Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009633.1 Hibiscus syriacus cultivar Beakdansim tig00117032_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: 2608659
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 13
Found at i:1722790 original size:23 final size:22
Alignment explanation
Indices: 1722751--1722795 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1722741 TTATTATATT
*
1722751 TTTAATATTTTGTATTTAATTTA
1 TTTAATATTTTGAATTT-ATTTA
1722774 TTTAAGTATTTT-AATTTATTTA
1 TTTAA-TATTTTGAATTTATTTA
1722796 ATATTTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTAATATTTTGAATTTATTTA
Found at i:1722802 original size:17 final size:18
Alignment explanation
Indices: 1722765--1722803 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1722755 ATATTTTGTA
1722765 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
1722783 TTTAATTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
1722800 TTTA
1 TTTA
1722804 CTTATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:1725186 original size:35 final size:36
Alignment explanation
Indices: 1725122--1725204 Score: 104
Period size: 35 Copynumber: 2.4 Consensus size: 36
1725112 TTCAGTTAAT
1725122 TTTGTT-TA-TTACCATTTAATATCAGTTATTGTAA-
1 TTTGTTATATTTACCATTTAATATCA-TTATTGTAAG
1725156 TTTGGTTATCATTTACCATTTAATA-C-TTATTGTAAG
1 TTT-GTTAT-ATTTACCATTTAATATCATTATTGTAAG
1725192 TTTGTTATATTTA
1 TTTGTTATATTTA
1725205 AAATTATTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
34 8 0.18
35 17 0.39
36 4 0.09
37 2 0.05
38 13 0.30
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.54
Consensus pattern (36 bp):
TTTGTTATATTTACCATTTAATATCATTATTGTAAG
Found at i:1730203 original size:2 final size:2
Alignment explanation
Indices: 1730196--1730261 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
1730186 TATCTTCCAA
1730196 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
1730238 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
1730262 TTCATTATCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1732038 original size:18 final size:19
Alignment explanation
Indices: 1732006--1732045 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
1731996 AATTTGATGC
* *
1732006 TGCCGAGGAAGAATTCATT
1 TGCCGAGGAAAAATTAATT
1732025 TGCC-AGGAAAAATTAATT
1 TGCCGAGGAAAAATTAATT
1732043 TGC
1 TGC
1732046 TAGGGCATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (19 bp):
TGCCGAGGAAAAATTAATT
Found at i:1736809 original size:20 final size:20
Alignment explanation
Indices: 1736784--1736821 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1736774 AAATTGATCC
*
1736784 CCAACGACTCTAAACGACAT
1 CCAACGACTCGAAACGACAT
1736804 CCAACGACTCGAAACGAC
1 CCAACGACTCGAAACGAC
1736822 CACAACAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.37, G:0.13, T:0.11
Consensus pattern (20 bp):
CCAACGACTCGAAACGACAT
Found at i:1758403 original size:30 final size:30
Alignment explanation
Indices: 1758367--1758450 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
1758357 AAGCTCATAA
* * *
1758367 AAAATAACATGCAAACGTTATCAAACAATC
1 AAAATAACATACAAACGTGAACAAACAATC
* *
1758397 AAAATAATATACAAACGTGAACAAACAATT
1 AAAATAACATACAAACGTGAACAAACAATC
* * *
1758427 AAAATAATATATAAACATGAACAA
1 AAAATAACATACAAACGTGAACAA
1758451 TCAAAATAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.60, C:0.14, G:0.06, T:0.20
Consensus pattern (30 bp):
AAAATAACATACAAACGTGAACAAACAATC
Found at i:1758651 original size:26 final size:26
Alignment explanation
Indices: 1758617--1758666 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
1758607 ATATACAAAC
*
1758617 AATCAAAATAATAT-ACAAATATGAAT
1 AATCAAAATAAAATGA-AAATATGAAT
1758643 AATCAAAATAAAATGAAAATATGA
1 AATCAAAATAAAATGAAAATATGA
1758667 TTTGAGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (26 bp):
AATCAAAATAAAATGAAAATATGAAT
Found at i:1765580 original size:4 final size:4
Alignment explanation
Indices: 1765573--1765606 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
1765563 AATCAAAGAA
1765573 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AA
1765607 GAACACAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:1769050 original size:20 final size:20
Alignment explanation
Indices: 1769025--1769063 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1769015 GCCAATTATA
1769025 CTACAG-TTCTCATATCATAC
1 CTACAGCTT-TCATATCATAC
1769045 CTACAGCTTTCATATCATA
1 CTACAGCTTTCATATCATA
1769064 TAACATGGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.36
Consensus pattern (20 bp):
CTACAGCTTTCATATCATAC
Found at i:1769252 original size:2 final size:2
Alignment explanation
Indices: 1769245--1769270 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1769235 TATAACAGTA
1769245 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
1769271 GCATGTACAT
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:1773621 original size:203 final size:203
Alignment explanation
Indices: 1773267--1773679 Score: 783
Period size: 203 Copynumber: 2.0 Consensus size: 203
1773257 GAATTCTCTA
*
1773267 ACAAT-AACTTGCATGTTACTTGCGAGGTGATTTTCAGAATTGGAACGAATGTTCACAATATTCA
1 ACAATCAACTTGCATGTTACTTGCGAGGCGATTTTCAGAATTGGAACGAATGTTCACAATATTCA
1773331 TTTCCTACACAAATTTAGTCATAACAGATAGAACATTGAGATATACTTATTACAAAAGGAGGAAT
66 TTTCCTACACAAATTTAGTCATAACAGATAGAACATTGAGATATACTTATTACAAAAGGAGGAAT
*
1773396 CATTATCAAAATTTTGGTTTAGAAGAATATGATTATAATCTAGGGGTATATACTGATAGACACCC
131 CATTATCAAAATTTTGGTTTAGAAGAATACGATTATAATCTAGGGGTATATACTGATAGACACCC
1773461 TATGACAG
196 TATGACAG
*
1773469 ACAATCAACTTGCATGTTACTTGCGAGGCGATTTTCAGAATTGGAATGAATGTTCACAATATTCA
1 ACAATCAACTTGCATGTTACTTGCGAGGCGATTTTCAGAATTGGAACGAATGTTCACAATATTCA
1773534 TTTCCTACACAAATTTAGTCATAACAGATAGAACATTGAGATATACTTATTACAAAAGGAGGAAT
66 TTTCCTACACAAATTTAGTCATAACAGATAGAACATTGAGATATACTTATTACAAAAGGAGGAAT
1773599 CATTATCAAAATTTTGGTTTAGAAGAATACGATTATAATCTAGGGGTATATACTGATAGACACCC
131 CATTATCAAAATTTTGGTTTAGAAGAATACGATTATAATCTAGGGGTATATACTGATAGACACCC
*
1773664 TATGTCAG
196 TATGACAG
1773672 ACAATCAA
1 ACAATCAA
1773680 ATGAATTACC
Statistics
Matches: 206, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
202 5 0.02
203 201 0.98
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (203 bp):
ACAATCAACTTGCATGTTACTTGCGAGGCGATTTTCAGAATTGGAACGAATGTTCACAATATTCA
TTTCCTACACAAATTTAGTCATAACAGATAGAACATTGAGATATACTTATTACAAAAGGAGGAAT
CATTATCAAAATTTTGGTTTAGAAGAATACGATTATAATCTAGGGGTATATACTGATAGACACCC
TATGACAG
Found at i:1786355 original size:46 final size:46
Alignment explanation
Indices: 1786302--1786722 Score: 594
Period size: 46 Copynumber: 9.2 Consensus size: 46
1786292 AAACGAATCT
* * *
1786302 ATAACTAAATTGCAAGAAATGATGCATTAAGGTATGAAAGGATGCC
1 ATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCC
* *
1786348 ATAACTAAAATGCATGAAATGATGCATTAAGGCATGAACGGATTCC
1 ATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCC
* * * * *
1786394 ATAACAAAAATGAATGAAAGGATGCATTAAAGCATAAAAGGATGCC
1 ATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCC
* * * * *
1786440 AAAACTAAAATACATGAAAGGATGCATTAAGGCATGTATGGATGCC
1 ATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCC
* *
1786486 ATAACTAAAATGCATGAAATGATGCATTAAGGAATGAAAGGATGAC
1 ATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCC
1786532 ATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCC
1 ATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCC
* *
1786578 ATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAACA-GATGTC
1 ATAACTAAAATGCATGAAATGATGCATTAAGGCATGAA-AGGATGCC
* *
1786624 ATAACTAAAATGTATGAAATGATGCA-TAAGGCATGAAAGGATGTC
1 ATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCC
* * *
1786669 ATAACTAAAATACATGAAAGGATGCATTAAGGCATTAAAGGATGCC
1 ATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCC
*
1786715 ACAACTAA
1 ATAACTAA
1786723 GATTAATGAA
Statistics
Matches: 333, Mismatches: 39, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
44 1 0.00
45 40 0.12
46 291 0.87
47 1 0.00
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (46 bp):
ATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCC
Found at i:1786384 original size:20 final size:20
Alignment explanation
Indices: 1786317--1786385 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 20
1786307 TAAATTGCAA
*
1786317 GAAATGATGCATTAAGGTAT
1 GAAATGATGCATTAAGGCAT
* *
1786337 GAAAGGATGCCATAACTAAAATGCAT
1 GAAATGATG-CAT---T--AAGGCAT
1786363 GAAATGATGCATTAAGGCAT
1 GAAATGATGCATTAAGGCAT
1786383 GAA
1 GAA
1786386 CGGATTCCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
20 17 0.45
21 3 0.08
22 1 0.03
24 1 0.03
25 3 0.08
26 13 0.34
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.23
Consensus pattern (20 bp):
GAAATGATGCATTAAGGCAT
Found at i:1786509 original size:26 final size:25
Alignment explanation
Indices: 1786335--1786695 Score: 148
Period size: 26 Copynumber: 15.6 Consensus size: 25
1786325 GCATTAAGGT
1786335 ATGAAAGGATGCCATAACTAAAATGC
1 ATGAAAGGATG-CATAACTAAAATGC
* *
1786361 ATGAAATGATGCAT---T--AAGGC
1 ATGAAAGGATGCATAACTAAAATGC
* * * *
1786381 ATGAACGGATTCCATAACAAAAATGA
1 ATGAAAGGA-TGCATAACTAAAATGC
1786407 ATGAAAGGATGCAT---T-AAA-GC
1 ATGAAAGGATGCATAACTAAAATGC
* **** * *
1786427 ATAAAAGGATGCCAAAACTAAAATAC
1 ATGAAA-GGATGCATAACTAAAATGC
*
1786453 ATGAAAGGATGCAT---T--AAGGC
1 ATGAAAGGATGCATAACTAAAATGC
* *
1786473 ATGTATGGATGCCATAACTAAAATGC
1 ATGAAAGGATG-CATAACTAAAATGC
* * *
1786499 ATGAAATGATGCAT---T--AAGGA
1 ATGAAAGGATGCATAACTAAAATGC
1786519 ATGAAAGGATGACATAACTAAAATGC
1 ATGAAAGGATG-CATAACTAAAATGC
* *
1786545 ATGAAATGATGCAT---T--AAGGC
1 ATGAAAGGATGCATAACTAAAATGC
1786565 ATGAAAGGATGCCATAACTAAAATGC
1 ATGAAAGGATG-CATAACTAAAATGC
*
1786591 ATGAAAGGATGCAT---T--AAGGC
1 ATGAAAGGATGCATAACTAAAATGC
*
1786611 ATGAACA-GATGTCATAACTAAAATGT
1 ATGAA-AGGATG-CATAACTAAAATGC
* *
1786637 ATGAAATGATGC---A-T--AAGGC
1 ATGAAAGGATGCATAACTAAAATGC
*
1786656 ATGAAAGGATGTCATAACTAAAATAC
1 ATGAAAGGATG-CATAACTAAAATGC
1786682 ATGAAAGGATGCAT
1 ATGAAAGGATGCAT
1786696 TAAGGCATTA
Statistics
Matches: 240, Mismatches: 50, Indels: 91
0.63 0.13 0.24
Matches are distributed among these distances:
19 13 0.05
20 70 0.29
21 24 0.10
22 6 0.03
23 1 0.00
24 6 0.03
25 27 0.11
26 93 0.39
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (25 bp):
ATGAAAGGATGCATAACTAAAATGC
Found at i:1786524 original size:20 final size:20
Alignment explanation
Indices: 1786497--1786713 Score: 96
Period size: 20 Copynumber: 9.7 Consensus size: 20
1786487 TAACTAAAAT
*
1786497 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1786517 GAATGAAAGGATGACATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
1786543 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
1786563 GCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
1786589 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
1786609 GCATGAACA-GATGTCATAACTAAAAT
1 GCATGAA-AGGATG-CAT---T--AAG
* *
1786635 GTATGAAATGATGCA-TAAG
1 GCATGAAAGGATGCATTAAG
*
1786654 GCATGAAAGGATGTCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
1786680 ACATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
1786700 GCATTAAAGGATGC
1 GCATGAAAGGATGC
1786714 CACAACTAAG
Statistics
Matches: 151, Mismatches: 19, Indels: 54
0.67 0.08 0.24
Matches are distributed among these distances:
19 13 0.09
20 54 0.36
21 11 0.07
22 3 0.02
24 4 0.03
25 12 0.08
26 54 0.36
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:1792429 original size:19 final size:19
Alignment explanation
Indices: 1792405--1792452 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
1792395 GGGGGCAAAA
1792405 TGAAGTAAAGTTAGTTGGG
1 TGAAGTAAAGTTAGTTGGG
1792424 TGAAGTAAAGTTAGTTGGG
1 TGAAGTAAAGTTAGTTGGG
*
1792443 TTAAGTAAAG
1 TGAAGTAAAG
1792453 AGGAGTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.31
Consensus pattern (19 bp):
TGAAGTAAAGTTAGTTGGG
Found at i:1792652 original size:16 final size:17
Alignment explanation
Indices: 1792627--1792671 Score: 74
Period size: 16 Copynumber: 2.7 Consensus size: 17
1792617 CGATGCAAGT
1792627 GGTATCGATACTGAT-G
1 GGTATCGATACTGATGG
*
1792643 GGTATTGATACTGATGG
1 GGTATCGATACTGATGG
1792660 GGTATCGATACT
1 GGTATCGATACT
1792672 AACAAGGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.24, C:0.11, G:0.31, T:0.33
Consensus pattern (17 bp):
GGTATCGATACTGATGG
Found at i:1793351 original size:25 final size:25
Alignment explanation
Indices: 1793283--1793531 Score: 156
Period size: 20 Copynumber: 10.8 Consensus size: 25
1793273 AAAATGAATC
*
1793283 CATAACTAAAATGCATGAAATGATG
1 CATAACTAAAATGCATGAAAGGATG
*
1793308 CAT---T--AAGGCATGAAAGGATG
1 CATAACTAAAATGCATGAAAGGATG
*
1793328 CATAACTAAAATGTATGAAAGGATG
1 CATAACTAAAATGCATGAAAGGATG
* *
1793353 --T-A-T-TAAGGCATGAACA-GATG
1 CATAACTAAAATGCATGAA-AGGATG
*
1793373 CCATAACTAAAATGCATGAAAGAATG
1 -CATAACTAAAATGCATGAAAGGATG
* *
1793399 C---A-T-AAAGGCATGAAATGATG
1 CATAACTAAAATGCATGAAAGGATG
1793419 CCATAACTAAAATGCATGAAAGGATG
1 -CATAACTAAAATGCATGAAAGGATG
*
1793445 CAT---T--AAGGCATGAACA-GATG
1 CATAACTAAAATGCATGAA-AGGATG
*
1793465 TCATAACTAAAATGCATGAAATGATG
1 -CATAACTAAAATGCATGAAAGGATG
*
1793491 CAT---T--AAGGCATGAAAGGATG
1 CATAACTAAAATGCATGAAAGGATG
1793511 TCATAACTAAAATGCATGAAA
1 -CATAACTAAAATGCATGAAA
1793532 TGAATCATTA
Statistics
Matches: 171, Mismatches: 20, Indels: 65
0.67 0.08 0.25
Matches are distributed among these distances:
20 70 0.41
21 11 0.06
22 5 0.03
23 3 0.02
24 4 0.02
25 28 0.16
26 50 0.29
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.22
Consensus pattern (25 bp):
CATAACTAAAATGCATGAAAGGATG
Found at i:1793392 original size:46 final size:46
Alignment explanation
Indices: 1793282--1793566 Score: 416
Period size: 46 Copynumber: 6.2 Consensus size: 46
1793272 TAAAATGAAT
*
1793282 CCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
1793328 -CATAACTAAAATGTATGAAAGGATGTATTAAGGCATGAACA-GATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAA-AGGATG
* * *
1793373 CCATAACTAAAATGCATGAAAGAATGCATAAAGGCATGAAATGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1793419 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAACA-GATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAA-AGGATG
* *
1793465 TCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
1793511 TCATAACTAAAATGCATGAAATGAAT-CATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAA-GGATGCATTAAGGCATGAAAGGATG
*
1793557 CCAGAACTAA
1 CCATAACTAA
1793567 GATTAATGAA
Statistics
Matches: 218, Mismatches: 15, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
45 42 0.19
46 173 0.79
47 3 0.01
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:1813839 original size:12 final size:12
Alignment explanation
Indices: 1813822--1813846 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1813812 AGTCTCTCGT
1813822 CCATAACCACAA
1 CCATAACCACAA
1813834 CCATAACCACAA
1 CCATAACCACAA
1813846 C
1 C
1813847 TCGGCCTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.44, G:0.00, T:0.08
Consensus pattern (12 bp):
CCATAACCACAA
Found at i:1823634 original size:2 final size:2
Alignment explanation
Indices: 1823627--1823665 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1823617 TTTAAACCAA
*
1823627 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1823666 ATAGTGACTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1824936 original size:10 final size:9
Alignment explanation
Indices: 1824914--1824946 Score: 50
Period size: 8 Copynumber: 3.7 Consensus size: 9
1824904 TTTACAAATA
1824914 ATAATATTT
1 ATAATATTT
1824923 ATAATATATT
1 ATAATAT-TT
1824933 ATAATA-TT
1 ATAATATTT
1824941 ATAATA
1 ATAATA
1824947 ACGTCACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.35
9 7 0.30
10 8 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
ATAATATTT
Found at i:1832462 original size:19 final size:19
Alignment explanation
Indices: 1832440--1832480 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1832430 CCCAACCAAG
1832440 TCAGACCGGTCCAACCGGT
1 TCAGACCGGTCCAACCGGT
* **
1832459 TCAGACTGGTTTAACCGGT
1 TCAGACCGGTCCAACCGGT
1832478 TCA
1 TCA
1832481 ATAGACCCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.24
Consensus pattern (19 bp):
TCAGACCGGTCCAACCGGT
Found at i:1834730 original size:31 final size:30
Alignment explanation
Indices: 1834695--1834796 Score: 73
Period size: 31 Copynumber: 3.2 Consensus size: 30
1834685 GTCCATAAGA
1834695 AATTATCAGTCGATGCTGAACCGATACAAGG
1 AATTATCAGTCG-TGCTGAACCGATACAAGG
* *
1834726 AATTATTAACAG-CG-GCTGAACCTGCCAGAGATAGG
1 AATTA-T--CAGTCGTGCTGAACC-G--ATACA-AGG
* *
1834761 AATTACCAGTCGGTGCTGAACCTATACAAGG
1 AATTATCAGTC-GTGCTGAACCGATACAAGG
1834792 AATTA
1 AATTA
1834797 CTAGCAATGA
Statistics
Matches: 55, Mismatches: 6, Indels: 20
0.68 0.07 0.25
Matches are distributed among these distances:
31 21 0.38
32 8 0.15
33 3 0.05
34 7 0.13
35 16 0.29
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (30 bp):
AATTATCAGTCGTGCTGAACCGATACAAGG
Found at i:1834811 original size:66 final size:66
Alignment explanation
Indices: 1834695--1834821 Score: 182
Period size: 66 Copynumber: 1.9 Consensus size: 66
1834685 GTCCATAAGA
* * * *
1834695 AATTATCAGTCGATGCTGAACCGATACAAGGAATTATTAACAGCGGCTGAACCTGCCAGAGATAG
1 AATTACCAGTCGATGCTGAACCGATACAAGGAATTACTAACAACGACTGAACCTGCCAGAGATAG
1834760 G
66 G
* * * *
1834761 AATTACCAGTCGGTGCTGAACCTATACAAGGAATTACTAGCAATGACTGAACCTGCCAGAG
1 AATTACCAGTCGATGCTGAACCGATACAAGGAATTACTAACAACGACTGAACCTGCCAGAG
1834822 TCTTCATACC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (66 bp):
AATTACCAGTCGATGCTGAACCGATACAAGGAATTACTAACAACGACTGAACCTGCCAGAGATAG
G
Found at i:1841222 original size:13 final size:13
Alignment explanation
Indices: 1841221--1841263 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
1841211 CCGTTGACCC
*
1841221 GACCCGACCCATT
1 GACCCGACCCGTT
*
1841234 TACCCGACCCGTT
1 GACCCGACCCGTT
1841247 GACCCGACCCGTT
1 GACCCGACCCGTT
1841260 GACC
1 GACC
1841264 GTTGACCAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.19, C:0.47, G:0.19, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1841250 original size:8 final size:8
Alignment explanation
Indices: 1841239--1841285 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
1841229 CCATTTACCC
1841239 GACCCGTT
1 GACCCGTT
1841247 GACCC---
1 GACCCGTT
1841252 GACCCGTT
1 GACCCGTT
1841260 GA-CCGTT
1 GACCCGTT
*
1841267 GACCAGTT
1 GACCCGTT
1841275 GA-CCGTT
1 GACCCGTT
1841282 GACC
1 GACC
1841286 GGAGTTGACC
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
5 5 0.16
7 13 0.41
8 14 0.44
ACGTcount: A:0.17, C:0.36, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:1841257 original size:18 final size:18
Alignment explanation
Indices: 1841199--1841244 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1841189 ACCGGTCACA
* *
1841199 ACCCAACCCGACCCGTTG
1 ACCCGACCCGACCCATTG
*
1841217 ACCCGACCCGACCCATTT
1 ACCCGACCCGACCCATTG
1841235 ACCCGACCCG
1 ACCCGACCCG
1841245 TTGACCCGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.22, C:0.52, G:0.15, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCATTG
Found at i:1841267 original size:7 final size:7
Alignment explanation
Indices: 1841255--1841286 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1841245 TTGACCCGAC
1841255 CCGTTGA
1 CCGTTGA
1841262 CCGTTGA
1 CCGTTGA
1841269 CCAGTTGA
1 CC-GTTGA
1841277 CCGTTGA
1 CCGTTGA
1841284 CCG
1 CCG
1841287 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.16, C:0.31, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:1841275 original size:15 final size:15
Alignment explanation
Indices: 1841252--1841295 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
1841242 CCGTTGACCC
*
1841252 GACCCGTTGACCGTT
1 GACCAGTTGACCGTT
1841267 GACCAGTTGACCGTT
1 GACCAGTTGACCGTT
1841282 GACCGGAGTTGACC
1 GACC--AGTTGACC
1841296 ACTGTTGACC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 18 0.69
17 8 0.31
ACGTcount: A:0.18, C:0.30, G:0.30, T:0.23
Consensus pattern (15 bp):
GACCAGTTGACCGTT
Found at i:1842607 original size:18 final size:18
Alignment explanation
Indices: 1842581--1842616 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1842571 TCGAAAGGAC
*
1842581 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1842599 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1842617 CGGATGGAAG
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:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1843789 original size:24 final size:23
Alignment explanation
Indices: 1843755--1843857 Score: 86
Period size: 24 Copynumber: 4.4 Consensus size: 23
1843745 ATTTTCGATT
* *
1843755 TGATTTCTGATTTGATACTTGAC
1 TGATTTATGATCTGATACTTGAC
1843778 ATGGA-TTATGATCTGATA-TATGAC
1 -T-GATTTATGATCTGATACT-TGAC
* *
1843802 TGGA-TTCTGATCTGTTACTTGACC
1 T-GATTTATGATCTGATACTTGA-C
* *
1843826 TGATTTCTGATATGATACTTGAC
1 TGATTTATGATCTGATACTTGAC
1843849 TGATTTATG
1 TGATTTATG
1843858 TTTTGATTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
23 30 0.45
24 35 0.52
25 2 0.03
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (23 bp):
TGATTTATGATCTGATACTTGAC
Found at i:1843812 original size:23 final size:24
Alignment explanation
Indices: 1843759--1843848 Score: 96
Period size: 24 Copynumber: 3.8 Consensus size: 24
1843749 TCGATTTGAT
*
1843759 TTCTGATTTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
*
1843783 TTATGATCTGATA-TATGAC-TGGA
1 TTCTGATCTGATACT-TGACATGGA
* *
1843806 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
1843829 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
1843849 TGATTTATGT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
23 22 0.39
24 34 0.61
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.42
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:1843842 original size:47 final size:47
Alignment explanation
Indices: 1843759--1843850 Score: 107
Period size: 47 Copynumber: 2.0 Consensus size: 47
1843749 TCGATTTGAT
* *
1843759 TTCTGATTTGATACTTGACATGGATTATGATCTGATA-TATGACTGGA
1 TTCTGATCTGATACTTGACATGGATTATGATATGATACT-TGACTGGA
* * *
1843806 TTCTGATCTGTTACTTGACCT-GATTTCTGATATGATACTTGACTG
1 TTCTGATCTGATACTTGACATGGA-TTATGATATGATACTTGACTG
1843851 ATTTATGTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
46 2 0.05
47 35 0.92
48 1 0.03
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (47 bp):
TTCTGATCTGATACTTGACATGGATTATGATATGATACTTGACTGGA
Found at i:1846047 original size:13 final size:13
Alignment explanation
Indices: 1846044--1846084 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
1846034 CCGTTGACCC
*
1846044 GACCCGACCCATT
1 GACCCGACCCGTT
1846057 -ACCCGACCCGTT
1 GACCCGACCCGTT
1846069 GACCCGACCCGTT
1 GACCCGACCCGTT
1846082 GAC
1 GAC
1846085 GTTGACCAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.20, C:0.46, G:0.20, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1846060 original size:17 final size:18
Alignment explanation
Indices: 1846029--1846066 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1846019 CACAACCCAA
*
1846029 CCGACCCGTTGACCCGAC
1 CCGACCCATTGACCCGAC
1846047 CCGACCCATT-ACCCGAC
1 CCGACCCATTGACCCGAC
1846064 CCG
1 CCG
1846067 TTGACCCGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.18, C:0.53, G:0.18, T:0.11
Consensus pattern (18 bp):
CCGACCCATTGACCCGAC
Found at i:1846114 original size:16 final size:14
Alignment explanation
Indices: 1846074--1846105 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1846064 CCGTTGACCC
*
1846074 GACCCGTTGACGTT
1 GACCAGTTGACGTT
1846088 GACCAGTTGACGTT
1 GACCAGTTGACGTT
1846102 GACC
1 GACC
1846106 GGAGTTGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (14 bp):
GACCAGTTGACGTT
Found at i:1847404 original size:17 final size:17
Alignment explanation
Indices: 1847379--1847413 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1847369 TCGAAAGGAC
*
1847379 TGAAGTAAATGATAAGA
1 TGAAGTAAATAATAAGA
*
1847396 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
1847413 T
1 T
1847414 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (17 bp):
TGAAGTAAATAATAAGA
Found at i:1848566 original size:24 final size:24
Alignment explanation
Indices: 1848542--1848625 Score: 86
Period size: 24 Copynumber: 3.6 Consensus size: 24
1848532 TCGATTTGAT
1848542 TTCTGAT-TGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
* *
1848565 TTATGATCTGATA--TGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
1848587 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
1848610 TTTCTGATATGATACT
1 -TTCTGATCTGATACT
1848626 GACCTGATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
22 19 0.38
23 8 0.16
24 23 0.46
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:1854860 original size:30 final size:29
Alignment explanation
Indices: 1854826--1854883 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
1854816 CTCAACAACC
1854826 AAGTGTAGGTAGAGA-TCACTTCAAAAAAAA
1 AAGTGTAGGTAGAGACT-ACTT-AAAAAAAA
1854856 AAGTGTAGGTAGAGACTACTTAAAAAAA
1 AAGTGTAGGTAGAGACTACTTAAAAAAA
1854884 GTTTAGGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 7 0.26
30 19 0.70
31 1 0.04
ACGTcount: A:0.50, C:0.09, G:0.21, T:0.21
Consensus pattern (29 bp):
AAGTGTAGGTAGAGACTACTTAAAAAAAA
Found at i:1857012 original size:21 final size:21
Alignment explanation
Indices: 1856983--1857029 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1856973 ATTCTGACTA
1856983 TCGCATTGCAATTTCCCAAAT
1 TCGCATTGCAATTTCCCAAAT
* * * *
1857004 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCAATTTCCCAAAT
1857025 TCGCA
1 TCGCA
1857030 ATGCGAATAC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (21 bp):
TCGCATTGCAATTTCCCAAAT
Found at i:1857050 original size:20 final size:20
Alignment explanation
Indices: 1857025--1857190 Score: 196
Period size: 20 Copynumber: 8.3 Consensus size: 20
1857015 TTTTCCTAAT
*
1857025 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
1857045 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
* *
1857065 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCG-ATTACGTAAA
1857086 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
*
1857106 TCGCATTGCGATTACGT-AA
1 TCGCAATGCGATTACGTAAA
*
1857125 TCGCATTGCGATTTACGT-AA
1 TCGCAATGCGA-TTACGTAAA
*
1857145 TCGCATTGCGATTTACGT-AA
1 TCGCAATGCGA-TTACGTAAA
* *
1857165 TCGCATTGCAATTTA-GTAAA
1 TCGCAATGCGA-TTACGTAAA
1857185 TCGCAA
1 TCGCAA
1857191 CGAGATTCTG
Statistics
Matches: 135, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
19 15 0.11
20 102 0.76
21 18 0.13
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:1858073 original size:24 final size:24
Alignment explanation
Indices: 1858046--1858099 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
1858036 GTATTCGAAA
1858046 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTTGGTCAATACTCGGAC
*
1858070 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAC
1858094 TTTGAT
1 TTTGAT
1858100 GATTTTTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGGAC
Found at i:1860649 original size:19 final size:19
Alignment explanation
Indices: 1860607--1860665 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
1860597 CAATCATCTT
* *
1860607 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAATGC-GA
1860627 AATGACTATCGCAATGCGA
1 AATGACTATCGCAATGCGA
**
1860646 AATGAAAATCGCAATGCGA
1 AATGACTATCGCAATGCGA
1860665 A
1 A
1860666 TTTAGTTTCG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
19 20 0.57
20 15 0.43
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (19 bp):
AATGACTATCGCAATGCGA
Found at i:1860682 original size:19 final size:18
Alignment explanation
Indices: 1860660--1860716 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
1860650 AAAATCGCAA
1860660 TGCGAATTTAGTTTCGCGT
1 TGCGAATTTA-TTTCGCGT
1860679 TGCG-ATTT-TTT--CGT
1 TGCGAATTTATTTCGCGT
*
1860693 TGCGATTTTCATTTCGCGT
1 TGCGAATTT-ATTTCGCGT
1860712 TGCGA
1 TGCGA
1860717 TTTTCATTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
14 7 0.22
15 3 0.09
16 3 0.09
17 3 0.09
18 4 0.12
19 12 0.38
ACGTcount: A:0.12, C:0.18, G:0.25, T:0.46
Consensus pattern (18 bp):
TGCGAATTTATTTCGCGT
Found at i:1860717 original size:19 final size:19
Alignment explanation
Indices: 1860671--1860725 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 19
1860661 GCGAATTTAG
1860671 TTTCGCGTTGCGA-TTT--
1 TTTCGCGTTGCGATTTTCA
1860687 TTT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
1860704 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
1860723 TTT
1 TTT
1860726 GCCTTCAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.24
15 3 0.09
16 3 0.09
17 3 0.09
19 17 0.50
ACGTcount: A:0.09, C:0.18, G:0.20, T:0.53
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:1860840 original size:14 final size:14
Alignment explanation
Indices: 1860821--1860857 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1860811 CATCAATTAA
1860821 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1860835 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1860849 ACAAATCAA
1 ACAAATCAA
1860858 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1862995 original size:94 final size:94
Alignment explanation
Indices: 1862882--1863152 Score: 380
Period size: 94 Copynumber: 3.0 Consensus size: 94
1862872 GCATTACTTC
* *
1862882 AACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTTTAGCAGA
1 AACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGA
1862947 ATTGGCAGCAAACGAACAAATTTACTTTA
66 ATTGGCAGCAAACGAACAAATTTACTTTA
*
1862976 AACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCATA
1 AACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGA
* * *
1863041 ATTGGCAGC-AAC---CGAATATAC-TTC
66 ATTGGCAGCAAACGAACAAATTTACTTTA
*
1863065 AACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGTTTAGCAG
1 AACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAG
* * *
1863126 TATTGGCAGCAACCGAATAAATTTACT
65 AATTGGCAGCAAACGAACAAATTTACT
1863153 AACCAATCTA
Statistics
Matches: 158, Mismatches: 13, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
86 24 0.15
87 2 0.01
89 18 0.11
90 40 0.25
93 3 0.02
94 71 0.45
ACGTcount: A:0.48, C:0.18, G:0.13, T:0.21
Consensus pattern (94 bp):
AACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGA
ATTGGCAGCAAACGAACAAATTTACTTTA
Found at i:1864862 original size:20 final size:19
Alignment explanation
Indices: 1864817--1864906 Score: 57
Period size: 20 Copynumber: 4.9 Consensus size: 19
1864807 TCTTTTGGTT
*
1864817 GAAATGAAAATCGCAACTA
1 GAAATGAAAATCGCAACCA
* *
1864836 GAGAATGAAAATCTCAACGCG
1 GA-AATGAAAATCGCAAC-CA
**
1864857 GAAATGACTATCGCAA-C-
1 GAAATGAAAATCGCAACCA
*
1864874 G--A-GAGAATCGCAA-CA
1 GAAATGAAAATCGCAACCA
1864889 CGAAATGAAAATCGCAAC
1 -GAAATGAAAATCGCAAC
1864907 GAGAGAATCG
Statistics
Matches: 54, Mismatches: 9, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 1 0.02
17 1 0.02
18 2 0.04
19 12 0.22
20 25 0.46
21 2 0.04
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACCA
Found at i:1864885 original size:14 final size:14
Alignment explanation
Indices: 1864866--1864919 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1864856 GGAAATGACT
1864866 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
1864880 ATCGCAACACGAAATGAAA
1 ATCGC-A-ACG--A-GAGA
1864899 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1864913 ATCGCAA
1 ATCGCAA
1864920 TGCGATTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 15 0.45
15 2 0.06
16 3 0.09
17 3 0.09
18 2 0.06
19 8 0.24
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1864903 original size:33 final size:33
Alignment explanation
Indices: 1864857--1864919 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
1864847 TCTCAACGCG
**
1864857 GAAATGACTATCGCAACGAGAGAATCGCAACAC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACAC
1864890 GAAATGAAAATCGCAACGAGAGAATCGCAA
1 GAAATGAAAATCGCAACGAGAGAATCGCAA
1864920 TGCGATTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACAC
Found at i:1865551 original size:20 final size:20
Alignment explanation
Indices: 1865528--1865641 Score: 129
Period size: 20 Copynumber: 5.7 Consensus size: 20
1865518 CGATAGTCAG
*
1865528 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACCT
*
1865548 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACCT
*
1865568 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACCT
* * *
1865589 AATCGCGTTGCGATTTTCCT
1 ATTCGCATTGCGATTTACCT
* ** *
1865609 AATCGTGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACCT
1865629 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1865642 ATTAGGAAAA
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
20 61 0.77
21 18 0.23
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACCT
Found at i:1865580 original size:41 final size:41
Alignment explanation
Indices: 1865528--1865641 Score: 176
Period size: 41 Copynumber: 2.8 Consensus size: 41
1865518 CGATAGTCAG
1865528 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTA
* * *
1865569 ATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTA
**
1865610 A-TCGTGTTGCGATTTACGTATTCGCATTGCGA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGA
1865642 ATTAGGAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 26 0.40
41 39 0.60
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (41 bp):
ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTA
Found at i:1865662 original size:21 final size:21
Alignment explanation
Indices: 1865638--1865683 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1865628 TATTCGCATT
1865638 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
1865659 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1865680 GCGA
1 GCGA
1865684 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1866471 original size:19 final size:20
Alignment explanation
Indices: 1866442--1866481 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1866432 AAATAAAATA
* *
1866442 ATATATTAAAATTTTATTTT
1 ATATATTAAAAGTTTAATTT
1866462 ATAT-TTAAAAGTTTAATTT
1 ATATATTAAAAGTTTAATTT
1866481 A
1 A
1866482 GCTCTAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
ATATATTAAAAGTTTAATTT
Found at i:1866480 original size:20 final size:20
Alignment explanation
Indices: 1866442--1866480 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1866432 AAATAAAATA
*
1866442 ATATATTAAAATTTTATTTT
1 ATATATTAAAATTTAATTTT
1866462 ATAT-TTAAAAGTTTAATTT
1 ATATATTAAAA-TTTAATTT
1866481 AGCTCTAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
ATATATTAAAATTTAATTTT
Found at i:1867498 original size:16 final size:17
Alignment explanation
Indices: 1867479--1867530 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
1867469 TTTTTATTTT
1867479 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
1867495 AATTACTCATAA-TTT--
1 AATTACTC-TAACTTTCA
*
1867510 AATAACTCTAACTTTCA
1 AATTACTCTAACTTTCA
1867527 AATT
1 AATT
1867531 TATTCTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 10 0.34
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:1869896 original size:21 final size:21
Alignment explanation
Indices: 1869872--1869935 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
1869862 CAGTTTTCTC
1869872 AATTTTTGCAGATTTATCTGT
1 AATTTTTGCAGATTTATCTGT
* *
1869893 AATTTTT----ATTT-TTTGA
1 AATTTTTGCAGATTTATCTGT
*
1869909 ATATTTTTGCAGATTAATCTGT
1 A-ATTTTTGCAGATTTATCTGT
1869931 AATTT
1 AATTT
1869936 CTATGTAGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 12
0.65 0.10 0.24
Matches are distributed among these distances:
16 4 0.12
17 10 0.31
21 14 0.44
22 4 0.12
ACGTcount: A:0.27, C:0.06, G:0.11, T:0.56
Consensus pattern (21 bp):
AATTTTTGCAGATTTATCTGT
Found at i:1877318 original size:28 final size:25
Alignment explanation
Indices: 1877287--1877340 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 25
1877277 TAGCGTTAAT
1877287 ATTAATATTTCTGATAAAAAAATATTTA
1 ATTAATATTT-T-AT-AAAAAATATTTA
* *
1877315 ATTATTATTTTATTAAAAATATTTA
1 ATTAATATTTTATAAAAAATATTTA
1877340 A
1 A
1877341 AAAATATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.50
26 2 0.08
27 1 0.04
28 9 0.38
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
ATTAATATTTTATAAAAAATATTTA
Found at i:1878349 original size:31 final size:31
Alignment explanation
Indices: 1878242--1878353 Score: 100
Period size: 31 Copynumber: 3.5 Consensus size: 31
1878232 CATTAGGTCC
*
1878242 ATAAGGAATTATCAGTCGGTGTTGAACCTAT
1 ATAAGGAATTACCAGTCGGTGTTGAACCTAT
* * * * * *
1878273 ACAAGAAATTACCAG-CAGCGACTGAACCTGCCAG
1 ATAAGGAATTACCAGTCGGTG-TTGAACCT---AT
*
1878307 AGATAGGAATTACCAGTCGGTGTTGAACCTAT
1 ATA-AGGAATTACCAGTCGGTGTTGAACCTAT
1878339 ATAAGGAATTACCAG
1 ATAAGGAATTACCAG
1878354 CATCGACTGA
Statistics
Matches: 61, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
30 3 0.05
31 31 0.51
32 3 0.05
34 3 0.05
35 18 0.30
36 3 0.05
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (31 bp):
ATAAGGAATTACCAGTCGGTGTTGAACCTAT
Found at i:1878351 original size:66 final size:66
Alignment explanation
Indices: 1878245--1878368 Score: 212
Period size: 66 Copynumber: 1.9 Consensus size: 66
1878235 TAGGTCCATA
*
1878245 AGGAATTATCAGTCGGTGTTGAACCTATACAAGAAATTACCAGCAGCGACTGAACCTGCCAGAGA
1 AGGAATTACCAGTCGGTGTTGAACCTATACAAGAAATTACCAGCAGCGACTGAACCTGCCAGAGA
1878310 T
66 T
* * *
1878311 AGGAATTACCAGTCGGTGTTGAACCTATATAAGGAATTACCAGCATCGACTGAACCTG
1 AGGAATTACCAGTCGGTGTTGAACCTATACAAGAAATTACCAGCAGCGACTGAACCTG
1878369 TAAGAGTCTT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.23
Consensus pattern (66 bp):
AGGAATTACCAGTCGGTGTTGAACCTATACAAGAAATTACCAGCAGCGACTGAACCTGCCAGAGA
T
Found at i:1878365 original size:31 final size:31
Alignment explanation
Indices: 1878264--1878367 Score: 77
Period size: 31 Copynumber: 3.2 Consensus size: 31
1878254 CAGTCGGTGT
* *
1878264 TGAACCTATACAAGAAATTACCAGCAGCGAC
1 TGAACCTATACAAGGAATTACCAGCATCGAC
* * **
1878295 TGAACCTGCCAGAGATAGGAATTACCAG--TCGGTGT
1 TGAACCT---ATACA-AGGAATTACCAGCATC-G-AC
*
1878330 TGAACCTATATAAGGAATTACCAGCATCGAC
1 TGAACCTATACAAGGAATTACCAGCATCGAC
1878361 TGAACCT
1 TGAACCT
1878368 GTAAGAGTCT
Statistics
Matches: 55, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
31 26 0.47
32 4 0.07
33 3 0.05
34 4 0.07
35 18 0.33
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (31 bp):
TGAACCTATACAAGGAATTACCAGCATCGAC
Found at i:1883930 original size:10 final size:9
Alignment explanation
Indices: 1883912--1883945 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 9
1883902 GCTTATTACC
1883912 TTTTTTTCT
1 TTTTTTTCT
1883921 TTTCTTTTCT
1 TTT-TTTTCT
1883931 TTTTTTT-T
1 TTTTTTTCT
1883939 TTTTTTT
1 TTTTTTT
1883946 GCTCCCTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.33
9 7 0.29
10 9 0.38
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:1885373 original size:30 final size:30
Alignment explanation
Indices: 1885337--1885583 Score: 279
Period size: 30 Copynumber: 8.2 Consensus size: 30
1885327 GTAGGTCAAC
* *
1885337 CCTTTAAGTTTATATTTTTACTATTTTAGT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGT
* *
1885367 CCTTTAA-TTT-TATGTTTTTGTTATTTTAAT
1 CCTTTAAGTTTCTAT-TTTTT-CTATTTTAGT
*
1885397 CTTTTAAGTTTCTATTTTTT-TATTTTAGT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGT
* * * *
1885426 CCTTTAACTTTTTGTTTTTTTTCTTTTTTAGT
1 CCTTTAA--GTTTCTATTTTTTCTATTTTAGT
*
1885458 CCTTTAAGTTTTTATTTTTTCTATTTTAGT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGT
1885488 CCTTTAAGTTTCTA-TTTTTCTATTTTAGT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGT
*
1885517 CCTTTAACTTTCTATTTTTTCTATTTTAGT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGT
* * *
1885547 CCCTTAAGTTCCTATTTTTGT-TATTTTGGT
1 CCTTTAAGTTTCTATTTTT-TCTATTTTAGT
*
1885577 CCATTAA
1 CCTTTAA
1885584 ATCACTGAGT
Statistics
Matches: 187, Mismatches: 21, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
28 3 0.02
29 49 0.26
30 98 0.52
31 19 0.10
32 18 0.10
ACGTcount: A:0.17, C:0.12, G:0.07, T:0.64
Consensus pattern (30 bp):
CCTTTAAGTTTCTATTTTTTCTATTTTAGT
Found at i:1885462 original size:91 final size:88
Alignment explanation
Indices: 1885337--1885573 Score: 289
Period size: 91 Copynumber: 2.6 Consensus size: 88
1885327 GTAGGTCAAC
* * * *
1885337 CCTTTAAGTTTATATTTTTACTATTTTAGTCCTTTAATTTTATGTTTTTGTTATTTTAATCTTTT
1 CCTTTAACTTTCTATTTTTTCTATTTTAGTCCTTTAATTTTAT-TTTTTGTTATTTTAATCCTTT
*
1885402 AAGTTTCTATTTTTTTATTTTAGT
65 AAGTTTCTATTTTTCTATTTTAGT
* * * * *
1885426 CCTTTAACTTTTTGTTTTTTTTCTTTTTTAGTCCTTTAAGTTTTTATTTTTT-CTATTTTAGTCC
1 CCTTTAAC--TTTCTATTTTTTCTATTTTAGTCCTTTAA--TTTTATTTTTTGTTATTTTAATCC
1885490 TTTAAGTTTCTATTTTTCTATTTTAGT
62 TTTAAGTTTCTATTTTTCTATTTTAGT
* *
1885517 CCTTTAACTTTCTATTTTTTCTATTTTAGTCCCTTAAGTTCCTA-TTTTTGTTATTTT
1 CCTTTAACTTTCTATTTTTTCTATTTTAGTCCTTTAA-TT-TTATTTTTTGTTATTTT
1885574 GGTCCATTAA
Statistics
Matches: 126, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
88 7 0.06
89 40 0.32
91 68 0.54
92 5 0.04
93 6 0.05
ACGTcount: A:0.17, C:0.12, G:0.06, T:0.65
Consensus pattern (88 bp):
CCTTTAACTTTCTATTTTTTCTATTTTAGTCCTTTAATTTTATTTTTTGTTATTTTAATCCTTTA
AGTTTCTATTTTTCTATTTTAGT
Found at i:1885516 original size:59 final size:60
Alignment explanation
Indices: 1885337--1885583 Score: 282
Period size: 59 Copynumber: 4.1 Consensus size: 60
1885327 GTAGGTCAAC
* * * * * * *
1885337 CCTTTAAGTTTATATTTTTACTATTTTAGTCCTTTAATTTTATGTTTTTGTTATTTTAAT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGTCCTTTAAGTTTCTATTTTTGCTATTTTAGT
* * * * * *
1885397 CTTTTAAGTTTCTATTTTTT-TATTTTAGTCCTTTAACTTTTTGTTTTTTTTCTTTTTTAGT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGTCCTTTAA--GTTTCTATTTTTGCTATTTTAGT
*
1885458 CCTTTAAGTTTTTATTTTTTCTATTTTAGTCCTTTAAGTTTCTATTTTT-CTATTTTAGT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGTCCTTTAAGTTTCTATTTTTGCTATTTTAGT
* * * * *
1885517 CCTTTAACTTTCTATTTTTTCTATTTTAGTCCCTTAAGTTCCTATTTTTGTTATTTTGGT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGTCCTTTAAGTTTCTATTTTTGCTATTTTAGT
*
1885577 CCATTAA
1 CCTTTAA
1885584 ATCACTGAGT
Statistics
Matches: 161, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
59 70 0.43
60 40 0.25
61 35 0.22
62 16 0.10
ACGTcount: A:0.17, C:0.12, G:0.07, T:0.64
Consensus pattern (60 bp):
CCTTTAAGTTTCTATTTTTTCTATTTTAGTCCTTTAAGTTTCTATTTTTGCTATTTTAGT
Found at i:1891042 original size:29 final size:29
Alignment explanation
Indices: 1891010--1891066 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1891000 ATTTCAAAAT
1891010 TATAATTATGAAA-AAAATATTAATTTATA
1 TATAATTAT-AAATAAAATATTAATTTATA
* *
1891039 TATATTTATAAATAAAATATTTATTTAT
1 TATAATTATAAATAAAATATTAATTTAT
1891067 TTAGAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TATAATTATAAATAAAATATTAATTTATA
Found at i:1891161 original size:20 final size:19
Alignment explanation
Indices: 1891122--1891163 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1891112 TTTCTTCGAT
1891122 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1891141 ATTAAAATAATTAATATATA
1 ATTAAAA-AATAAATAAATA
1891161 ATT
1 ATT
1891164 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1893144 original size:76 final size:76
Alignment explanation
Indices: 1893018--1893961 Score: 1674
Period size: 76 Copynumber: 12.4 Consensus size: 76
1893008 AGGTCCTAAA
* *
1893018 AAACATCATGCACTGAAGGGA-TTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGTA-GGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
1893082 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* * *
1893094 AAACATGATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1893159 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
1893170 AAATATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCACCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1893235 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1893246 AAACATCATGCACTGTAGGACTTACAGATGACACTAAGGCTTTGAAAACATCCAAAAAGCTCCCG
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACAT-CAAAAAGCTCCCG
1893311 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* * *
1893323 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1893388 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1893399 AAATATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1893464 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1893475 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1893540 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
1893551 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1893616 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1893627 AAACATCATGCATTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1893692 AGGCTTTTTGG
66 AGGCTTTTTGG
1893703 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
1893768 AGGCTTTTTTG
66 AGGCTTTTTGG
*
1893779 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAATATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1893844 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1893855 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCCAAAAAGCTCCCG
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACAT-CAAAAAGCTCCCG
1893920 AAGGCTTTTTGG
65 AAGGCTTTTTGG
*
1893932 AAACATCATGCACTGCAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
1893962 TGAGAAATAG
Statistics
Matches: 833, Mismatches: 32, Indels: 5
0.96 0.04 0.01
Matches are distributed among these distances:
75 3 0.00
76 705 0.85
77 125 0.15
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:1899436 original size:17 final size:16
Alignment explanation
Indices: 1899416--1899519 Score: 66
Period size: 17 Copynumber: 6.2 Consensus size: 16
1899406 ATTTCTCCCC
1899416 TTTTTCTTTTTCCCTTT
1 TTTTTCTTTTT-CCTTT
*
1899433 TTTTCCTTTTTTCTCATTT
1 TTTTTC-TTTTTC-C-TTT
* * *
1899452 TTCTT-TTTTTCATCT
1 TTTTTCTTTTTCCTTT
*
1899467 TTTTCCTTTTTTCCTTT
1 TTTTTC-TTTTTCCTTT
* *
1899484 TTTCTCATTTTCCTTT
1 TTTTTCTTTTTCCTTT
* *
1899500 TTTCATCTTTTTTCTTT
1 TTT-TTCTTTTTCCTTT
1899517 TTT
1 TTT
1899520 CTTTCTTTGC
Statistics
Matches: 66, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
15 5 0.08
16 12 0.18
17 37 0.56
18 6 0.09
19 6 0.09
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTCTTTTTCCTTT
Found at i:1899490 original size:42 final size:41
Alignment explanation
Indices: 1899420--1899520 Score: 157
Period size: 41 Copynumber: 2.4 Consensus size: 41
1899410 CTCCCCTTTT
*
1899420 TCTTTTTCCCTTTTTTTCCTTTTTTCTCATTTTTCTTTTTTTCA
1 TCTTTTT-CC-TTTTTTCCTTTTTTCTCA-TTTTCCTTTTTTCA
1899464 TCTTTTTCCTTTTTTCCTTTTTTCTCATTTTCCTTTTTTCA
1 TCTTTTTCCTTTTTTCCTTTTTTCTCATTTTCCTTTTTTCA
*
1899505 TCTTTTTTCTTTTTTC
1 TCTTTTTCCTTTTTTC
1899521 TTTCTTTGCT
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
41 28 0.51
42 18 0.33
43 2 0.04
44 7 0.13
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (41 bp):
TCTTTTTCCTTTTTTCCTTTTTTCTCATTTTCCTTTTTTCA
Found at i:1899518 original size:8 final size:8
Alignment explanation
Indices: 1899416--1899523 Score: 83
Period size: 8 Copynumber: 13.1 Consensus size: 8
1899406 ATTTCTCCCC
1899416 TTTTTCTT
1 TTTTTCTT
**
1899424 TTTCCCTT
1 TTTTTCTT
*
1899432 TTTTTCCT
1 TTTTTCTT
*
1899440 TTTTTCTCA
1 TTTTTCT-T
1899449 TTTTTCTT
1 TTTTTCTT
*
1899457 TTTTTCATC
1 TTTTTC-TT
*
1899466 TTTTTCCT
1 TTTTTCTT
*
1899474 TTTTTCCT
1 TTTTTCTT
*
1899482 TTTTTCTC
1 TTTTTCTT
* *
1899490 ATTTTCCT
1 TTTTTCTT
1899498 TTTTTCATCT
1 TTTTTC-T-T
1899508 TTTTTC-T
1 TTTTTCTT
1899515 TTTTTCTT
1 TTTTTCTT
1899523 T
1 T
1899524 CTTTGCTGGA
Statistics
Matches: 77, Mismatches: 18, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
7 7 0.09
8 49 0.64
9 14 0.18
10 7 0.09
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTCTT
Found at i:1899520 original size:17 final size:16
Alignment explanation
Indices: 1899431--1899521 Score: 89
Period size: 17 Copynumber: 5.5 Consensus size: 16
1899421 CTTTTTCCCT
1899431 TTTTTTC-CTTTTTTC
1 TTTTTTCTCTTTTTTC
1899446 TCATTTTTCT-TTTTTTC
1 T--TTTTTCTCTTTTTTC
1899463 ATCTTTTTC-CTTTTTTCC
1 -T-TTTTTCTCTTTTTT-C
* *
1899481 TTTTTTCTCATTTTCC
1 TTTTTTCTCTTTTTTC
1899497 TTTTTTCATCTTTTTTC
1 TTTTTTC-TCTTTTTTC
1899514 TTTTTTCT
1 TTTTTTCT
1899522 TTCTTTGCTG
Statistics
Matches: 63, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
15 1 0.02
16 15 0.24
17 45 0.71
18 2 0.03
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTCTCTTTTTTC
Found at i:1904663 original size:24 final size:22
Alignment explanation
Indices: 1904624--1904685 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
1904614 TCTAACAGAC
*
1904624 AAATAAAATAATTAATACCTGAATA
1 AAAT-AAATAAATAATA--TGAATA
*
1904649 AAATAAATAAATAATATTAATA
1 AAATAAATAAATAATATGAATA
*
1904671 AAAT-AATAAAAAATA
1 AAATAAATAAATAATA
1904686 ATAAGTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 10 0.29
22 9 0.26
24 11 0.32
25 4 0.12
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (22 bp):
AAATAAATAAATAATATGAATA
Found at i:1904673 original size:22 final size:21
Alignment explanation
Indices: 1904645--1904685 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1904635 TTAATACCTG
*
1904645 AATAAAATAAATAAATAATATT
1 AATAAAAT-AATAAAAAATATT
1904667 AATAAAATAATAAAAAATA
1 AATAAAATAATAAAAAATA
1904686 ATAAGTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AATAAAATAATAAAAAATATT
Found at i:1904678 original size:25 final size:25
Alignment explanation
Indices: 1904650--1904698 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1904640 ACCTGAATAA
*
1904650 AATAAATAAATAAT-ATTAATAAAAT
1 AATAAA-AAATAATAAGTAATAAAAT
1904675 AATAAAAAATAATAAGTAATAAAA
1 AATAAAAAATAATAAGTAATAAAA
1904699 AATTTGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (25 bp):
AATAAAAAATAATAAGTAATAAAAT
Found at i:1904687 original size:18 final size:18
Alignment explanation
Indices: 1904645--1904701 Score: 62
Period size: 17 Copynumber: 3.0 Consensus size: 18
1904635 TTAATACCTG
1904645 AATAAAATAAATAAATAATATT
1 AATAAAAT-AATAAA-AA-A-T
1904667 AATAAAATAATAAAAAAT
1 AATAAAATAATAAAAAAT
*
1904685 AAT-AAGTAATAAAAAAT
1 AATAAAATAATAAAAAAT
1904702 TTGAAAGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
17 13 0.38
18 4 0.12
19 1 0.03
20 2 0.06
21 6 0.18
22 8 0.24
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
AATAAAATAATAAAAAAT
Found at i:1905207 original size:29 final size:29
Alignment explanation
Indices: 1905175--1905231 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1905165 ATTTCAAAAT
1905175 TATAATTATGAAA-AAAATATTAATTTATA
1 TATAATTAT-AAATAAAATATTAATTTATA
* *
1905204 TATATTTATAAATAAAATATTTATTTAT
1 TATAATTATAAATAAAATATTAATTTAT
1905232 TTAGAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TATAATTATAAATAAAATATTAATTTATA
Found at i:1905416 original size:119 final size:117
Alignment explanation
Indices: 1905196--1905428 Score: 282
Period size: 117 Copynumber: 2.0 Consensus size: 117
1905186 AAAAAATATT
* * *
1905196 AATTTATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGT
1 AATTAATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAAGACTACTAGGT
*
1905261 GCCTTAAGACAGCTCTTTTCTTCGATATTAAAAAATAAATAATAATTAAAAC
66 GCCTTAAGACAGCTCTTTTCTTCAATATTAAAAAATAAATAATAATTAAAAC
*
1905313 AATTAATATATAATTTATAAAATAAGATATTTATTTATTTA-AAA-AT-AGAAAATAGACATAC-
1 AATTAATATAT-ATTTAT-AAATAAAATATTTATTTATTTAGAAATATCAGAAAA-AGAC-TACT
* ** * *
1905374 AGTTGTTTTAAGACTGCTC-TTTCTT-AATATTGAAAAATAAATAA-ATATTAAAAC
62 AGGTGCCTTAAGACAGCTCTTTTCTTCAATATTAAAAAATAAATAATA-ATTAAAAC
1905428 A
1 A
1905429 TGATTAAAAT
Statistics
Matches: 101, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
114 1 0.01
115 26 0.26
116 12 0.12
117 30 0.30
118 11 0.11
119 21 0.21
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.38
Consensus pattern (117 bp):
AATTAATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAAGACTACTAGGT
GCCTTAAGACAGCTCTTTTCTTCAATATTAAAAAATAAATAATAATTAAAAC
Found at i:1905495 original size:2 final size:2
Alignment explanation
Indices: 1905480--1905516 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1905470 AGTAAAATAA
*
1905480 AT AT AT TT AT -T 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
1905517 GGCTAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:1916025 original size:15 final size:17
Alignment explanation
Indices: 1916005--1916036 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1915995 GTTTAAAGTA
1916005 ATTTT-AAGA-AAAAAT
1 ATTTTAAAGATAAAAAT
1916020 ATTTTAAAGATAAAAAT
1 ATTTTAAAGATAAAAAT
1916037 TAATCGGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 4 0.27
17 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (17 bp):
ATTTTAAAGATAAAAAT
Found at i:1916180 original size:22 final size:22
Alignment explanation
Indices: 1916152--1916196 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1916142 CGTCTTAAAT
1916152 GTGGAACTTGCAAATTCGAGTA
1 GTGGAACTTGCAAATTCGAGTA
1916174 GTGGAACTTGCAAATTCGAGTA
1 GTGGAACTTGCAAATTCGAGTA
1916196 G
1 G
1916197 AAAATTGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (22 bp):
GTGGAACTTGCAAATTCGAGTA
Found at i:1921556 original size:15 final size:15
Alignment explanation
Indices: 1921536--1921566 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1921526 CAACAAATAG
1921536 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1921551 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1921566 A
1 A
1921567 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1921763 original size:20 final size:20
Alignment explanation
Indices: 1921727--1921764 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1921717 ATCTTATTCT
**
1921727 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1921747 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1921765 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1923183 original size:20 final size:20
Alignment explanation
Indices: 1923134--1923184 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1923124 TATACCTAAG
*
1923134 TAAATTTTTAATATTTGTAT
1 TAAAATTTTAATATTTGTAT
*
1923154 TATAAA-TTTAATATTTTTAT
1 TA-AAATTTTAATATTTGTAT
1923174 TAAAATTTTAA
1 TAAAATTTTAA
1923185 CTTTGTTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 3 0.11
20 22 0.81
21 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TAAAATTTTAATATTTGTAT
Found at i:1923285 original size:16 final size:18
Alignment explanation
Indices: 1923255--1923298 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
1923245 CTTTATTTAA
1923255 AATTTGTG-TCTCATG-T
1 AATTTGTGTTCTCATGTT
1923271 AATTTGTGTTC-CATGTT
1 AATTTGTGTTCTCATGTT
*
1923288 ATTTTGTGTTC
1 AATTTGTGTTC
1923299 GTAAAAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.16, C:0.11, G:0.18, T:0.55
Consensus pattern (18 bp):
AATTTGTGTTCTCATGTT
Found at i:1923567 original size:33 final size:33
Alignment explanation
Indices: 1923530--1923620 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 33
1923520 AAATAATAAC
1923530 TATTAAATTATTATCAAACGTGGTACT-AGTGGT
1 TATTAAATTATTATCAAACGTGGTACTGA-TGGT
*
1923563 TATTAAATTATTATCAAATGTGGTACTGATGGT
1 TATTAAATTATTATCAAACGTGGTACTGATGGT
* * *
1923596 TACTAAACTATTATCAAAGGTGGTA
1 TATTAAATTATTATCAAACGTGGTA
1923621 ATTAACTATT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 52 0.98
34 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (33 bp):
TATTAAATTATTATCAAACGTGGTACTGATGGT
Found at i:1923857 original size:16 final size:16
Alignment explanation
Indices: 1923828--1923952 Score: 58
Period size: 16 Copynumber: 7.8 Consensus size: 16
1923818 GTTCAGGTTA
* * *
1923828 TTTCGGTTCAGATTGT
1 TTTCGATTCGGATTAT
1923844 TTTCGATTCGGATTAAT
1 TTTCGATTCGGATT-AT
*
1923861 TTT-GATTCGGTTTAT
1 TTTCGATTCGGATTAT
* ** *
1923876 TTTCGGTTATGATTGTT
1 TTTCGATTCGGATT-AT
* **
1923893 TTTTG-TTC-GAGTTGC
1 TTTCGATTCGGA-TTAT
1923908 TTTCGATTCGGATTAT
1 TTTCGATTCGGATTAT
* * ** *
1923924 TTTTGGTTCAAACTAT
1 TTTCGATTCGGATTAT
1923940 TTTCGATTCGGAT
1 TTTCGATTCGGAT
1923953 CAAATTGGAT
Statistics
Matches: 77, Mismatches: 26, Indels: 12
0.67 0.23 0.10
Matches are distributed among these distances:
15 11 0.14
16 55 0.71
17 11 0.14
ACGTcount: A:0.16, C:0.11, G:0.21, T:0.52
Consensus pattern (16 bp):
TTTCGATTCGGATTAT
Found at i:1927207 original size:5 final size:5
Alignment explanation
Indices: 1927197--1927287 Score: 175
Period size: 5 Copynumber: 18.4 Consensus size: 5
1927187 CTTGAATATA
1927197 TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG T-ATG TAATG
1 TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG
1927246 TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG TA
1 TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG TA
1927288 TATAATAATA
Statistics
Matches: 85, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.05
5 81 0.95
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.41
Consensus pattern (5 bp):
TAATG
Found at i:1927297 original size:3 final size:3
Alignment explanation
Indices: 1927289--1927346 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
1927279 TGTAATGTAT
1927289 ATA ATA AT- ATA AT- ATA AT- ATA ATA ATA AT- ATA AT- ATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
1927330 ATA ATA AT- ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA
1927347 CTAGTATAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
2 12 0.25
3 33 0.69
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:1927300 original size:5 final size:5
Alignment explanation
Indices: 1927194--1927539 Score: 124
Period size: 5 Copynumber: 69.2 Consensus size: 5
1927184 TTACTTGAAT
* * * * * * * * *
1927194 ATATA ATGTA ATGTA ATGTA ATGTA ATGTA ATGTA ATGTA ATGT- ATGTA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * * * * * * * *
1927243 ATGTA ATGTA ATGTA ATGTA ATGTA ATGTA ATGTA ATGTA ATGTA TATAATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA -AT-ATA
1927295 ATATA ATATA ATATA ATAATA ATATA ATATA ATA-A ATAATA ATAT- A-ATA
1 ATATA ATATA ATATA AT-ATA ATATA ATATA ATATA AT-ATA ATATA ATATA
* * * * * *
1927344 ATACTA GTATA ATATA TAGTATA GTATA GTA-C A-ATA GTATA ATACA
1 ATA-TA ATATA ATATA -A-TATA ATATA ATATA ATATA ATATA ATATA
* * * * * * *
1927390 GTAAGTA CATATA GTATA GTATA GTATA GTATA ATATA GTACA ATAT-
1 AT-A-TA -ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * *
1927437 ATAGTA CA-ATA ATAT- ATATA ATACA ATATA TTAT- ATA-A ATATA CTAT-
1 ATA-TA -ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * * * * *
1927484 ATATT ATCTT ATATA ATATA CTATA ATATA TTATA CTA-A ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1927533 TATATA A
1 -ATATA A
1927540 AAGGTCTCGA
Statistics
Matches: 281, Mismatches: 34, Indels: 52
0.77 0.09 0.14
Matches are distributed among these distances:
3 3 0.01
4 28 0.10
5 214 0.76
6 26 0.09
7 9 0.03
8 1 0.00
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:1927300 original size:8 final size:8
Alignment explanation
Indices: 1927287--1927346 Score: 79
Period size: 8 Copynumber: 7.4 Consensus size: 8
1927277 AATGTAATGT
1927287 ATATAATA
1 ATATAATA
1927295 ATATAATATA
1 ATAT-A-ATA
1927305 ATATAATA
1 ATATAATA
1927313 ATA-ATATA
1 ATATA-ATA
1927321 ATATAATA
1 ATATAATA
1927329 A-ATAATA
1 ATATAATA
1927336 ATATAATA
1 ATATAATA
1927344 ATA
1 ATA
1927347 CTAGTATAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
7 8 0.17
8 29 0.62
9 3 0.06
10 7 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
ATATAATA
Found at i:1927386 original size:41 final size:37
Alignment explanation
Indices: 1927341--1927442 Score: 118
Period size: 41 Copynumber: 2.6 Consensus size: 37
1927331 TAATAATATA
1927341 ATAATACTAGTATAATATATAGTATAGTATAGTACAATAGT
1 ATAATACTAGTA-AATATATAGTATAGTATAGT---ATAGT
*
1927382 ATAATAC-AGTAAGTACATATAGTATAGTATAGTATAGT
1 ATAATACTAGTAA--ATATATAGTATAGTATAGTATAGT
1927420 ATAATA-TAGTACAATATATAGTA
1 ATAATACTAGTA-AATATATAGTA
1927443 CAATAATATA
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
37 9 0.16
38 15 0.27
39 2 0.04
40 4 0.07
41 25 0.45
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.35
Consensus pattern (37 bp):
ATAATACTAGTAAATATATAGTATAGTATAGTATAGT
Found at i:1927443 original size:46 final size:45
Alignment explanation
Indices: 1927349--1927456 Score: 116
Period size: 46 Copynumber: 2.4 Consensus size: 45
1927339 TAATAATACT
* * *
1927349 AGTATAAT-ATATAGTATAGTATAGTACAATAGTATAATACAGTA
1 AGTACAATAATATAGTATAGTATAGTAAAATAGTACAATACAGTA
* *
1927393 AGTACATATAGTATAGTATAGTATAGTATAATATAGTACAATATA-T-
1 AGTACA-ATAATATAGTATAGTATAGTA-AA-ATAGTACAATACAGTA
1927439 AGTACAATAATATA-TATA
1 AGTACAATAATATAGTATA
1927457 ATACAATATA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
44 9 0.17
45 9 0.17
46 23 0.43
47 2 0.04
48 11 0.20
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.35
Consensus pattern (45 bp):
AGTACAATAATATAGTATAGTATAGTAAAATAGTACAATACAGTA
Found at i:1927453 original size:2 final size:2
Alignment explanation
Indices: 1927448--1927538 Score: 56
Period size: 2 Copynumber: 48.5 Consensus size: 2
1927438 TAGTACAATA
* *
1927448 AT AT AT AT A- AT AC A- AT AT AT -T AT AT AA AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* *
1927488 -T AT CT -T AT AT A- AT AT ACT AT A- AT AT AT -T AT ACT AA AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT
1927527 A- AT AT AT AT AT A
1 AT AT AT AT AT AT A
1927539 AAAGGTCTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 24
0.70 0.06 0.24
Matches are distributed among these distances:
1 9 0.13
2 56 0.79
3 6 0.08
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1927506 original size:24 final size:25
Alignment explanation
Indices: 1927463--1927535 Score: 98
Period size: 24 Copynumber: 3.0 Consensus size: 25
1927453 TATAATACAA
1927463 TATATTATATAAATATACTATATAT
1 TATATTATATAAATATACTATATAT
*
1927488 TATCTTATAT-AATATACTATA-A-
1 TATATTATATAAATATACTATATAT
*
1927510 TATATTATACTAAATATAATATATAT
1 TATATTATA-TAAATATACTATATAT
1927536 ATAAAAGGTC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 8 0.20
23 2 0.05
24 21 0.51
25 10 0.24
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (25 bp):
TATATTATATAAATATACTATATAT
Found at i:1938149 original size:31 final size:32
Alignment explanation
Indices: 1938097--1938181 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 32
1938087 CTAATGTGAC
* * *
1938097 TCTTAGGTAGGCTCTGCGGCCCTGAGAT-TAT
1 TCTTAGGTAGGCCCTGTGGCCCTAAGATGTAT
* *
1938128 TCTTGGGTAGGCCCTGTGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGTGGCCCTAAGATGTAT
*
1938160 TCTTAGGTAGGCCCCGTGGCCC
1 TCTTAGGTAGGCCCTGTGGCCC
1938182 CGAACTTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 24 0.52
32 22 0.48
ACGTcount: A:0.13, C:0.26, G:0.32, T:0.29
Consensus pattern (32 bp):
TCTTAGGTAGGCCCTGTGGCCCTAAGATGTAT
Found at i:1940147 original size:5 final size:5
Alignment explanation
Indices: 1940137--1940195 Score: 55
Period size: 5 Copynumber: 11.4 Consensus size: 5
1940127 AAAATAAATG
* * * *
1940137 TACAA TACAA TATAA TGTACAA TACAA TACAA TGCAA TGCAC TACAA TACAA
1 TACAA TACAA TACAA --TACAA TACAA TACAA TACAA TACAA TACAA TACAA
*
1940189 TATAA TA
1 TACAA TA
1940196 TATATTATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
5 41 0.91
7 4 0.09
ACGTcount: A:0.53, C:0.17, G:0.05, T:0.25
Consensus pattern (5 bp):
TACAA
Found at i:1940155 original size:17 final size:16
Alignment explanation
Indices: 1940129--1940170 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 16
1940119 TAAATATAAA
1940129 AATAAATGTACAATAC
1 AATAAATGTACAATAC
1940145 AATATAATGTACAATAC
1 AATA-AATGTACAATAC
1940162 AATACAATG
1 AATA-AATG
1940171 CAATGCACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.26
Consensus pattern (16 bp):
AATAAATGTACAATAC
Found at i:1940239 original size:20 final size:19
Alignment explanation
Indices: 1940216--1940270 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
1940206 AATACAAATT
1940216 TATATAATATATTATATAAG
1 TATATAATATA-TATATAAG
*
1940236 TATATTATATA-ATATAAAG
1 TATATAATATATATAT-AAG
*
1940255 -ATATATTATATATATA
1 TATATAATATATATATA
1940271 CTATTAGGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 13 0.43
19 7 0.23
20 10 0.33
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (19 bp):
TATATAATATATATATAAG
Found at i:1940246 original size:27 final size:26
Alignment explanation
Indices: 1940195--1940251 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
1940185 ACAATATAAT
1940195 ATATATTATATAATACAAATTTATATA
1 ATATATTATATAATA-AAATTTATATA
*
1940222 ATATATTATATAAGT-ATA-TTATATA
1 ATATATTATATAA-TAAAATTTATATA
1940247 ATATA
1 ATATA
1940252 AAGATATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 12 0.43
26 2 0.07
27 13 0.46
28 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
ATATATTATATAATAAAATTTATATA
Found at i:1940719 original size:27 final size:26
Alignment explanation
Indices: 1940687--1940835 Score: 110
Period size: 27 Copynumber: 5.6 Consensus size: 26
1940677 TATACTATAC
*
1940687 ATACTATATAACATAATATTATAAAGT
1 ATACTATATAATATAATATTATAAA-T
* *
1940714 ATACTATGTAATATAAATATATATAGTAT
1 ATACTATATAATAT-AATAT-TATA-AAT
*
1940743 ATATTATATACCATATAA-A--AT-AAT
1 ATACTATATA--ATATAATATTATAAAT
* *
1940767 AAAC-ATATAATATTTATATTATAATAT
1 ATACTATATAATA-TAATATTATAA-AT
* *
1940794 ATACTATATAATATTATCTTATATAAT
1 ATACTATATAATATAATATTATA-AAT
1940821 ATACTATATAATATA
1 ATACTATATAATATA
1940836 CACCGTACTA
Statistics
Matches: 97, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
21 3 0.03
22 2 0.02
23 6 0.06
24 4 0.04
25 2 0.02
26 3 0.03
27 42 0.43
28 14 0.14
29 14 0.14
30 3 0.03
31 4 0.04
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (26 bp):
ATACTATATAATATAATATTATAAAT
Found at i:1940807 original size:12 final size:12
Alignment explanation
Indices: 1940792--1940836 Score: 63
Period size: 12 Copynumber: 3.5 Consensus size: 12
1940782 ATATTATAAT
1940792 ATATACTATATA
1 ATATACTATATA
1940804 ATATTATCTTATATA
1 ATA-TA-C-TATATA
1940819 ATATACTATATA
1 ATATACTATATA
1940831 ATATAC
1 ATATAC
1940837 ACCGTACTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 15 0.50
13 3 0.10
14 3 0.10
15 9 0.30
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (12 bp):
ATATACTATATA
Found at i:1940854 original size:7 final size:7
Alignment explanation
Indices: 1940699--1940835 Score: 61
Period size: 7 Copynumber: 19.1 Consensus size: 7
1940689 ACTATATAAC
1940699 ATAATATT
1 ATAATA-T
1940707 ATAA-AGT
1 ATAATA-T
*
1940714 ATACTAT
1 ATAATAT
*
1940721 GTAATAT
1 ATAATAT
1940728 A-AATAT
1 ATAATAT
1940734 ATATAGTAT
1 ATA-A-TAT
*
1940743 ATATTAT
1 ATAATAT
1940750 ATACCATAT
1 ATA--ATAT
*
1940759 AAAATA-
1 ATAATAT
*
1940765 ATAAACAT
1 AT-AATAT
1940773 ATAATAT
1 ATAATAT
*
1940780 -TTATATT
1 ATAATA-T
1940787 ATAATAT
1 ATAATAT
*
1940794 ATACTAT
1 ATAATAT
1940801 ATAATATT
1 ATAATA-T
**
1940809 ATCTTAT
1 ATAATAT
1940816 AT-A-AT
1 ATAATAT
*
1940821 ATACTAT
1 ATAATAT
1940828 ATAATAT
1 ATAATAT
1940835 A
1 A
1940836 CACCGTACTA
Statistics
Matches: 96, Mismatches: 20, Indels: 27
0.67 0.14 0.19
Matches are distributed among these distances:
5 4 0.04
6 11 0.11
7 53 0.55
8 17 0.18
9 11 0.11
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.42
Consensus pattern (7 bp):
ATAATAT
Found at i:1942014 original size:20 final size:21
Alignment explanation
Indices: 1941989--1942028 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1941979 CTTTACATAG
*
1941989 TAGTATTGATACCAT-AGGCA
1 TAGTATCGATACCATCAGGCA
1942009 TAGTATCGATACCATCAGGC
1 TAGTATCGATACCATCAGGC
1942029 CCCAACGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCA
Found at i:1942168 original size:20 final size:21
Alignment explanation
Indices: 1942129--1942169 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1942119 TGTAGAGATT
**
1942129 TCATCCCCAAACGGCTAGAAA
1 TCATCCCCAAACAACTAGAAA
1942150 TCATCCCC-AACAACTAGAAA
1 TCATCCCCAAACAACTAGAAA
1942170 CGGCCACAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.41, C:0.34, G:0.10, T:0.15
Consensus pattern (21 bp):
TCATCCCCAAACAACTAGAAA
Found at i:1942938 original size:20 final size:20
Alignment explanation
Indices: 1942901--1942940 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1942891 CTCTAAATCA
* *
1942901 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATCTAATTTTG
1942921 TTTTTCAAAATCTAATTTTG
1 TTTTTCAAAATCTAATTTTG
1942941 CTTTAAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.57
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTG
Found at i:1948976 original size:22 final size:21
Alignment explanation
Indices: 1948951--1949023 Score: 53
Period size: 22 Copynumber: 3.5 Consensus size: 21
1948941 CCCAAAGACT
1948951 ACATAATTTGCACTAAAGTGCC
1 ACATAATTTGCACTAAA-TGCC
* * *
1948973 ACATATTTTTC-CTGAAA-GAC
1 ACATAATTTGCACT-AAATGCC
* *
1948993 ACATAGTTTGCACCAAAATGCC
1 ACATAATTTGCA-CTAAATGCC
1949015 ACAT-ATTTG
1 ACATAATTTG
1949024 TCCCGAGGAC
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
20 11 0.28
21 9 0.23
22 19 0.49
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (21 bp):
ACATAATTTGCACTAAATGCC
Found at i:1948997 original size:42 final size:41
Alignment explanation
Indices: 1948913--1949042 Score: 136
Period size: 42 Copynumber: 3.1 Consensus size: 41
1948903 CCACAACTCG
* * *
1948913 TAATTTGCACGAAGTGCCATATAATTGTCCCAAAGACTACA
1 TAATTTGCACAAAGTGCCACATATTTGTCCCAAAGACTACA
* *
1948954 TAATTTGCACTAAAGTGCCACATATTTTTCCTGAAAGAC-ACA
1 TAATTTGCAC-AAAGTGCCACATATTTGTCC-CAAAGACTACA
* * * * *
1948996 TAGTTTGCACCAAAATGCCACATATTTGTCCCGAGGACCACA
1 TAATTTGCA-CAAAGTGCCACATATTTGTCCCAAAGACTACA
1949038 TAATT
1 TAATT
1949043 GTCTCGAATG
Statistics
Matches: 73, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
41 14 0.19
42 52 0.71
43 7 0.10
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (41 bp):
TAATTTGCACAAAGTGCCACATATTTGTCCCAAAGACTACA
Found at i:1949672 original size:53 final size:55
Alignment explanation
Indices: 1949615--1949740 Score: 188
Period size: 55 Copynumber: 2.3 Consensus size: 55
1949605 TCGAAATTGC
*
1949615 AAGGGTATCGATAC-CTCC-CAGTGTACCGATACACATGT-AGCAC-CAAATGTTTT
1 AAGGGTATCGATACACTCCTCAGTGTACCGATACACATATGA-CACTC-AATGTTTT
1949668 AAGGGTATCGATACACTCCTCAGTGTACCGATACACATATGACACTCAATGTTTT
1 AAGGGTATCGATACACTCCTCAGTGTACCGATACACATATGACACTCAATGTTTT
*
1949723 AAAGGTATCGATACACTC
1 AAGGGTATCGATACACTC
1949741 TCCCTTTTAA
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
53 14 0.21
54 4 0.06
55 47 0.70
56 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (55 bp):
AAGGGTATCGATACACTCCTCAGTGTACCGATACACATATGACACTCAATGTTTT
Found at i:1950781 original size:15 final size:15
Alignment explanation
Indices: 1950760--1950796 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1950750 TGAGACATTA
1950760 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
*
1950775 TCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
1950790 CCCGCCC
1 CCCGCCC
1950797 AGCTAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.05, C:0.68, G:0.19, T:0.08
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:1952106 original size:117 final size:118
Alignment explanation
Indices: 1951857--1952140 Score: 414
Period size: 117 Copynumber: 2.4 Consensus size: 118
1951847 CAAATGGCGT
* * *
1951857 AGGTGCCAACTTAAGGGAGCACCTTAGG-TCTATAAGGTCTTACCCTAGCCGAAACAAAGGTGCC
1 AGGTGCCACCCTAAGGGAGTACCTTAGGTTC-ATAAGGTCTTACCCTAGCCGAAACAAAGGTGCC
1951921 CACATAAGGGGTGTGCCCTCATGCCCATAAGGACTTACCCAATGCACATAGTAG
65 CACATAAGGGGTGTGCCCTCATGCCCATAAGGACTTACCCAATGCACATAGTAG
* * * *
1951975 AAGTGTCACCCTAAGGGAGTACCTTAGGGTTCATAAGGTCTTACCCTAGCTGAAACGAAGGTGCC
1 AGGTGCCACCCTAAGGGAGTACCTTA-GGTTCATAAGGTCTTACCCTAGCCGAAACAAAGGTGCC
* *
1952040 CACCTGA-GGGTGTGCCCTCA-GTCCCAT-AGGACTTACCCAATGCACATAGTAG
65 CACATAAGGGGTGTGCCCTCATG-CCCATAAGGACTTACCCAATGCACATAGTAG
*
1952092 AGGTGCCACCCTAAGGGAGTACCTTAGGTCCATAAGGTCTTACCACTAG
1 AGGTGCCACCCTAAGGGAGTACCTTAGGTTCATAAGGTCTTACC-CTAG
1952141 GCTCATTGGG
Statistics
Matches: 150, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
116 17 0.11
117 54 0.36
118 39 0.26
119 38 0.25
120 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.21
Consensus pattern (118 bp):
AGGTGCCACCCTAAGGGAGTACCTTAGGTTCATAAGGTCTTACCCTAGCCGAAACAAAGGTGCCC
ACATAAGGGGTGTGCCCTCATGCCCATAAGGACTTACCCAATGCACATAGTAG
Found at i:1952134 original size:59 final size:59
Alignment explanation
Indices: 1951945--1952135 Score: 178
Period size: 59 Copynumber: 3.3 Consensus size: 59
1951935 GCCCTCATGC
* *
1951945 CCATAAGGACTTACCCAATGCACATAGTAGAAGTGTCACCCTAAGGGAGTACCTTAGGGT
1 CCATAAGGACTTACCCAATGCACATAGTAGAGGTGCCACCCTAAGGGAGTACCTTA-GGT
* * * ** * * * * *
1952005 TCATAAGGTCTTACCCTA-GCTGAAACG-A-AGGTGCC-CACCTGAGGGTGTGCCCTCA-GT
1 CCATAAGGACTTACCCAATGCACATA-GTAGAGGTGCCAC-CCTAAGGGAGT-ACCTTAGGT
1952062 CCCAT-AGGACTTACCCAATGCACATAGTAGAGGTGCCACCCTAAGGGAGTACCTTAGGT
1 -CCATAAGGACTTACCCAATGCACATAGTAGAGGTGCCACCCTAAGGGAGTACCTTAGGT
*
1952121 CCATAAGGTCTTACC
1 CCATAAGGACTTACC
1952136 ACTAGGCTCA
Statistics
Matches: 98, Mismatches: 23, Indels: 21
0.69 0.16 0.15
Matches are distributed among these distances:
57 15 0.15
58 30 0.31
59 36 0.37
60 17 0.17
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.22
Consensus pattern (59 bp):
CCATAAGGACTTACCCAATGCACATAGTAGAGGTGCCACCCTAAGGGAGTACCTTAGGT
Found at i:1952452 original size:16 final size:16
Alignment explanation
Indices: 1952427--1952460 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1952417 GAATCATACT
*
1952427 TAAATTAGATAAAGCA
1 TAAATCAGATAAAGCA
1952443 TAAATCAGATAAAGCA
1 TAAATCAGATAAAGCA
1952459 TA
1 TA
1952461 CGGTAGTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.24
Consensus pattern (16 bp):
TAAATCAGATAAAGCA
Found at i:1953021 original size:13 final size:13
Alignment explanation
Indices: 1953003--1953027 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1952993 TTGACTTTTT
1953003 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
1953016 GGTCAAAGTCAA
1 GGTCAAAGTCAA
1953028 AGTCAACAAA
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:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (13 bp):
GGTCAAAGTCAAC
Found at i:1953078 original size:18 final size:18
Alignment explanation
Indices: 1953055--1953101 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
1953045 ACGTGCAGGT
1953055 CAACGGTCAGGTCAAAGC
1 CAACGGTCAGGTCAAAGC
* * *
1953073 CAACGGTTCGGGTCAAGGT
1 CAACGG-TCAGGTCAAAGC
1953092 CAACGGTCAG
1 CAACGGTCAG
1953102 ACCGGTTTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.28, C:0.26, G:0.32, T:0.15
Consensus pattern (18 bp):
CAACGGTCAGGTCAAAGC
Found at i:1953144 original size:20 final size:20
Alignment explanation
Indices: 1953115--1953159 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1953105 GGTTTAGGTT
*
1953115 GACTCTAGTCAGTTCGGGTG
1 GACTCGAGTCAGTTCGGGTG
1953135 GACTCGAGTCAGTTCGGGTG
1 GACTCGAGTCAGTTCGGGTG
1953155 GACTC
1 GACTC
1953160 AGATCGGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.22, G:0.36, T:0.27
Consensus pattern (20 bp):
GACTCGAGTCAGTTCGGGTG
Found at i:1953180 original size:14 final size:15
Alignment explanation
Indices: 1953143--1953182 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1953133 TGGACTCGAG
*
1953143 TCAGTTCGGGTGGAC
1 TCAGATCGGGTGGAC
*
1953158 TCAGATCGGGTTGAC
1 TCAGATCGGGTGGAC
1953173 TC-GATCGGGT
1 TCAGATCGGGT
1953183 CAAACAGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.15, C:0.20, G:0.38, T:0.28
Consensus pattern (15 bp):
TCAGATCGGGTGGAC
Found at i:1957357 original size:27 final size:27
Alignment explanation
Indices: 1957308--1957367 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
1957298 GTGCAATATG
* * * *
1957308 CACTCAAAAGTGTCTCTAGATAAATTC
1 CACTAAAAAGTGCCTATACATAAATTC
* *
1957335 CACTAAAAAGTGCCTATACATAACTTG
1 CACTAAAAAGTGCCTATACATAAATTC
1957362 CACTAA
1 CACTAA
1957368 TGTGTCATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (27 bp):
CACTAAAAAGTGCCTATACATAAATTC
Done.