Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold47
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: 2157611
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 149227 characters in sequence are not A, C, G, or T
File 4 of 15
Found at i:350248 original size:115 final size:119
Alignment explanation
Indices: 350064--350289 Score: 277
Period size: 115 Copynumber: 1.9 Consensus size: 119
350054 TTGATCTAAC
* *
350064 ATAATTAAATAAAATAGACTCTAAATAAATAAATTAAATATGAGCGTGAGTCTTATTTTATCTAA
1 ATAATTAAATAAAATAGACTCTAAATAAATAAATTAAATATGAGCGTGAGACTTATTCTATCTAA
** *
350129 TATATAT-T-TA-TTATTGGGCTTT-ATTTTAAATTAAATAATTTATAACTCAAT
66 TATATATATATATTTA-TAAGATTTGATTTTAAATTAAATAATTTATAACTCAAT
* * * * *
350180 ATAATTAAATAAAATA-AGTCTAAATTAATTAATTAAATATGCATG-TTGA-ACTTATTCTATTT
1 ATAATTAAATAAAATAGACTCTAAATAAATAAATTAAATATG-A-GCGTGAGACTTATTCTATCT
*
350242 ATTATATATATATATTTATAAGATTTGATTTTAAATTAAATAATTTAT
64 AATATATATATATATTTATAAGATTTGATTTTAAATTAAATAATTTAT
350290 GACCTTATTT
Statistics
Matches: 93, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
115 40 0.43
116 21 0.23
117 8 0.09
118 24 0.26
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (119 bp):
ATAATTAAATAAAATAGACTCTAAATAAATAAATTAAATATGAGCGTGAGACTTATTCTATCTAA
TATATATATATATTTATAAGATTTGATTTTAAATTAAATAATTTATAACTCAAT
Found at i:350680 original size:2 final size:2
Alignment explanation
Indices: 350668--350700 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
350658 TAAGCCAATG
*
350668 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
350701 GAATCTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:350796 original size:17 final size:17
Alignment explanation
Indices: 350776--350830 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
350766 TAAAAAATTT
*
350776 AAATAAAAATATTATAA
1 AAATAAAATTATTATAA
*
350793 AAATAAAATTA-AATAAA
1 AAATAAAATTATTAT-AA
350810 AAATAAAATTCATT-TAA
1 AAATAAAATT-ATTATAA
350827 AAAT
1 AAAT
350831 TAATTTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
16 2 0.06
17 28 0.88
18 2 0.06
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATAAAATTATTATAA
Found at i:351902 original size:2 final size:2
Alignment explanation
Indices: 351895--351929 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
351885 CTCCTTGCTT
351895 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
351930 CTTGGTGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:354310 original size:79 final size:80
Alignment explanation
Indices: 354197--354351 Score: 190
Period size: 79 Copynumber: 1.9 Consensus size: 80
354187 ATATTTTCCG
* * * *
354197 ATGAGAAATTTAATATTTTGGAGATAATAACGGGGTTGGAGTGTTCCCTTGAAAATAACGAGGCT
1 ATGAGAAATTCAATATTTTGGAGATAATAACGGGGTTGGAGTATCCCCTCGAAAATAACGAGGCT
354262 GGAGTATCCCCAATT
66 GGAGTATCCCCAATT
* * * *
354277 ATGAGAAA-TCAATATTTTGG-GAATAA-AGCCGGGGTTGGAGTATCCCCTCGGAAGTAACGGGG
1 ATGAGAAATTCAATATTTTGGAG-ATAATA-ACGGGGTTGGAGTATCCCCTCGAAAATAACGAGG
*
354339 TTGGAGTATCCCC
64 CTGGAGTATCCCC
354352 GATGAAATAA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
78 2 0.03
79 54 0.84
80 8 0.12
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (80 bp):
ATGAGAAATTCAATATTTTGGAGATAATAACGGGGTTGGAGTATCCCCTCGAAAATAACGAGGCT
GGAGTATCCCCAATT
Found at i:354346 original size:28 final size:28
Alignment explanation
Indices: 354306--354377 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
354296 GGAATAAAGC
** *
354306 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
354334 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
354362 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
354378 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:354435 original size:52 final size:52
Alignment explanation
Indices: 354365--354764 Score: 237
Period size: 52 Copynumber: 7.6 Consensus size: 52
354355 GAAATAACGA
*
354365 GGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTTGGAAATAAAATCGG
* ** * * * *
354417 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTG-TTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-GTGAAAAATTGATGTTTTTGGAAATAAAATCGG
*** * * *
354469 GGTTGGAGTATCCCCGATTGTGAAAAAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGA-T-GT-TTTTGGAAATAAAATCGG
* * ** * *
354524 GGTTGGAGTATCCCCAATTATGAAAAATCAAT-ATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTTGGAAATAAAATCGG
* * **** * *
354575 GGTTGGAGTATCCCC--TCG-GAAATAACGGGGTTGAAGTATCCCCGATGAT-TAA-CGG
1 GGTTGGAGTATCCCCGATTGTGAAA-AA-----TTGATGT-TTTTGGA-AATAAAATCGG
* * *
354630 GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGAAAAAAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAA-AAATTGATG-TTTTTGGAAATAAAATCGG
* * *
354684 AGTTGGAGTAT-CCCGATTAT-AGAAAATT-A-GTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGA-AAAATTGATGT-TTTTGGAAATAAAATCGG
* * * *
354734 AGTTGGAATATCCCCGATTGTGGAGAATTGA
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGA
354765 GAAACTAAAC
Statistics
Matches: 262, Mismatches: 60, Indels: 52
0.70 0.16 0.14
Matches are distributed among these distances:
48 4 0.02
49 4 0.02
50 28 0.11
51 47 0.18
52 60 0.23
53 28 0.11
54 17 0.06
55 60 0.23
56 4 0.02
57 4 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTTGGAAATAAAATCGG
Found at i:354517 original size:55 final size:53
Alignment explanation
Indices: 354365--354589 Score: 203
Period size: 55 Copynumber: 4.3 Consensus size: 53
354355 GAAATAACGA
* *** *
354365 GGTTGGAGTATCCTCGATTGTGAAAAATTGA-TGT-TTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAAAAAATTGTGTTTT-GAAATAAAACCGG
* **
354417 AGTTGGAGTATCCCCGA-T-T-AAAGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAAAAAATT-GTGTTTTG-AAATAAAACCGG
*
354469 GGTTGGAGTATCCCCGATTGTGAAAAAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAAAAAATT-GTGTTTT-GAAATAAAACCGG
* * ** * * **
354524 GGTTGGAGTATCCCCAATTATGAAAAATCAA-TAT-TTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAAAAAATTGTGTTTTGAAATAAAACCGG
354575 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
354590 TCGGAAATAA
Statistics
Matches: 143, Mismatches: 22, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
49 4 0.03
50 2 0.01
51 29 0.20
52 49 0.34
53 2 0.01
54 2 0.01
55 54 0.38
56 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (53 bp):
GGTTGGAGTATCCCCGATTGTGAAAAAAAAATTGTGTTTTGAAATAAAACCGG
Found at i:354576 original size:106 final size:104
Alignment explanation
Indices: 354365--354589 Score: 254
Period size: 106 Copynumber: 2.1 Consensus size: 104
354355 GAAATAACGA
* *** * *
354365 GGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTTTTGGAAATAAAATCGGAGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTGTGAAAAAAAAATGTTTTTAGAAATAAAACCGGAGTTGGAGTATCC
* * *** *
354430 CCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGG
66 CCAATTAAAGAAAAATCAATATTTTGAAAATAAAACCGG
* *
354469 GGTTGGAGTATCCCCGATTGTGAAAAAAAAATTAGTGTTTTAGCAATAAAACCGGGGTTGGAGTA
1 GGTTGGAGTATCCCCGATTGTGAAAAAAAAA-T-GT-TTTTAGAAATAAAACCGGAGTTGGAGTA
* * **
354534 TCCCCAATT-ATGAAAAATCAATATTTTGGAAATAAAGTCGG
63 TCCCCAATTAAAGAAAAATCAATATTTTGAAAATAAAACCGG
354575 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
354590 TCGGAAATAA
Statistics
Matches: 100, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
104 27 0.27
105 1 0.01
106 40 0.40
107 32 0.32
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (104 bp):
GGTTGGAGTATCCCCGATTGTGAAAAAAAAATGTTTTTAGAAATAAAACCGGAGTTGGAGTATCC
CCAATTAAAGAAAAATCAATATTTTGAAAATAAAACCGG
Found at i:354639 original size:27 final size:28
Alignment explanation
Indices: 354572--354647 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 28
354562 GAAATAAAGT
***
354572 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
354600 CGGGGTTGAAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
354627 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
354648 TGTGAAGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 24 0.57
28 18 0.43
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:357323 original size:20 final size:20
Alignment explanation
Indices: 357298--357350 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
357288 TACCACTGTT
357298 TGTATCGATACATGGGACAA
1 TGTATCGATACATGGGACAA
*
357318 TGTATCGATACATGGGACAG
1 TGTATCGATACATGGGACAA
*
357338 TGTATCAATACAT
1 TGTATCGATACAT
357351 TGTATTGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (20 bp):
TGTATCGATACATGGGACAA
Found at i:366097 original size:13 final size:13
Alignment explanation
Indices: 366079--366103 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
366069 CATTATGCTT
366079 TGTATCGATACAA
1 TGTATCGATACAA
366092 TGTATCGATACA
1 TGTATCGATACA
366104 TGCTCATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:366099 original size:33 final size:32
Alignment explanation
Indices: 366057--366122 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
366047 TACACACCTA
* *
366057 AATGTATCGATACATTATGCTTTGTATCGATAC
1 AATGTATCGATACATGAT-CATTGTATCGATAC
*
366090 AATGTATCGATACATGCTCATTGTATCGATAC
1 AATGTATCGATACATGATCATTGTATCGATAC
366122 A
1 A
366123 TAGACAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATGATCATTGTATCGATAC
Found at i:366134 original size:20 final size:19
Alignment explanation
Indices: 366088--366145 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 19
366078 TTGTATCGAT
366088 ACAA-TGTATCGATACATG
1 ACAATTGTATCGATACATG
*
366106 -CTCATTGTATCGATACATAG
1 AC-AATTGTATCGATACAT-G
366126 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
366145 A
1 A
366146 GATTGGCAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
17 1 0.03
18 1 0.03
19 15 0.44
20 16 0.47
21 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (19 bp):
ACAATTGTATCGATACATG
Found at i:366214 original size:13 final size:13
Alignment explanation
Indices: 366196--366242 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
366186 TGGGACAATA
366196 TATCGATACATTG
1 TATCGATACATTG
366209 TATCGATACA-TG
1 TATCGATACATTG
366221 -AT-GA-A-ATTG
1 TATCGATACATTG
366230 TATCGATACATTG
1 TATCGATACATTG
366243 CTTGTAACGG
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
8 1 0.03
9 3 0.10
10 4 0.14
11 4 0.14
12 3 0.10
13 14 0.48
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:366215 original size:33 final size:34
Alignment explanation
Indices: 366173--366242 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 34
366163 CTACCACTGT
366173 TTGTATCGATACATG-GGACAA-TATATCGATACA
1 TTGTATCGATACATGAGGA-AATTATATCGATACA
* *
366206 TTGTATCGATACATGATGAAATTGTATCGATACA
1 TTGTATCGATACATGAGGAAATTATATCGATACA
366240 TTG
1 TTG
366243 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 17 0.52
34 16 0.48
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (34 bp):
TTGTATCGATACATGAGGAAATTATATCGATACA
Found at i:367544 original size:18 final size:18
Alignment explanation
Indices: 367523--367558 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
367513 ATGTAGATCG
*
367523 AAAATTAAATAATTTTGA
1 AAAATGAAATAATTTTGA
*
367541 AAAATGAAATATTTTTGA
1 AAAATGAAATAATTTTGA
367559 GATTTTTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
AAAATGAAATAATTTTGA
Found at i:368007 original size:51 final size:52
Alignment explanation
Indices: 367921--368026 Score: 178
Period size: 51 Copynumber: 2.1 Consensus size: 52
367911 ATTCTAACAA
* *
367921 AAAATAATTTTTGAACTCGGACTTCACTCATCACTAATAGCATGC-CAAGAG
1 AAAATAATTTTTGAACTCGAACTTCACTCAACACTAATAGCATGCACAAGAG
*
367972 AAAATAATTTTTGAACTCGAACTTCGCTCAACACTAATAGCATGCACAAGAG
1 AAAATAATTTTTGAACTCGAACTTCACTCAACACTAATAGCATGCACAAGAG
368024 AAA
1 AAA
368027 GTACTATAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
51 42 0.82
52 9 0.18
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25
Consensus pattern (52 bp):
AAAATAATTTTTGAACTCGAACTTCACTCAACACTAATAGCATGCACAAGAG
Found at i:372789 original size:29 final size:29
Alignment explanation
Indices: 372747--372811 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
372737 AAAAAATTAT
*
372747 TTAAGAAAGCTTCAATCTTTTTATTTAGA
1 TTAATAAAGCTTCAATCTTTTTATTTAGA
372776 TTAATAAAGCTTCAATCTTTTTATTTAGA
1 TTAATAAAGCTTCAATCTTTTTATTTAGA
372805 TTAATAA
1 TTAATAA
372812 TTATTAATCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.46
Consensus pattern (29 bp):
TTAATAAAGCTTCAATCTTTTTATTTAGA
Found at i:375499 original size:9 final size:9
Alignment explanation
Indices: 375485--375522 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
375475 AAAAAATTTC
375485 TATTTAAAT
1 TATTTAAAT
375494 TATTTAAAT
1 TATTTAAAT
*
375503 TTTATTAAAT
1 TAT-TTAAAT
375513 TATTTAAAT
1 TATTTAAAT
375522 T
1 T
375523 TAAATTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TATTTAAAT
Found at i:375504 original size:15 final size:16
Alignment explanation
Indices: 375454--375538 Score: 61
Period size: 15 Copynumber: 5.3 Consensus size: 16
375444 AGTTCACAAG
375454 ATATT-AATCTATTTAA
1 ATATTAAAT-TATTTAA
** **
375470 ATATTAAAAAATTTCT
1 ATATTAAATTATTTAA
375486 AT-TTAAATTATTTAA
1 ATATTAAATTATTTAA
375501 ATTTTATTAAATTATTTAA
1 A---TATTAAATTATTTAA
*
375520 AT-TTAAATTA-ATAA
1 ATATTAAATTATTTAA
375534 ATATT
1 ATATT
375539 TTTAAAAAGA
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
14 5 0.09
15 20 0.37
16 12 0.22
17 2 0.04
18 1 0.02
19 14 0.26
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATTAAATTATTTAA
Found at i:375512 original size:19 final size:21
Alignment explanation
Indices: 375461--375523 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 21
375451 AAGATATTAA
*
375461 TCTATTTAAA-TATTAAAAAATT
1 TCTATTTAAATTATT--TAAATT
375483 TCTATTTAAATTATTTAAATT
1 TCTATTTAAATTATTTAAATT
375504 T-TA-TTAAATTATTTAAATT
1 TCTATTTAAATTATTTAAATT
375523 T
1 T
375524 AAATTAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
19 17 0.44
20 2 0.05
21 6 0.15
22 10 0.26
23 4 0.10
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (21 bp):
TCTATTTAAATTATTTAAATT
Found at i:375516 original size:104 final size:104
Alignment explanation
Indices: 375382--375654 Score: 297
Period size: 104 Copynumber: 2.6 Consensus size: 104
375372 GAAAGGCATC
*
375382 CTATTTAAATATAT-AATTTT-TTAAATTTATTTATATATAAATTAATAAATATTTAAAAATAGA
1 CTATTTAAATATATAAATTTTATTAAA-TTATTTAAAT-TAAATTAATAAATATTTAAAAATAGA
*
375445 GTTCACAAGATATT-AATCTATTTAAATATTAA-AAA-ATTT
64 GTTCACAAGATATTAAATCAATTTAAA-ATTAATAAATATTT
* *
375484 CTATTTAAATTATTTAAATTTTATTAAATTATTTAAATTTAAATTAATAAATATTTTTAAAA-AG
1 CTATTTAAA-TATATAAATTTTATTAAATTATTTAAA-TTAAATTAATAAATA-TTTAAAAATAG
* * * *
375548 AGTTTACATGATATTAAATGAATTTAAAATTAATAAACTTTTTT
63 AGTTCACAAGATATTAAATCAATTTAAAATTAATAAA--TATTT
* * * * *
375592 CTATTTAAATATGTAATTTTTATTAATTTATTTAAATTCAAATCAACTAAATATTAAAAAATA
1 CTATTTAAATATATAAATTTTATTAAATTATTTAAATT-AAATTAA-TAAATATTTAAAAATA
375655 AAGTCTAAAT
Statistics
Matches: 144, Mismatches: 14, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
102 9 0.06
103 4 0.03
104 48 0.33
105 26 0.18
106 2 0.01
107 36 0.25
108 19 0.13
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (104 bp):
CTATTTAAATATATAAATTTTATTAAATTATTTAAATTAAATTAATAAATATTTAAAAATAGAGT
TCACAAGATATTAAATCAATTTAAAATTAATAAATATTT
Found at i:377943 original size:40 final size:40
Alignment explanation
Indices: 377875--377954 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
377865 TGTCAATTAG
* ** * *
377875 TTGTTGTAAATAATATGGTAATGGTATCAGTATCTTAGGA
1 TTGTTGCAAATAATATGGTAATAATATCAATATATTAGGA
*
377915 TTGTTGCAAATAATATGGTAGTAATATCAATATATTAGGA
1 TTGTTGCAAATAATATGGTAATAATATCAATATATTAGGA
377955 GTCTGTTTAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (40 bp):
TTGTTGCAAATAATATGGTAATAATATCAATATATTAGGA
Found at i:379137 original size:26 final size:25
Alignment explanation
Indices: 379101--379149 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
379091 TTACTAGATA
*
379101 TGTTTTGACTCAATATTAATTTCATT
1 TGTTTCGACTCAATATT-ATTTCATT
*
379127 TGTTTCGACTCGATATTATTTCA
1 TGTTTCGACTCAATATTATTTCA
379150 ATATAATCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.51
Consensus pattern (25 bp):
TGTTTCGACTCAATATTATTTCATT
Found at i:382095 original size:21 final size:21
Alignment explanation
Indices: 382035--382096 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
382025 CCATTCATTT
*
382035 TTTTACTTTTTATTTTTTTGTA
1 TTTTA-TTATTATTTTTTTGTA
382057 TTTT-TTAATCT-TTTTTTTGTA
1 TTTTATT-AT-TATTTTTTTGTA
382078 TTTTATTATTATTATTTTT
1 TTTTATTATTATT-TTTTT
382097 TTAAAAAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
20 3 0.09
21 19 0.56
22 12 0.35
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.77
Consensus pattern (21 bp):
TTTTATTATTATTTTTTTGTA
Found at i:382983 original size:21 final size:21
Alignment explanation
Indices: 382957--383009 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
382947 AAAAAAATTA
* *
382957 TATCGATACATGCTTATAATG
1 TATCGATACATACTTACAATG
* *
382978 TATCGACACATACTTGCAATG
1 TATCGATACATACTTACAATG
*
382999 TATTGATACAT
1 TATCGATACAT
383010 TATGGGTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (21 bp):
TATCGATACATACTTACAATG
Found at i:385592 original size:97 final size:97
Alignment explanation
Indices: 385409--385605 Score: 281
Period size: 97 Copynumber: 2.0 Consensus size: 97
385399 TTAACCTCCT
* * *
385409 ATTTTTTCGAGGAGATACTCTAACTCCGTTTTTAAACTTGTTAAGATTTAAATCTTATTTTTGCC
1 ATTTTTTCGAGAAGATACTCCAACTCCGTTTTTAAACTTGTCAAGATTTAAATCTTATTTTTGCC
* * *
385474 TAAATTGTCATCCTCGGGGACACTT-CAACCCC
66 AAAATTGTCATCATCGAGGACA-TTCCAACCCC
385506 ATTTTTTCGAGAAGATACTCCAAC-CTCGTTTTTAAACTTGTCAAGATTTAAATCTTATTTTTGC
1 ATTTTTTCGAGAAGATACTCCAACTC-CGTTTTTAAACTTGTCAAGATTTAAATCTTATTTTTGC
* * *
385570 CAAAATTGTCTTCATTGAGGACATTCCAATCCC
65 CAAAATTGTCATCATCGAGGACATTCCAACCCC
385603 ATT
1 ATT
385606 CTTCTAAGGG
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
96 3 0.03
97 86 0.97
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (97 bp):
ATTTTTTCGAGAAGATACTCCAACTCCGTTTTTAAACTTGTCAAGATTTAAATCTTATTTTTGCC
AAAATTGTCATCATCGAGGACATTCCAACCCC
Found at i:385620 original size:97 final size:98
Alignment explanation
Indices: 385421--385627 Score: 251
Period size: 97 Copynumber: 2.1 Consensus size: 98
385411 TTTTTCGAGG
* * *
385421 AGATACTCTAA-CTCCGTTTTTAAACTTGTTAAGATTTAAATCTTATTTTTGCCTAAATTGTCAT
1 AGATACTCCAACCTCCGTTTTTAAACTTGTCAAGATTTAAATCTTATTTTTGCCAAAATTGTCAT
* * * *
385485 CCTCGGGGACACTTCAACCCCATTTTTTCGAGA
66 CATCGAGGACACTTCAACCCCATTTTCTCAAGA
*
385518 AGATACTCCAACCT-CGTTTTTAAACTTGTCAAGATTTAAATCTTATTTTTGCCAAAATTGTCTT
1 AGATACTCCAACCTCCGTTTTTAAACTTGTCAAGATTTAAATCTTATTTTTGCCAAAATTGTCAT
* * *
385582 CATTGAGGACA-TTCCAATCCCATTCTTCT-AAGG
66 CATCGAGGACACTT-CAACCCCATT-TTCTCAAGA
* *
385615 GGATACTGCAACC
1 AGATACTCCAACC
385628 CTATTTTTCA
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
96 2 0.02
97 87 0.93
98 5 0.05
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (98 bp):
AGATACTCCAACCTCCGTTTTTAAACTTGTCAAGATTTAAATCTTATTTTTGCCAAAATTGTCAT
CATCGAGGACACTTCAACCCCATTTTCTCAAGA
Found at i:390053 original size:28 final size:30
Alignment explanation
Indices: 389968--390065 Score: 137
Period size: 30 Copynumber: 3.3 Consensus size: 30
389958 CTGACTCATA
* *
389968 GGCTTTAAAAAGATATGCCATTAACTTGTG
1 GGCTTTAAAAGGAGATGCCATTAACTTGTG
* *
389998 GGTTTTAAAAGGAGATGCCACTAACTTGTG
1 GGCTTTAAAAGGAGATGCCATTAACTTGTG
*
390028 GGCTTTAAAAGG-G-TGCCATTGACTTGTG
1 GGCTTTAAAAGGAGATGCCATTAACTTGTG
390056 GGCTTTAAAA
1 GGCTTTAAAA
390066 AGTATGCCAC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
28 23 0.38
29 1 0.02
30 37 0.61
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.32
Consensus pattern (30 bp):
GGCTTTAAAAGGAGATGCCATTAACTTGTG
Found at i:390085 original size:18 final size:19
Alignment explanation
Indices: 390062--390097 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
390052 TGTGGGCTTT
390062 AAAAA-GTATGCCACTAAA
1 AAAAAGGTATGCCACTAAA
390080 AAAAAGGTATGCCACTAA
1 AAAAAGGTATGCCACTAA
390098 TTCTGGGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.53, C:0.17, G:0.14, T:0.17
Consensus pattern (19 bp):
AAAAAGGTATGCCACTAAA
Found at i:390188 original size:28 final size:28
Alignment explanation
Indices: 390101--390691 Score: 526
Period size: 28 Copynumber: 20.7 Consensus size: 28
390091 CCACTAATTC
* * *
390101 TGGGCTTTGAAAGGAAATGCTACTAACTTG
1 TGGGCTTTGAAAGG--GTGCCACTGACTTG
*
390131 TGAGCTTTGAAAGGAGATGCCACTGACTTG
1 TGGGCTTTGAAAGG-G-TGCCACTGACTTG
*
390161 TGGGCTTTGAGAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* * * *
390189 TGGACTTAGAAAAGGTGCCGCTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
390217 TGGGCTTTGAAAGGGGATGCCACTAACTTA
1 TGGGCTTTGAAA-GGG-TGCCACTGACTTG
390247 TGGGCTTT-AAGAGGGTGCCACTGACTTG
1 TGGGCTTTGAA-AGGGTGCCACTGACTTG
* * **
390275 TGAGCTTTGAGATTGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* ** *
390303 TGGACTTAAAAAGGGTGCCGCTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
390331 TGGGCTTTGAAAGGGGATGCCACTAACTTA
1 TGGGCTTTGAAA-GGG-TGCCACTGACTTG
390361 TGGGCTTT-AAGAGGGTGCCACTGACTTG
1 TGGGCTTTGAA-AGGGTGCCACTGACTTG
* * *
390389 TGAGCTTTGAGATGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* ** *
390417 TGGACTTAAAAAGGGTGCCACTAACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
390445 TGGGCTTTGAAAGGGGATGCCACTAACTTA
1 TGGGCTTTGAAA-GGG-TGCCACTGACTTG
** *
390475 TGGGCTTT-AAGAGGGTGCCACCAACTTA
1 TGGGCTTTGAA-AGGGTGCCACTGACTTG
*
390503 TGGGCTTTAAAAGGGTGCCACTG-CTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
**
390530 TGGGCTTTGAAAATGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* **
390558 TGGGTTTTGAAAATGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
** * * *
390586 TATGCTTTAAAAGGGGATGCCACTAACTTA
1 TGGGCTTTGAAA-GGG-TGCCACTGACTTG
* * ** *
390616 TGAGCTTTAAAAATGTGCCATTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* * * *
390644 TGGGATTTAAAAAGGTGCCACTAACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
390672 TGGGCTTT-AGAAGGGTGCCA
1 TGGGCTTTGA-AAGGGTGCCA
390692 TAGAGTTATG
Statistics
Matches: 461, Mismatches: 83, Indels: 36
0.79 0.14 0.06
Matches are distributed among these distances:
27 24 0.05
28 290 0.63
29 31 0.07
30 116 0.25
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (28 bp):
TGGGCTTTGAAAGGGTGCCACTGACTTG
Found at i:390303 original size:114 final size:113
Alignment explanation
Indices: 390101--390679 Score: 698
Period size: 114 Copynumber: 5.1 Consensus size: 113
390091 CCACTAATTC
** * * * *
390101 TGGGCTTTGAAAGGAAATGCTACTAACTTGTGAGCTTTGAA-AGGAGATGCCACTGACTTGTGGG
1 TGGGCTTTGAAAGGGGATGCCACTAACTTATGGGCTTT-AAGAGG-G-TGCCACTGACTTGTGAG
*
390165 CTTTGAGAGGGTGCCACTGACTTGTGGACTTAGAAAAGGTGCCGCTGACTTG
63 CTTTGAGAGGGTGCCACTGACTTGTGGACTTA-AAAAGGTGCCACTGACTTG
390217 TGGGCTTTGAAAGGGGATGCCACTAACTTATGGGCTTTAAGAGGGTGCCACTGACTTGTGAGCTT
1 TGGGCTTTGAAAGGGGATGCCACTAACTTATGGGCTTTAAGAGGGTGCCACTGACTTGTGAGCTT
** *
390282 TGAGATTGTGCCACTGACTTGTGGACTTAAAAAGGGTGCCGCTGACTTG
66 TGAGAGGGTGCCACTGACTTGTGGACTTAAAAA-GGTGCCACTGACTTG
390331 TGGGCTTTGAAAGGGGATGCCACTAACTTATGGGCTTTAAGAGGGTGCCACTGACTTGTGAGCTT
1 TGGGCTTTGAAAGGGGATGCCACTAACTTATGGGCTTTAAGAGGGTGCCACTGACTTGTGAGCTT
* *
390396 TGAGATGGTGCCACTGACTTGTGGACTTAAAAAGGGTGCCACTAACTTG
66 TGAGAGGGTGCCACTGACTTGTGGACTTAAAAA-GGTGCCACTGACTTG
** * *
390445 TGGGCTTTGAAAGGGGATGCCACTAACTTATGGGCTTTAAGAGGGTGCCACCAACTTATGGGCTT
1 TGGGCTTTGAAAGGGGATGCCACTAACTTATGGGCTTTAAGAGGGTGCCACTGACTTGTGAGCTT
* * * * *
390510 TAAAAGGGTGCCACTG-CTTGTGGGCTTTGAAAATGTGCCACTGACTTG
66 TGAGAGGGTGCCACTGACTTGTGGAC-TTAAAAAGGTGCCACTGACTTG
* ** * * ** * * *
390558 TGGGTTTTGAAA-ATG-TGCCACTGACTTGTATGCTTTAAAAGGGGATGCCACTAACTTATGAGC
1 TGGGCTTTGAAAGGGGATGCCACTAACTTATGGGCTTTAAGA-GGG-TGCCACTGACTTGTGAGC
* * ** * * *
390621 TTTAAAAATGTGCCATTGACTTGTGGGATTTAAAAAGGTGCCACTAACTTG
64 TTTGAGAGGGTGCCACTGACTTGT-GGACTTAAAAAGGTGCCACTGACTTG
390672 TGGGCTTT
1 TGGGCTTT
390680 AGAAGGGTGC
Statistics
Matches: 415, Mismatches: 41, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
111 20 0.05
112 4 0.01
113 67 0.16
114 283 0.68
115 5 0.01
116 36 0.09
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (113 bp):
TGGGCTTTGAAAGGGGATGCCACTAACTTATGGGCTTTAAGAGGGTGCCACTGACTTGTGAGCTT
TGAGAGGGTGCCACTGACTTGTGGACTTAAAAAGGTGCCACTGACTTG
Found at i:390714 original size:86 final size:86
Alignment explanation
Indices: 390148--390714 Score: 473
Period size: 86 Copynumber: 6.7 Consensus size: 86
390138 TGAAAGGAGA
* * * *
390148 TGCCACTGACTTGTGGGCTTTGAGAGGGTGCCACT-GACTTGTGGACTTAG-AAAAGGTGCCGCT
1 TGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTAGACTTGTGGACTTTGAAAAAGGTGCCACT
**
390211 GACTTGTGGGCTTTGAAAGGGG
66 GACTTGTGGGCTTT-AAAAAGG
* * * * **
390233 ATGCCACTAACTTATGGGCTTTAAGAGGGTGCCACT-GACTTGT-GAGCTTTG-AGATTGTGCCA
1 -TGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTAGACTTGTGGA-CTTTGAAAAAGGTGCCA
*
390295 CTGACTTGTGGAC-TTAAAAAGGG
64 CTGACTTGTGGGCTTTAAAAA-GG
* * * * * *
390318 TGCCGCTGACTTGTGGGCTTTGAAAGGGGATGCCACTA-ACTTATGGGCTTT-AAGAGGGTGCCA
1 TGCCACTGACTTGTGGGCTTT-AAAAGGG-TGCCACTAGACTTGTGGACTTTGAAAAAGGTGCCA
* * * *
390381 CTGACTTGTGAGCTTTGAGATGG
64 CTGACTTGTGGGCTTTAAAAAGG
* * * **
390404 TGCCACTGACTTGTGGACTTAAAAAGGGTGCCACTA-ACTTGTGGGCTTTGAAAGGGGATGCCAC
1 TGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTAGACTTGTGGACTTTGAAAAAGG-TGCCAC
* * * *
390468 TAACTTATGGGCTTTAAGAGGG
65 TGACTTGTGGGCTTTAAAAAGG
** * * *
390490 TGCCACCAACTTATGGGCTTTAAAAGGGTGCCACT-G-CTTGTGGGCTTTG-AAAATGTGCCACT
1 TGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTAGACTTGTGGACTTTGAAAAAGGTGCCACT
* * *
390552 GACTTGTGGGTTTTGAAAATG
66 GACTTGTGGGCTTTAAAAAGG
** * *
390573 TGCCACTGACTTGTATGCTTTAAAAGGGGATGCCACTA-ACTTAT-GAGCTTT-AAAAATGTGCC
1 TGCCACTGACTTGTGGGCTTTAAAA-GGG-TGCCACTAGACTTGTGGA-CTTTGAAAAAGGTGCC
* *
390635 ATTGACTTGTGGGATTTAAAAAGG
63 ACTGACTTGTGGGCTTTAAAAAGG
* * * *
390659 TGCCACTAACTTGTGGGCTTTAGAAGGGTGCCA-TAGAGTTATGGACTTTTGAAAAA
1 TGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTAGACTTGTGGAC-TTTGAAAAA
390715 AAATGTGCTA
Statistics
Matches: 392, Mismatches: 68, Indels: 42
0.78 0.14 0.08
Matches are distributed among these distances:
83 43 0.11
84 58 0.15
85 51 0.13
86 235 0.60
87 5 0.01
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (86 bp):
TGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTAGACTTGTGGACTTTGAAAAAGGTGCCACT
GACTTGTGGGCTTTAAAAAGG
Found at i:390836 original size:30 final size:30
Alignment explanation
Indices: 390686--390896 Score: 144
Period size: 30 Copynumber: 6.9 Consensus size: 30
390676 CTTTAGAAGG
* * *
390686 GTGCCATAGAGTTATGGACTTTTGAAAAAAAA
1 GTGCCACAGAGTTGTGGAC-TTT-AAAAAAGA
* * * *
390718 TGTGCTACGGAGTTATTGAC-TTAAAAAATGA
1 -GTGCCACAGAGTTGTGGACTTTAAAAAA-GA
* *
390749 -TGCCACGGAGTTGT-GAGCTTT-AAAAAGG
1 GTGCCACAGAGTTGTGGA-CTTTAAAAAAGA
* * *
390777 GATGCCACTGAGTTGTGGGCTTTTAAAAAGA
1 G-TGCCACAGAGTTGTGGACTTTAAAAAAGA
* *
390808 GTGTCACAGAGTTGTGAACTTTAAAAAAGA
1 GTGCCACAGAGTTGTGGACTTTAAAAAAGA
* * * *
390838 GGGTGCTATAGAATTGTGGACTTTAAAAGAG-
1 --GTGCCACAGAGTTGTGGACTTTAAAAAAGA
*
390869 GTGCCACAAAGTTGTGGACTTTAAAAAA
1 GTGCCACAGAGTTGTGGACTTTAAAAAA
390897 AGAGGGTGCC
Statistics
Matches: 142, Mismatches: 27, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
28 3 0.02
29 41 0.29
30 49 0.35
31 11 0.08
32 23 0.16
33 15 0.11
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.28
Consensus pattern (30 bp):
GTGCCACAGAGTTGTGGACTTTAAAAAAGA
Found at i:390865 original size:61 final size:61
Alignment explanation
Indices: 390749--390924 Score: 189
Period size: 62 Copynumber: 2.9 Consensus size: 61
390739 TAAAAAATGA
* * * * *
390749 TGCCACGGAGTTGTGAGCTTT-AAAAAG-GGATGCCACTGAGTTGTGGGCTTTTAAAAAGA-G
1 TGCCACAGAGTTGTGAACTTTAAAAAAGAGGGTGCCA-TGAATTGTGGAC-TTTAAAAAGAGG
* *
390809 TGTCACAGAGTTGTGAACTTTAAAAAAGAGGGTGCTATAGAATTGTGGACTTT-AAAAGAGG
1 TGCCACAGAGTTGTGAACTTTAAAAAAGAGGGTGCCAT-GAATTGTGGACTTTAAAAAGAGG
* * *
390870 TGCCACAAAGTTGTGGACTTTAAAAAAAGAGGGTGCCATGAAGTTGAGGACTTTA
1 TGCCACAGAGTTGTGAACTTT-AAAAAAGAGGGTGCCATGAA-TTGTGGACTTTA
390925 TGGGGATTGA
Statistics
Matches: 97, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
60 24 0.25
61 32 0.33
62 41 0.42
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (61 bp):
TGCCACAGAGTTGTGAACTTTAAAAAAGAGGGTGCCATGAATTGTGGACTTTAAAAAGAGG
Found at i:390914 original size:33 final size:32
Alignment explanation
Indices: 390757--390924 Score: 133
Period size: 30 Copynumber: 5.4 Consensus size: 32
390747 GATGCCACGG
*
390757 AGTTGT-GAGCTTT-AAAAAG-GGATGCCACTG-
1 AGTTGTGGA-CTTTAAAAAAGAGGGTGCCA-TGA
* * *
390787 AGTTGTGGGCTTTTAAAAAGAGTGT-CACA-G-
1 AGTTGTGGACTTTAAAAAAGAGGGTGC-CATGA
* *
390817 AGTTGTGAACTTTAAAAAAGAGGGTGCTATAGA
1 AGTTGTGGACTTTAAAAAAGAGGGTGCCAT-GA
**
390850 A-TTGTGGACTTT--AAAAGA-GGTGCCACAA
1 AGTTGTGGACTTTAAAAAAGAGGGTGCCATGA
390878 AGTTGTGGACTTTAAAAAAAGAGGGTGCCATGA
1 AGTTGTGGACTTT-AAAAAAGAGGGTGCCATGA
*
390911 AGTTGAGGACTTTA
1 AGTTGTGGACTTTA
390925 TGGGGATTGA
Statistics
Matches: 110, Mismatches: 15, Indels: 24
0.74 0.10 0.16
Matches are distributed among these distances:
28 2 0.02
29 17 0.15
30 39 0.35
31 9 0.08
32 22 0.20
33 21 0.19
ACGTcount: A:0.34, C:0.10, G:0.29, T:0.27
Consensus pattern (32 bp):
AGTTGTGGACTTTAAAAAAGAGGGTGCCATGA
Found at i:398238 original size:45 final size:45
Alignment explanation
Indices: 398164--398254 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
398154 TACGCCAGAG
* **
398164 TAGTTTGGGACGATGAAACAGCCTGTTGATCACACCACTCAAAGT
1 TAGTTTGGGACGATAAAACAGCCCATTGATCACACCACTCAAAGT
* *
398209 TAGTTTGGGATGATAAAATAGCCCATTGATCACACCACTCAAAGT
1 TAGTTTGGGACGATAAAACAGCCCATTGATCACACCACTCAAAGT
398254 T
1 T
398255 TTGACACAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (45 bp):
TAGTTTGGGACGATAAAACAGCCCATTGATCACACCACTCAAAGT
Found at i:399697 original size:52 final size:50
Alignment explanation
Indices: 399640--399769 Score: 136
Period size: 52 Copynumber: 2.5 Consensus size: 50
399630 TACCTACATA
* *
399640 TATCGATACATTGAAGAATGTATCGATACATCTGGGTCAAAAACCT-AGAATG
1 TATCGATACAATGAA-AATGTATCGATACATCTCGGT-AAAAA-CTGAGAATG
* * * * *
399692 TATCGATATAATGAAAAATATATCGATACATTTCGGTTAAAACTGAGAATT
1 TATCGATACAATG-AAAATGTATCGATACATCTCGGTAAAAACTGAGAATG
* *
399743 TATTGGTACAATGAAAATGTATCGATA
1 TATCGATACAATGAAAATGTATCGATA
399770 TATTTTCATT
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
50 15 0.23
51 19 0.29
52 29 0.45
53 2 0.03
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.31
Consensus pattern (50 bp):
TATCGATACAATGAAAATGTATCGATACATCTCGGTAAAAACTGAGAATG
Found at i:399879 original size:21 final size:20
Alignment explanation
Indices: 399838--399880 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
399828 ATATGTATTG
*
399838 ATACATTCACTTATGTATCA
1 ATACATTCACTTATATATCA
399858 ATACATTCACTTATTATATCA
1 ATACATTCACTTA-TATATCA
399879 AT
1 AT
399881 GCAAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.37, C:0.19, G:0.02, T:0.42
Consensus pattern (20 bp):
ATACATTCACTTATATATCA
Found at i:403676 original size:64 final size:67
Alignment explanation
Indices: 403542--403703 Score: 231
Period size: 70 Copynumber: 2.4 Consensus size: 67
403532 TAACTAGATA
*
403542 TATCGATACATTGAAAAATATATCGATACATTGAAAAATATATCGATACATCTAGGTAAAAGACA
1 TATCGATACATTGAAAAATGTATCGATACATTGAAAAATATATCGATA-ATCT--GTAAAAGACA
403607 GAATG
63 GAATG
* * *
403612 TATCGATACATTCAAATATGTATCGATACATTGAAAAATGTATCGAT-AT-T-TAAAAGACAGAA
1 TATCGATACATTGAAAAATGTATCGATACATTGAAAAATATATCGATAATCTGTAAAAGACAGAA
403674 TG
66 TG
*
403676 TGTCGATACATTGAAAAATGTATCGATA
1 TATCGATACATTGAAAAATGTATCGATA
403704 TTTAAAAGAC
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
64 39 0.46
67 1 0.01
68 2 0.02
70 43 0.51
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (67 bp):
TATCGATACATTGAAAAATGTATCGATACATTGAAAAATATATCGATAATCTGTAAAAGACAGAA
TG
Found at i:403681 original size:24 final size:24
Alignment explanation
Indices: 403648--403727 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
403638 TACATTGAAA
403648 AATGTATCGATATTTAAAAGACAG
1 AATGTATCGATATTTAAAAGACAG
* * *
403672 AATGTGTCGATACATT----GA-AA
1 AATGTATCGATA-TTTAAAAGACAG
403692 AATGTATCGATATTTAAAAGACAG
1 AATGTATCGATATTTAAAAGACAG
*
403716 AATGTGTCGATA
1 AATGTATCGATA
403728 CATTGAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
19 2 0.05
20 12 0.28
21 2 0.05
23 2 0.05
24 23 0.53
25 2 0.05
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (24 bp):
AATGTATCGATATTTAAAAGACAG
Found at i:403701 original size:20 final size:20
Alignment explanation
Indices: 403542--403747 Score: 128
Period size: 20 Copynumber: 9.4 Consensus size: 20
403532 TAACTAGATA
*
403542 TATCGATACATTGAAAAATA
1 TATCGATACATTGAAAAATG
*
403562 TATCGATACATTGAAAAATA
1 TATCGATACATTGAAAAATG
403582 TATCGATACATCTAGGTAAAAGACAGAATG
1 TATCGATACAT-T--G----A-A-A-AATG
* *
403612 TATCGATACATTCAAATATG
1 TATCGATACATTGAAAAATG
403632 TATCGATACATTGAAAAATG
1 TATCGATACATTGAAAAATG
* *
403652 TATCGATA-TTTAAAAGACAGAATG
1 TATCGATACATT----GA-AAAATG
*
403676 TGTCGATACATTGAAAAATG
1 TATCGATACATTGAAAAATG
* *
403696 TATCGATA-TTTAAAAGACAGAATG
1 TATCGATACATT----GA-AAAATG
*
403720 TGTCGATACATTGAAAAATG
1 TATCGATACATTGAAAAATG
403740 TATCGATA
1 TATCGATA
403748 TATCTTGGTA
Statistics
Matches: 147, Mismatches: 17, Indels: 44
0.71 0.08 0.21
Matches are distributed among these distances:
19 4 0.03
20 84 0.57
21 6 0.04
22 1 0.01
23 6 0.04
24 24 0.16
25 4 0.03
27 1 0.01
28 1 0.01
29 2 0.01
30 14 0.10
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.30
Consensus pattern (20 bp):
TATCGATACATTGAAAAATG
Found at i:403765 original size:44 final size:44
Alignment explanation
Indices: 403629--403748 Score: 231
Period size: 44 Copynumber: 2.7 Consensus size: 44
403619 ACATTCAAAT
*
403629 ATGTATCGATACATTGAAAAATGTATCGATATTTAAAAGACAGA
1 ATGTGTCGATACATTGAAAAATGTATCGATATTTAAAAGACAGA
403673 ATGTGTCGATACATTGAAAAATGTATCGATATTTAAAAGACAGA
1 ATGTGTCGATACATTGAAAAATGTATCGATATTTAAAAGACAGA
403717 ATGTGTCGATACATTGAAAAATGTATCGATAT
1 ATGTGTCGATACATTGAAAAATGTATCGATAT
403749 ATCTTGGTAA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
44 75 1.00
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.31
Consensus pattern (44 bp):
ATGTGTCGATACATTGAAAAATGTATCGATATTTAAAAGACAGA
Found at i:404458 original size:44 final size:44
Alignment explanation
Indices: 404410--404493 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
404400 ACTTGGACTT
* *
404410 AAAGATAAGAA-AGGTGCTAATGTGCTAATTTAAGGCCAGCTACA
1 AAAGATAAGAAGA-GTGCCAATGTACTAATTTAAGGCCAGCTACA
* *
404454 AAAGATGAGAAGAGTGCCAATGTACTGATTTAAGGCCAGC
1 AAAGATAAGAAGAGTGCCAATGTACTAATTTAAGGCCAGC
404494 GATATTAGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
44 34 0.97
45 1 0.03
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.21
Consensus pattern (44 bp):
AAAGATAAGAAGAGTGCCAATGTACTAATTTAAGGCCAGCTACA
Found at i:404716 original size:32 final size:32
Alignment explanation
Indices: 404680--404798 Score: 118
Period size: 32 Copynumber: 3.7 Consensus size: 32
404670 TGGTGTTTTG
*
404680 AAAAAGATTGCCACTGACTTGTGTGGGCCTTTA
1 AAAAAGAGTGCCACTGACTTGTGT-GGCCTTTA
* * *
404713 AAAAAAAGTGCCACCGACTTGTGTGGCC-TTG
1 AAAAAGAGTGCCACTGACTTGTGTGGCCTTTA
* *
404744 AAAAAG-GTTGCCA-TCGACTTGTGTGGACTTTG
1 AAAAAGAG-TGCCACT-GACTTGTGTGGCCTTTA
* *
404776 AAAAGGGGTGCCACTGACTTGTG
1 AAAAAGAGTGCCACTGACTTGTG
404799 GTCTATAAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
30 1 0.01
31 24 0.33
32 25 0.34
33 23 0.32
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (32 bp):
AAAAAGAGTGCCACTGACTTGTGTGGCCTTTA
Found at i:404813 original size:28 final size:28
Alignment explanation
Indices: 404688--405048 Score: 234
Period size: 28 Copynumber: 12.4 Consensus size: 28
404678 TGAAAAAGAT
**
404688 TGCCACTGACTTGTGTGGGCCTTTAAAAAAAAG
1 TGCCACTGAC-T-TGTGGG-C-TT-AAAAAGGG
* *
404721 TGCCACCGACTTGTGTGGCCTTGAAAAAGGT
1 TGCCACTGACTTGTG-GG-CTT-AAAAAGGG
*
404752 TGCCA-TCGACTTGTGTGGACTTTGAAAAGGGG
1 TGCCACT-GACTTGTG-GG-C-TT-AAAAAGGG
*
404784 TGCCACTGACTTGTGGTC-TATAAAAGGG
1 TGCCACTGACTTGTGGGCTTA-AAAAGGG
* * * * *
404812 TGCCACCGACTTGTGGGTTTCAAAACGA
1 TGCCACTGACTTGTGGGCTTAAAAAGGG
***
404840 TGCCACTTG-CTTGTGGGCTTTGGAAGGG
1 TGCCAC-TGACTTGTGGGCTTAAAAAGGG
** *
404868 TGCCACCAACTTGTGGGCTTAAAAATGG
1 TGCCACTGACTTGTGGGCTTAAAAAGGG
**
404896 TGCCACTTG-CTTGTGGGCTTTGGAAA-GG
1 TGCCAC-TGACTTGTGGGC-TTAAAAAGGG
*
404924 TGCC-GTCGACTTGTGGGCTTAAAAAGGG
1 TGCCACT-GACTTGTGGGCTTAAAAAGGG
*
404952 TGCCACTTG-CTTGTGGGCTTTGAAAAGGGG
1 TGCCAC-TGACTTGTGGGC-TT-AAAAAGGG
* *
404982 TGCCACTGACCTGTGGTCTCT-AAAAGGG
1 TGCCACTGACTTGTGGGCT-TAAAAAGGG
* *
405010 TGCCACTGACTTATGGGCTTCAAAAGGG
1 TGCCACTGACTTGTGGGCTTAAAAAGGG
*
405038 TGCCATTGACT
1 TGCCACTGACT
405049 CATGCATCTT
Statistics
Matches: 262, Mismatches: 46, Indels: 45
0.74 0.13 0.13
Matches are distributed among these distances:
26 1 0.00
27 8 0.03
28 151 0.58
29 13 0.05
30 23 0.09
31 29 0.11
32 27 0.10
33 10 0.04
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTAAAAAGGG
Found at i:404868 original size:56 final size:56
Alignment explanation
Indices: 404807--405029 Score: 261
Period size: 56 Copynumber: 3.9 Consensus size: 56
404797 TGGTCTATAA
* * *
404807 AAGGGTGCCACCGACTTGTGGGTTTCAAAACGATGCCACTTGCTTGTGGGCTTTGG
1 AAGGGTGCCACCGACTTGTGGGCTTAAAAACGGTGCCACTTGCTTGTGGGCTTTGG
* *
404863 AAGGGTGCCACCAACTTGTGGGCTTAAAAATGGTGCCACTTGCTTGTGGGCTTTGG
1 AAGGGTGCCACCGACTTGTGGGCTTAAAAACGGTGCCACTTGCTTGTGGGCTTTGG
* ** * *
404919 AAAGGTGCCGTCGACTTGTGGGCTTAAAAAGGGTGCCACTTGCTTGTGGGCTTTGAA
1 AAGGGTGCCACCGACTTGTGGGCTTAAAAACGGTGCCACTTGCTTGTGGGCTTTG-G
* * * * *
404976 AAGGGGTGCCACTGACCTGTGGTCTCT-AAAAGGGTGCCAC-TGACTTATGGGCTT
1 AA-GGGTGCCACCGACTTGTGGGCT-TAAAAACGGTGCCACTTG-CTTGTGGGCTT
405030 CAAAAGGGTG
Statistics
Matches: 145, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
56 101 0.70
57 4 0.03
58 39 0.27
59 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.32, T:0.28
Consensus pattern (56 bp):
AAGGGTGCCACCGACTTGTGGGCTTAAAAACGGTGCCACTTGCTTGTGGGCTTTGG
Found at i:410815 original size:15 final size:15
Alignment explanation
Indices: 410776--410820 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
410766 GTGTATCAAC
*
410776 AATTTTGTGGTGGGT
1 AATTTTGTGGTGGAT
**
410791 AATTAGGTGGTGGAT
1 AATTTTGTGGTGGAT
*
410806 GATTTTGTGGTGGAT
1 AATTTTGTGGTGGAT
410821 TTGGCGAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.18, C:0.00, G:0.40, T:0.42
Consensus pattern (15 bp):
AATTTTGTGGTGGAT
Found at i:419497 original size:50 final size:49
Alignment explanation
Indices: 419421--419582 Score: 171
Period size: 50 Copynumber: 3.4 Consensus size: 49
419411 AAAGTCACAT
* * *
419421 TTTTACCTAGATGTATCGATAGATTTTTCAATGTGTCGATACATTCTGTC
1 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATT-TGTC
*
419471 TTTTACCCAGATGTATCGATACATTTTTTAATGTATCGATACA--TG--
1 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTTGTC
** *
419516 ---TA-TGA-ATGTATCGATACATTCTTCAATGTATCGATACATTTTGTC
1 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACA-TTTGTC
419561 TTTTTACCCAGATGTATCGATA
1 -TTTTACCCAGATGTATCGATA
419583 TATTGAATAT
Statistics
Matches: 91, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
40 31 0.34
41 1 0.01
42 2 0.02
43 2 0.02
47 2 0.02
49 2 0.02
50 40 0.44
51 11 0.12
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (49 bp):
TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTTGTC
Found at i:419506 original size:20 final size:20
Alignment explanation
Indices: 419481--419557 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 20
419471 TTTTACCCAG
*
419481 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTCA
* * *
419501 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
419521 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
419541 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
419558 GTCTTTTTAC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:423297 original size:21 final size:21
Alignment explanation
Indices: 423271--423346 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
423261 TTCTACAATT
423271 TGTATCGATACAAACAGTAAA
1 TGTATCGATACAAACAGTAAA
* *
423292 TGTATCGATACATA-AGTGAA
1 TGTATCGATACAAACAGTAAA
* *
423312 TGTATCGATACAAGC-CTGAAA
1 TGTATCGATACAAACAGT-AAA
423333 TGTATCGATACAAA
1 TGTATCGATACAAA
423347 ACCACCCTGC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 18 0.39
21 28 0.61
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.26
Consensus pattern (21 bp):
TGTATCGATACAAACAGTAAA
Found at i:426973 original size:50 final size:51
Alignment explanation
Indices: 426919--427048 Score: 163
Period size: 52 Copynumber: 2.5 Consensus size: 51
426909 GCGACAATAG
* * *
426919 CGATACATTTTTTATTGTATCAATACATTCTAGG-TTTGATCCAAATGTAT
1 CGATACATTTTTCATTGTATCAATACATTCTAGGTTTTGACCCAAATATAT
* *
426969 CGATACATTTTTCATTATATCAATACATTCTCGGTTTTTGACCCAAATATAT
1 CGATACATTTTTCATTGTATCAATACATTCTAGG-TTTTGACCCAAATATAT
* * * *
427021 CGACACATTCTTCAATGTATCGATACAT
1 CGATACATTTTTCATTGTATCAATACAT
427049 CCAATTAAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
50 31 0.46
52 37 0.54
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (51 bp):
CGATACATTTTTCATTGTATCAATACATTCTAGGTTTTGACCCAAATATAT
Found at i:432069 original size:21 final size:21
Alignment explanation
Indices: 432045--432085 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
432035 CTTTTCTCCT
* *
432045 CTAATTCATTTATTTTCTTTC
1 CTAATTCACTTAATTTCTTTC
432066 CTAATTCACTTAATTTCTTT
1 CTAATTCACTTAATTTCTTT
432086 TCAAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.20, G:0.00, T:0.59
Consensus pattern (21 bp):
CTAATTCACTTAATTTCTTTC
Found at i:437673 original size:52 final size:52
Alignment explanation
Indices: 437595--437722 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
437585 CGAAATATGA
*
437595 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
437647 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
437699 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
437723 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 21 0.28
52 48 0.65
53 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:437749 original size:13 final size:13
Alignment explanation
Indices: 437731--437755 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
437721 CAAAGATCAG
437731 TGTATCGATACAA
1 TGTATCGATACAA
437744 TGTATCGATACA
1 TGTATCGATACA
437756 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:437833 original size:33 final size:33
Alignment explanation
Indices: 437796--437862 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
437786 AGTAGCTTAA
437796 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
437829 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
437862 A
1 A
437863 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:437836 original size:13 final size:13
Alignment explanation
Indices: 437818--437842 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
437808 CAAAAAAATA
437818 TGTATCGATACAT
1 TGTATCGATACAT
437831 TGTATCGATACA
1 TGTATCGATACA
437843 ACATTTTATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:441754 original size:24 final size:23
Alignment explanation
Indices: 441711--441768 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
441701 TATGAATGAT
*
441711 AATATAGTATATAATTATTAATA
1 AATATAGTAAATAATTATTAATA
*
441734 AATATTAGTAAAT-ATTGATTAACA
1 AATA-TAGTAAATAATT-ATTAATA
*
441758 TA-ATAGTAAAT
1 AATATAGTAAAT
441769 CTTTGATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 8 0.27
23 8 0.27
24 14 0.47
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.40
Consensus pattern (23 bp):
AATATAGTAAATAATTATTAATA
Found at i:441782 original size:22 final size:22
Alignment explanation
Indices: 441733--441784 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
441723 AATTATTAAT
*
441733 AAATATTAGTAAATATTGATTA
1 AAATAATAGTAAATATTGATTA
* *
441755 ACATAATAGTAAATCTTTGA-TA
1 AAATAATAGTAAAT-ATTGATTA
441777 AAATAATA
1 AAATAATA
441785 TAATAGTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.37
Consensus pattern (22 bp):
AAATAATAGTAAATATTGATTA
Found at i:446343 original size:125 final size:126
Alignment explanation
Indices: 446114--446361 Score: 428
Period size: 125 Copynumber: 2.0 Consensus size: 126
446104 CAGTAAGATG
446114 TTAAGGAAACTAGACAATGAATTAAAATAACGGCGATGACATTGAAGAATATGACAAATTTATAA
1 TTAAGGAAACTAGACAATGAATTAAAATAACGGCGATGACATTGAAGAATATGACAAATTTATAA
*
446179 CTAAAAAAATTGTCAATCTTAACTAGCAGCAATGGCC-TTTTGGCATCAACTTTTGTTAAA
66 CTAAAAAAATTGTCAACCTTAACTAGCAGCAATGGCCTTTTTGGCATCAACTTTTGTTAAA
* * *
446239 TTAAGGCAACTAGACAATGAATTAAAATAACTGTGATGACATTGAAGAATATGACAAATTTATAA
1 TTAAGGAAACTAGACAATGAATTAAAATAACGGCGATGACATTGAAGAATATGACAAATTTATAA
*
446304 CT-AAAAAATTGTCAACCTTAACTAGCAGGAATGGTCCTTTTTGGCATCAACTTTTGTT
66 CTAAAAAAATTGTCAACCTTAACTAGCAGCAATGG-CCTTTTTGGCATCAACTTTTGTT
446362 CAGATCATAA
Statistics
Matches: 116, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
124 30 0.26
125 66 0.57
126 20 0.17
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (126 bp):
TTAAGGAAACTAGACAATGAATTAAAATAACGGCGATGACATTGAAGAATATGACAAATTTATAA
CTAAAAAAATTGTCAACCTTAACTAGCAGCAATGGCCTTTTTGGCATCAACTTTTGTTAAA
Found at i:451714 original size:15 final size:16
Alignment explanation
Indices: 451696--451729 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
451686 TATTACTAGT
451696 TATTT-TATAATATTA
1 TATTTATATAATATTA
451711 TATTTAATATAATATTA
1 TATTT-ATATAATATTA
451728 TA
1 TA
451730 AATCATCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
17 12 0.71
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTATATAATATTA
Found at i:452664 original size:20 final size:21
Alignment explanation
Indices: 452619--452674 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
452609 TCAATTCTAT
452619 TAAAA-TTAATTATATAAAAA
1 TAAAATTTAATTATATAAAAA
* *
452639 TCAAATTTAATT-TATAATAA
1 TAAAATTTAATTATATAAAAA
*
452659 TAAAA-TAAATTATATA
1 TAAAATTTAATTATATA
452675 TAAGTATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 5 0.17
20 19 0.63
21 6 0.20
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAAATTTAATTATATAAAAA
Found at i:453458 original size:2 final size:2
Alignment explanation
Indices: 453445--453493 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
453435 ATTCAGCACT
*
453445 TA TA TT 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
453487 TA TA TA T
1 TA TA TA T
453494 TAAACATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:454280 original size:22 final size:23
Alignment explanation
Indices: 454252--454295 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
454242 AAGTTTGATA
*
454252 TTTGCAT-TTATTTTTAAGTTTG
1 TTTGCATATTATTTTAAAGTTTG
*
454274 TTTGCATATTCTTTTAAAGTTT
1 TTTGCATATTATTTTAAAGTTT
454296 AAGATTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.20, C:0.07, G:0.11, T:0.61
Consensus pattern (23 bp):
TTTGCATATTATTTTAAAGTTTG
Found at i:454656 original size:21 final size:21
Alignment explanation
Indices: 454613--454656 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
454603 ATTTTTATAA
*
454613 TTAAATTTAAATAAAATATTTT
1 TTAAATTTAAAT-AAATAATTT
454635 TTAATATTTAAAT-AATAATTT
1 TTAA-ATTTAAATAAATAATTT
454656 T
1 T
454657 GATCAAATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 4 0.20
23 8 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTAAATTTAAATAAATAATTT
Found at i:455890 original size:29 final size:30
Alignment explanation
Indices: 455826--455898 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
455816 CATTTGTTTC
455826 ATTA-TTTTAATTTATATTTGAATTTTATA
1 ATTATTTTTAATTTATATTTGAATTTTATA
* * *
455855 ATAATTTTTATTTTGATATTTGTATTTT-T-
1 ATTATTTTTAATTT-ATATTTGAATTTTATA
455884 ATTATTTTTAATTTA
1 ATTATTTTTAATTTA
455899 AATAATTATA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
28 1 0.03
29 15 0.41
30 9 0.24
31 12 0.32
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (30 bp):
ATTATTTTTAATTTATATTTGAATTTTATA
Found at i:456042 original size:3 final size:3
Alignment explanation
Indices: 456034--456059 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
456024 ATTAGATTTT
456034 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
456060 TATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:456064 original size:3 final size:3
Alignment explanation
Indices: 456058--456083 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
456048 GATGATGATG
456058 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
456084 ATACATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:457916 original size:20 final size:19
Alignment explanation
Indices: 457891--457963 Score: 110
Period size: 20 Copynumber: 3.7 Consensus size: 19
457881 TTTTCACAAT
457891 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATT-TTCA
*
457911 TTGTATCGAAACATTATTCA
1 TTGTATCGATACATT-TTCA
457931 TTGTATCGATACATTTTGCA
1 TTGTATCGATACATTTT-CA
457951 TTGTATCGATACA
1 TTGTATCGATACA
457964 ATGTATCGAT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
19 2 0.04
20 47 0.96
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (19 bp):
TTGTATCGATACATTTTCA
Found at i:457970 original size:13 final size:13
Alignment explanation
Indices: 457952--457997 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
457942 CATTTTGCAT
457952 TGTATCGATACAA
1 TGTATCGATACAA
*
457965 TGTATCGATACAT
1 TGTATCGATACAA
* *
457978 TTTAT-GA-GCAA
1 TGTATCGATACAA
457989 TGTATCGAT
1 TGTATCGAT
457998 GCATAGCTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
11 6 0.23
12 4 0.15
13 16 0.62
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:460407 original size:51 final size:50
Alignment explanation
Indices: 460332--460543 Score: 246
Period size: 51 Copynumber: 4.2 Consensus size: 50
460322 AAATTTCTAG
* * * *
460332 ATTTTTCAT-CTCGGGGATACTCCAATCCCGGTTTCATTTCCAAAACATCA
1 ATTTTTCATAATCGGGGATACTCCAA-CCCGATTTTATTTCCAAAACACCA
* * *
460382 ATTTTTCTTAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACACCC
1 ATTTTTCATAATCGGGGATACTCCAAC-CCGATTTTATTTCCAAAACACCA
* *
460433 ATTTTCCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCG
1 ATTTTTCATAATCGGGGATACTCCAAC-CCGATTTTATTTCCAAAACACCA
* * * * * *
460484 ACTTTTCACAATCGGGGATACTCCGACCCCGGTTTTATTTCTAAAACATCA
1 ATTTTTCATAATCGGGGATACTCC-AACCCGATTTTATTTCCAAAACACCA
460535 ATTTTTCAT
1 ATTTTTCAT
460544 CAGGGATACT
Statistics
Matches: 138, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
50 9 0.07
51 127 0.92
52 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.11, T:0.35
Consensus pattern (50 bp):
ATTTTTCATAATCGGGGATACTCCAACCCGATTTTATTTCCAAAACACCA
Found at i:460520 original size:102 final size:102
Alignment explanation
Indices: 460342--460562 Score: 279
Period size: 102 Copynumber: 2.2 Consensus size: 102
460332 ATTTTTCATC
* * * **
460342 TCGGGGATACTCCAATCCCGGTTTCATTTCCAAAACATCAATTTTTCTTAATCGGGGATACTCCA
1 TCGGGGATACTCCAATCCCGATTTCATTTCCAAAACACCAACTTTTCACAATCGGGGATACTCCA
*
460407 ACTCCGATTTTATTTCTAAAACACCCATTTTCCATAA
66 ACCCCGATTTTATTTCTAAAACACCCATTTTCCATAA
* *
460444 TCGGGGATACTCCAA-CTCCGATTTTATTTCCAAAACACCGACTTTTCACAATCGGGGATACTCC
1 TCGGGGATACTCCAATC-CCGATTTCATTTCCAAAACACCAACTTTTCACAATCGGGGATACTCC
* * * * *
460508 GACCCCGGTTTTATTTCTAAAACATCAATTTT---TCA
65 AACCCCGATTTTATTTCTAAAACACCCATTTTCCATAA
*
460543 TCAGGGATACTCCAATCCCG
1 TCGGGGATACTCCAATCCCG
460563 TTATTTTTGA
Statistics
Matches: 103, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
99 19 0.18
100 1 0.01
101 1 0.01
102 82 0.80
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.32
Consensus pattern (102 bp):
TCGGGGATACTCCAATCCCGATTTCATTTCCAAAACACCAACTTTTCACAATCGGGGATACTCCA
ACCCCGATTTTATTTCTAAAACACCCATTTTCCATAA
Found at i:460738 original size:79 final size:79
Alignment explanation
Indices: 460497--460841 Score: 395
Period size: 79 Copynumber: 4.5 Consensus size: 79
460487 TTTCACAATC
* * * * *
460497 GGGGATACTCCGACCCCGGTTTTATTTCTAAAACATCAATTTTTC---ATCAGGGATACTCCAAT
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATATCAATTTTTCATAATCGGGGATACTCCAAC
*
460559 CCCGTTATTTTTGA
66 CCCGTTATTTTCGA
* * * *
460573 GGGGATACCCCAA-CCCTAGTTTTATTTCTAAAACATCAATTTTTCAT--T-GGGGATACTCTAA
1 GGGGATACTCCAACCCCGA-TTTTATTTCTAAAATATCAATTTTTCATAATCGGGGATACTCCAA
* *
460634 -CCCGTTATTTCCAA
65 CCCCGTTATTTTCGA
* *
460648 GGGGATACTCCAACCCCGATTTTATTTCTAAAATATTAATTTATCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATATCAATTTTTCATAATCGGGGATACTCCAAC
*
460713 CCCGTTATTTTTGA
66 CCCGTTATTTTCGA
* * * *
460727 GGGGATACTCCAATCCCGATTTTATTTCT-AAATCATCGATTTTTCACAATCGGGGATACTCTAA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAAT-ATCAATTTTTCATAATCGGGGATACTCCAA
460791 CCCCGTTATTTTCGA
65 CCCCGTTATTTTCGA
* * *
460806 GGGGATATTCCAACCCCG-TTATTATCTCCAAAATAT
1 GGGGATACTCCAACCCCGATT-TTATTTCTAAAATAT
460842 TAAATTTCTC
Statistics
Matches: 229, Mismatches: 29, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
75 51 0.22
76 52 0.23
77 2 0.01
78 18 0.08
79 102 0.45
80 4 0.02
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAATATCAATTTTTCATAATCGGGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:462686 original size:15 final size:15
Alignment explanation
Indices: 462666--462717 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
462656 GAGAATTAAA
*
462666 ATTATTTTTTTATTT
1 ATTATTTTATTATTT
462681 ATTA-TTTATTATTT
1 ATTATTTTATTATTT
462695 ATTATTTTATTATTT
1 ATTATTTTATTATTT
*
462710 ATTGTTTT
1 ATTATTTT
462718 GAAATAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.38
15 21 0.62
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (15 bp):
ATTATTTTATTATTT
Found at i:462687 original size:7 final size:7
Alignment explanation
Indices: 462667--462712 Score: 69
Period size: 7 Copynumber: 6.7 Consensus size: 7
462657 AGAATTAAAA
462667 TTATT-T
1 TTATTAT
462673 TT-TTAT
1 TTATTAT
462679 TTATTAT
1 TTATTAT
462686 TTATTAT
1 TTATTAT
462693 TTATTATT
1 TTATTA-T
462701 TTATTAT
1 TTATTAT
462708 TTATT
1 TTATT
462713 GTTTTGAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 2 0.05
6 5 0.14
7 23 0.62
8 7 0.19
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTATTAT
Found at i:462693 original size:22 final size:23
Alignment explanation
Indices: 462666--462717 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
462656 GAGAATTAAA
*
462666 ATTATTTTTTTA-TTTATTATTT
1 ATTATTTTATTATTTTATTATTT
462688 ATTA-TTTATTATTTTATTATTT
1 ATTATTTTATTATTTTATTATTT
*
462710 ATTGTTTT
1 ATTATTTT
462718 GAAATAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 6 0.23
22 17 0.65
23 3 0.12
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (23 bp):
ATTATTTTATTATTTTATTATTT
Found at i:464410 original size:27 final size:29
Alignment explanation
Indices: 464377--464433 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
464367 TTTGTCGGTT
464377 TTAAAT-ATATATT-TTAAATATATTTTA
1 TTAAATAATATATTATTAAATATATTTTA
*
464404 TTAAATAAATATTTTATTAAATATATTTTA
1 TTAAAT-AATATATTATTAAATATATTTTA
464434 AATATTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 6 0.23
29 6 0.23
30 14 0.54
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TTAAATAATATATTATTAAATATATTTTA
Found at i:464415 original size:16 final size:16
Alignment explanation
Indices: 464396--464426 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
464386 TATTTTAAAT
464396 ATATTTTATTAAATAA
1 ATATTTTATTAAATAA
464412 ATATTTTATTAAATA
1 ATATTTTATTAAATA
464427 TATTTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATTTTATTAAATAA
Found at i:464434 original size:27 final size:26
Alignment explanation
Indices: 464375--464437 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
464365 GTTTTGTCGG
* *
464375 TTTTAAATATATATTTTAAATATATT
1 TTTTAAATAAATATTTTAAATATATA
464401 TTATTAAATAAATATTTTATTAA-ATATA
1 TT-TTAAATAAATATTTTA--AATATATA
464429 TTTTAAATA
1 TTTTAAATA
464438 TTAAATCGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 2 0.06
27 22 0.69
28 6 0.19
29 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTTAAATAAATATTTTAAATATATA
Found at i:466139 original size:34 final size:32
Alignment explanation
Indices: 466059--466144 Score: 93
Period size: 34 Copynumber: 2.6 Consensus size: 32
466049 ATTACTATCG
* *
466059 TTTTAATAATTTTAATTATTTAACATAAATATA
1 TTTTAATTATTTT-ATTATTTAAAATAAATATA
*
466092 TTTTATTCATATTTTATTATTTAAAATAAATATAAA
1 TTTTAAT--TATTTTATTATTTAAAATAAATAT--A
466128 TTTTAATTA-TTTATTAT
1 TTTTAATTATTTTATTAT
466145 ATATAGATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
33 14 0.31
34 19 0.42
35 5 0.11
36 7 0.16
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (32 bp):
TTTTAATTATTTTATTATTTAAAATAAATATA
Found at i:466612 original size:17 final size:16
Alignment explanation
Indices: 466590--466621 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
466580 TTTTAAAGAA
466590 GAAAAAAAAAAGAAAAG
1 GAAAAAAAAAA-AAAAG
466607 GAAAAAAAAAAAAAA
1 GAAAAAAAAAAAAAA
466622 CCTTAAACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (16 bp):
GAAAAAAAAAAAAAAG
Found at i:466793 original size:20 final size:21
Alignment explanation
Indices: 466761--466799 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
466751 TTTAATTAAA
466761 AATTTTAAGTATTAAATATAT
1 AATTTTAAGTATTAAATATAT
466782 AATTTTAA-TATTAAATAT
1 AATTTTAAGTATTAAATAT
466800 GTTATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (21 bp):
AATTTTAAGTATTAAATATAT
Found at i:466863 original size:15 final size:15
Alignment explanation
Indices: 466833--466868 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
466823 TTCATTTGAA
466833 TTAATTATATAATTT
1 TTAATTATATAATTT
466848 TTAA-TATATAATTT
1 TTAATTATATAATTT
*
466862 TTTATTA
1 TTAATTA
466869 AAGATTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTAATTATATAATTT
Found at i:467258 original size:23 final size:21
Alignment explanation
Indices: 467220--467283 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 21
467210 ATAGCATTTC
* *
467220 TCTTTTTTTTATTTATTATGTT
1 TCTTTTTATTA-TTATTATATT
*
467242 TCTATTTTATTTCTTATATATATT
1 TCT-TTTTA-TTATTAT-TATATT
467266 TCTTTTTATTATTATTAT
1 TCTTTTTATTATTATTAT
467284 TATTACCTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
21 3 0.09
22 9 0.26
23 13 0.37
24 10 0.29
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (21 bp):
TCTTTTTATTATTATTATATT
Found at i:467363 original size:2 final size:2
Alignment explanation
Indices: 467356--467415 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
467346 TTTTGGTCTC
467356 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
467398 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
467416 CTATCTCTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:467658 original size:21 final size:19
Alignment explanation
Indices: 467627--467665 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
467617 TATAATTTTT
467627 TTTAAAAAAATTATAAATA
1 TTTAAAAAAATTATAAATA
*
467646 TTTAAATATAAATTTTAAAT
1 TTTAAA-A-AAATTATAAAT
467666 TTTTTGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTAAAAAAATTATAAATA
Found at i:468560 original size:29 final size:29
Alignment explanation
Indices: 468490--468560 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
468480 TAATAATTCA
* * * *
468490 TATATTTATGTTATGTATAGATATTTTTT
1 TATATTTATATTATATATAGAAATTATTT
* *
468519 TATA-TCATAATTATATATATAAATTATTT
1 TATATTTAT-ATTATATATAGAAATTATTT
468548 TATATTTATATTA
1 TATATTTATATTA
468561 AATTTGATAC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
28 3 0.09
29 27 0.82
30 3 0.09
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (29 bp):
TATATTTATATTATATATAGAAATTATTT
Found at i:468623 original size:16 final size:16
Alignment explanation
Indices: 468604--468655 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
468594 TTTTAAAATA
468604 TATATATAAATTATAT
1 TATATATAAATTATAT
* * *
468620 TATATTTTATTTATAT
1 TATATATAAATTATAT
468636 TATACTTATATAATTATAT
1 TATA--TATA-AATTATAT
468655 T
1 T
468656 TAATATTATT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
16 17 0.63
18 2 0.07
19 8 0.30
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TATATATAAATTATAT
Found at i:472339 original size:22 final size:19
Alignment explanation
Indices: 472296--472333 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
472286 TTTACGTGTC
472296 ATAAATTATATATAAATTA
1 ATAAATTATATATAAATTA
*
472315 ATAAATATTTATATAAATT
1 ATAAAT-TATATATAAATT
472334 TTAATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAAATTATATATAAATTA
Found at i:473524 original size:25 final size:27
Alignment explanation
Indices: 473461--473531 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 27
473451 TATGTACTCG
*
473461 TAAATTTTTATATATTTTATTATATAA
1 TAAATTTTAATATATTTTATTATATAA
*
473488 TAATTATATTTAAAATATTTTA-TATAT-A
1 TAA--AT-TTTAATATATTTTATTATATAA
473516 TAAATTTTAATATATT
1 TAAATTTTAATATATT
473532 AATAATTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
25 10 0.26
26 2 0.05
27 3 0.08
28 4 0.11
29 7 0.18
30 12 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TAAATTTTAATATATTTTATTATATAA
Found at i:474001 original size:2 final size:2
Alignment explanation
Indices: 473994--474039 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
473984 AATTGACTTG
*
473994 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
474036 AT AT
1 AT AT
474040 TGAAATGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:477285 original size:2 final size:2
Alignment explanation
Indices: 477278--477324 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
477268 TTTTATGATA
477278 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
477320 CT CT C
1 CT CT C
477325 ACACACACAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:478221 original size:15 final size:16
Alignment explanation
Indices: 478201--478230 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
478191 AATTTTAATT
478201 TTAAATTA-AATTTTA
1 TTAAATTATAATTTTA
478216 TTAAATTATAATTTT
1 TTAAATTATAATTTT
478231 TAATTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAAATTATAATTTTA
Found at i:478748 original size:13 final size:13
Alignment explanation
Indices: 478717--478753 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
478707 AAAGCATCAT
478717 TAAAAATAA--AA
1 TAAAAATAATTAA
478728 TAAAAAATAATTAA
1 T-AAAAATAATTAA
478742 TAAAAATAATTA
1 TAAAAATAATTA
478754 TTTCCTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 1 0.04
12 8 0.35
13 11 0.48
14 3 0.13
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
TAAAAATAATTAA
Found at i:478788 original size:26 final size:25
Alignment explanation
Indices: 478735--478788 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
478725 AAATAAAAAA
*
478735 TAATTAATAAAAATAATTATTTCCT
1 TAATTAATAAAAATAATTATTTACT
* * *
478760 TAATTGAATAAAAATGATTCTTTATT
1 TAATT-AATAAAAATAATTATTTACT
478786 TAA
1 TAA
478789 ATATATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (25 bp):
TAATTAATAAAAATAATTATTTACT
Found at i:479389 original size:12 final size:13
Alignment explanation
Indices: 479366--479399 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
479356 TTTTAAAATA
479366 AAATATAATATAT
1 AAATATAATATAT
479379 AAATA-AATATAT
1 AAATATAATATAT
*
479391 AAATTTAAT
1 AAATATAAT
479400 TTATTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATATAATATAT
Found at i:479849 original size:11 final size:11
Alignment explanation
Indices: 479835--479906 Score: 57
Period size: 11 Copynumber: 6.9 Consensus size: 11
479825 TGATATAAAA
*
479835 ATAAATATAAC
1 ATAAATATAAT
*
479846 ATAAA-AAAACT
1 ATAAATATAA-T
479857 A-AAATATAAT
1 ATAAATATAAT
479867 A-AAATATAA-
1 ATAAATATAAT
*
479876 A-AAAAATAAT
1 ATAAATATAAT
479886 AT-AATCATAAT
1 ATAAAT-ATAAT
479897 ATAAATATAA
1 ATAAATATAA
479907 AAAATATTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
9 8 0.16
10 19 0.38
11 20 0.40
12 3 0.06
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.26
Consensus pattern (11 bp):
ATAAATATAAT
Found at i:479873 original size:31 final size:31
Alignment explanation
Indices: 479835--479910 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
479825 TGATATAAAA
479835 ATAAATATAACATAAAAA-AACTAAAAT-ATAAT
1 ATAAATATAA-A-AAAAATAA-TAAAATCATAAT
*
479867 A-AAATATAAAAAAAATAATATAATCATAAT
1 ATAAATATAAAAAAAATAATAAAATCATAAT
479897 ATAAATATAAAAAA
1 ATAAATATAAAAAA
479911 TATTAAAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
29 10 0.25
30 9 0.22
31 20 0.50
32 1 0.03
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (31 bp):
ATAAATATAAAAAAAATAATAAAATCATAAT
Found at i:479879 original size:9 final size:10
Alignment explanation
Indices: 479856--479913 Score: 66
Period size: 9 Copynumber: 5.8 Consensus size: 10
479846 ATAAAAAAAC
479856 TAAAATATAA
1 TAAAATATAA
479866 TAAAATATAA
1 TAAAATATAA
*
479876 -AAAAAATAA
1 TAAAATATAA
*
479885 TATAATCATAA
1 TAAAAT-ATAA
479896 TATAAATATAA
1 TA-AAATATAA
479907 -AAAATAT
1 TAAAATAT
479914 TAAAATTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
9 14 0.34
10 14 0.34
11 10 0.24
12 3 0.07
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (10 bp):
TAAAATATAA
Found at i:479918 original size:9 final size:9
Alignment explanation
Indices: 479857--479918 Score: 52
Period size: 10 Copynumber: 6.2 Consensus size: 9
479847 TAAAAAAACT
479857 AAAATATAA
1 AAAATATAA
479866 TAAAATATAA
1 -AAAATATAA
*
479876 AAAAAATAA
1 AAAATATAA
*
479885 TATAATCATAA
1 -AAAAT-ATAA
479896 TATAAATATAA
1 -A-AAATATAA
479907 AAAATATTAA
1 AAAATA-TAA
479917 AA
1 AA
479919 TTTATATAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
9 13 0.30
10 18 0.41
11 10 0.23
12 3 0.07
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAATATAA
Found at i:479989 original size:19 final size:20
Alignment explanation
Indices: 479955--479994 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
479945 ATTGAGAATT
*
479955 ATTTGAATAATGTTAATTAA
1 ATTTGAATAATGTTAAATAA
*
479975 ATTTG-ATAATTTTAAATAA
1 ATTTGAATAATGTTAAATAA
479994 A
1 A
479995 ATGCAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATTTGAATAATGTTAAATAA
Found at i:479996 original size:20 final size:20
Alignment explanation
Indices: 479955--479996 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
479945 ATTGAGAATT
*
479955 ATTTGAATAATGTTAATTAA
1 ATTTGAATAATGTTAATAAA
*
479975 ATTTG-ATAATTTTAAATAAA
1 ATTTGAATAATGTT-AATAAA
479995 AT
1 AT
479997 GCAAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATTTGAATAATGTTAATAAA
Found at i:480133 original size:13 final size:14
Alignment explanation
Indices: 480115--480143 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
480105 TAATTATAAG
480115 TATAATT-TTTTAT
1 TATAATTATTTTAT
480128 TATAATTATTTTAT
1 TATAATTATTTTAT
480142 TA
1 TA
480144 AAGATTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATAATTATTTTAT
Found at i:480608 original size:19 final size:17
Alignment explanation
Indices: 480584--480627 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
480574 TCATGAATTT
480584 AATATAATAAAATAATTAA
1 AATATAATAAAAT-A-TAA
*
480603 AATATAATATAATATAA
1 AATATAATAAAATATAA
480620 AA-ATAATA
1 AATATAATA
480628 TGAATATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 6 0.25
17 5 0.21
18 1 0.04
19 12 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AATATAATAAAATATAA
Found at i:480644 original size:17 final size:16
Alignment explanation
Indices: 480589--480636 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
480579 AATTTAATAT
*
480589 AATAAAATAAT-TAAA
1 AATAATATAATATAAA
480604 ATATAATATAATATAAA
1 A-ATAATATAATATAAA
480621 AATAATATGAATATAA
1 AATAATAT-AATATAA
480637 CATTAATAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 1 0.03
16 16 0.55
17 12 0.41
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (16 bp):
AATAATATAATATAAA
Found at i:495633 original size:79 final size:79
Alignment explanation
Indices: 495514--495858 Score: 370
Period size: 79 Copynumber: 4.4 Consensus size: 79
495504 AATTTAATAT
* * * *
495514 TTTGGAGATAATAA-CGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGGTT
1 TTTGGAAATAA-AATCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATT
*
495578 GTGAAAAATCGATGA
65 ATGAAAAATCGATGA
* * * * *
495593 TTGGGAAATAAAATTGGGATTAGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTA
1 TTTGGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTA
* *
495658 TGAGAAATCAAT-A
66 TGAAAAATCGATGA
* ** *
495671 TTCTGGAAATAAAGTCGGGGTTGGAGTATCCCCTCGGAGGTAATGGGGTTGGAGTATCCCCGATT
1 TT-TGGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATT
* * * *
495736 ATTAAAAATTGAAGT
65 ATGAAAAATCGATGA
* * * *
495751 TTTAGAAATAAAACCGGGGTTGGAGTATCCCCGCGGAAACAACGGGGTTGGAGTATCCCCGATTA
1 TTTGGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTA
* * * *
495816 TGAGAAATTGAAGT
66 TGAAAAATCGATGA
* * * *
495830 TTTAGAAATAAAACCAGGGTTGAAGTATC
1 TTTGGAAATAAAATCGGGGTTGGAGTATC
495859 TCCGATTATG
Statistics
Matches: 224, Mismatches: 39, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
78 5 0.02
79 217 0.97
80 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (79 bp):
TTTGGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTA
TGAAAAATCGATGA
Found at i:495797 original size:158 final size:158
Alignment explanation
Indices: 495528--495823 Score: 412
Period size: 158 Copynumber: 1.9 Consensus size: 158
495518 GAGATAATAA
* * * *
495528 CGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGAAGA
* ** * *
495593 TTGGGAAATAAAATTGGGATTAGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTA
66 TTGAGAAATAAAACCGGGATTAGAGTATCCCCGCGGAAACAACGGGGTTGGAGTATCCCCAATTA
495658 TGAGAAATCAATATTCTGGAAATAAAGT
131 TGAGAAATCAATATTCTGGAAATAAAGT
* ** * * * *
495686 CGGGGTTGGAGTATCCCCTCGGAGGTAATGGGGTTGGAGTATCCCCGATTATTAAAAATTGAAGT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGAAGA
* * * *
495751 TTTAGAAATAAAACCGGGGTTGGAGTATCCCCGCGGAAACAACGGGGTTGGAGTATCCCCGATTA
66 TTGAGAAATAAAACCGGGATTAGAGTATCCCCGCGGAAACAACGGGGTTGGAGTATCCCCAATTA
495816 TGAGAAAT
131 TGAGAAAT
495824 TGAAGTTTTA
Statistics
Matches: 118, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
158 118 1.00
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (158 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGAAGA
TTGAGAAATAAAACCGGGATTAGAGTATCCCCGCGGAAACAACGGGGTTGGAGTATCCCCAATTA
TGAGAAATCAATATTCTGGAAATAAAGT
Found at i:495871 original size:51 final size:51
Alignment explanation
Indices: 495795--495912 Score: 184
Period size: 51 Copynumber: 2.3 Consensus size: 51
495785 GGAAACAACG
*
495795 GGGTTGGAGTATCCCCGATTATGAGAAATTGAA-GTTTTAGAAATAAAACCA
1 GGGTTGGAGTATCCCCGATTATGAGAAATT-AATATTTTAGAAATAAAACCA
* * *
495846 GGGTTGAAGTATCTCCGATTATGAGAAATTAATATTTTAGAAATAAAACCG
1 GGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAACCA
495897 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
495913 TCGAAAATAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 2 0.03
51 58 0.97
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.29
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAACCA
Found at i:495875 original size:130 final size:129
Alignment explanation
Indices: 495716--496124 Score: 651
Period size: 130 Copynumber: 3.1 Consensus size: 129
495706 GGAGGTAATG
* * *
495716 GGGTTGGAGTATCCCCGATTATTAAAAATTGAA-GTTTTAGAAATAAAACCGGGGTTGGAGTATC
1 GGGTTGGAGTATCCCCGATTATGAGAAATT-AATATTTTAGAAATAAAACCGGGGTTGGAGTATC
* *
495780 CCCGCGGAAACAACGGGGTTGGAGTATCCCCGATTATGAGAAATTGAAGTTTTAGAAATAAAACC
65 CCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTGAAGTTTTAGAAATAAAACC
* *
495845 AGGGTTGAAGTATCTCCGATTATGAGAAATTAATATTTTAGAAATAAAACCGGGGTTGGAGTATC
1 -GGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAACCGGGGTTGGAGTATC
* *
495910 CCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGAAGTTTTAGAAATAAAATC
65 CCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTGAAGTTTTAGAAATAAAA-C
*
495975 G
129 C
*
495976 GGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAATCGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAACCGGGGTTGGAGTATCC
*
496041 CCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTGATA-TTTTAGAAATAAAACC
66 CCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTGA-AGTTTTAGAAATAAAACC
496105 GAGGTTGGAGTATCCCCGAT
1 G-GGTTGGAGTATCCCCGAT
496125 GATTAACGGG
Statistics
Matches: 258, Mismatches: 17, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
129 4 0.02
130 252 0.98
131 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.27
Consensus pattern (129 bp):
GGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAACCGGGGTTGGAGTATCC
CCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTGAAGTTTTAGAAATAAAACC
Found at i:495978 original size:79 final size:79
Alignment explanation
Indices: 495846--495991 Score: 231
Period size: 79 Copynumber: 1.8 Consensus size: 79
495836 AATAAAACCA
* *
495846 GGGTTGAAGTATCTCCGATTATGAGAAATTAATATTTTAGAAATAAAACCGGGGTTGGAGTATCC
1 GGGTTGAAGTATCCCCGATTATGAAAAATTAATATTTTAGAAATAAAACCGGGGTTGGAGTATCC
495911 CCTCGAAAATAACG
66 CCTCGAAAATAACG
* * *
495925 GGGTTGGAGTATCCCCGATTATGAAAAATTGAA-GTTTTAGAAATAAAATCGGGGTTGGAGTATC
1 GGGTTGAAGTATCCCCGATTATGAAAAATT-AATATTTTAGAAATAAAACCGGGGTTGGAGTATC
495989 CCC
65 CCC
495992 GATTATGAGA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
79 59 0.97
80 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.28
Consensus pattern (79 bp):
GGGTTGAAGTATCCCCGATTATGAAAAATTAATATTTTAGAAATAAAACCGGGGTTGGAGTATCC
CCTCGAAAATAACG
Found at i:495990 original size:51 final size:51
Alignment explanation
Indices: 495923--496042 Score: 206
Period size: 51 Copynumber: 2.4 Consensus size: 51
495913 TCGAAAATAA
*
495923 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGAA-GTTTTAGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATT-AATATTTTAGAAATAAAAT
*
495974 CGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTAATATTTTAGAAATAAAAT
496025 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
496043 TCAGAAATAA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
50 2 0.03
51 64 0.97
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATTAATATTTTAGAAATAAAAT
Found at i:496057 original size:79 final size:78
Alignment explanation
Indices: 495974--496162 Score: 281
Period size: 79 Copynumber: 2.4 Consensus size: 78
495964 GAAATAAAAT
* *
495974 CGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAATCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAACCGAGGTTGGAGTAT
496039 CCCCTCA-GAAATAA
66 CCCC-CATG-AATAA
*
496053 CGGGGTTGGAGTATCCCCGATTATGAGAAATTGATATTTTAGAAATAAAACCGAGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAACCGAGGTTGGAGTAT
* *
496118 CCCCGATGATTAA
66 CCCCCATGAATAA
* * *
496131 CGGGGTTGGAGTATCCTCGATTGTGAAAAATT
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATT
496163 GAGAAACTTA
Statistics
Matches: 101, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
78 34 0.34
79 67 0.66
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.29
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAACCGAGGTTGGAGTAT
CCCCCATGAATAA
Found at i:497447 original size:41 final size:41
Alignment explanation
Indices: 497396--497474 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
497386 CTCCCATTGT
*
497396 ATTTTTTTATTTCCTTTCCCATGTTGCCAATTGTTGTATGC
1 ATTTTTTTATTTCCTTTCCCATGCTGCCAATTGTTGTATGC
497437 ATTTTTTTATTTCCTTTCCCATGCTGCCAATTGTTGTA
1 ATTTTTTTATTTCCTTTCCCATGCTGCCAATTGTTGTA
497475 AGTTCCCACC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.15, C:0.20, G:0.11, T:0.53
Consensus pattern (41 bp):
ATTTTTTTATTTCCTTTCCCATGCTGCCAATTGTTGTATGC
Found at i:497646 original size:12 final size:13
Alignment explanation
Indices: 497626--497654 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
497616 ATTATTATTT
497626 TTTTGAATTTTAA
1 TTTTGAATTTTAA
497639 TTTT-AATTTTAA
1 TTTTGAATTTTAA
497651 TTTT
1 TTTT
497655 TGATTTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
TTTTGAATTTTAA
Found at i:498804 original size:20 final size:20
Alignment explanation
Indices: 498757--498811 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
498747 AAAAAAATAT
* *
498757 AATATATCGATATATTGAAA
1 AATATATCGATACATTCAAA
* *
498777 AATGTATCGATACATTCACA
1 AATATATCGATACATTCAAA
*
498797 CATATATCGATACAT
1 AATATATCGATACAT
498812 CTAGGTAGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.33
Consensus pattern (20 bp):
AATATATCGATACATTCAAA
Found at i:499646 original size:15 final size:17
Alignment explanation
Indices: 499623--499669 Score: 71
Period size: 15 Copynumber: 2.9 Consensus size: 17
499613 TTGTTAAAAA
499623 AAAGAAAGAAAAAAA-G
1 AAAGAAAGAAAAAAAGG
*
499639 AAA-TAAGAAAAAAAGG
1 AAAGAAAGAAAAAAAGG
499655 AAAGAAAGAAAAAAA
1 AAAGAAAGAAAAAAA
499670 AGGCAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 10 0.37
16 7 0.26
17 10 0.37
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (17 bp):
AAAGAAAGAAAAAAAGG
Found at i:499650 original size:16 final size:17
Alignment explanation
Indices: 499618--499671 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 17
499608 ACGTTTTGTT
499618 AAAAA-AAAGAAAG-AA
1 AAAAAGAAAGAAAGAAA
*
499633 AAAAAGAAA-TAAGAAA
1 AAAAAGAAAGAAAGAAA
*
499649 AAAAGGAAAGAAAGAAA
1 AAAAAGAAAGAAAGAAA
499666 AAAAAG
1 AAAAAG
499672 GCAAAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 8 0.25
16 13 0.41
17 11 0.34
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (17 bp):
AAAAAGAAAGAAAGAAA
Found at i:500573 original size:7 final size:8
Alignment explanation
Indices: 500556--500586 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
500546 AGAAAGATGG
500556 AAAGAAAA
1 AAAGAAAA
500564 AAAG-AAA
1 AAAGAAAA
500571 AAAGAAAA
1 AAAGAAAA
500579 AAAGAAAA
1 AAAGAAAA
500587 GGGAGAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:500574 original size:15 final size:15
Alignment explanation
Indices: 500556--500586 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
500546 AGAAAGATGG
500556 AAAGAAAAAAAGAAA
1 AAAGAAAAAAAGAAA
500571 AAAGAAAAAAAGAAA
1 AAAGAAAAAAAGAAA
500586 A
1 A
500587 GGGAGAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAGAAA
Done.