Period size: 3 Copynumber: 13.0 Consensus size: 3
557645 TAAAAAATAA
557655 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATGT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT AT-T ATT ATT
557696 TTAAAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 30 0.83
4 6 0.17
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:559725 original size:19 final size:19
Alignment explanation
Indices: 559703--560002 Score: 304
Period size: 19 Copynumber: 17.4 Consensus size: 19
559693 ACGGAAATAC
*
559703 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
559722 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
559736 AATCGCAATGCGGAAATG-A
1 AATCGCAATGC-GAAATGAA
*
559755 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
559769 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
559787 AATCGC-ATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
559805 AATCGCAA--CG--ACGAG
1 AATCGCAATGCGAAATGAA
559820 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
559839 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
559858 AA-CGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
559871 AATCGCAATGCGAAAT-TA
1 AATCGCAATGCGAAATGAA
559889 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
559908 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
559927 AATCGCAATGC-AAATGAA
1 AATCGCAATGCGAAATGAA
559945 AATCG-AA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
559958 AATCGCAATGCG-AATGAA
1 AATCGCAATGCGAAATGAA
559976 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
559995 AATCGCAA
1 AATCGCAA
560003 CGAGATAACC
Statistics
Matches: 237, Mismatches: 11, Indels: 66
0.75 0.04 0.21
Matches are distributed among these distances:
13 8 0.03
14 28 0.12
15 16 0.07
16 18 0.08
17 18 0.08
18 59 0.25
19 87 0.37
20 3 0.01
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:559814 original size:50 final size:53
Alignment explanation
Indices: 559731--560002 Score: 329
Period size: 50 Copynumber: 5.2 Consensus size: 53
559721 AAATCCCAAC
559731 ATGAAAATCGCAATGCGGAAATG-AAATCGCAACGA-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGATGAGAATCGCAATGCGAA
*
559783 ATG-AAATCGC-ATGCGAAATGAAAATCGCAACGACGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGATGAGAATCGCAATGCGAA
*
559834 ATGAAAATCGCAATGCGAAATGAAAA-CGCAACGA-CAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGATGAGAATCGCAATGCGAA
* *
559885 AT-TAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-AA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAGAATCGCAATGCGAA
*
559940 ATGAAAATCG-AA--CGAAA-G--AATCGCAATGCGAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-ATGAGAATCGCAATGCGAA
559990 ATGAAAATCGCAA
1 ATGAAAATCGCAA
560003 CGAGATAACC
Statistics
Matches: 202, Mismatches: 5, Indels: 27
0.86 0.02 0.12
Matches are distributed among these distances:
49 23 0.11
50 62 0.31
51 52 0.26
52 19 0.09
53 21 0.10
55 7 0.03
56 18 0.09
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGATGAGAATCGCAATGCGAA
Found at i:559908 original size:69 final size:69
Alignment explanation
Indices: 559703--560040 Score: 278
Period size: 69 Copynumber: 4.9 Consensus size: 69
559693 ACGGAAATAC
* * *
559703 AATCGCAACGCGAAATGAAAATCCCAACATGA-AAATCGCAATGCGGAAATGAAATCGCAA--CG
1 AATCGCAATGCGAAATGAAAATCGCAAC--GACAAATCGCAATGC-GAAATTAAATCGCAATGCG
*
559765 --A-GAG
63 AAATGAA
* * * *
559769 AATCGCAATGCGAAATG-AAATCGCATGCGAAATGAAAATCGCAA--CGACGA--GAATCGCAAT
1 AATCGCAATGCGAAATGAAAATCGCA-ACG--A--CAAATCGCAATGCGA-AATTAAATCGCAAT
559829 GCGAAATGAA
60 GCGAAATGAA
559839 AATCGCAATGCGAAATGAAAA-CGCAACGACAGAATCGCAATGCGAAATTAAATCGCAATGCGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGACA-AATCGCAATGCGAAATTAAATCGCAATGCGAA
559903 ATGAA
65 ATGAA
* * *
559908 AATCGCAATGCGAAATGAAAATCGCAATG-CAAAT-GAAAATCGAACGAAA--GAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCGCAACGACAAATCG-CAAT-G--CGAAATTAAATCGCAATGC
559969 G-AATGAA
62 GAAATGAA
* * * *
559976 AATCGCAATGCGAAATGAAAATCGCAACGAGATAACCGCAATGCGAAATTATAAACGCATTGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGACA-AATCGCAATGCGAAATTA-AATCGCAATGCGA
560041 TTTTCATTTC
Statistics
Matches: 222, Mismatches: 20, Indels: 55
0.75 0.07 0.19
Matches are distributed among these distances:
64 1 0.00
65 16 0.07
66 28 0.13
67 12 0.05
68 43 0.19
69 69 0.31
70 44 0.20
71 9 0.04
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (69 bp):
AATCGCAATGCGAAATGAAAATCGCAACGACAAATCGCAATGCGAAATTAAATCGCAATGCGAAA
TGAA
Found at i:559962 original size:31 final size:35
Alignment explanation
Indices: 559703--560002 Score: 244
Period size: 37 Copynumber: 8.7 Consensus size: 35
559693 ACGGAAATAC
*
559703 AATCGCAACGCGAAATGAAAATCCCAA--C--ATGAA
1 AATCGCAA-GCGAAATG-AAATCGCAATGCAAATGAA
* *
559736 AATCGCAATGCGGAAATGAAATCGCAA--C-GA-GAG
1 AATCGCAA-GC-GAAATGAAATCGCAATGCAAATGAA
559769 AATCGCAATGCGAAATGAAATCGC-ATGCGAAATGAA
1 AATCGCAA-GCGAAATGAAATCGCAATGC-AAATGAA
*
559805 AATCGCAA-CG--ACGAGAATCGCAATGCGAAATGAA
1 AATCGCAAGCGAAATGA-AATCGCAATGC-AAATGAA
* * *
559839 AATCGCAATGCGAAATGAAAACGCAACG-ACA-G--
1 AATCGCAA-GCGAAATGAAATCGCAATGCAAATGAA
*
559871 AATCGCAATGCGAAATTAAATCGCAATGCGAAATGAA
1 AATCGCAA-GCGAAATGAAATCGCAATGC-AAATGAA
559908 AATCGCAATGCGAAATGAAAATCGCAATGCAAATGAA
1 AATCGCAA-GCGAAATG-AAATCGCAATGCAAATGAA
*
559945 AATCG-AA-CGAAA-G-AATCGCAATGCGAATGAA
1 AATCGCAAGCGAAATGAAATCGCAATGCAAATGAA
559976 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAA-GCGAAATG-AAATCGCAA
560003 CGAGATAACC
Statistics
Matches: 226, Mismatches: 16, Indels: 46
0.78 0.06 0.16
Matches are distributed among these distances:
31 23 0.10
32 43 0.19
33 40 0.18
34 42 0.19
35 5 0.02
36 14 0.06
37 44 0.19
38 15 0.07
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (35 bp):
AATCGCAAGCGAAATGAAATCGCAATGCAAATGAA
Found at i:560136 original size:19 final size:19
Alignment explanation
Indices: 560031--560128 Score: 131
Period size: 19 Copynumber: 5.6 Consensus size: 19
560021 AAATTATAAA
560031 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
560050 C-CATTGCGA-TTTCATTT
1 CGCATTGCGATTTTCATTT
*
560067 CGCATTGCGA---TC-TCT
1 CGCATTGCGATTTTCATTT
560082 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
560099 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
560118 CGCATTGCGAT
1 CGCATTGCGAT
560129 AGTCATTTTT
Statistics
Matches: 70, Mismatches: 2, Indels: 14
0.81 0.02 0.16
Matches are distributed among these distances:
13 6 0.09
15 4 0.06
16 4 0.06
17 13 0.19
18 16 0.23
19 27 0.39
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:560252 original size:14 final size:14
Alignment explanation
Indices: 560233--560269 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
560223 CATCAATTAC
560233 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
560247 ACAAATCATCTTTT
1 ACAAATCAACTTTT
560261 ACAAATCAA
1 ACAAATCAA
560270 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:562189 original size:20 final size:19
Alignment explanation
Indices: 562164--562228 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
562154 TAGTTTACTT
*
562164 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-TAAAA
* *
562184 TCGCAATGCGAAACCAAAA
1 TCGCAACGCGAAACTAAAA
562203 TCGCAACGCGAAA-TAAAA
1 TCGCAACGCGAAACTAAAA
562221 TCGCAACG
1 TCGCAACG
562229 ACAGAATCGC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
18 12 0.30
19 16 0.40
20 12 0.30
ACGTcount: A:0.46, C:0.26, G:0.15, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:562204 original size:19 final size:18
Alignment explanation
Indices: 562180--562298 Score: 83
Period size: 19 Copynumber: 6.8 Consensus size: 18
562170 CACGAAACTT
562180 AAAATCGCAATGCGAAACC
1 AAAATCGCAATGCGAAA-C
* *
562199 AAAATCGCAACGCGAAAT
1 AAAATCGCAATGCGAAAC
562217 AAAATCGCAA--CG--AC
1 AAAATCGCAATGCGAAAC
* *
562231 AGAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAA-C
562250 AAAATCGCAA--CG-AA-
1 AAAATCGCAATGCGAAAC
* * *
562264 AGAATCGCAACGCGAAATG
1 AAAATCGCAATGCGAAA-C
562283 AAAATCGGCAATGCGA
1 AAAATC-GCAATGCGA
562299 TTTGGTTTCG
Statistics
Matches: 80, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
14 19 0.24
16 8 0.10
17 4 0.05
18 11 0.14
19 30 0.38
20 8 0.10
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (18 bp):
AAAATCGCAATGCGAAAC
Found at i:562238 original size:14 final size:14
Alignment explanation
Indices: 562219--562275 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
562209 CGCGAAATAA
*
562219 AATCGCAACGACAG
1 AATCGCAACGAAAG
562233 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
562250 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
562266 AATCGCAACG
1 AATCGCAACG
562276 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:562259 original size:33 final size:33
Alignment explanation
Indices: 562201--562289 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
562191 GCGAAACCAA
*
562201 AATCGCAACGCGAAAT-AAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
562233 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
562266 AATCGCAACGCGAAATGAAAATCG
1 AATCGCAACGCGAAATGAAAATCG
562290 GCAATGCGAT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 15 0.28
33 38 0.72
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:562339 original size:33 final size:33
Alignment explanation
Indices: 562294--562384 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
562284 AAATCGGCAA
562294 TGCGA-TTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
562326 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
562359 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
562385 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 5 0.09
33 48 0.87
34 2 0.04
ACGTcount: A:0.08, C:0.19, G:0.29, T:0.45
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:562347 original size:19 final size:19
Alignment explanation
Indices: 562294--562421 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
562284 AAATCGGCAA
562294 TGCGA-TTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
562312 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
562326 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
562345 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
562359 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
562378 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
562397 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
562417 TGCGA
1 TGCGA
562422 AAGGTTTCTT
Statistics
Matches: 89, Mismatches: 9, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 7 0.08
19 42 0.47
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:562597 original size:92 final size:93
Alignment explanation
Indices: 562459--563106 Score: 1144
Period size: 92 Copynumber: 7.1 Consensus size: 93
562449 TTGAATGGAT
562459 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA-TTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
*
562523 TTTTAGCAGAATTGGCAGCAACCGAACA
66 GTTTAGCAGAATTGGCAGCAACCGAACA
562551 AATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTT-AAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
562614 GTTTAGCAGAATTGGCAGCAACCGAACA
66 GTTTAGCAGAATTGGCAGCAACCGAACA
562642 AATTTACTTTCAACCAAAAGACAAAACAAAGAC-AA-A-TATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
562704 GTTTAGCAGAATTGGCAGCAACCGAACA
66 GTTTAGCAGAATTGGCAGCAACCGAACA
562732 AATTTACTTTCAACCAAAAGACAAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AATTTACTTTCAACCAAAAGAC-AAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
562797 AGTTTAGCAGAATTGGCAGCAACCGAACA
65 AGTTTAGCAGAATTGGCAGCAACCGAACA
562826 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
562890 GTTTAGCAGAATTGGCAGC-ACCGAAACA
66 GTTTAGCAGAATTGGCAGCAACCG-AACA
562918 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TACTTTCACAGTGTTAAAGAATACAC
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA-TTTCACAGTGTTAAAGAATACAC
*
562982 AG-TTAGCAGAATT-GCA-AAACCGAACA
65 AGTTTAGCAGAATTGGCAGCAACCGAACA
563008 AA-TTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
*
563071 GTTTAGCAGAATTGGCAGCAACCGAATA
66 GTTTAGCAGAATTGGCAGCAACCGAACA
563099 AATTTACT
1 AATTTACT
563107 AAGCAATCTA
Statistics
Matches: 537, Mismatches: 4, Indels: 30
0.94 0.01 0.05
Matches are distributed among these distances:
88 40 0.07
89 46 0.09
90 71 0.13
91 112 0.21
92 150 0.28
93 42 0.08
94 76 0.14
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (93 bp):
AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAACA
Found at i:563104 original size:181 final size:185
Alignment explanation
Indices: 562459--563106 Score: 1140
Period size: 181 Copynumber: 3.5 Consensus size: 185
562449 TTGAATGGAT
562459 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA-TTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACA
*
562523 TTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACC-AAAGACAAAACAAAGACAAAT
65 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
562587 ACTATTTCACAGTGTT-AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACA
130 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACA
562642 AATTTACTTTCAACCAAAAGACAAAACAAAGAC-AA-ATATTTCACAGTGTTAAAGAATACACAG
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAG
562705 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAACAAAGACAAAT
66 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGAC-AAAACAAAGACAAAT
562770 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACA
130 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACA
562826 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAG
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAG
562891 TTTAGCAGAATTGGCAGC-ACCGAAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
66 TTTAGCAGAATTGGCAGCAACCG-AACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
*
562955 A-TACTTTCACAGTGTTAAAGAATACACAG-TTAGCAGAATT-GCA-AAACCGAACA
130 ACTA-TTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACA
563008 AA-TTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACA
*
563071 GTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
65 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
563107 AAGCAATCTA
Statistics
Matches: 452, Mismatches: 3, Indels: 22
0.95 0.01 0.05
Matches are distributed among these distances:
180 17 0.04
181 141 0.31
182 23 0.05
183 67 0.15
184 85 0.19
185 47 0.10
186 72 0.16
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (185 bp):
AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAG
TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACA
Found at i:564733 original size:19 final size:18
Alignment explanation
Indices: 564694--564805 Score: 95
Period size: 14 Copynumber: 6.8 Consensus size: 18
564684 GTTGAAATGA
564694 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
564709 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
564726 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
564742 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
564759 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
564775 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
564792 AAATCGCAATGCGA
1 AAATCGCAACGCGA
564806 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 25
0.73 0.04 0.23
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
18 12 0.15
19 16 0.20
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:564737 original size:33 final size:33
Alignment explanation
Indices: 564687--564800 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
564677 AGATTTGGTT
564687 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
564720 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
564753 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
564786 GAAATG-AAATCGCAA
1 GAAATGAAAATCGCAA
564801 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 9 0.12
33 68 0.88
ACGTcount: A:0.45, C:0.21, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:564836 original size:14 final size:14
Alignment explanation
Indices: 564817--564871 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
564807 TTTGGTTTCG
564817 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
564831 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
564850 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
564864 CGTTGCGA
1 CGTTGCGA
564872 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:564849 original size:33 final size:33
Alignment explanation
Indices: 564801--564871 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
564791 GAAATCGCAA
**
564801 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
564834 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
564867 TGCGA
1 TGCGA
564872 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:564879 original size:33 final size:33
Alignment explanation
Indices: 564812--564893 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
564802 GCGATTTTGG
***
564812 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
564845 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
564878 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
564894 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:564898 original size:20 final size:20
Alignment explanation
Indices: 564824--564912 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
564814 TCGCGTTGCG
564824 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
564844 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
564857 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
564877 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
564897 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
564913 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:565026 original size:28 final size:30
Alignment explanation
Indices: 564994--565056 Score: 85
Period size: 33 Copynumber: 2.1 Consensus size: 30
564984 TACTAACTTG
564994 AAATCGCAACG-AGAA-TAACGCGAAATGA
1 AAATCGCAACGAAGAACTAACGCGAAATGA
565022 AAATCGCAACGACAGAATCGTAACGCGAAATGA
1 AAATCGCAACGA-AGAA-C-TAACGCGAAATGA
565055 AA
1 AA
565057 TCTAAGTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
28 11 0.37
30 4 0.13
33 15 0.50
ACGTcount: A:0.49, C:0.19, G:0.21, T:0.11
Consensus pattern (30 bp):
AAATCGCAACGAAGAACTAACGCGAAATGA
Found at i:565286 original size:22 final size:22
Alignment explanation
Indices: 565234--565288 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
565224 TGGTTGTGAG
**
565234 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
565256 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
565278 GGATTTCTTCG
1 GGATTTCTTCG
565289 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:565455 original size:20 final size:20
Alignment explanation
Indices: 565430--565620 Score: 192
Period size: 20 Copynumber: 9.6 Consensus size: 20
565420 CTTTAAATAT
565430 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
565450 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
565472 -TCGTTGCGATTTACGAATA
1 CGCGTTGCGATTTACGGATA
*
565491 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
565511 CGCATTGCGA-TTACCCATA
1 CGCGTTGCGATTTACGGATA
565530 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
565550 CACGTTGCGA-TTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
565569 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
565589 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
565609 CGCGTTGCGATT
1 CGCGTTGCGATT
565621 ATGGAAAATC
Statistics
Matches: 141, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
19 35 0.25
20 89 0.63
21 15 0.11
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:565595 original size:39 final size:39
Alignment explanation
Indices: 565429--565600 Score: 184
Period size: 39 Copynumber: 4.3 Consensus size: 39
565419 GCTTTAAATA
* *
565429 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGA-TTACGGATACGCGTTGCGA-TTTACGGAT
** * *
565470 TATCGTTGCGATTTACGAATACGCGTTGCGATATACGGAT
1 TCGCGTTGCGA-TTACGGATACGCGTTGCGATTTACGGAT
* * **
565510 ACGCATTGCGATTACCCATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTACGGATACGCGTTGCGATTTACGGAT
* * *
565549 ACACGTTGCGATTACGGATACGCGTTGCGATTTATGTG-T
1 TCGCGTTGCGATTACGGATACGCGTTGCGATTTACG-GAT
565588 TCGCGTTGCGATT
1 TCGCGTTGCGATT
565601 TTCATATTCG
Statistics
Matches: 110, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
39 68 0.62
40 14 0.13
41 28 0.25
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (39 bp):
TCGCGTTGCGATTACGGATACGCGTTGCGATTTACGGAT
Found at i:565615 original size:59 final size:58
Alignment explanation
Indices: 565421--565621 Score: 217
Period size: 59 Copynumber: 3.4 Consensus size: 58
565411 ATAATGGCGC
**
565421 TTTA-AATATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGA
1 TTTACAATA-CGCGTTGCGA-TTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGA
* *** *
565481 TTTACGAATACGCGTTGCGATATACGGATACGCATTGCGA-TTACCCATACGCGTTGCGA
1 TTTAC-AATACGCGTTGCGAT-TACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGA
* * *
565540 TTTACGGATACACGTTGCGATTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGA
1 TTTAC-AATACGCGTTGCGATTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGA
* *
565599 TTTTCATATTCGCGTTGCGATTA
1 TTTACA-ATACGCGTTGCGATTA
565622 TGGAAAATCG
Statistics
Matches: 117, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
58 17 0.15
59 64 0.55
60 5 0.04
61 27 0.23
62 4 0.03
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (58 bp):
TTTACAATACGCGTTGCGATTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGA
Found at i:565701 original size:20 final size:20
Alignment explanation
Indices: 565676--565727 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
565666 AAGAATCGCG
*
565676 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
565696 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
565716 TTGCGATTCTGG
1 TTGCGATTCTGG
565728 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:586777 original size:25 final size:25
Alignment explanation
Indices: 586730--586777 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
586720 AAAAGAAATG
**
586730 ACCCTATCAAATCGGTTGGATTGAA
1 ACCCTATCAAATCGGTTAAATTGAA
586755 ACCC-ATCAAATTCGGTTAAATTG
1 ACCCTATCAAA-TCGGTTAAATTG
586778 TCATCTTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (25 bp):
ACCCTATCAAATCGGTTAAATTGAA
Found at i:589591 original size:19 final size:19
Alignment explanation
Indices: 589567--589604 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
589557 ACACCAGGGG
589567 ATGGTGCTATATGTATTTT
1 ATGGTGCTATATGTATTTT
589586 ATGGTGCTATATGTATTTT
1 ATGGTGCTATATGTATTTT
589605 CAAAATTTGT
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:0.21, C:0.05, G:0.21, T:0.53
Consensus pattern (19 bp):
ATGGTGCTATATGTATTTT
Found at i:592082 original size:12 final size:14
Alignment explanation
Indices: 592037--592080 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
592027 TAGTACCTTT
*
592037 AAAATTTCATTATA
1 AAAATTTTATTATA
592051 AAAATTTTATTATA
1 AAAATTTTATTATA
592065 AAAATTTTATTA-A
1 AAAATTTTATTATA
592078 AAA
1 AAA
592081 TTAAAAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 4 0.14
14 25 0.86
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAATTTTATTATA
Found at i:592777 original size:16 final size:16
Alignment explanation
Indices: 592756--592787 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
592746 GAGTTCAGCC
*
592756 TTAAATTTTTAAAATT
1 TTAAATTATTAAAATT
592772 TTAAATTATTAAAATT
1 TTAAATTATTAAAATT
592788 ATGAAATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAATTATTAAAATT
Found at i:592882 original size:77 final size:77
Alignment explanation
Indices: 592780--592936 Score: 314
Period size: 77 Copynumber: 2.0 Consensus size: 77
592770 TTTTAAATTA
592780 TTAAAATTATGAAATAACTGAGAAAATGAATGGTCTTAAAGTAATTGGATTGTTTTTACAATTTC
1 TTAAAATTATGAAATAACTGAGAAAATGAATGGTCTTAAAGTAATTGGATTGTTTTTACAATTTC
592845 ATTTGTAATTTT
66 ATTTGTAATTTT
592857 TTAAAATTATGAAATAACTGAGAAAATGAATGGTCTTAAAGTAATTGGATTGTTTTTACAATTTC
1 TTAAAATTATGAAATAACTGAGAAAATGAATGGTCTTAAAGTAATTGGATTGTTTTTACAATTTC
592922 ATTTGTAATTTT
66 ATTTGTAATTTT
592934 TTA
1 TTA
592937 CGTCTTTAAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 80 1.00
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (77 bp):
TTAAAATTATGAAATAACTGAGAAAATGAATGGTCTTAAAGTAATTGGATTGTTTTTACAATTTC
ATTTGTAATTTT
Found at i:594274 original size:18 final size:18
Alignment explanation
Indices: 594251--594299 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
594241 GGGAGAGATA
*
594251 TTTTTTTAAAAAAGAATG
1 TTTTTTTAAAAAAGAAAG
* * *
594269 TTTTTTTAGAATATAAAG
1 TTTTTTTAAAAAAGAAAG
*
594287 TATTTTTAAAAAA
1 TTTTTTTAAAAAA
594300 AATCTAAAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (18 bp):
TTTTTTTAAAAAAGAAAG
Found at i:595805 original size:5 final size:5
Alignment explanation
Indices: 595795--595832 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
595785 AACACCACCG
595795 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
595833 TCAAACAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:597068 original size:30 final size:30
Alignment explanation
Indices: 597034--597118 Score: 77
Period size: 30 Copynumber: 2.8 Consensus size: 30
597024 ATAAAAGTTT
*
597034 GATAATATAATAATTATTTTATAGT-ATTTA
1 GATAATATAATAA-TATTTTATAATCATTTA
* *
597064 GATAA-ATTATTAATAATTTATAATCATTTA
1 GATAATA-TAATAATATTTTATAATCATTTA
*
597094 -ATAAATTTAATAAATATTTTATAAT
1 GAT-AATATAAT-AATATTTTATAAT
597119 TTTTTAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
29 12 0.27
30 20 0.45
31 12 0.27
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (30 bp):
GATAATATAATAATATTTTATAATCATTTA
Found at i:597086 original size:18 final size:21
Alignment explanation
Indices: 597059--597117 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 21
597049 ATTTTATAGT
*
597059 ATTTAGATAAATTA-TTAAT-A
1 ATTTA-ATAAATCATTTAATAA
597079 ATTT-AT-AATCATTTAATAA
1 ATTTAATAAATCATTTAATAA
*
597098 ATTTAATAAAT-ATTTTATAA
1 ATTTAATAAATCATTTAATAA
597118 TTTTTTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
17 4 0.12
18 7 0.21
19 5 0.15
20 14 0.42
21 3 0.09
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
ATTTAATAAATCATTTAATAA
Found at i:602283 original size:52 final size:52
Alignment explanation
Indices: 602175--602286 Score: 138
Period size: 52 Copynumber: 2.2 Consensus size: 52
602165 AATAATATTC
* *** *
602175 TTTTATTTAAATTTATCACGTTGAAGTGATAAGTTTCAAAAAATATAATTAT
1 TTTTATTAAAATTTATCACGACAAAGTGATAAGTTTCAAAAAAAATAATTAT
*
602227 TTTTATTAAAATTTATCACGACAAAGTGATAAGTTTTAATAAAAAAT-A-TAT
1 TTTTATTAAAATTTATCACGACAAAGTGATAAGTTTCAA-AAAAAATAATTAT
602278 ATTTTATTA
1 -TTTTATTA
602287 GAACTTGTGA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
51 3 0.06
52 43 0.83
53 6 0.12
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (52 bp):
TTTTATTAAAATTTATCACGACAAAGTGATAAGTTTCAAAAAAAATAATTAT
Found at i:613848 original size:32 final size:31
Alignment explanation
Indices: 613806--613895 Score: 126
Period size: 31 Copynumber: 2.9 Consensus size: 31
613796 CAAAAATTAA
* *
613806 GGTACTAAAATGAAACAAAAAGTTAACATTGG
1 GGTACTAAAATGAAACAAAAAGTAAACA-TCG
* *
613838 GGTACCAAAATGAAATAAAAAGTAAACATCG
1 GGTACTAAAATGAAACAAAAAGTAAACATCG
*
613869 GGTACTAAAATGAAACTAAAAGTAAAC
1 GGTACTAAAATGAAACAAAAAGTAAAC
613896 GTTATGTATG
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 26 0.51
32 25 0.49
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (31 bp):
GGTACTAAAATGAAACAAAAAGTAAACATCG
Found at i:616529 original size:14 final size:14
Alignment explanation
Indices: 616510--616552 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
616500 ATAACTTTCG
*
616510 TTAAATTTTAATTT
1 TTAAATTTTAATTA
616524 TTAAA-TTTAATTA
1 TTAAATTTTAATTA
*
616537 TTCAATTTT-ATTA
1 TTAAATTTTAATTA
616550 TTA
1 TTA
616553 CTCCATCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (14 bp):
TTAAATTTTAATTA
Done.