Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008955.1 Hibiscus syriacus cultivar Beakdansim tig00112285_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: 4658001
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 23
Found at i:535885 original size:2 final size:2
Alignment explanation
Indices: 535878--535904 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
535868 TTAAAGAAAC
535878 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
535905 AAAAAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:535981 original size:18 final size:17
Alignment explanation
Indices: 535958--536000 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
535948 ATATATATGT
535958 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
535976 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
535993 ATAA-AATA
1 ATAATAATA
536001 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:536673 original size:17 final size:17
Alignment explanation
Indices: 536651--536693 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
536641 GGCTCCTCCT
*
536651 TCGTGAAATCGAGTCCG
1 TCGTGAAATCGAGTCCA
536668 TCGTGAAATCGAGTCCA
1 TCGTGAAATCGAGTCCA
*
536685 TCTTGAAAT
1 TCGTGAAAT
536694 GATTTGAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (17 bp):
TCGTGAAATCGAGTCCA
Found at i:537502 original size:106 final size:106
Alignment explanation
Indices: 537306--537731 Score: 627
Period size: 106 Copynumber: 4.0 Consensus size: 106
537296 AGTATTGTTC
* * * * *
537306 CGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTATGGAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
*
537371 ACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAACCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
*
537412 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
** * * *
537477 ACCAGTCGTCCTTTCATTGTAAAGTTGAACTTGTGCTGTCT
66 ACCAACCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
* ** * *
537518 TGAGTCCAATGCCCTTCGCTTTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
*
537583 ACCAACCGTCCCTTCAATGTGAAGTTGAACTTGTGTTGTCT
66 ACCAACCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
* * * *
537624 TGAGTCCAATATCCTTCGCTGTGAAGTCGAAATTGGATCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
** *
537689 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAACCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
537730 CG
1 CG
537732 GGTGGCGTGA
Statistics
Matches: 285, Mismatches: 35, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
106 285 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAACCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
Found at i:538390 original size:37 final size:37
Alignment explanation
Indices: 538348--538419 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
538338 AAGATATATG
* * *
538348 TTGTTTCATGAGAAACGGTCTCAAGGGAGACAAAATT
1 TTGTTTCAAGAAAAACGGTCTCAAGAGAGACAAAATT
* *
538385 TTGTTTTAAGAAAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAAAAACGGTCTCAAGAGAGACAAAA
538420 CTTAGTTCCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.26
Consensus pattern (37 bp):
TTGTTTCAAGAAAAACGGTCTCAAGAGAGACAAAATT
Found at i:538442 original size:37 final size:36
Alignment explanation
Indices: 538360--538474 Score: 97
Period size: 37 Copynumber: 3.1 Consensus size: 36
538350 GTTTCATGAG
* * * **
538360 AAACGGTCTCAAGGGAGACAAAATTTTGTTTTAAGAA
1 AAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAGAA
538397 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAA-AA
1 AAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAGAA
* * ** *
538433 GAAATTGTCTCACGAGAAGATGAAATTAGTTCCAAGGA
1 -AAACTGTCTCAAGAG-AGACAAAATTAGTTCCAAGAA
538471 AAAC
1 AAAC
538475 ATATTCAAAG
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
36 2 0.03
37 54 0.86
38 7 0.11
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (36 bp):
AAACTGTCTCAAGAGAGACAAAATTAGTTCCAAGAA
Found at i:538645 original size:36 final size:38
Alignment explanation
Indices: 538591--538667 Score: 104
Period size: 36 Copynumber: 2.1 Consensus size: 38
538581 GAAACAATTT
*
538591 CAAAGGTTTTTTTCCAAGGAAAAATGTCTCAAGAGAGA
1 CAAAGGTTTGTTTCCAAGGAAAAATGTCTCAAGAGAGA
* **
538629 CAAA-GTTTGTTT-CAAGGGAAGCTGTCTCAAGAGAGA
1 CAAAGGTTTGTTTCCAAGGAAAAATGTCTCAAGAGAGA
538665 CAA
1 CAA
538668 TGGTGAGCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 24 0.69
37 7 0.20
38 4 0.11
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (38 bp):
CAAAGGTTTGTTTCCAAGGAAAAATGTCTCAAGAGAGA
Found at i:540257 original size:21 final size:19
Alignment explanation
Indices: 540240--540296 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
540230 TTCCTTTTGA
540240 TTTTTGCTTCTTTTCTTTT
1 TTTTTGCTTCTTTTCTTTT
* * *
540259 TTGTT-CTTGTTTT-TTCT
1 TTTTTGCTTCTTTTCTTTT
540276 TTTTTGCTTCTTTTCTTTT
1 TTTTTGCTTCTTTTCTTTT
540295 TT
1 TT
540297 GTTCTTGATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
17 7 0.23
18 14 0.47
19 9 0.30
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (19 bp):
TTTTTGCTTCTTTTCTTTT
Found at i:540265 original size:15 final size:16
Alignment explanation
Indices: 540240--540302 Score: 74
Period size: 16 Copynumber: 3.8 Consensus size: 16
540230 TTCCTTTTGA
540240 TTTTTGCTTCTTTTCT
1 TTTTTGCTTCTTTTCT
*
540256 TTTTTGTTCTTGTTTTTTCT
1 TTTTTG--C-T-TCTTTTCT
540276 TTTTTGCTTCTTTTCT
1 TTTTTGCTTCTTTTCT
540292 TTTTTG-TTCTT
1 TTTTTGCTTCTT
540303 GATTGAATCT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
15 5 0.12
16 19 0.46
17 1 0.02
18 2 0.05
19 1 0.02
20 13 0.32
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (16 bp):
TTTTTGCTTCTTTTCT
Found at i:540302 original size:10 final size:10
Alignment explanation
Indices: 540252--540289 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
540242 TTTGCTTCTT
540252 TTCTTTTTTG
1 TTCTTTTTTG
540262 TTCTTGTTTT-
1 TTCTT-TTTTG
540272 TTCTTTTTTG
1 TTCTTTTTTG
540282 CTTCTTTT
1 -TTCTTTT
540290 CTTTTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.16
10 10 0.40
11 11 0.44
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (10 bp):
TTCTTTTTTG
Found at i:543768 original size:11 final size:11
Alignment explanation
Indices: 543749--543808 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
543739 TTAGTAAAAT
*
543749 AAAATAAATAG
1 AAAAAAAATAG
*
543760 AAAAAAAATAC
1 AAAAAAAATAG
*
543771 AAAAAAAATGG
1 AAAAAAAATAG
* *
543782 GAAATAAATAG
1 AAAAAAAATAG
*
543793 -AAAAAAATAC
1 AAAAAAAATAG
543803 AAAAAA
1 AAAAAA
543809 TAAATGGGAA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
10 8 0.21
11 31 0.79
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.12
Consensus pattern (11 bp):
AAAAAAAATAG
Found at i:543792 original size:33 final size:34
Alignment explanation
Indices: 543750--543818 Score: 115
Period size: 33 Copynumber: 2.1 Consensus size: 34
543740 TAGTAAAATA
543750 AAATAAATAGAAAAAAAATAC-AAAAA-AAATGGG
1 AAATAAATAG-AAAAAAATACAAAAAATAAATGGG
543783 AAATAAATAGAAAAAAATACAAAAAATAAATGGG
1 AAATAAATAGAAAAAAATACAAAAAATAAATGGG
543817 AA
1 AA
543819 GAGAAAAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 10 0.29
33 15 0.44
34 9 0.26
ACGTcount: A:0.72, C:0.03, G:0.12, T:0.13
Consensus pattern (34 bp):
AAATAAATAGAAAAAAATACAAAAAATAAATGGG
Found at i:544653 original size:38 final size:40
Alignment explanation
Indices: 544587--544663 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
544577 AAAATGAAAA
*
544587 ATATATATACATCAAAGTATTAATAAAATA-AATAAGCTAT
1 ATATATATACAACAAAGTATTAATAAAATAGAA-AAGCTAT
*
544627 ATATATATACAACAAA-TATTTA-AAAATAGAAAAGCTA
1 ATATATATACAACAAAGTATTAATAAAATAGAAAAGCTA
544664 CCCTCTCACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 12 0.35
39 7 0.21
40 15 0.44
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (40 bp):
ATATATATACAACAAAGTATTAATAAAATAGAAAAGCTAT
Found at i:545172 original size:17 final size:18
Alignment explanation
Indices: 545139--545174 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
545129 ATATACGTAT
*
545139 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
545157 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
545174 A
1 A
545175 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:547038 original size:25 final size:27
Alignment explanation
Indices: 547009--547066 Score: 84
Period size: 25 Copynumber: 2.2 Consensus size: 27
546999 CCCAGTTGCA
*
547009 AGCTGCCCAGGAGGGGACCAC-GCC-T
1 AGCTGCCCAGGAGGAGACCACTGCCAT
*
547034 AGCTGCCTAGGAGGAGACCACTGCCAT
1 AGCTGCCCAGGAGGAGACCACTGCCAT
547061 AGCTGC
1 AGCTGC
547067 TCACCCCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 19 0.66
26 3 0.10
27 7 0.24
ACGTcount: A:0.22, C:0.33, G:0.33, T:0.12
Consensus pattern (27 bp):
AGCTGCCCAGGAGGAGACCACTGCCAT
Found at i:547568 original size:21 final size:20
Alignment explanation
Indices: 547530--547568 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
547520 TAATGGATGA
*
547530 TTGTTTTTGTATGTTGTTAT
1 TTGTTTTTGTATGATGTTAT
*
547550 TTGTTTTGTTTATGATGTT
1 TTGTTTT-TGTATGATGTT
547569 TAATGCCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.10, C:0.00, G:0.21, T:0.69
Consensus pattern (20 bp):
TTGTTTTTGTATGATGTTAT
Found at i:553503 original size:201 final size:198
Alignment explanation
Indices: 553138--553691 Score: 596
Period size: 199 Copynumber: 2.8 Consensus size: 198
553128 TGCAATGTAT
* *
553138 AAGTAATAGGTAAATTTACAATGTAAACAGTAAAAGTATA-TCGGTATAATGATAATA-GCATAA
1 AAGTAATAGGTAAATTTACAATGTAAACAGTAAAAGTATACT-AGTATAATGATAATAGGCGTAA
* * * * * *
553201 ACACATCATATCAATACTTTGTTATATCA-ATATTGATACTTTAATTCCAGTATGCATCTCAAAC
65 ATAAAT--TATCAATACTTTATT-TAT-AGGTATCGATACTTTTATTCCAGTATGCATCTCAAAC
* * ***
553265 AATTTTCACGCAAAAAGTATCAATACACATATATAAAGTATCGATATACTTAGAATTTTGAAACC
126 AATTTGCACGCAAAAAGTATCGATACACATATATAAAGTATC-A-ATACTTAGAATTCCAAAACC
*
553330 TATTACTTTA
189 TATTACTATA
* * * * * *
553340 AAGTAATAGGTAAATTTACAATGTAAATAGTAAAAATCTACTTGTTTAATGATAATAGGTGTAAA
1 AAGTAATAGGTAAATTTACAATGTAAACAGTAAAAGTATACTAGTATAATGATAATAGGCGTAAA
*** *
553405 TATAATGTATCAATACTTT-TTTATAGGTATCGATACTTTTATTCCAGTATATTTCTCATACAAT
66 TA-AAT-TATCAATACTTTATTTATAGGTATCGATACTTTTATTCCAGTATGCATCTCAAACAAT
* * **
553469 TTGCACGCAAAAAGTATCGATACACTTGTATAAAGTATCAATACTTTTAATTCCAAAACCTATTA
129 TTGCACGCAAAAAGTATCGATACACATATATAAAGTATCAATACTTAGAATTCCAAAACCTATTA
553534 CTATA
194 CTATA
* ** * * *
553539 AAGTAATAGGTAAATTAACAATGTAAAGGGTAAAAGTTTACTAGTATAATGATCATAGGCGTATA
1 AAGTAATAGGTAAATTTACAATGTAAACAGTAAAAGTATACTAGTATAATGATAATAGGCGTAAA
* * * *
553604 TACCAATTATCGATACTTTATATATAGGTAGCGATAATTTTAGTT-CAGTATGCATCTCAAACAA
66 TA--AATTATCAATACTTTATTTATAGGTATCGATACTTTTA-TTCCAGTATGCATCTCAAACAA
** *
553668 TTTGCACTTAAAATGTATCGATAC
128 TTTGCACGCAAAAAGTATCGATAC
553692 TCGGAATTTC
Statistics
Matches: 296, Mismatches: 49, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
199 92 0.31
200 60 0.20
201 71 0.24
202 52 0.18
203 19 0.06
204 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (198 bp):
AAGTAATAGGTAAATTTACAATGTAAACAGTAAAAGTATACTAGTATAATGATAATAGGCGTAAA
TAAATTATCAATACTTTATTTATAGGTATCGATACTTTTATTCCAGTATGCATCTCAAACAATTT
GCACGCAAAAAGTATCGATACACATATATAAAGTATCAATACTTAGAATTCCAAAACCTATTACT
ATA
Found at i:555098 original size:179 final size:178
Alignment explanation
Indices: 554729--555101 Score: 435
Period size: 179 Copynumber: 2.1 Consensus size: 178
554719 TTTATATATG
* * * **
554729 AGTATTGATACATTTGGTGTGCAAATTGTTTGAGAAGCATACTAGAAAAAATTATCGATATGTAT
1 AGTATTGATACATTTTGAGTGCAAATTGTTTGAGAAGCATACTAGAAAAAAGTATCGATACCTAT
* * * * * * * * *
554794 ATTAAACGTATCAATACTTTATGTTTACGACTATTACCATTAAACCGATATATTTTTACACTTTA
66 ATAAAAAGTATCAATAATTGATATATACGACTATGACCATTAAACCGATAAACTTTTACACTTTA
* **
554859 CATTGCAAATTTACCTATTACTTTAAAGTAATCAGTTTCGAAATTCCA
131 CATTGCAAATTTACCTATTACTTTAAAGTAATCAGTTTCAAAATTAAA
* * *
554907 AGTATCGATACATTTTGAGTGCAAATTGTTTGAGATGCATACTAGACTAAAAGTATCGATACCTA
1 AGTATTGATACATTTTGAGTGCAAATTGTTTGAGAAGCATACTAGA-AAAAAGTATCGATACCTA
* * * * * * *
554972 TATAAAAAGTATCGATAATTGGTATATACGCCTATGATCATTATACCGGTAAACTTTTACCCTTT
65 TATAAAAAGTATCAATAATTGATATATACGACTATGACCATTAAACCGATAAACTTTTACACTTT
** *
555037 ACATTGTTAATTTACCTATTTCTTTATAA-TAAT-AGGTTTCAAAATTAAA
130 ACATTGCAAATTTACCTATTACTTTA-AAGTAATCA-GTTTCAAAATTAAA
555086 AGTATTGATACATTTT
1 AGTATTGATACATTTT
555102 ACAAGTGTAT
Statistics
Matches: 161, Mismatches: 31, Indels: 5
0.82 0.16 0.03
Matches are distributed among these distances:
178 43 0.27
179 116 0.72
180 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (178 bp):
AGTATTGATACATTTTGAGTGCAAATTGTTTGAGAAGCATACTAGAAAAAAGTATCGATACCTAT
ATAAAAAGTATCAATAATTGATATATACGACTATGACCATTAAACCGATAAACTTTTACACTTTA
CATTGCAAATTTACCTATTACTTTAAAGTAATCAGTTTCAAAATTAAA
Found at i:555442 original size:202 final size:199
Alignment explanation
Indices: 554908--555461 Score: 616
Period size: 200 Copynumber: 2.8 Consensus size: 199
554898 GAAATTCCAA
* * * *
554908 GTATCGATACATTTTGAGTGCAAATTGTTTGAGATGCATACTAGACTAAAAGTATCGATACCTAT
1 GTATCGATACTTTTTGCGTGCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATACCTAT
* * * *
554973 ATAAAAAGTATCGATAATTG-GTATATACGCCTATGATCATTATACCGGTAAACTTTTACCCTTT
66 ATAAAAAGTATCGATAATTGTGT-T-TACTCCTATTATCATTATACCGATAAACTTTTACCATTT
*
555037 ACATTGTT-AATTTACCTATTTCTTTATAATAATAGGTTTCAAAATTAAAAGTATTGATACATTT
129 ACATT-TTAAATTTACCTATTACTTTATAATAATAGGTTTCAAAATTAAAAGTATTGATACATTT
555101 TACAAGT
193 TACAAGT
* * ** * * * *
555108 GTATCGATACTTTTTGCGTACAAATTCTTTGAGAAACATACTGGAAAAAAAGTTTTGATGCCTAT
1 GTATCGATACTTTTTGCGTGCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATACCTAT
* * * * * *
555173 AAAAAAAGTATCGATACATTATATTTACTCCTATTATCATTAAACCAATAGA-TATTTACCATTT
66 ATAAAAAGTATCGATA-ATTGTGTTTACTCCTATTATCATTATACCGATAAACT-TTTACCATTT
* * **
555237 ACATTTTAAATTTACATATTACTTTA-AAGTAATAGGTTTCGAAATTATGAGTATATCGATAC-T
129 ACATTTTAAATTTACCTATTACTTTATAA-TAATAGGTTTCAAAATTAAAAGTAT-T-GATACAT
* *
555300 TTATATATGT
191 TT-TACAAGT
* * * *
555310 GTATTGATACTTTTTGCGTGCAAATTGTTTGAGATGCATACTGGAATTAAAGTATCGATATCGAT
1 GTATCGATACTTTTTGCGTGCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATACCTAT
* * * * *
555375 ATAACAAAGTATCGATAAGTTGTGTTTA-TTCTATTAACATTATACCGATATACTTTTATCGTTT
66 ATAA-AAAGTATCGATAA-TTGTGTTTACTCCTATTATCATTATACCGATAAACTTTTACCATTT
*
555439 ACATTGTAAATTTACCTATTACT
129 ACATTTTAAATTTACCTATTACT
555462 CCTACATTGC
Statistics
Matches: 290, Mismatches: 53, Indels: 20
0.80 0.15 0.06
Matches are distributed among these distances:
199 5 0.02
200 141 0.49
201 8 0.03
202 116 0.40
203 20 0.07
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (199 bp):
GTATCGATACTTTTTGCGTGCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATACCTAT
ATAAAAAGTATCGATAATTGTGTTTACTCCTATTATCATTATACCGATAAACTTTTACCATTTAC
ATTTTAAATTTACCTATTACTTTATAATAATAGGTTTCAAAATTAAAAGTATTGATACATTTTAC
AAGT
Found at i:557959 original size:318 final size:314
Alignment explanation
Indices: 557336--557970 Score: 1161
Period size: 318 Copynumber: 2.0 Consensus size: 314
557326 CCCACTTCCC
557336 CCTTAAGGCTCTCAAGTGGCTCTTCGATTCTGTATTGTCTTTGCAAACAATCAGAAATGACTTCT
1 CCTTAAGGCTCTCAAGTGGCTCTTCGATTCTGTATTGTCTTTGCAAACAATCAGAAATGACTTCT
557401 TTTTATCTACGTCAACTCAGACATCAAAATGTCAAATTTACTTGCAATATCCTGAATAATCCCCC
66 TTTTATCTACGTCAACTCAGACATCAAAATGTCAAATTTACTTGCAATATCCTGAATAATCCCCC
557466 TACTATTCTCTTCTACCTTCTTCTTCTTCTTTCGTTCTCTTCCTCTTGCTAACCTACAAAATTAA
131 TACTATTCTCTTCTACC-TCTTCTTCTTCTTTCGTTCTCTTCCTCTTGCTAACCTACAAAATTAA
557531 ATTACAATATTAATATATTTTTTTATATTCTTAATATTATATAATTACTTTTATTTCCCTTTCTT
195 ATTACAATATTAATATATTTTTTTATATTCTTAATATTATATAATTACTTTTATTTCCCTTTCTT
557596 GCTTGCTCGGTCTTTTCAACTTCAATTTTGCCATCACTCAAACTACTTCTTTCTT
260 GCTTGCTCGGTCTTTTCAACTTCAATTTTGCCATCACTCAAACTACTTCTTTCTT
557651 CCTTAAGGCTCTCAAGTGGCTCTTCGATTCTGTATTGTCTTTGCAAACAATCAGAAATGACTTCT
1 CCTTAAGGCTCTCAAGTGGCTCTTCGATTCTGTATTGTCTTTGCAAACAATCAGAAATGACTTCT
557716 TTTTATCTACGTCAACTCAGACATCAAAATGTCAAATTTACTTGCAATATCCTGAACATAATCCC
66 TTTTATCTACGTCAACTCAGACATCAAAATGTCAAATTTACTTGCAATATCCTG-A-ATAATCCC
557781 CCTACTACATTCTCTTCTA-C-CTTC-TCTTC-TTCGTTCTCTTCCTCTTTGCTAATAACCTACA
129 CCTACT--ATTCTCTTCTACCTCTTCTTCTTCTTTCGTTCTCTTCCTC-TTGC---TAACCTACA
557842 AAATTAAATTACAATATTAATATATTTTTTTATATTCTTAATATTATATAATTACTTTTATTTCC
188 AAATTAAATTACAATATTAATATATTTTTTTATATTCTTAATATTATATAATTACTTTTATTTCC
557907 CTTTCTTGCTTGCTCGGTCTTTTCAACTTCAATTTTGCCATCACTCAAACTACTTCTTTCTT
253 CTTTCTTGCTTGCTCGGTCTTTTCAACTTCAATTTTGCCATCACTCAAACTACTTCTTTCTT
557969 CC
1 CC
557971 CCGTACACGG
Statistics
Matches: 312, Mismatches: 0, Indels: 13
0.96 0.00 0.04
Matches are distributed among these distances:
314 15 0.05
315 128 0.41
316 5 0.02
317 14 0.04
318 139 0.45
319 11 0.04
ACGTcount: A:0.26, C:0.24, G:0.07, T:0.43
Consensus pattern (314 bp):
CCTTAAGGCTCTCAAGTGGCTCTTCGATTCTGTATTGTCTTTGCAAACAATCAGAAATGACTTCT
TTTTATCTACGTCAACTCAGACATCAAAATGTCAAATTTACTTGCAATATCCTGAATAATCCCCC
TACTATTCTCTTCTACCTCTTCTTCTTCTTTCGTTCTCTTCCTCTTGCTAACCTACAAAATTAAA
TTACAATATTAATATATTTTTTTATATTCTTAATATTATATAATTACTTTTATTTCCCTTTCTTG
CTTGCTCGGTCTTTTCAACTTCAATTTTGCCATCACTCAAACTACTTCTTTCTT
Found at i:559834 original size:20 final size:20
Alignment explanation
Indices: 559805--559847 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
559795 ATTCCACTAC
*
559805 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
559825 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
559845 ATG
1 ATG
559848 GGATTTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:560224 original size:3 final size:3
Alignment explanation
Indices: 560216--560268 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
560206 ATTATTTCCT
560216 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
560264 TTC TT
1 TTC TT
560269 TTTACACTGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:564752 original size:20 final size:20
Alignment explanation
Indices: 564729--564771 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
564719 ATTCCACCAC
**
564729 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATAATCCTAA
*
564749 ATGCATCTATATAATCCTAA
1 ATGCAACTATATAATCCTAA
564769 ATG
1 ATG
564772 GGCTTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATAATCCTAA
Found at i:564883 original size:22 final size:22
Alignment explanation
Indices: 564829--564877 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
564819 CTTTTTATGG
564829 AGTTATCACACCCCCAAACTTA
1 AGTTATCACACCCCCAAACTTA
564851 AGTTATCACACCCCCAAACTTA
1 AGTTATCACACCCCCAAACTTA
564873 AGTTA
1 AGTTA
564878 CAACACATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.37, C:0.33, G:0.06, T:0.24
Consensus pattern (22 bp):
AGTTATCACACCCCCAAACTTA
Found at i:566479 original size:21 final size:21
Alignment explanation
Indices: 566453--566492 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
566443 ATTGCAATTC
566453 TTTTAAATTCCTAAAGTATTG
1 TTTTAAATTCCTAAAGTATTG
566474 TTTTAAATTCCTAAAGTAT
1 TTTTAAATTCCTAAAGTAT
566493 CGATACTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (21 bp):
TTTTAAATTCCTAAAGTATTG
Found at i:576975 original size:21 final size:21
Alignment explanation
Indices: 576949--576991 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
576939 ACGAATGTAA
576949 AAACATGGAAA-ATATAAAAAT
1 AAACAT-GAAATATATAAAAAT
576970 AAACATGAAATATATAAAAAT
1 AAACATGAAATATATAAAAAT
576991 A
1 A
576992 CAAAGTATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (21 bp):
AAACATGAAATATATAAAAAT
Found at i:580709 original size:5 final size:5
Alignment explanation
Indices: 580699--580730 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
580689 TAATAAACAA
580699 AAAAT AAAAT AAAAT AAAAT -AAAT -AAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
580731 CATAGTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:583293 original size:177 final size:177
Alignment explanation
Indices: 582997--583350 Score: 708
Period size: 177 Copynumber: 2.0 Consensus size: 177
582987 GGATGGTATG
582997 CCATATCTGCAATTGTTTGATACTGATATCAACATGGTTATGGTAGTTTATGCATTAGAAATTAA
1 CCATATCTGCAATTGTTTGATACTGATATCAACATGGTTATGGTAGTTTATGCATTAGAAATTAA
583062 AACAATGATCATTGCCATTACAGGGTGAGAAAGCTGGGGGCTCTGATCAGCCAGACTTATTCGAG
66 AACAATGATCATTGCCATTACAGGGTGAGAAAGCTGGGGGCTCTGATCAGCCAGACTTATTCGAG
583127 GAGAACTTTAAAGAACTGACAAAATGGGTAGATATAAAGTCATCTAA
131 GAGAACTTTAAAGAACTGACAAAATGGGTAGATATAAAGTCATCTAA
583174 CCATATCTGCAATTGTTTGATACTGATATCAACATGGTTATGGTAGTTTATGCATTAGAAATTAA
1 CCATATCTGCAATTGTTTGATACTGATATCAACATGGTTATGGTAGTTTATGCATTAGAAATTAA
583239 AACAATGATCATTGCCATTACAGGGTGAGAAAGCTGGGGGCTCTGATCAGCCAGACTTATTCGAG
66 AACAATGATCATTGCCATTACAGGGTGAGAAAGCTGGGGGCTCTGATCAGCCAGACTTATTCGAG
583304 GAGAACTTTAAAGAACTGACAAAATGGGTAGATATAAAGTCATCTAA
131 GAGAACTTTAAAGAACTGACAAAATGGGTAGATATAAAGTCATCTAA
583351 ATATGAAACC
Statistics
Matches: 177, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
177 177 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (177 bp):
CCATATCTGCAATTGTTTGATACTGATATCAACATGGTTATGGTAGTTTATGCATTAGAAATTAA
AACAATGATCATTGCCATTACAGGGTGAGAAAGCTGGGGGCTCTGATCAGCCAGACTTATTCGAG
GAGAACTTTAAAGAACTGACAAAATGGGTAGATATAAAGTCATCTAA
Found at i:592170 original size:29 final size:28
Alignment explanation
Indices: 592111--592171 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
592101 AGGCTCCCAA
* ** **
592111 TTTTTTGTATTTATAATTAGGGCCTTCT
1 TTTTTTATATTTATAATTAGAACCTAAT
592139 TTTTTTATATTTATAATTAGTAACCTAAT
1 TTTTTTATATTTATAATTAG-AACCTAAT
592168 TTTT
1 TTTT
592172 ATAATTTCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.59
Consensus pattern (28 bp):
TTTTTTATATTTATAATTAGAACCTAAT
Found at i:594101 original size:21 final size:21
Alignment explanation
Indices: 594075--594119 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
594065 GTTTACCGCG
* *
594075 ATTGCGGCCATAGTGGGCGCT
1 ATTGCGACCATAGCGGGCGCT
*
594096 ATTGCGACCGTAGCGGGCGCT
1 ATTGCGACCATAGCGGGCGCT
594117 ATT
1 ATT
594120 ACGGGTGTAG
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:0.36, T:0.24
Consensus pattern (21 bp):
ATTGCGACCATAGCGGGCGCT
Found at i:595947 original size:5 final size:5
Alignment explanation
Indices: 595937--595968 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
595927 ATTTTCTATA
595937 ATTTT ATTTT ATTTT ATTTT A-TTT A-TTT ATTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
595969 ATCTTCCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:596714 original size:29 final size:31
Alignment explanation
Indices: 596667--596724 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 31
596657 GTTTAATATA
596667 TAAATTTATTTTAAAAAT-ATATA-AAATTT
1 TAAATTTATTTTAAAAATAATATATAAATTT
***
596696 TAAATTTATTTTTTTAATAATATATAAAT
1 TAAATTTATTTTAAAAATAATATATAAAT
596725 CTTTGTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.62
30 5 0.21
31 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
TAAATTTATTTTAAAAATAATATATAAATTT
Found at i:597305 original size:5 final size:5
Alignment explanation
Indices: 597295--597329 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
597285 GAAGATAAAT
597295 AATTA AATTA AATTA AATTA AA-TA AATTTA AATTA
1 AATTA AATTA AATTA AATTA AATTA AA-TTA AATTA
597330 TAAAAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 20 0.71
6 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATTA
Found at i:601593 original size:22 final size:21
Alignment explanation
Indices: 601555--601601 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
601545 AATTTTATGT
*
601555 TTTTTTTTTTAAATATAT-AA
1 TTTTATTTTTAAATATATAAA
601575 TTTTATTTTTAAATTTATATAAA
1 TTTTATTTTTAAA--TATATAAA
601598 TTTT
1 TTTT
601602 TTAAAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 12 0.52
22 5 0.22
23 6 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTATTTTTAAATATATAAA
Found at i:601603 original size:20 final size:21
Alignment explanation
Indices: 601558--601609 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
601548 TTTATGTTTT
*
601558 TTTTTTTAAA--TATATAATT
1 TTTTTTTAAATTTATATAATA
601577 TTATTTTTAAATTTATATAA-A
1 TT-TTTTTAAATTTATATAATA
*
601598 TTTTTTAAAATT
1 TTTTTTTAAATT
601610 ATCATGTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 2 0.07
20 17 0.61
21 2 0.07
22 7 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTTTTAAATTTATATAATA
Found at i:603363 original size:30 final size:30
Alignment explanation
Indices: 603327--603393 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
603317 AGAAAAATAT
*
603327 AACATGATGCAAGAAAATTTGCTTAGCTAA
1 AACATGATGCAAGAAAACTTGCTTAGCTAA
*
603357 AACATGATGCAAGAAAGCTTGCTTAGCTAA
1 AACATGATGCAAGAAAACTTGCTTAGCTAA
603387 AACATGA
1 AACATGA
603394 GCCACTCTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (30 bp):
AACATGATGCAAGAAAACTTGCTTAGCTAA
Found at i:607519 original size:56 final size:57
Alignment explanation
Indices: 607412--607546 Score: 159
Period size: 56 Copynumber: 2.3 Consensus size: 57
607402 CCACAATTCG
* *
607412 TGCGTATGTGTTTGTTCTTGTTTTTTTTCTTTTCTTTTCTAAGTATACAGTTATTCGTAAT
1 TGCGTA-GTGTCTGTTCTTG-TTTTTTTCTTTCCTTTTCTAAGTATACAGTTATTCGT--T
* * *
607473 TTCGTA-TGTCTGTTCTTG-TTTTTT-TTTCCTTTTTTAAGTATGCAGTTATTCGTT
1 TGCGTAGTGTCTGTTCTTGTTTTTTTCTTTCCTTTTCTAAGTATACAGTTATTCGTT
607527 TGCGTATGTGTCTGTTCTTG
1 TGCGTA-GTGTCTGTTCTTG
607547 ATAATCACAG
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
54 6 0.09
56 38 0.58
57 6 0.09
59 11 0.17
61 5 0.08
ACGTcount: A:0.12, C:0.13, G:0.17, T:0.59
Consensus pattern (57 bp):
TGCGTAGTGTCTGTTCTTGTTTTTTTCTTTCCTTTTCTAAGTATACAGTTATTCGTT
Found at i:612323 original size:31 final size:31
Alignment explanation
Indices: 612285--612379 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
612275 GAACCTTGAC
* *
612285 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* **
612316 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
612347 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
612378 AA
1 AA
612380 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 49 0.94
32 3 0.06
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:613695 original size:64 final size:63
Alignment explanation
Indices: 613574--613714 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 63
613564 GCACTACACC
* * *
613574 ATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGGATGCATCAATGCACTC-CTT
1 ATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGAATGCATCAATGCAC-CGCAT
* * * **
613638 ATGCATCGATGCCTAAATCCTATTCGATGTTTTCTTTTTAAAT-TAATGCATTGATGCACCGCAT
1 ATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGAATGCATCAATGCACCGCAT
*
613702 GTGCATCGATGCA
1 ATGCATCGATGCA
613715 CCTTAAACAA
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
63 1 0.02
64 53 0.83
65 7 0.11
66 3 0.05
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (63 bp):
ATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGAATGCATCAATGCACCGCAT
Found at i:618753 original size:30 final size:30
Alignment explanation
Indices: 618717--618783 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
618707 AGAAAAATAT
*
618717 AACATGATGTAAGAAAACTTGCTTAGCTAA
1 AACATGATGCAAGAAAACTTGCTTAGCTAA
*
618747 AACATGATGCAAGAAAGCTTGCTTAGCTAA
1 AACATGATGCAAGAAAACTTGCTTAGCTAA
618777 AACATGA
1 AACATGA
618784 GCCACTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (30 bp):
AACATGATGCAAGAAAACTTGCTTAGCTAA
Found at i:621900 original size:16 final size:15
Alignment explanation
Indices: 621879--621908 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
621869 TTATATAGAA
621879 AATTATTATATTTTAT
1 AATTATTAT-TTTTAT
621895 AATTATTATTTTTA
1 AATTATTATTTTTA
621909 CTGAATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
AATTATTATTTTTAT
Found at i:622901 original size:16 final size:16
Alignment explanation
Indices: 622876--622917 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
622866 TGAAAAATTA
622876 GCAAAGTTGAAAGTTG
1 GCAAAGTTGAAAGTTG
*
622892 GCAAAATTGAAAGTTG
1 GCAAAGTTGAAAGTTG
622908 GCAAAGTTGA
1 GCAAAGTTGA
622918 CATCTTTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.40, C:0.07, G:0.29, T:0.24
Consensus pattern (16 bp):
GCAAAGTTGAAAGTTG
Found at i:624407 original size:20 final size:20
Alignment explanation
Indices: 624382--624419 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
624372 AATTTAGCTG
624382 CCACCAATTTTGACTTTAAC
1 CCACCAATTTTGACTTTAAC
624402 CCACCAATTTTGACTTTA
1 CCACCAATTTTGACTTTA
624420 CAATCTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.05, T:0.37
Consensus pattern (20 bp):
CCACCAATTTTGACTTTAAC
Found at i:626437 original size:17 final size:17
Alignment explanation
Indices: 626400--626431 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
626390 ATCGTCGACC
626400 AAATTCTACTATTCACA
1 AAATTCTACTATTCACA
626417 AAATT-TACTATTCAC
1 AAATTCTACTATTCAC
626432 GTAAATAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATTCTACTATTCACA
Found at i:626919 original size:20 final size:20
Alignment explanation
Indices: 626894--626931 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
626884 AATTTAGCTG
626894 CCACCAATTTTGACTTTAAC
1 CCACCAATTTTGACTTTAAC
626914 CCACCAATTTTGACTTTA
1 CCACCAATTTTGACTTTA
626932 CACGATGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.05, T:0.37
Consensus pattern (20 bp):
CCACCAATTTTGACTTTAAC
Found at i:630601 original size:16 final size:16
Alignment explanation
Indices: 630576--630649 Score: 121
Period size: 16 Copynumber: 4.6 Consensus size: 16
630566 TGAAAAATTA
630576 GCAAAGTTGAAAGTTG
1 GCAAAGTTGAAAGTTG
*
630592 GCAAAATTGAAAGTTG
1 GCAAAGTTGAAAGTTG
630608 GCAAAGTTGAAAGTTG
1 GCAAAGTTGAAAGTTG
* *
630624 GCAAAATTGAATGTTG
1 GCAAAGTTGAAAGTTG
630640 GCAAAGTTGA
1 GCAAAGTTGA
630650 CATCTTTGGT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 53 1.00
ACGTcount: A:0.39, C:0.07, G:0.28, T:0.26
Consensus pattern (16 bp):
GCAAAGTTGAAAGTTG
Found at i:630613 original size:32 final size:32
Alignment explanation
Indices: 630576--630649 Score: 139
Period size: 32 Copynumber: 2.3 Consensus size: 32
630566 TGAAAAATTA
630576 GCAAAGTTGAAAGTTGGCAAAATTGAAAGTTG
1 GCAAAGTTGAAAGTTGGCAAAATTGAAAGTTG
*
630608 GCAAAGTTGAAAGTTGGCAAAATTGAATGTTG
1 GCAAAGTTGAAAGTTGGCAAAATTGAAAGTTG
630640 GCAAAGTTGA
1 GCAAAGTTGA
630650 CATCTTTGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.39, C:0.07, G:0.28, T:0.26
Consensus pattern (32 bp):
GCAAAGTTGAAAGTTGGCAAAATTGAAAGTTG
Found at i:634931 original size:14 final size:14
Alignment explanation
Indices: 634905--634942 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
634895 TCTTAAAATT
634905 AATTATATTTTTAAA
1 AATTAT-TTTTTAAA
634920 AATTATTTTTTAAA
1 AATTATTTTTTAAA
*
634934 AAATATTTT
1 AATTATTTT
634943 ATGATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTATTTTTTAAA
Found at i:635092 original size:17 final size:18
Alignment explanation
Indices: 635072--635113 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
635062 TATTTTTAAA
635072 TATTA-AAATAAT-TTATT
1 TATTATAAA-AATATTATT
635089 TATTATAAAAATATTATT
1 TATTATAAAAATATTATT
635107 T-TTATAA
1 TATTATAA
635114 TTTTATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TATTATAAAAATATTATT
Found at i:635118 original size:28 final size:29
Alignment explanation
Indices: 635087--635167 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 29
635077 AAATAATTTA
* *
635087 TTTATTATAAAAATATTATTTTTATA-AT
1 TTTATTATAAAAATATTATATTGATATAT
635115 TTTATTA-ATAAAATATTAATATTGATATAT
1 TTTATTATA-AAAATATT-ATATTGATATAT
635145 TTTATTGAAATAAAAATATTATA
1 TTTATT---ATAAAAATATTATA
635168 AATTATATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
27 1 0.02
28 15 0.34
29 7 0.16
30 8 0.18
32 3 0.07
33 9 0.20
34 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (29 bp):
TTTATTATAAAAATATTATATTGATATAT
Found at i:635235 original size:23 final size:23
Alignment explanation
Indices: 635206--635250 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
635196 AGTGTTATAT
635206 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
635229 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
635251 AAATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:635256 original size:23 final size:23
Alignment explanation
Indices: 635207--635275 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
635197 GTGTTATATT
* * **
635207 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTTATTAAA
635230 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTTATTAAA
*
635253 ATATTATTAGAT-TATTATATTAA
1 ATATT-TTAAATATATT-TATTAA
635276 TATTAAATAG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
23 28 0.72
24 11 0.28
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTTATTAAA
Found at i:635415 original size:18 final size:20
Alignment explanation
Indices: 635392--635435 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
635382 AATAAAAAAA
635392 ATAATAT-CTT-A-TATTATT
1 ATAATATACTTGATTATT-TT
635410 ATAATATACTTGATTATTTT
1 ATAATATACTTGATTATTTT
635430 ATAATA
1 ATAATA
635436 ATATTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.30
19 3 0.13
20 9 0.39
21 4 0.17
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (20 bp):
ATAATATACTTGATTATTTT
Found at i:635480 original size:22 final size:22
Alignment explanation
Indices: 635424--635476 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
635414 TATACTTGAT
* *
635424 TATTTTATAATAATATTAAAAA
1 TATTATATAATATTATTAAAAA
* *
635446 TATTATATTATATTATTAGAAA
1 TATTATATAATATTATTAAAAA
635468 TATTA-ATAA
1 TATTATATAA
635477 ATATATTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TATTATATAATATTATTAAAAA
Found at i:635897 original size:21 final size:21
Alignment explanation
Indices: 635871--635912 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
635861 TACAACATTC
635871 AAAGGGACAATTTGAAATTTT
1 AAAGGGACAATTTGAAATTTT
*
635892 AAAGGGACAATTTGAAGTTTT
1 AAAGGGACAATTTGAAATTTT
635913 GACCCATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.33
Consensus pattern (21 bp):
AAAGGGACAATTTGAAATTTT
Found at i:637648 original size:195 final size:194
Alignment explanation
Indices: 637313--637704 Score: 667
Period size: 195 Copynumber: 2.0 Consensus size: 194
637303 TTTTTATCTA
* *
637313 TTTCATCTCATTCTTCACTTAATTTCTTCATTCCTTCTCATTTTTCTTCTCTCATTTTCCTCTAC
1 TTTCATCTCATTCTTCACTTAATTTCTTCATACCTTCTCATTTTTCTCCTCTCATTTTCCTCTAC
637378 AAGTTCCATAGCACAAAGGTAAGTTCTTGAGCCTCTTTCATACTTCAATTCCATTCATTTTCCCT
66 AAGTTCCATAGCACAAAGGTAAGTTCTTGAGCCTCTTTCATACTTCAATTCCATTCATTTTCCCT
* * * * *
637443 CCAACAACATCATTTTAATGAATTATAGTCTTGGGTCCTTTCTAGCTAAAGAAAAAGTGGGGGT
131 CCAACAACATCATTTTAATGAATTAAAGTCTTGGGTCCTTCCCAACTAAAGAAAAAGTGGAGGT
*
637507 TTTCATCTCATTCTTCTCTTAATTTCTTCACTACCTTCTCATTTTTCTCCTCTCATTTTCCTCTA
1 TTTCATCTCATTCTTCACTTAATTTCTTCA-TACCTTCTCATTTTTCTCCTCTCATTTTCCTCTA
* * *
637572 CAAGTTCCATAGCACAAAGGTAAGTTCTTGAGTCTCTTTCATACTTCAATTTCATTCCTTTTCCC
65 CAAGTTCCATAGCACAAAGGTAAGTTCTTGAGCCTCTTTCATACTTCAATTCCATTCATTTTCCC
*
637637 TCCAGCAACATCATTTTAATGAATTAAAGTCTTGGGTCCTTCCCAACTAAAGAAAAAGTGGAGGT
130 TCCAACAACATCATTTTAATGAATTAAAGTCTTGGGTCCTTCCCAACTAAAGAAAAAGTGGAGGT
637702 TTT
1 TTT
637705 GATCGCTTGT
Statistics
Matches: 185, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
194 29 0.16
195 156 0.84
ACGTcount: A:0.24, C:0.25, G:0.10, T:0.41
Consensus pattern (194 bp):
TTTCATCTCATTCTTCACTTAATTTCTTCATACCTTCTCATTTTTCTCCTCTCATTTTCCTCTAC
AAGTTCCATAGCACAAAGGTAAGTTCTTGAGCCTCTTTCATACTTCAATTCCATTCATTTTCCCT
CCAACAACATCATTTTAATGAATTAAAGTCTTGGGTCCTTCCCAACTAAAGAAAAAGTGGAGGT
Found at i:652630 original size:21 final size:21
Alignment explanation
Indices: 652568--652630 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
652558 AATGCTAACT
*
652568 CCAATTTCGCAACAT-AGTTT-
1 CCAAATTCGCAAC-TCAGTTTC
* * *
652588 CCAAATTAGCAACGCGAATTTC
1 CCAAATTCGCAACTC-AGTTTC
652610 CCAAATTCGCAACTCAGTTTC
1 CCAAATTCGCAACTCAGTTTC
652631 TGCAATCATA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
20 11 0.33
21 9 0.27
22 13 0.39
ACGTcount: A:0.32, C:0.29, G:0.11, T:0.29
Consensus pattern (21 bp):
CCAAATTCGCAACTCAGTTTC
Found at i:652762 original size:20 final size:20
Alignment explanation
Indices: 652739--652821 Score: 57
Period size: 20 Copynumber: 4.2 Consensus size: 20
652729 TTCTAAATCC
**
652739 CAACACGAATTTTGTTTTCG
1 CAACACGAATTTTAATTTCG
* *
652759 CAACTC-AATTTTTGAA-TTAG
1 CAACACGAA-TTTT-AATTTCG
*
652779 CAACACAAATTTTAATTTCG
1 CAACACGAATTTTAATTTCG
* *
652799 CAACA-G-CTTTTATTTTCG
1 CAACACGAATTTTAATTTCG
652817 CAACA
1 CAACA
652822 AAAATGTTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
18 15 0.30
19 4 0.08
20 29 0.58
21 2 0.04
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
CAACACGAATTTTAATTTCG
Found at i:653181 original size:17 final size:16
Alignment explanation
Indices: 653143--653177 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
653133 GTTGATCATA
653143 TTTGGATAGATTTGTG
1 TTTGGATAGATTTGTG
653159 TTTGGATAGATTTGTG
1 TTTGGATAGATTTGTG
653175 TTT
1 TTT
653178 TGGAGGGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.54
Consensus pattern (16 bp):
TTTGGATAGATTTGTG
Found at i:653629 original size:12 final size:12
Alignment explanation
Indices: 653608--653641 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
653598 ACCACATTTC
*
653608 CAATACCAAACA
1 CAATAACAAACA
653620 CAATAACAAACA
1 CAATAACAAACA
*
653632 CAATATCAAA
1 CAATAACAAA
653642 ACCCATAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.62, C:0.26, G:0.00, T:0.12
Consensus pattern (12 bp):
CAATAACAAACA
Found at i:653780 original size:24 final size:24
Alignment explanation
Indices: 653762--653808 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
653752 AGTCAGTATT
653762 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATCTTGGTCAATACC
* *
653786 CGGACTTTGATCTTGGTCAATAC
1 CGAAATTTGATCTTGGTCAATAC
653809 TCGGATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATCTTGGTCAATACC
Found at i:653813 original size:24 final size:24
Alignment explanation
Indices: 653767--653820 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
653757 GTATTCGAAA
653767 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
653791 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
653815 TTTGAT
1 TTTGAT
653821 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:654007 original size:3 final size:3
Alignment explanation
Indices: 653999--654023 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
653989 AACCCTGAAA
653999 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
654024 CCCCGAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:656515 original size:29 final size:29
Alignment explanation
Indices: 656478--656540 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
656468 TGAAAGTGCT
* ** *
656478 ATTCACGTTGCGATTGTTGCGAAAGTCAA
1 ATTCGCGTTGCGATTGTTGAAAAAGACAA
656507 ATTCGCGTTGCGATTGTTGAAAAAGACAA
1 ATTCGCGTTGCGATTGTTGAAAAAGACAA
656536 ATTCG
1 ATTCG
656541 TAACGCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (29 bp):
ATTCGCGTTGCGATTGTTGAAAAAGACAA
Found at i:656580 original size:20 final size:20
Alignment explanation
Indices: 656555--656623 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
656545 GCAAAAATTA
656555 CAACGCGAATTTGACTATCG
1 CAACGCGAATTTGACTATCG
*
656575 CAACGCGAATTTGACTTTCG
1 CAACGCGAATTTGACTATCG
*** * *
656595 CGTTGTGAATTTTACTATCG
1 CAACGCGAATTTGACTATCG
*
656615 CAATGCGAA
1 CAACGCGAA
656624 AATCTCAATG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (20 bp):
CAACGCGAATTTGACTATCG
Found at i:658151 original size:21 final size:21
Alignment explanation
Indices: 658125--658260 Score: 116
Period size: 21 Copynumber: 6.5 Consensus size: 21
658115 GTGAATCGGG
658125 CTCTTGAACGGTGGGAGGGAT-
1 CTCTTGAACGGTGGGAGGG-TC
*
658146 CTCTTGAATGGTGGGAGGGTC
1 CTCTTGAACGGTGGGAGGGTC
* * *
658167 CTATTGAACGATGAGAGGGTC
1 CTCTTGAACGGTGGGAGGGTC
*
658188 CTTTTGAACGGTGGGAAGGG-C
1 CTCTTGAACGGTGGG-AGGGTC
* * *
658209 CTCTTGAACGATGAGATGAG-C
1 CTCTTGAACGGTGGGA-GGGTC
** * *
658230 CTCTTGAACAATAGGAGGGGC
1 CTCTTGAACGGTGGGAGGGTC
658251 CTCTTGAACG
1 CTCTTGAACG
658261 ATGACAGATG
Statistics
Matches: 94, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
20 4 0.04
21 86 0.91
22 4 0.04
ACGTcount: A:0.23, C:0.17, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGTC
Found at i:658237 original size:42 final size:42
Alignment explanation
Indices: 658146--658264 Score: 134
Period size: 42 Copynumber: 2.8 Consensus size: 42
658136 TGGGAGGGAT
* * *
658146 CTCTTGAATGGTGGG-AGGGTCCTATTGAACGATGAGAGGGTC
1 CTCTTGAACGGTGGGAAGGG-CCTCTTGAACGATGAGAGAGTC
*
658188 CTTTTGAACGGTGGGAAGGGCCTCTTGAACGATGAGATGAG-C
1 CTCTTGAACGGTGGGAAGGGCCTCTTGAACGATGAGA-GAGTC
** * *
658230 CTCTTGAACAATAGGAGGGGCCTCTTGAACGATGA
1 CTCTTGAACGGTGGGAAGGGCCTCTTGAACGATGA
658265 CAGATGAATC
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 60 0.91
43 6 0.09
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.24
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAAGGGCCTCTTGAACGATGAGAGAGTC
Found at i:658647 original size:42 final size:43
Alignment explanation
Indices: 658555--658650 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 43
658545 GTAGAGCGGC
** *
658555 TACCTCATCACGTAAAGTAGATACCTCACCACGTAAAGCACCA
1 TACCTCATCACGTAAAACAGATACCTCACCAAGTAAAGCACCA
** ** *
658598 T-TGTCATCACGTAAAACATCTACCTCACCAAGTAAAG-ACCG
1 TACCTCATCACGTAAAACAGATACCTCACCAAGTAAAGCACCA
658639 TACCTCATCACG
1 TACCTCATCACG
658651 CCATGCACCA
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
41 4 0.10
42 37 0.88
43 1 0.02
ACGTcount: A:0.35, C:0.32, G:0.11, T:0.21
Consensus pattern (43 bp):
TACCTCATCACGTAAAACAGATACCTCACCAAGTAAAGCACCA
Found at i:658686 original size:63 final size:63
Alignment explanation
Indices: 658592--658713 Score: 140
Period size: 63 Copynumber: 1.9 Consensus size: 63
658582 ACCACGTAAA
* *
658592 GCACCATTGTCATCACGTAAAACATCTACCTCACCAAGTAAAG-ACCGTACCTCATCACGCCAT
1 GCACCATTATCATCACGTAAAACATCTACCTCACCAAGCAAAGCACCG-ACCTCATCACGCCAT
* ** * * *
658655 GCACCATTATCGTCACGTAAAGTA-CTGACCTCATCACGCAAAGCACTGACCTCATCACG
1 GCACCATTATCATCACGTAAAACATCT-ACCTCACCAAGCAAAGCACCGACCTCATCACG
658714 TAACTCCCCT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
62 2 0.04
63 44 0.90
64 3 0.06
ACGTcount: A:0.32, C:0.34, G:0.13, T:0.20
Consensus pattern (63 bp):
GCACCATTATCATCACGTAAAACATCTACCTCACCAAGCAAAGCACCGACCTCATCACGCCAT
Found at i:658691 original size:21 final size:21
Alignment explanation
Indices: 658667--658716 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
658657 ACCATTATCG
*
658667 TCACGTAAAGTACTGACCTCA
1 TCACGTAAAGCACTGACCTCA
*
658688 TCACGCAAAGCACTGACCTCA
1 TCACGTAAAGCACTGACCTCA
658709 TCACGTAA
1 TCACGTAA
658717 CTCCCCTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.32, G:0.14, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCACTGACCTCA
Found at i:660265 original size:19 final size:20
Alignment explanation
Indices: 660227--660267 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
660217 ACTTAAATTT
660227 GCAACGCGAAAATGAAAATC
1 GCAACGCGAAAATGAAAATC
*
660247 GCAACGCGAAACT-AAAATC
1 GCAACGCGAAAATGAAAATC
660266 GC
1 GC
660268 GTTGCGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (20 bp):
GCAACGCGAAAATGAAAATC
Found at i:660860 original size:19 final size:20
Alignment explanation
Indices: 660820--660867 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
660810 TAAACGTGCT
*
660820 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTATGTG
660840 TTGCGAATTTGAC-TATGTG
1 TTGCGAATTTGACTTATGTG
*
660859 TTGTGAATT
1 TTGCGAATT
660868 ACAAATTCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.19, C:0.10, G:0.25, T:0.46
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGTG
Found at i:660881 original size:21 final size:21
Alignment explanation
Indices: 660855--660916 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
660845 AATTTGACTA
*
660855 TGTGTTGTGAATTACAAATTC
1 TGTGTTGCGAATTACAAATTC
660876 TGTGTTGCGAATTACAAATTC
1 TGTGTTGCGAATTACAAATTC
* * *
660897 -GCGTTGCGATTTACATATTC
1 TGTGTTGCGAATTACAAATTC
660917 ACGTTGCGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (21 bp):
TGTGTTGCGAATTACAAATTC
Found at i:660904 original size:20 final size:20
Alignment explanation
Indices: 660858--660928 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
660848 TTGACTATGT
* *
660858 GTTGTGAATTACAAATTCTGT
1 GTTGCGAATTACAAATTC-GC
660879 GTTGCGAATTACAAATTCGC
1 GTTGCGAATTACAAATTCGC
* * *
660899 GTTGCGATTTACATATTCAC
1 GTTGCGAATTACAAATTCGC
660919 GTTGCGAATT
1 GTTGCGAATT
660929 TGAAAAATTG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
20 27 0.61
21 17 0.39
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (20 bp):
GTTGCGAATTACAAATTCGC
Found at i:666147 original size:18 final size:18
Alignment explanation
Indices: 666126--666293 Score: 264
Period size: 18 Copynumber: 9.3 Consensus size: 18
666116 TGTCTCGTAT
666126 GACCACTATGTCCCGAAG
1 GACCACTATGTCCCGAAG
* *
666144 GACCACTGTGTCCCTAAG
1 GACCACTATGTCCCGAAG
*
666162 GACCATTATGTCCCGAAG
1 GACCACTATGTCCCGAAG
666180 GACCACTATGTCCCGAAG
1 GACCACTATGTCCCGAAG
*
666198 GACCATTATGTCCCGAAG
1 GACCACTATGTCCCGAAG
666216 GACCACTATGTCCCGAAG
1 GACCACTATGTCCCGAAG
*
666234 GACCATTATGTCCCGAAG
1 GACCACTATGTCCCGAAG
* *
666252 GACCATTATGTCCCGAAA
1 GACCACTATGTCCCGAAG
*
666270 GACCACTATGTCCCGAAT
1 GACCACTATGTCCCGAAG
666288 GACCAC
1 GACCAC
666294 GTAGACCCTC
Statistics
Matches: 138, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 138 1.00
ACGTcount: A:0.28, C:0.32, G:0.21, T:0.20
Consensus pattern (18 bp):
GACCACTATGTCCCGAAG
Found at i:673149 original size:42 final size:42
Alignment explanation
Indices: 673090--673181 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
673080 CCCGAAATCT
* *
673090 CGTGTTTGTTTCACGTAATTCGTTTTCCGTAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCC
*
673132 CGTGTTTGTTTCACGTAATTTGTTTTCCGGAAAATATTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCC
*
673174 AGTGTTTG
1 CGTGTTTG
673182 GTTGGAGGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.17, C:0.16, G:0.18, T:0.48
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCC
Found at i:673562 original size:28 final size:29
Alignment explanation
Indices: 673470--673599 Score: 117
Period size: 30 Copynumber: 4.4 Consensus size: 29
673460 AATAATCAAT
* *
673470 TATATTATAATAATATA-AGATATTATATTTT
1 TATATT-TAATAATATATA-ATAAT-TATTTA
673501 TAT-TTTAATAATATATAATAAATTATTTA
1 TATATTTAATAATATATAAT-AATTATTTA
673530 TATATTTAATAATGA-ATAAT-ATTATTTA
1 TATATTTAATAAT-ATATAATAATTATTTA
* * *
673558 TATATTTAATATTAATATAATAATCTAATAA
1 TATATTTAATAAT-ATATAATAAT-TATTTA
673589 TAT-TTTAATAA
1 TATATTTAATAA
673600 AGATATTTAA
Statistics
Matches: 85, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
28 21 0.25
29 25 0.29
30 28 0.33
31 11 0.13
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (29 bp):
TATATTTAATAATATATAATAATTATTTA
Found at i:673597 original size:19 final size:18
Alignment explanation
Indices: 673505--673599 Score: 57
Period size: 19 Copynumber: 5.0 Consensus size: 18
673495 TATTTTTATT
*
673505 TTAATAATA-TATAATAAA
1 TTAATAATATTTTAAT-AA
* *
673523 TTATTTATATATTTAATAA
1 TTAATAATAT-TTTAATAA
* *
673542 TGAATAATATTATTTATATAT
1 TTAATAATA-T-TTTA-ATAA
* * *
673563 TTAATATTAATATAATAA
1 TTAATAATATTTTAATAA
673581 TCTAATAATATTTTAATAA
1 T-TAATAATATTTTAATAA
673600 AGATATTTAA
Statistics
Matches: 57, Mismatches: 15, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
18 11 0.19
19 25 0.44
20 11 0.19
21 10 0.18
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
TTAATAATATTTTAATAA
Found at i:673620 original size:23 final size:23
Alignment explanation
Indices: 673594--673638 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
673584 AATAATATTT
673594 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
673617 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
673639 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:674847 original size:296 final size:296
Alignment explanation
Indices: 674306--675193 Score: 1697
Period size: 296 Copynumber: 3.0 Consensus size: 296
674296 CTCTCTTTTT
* *
674306 CCACATTATCAAAATAATC-AAAAAACTAATTTGAATTAACCTAGATTTTTGGTTCAGATGTCGA
1 CCACATCATCAAAATAATCAAAAAAACTAATTTGAATTAACCTAGATTTTTGGTTCGGATGTCGA
674370 ATTAGTCAAATTTAGTGTATGGAATGTGACATTTAATTTGATTATGATAGCTCAAATTAAGATTT
66 ATTAGTCAAATTTAGTGTATGGAATGTGACATTTAATTTGATTATGATAGCTCAAATTAAGATTT
674435 TATGCGTTAAGAAATCAAAATCTTAAAATGTGCTACTTGAAATTTAAAATCTAATAATATAAATA
131 TATGCGTTAAGAAATCAAAATCTTAAAATGTG-TACTTGAAATTTAAAATCTAATAATATAAATA
* **
674500 TTACAATTTCGAATAACCAACTTTTGATCATCTTAAATAGTATCTCTAACATCCATAACAGCAAT
195 TTACAATTTCGAATAACCAACTTTTGATCATCGTAAATAGTATCTCTAACATCCATAACTCCAAT
674565 ACTATATTTCATGTTTAAAGTATGATATACCAGCTTC
260 ACTATATTTCATGTTTAAAGTATGATATACCAGCTTC
674602 CCACATCATCAAAATAATCAAAAAAACTAATTTGAATTAACCTAGATTTTTGGTTCGGATGTCGA
1 CCACATCATCAAAATAATCAAAAAAACTAATTTGAATTAACCTAGATTTTTGGTTCGGATGTCGA
674667 ATTAGTCAAATTTAGTGTATGGAATGTGACATTTAATTTGATTATGATAGCTCAAATTAAGATTT
66 ATTAGTCAAATTTAGTGTATGGAATGTGACATTTAATTTGATTATGATAGCTCAAATTAAGATTT
674732 TATGCGTTAAGAAATCAAAATCTTAAAATGTGTACTTGAAATTTAAAATCTAATAATATAAATAT
131 TATGCGTTAAGAAATCAAAATCTTAAAATGTGTACTTGAAATTTAAAATCTAATAATATAAATAT
674797 TACAATTTCGAATAACCAACTTTTGATCATCGTAAATAGTATCTCTAACATCCATAACTCCAATA
196 TACAATTTCGAATAACCAACTTTTGATCATCGTAAATAGTATCTCTAACATCCATAACTCCAATA
674862 CTATATTTCATGTTTAAAGTATGATATACCAGCTTC
261 CTATATTTCATGTTTAAAGTATGATATACCAGCTTC
674898 CCACATCATCAAAATAATCAAAAAAACTAATTTGAATTAACCTAGATTTTTGGTTCGGATGTCGA
1 CCACATCATCAAAATAATCAAAAAAACTAATTTGAATTAACCTAGATTTTTGGTTCGGATGTCGA
*
674963 ATTTGTCAAATTTAGTGTATGGAATGTGACATTTAATTTGATTATGATAGCTCAAATTAAGATTT
66 ATTAGTCAAATTTAGTGTATGGAATGTGACATTTAATTTGATTATGATAGCTCAAATTAAGATTT
675028 TATGCGTTAAGAAATCAAAATCTTAAAATGTGTACTTGAAATTTAAAATCTAATAATATAAATAT
131 TATGCGTTAAGAAATCAAAATCTTAAAATGTGTACTTGAAATTTAAAATCTAATAATATAAATAT
675093 TACAATTTCGAATAACCAACTTTTGATCATCGTAAATAGTATCTCTAACATCCATAACTCCAATA
196 TACAATTTCGAATAACCAACTTTTGATCATCGTAAATAGTATCTCTAACATCCATAACTCCAATA
*
675158 CTATATTTCATGTTTAAAGTATGATATACCATCTTC
261 CTATATTTCATGTTTAAAGTATGATATACCAGCTTC
675194 ATTTGTTTAT
Statistics
Matches: 584, Mismatches: 7, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
296 443 0.76
297 141 0.24
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (296 bp):
CCACATCATCAAAATAATCAAAAAAACTAATTTGAATTAACCTAGATTTTTGGTTCGGATGTCGA
ATTAGTCAAATTTAGTGTATGGAATGTGACATTTAATTTGATTATGATAGCTCAAATTAAGATTT
TATGCGTTAAGAAATCAAAATCTTAAAATGTGTACTTGAAATTTAAAATCTAATAATATAAATAT
TACAATTTCGAATAACCAACTTTTGATCATCGTAAATAGTATCTCTAACATCCATAACTCCAATA
CTATATTTCATGTTTAAAGTATGATATACCAGCTTC
Found at i:675547 original size:3 final size:3
Alignment explanation
Indices: 675539--675606 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
675529 GACATGATAC
675539 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
675587 CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CT
675607 CTGTTTAACA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:676651 original size:17 final size:17
Alignment explanation
Indices: 676629--676666 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
676619 AAATCCCCAA
676629 AAACCAATTCCCAATAT
1 AAACCAATTCCCAATAT
676646 AAACCAATTCCCAATAT
1 AAACCAATTCCCAATAT
676663 AAAC
1 AAAC
676667 AAGTGAATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (17 bp):
AAACCAATTCCCAATAT
Found at i:678447 original size:17 final size:18
Alignment explanation
Indices: 678425--678458 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
678415 TGATATATTG
678425 ATGTTGT-GACATTGTTA
1 ATGTTGTAGACATTGTTA
*
678442 ATGTTGTAGTCATTGTT
1 ATGTTGTAGACATTGTT
678459 GTGCATTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.06, G:0.24, T:0.50
Consensus pattern (18 bp):
ATGTTGTAGACATTGTTA
Found at i:688499 original size:109 final size:105
Alignment explanation
Indices: 688344--688540 Score: 349
Period size: 107 Copynumber: 1.8 Consensus size: 105
688334 GTCAATGAAC
688344 AAGTCCCCTATTTCGTTTTAAACATGTTTTTCCCCTTTCCCTTGCAATTTTGTTGAGTTTTGTGT
1 AAGTCCCCTATTTCGTTTTAAACATGTTTTTCCCCTTTCCCTTGCAATTTTGTTGAG-TTT-TGT
688409 CAGACGTGTTTTTTTCTTTTCCCTTGTAATATTATTTTAAAT
64 CAGACGTGTTTTTTTCTTTTCCCTTGTAATATTATTTTAAAT
688451 AAGTCCCCTAGTTTCGTTTTAAACATGTTTTTTCCCCTTTCCCTTGCAATTTTGTTGAGTTTTGT
1 AAGTCCCCTA-TTTCGTTTTAAACATG-TTTTTCCCCTTTCCCTTGCAATTTTGTTGAGTTTTGT
*
688516 CAGATGTGTTTTTTTCTTTTCCCTT
64 CAGACGTGTTTTTTTCTTTTCCCTT
688541 TCCTCTTTCA
Statistics
Matches: 87, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
107 37 0.43
108 19 0.22
109 31 0.36
ACGTcount: A:0.16, C:0.20, G:0.13, T:0.52
Consensus pattern (105 bp):
AAGTCCCCTATTTCGTTTTAAACATGTTTTTCCCCTTTCCCTTGCAATTTTGTTGAGTTTTGTCA
GACGTGTTTTTTTCTTTTCCCTTGTAATATTATTTTAAAT
Found at i:701051 original size:2 final size:2
Alignment explanation
Indices: 701044--701076 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
701034 TATGCTCTGA
701044 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
701077 ACTTACAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:704816 original size:21 final size:21
Alignment explanation
Indices: 704777--704816 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
704767 TAAAGAGAAA
** *
704777 CAAACAGCAAGTAGTAAATAG
1 CAAACAGCAAACAGCAAATAG
704798 CAAACAGCAAACAGCAAAT
1 CAAACAGCAAACAGCAAAT
704817 TGAAAAGGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.20, G:0.15, T:0.10
Consensus pattern (21 bp):
CAAACAGCAAACAGCAAATAG
Found at i:720910 original size:83 final size:83
Alignment explanation
Indices: 720807--720964 Score: 289
Period size: 83 Copynumber: 1.9 Consensus size: 83
720797 TCGAGAGAGT
* *
720807 TTTACTCCATCTAAATATCTTTTAATATCTAAATTTAAACAAATAATAATATCTTTTAAATTTAA
1 TTTACTCCAACCAAATATCTTTTAATATCTAAATTTAAACAAATAATAATATCTTTTAAATTTAA
720872 AATATTAAACCTGAAAGA
66 AATATTAAACCTGAAAGA
*
720890 TTTACTCCAACCATATATCTTTTAATATCTAAATTTAAACAAATAATAATATCTTTTAAATTTAA
1 TTTACTCCAACCAAATATCTTTTAATATCTAAATTTAAACAAATAATAATATCTTTTAAATTTAA
720955 AATATTAAAC
66 AATATTAAAC
720965 ATATATACAC
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 72 1.00
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.41
Consensus pattern (83 bp):
TTTACTCCAACCAAATATCTTTTAATATCTAAATTTAAACAAATAATAATATCTTTTAAATTTAA
AATATTAAACCTGAAAGA
Found at i:727007 original size:3 final size:3
Alignment explanation
Indices: 726999--727032 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
726989 TTAGTGAGGC
*
726999 ATA ATA ATA ATA ATA ATA ATA TATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
727033 CCATAATGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:727265 original size:23 final size:23
Alignment explanation
Indices: 727232--727289 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
727222 AGCTCGTATA
* *
727232 AATGCAACGAAGCGCCATGTA-G
1 AATGCACCGAAGCGCCACGTAGG
* *
727254 AATTGCACCGAAGTGCCGCGTAGG
1 AA-TGCACCGAAGCGCCACGTAGG
727278 AATGCACCGAAG
1 AATGCACCGAAG
727290 TGCTATATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 2 0.07
23 25 0.83
24 3 0.10
ACGTcount: A:0.33, C:0.24, G:0.29, T:0.14
Consensus pattern (23 bp):
AATGCACCGAAGCGCCACGTAGG
Found at i:727328 original size:22 final size:20
Alignment explanation
Indices: 727294--727358 Score: 51
Period size: 22 Copynumber: 3.0 Consensus size: 20
727284 CCGAAGTGCT
727294 ATATAAAATTTCCATAAGGACC
1 ATATAAAA-TTCC-TAAGGACC
* *
727316 ATATAGAAATTCCTTAAGAATC
1 ATATA-AAATTCC-TAAGGACC
*
727338 ATATACATATTCC-AAGGACC
1 ATATA-AAATTCCTAAGGACC
727358 A
1 A
727359 ATTATGCGTC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
20 6 0.17
22 26 0.74
23 3 0.09
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.28
Consensus pattern (20 bp):
ATATAAAATTCCTAAGGACC
Found at i:737687 original size:23 final size:23
Alignment explanation
Indices: 737623--737687 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 23
737613 CACCACAGCT
* *
737623 CGTATAAATGCACCGAAGTGTCA
1 CGTAGAAATGCACCGAAGTGACA
* * * * * *
737646 TGTAGAATTGAAACAAAGTGACG
1 CGTAGAAATGCACCGAAGTGACA
737669 CGTAGAAATGCACCGAAGT
1 CGTAGAAATGCACCGAAGT
737688 TCCATATAAG
Statistics
Matches: 29, Mismatches: 13, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGACA
Found at i:738505 original size:21 final size:21
Alignment explanation
Indices: 738475--738532 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
738465 AAATTGGTCT
*
738475 TAGGGTATCGATACCCATTCA
1 TAGGGTATCGATACCCAATCA
* *
738496 TAGGGCATCGGTACCCAATCA
1 TAGGGTATCGATACCCAATCA
738517 TAGGGTATCGATACCC
1 TAGGGTATCGATACCC
738533 CTTGCCCACA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (21 bp):
TAGGGTATCGATACCCAATCA
Found at i:741608 original size:3 final size:3
Alignment explanation
Indices: 741602--741684 Score: 148
Period size: 3 Copynumber: 27.7 Consensus size: 3
741592 TTTTTACCCA
*
741602 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
741650 TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
741685 AATATATATT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:742062 original size:169 final size:167
Alignment explanation
Indices: 741781--742116 Score: 604
Period size: 169 Copynumber: 2.0 Consensus size: 167
741771 AGACCCAAAA
741781 GGAAACCTAAACCAATTTAGGGTTTCAGTTAGGGTTTCCTAACCTAATCCATGCCAGCCGCTCTA
1 GGAAACCTAAACCAATTTAGGGTTTCAGTTAGGGTTTCCTAACCTAATCCATGCCAGCCGCTCTA
741846 GCCAGCCGCCTCAGACTAACCGTTGGATCTGGCAAGATCCAACGGTCCAGATGGCTCCAGATGGA
66 GCCAGCCGCCTCAGACTAACCGTTGGATCTGGCAAGATCCAACGGTCCAGATGGCTCCAGATGGA
741911 AAAAGTAGGGTATGATACCCTAGGG-C-CGCGGCCGC
131 AAAAGTAGGGTATGATACCCTAGGGCCACGCGGCCGC
741946 GGAAACCCTAAACCAATTTAGGGTTTCAGTTAGGGTTTCCTAACCCTAATCCCATGCCAGCCGCC
1 GGAAA-CCTAAACCAATTTAGGGTTTCAGTTAGGGTTTCCTAA-CCTAAT-CCATGCCAGCCG-C
742011 TCTAGCCAGCCGCCTCAGACTAACCGTTGGATCTGGCAAGATCCAACGGTCCAGATGGCTCCAGA
62 TCTAGCCAGCCGCCTCAGACTAACCGTTGGATCTGGCAAGATCCAACGGTCCAGATGGCTCCAGA
**
742076 TGGAAACCGTAGGGTATGATACCCTAGGGCCACGCGGCCGC
127 TGGAAAAAGTAGGGTATGATACCCTAGGGCCACGCGGCCGC
742117 CGCTGCTGCT
Statistics
Matches: 163, Mismatches: 2, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
165 5 0.03
166 37 0.23
167 6 0.04
168 12 0.07
169 93 0.57
170 1 0.01
171 9 0.06
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.20
Consensus pattern (167 bp):
GGAAACCTAAACCAATTTAGGGTTTCAGTTAGGGTTTCCTAACCTAATCCATGCCAGCCGCTCTA
GCCAGCCGCCTCAGACTAACCGTTGGATCTGGCAAGATCCAACGGTCCAGATGGCTCCAGATGGA
AAAAGTAGGGTATGATACCCTAGGGCCACGCGGCCGC
Found at i:743292 original size:13 final size:13
Alignment explanation
Indices: 743274--743313 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
743264 TATATATAAA
743274 TAAATATTTATTT
1 TAAATATTTATTT
*
743287 TAAATAAATTATTT
1 TAAAT-ATTTATTT
743301 T-AATATTTATTT
1 TAAATATTTATTT
743313 T
1 T
743314 TCAATATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:747301 original size:15 final size:16
Alignment explanation
Indices: 747272--747304 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
747262 TTTGGGATCA
*
747272 ATACCTTTTTGCATAC
1 ATACATTTTTGCATAC
747288 ATACATTTTT-CATAC
1 ATACATTTTTGCATAC
747303 AT
1 AT
747305 TCATCATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.30, C:0.21, G:0.03, T:0.45
Consensus pattern (16 bp):
ATACATTTTTGCATAC
Found at i:754229 original size:17 final size:17
Alignment explanation
Indices: 754200--754260 Score: 77
Period size: 17 Copynumber: 3.6 Consensus size: 17
754190 ATGCTTGAAG
* *
754200 AAAAGAAAGAAAAAGAA
1 AAAAGAAAAAAAAAAAA
*
754217 AAGAGAAAAAAAAAAAA
1 AAAAGAAAAAAAAAAAA
* *
754234 AAAAGAAAAAAGAGAAA
1 AAAAGAAAAAAAAAAAA
754251 AAAAGAAAAA
1 AAAAGAAAAA
754261 GGGGTCAAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAAAAAAAA
Found at i:754236 original size:24 final size:24
Alignment explanation
Indices: 754200--754260 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
754190 ATGCTTGAAG
* * *
754200 AAAAGAAAGAAAAAGAAAAGAGAA
1 AAAAAAAAAAAAAAGAAAAAAGAA
*
754224 AAAAAAAAAAAAAAGAAAAAAGAG
1 AAAAAAAAAAAAAAGAAAAAAGAA
*
754248 AAAAAAAGAAAAA
1 AAAAAAAAAAAAA
754261 GGGGTCAAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAAAAAAGAAAAAAGAA
Found at i:755490 original size:83 final size:83
Alignment explanation
Indices: 755396--755945 Score: 1030
Period size: 83 Copynumber: 6.6 Consensus size: 83
755386 TAAATGAAAG
* * * *
755396 TTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TCGAACAGAAACAATCA
1 TTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG-GCAGAACCAATCA
755460 TTGAATTTGGAAGATGAAT
65 TTGAATTTGGAAGATGAAT
755479 TTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
1 TTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
755544 TGAATTTGGAAGATGAAT
66 TGAATTTGGAAGATGAAT
755562 TTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
1 TTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
755627 TGAATTTGGAAGATGAAT
66 TGAATTTGGAAGATGAAT
*
755645 TTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAATCAT
1 TTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
755710 TGAATTTGGAAGATGAAT
66 TGAATTTGGAAGATGAAT
755728 TTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
1 TTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
755793 TGAATTTGGAAGATGAAT
66 TGAATTTGGAAGATGAAT
*
755811 TTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCAT
1 TTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
755876 TGAATTTGGAAGATGAAT
66 TGAATTTGGAAGATGAAT
755894 TTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 TTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
755946 TAAGAACTAC
Statistics
Matches: 458, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
83 456 1.00
84 2 0.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (83 bp):
TTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
TGAATTTGGAAGATGAAT
Found at i:757040 original size:213 final size:214
Alignment explanation
Indices: 756661--757342 Score: 1053
Period size: 213 Copynumber: 3.2 Consensus size: 214
756651 GCAAAGATTT
*
756661 AAATCTATCATTGATGGATCAGCTTTTCCAGAGAAGTTCATAATGAGAAGACTCATCTG-AAGAA
1 AAATCCATCATTGATGGATCAGCTTTTCCAGA-AAGTTCATAATGAG-A-ACTCATCTGAAAGAA
756725 GGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACC-TTTGCTCAATCCATCATTTGATGGATCAG
63 -GAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAATCCATCATTTGATGGATCAG
*
756789 TATTTCCAGAAAAGTTCAT-ATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
127 TATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
756853 AGAGCTTGTTCAACC-TTTGCTC
192 AGAGCTTGTTCAACCTTTTGCTC
756875 -AATCCATCATTTGATGGATCAGCTTTTCCAGAAAGTTCATAATGAGAACTCATCTGAAAGAAGA
1 AAATCCATCA-TTGATGGATCAGCTTTTCCAGAAAGTTCATAATGAGAACTCATCTGAAAGAAGA
756939 AGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGTA
65 AGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC-AATCCATCATTTGATGGATCAGTA
757004 TTTCCAGAGAAGTTCATAATGAGAAGAACT-ATCTGAAGAA-G--GAAGAAGTTCATAATGAGAG
129 TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAG
757065 AGCTTGTTCAACCTTTTGCTC
194 AGCTTGTTCAACCTTTTGCTC
757086 AAATCCATCATTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAAC-CATCTGAAGA
1 AAATCCATCATTGATGGATCAGCTTTTCC--AGAAAGTTCATAAT--G-AGAACTCATCTG-A-A
* * * * *
757150 AGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACATGAATTCATCAATTGATGGA
59 AGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC-TCAATCCATCATTTGATGGA
*
757215 TCAGCT-TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGACGTTCAT
123 TCAG-TATTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
757279 AATGAGAAGAGCTTGTTCAACCTTTTGCTC
186 AATGAG-AGAGCTTGTTCAACCTTTTGCTC
757309 AAATCCATCATTTGATGGATCAGCTTTTCCAGAA
1 AAATCCATCA-TTGATGGATCAGCTTTTCCAGAA
757343 CTTGTTCAAC
Statistics
Matches: 437, Mismatches: 8, Indels: 38
0.90 0.02 0.08
Matches are distributed among these distances:
210 33 0.08
211 69 0.16
212 23 0.05
213 86 0.20
214 34 0.08
215 7 0.02
216 6 0.01
217 72 0.16
218 23 0.05
219 10 0.02
220 1 0.00
222 21 0.05
223 33 0.08
224 19 0.04
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (214 bp):
AAATCCATCATTGATGGATCAGCTTTTCCAGAAAGTTCATAATGAGAACTCATCTGAAAGAAGAA
GAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAATCCATCATTTGATGGATCAGTATT
TCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAGAG
CTTGTTCAACCTTTTGCTC
Found at i:757371 original size:53 final size:53
Alignment explanation
Indices: 757290--757394 Score: 158
Period size: 53 Copynumber: 2.0 Consensus size: 53
757280 ATGAGAAGAG
* *
757290 CTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAA
1 CTTGTTCAACCTTTTACTCAAATCCATCAATTGATGGATCAGCTTTTCCAGAA
* *
757343 CTTGTTCAACCTTTTACAT-GAATTCATCAATTGATGGATCAGCTTTTCCAGA
1 CTTGTTCAACCTTTTAC-TCAAATCCATCAATTGATGGATCAGCTTTTCCAGA
757395 GAAAGTTCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
53 46 0.98
54 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (53 bp):
CTTGTTCAACCTTTTACTCAAATCCATCAATTGATGGATCAGCTTTTCCAGAA
Found at i:757447 original size:166 final size:166
Alignment explanation
Indices: 757173--757507 Score: 643
Period size: 166 Copynumber: 2.0 Consensus size: 166
757163 CATAATGAGA
757173 AGAACTTGTTCAACCTTTTACATGAATTCATCAATTGATGGATCAGCTTTTCCAGAGAAAGTTCA
1 AGAACTTGTTCAACCTTTTACATGAATTCATCAATTGATGGATCAGCTTTTCCAGAGAAAGTTCA
*
757238 TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGACGTTCATAATGAGAAGAGCTTGTTCAACCTT
66 TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTT
* *
757303 TTGCTCAAATCCATCATTTGATGGATCAGCTTTTCC
131 TTGCTCAAATCCATCACTTGATGGAGCAGCTTTTCC
757339 AGAACTTGTTCAACCTTTTACATGAATTCATCAATTGATGGATCAGCTTTTCCAGAGAAAGTTCA
1 AGAACTTGTTCAACCTTTTACATGAATTCATCAATTGATGGATCAGCTTTTCCAGAGAAAGTTCA
757404 TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTT
66 TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTT
757469 TTGCTCAAATCCATCACTTGATGGAGCAGCTTTTCC
131 TTGCTCAAATCCATCACTTGATGGAGCAGCTTTTCC
757505 AGA
1 AGA
757508 GAAGTTCATA
Statistics
Matches: 166, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
166 166 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (166 bp):
AGAACTTGTTCAACCTTTTACATGAATTCATCAATTGATGGATCAGCTTTTCCAGAGAAAGTTCA
TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTT
TTGCTCAAATCCATCACTTGATGGAGCAGCTTTTCC
Found at i:757553 original size:112 final size:113
Alignment explanation
Indices: 757339--757576 Score: 381
Period size: 112 Copynumber: 2.1 Consensus size: 113
757329 CAGCTTTTCC
* * *
757339 AGAACTTGTTCAACCTTTTACATGAATTCATCAATTGATGGATCAGCTTTTCCAGAGAAAGTTCA
1 AGAACTTGTTCAACCTTTTACATAAATCCATCAATTGATGGAGCAGCTTTTCCAGAGAAAGTTCA
*
757404 TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
66 TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGA
* * *
757452 AGAGCTTGTTCAACCTTTTGC-TCAAATCCATCACTTGATGGAGCAGCTTTTCCAGAG-AAGTTC
1 AGAACTTGTTCAACCTTTTACAT-AAATCCATCAATTGATGGAGCAGCTTTTCCAGAGAAAGTTC
*
757515 ATAATGAGAAGAACTCATTTGAAGAAGGAAGAAGAAGTTCATAATAAGA
65 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGA
757564 AGAACTTGTTCAA
1 AGAACTTGTTCAA
757577 TAATTCTATC
Statistics
Matches: 115, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
112 66 0.57
113 49 0.43
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (113 bp):
AGAACTTGTTCAACCTTTTACATAAATCCATCAATTGATGGAGCAGCTTTTCCAGAGAAAGTTCA
TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGA
Found at i:757900 original size:3 final size:3
Alignment explanation
Indices: 757894--757964 Score: 124
Period size: 3 Copynumber: 23.7 Consensus size: 3
757884 TTTTTACCCA
*
757894 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
757942 TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
757965 AATATATATT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:759408 original size:13 final size:13
Alignment explanation
Indices: 759392--759431 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
759382 ATATAATAAA
759392 TAAATATTTATTT
1 TAAATATTTATTT
*
759405 TAAATAAATTATTT
1 TAAAT-ATTTATTT
759419 T-AATATTTATTT
1 TAAATATTTATTT
759431 T
1 T
759432 TCAATATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:763031 original size:23 final size:23
Alignment explanation
Indices: 763005--763048 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
762995 AAAGTGTCAT
* *
763005 GTAGAATTGCACCGAAGTGCCGC
1 GTAGAAATACACCGAAGTGCCGC
*
763028 GTAGAAATACACCGATGTGCC
1 GTAGAAATACACCGAAGTGCC
763049 ATATAAGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (23 bp):
GTAGAAATACACCGAAGTGCCGC
Found at i:768519 original size:23 final size:23
Alignment explanation
Indices: 768493--768536 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
768483 AAAGTGTCAT
* *
768493 GTAGAATTGCACCGAAGTGCCGC
1 GTAGAAATACACCGAAGTGCCGC
*
768516 GTAGAAATACACCGATGTGCC
1 GTAGAAATACACCGAAGTGCC
768537 ATATAAGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (23 bp):
GTAGAAATACACCGAAGTGCCGC
Found at i:774571 original size:22 final size:22
Alignment explanation
Indices: 774546--774588 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
774536 AAAATGTCCA
*
774546 TAAGAACCACATAGATATTCCT
1 TAAGAACCACATACATATTCCT
* *
774568 TAAGAATCATATACATATTCC
1 TAAGAACCACATACATATTCC
774589 AAGTACCAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (22 bp):
TAAGAACCACATACATATTCCT
Found at i:775288 original size:35 final size:35
Alignment explanation
Indices: 775229--775296 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
775219 GATGTTTCCA
* *
775229 GGTATCGATACCTGCCTTCTGGTATCGATACCTAT
1 GGTATCGATACATCCCTTCTGGTATCGATACCTAT
*
775264 GGTATCGATACTATCCCTTC-GGTATTGATACCT
1 GGTATCGATAC-ATCCCTTCTGGTATCGATACCT
775297 TATGAAGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 23 0.79
36 6 0.21
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (35 bp):
GGTATCGATACATCCCTTCTGGTATCGATACCTAT
Found at i:775790 original size:18 final size:19
Alignment explanation
Indices: 775758--775795 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
775748 CTCATAATTC
775758 TTTGAGTTTCTATACCTCTT
1 TTTGAGTTTCTATA-CTCTT
775778 TTTGA-TTTC-ATACTCTT
1 TTTGAGTTTCTATACTCTT
775795 T
1 T
775796 CCTAATGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 4 0.22
20 5 0.28
ACGTcount: A:0.16, C:0.18, G:0.08, T:0.58
Consensus pattern (19 bp):
TTTGAGTTTCTATACTCTT
Found at i:776214 original size:22 final size:22
Alignment explanation
Indices: 776169--776214 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
776159 GTTGCTTGTC
***
776169 TTTTGGATATAATACATTGTTT
1 TTTTGGATATAATACATACATT
776191 TTTTGGATATAATACATACATT
1 TTTTGGATATAATACATACATT
776213 TT
1 TT
776215 ATCTAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.52
Consensus pattern (22 bp):
TTTTGGATATAATACATACATT
Found at i:795053 original size:80 final size:80
Alignment explanation
Indices: 794920--795079 Score: 311
Period size: 80 Copynumber: 2.0 Consensus size: 80
794910 AAATCCACTA
794920 GAATTCATTGTGATATGGATATTCAAGAGACGTCAAGAGAAAACAAAAGATATGGGCATTGTAGA
1 GAATTCATTGTGATATGGATATTCAAGAGACGTCAAGAGAAAACAAAAGATATGGGCATTGTAGA
794985 AACCTAGGACACAAT
66 AACCTAGGACACAAT
*
795000 GAATTCATTGTGATATGGATATTCAGGAGACGTCAAGAGAAAACAAAAGATATGGGCATTGTAGA
1 GAATTCATTGTGATATGGATATTCAAGAGACGTCAAGAGAAAACAAAAGATATGGGCATTGTAGA
795065 AACCTAGGACACAAT
66 AACCTAGGACACAAT
795080 AGAAAAAATG
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (80 bp):
GAATTCATTGTGATATGGATATTCAAGAGACGTCAAGAGAAAACAAAAGATATGGGCATTGTAGA
AACCTAGGACACAAT
Found at i:796132 original size:21 final size:21
Alignment explanation
Indices: 796103--796203 Score: 85
Period size: 21 Copynumber: 4.8 Consensus size: 21
796093 TAAGGACCAC
*
796103 TCCATAAGGATCACATATATAT
1 TCCA-AAGGACCACATATATAT
* * *
796125 TCCAAAGGACCAAATATGTGT
1 TCCAAAGGACCACATATATAT
** * *
796146 TCTGAAGAACCACATATATGT
1 TCCAAAGGACCACATATATAT
**
796167 TCCAAAGGATTACATATATAT
1 TCCAAAGGACCACATATATAT
* *
796188 CCCGAAGGACCACATA
1 TCCAAAGGACCACATA
796204 GAACCCTTGA
Statistics
Matches: 60, Mismatches: 19, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
21 56 0.93
22 4 0.07
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.26
Consensus pattern (21 bp):
TCCAAAGGACCACATATATAT
Found at i:796200 original size:42 final size:42
Alignment explanation
Indices: 796108--796203 Score: 102
Period size: 42 Copynumber: 2.3 Consensus size: 42
796098 ACCACTCCAT
* * * * *
796108 AAGGATCACATATATATTCCAAAGGACCAAATATGTGTTCTG
1 AAGGACCACATATATATTCCAAAGGACCAAATATATATCCCG
* * ** *
796150 AAGAACCACATATATGTTCCAAAGGATTACATATATATCCCG
1 AAGGACCACATATATATTCCAAAGGACCAAATATATATCCCG
796192 AAGGACCACATA
1 AAGGACCACATA
796204 GAACCCTTGA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.25
Consensus pattern (42 bp):
AAGGACCACATATATATTCCAAAGGACCAAATATATATCCCG
Found at i:803371 original size:23 final size:21
Alignment explanation
Indices: 803345--803404 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
803335 CACCTAAACT
*
803345 TGTCCCGAAGGACCGTACATATA
1 TGTCCCGAAGGACC--ACATAAA
* * *
803368 TGTCCCTAAGAACCACTTAAA
1 TGTCCCGAAGGACCACATAAA
803389 TGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
803405 TCCTTAAGGA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 19 0.61
23 12 0.39
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATAAA
Found at i:806062 original size:2 final size:2
Alignment explanation
Indices: 806055--806080 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
806045 TTTAATAATA
806055 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
806081 TTAAAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:806207 original size:10 final size:10
Alignment explanation
Indices: 806192--806232 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
806182 AATTATCAAC
806192 AAATAACATA
1 AAATAACATA
*
806202 AAATAAAATA
1 AAATAACATA
806212 AAATAACATA
1 AAATAACATA
*
806222 ACATAACATA
1 AAATAACATA
806232 A
1 A
806233 TCAAAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.20
Consensus pattern (10 bp):
AAATAACATA
Found at i:806480 original size:55 final size:55
Alignment explanation
Indices: 806415--806791 Score: 412
Period size: 55 Copynumber: 7.0 Consensus size: 55
806405 ATAATAAGTT
* * * *
806415 AGACTTGAAAAATCTTCGGA-AGACGGGTCCGCTCCCTATTCCTTCAGGGAGTATA
1 AGACTCGAAAAATCTTC-AACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATA
* * * * * * *
806470 GGACTCGAAAAATATTCGACAAACAGGTTCGCTCCCTATTCGTTCAGGGAGTATA
1 AGACTCGAAAAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATA
* * * * *
806525 AGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA
1 AGACTCGAAAAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATA
* *
806580 AGACTCGAATAATCTTCAATAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATA
1 AGACTCGAAAAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATA
* * * * *
806635 GGACTCG----ATCTTCAACAAATGTGTCAGCTCCCTTTTCCTTCAGAGAGTATA
1 AGACTCGAAAAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATA
* * * *
806686 GGACTTGAAAAATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATA
1 AGACTCGAAAAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATA
* * *
806741 AGACTTG----ATCTTCAACAAACGTGTCCGCTCCCTATTCTTTCAGAGAGTATA
1 AGACTCGAAAAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATA
806792 GAACTCAATA
Statistics
Matches: 282, Mismatches: 35, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
51 87 0.31
54 2 0.01
55 193 0.68
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (55 bp):
AGACTCGAAAAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATA
Found at i:806700 original size:106 final size:106
Alignment explanation
Indices: 806445--806797 Score: 463
Period size: 106 Copynumber: 3.3 Consensus size: 106
806435 AGACGGGTCC
* * * * *
806445 GCTCCCTATTCCTTCAGGGAGTATAGGACTCGAAAAATATTCGACAAACAGGTTCGCTCCCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGAAAAATCTTCAACAAACGGGTCCGCTCCCTATT
* * *
806510 CGTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCT
66 CCTTCAGAGAGTATAAGACTCG----ATCTTCAACAAACGTGTCA
* * * * *
806555 GCTCCCTATTCATTCAGGGAGTATAAGACTCGAATAATCTTCAATAAACGGGTCCGCTCCCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGAAAAATCTTCAACAAACGGGTCCGCTCCCTATT
* *
806620 CCTTCAGAGAGTATAGGACTCGATCTTCAACAAATGTGTCA
66 CCTTCAGAGAGTATAAGACTCGATCTTCAACAAACGTGTCA
* * * *
806661 GCTCCCTTTTCCTTCAGAGAGTATAGGACTTGAAAAATCTTCAACAAACGTGTCTGCTCCCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGAAAAATCTTCAACAAACGGGTCCGCTCCCTATT
* *
806726 CCTTCAGAGAGTATAAGACTTGATCTTCAACAAACGTGTCC
66 CCTTCAGAGAGTATAAGACTCGATCTTCAACAAACGTGTCA
* *
806767 GCTCCCTATTCTTTCAGAGAGTATAGAACTC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTC
806798 AATATTCATA
Statistics
Matches: 213, Mismatches: 30, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
106 137 0.64
110 76 0.36
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (106 bp):
GCTCCCTATTCCTTCAGAGAGTATAGGACTCGAAAAATCTTCAACAAACGGGTCCGCTCCCTATT
CCTTCAGAGAGTATAAGACTCGATCTTCAACAAACGTGTCA
Found at i:806923 original size:37 final size:37
Alignment explanation
Indices: 806816--806925 Score: 134
Period size: 37 Copynumber: 3.0 Consensus size: 37
806806 TAAAATGAGT
* *
806816 TTGCTTCACTACT-TTTCAGTGAATGCTTATAGA-TGAT
1 TTGCTTCACTACTCTTTC-GTGAAGGCTTA-AGATTGAA
* *
806853 TTACTTCACTACTCTTCCGTGAAGGCTTAAGATTGAA
1 TTGCTTCACTACTCTTTCGTGAAGGCTTAAGATTGAA
* *
806890 TTGCTTCACTGCTCTTTCGTGAAGGATTAAGATTGA
1 TTGCTTCACTACTCTTTCGTGAAGGCTTAAGATTGA
806926 CTTGTTTCGA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
36 3 0.05
37 57 0.90
38 3 0.05
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (37 bp):
TTGCTTCACTACTCTTTCGTGAAGGCTTAAGATTGAA
Done.