Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397264.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_130.0, 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: 8132550
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 35170 characters in sequence are not A, C, G, or T
File 10 of 14
Found at i:5008379 original size:2 final size:2
Alignment explanation
Indices: 5008372--5008405 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5008362 GCTGATAACA
5008372 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
5008406 GATCAGATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:5012508 original size:2 final size:2
Alignment explanation
Indices: 5012496--5012526 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5012486 GTATCCCCTT
*
5012496 TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5012527 TAGATGGGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:5017117 original size:6 final size:6
Alignment explanation
Indices: 5017094--5017120 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5017084 AAGAGAGGGA
5017094 GAGAGT GAGAGT GAGAGT GAGAGT GAG
1 GAGAGT GAGAGT GAGAGT GAGAGT GAG
5017121 GGGATAGTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.52, T:0.15
Consensus pattern (6 bp):
GAGAGT
Found at i:5021770 original size:34 final size:33
Alignment explanation
Indices: 5021714--5021784 Score: 79
Period size: 34 Copynumber: 2.1 Consensus size: 33
5021704 ATAGCCAGCA
* * * *
5021714 GGGCTTCTTTTGGTACATAAACAATCAGAATTT
1 GGGCCTCTTTGGGTACATAAACAATCAAAACTT
* *
5021747 GGGCCTCTTTGGGTGCATGAAACACTCAAAACTT
1 GGGCCTCTTTGGGTACAT-AAACAATCAAAACTT
5021781 GGGC
1 GGGC
5021785 TTCTACCTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
33 15 0.48
34 16 0.52
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.30
Consensus pattern (33 bp):
GGGCCTCTTTGGGTACATAAACAATCAAAACTT
Found at i:5023592 original size:59 final size:59
Alignment explanation
Indices: 5023524--5023640 Score: 207
Period size: 59 Copynumber: 2.0 Consensus size: 59
5023514 ATTTCTAATG
* *
5023524 CATCCTTGTGAGAAAAGTATAACTAGCTATGAACACCAACAACGTCAAGGTCACAACTA
1 CATCCTTGTGACAAAAGTATAACAAGCTATGAACACCAACAACGTCAAGGTCACAACTA
*
5023583 CATCCTTGTGACAAAAGTATAACAAGCTATGAACACCAACAATGTCAAGGTCACAACT
1 CATCCTTGTGACAAAAGTATAACAAGCTATGAACACCAACAACGTCAAGGTCACAACT
5023641 TCAAGACTCT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.21
Consensus pattern (59 bp):
CATCCTTGTGACAAAAGTATAACAAGCTATGAACACCAACAACGTCAAGGTCACAACTA
Found at i:5037556 original size:2 final size:2
Alignment explanation
Indices: 5037536--5037576 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
5037526 ATTATTCTCA
* *
5037536 AT AT -T AT AT AT GT AG 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
5037577 CAAAGTATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5043540 original size:2 final size:2
Alignment explanation
Indices: 5043528--5043567 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5043518 TGATACATAC
*
5043528 AT AT GT 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
5043568 TGGTTTAGCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5048671 original size:27 final size:25
Alignment explanation
Indices: 5048623--5048676 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
5048613 ATTTAATAAC
*
5048623 TTTTTATTATTATATTAATATAAAA
1 TTTTTATTATTACATTAATATAAAA
* *
5048648 TTTTTTTTATTACATATAATTATATAA
1 TTTTTATTATTACAT-TAA-TATAAAA
5048675 TT
1 TT
5048677 AAATATGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 13 0.54
26 3 0.12
27 8 0.33
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTTTATTATTACATTAATATAAAA
Found at i:5050654 original size:17 final size:17
Alignment explanation
Indices: 5050632--5050668 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
5050622 CAAAGATCAA
5050632 ATTAATAT-TATATATAT
1 ATTAATATATAT-TATAT
5050649 ATTAATATATATTATAT
1 ATTAATATATATTATAT
5050666 ATT
1 ATT
5050669 TTGGTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTAATATATATTATAT
Found at i:5064910 original size:19 final size:20
Alignment explanation
Indices: 5064866--5064915 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
5064856 AGATAAATTT
*
5064866 TTAATTTTTATTTAAATAAA
1 TTAATTTTTAATTAAATAAA
*
5064886 TAAATTTTATAATT-AAT-AA
1 TTAATTTT-TAATTAAATAAA
*
5064905 TTAATTATTAA
1 TTAATTTTTAA
5064916 AATATTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 3 0.12
19 8 0.32
20 10 0.40
21 4 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAATTTTTAATTAAATAAA
Found at i:5065001 original size:22 final size:21
Alignment explanation
Indices: 5064947--5065007 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
5064937 TCGTATGATG
*
5064947 AATTATGATAT-ATTAAAATTAT
1 AATT-TGATATAATTAATA-TAT
5064969 AA-TTGATATAATTAATATACT
1 AATTTGATATAATTAATATA-T
5064990 AATTTGATATAA-TAATAT
1 AATTTGATATAATTAATAT
5065008 GATTATGGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
20 8 0.23
21 16 0.46
22 11 0.31
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (21 bp):
AATTTGATATAATTAATATAT
Found at i:5073508 original size:30 final size:31
Alignment explanation
Indices: 5073421--5073533 Score: 99
Period size: 30 Copynumber: 3.7 Consensus size: 31
5073411 ATATTAAAAA
* *
5073421 AAATTAAATAAATTTTTAT-ATTTTTA-ATT
1 AAATCAAATAAATTTTTATAATTTTTATTTT
* * * * *
5073450 ATATTCAATTAAGTTTTTGT-ATTGTTATTTT
1 A-AATCAAATAAATTTTTATAATTTTTATTTT
* *
5073481 GAATCAGATAAATTTTT-TAATTTTTATTTT
1 AAATCAAATAAATTTTTATAATTTTTATTTT
*
5073511 AAATTAAATAAATTTTTATAATT
1 AAATCAAATAAATTTTTATAATT
5073534 AATAATTAAT
Statistics
Matches: 64, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
29 2 0.03
30 55 0.86
31 7 0.11
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (31 bp):
AAATCAAATAAATTTTTATAATTTTTATTTT
Found at i:5073642 original size:23 final size:23
Alignment explanation
Indices: 5073585--5073654 Score: 72
Period size: 22 Copynumber: 3.0 Consensus size: 23
5073575 CGTATGATGT
* *
5073585 TAATATGATATATTAAAATATTA
1 TAATTTGATATAATAAAATATTA
*
5073608 TAA-TTGATATAATATAATA-TA
1 TAATTTGATATAATAAAATATTA
*
5073629 CTAATTTGATATAATAATATGATTA
1 -TAATTTGATATAATAAAAT-ATTA
5073654 T
1 T
5073655 GGTGATATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 2 0.05
22 16 0.42
23 16 0.42
24 2 0.05
25 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (23 bp):
TAATTTGATATAATAAAATATTA
Found at i:5079310 original size:27 final size:26
Alignment explanation
Indices: 5079260--5079310 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
5079250 CTTTTTTTTT
*
5079260 AATATATATAGCTCAATTTAAAATTA
1 AATATATATAGCTCAATATAAAATTA
* *
5079286 AATATCATATAGTTCAATATGAAAT
1 AATAT-ATATAGCTCAATATAAAAT
5079311 ATCTTAACTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.24
27 16 0.76
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37
Consensus pattern (26 bp):
AATATATATAGCTCAATATAAAATTA
Found at i:5081448 original size:55 final size:55
Alignment explanation
Indices: 5081356--5081459 Score: 138
Period size: 55 Copynumber: 1.9 Consensus size: 55
5081346 AATTTGGGTT
* * * * *
5081356 ATGAATCCTCTCTGAAATACTCATTTATCTTCCCATACTTCTTGCCATACCGGTC
1 ATGAATCCTCTCTGAAATACTCATTCATCCTCACATACTCCATGCCATACCGGTC
*
5081411 ATGAATCCTCTCT-AGAATACTTATTCATCCTCACATACTCCATGCCATA
1 ATGAATCCTCTCTGA-AATACTCATTCATCCTCACATACTCCATGCCATA
5081460 TGCAAAAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 1 0.02
55 41 0.98
ACGTcount: A:0.27, C:0.31, G:0.08, T:0.35
Consensus pattern (55 bp):
ATGAATCCTCTCTGAAATACTCATTCATCCTCACATACTCCATGCCATACCGGTC
Found at i:5085483 original size:303 final size:303
Alignment explanation
Indices: 5085133--5085769 Score: 935
Period size: 304 Copynumber: 2.1 Consensus size: 303
5085123 CCTCATTATG
* * *
5085133 ACAACCACAAACAGGATGAGAAAGGTTAGTCAGGACAGCATTTTCTTGCCGTTATATACTTGGCT
1 ACAACCAGAAACAGGATGAGAAAGGTTAGTCAGGACAGCACTTTCTTGCCATTATATACTTGGCT
* *
5085198 ATTTACAAGCCC-AATGATCGCTAAATTTTTTTTTTCTATGT-ATA-ATGACGGACCGGCGCAGA
66 ATTTACAA-CCCGAATGATCGCTAAA--ATTTTTTTCTATGTAATAGATGACGGACCGGAGCAGA
*
5085260 AGACCATAGTAACATAATTCATCAAGCAAAAGAAAAATCCTTGCAAGAAGCTGCTTACACAGATG
128 AGACCATAGTAACATAATACATCAAGCAAAAGAAAAATCCTTGCAAGAAGCTGCTTACACAGATG
* *
5085325 AGGCAACAGGACAAGATTGTTTAGCTCCTGCAGCTGAAGATAAAAATA-CTCATGGAAATGAGAC
193 AGGCAACAGGACAAGATTGTTTAGCTCCTGCAGCTGAAAATAAAAATATC-CAGGGAAATGAGAC
5085389 AGATTTAGTTTCCT-GTGAACCTGATGAAATAGCATCTCCTCATGTTC
257 AGATTTAGTTT-CTAGTGAACCTGATGAAATAGCATCTCCTCATGTTC
* * *
5085436 ACAACCAGAAACAGGATGAGAAAGGTTAGTC-GGTACAGCACTTTCTTGCCATTATGTGCTTGTC
1 ACAACCAGAAACAGGATGAGAAAGGTTAGTCAGG-ACAGCACTTTCTTGCCATTATATACTTGGC
* * *
5085500 TATTTACAACCCGAATGATTGCTAAAATTTTTTTCTATGTAATATGATGATGGACTGGAGCAGAA
65 TATTTACAACCCGAATGATCGCTAAAATTTTTTTCTATGTAATA-GATGACGGACCGGAGCAGAA
* * * * * *
5085565 GACTATAGTAACATAATACCTGAAGCTAAGGAAAAATCCTTGCTAGAAGCTGCTTACACAGATGA
129 GACCATAGTAACATAATACATCAAGCAAAAGAAAAATCCTTGCAAGAAGCTGCTTACACAGATGA
* *
5085630 GGCAACAGGACAAGATTGTTTGGTTCCTGCAGCTGAAAATAAAAATATCCAGGGAAATGAGACAG
194 GGCAACAGGACAAGATTGTTTAGCTCCTGCAGCTGAAAATAAAAATATCCAGGGAAATGAGACAG
* * *
5085695 ATTTGGTTTCTAGTGAACCTGATGGAATAGCATCTCCTCATGTTG
259 ATTTAGTTTCTAGTGAACCTGATGAAATAGCATCTCCTCATGTTC
*
5085740 ACAACCAGAAGCAGGATGAGAAAGGTTAGT
1 ACAACCAGAAACAGGATGAGAAAGGTTAGT
5085770 ACATAGAGTA
Statistics
Matches: 301, Mismatches: 26, Indels: 13
0.89 0.08 0.04
Matches are distributed among these distances:
301 13 0.04
302 8 0.03
303 78 0.26
304 201 0.67
305 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (303 bp):
ACAACCAGAAACAGGATGAGAAAGGTTAGTCAGGACAGCACTTTCTTGCCATTATATACTTGGCT
ATTTACAACCCGAATGATCGCTAAAATTTTTTTCTATGTAATAGATGACGGACCGGAGCAGAAGA
CCATAGTAACATAATACATCAAGCAAAAGAAAAATCCTTGCAAGAAGCTGCTTACACAGATGAGG
CAACAGGACAAGATTGTTTAGCTCCTGCAGCTGAAAATAAAAATATCCAGGGAAATGAGACAGAT
TTAGTTTCTAGTGAACCTGATGAAATAGCATCTCCTCATGTTC
Found at i:5097006 original size:15 final size:15
Alignment explanation
Indices: 5096986--5097014 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5096976 ACTTTACAAT
5096986 GTAATATGATTACAG
1 GTAATATGATTACAG
5097001 GTAATATGATTACA
1 GTAATATGATTACA
5097015 AATAATGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (15 bp):
GTAATATGATTACAG
Found at i:5097020 original size:15 final size:15
Alignment explanation
Indices: 5096987--5097020 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5096977 CTTTACAATG
**
5096987 TAATATGATTACAGG
1 TAATATGATTACAAA
5097002 TAATATGATTACAAA
1 TAATATGATTACAAA
5097017 TAAT
1 TAAT
5097021 GTAATTGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (15 bp):
TAATATGATTACAAA
Found at i:5097316 original size:21 final size:20
Alignment explanation
Indices: 5097283--5097330 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
5097273 AATTTATATT
* *
5097283 TATTATTTTTATTTTTTAATA
1 TATT-TTTTTATTATATAATA
*
5097304 TATTTTTTATATTATATATTA
1 TATTTTTT-TATTATATAATA
5097325 TATTTT
1 TATTTT
5097331 AATTTGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TATTTTTTTATTATATAATA
Found at i:5097377 original size:26 final size:25
Alignment explanation
Indices: 5097305--5097418 Score: 79
Period size: 26 Copynumber: 4.2 Consensus size: 25
5097295 TTTTTAATAT
5097305 ATTTTTTATAT-TATATATTATATTTTA
1 ATTTTTTATATAT-TATA-TA-ATTTTA
5097332 ATTTGTTTTACTTATATTATATAAGTTTTA
1 A-TT-TTTTA--TATATTATATAA-TTTTA
* * *
5097362 ATTTTTTATATTTTATTTTTATTTTA
1 ATTTTTTATATATTA-TATAATTTTA
*
5097388 ATTTTTTAT-TATTATATTACATTTTT
1 ATTTTTTATATATTATA-TA-ATTTTA
5097414 ATTTT
1 ATTTT
5097419 AATTATAATA
Statistics
Matches: 71, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
24 1 0.01
25 5 0.07
26 30 0.42
27 4 0.06
28 7 0.10
29 8 0.11
30 8 0.11
31 7 0.10
32 1 0.01
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (25 bp):
ATTTTTTATATATTATATAATTTTA
Found at i:5097386 original size:19 final size:19
Alignment explanation
Indices: 5097248--5097430 Score: 70
Period size: 19 Copynumber: 9.6 Consensus size: 19
5097238 TAATGTCATA
5097248 TATTTT-AT-TTTTATTTAT
1 TATTTTAATATTTTA-TTAT
*
5097266 TATTATAA-ATTTATATTTAT
1 TATTTTAATATTT-TA-TTAT
* *
5097286 TATTTTTATTTTTTAATATAT
1 TATTTTAATATTTT-AT-TAT
5097307 T-TTTT-ATATTATATATTA-
1 TATTTTAATATT-T-TATTAT
5097325 TATTTTAAT-TTGTT-TTACT
1 TATTTTAATATT-TTATTA-T
*
5097344 TATATTATATAAGTTTTA--AT
1 TATTTTA-AT-A-TTTTATTAT
*
5097364 T-TTTT-ATATTTTATTTT
1 TATTTTAATATTTTATTAT
*
5097381 TATTTTAATTTTTTATTAT
1 TATTTTAATATTTTATTAT
*
5097400 TATATTACAT-TTTTATT-T
1 TATTTTA-ATATTTTATTAT
*
5097418 TAATTATAATATT
1 T-ATTTTAATATT
5097431 ANNNNNNNNN
Statistics
Matches: 127, Mismatches: 14, Indels: 47
0.68 0.07 0.25
Matches are distributed among these distances:
15 5 0.04
16 1 0.01
17 7 0.06
18 15 0.12
19 55 0.43
20 30 0.24
21 10 0.08
22 2 0.02
23 2 0.02
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (19 bp):
TATTTTAATATTTTATTAT
Found at i:5106720 original size:8 final size:8
Alignment explanation
Indices: 5106707--5106741 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
5106697 GAGGAAAAAT
5106707 AAATTTTA
1 AAATTTTA
5106715 AAATTTTA
1 AAATTTTA
5106723 AAATTTTA
1 AAATTTTA
5106731 AAATTTTA
1 AAATTTTA
5106739 AAA
1 AAA
5106742 GCCTTCTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AAATTTTA
Found at i:5118709 original size:7 final size:7
Alignment explanation
Indices: 5118697--5118727 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
5118687 GCTAAAAGAG
5118697 ATGGGTA
1 ATGGGTA
5118704 ATGGGTA
1 ATGGGTA
5118711 ATGGGTA
1 ATGGGTA
5118718 ATGGGTA
1 ATGGGTA
5118725 ATG
1 ATG
5118728 ACTTGTCTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.42, T:0.29
Consensus pattern (7 bp):
ATGGGTA
Found at i:5119418 original size:6 final size:6
Alignment explanation
Indices: 5119407--5119435 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5119397 GTAAAATTAG
5119407 AAATAA AAATAA AAATAA AAATAA AAATA
1 AAATAA AAATAA AAATAA AAATAA AAATA
5119436 TGAGACTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:5133080 original size:2 final size:2
Alignment explanation
Indices: 5133073--5133104 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5133063 GTAATTCTTA
*
5133073 AT AT AT AT AT GT 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
5133105 TTGAATCTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5144382 original size:61 final size:60
Alignment explanation
Indices: 5144240--5144383 Score: 146
Period size: 61 Copynumber: 2.4 Consensus size: 60
5144230 TAAATAAAAA
* **
5144240 ATATAAAAAAAATTAAATTAGAATAATTTTTAAAATAAAAAAATTAAAATATTATGATTTT
1 ATATAAAAAAAACTAAATT-GAATAATTTTTAAAATAAAAAAATTAAAATATTACAATTTT
* * *** * * *
5144301 ATGTGAAAGGGACTACATTGAAGTAATTTTTAAAATAAAGAGATTAAAATATTACAATTTT
1 ATATAAAAAAAACTAAATTGAA-TAATTTTTAAAATAAAAAAATTAAAATATTACAATTTT
*
5144362 GA-ATAAAAAAAAGTAAATTGAA
1 -ATATAAAAAAAACTAAATTGAA
5144384 AAATATAGAC
Statistics
Matches: 63, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
60 3 0.05
61 59 0.94
62 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (60 bp):
ATATAAAAAAAACTAAATTGAATAATTTTTAAAATAAAAAAATTAAAATATTACAATTTT
Found at i:5153861 original size:23 final size:23
Alignment explanation
Indices: 5153806--5153864 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
5153796 AGGTATTACG
**
5153806 TGACTGGTTGATATAACTTTGTG
1 TGACTGGTTGATATAACTTTGCA
* *
5153829 TGAATGGTTGATATGACTTTGCA
1 TGACTGGTTGATATAACTTTGCA
*
5153852 TGACTAGTTGATA
1 TGACTGGTTGATA
5153865 GGCACTGCGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.41
Consensus pattern (23 bp):
TGACTGGTTGATATAACTTTGCA
Found at i:5154018 original size:22 final size:22
Alignment explanation
Indices: 5153993--5154052 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
5153983 ATCAGTCACG
* *
5153993 CAATGCTTAAAAATTAATTTA-T
1 CAATACTTAAAAATTAA-TTACA
* *
5154015 CAATACTTATAAATCAATTACA
1 CAATACTTAAAAATTAATTACA
5154037 CAATACTTAAAAATTA
1 CAATACTTAAAAATTA
5154053 GTAATGTAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 3 0.10
22 28 0.90
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (22 bp):
CAATACTTAAAAATTAATTACA
Found at i:5154446 original size:28 final size:29
Alignment explanation
Indices: 5154391--5154446 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
5154381 ATAAAAAATT
*
5154391 AATTAAAATTATAATGAAAGATATTTTTA
1 AATTAAAATTATAATGAAAGATAATTTTA
* * *
5154420 AATTAAACTTATGA-GAAGGATAATTTT
1 AATTAAAATTATAATGAAAGATAATTTT
5154447 TCATAATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (29 bp):
AATTAAAATTATAATGAAAGATAATTTTA
Found at i:5154467 original size:2 final size:2
Alignment explanation
Indices: 5154460--5154490 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5154450 TAATTTTCTT
5154460 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5154491 CGATTGTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5160032 original size:28 final size:28
Alignment explanation
Indices: 5159986--5160044 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
5159976 ATGTAGATAG
5159986 AAAGGCGTGCTCGTAATAAATGGCT-ATT
1 AAAGGCGTGCTCGTAATAAAT-GCTGATT
* *
5160014 AAAGGCGTGCTTGTGATAAATGCTGATT
1 AAAGGCGTGCTCGTAATAAATGCTGATT
5160042 AAA
1 AAA
5160045 TTCACAAGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 3 0.11
28 25 0.89
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (28 bp):
AAAGGCGTGCTCGTAATAAATGCTGATT
Found at i:5160526 original size:81 final size:81
Alignment explanation
Indices: 5160382--5160547 Score: 199
Period size: 81 Copynumber: 2.0 Consensus size: 81
5160372 CATTTGGTAT
* * **
5160382 ATTGTTAGGAATGTGATTGTTGAAAATATAACTTTGTAACGTTTGGTACAATAACAGAAAGTGAT
1 ATTGTTAAGAATGTGATTGTTGAAAATATAACTTTGTAACATTTAATACAATAACAGAAAGTGAT
*
5160447 GATTGTAGGGAATATG
66 GATTGCAGGGAATATG
*** * * * *
5160463 ATTGTTAAGAATGTGATTGTTGCGTATATATCTTTGTAGCATTTAATATAATAA-TGAAGAGTGA
1 ATTGTTAAGAATGTGATTGTTGAAAATATAACTTTGTAACATTTAATACAATAACAGAA-AGTGA
*
5160527 TGATTGCAGGGAATGTG
65 TGATTGCAGGGAATATG
5160544 ATTG
1 ATTG
5160548 CTGAGAGGAT
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
80 3 0.04
81 68 0.96
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.37
Consensus pattern (81 bp):
ATTGTTAAGAATGTGATTGTTGAAAATATAACTTTGTAACATTTAATACAATAACAGAAAGTGAT
GATTGCAGGGAATATG
Found at i:5160872 original size:20 final size:20
Alignment explanation
Indices: 5160849--5160895 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
5160839 AAATCTATTA
*
5160849 ATAGATAG-AAAATTCTATCG
1 ATAGATAGTAAAA-TATATCG
*
5160869 ATAGATAGTATAATATATCG
1 ATAGATAGTAAAATATATCG
5160889 ATAGATA
1 ATAGATA
5160896 AATAGCCACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (20 bp):
ATAGATAGTAAAATATATCG
Found at i:5162200 original size:2 final size:2
Alignment explanation
Indices: 5162193--5162239 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
5162183 ATTAAAAGAA
5162193 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
5162235 AT AT A
1 AT AT A
5162240 CAATATTCAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5175271 original size:23 final size:23
Alignment explanation
Indices: 5175244--5175288 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5175234 TCTATGGGTG
*
5175244 TTCATGAATGTATGTGCATGCAT
1 TTCATGAATGTATATGCATGCAT
*
5175267 TTCATGAATGTATATGGATGCA
1 TTCATGAATGTATATGCATGCA
5175289 AACATATGTG
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:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (23 bp):
TTCATGAATGTATATGCATGCAT
Found at i:5181173 original size:90 final size:91
Alignment explanation
Indices: 5181059--5181239 Score: 319
Period size: 90 Copynumber: 2.0 Consensus size: 91
5181049 TTCCAAGGAA
*
5181059 ACCAAGATTCCATTCCCCTTGGACAATTGACTTGCAAGTTTTCAACTCCCTTCACCTGAATCTTG
1 ACCAAGATTCCATTCCCCTTGGACAATTGACTTGCAAGTTTTCAACCCCCTTCACCTGAATCTTG
5181124 CTTCAATGAACCCTAAAGGGTCGAAT
66 CTTCAATGAACCCTAAAGGGTCGAAT
* *
5181150 ACCAA-ATTCCATTCCCCTTGGACAATTGACTTTCAAGTTTTCAACCCCCTTCAGCTGAATCTTG
1 ACCAAGATTCCATTCCCCTTGGACAATTGACTTGCAAGTTTTCAACCCCCTTCACCTGAATCTTG
*
5181214 CTTCAATGAACCTTAAAGGGTCGAAT
66 CTTCAATGAACCCTAAAGGGTCGAAT
5181240 CAGTAGTGGT
Statistics
Matches: 86, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
90 81 0.94
91 5 0.06
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (91 bp):
ACCAAGATTCCATTCCCCTTGGACAATTGACTTGCAAGTTTTCAACCCCCTTCACCTGAATCTTG
CTTCAATGAACCCTAAAGGGTCGAAT
Found at i:5183769 original size:2 final size:2
Alignment explanation
Indices: 5183762--5183794 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5183752 AAAATTCACG
5183762 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
5183795 CACACACATT
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:5185047 original size:16 final size:16
Alignment explanation
Indices: 5185026--5185056 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5185016 AGGACTTGAC
5185026 CCTGGGAATACCATCA
1 CCTGGGAATACCATCA
5185042 CCTGGGAATACCATC
1 CCTGGGAATACCATC
5185057 CCTCTCTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.19
Consensus pattern (16 bp):
CCTGGGAATACCATCA
Found at i:5191173 original size:12 final size:12
Alignment explanation
Indices: 5191156--5191185 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5191146 AGAAAGCCTA
5191156 AGCATCATTGTC
1 AGCATCATTGTC
5191168 AGCATCATTGTC
1 AGCATCATTGTC
*
5191180 ATCATC
1 AGCATC
5191186 GTCTTCATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (12 bp):
AGCATCATTGTC
Found at i:5211611 original size:27 final size:27
Alignment explanation
Indices: 5211571--5211631 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
5211561 CTTAATATTA
5211571 TTTTTTGTAAATATATATAA-ATAAAAT
1 TTTTTTGTAAATATATA-AATATAAAAT
* *
5211598 TTTTTTGTATATATATAAATATAACAT
1 TTTTTTGTAAATATATAAATATAAAAT
5211625 TTGTTTT
1 TT-TTTT
5211632 TATTCTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 2 0.07
27 24 0.80
28 4 0.13
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (27 bp):
TTTTTTGTAAATATATAAATATAAAAT
Found at i:5256551 original size:2 final size:2
Alignment explanation
Indices: 5256514--5256539 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5256504 ACTATAGTTT
5256514 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5256540 CACCAGTATA
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):
TA
Found at i:5259332 original size:63 final size:64
Alignment explanation
Indices: 5259214--5259338 Score: 207
Period size: 63 Copynumber: 2.0 Consensus size: 64
5259204 ATACATAAAT
5259214 TAAAAATAGAGGTCAGATAACAATGCTTGTTTGAAACCTTCATCCAATCACCTCTAAGGACAAGC
1 TAAAAATAGAGGTCAGATAACAAT-CTTGTTTGAAACCTTCATCCAATCACCTCTAAGGACAAGC
* * *
5259279 TAAAAATAGAGGTCAGATAACAAT-TTGTTTGAATCTTTCATCCAATCATCTCTAAGGACA
1 TAAAAATAGAGGTCAGATAACAATCTTGTTTGAAACCTTCATCCAATCACCTCTAAGGACA
5259339 TTATGTAGAG
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 33 0.58
65 24 0.42
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.28
Consensus pattern (64 bp):
TAAAAATAGAGGTCAGATAACAATCTTGTTTGAAACCTTCATCCAATCACCTCTAAGGACAAGC
Found at i:5262233 original size:19 final size:19
Alignment explanation
Indices: 5262209--5262253 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
5262199 TTCAACTAGA
5262209 AAGTTAAGAAAACTTCTTG
1 AAGTTAAGAAAACTTCTTG
**
5262228 AAGTTAATCAAACTTCTTG
1 AAGTTAAGAAAACTTCTTG
5262247 AAGTTAA
1 AAGTTAA
5262254 TCATAAAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.33
Consensus pattern (19 bp):
AAGTTAAGAAAACTTCTTG
Found at i:5262254 original size:19 final size:19
Alignment explanation
Indices: 5262218--5262256 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
5262208 AAAGTTAAGA
5262218 AAACTTCTTGAAGTTAATC
1 AAACTTCTTGAAGTTAATC
5262237 AAACTTCTTGAAGTTAATC
1 AAACTTCTTGAAGTTAATC
5262256 A
1 A
5262257 TAAAGCAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (19 bp):
AAACTTCTTGAAGTTAATC
Found at i:5264759 original size:2 final size:2
Alignment explanation
Indices: 5264747--5264784 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
5264737 ATAAGATTTG
5264747 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5264785 TAATTTTTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5271370 original size:2 final size:2
Alignment explanation
Indices: 5271363--5271393 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5271353 TTATTAGTCT
5271363 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5271394 TAAAAGTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5276661 original size:2 final size:2
Alignment explanation
Indices: 5276654--5276684 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5276644 TTATAGTAAA
5276654 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5276685 CATGTTGATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5285033 original size:15 final size:14
Alignment explanation
Indices: 5285015--5285058 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
5285005 TATTTAAAAT
*
5285015 TAAAATTAATAATTA
1 TAAAA-TAATAATAA
*
5285030 TAAAAATAATTATAA
1 T-AAAATAATAATAA
5285045 TAAAATAATAATAA
1 TAAAATAATAATAA
5285059 CATCACATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 12 0.48
15 9 0.36
16 4 0.16
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAAAATAATAATAA
Found at i:5291523 original size:24 final size:24
Alignment explanation
Indices: 5291469--5291525 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
5291459 ATCATGTATT
*
5291469 TTTATTTAATCTAAAATATAAATA
1 TTTATTTAATCTAAAATAAAAATA
** *
5291493 TAAATTTAAT-TAACATAAAAATAA
1 TTTATTTAATCTAAAATAAAAAT-A
5291517 TTTATTTAA
1 TTTATTTAA
5291526 ATTTTTTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 10 0.38
24 16 0.62
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (24 bp):
TTTATTTAATCTAAAATAAAAATA
Found at i:5295573 original size:20 final size:18
Alignment explanation
Indices: 5295536--5295575 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
5295526 GGAGAGTAGG
*
5295536 AAAATTTATTAGTTAATA
1 AAAATTTATTAATTAATA
5295554 AAAATATTATTTAATTAATA
1 AAAAT-TTA-TTAATTAATA
5295574 AA
1 AA
5295576 TTAATAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 3 0.16
20 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
AAAATTTATTAATTAATA
Found at i:5296202 original size:17 final size:18
Alignment explanation
Indices: 5296182--5296216 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5296172 ATTAAGATTG
5296182 ATTAAAAATATT-ATTTA
1 ATTAAAAATATTAATTTA
*
5296199 ATTAAAATTATTAATTTA
1 ATTAAAAATATTAATTTA
5296217 TAAAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTAAAAATATTAATTTA
Found at i:5296222 original size:17 final size:17
Alignment explanation
Indices: 5296184--5296224 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5296174 TAAGATTGAT
5296184 TAAAAA-TATTATTTAA
1 TAAAAATTATTATTTAA
*
5296200 TTAAAATTATTAATTT-A
1 TAAAAATTATT-ATTTAA
5296217 TAAAAATT
1 TAAAAATT
5296225 TTACTATAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 5 0.24
17 12 0.57
18 4 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAAATTATTATTTAA
Found at i:5297230 original size:3 final size:3
Alignment explanation
Indices: 5297222--5297249 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5297212 TAACAATGGG
5297222 AGT AGT AGT AGT AGT AGT AGT AGT AGT A
1 AGT AGT AGT AGT AGT AGT AGT AGT AGT A
5297250 CAATGGAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
AGT
Found at i:5310559 original size:18 final size:20
Alignment explanation
Indices: 5310538--5310579 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
5310528 AAAGAAAATT
*
5310538 TTTTAAGTATTTT-GAGT-A
1 TTTTAAGCATTTTGGAGTGA
5310556 TTTTAAGCATTTTGGAGTGA
1 TTTTAAGCATTTTGGAGTGA
5310576 TTTT
1 TTTT
5310580 TGATATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.57
19 4 0.19
20 5 0.24
ACGTcount: A:0.24, C:0.02, G:0.19, T:0.55
Consensus pattern (20 bp):
TTTTAAGCATTTTGGAGTGA
Found at i:5310776 original size:22 final size:22
Alignment explanation
Indices: 5310751--5310793 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5310741 GTTTTTGTGT
*
5310751 ATTGCGTAACTAATTTTTAAAC
1 ATTGCATAACTAATTTTTAAAC
* *
5310773 ATTGTATTACTAATTTTTAAA
1 ATTGCATAACTAATTTTTAAA
5310794 TATTACGTGA
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:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (22 bp):
ATTGCATAACTAATTTTTAAAC
Found at i:5310808 original size:22 final size:21
Alignment explanation
Indices: 5310716--5310809 Score: 57
Period size: 22 Copynumber: 4.3 Consensus size: 21
5310706 AGTAGTTTTG
*
5310716 ATAATTTTTAAATATTATGTAA
1 ATAATTTTTAAATATTACGT-A
* *** *
5310738 ATAGTTTTTGTGTATTGCGTA
1 ATAATTTTTAAATATTACGTA
*
5310759 ACTAATTTTTAAACATT--GTA
1 A-TAATTTTTAAATATTACGTA
5310779 TTACTAATTTTTAAATATTACGTGA
1 --A-TAATTTTTAAATATTACGT-A
5310804 ATAATT
1 ATAATT
5310810 GATAAGGCGT
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
20 3 0.06
21 2 0.04
22 45 0.83
23 1 0.02
24 2 0.04
25 1 0.02
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (21 bp):
ATAATTTTTAAATATTACGTA
Found at i:5334776 original size:16 final size:17
Alignment explanation
Indices: 5334757--5334799 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
5334747 TCAAGACTTC
5334757 AAAGAGAGAGAAGAAG-
1 AAAGAGAGAGAAGAAGA
*
5334773 AAAGAGAGA-AAGGAGA
1 AAAGAGAGAGAAGAAGA
5334789 AAAGAGAGAGA
1 AAAGAGAGAGA
5334800 GAGTGTCTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 5 0.21
16 18 0.75
17 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (17 bp):
AAAGAGAGAGAAGAAGA
Found at i:5344567 original size:59 final size:59
Alignment explanation
Indices: 5344494--5344614 Score: 206
Period size: 59 Copynumber: 2.1 Consensus size: 59
5344484 TAATTTAAAA
* *
5344494 AAAATTATGAATTTCGAAATATAAATATATACATTGCTTCTTTATCATGATATTGAATC
1 AAAATTATGAATTTCGAAATATAAATATATACATTACTTCTTTAACATGATATTGAATC
* *
5344553 AAAATTATGAATTTCGGAATATAAATATATACATTACTTCTTTAAGATGATATTGAATC
1 AAAATTATGAATTTCGAAATATAAATATATACATTACTTCTTTAACATGATATTGAATC
5344612 AAA
1 AAA
5344615 TGATTGTTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (59 bp):
AAAATTATGAATTTCGAAATATAAATATATACATTACTTCTTTAACATGATATTGAATC
Found at i:5365471 original size:8 final size:8
Alignment explanation
Indices: 5365458--5365482 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5365448 TTCCCGATAA
5365458 ATGAAATC
1 ATGAAATC
5365466 ATGAAATC
1 ATGAAATC
5365474 ATGAAATC
1 ATGAAATC
5365482 A
1 A
5365483 CTGTATCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (8 bp):
ATGAAATC
Found at i:5369265 original size:13 final size:13
Alignment explanation
Indices: 5369247--5369272 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5369237 CAAGAATTGA
5369247 TAAGGAAATCCAG
1 TAAGGAAATCCAG
5369260 TAAGGAAATCCAG
1 TAAGGAAATCCAG
5369273 GGGCCATCCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.23, T:0.15
Consensus pattern (13 bp):
TAAGGAAATCCAG
Found at i:5370155 original size:21 final size:21
Alignment explanation
Indices: 5370126--5370165 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5370116 TTTAAATGAT
* *
5370126 AAAATTTTTCTAAATTTTATC
1 AAAAGTTTTCGAAATTTTATC
*
5370147 AAAAGTTTTGGAAATTTTA
1 AAAAGTTTTCGAAATTTTA
5370166 GGAAAAATTT
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:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (21 bp):
AAAAGTTTTCGAAATTTTATC
Found at i:5370284 original size:12 final size:13
Alignment explanation
Indices: 5370249--5370286 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
5370239 AATAAGCTTA
5370249 ATATAA-ATAAAT
1 ATATAAGATAAAT
5370261 ATATAAGATAAAT
1 ATATAAGATAAAT
*
5370274 ATATGAG-TAAAT
1 ATATAAGATAAAT
5370286 A
1 A
5370287 AAAATTCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (13 bp):
ATATAAGATAAAT
Found at i:5372810 original size:16 final size:16
Alignment explanation
Indices: 5372769--5372818 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
5372759 TTGACTGCCT
*
5372769 AAAACAAAAAAGAAAA
1 AAAACACAAAAGAAAA
*
5372785 AAAAGC-CAAAGGAAAA
1 AAAA-CACAAAAGAAAA
*
5372801 AAAACACAAAATAAAA
1 AAAACACAAAAGAAAA
5372817 AA
1 AA
5372819 CAAAAAATAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 1 0.04
16 26 0.93
17 1 0.04
ACGTcount: A:0.80, C:0.10, G:0.08, T:0.02
Consensus pattern (16 bp):
AAAACACAAAAGAAAA
Found at i:5378202 original size:51 final size:51
Alignment explanation
Indices: 5378117--5378220 Score: 172
Period size: 51 Copynumber: 2.0 Consensus size: 51
5378107 AAGGCAAGTG
*
5378117 CAGGGTGCCAGCAAGGGCGCACAGCATAGACCCCTGGGCGAGCCAGCCCGA
1 CAGGGTGCCAGCAAGGGCGCACAGCACAGACCCCTGGGCGAGCCAGCCCGA
* * *
5378168 CAGGGTGCCAGCATGGGCGCATAGCACAGGCCCCTGGGCGAGCCAGCCCGA
1 CAGGGTGCCAGCAAGGGCGCACAGCACAGACCCCTGGGCGAGCCAGCCCGA
5378219 CA
1 CA
5378221 AAGTCAGGTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.22, C:0.36, G:0.36, T:0.07
Consensus pattern (51 bp):
CAGGGTGCCAGCAAGGGCGCACAGCACAGACCCCTGGGCGAGCCAGCCCGA
Found at i:5378645 original size:15 final size:15
Alignment explanation
Indices: 5378625--5378666 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
5378615 TTTCCCTCTT
5378625 AAATATTTTGGAGG-G
1 AAATATTTTGG-GGTG
5378640 AAATATTTTGGGGTG
1 AAATATTTTGGGGTG
5378655 AAATA-TTTGGGG
1 AAATATTTTGGGG
5378667 AAAATTGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
AAATATTTTGGGGTG
Found at i:5378665 original size:14 final size:14
Alignment explanation
Indices: 5378625--5378671 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
5378615 TTTCCCTCTT
5378625 AAATATTTTGGAGGG
1 AAATATTTTGG-GGG
5378640 AAATATTTTGGGGTG
1 AAATATTTTGGGG-G
*
5378655 AAATA-TTTGGGGA
1 AAATATTTTGGGGG
5378668 AAAT
1 AAAT
5378672 TGGCTATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 4 0.13
14 9 0.30
15 17 0.57
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.34
Consensus pattern (14 bp):
AAATATTTTGGGGG
Found at i:5381449 original size:2 final size:2
Alignment explanation
Indices: 5381444--5381479 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5381434 CACACAAGGT
5381444 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5381480 AGATTAACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5399789 original size:25 final size:26
Alignment explanation
Indices: 5399751--5399812 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
5399741 TGAATGTAAG
5399751 TTAAAAC-ATTAATTG-A-CATTATA
1 TTAAAACTATTAATTGTAGCATTATA
5399774 TTAAAACCTATTAATTGTAGCATTATA
1 TTAAAA-CTATTAATTGTAGCATTATA
*
5399801 TTGAAATCTATT
1 TT-AAAACTATT
5399813 TGTAATACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 6 0.18
24 1 0.03
25 8 0.24
26 1 0.03
27 14 0.42
28 3 0.09
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (26 bp):
TTAAAACTATTAATTGTAGCATTATA
Found at i:5403033 original size:39 final size:39
Alignment explanation
Indices: 5402957--5403064 Score: 135
Period size: 39 Copynumber: 2.7 Consensus size: 39
5402947 AGCAATAGGT
* * ** *
5402957 AAAGGAGTGGTTCAATTGACTTAAATGGATGGGAACAAGG
1 AAAGGAGTGGTTGAGTCAACTT-AATGGATGGCAACAAGG
* *
5402997 AAAGGATTGTTTGAGTCAACTTAATGGATGGCAACAAGG
1 AAAGGAGTGGTTGAGTCAACTTAATGGATGGCAACAAGG
*
5403036 AAAGGAGTGGTTGAGTCTACTTAATGGAT
1 AAAGGAGTGGTTGAGTCAACTTAATGGAT
5403065 AGTAGAGCCT
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
39 42 0.72
40 16 0.28
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.26
Consensus pattern (39 bp):
AAAGGAGTGGTTGAGTCAACTTAATGGATGGCAACAAGG
Found at i:5407388 original size:18 final size:19
Alignment explanation
Indices: 5407365--5407402 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
5407355 TGGAAGGTTG
*
5407365 CTTCTT-TTTTAGTCATTC
1 CTTCTTATTTGAGTCATTC
5407383 CTTCTTAATTTGAGTCATTC
1 CTTCTT-ATTTGAGTCATTC
5407403 ATAAGGCCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.16, C:0.21, G:0.08, T:0.55
Consensus pattern (19 bp):
CTTCTTATTTGAGTCATTC
Found at i:5424257 original size:28 final size:28
Alignment explanation
Indices: 5424212--5424269 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
5424202 TAATGACTTC
*
5424212 ATAAAAACTTATTTAATTTAAAATAAAAAT
1 ATAAAAAC-TATTAAATTTAAAA-AAAAAT
*
5424242 ATAAAAA-TATTAAATTTAATAAAAAAT
1 ATAAAAACTATTAAATTTAAAAAAAAAT
5424269 A
1 A
5424270 AATGTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 7 0.27
28 12 0.46
30 7 0.27
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (28 bp):
ATAAAAACTATTAAATTTAAAAAAAAAT
Found at i:5424299 original size:22 final size:24
Alignment explanation
Indices: 5424274--5424328 Score: 73
Period size: 22 Copynumber: 2.4 Consensus size: 24
5424264 AAAATAAATG
5424274 TTTATTTAAA-TTTTTTAAA-TAA
1 TTTATTTAAATTTTTTTAAATTAA
5424296 TTTA--TAAATTTTTTTAAATTAA
1 TTTATTTAAATTTTTTTAAATTAA
5424318 TTTATCTTAAA
1 TTTAT-TTAAA
5424329 ATATTATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
20 4 0.14
21 9 0.32
22 11 0.39
25 4 0.14
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTATTTAAATTTTTTTAAATTAA
Found at i:5424308 original size:21 final size:21
Alignment explanation
Indices: 5424280--5424322 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
5424270 AATGTTTATT
5424280 TAAATTTTTTAAA-TAATTTA
1 TAAATTTTTTAAATTAATTTA
5424300 TAAATTTTTTTAAATTAATTTA
1 TAAA-TTTTTTAAATTAATTTA
5424322 T
1 T
5424323 CTTAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.19
21 9 0.43
22 8 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TAAATTTTTTAAATTAATTTA
Found at i:5429240 original size:33 final size:33
Alignment explanation
Indices: 5429203--5429265 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
5429193 ACTAAATTAG
*
5429203 TATATT-TCATCATTATCAATTATGATATGTCAA
1 TATATTAT-ATCATCATCAATTATGATATGTCAA
* *
5429236 TATATTATATTATCATTAATTATGATATGT
1 TATATTATATCATCATCAATTATGATATGT
5429266 TAACATATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 25 0.96
34 1 0.04
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (33 bp):
TATATTATATCATCATCAATTATGATATGTCAA
Found at i:5429430 original size:62 final size:60
Alignment explanation
Indices: 5429287--5429431 Score: 183
Period size: 55 Copynumber: 2.5 Consensus size: 60
5429277 ATTAATGCCA
5429287 TATGACATAAAATTACAAATGACATTTTGACTCAAAATAAAAATATAATTGAGGACTTATT
1 TATGACATAAAA-TACAAATGACATTTTGACTCAAAATAAAAATATAATTGAGGACTTATT
* * * * *
5429348 T-TG---TGACATA-AAATGTCATTTTGATTCAAAATAAAAATATAATTGAGGATTTATCT
1 TATGACATAAAATACAAATGACATTTTGACTCAAAATAAAAATATAATTGAGGACTTAT-T
5429404 TATGACATAAAATAACAAATGACATTTT
1 TATGACATAAAAT-ACAAATGACATTTT
5429432 ATCAATTATT
Statistics
Matches: 69, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
55 41 0.59
56 4 0.06
57 5 0.07
60 6 0.09
61 2 0.03
62 11 0.16
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.35
Consensus pattern (60 bp):
TATGACATAAAATACAAATGACATTTTGACTCAAAATAAAAATATAATTGAGGACTTATT
Found at i:5429519 original size:30 final size:29
Alignment explanation
Indices: 5429458--5429545 Score: 88
Period size: 34 Copynumber: 2.8 Consensus size: 29
5429448 AAGAGTTTAT
*
5429458 TTGATTCAAAATAAAAATATAATTAAGAACTTAG
1 TTGATTC-AAATAAAAATAT-A--AA-AACTTAA
5429492 TTGATTCGAAATAAAAATATAAAAACTTAA
1 TTGATTC-AAATAAAAATATAAAAACTTAA
*
5429522 TTGAAT-ATAATAAAAATATAAAAA
1 TTGATTCA-AATAAAAATATAAAAA
5429546 TTTATATAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
28 1 0.02
29 16 0.32
30 11 0.22
31 2 0.04
33 1 0.02
34 19 0.38
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.31
Consensus pattern (29 bp):
TTGATTCAAATAAAAATATAAAAACTTAA
Found at i:5436396 original size:14 final size:15
Alignment explanation
Indices: 5436368--5436398 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
5436358 ATTTCTTAAA
5436368 ATGATAAATAATAAC
1 ATGATAAATAATAAC
5436383 ATGATAAA-AATAAC
1 ATGATAAATAATAAC
5436397 AT
1 AT
5436399 AATTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (15 bp):
ATGATAAATAATAAC
Found at i:5436540 original size:9 final size:9
Alignment explanation
Indices: 5436483--5436548 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
5436473 AACTTTAAAA
*
5436483 AATTAAATT
1 AATTAATTT
5436492 AATTAATTT
1 AATTAATTT
5436501 AAATT-ATTT
1 -AATTAATTT
* *
5436510 TA-TAAATT
1 AATTAATTT
*
5436518 -ATTAA-TC
1 AATTAATTT
5436525 AATTAATTT
1 AATTAATTT
5436534 AATTAATTT
1 AATTAATTT
5436543 ATATTA
1 A-ATTA
5436549 TAAGTGTAGC
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
7 3 0.07
8 12 0.26
9 23 0.50
10 8 0.17
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (9 bp):
AATTAATTT
Found at i:5439667 original size:2 final size:2
Alignment explanation
Indices: 5439656--5439696 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
5439646 TAGAGAAGAT
*
5439656 TA TA -A TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5439697 AATGATGCAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:5453386 original size:24 final size:25
Alignment explanation
Indices: 5453333--5453391 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
5453323 AAGTTGTATC
5453333 ATTAATTTA-ATATATACATAATAA
1 ATTAATTTATATATATACATAATAA
*
5453357 AGTAATATTATATATATACA-AAT-A
1 ATTAAT-TTATATATATACATAATAA
*
5453381 TTTAATTTATA
1 ATTAATTTATA
5453392 CATTAGCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 5 0.17
24 10 0.33
25 6 0.20
26 9 0.30
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (25 bp):
ATTAATTTATATATATACATAATAA
Found at i:5453588 original size:22 final size:23
Alignment explanation
Indices: 5453563--5453608 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5453553 TATTAATTTC
5453563 ATATATATA-ATAAATTATACAT
1 ATATATATATATAAATTATACAT
* * *
5453585 ATATATGTATTTAATTTATACAT
1 ATATATATATATAAATTATACAT
5453608 A
1 A
5453609 ATTTGTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (23 bp):
ATATATATATATAAATTATACAT
Found at i:5458533 original size:37 final size:37
Alignment explanation
Indices: 5458489--5458562 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
5458479 AATTAGTTTG
5458489 ACAAATATAGTTTATCATACAGTCCCCACAAAATTAA
1 ACAAATATAGTTTATCATACAGTCCCCACAAAATTAA
*
5458526 ACAAATATAGTTTATTATACAGTCCCCACAAAATTAA
1 ACAAATATAGTTTATCATACAGTCCCCACAAAATTAA
5458563 GCAGGATGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.46, C:0.20, G:0.05, T:0.28
Consensus pattern (37 bp):
ACAAATATAGTTTATCATACAGTCCCCACAAAATTAA
Found at i:5463771 original size:18 final size:20
Alignment explanation
Indices: 5463736--5463778 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5463726 ATTTTATTAT
*
5463736 TATTTTTAAATGTATTAAGA
1 TATTTTTAAATGTATTAAAA
5463756 TATTTTTAAAT-T-TTAAAA
1 TATTTTTAAATGTATTAAAA
5463774 TATTT
1 TATTT
5463779 AAATAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
19 1 0.05
20 11 0.50
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TATTTTTAAATGTATTAAAA
Found at i:5472271 original size:20 final size:22
Alignment explanation
Indices: 5472220--5472274 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
5472210 GATGAATCTT
*
5472220 AATTTATAAATA-ATTTTTTAA
1 AATTAATAAATATATTTTTTAA
5472241 AATTAATAAATATATTTTTT-A
1 AATTAATAAATATATTTTTTAA
5472262 AATTAA-AAATATA
1 AATTAATAAATATA
5472275 AATTTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 7 0.22
21 18 0.56
22 7 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AATTAATAAATATATTTTTTAA
Found at i:5472280 original size:20 final size:22
Alignment explanation
Indices: 5472235--5472280 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
5472225 ATAAATAATT
*
5472235 TTTTAAAATTAATAAATAT-AT
1 TTTTAAAATTAATAAATATAAA
*
5472256 TTTTTAAATTAA-AAATATAAA
1 TTTTAAAATTAATAAATATAAA
5472277 TTTT
1 TTTT
5472281 TTTTAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTAAAATTAATAAATATAAA
Found at i:5472280 original size:21 final size:23
Alignment explanation
Indices: 5472229--5472282 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 23
5472219 TAATTTATAA
5472229 ATAATTTTTTAAAATTAATAAAT
1 ATAATTTTTTAAAATTAATAAAT
5472252 AT-ATTTTTT-AAATTAA-AAAT
1 ATAATTTTTTAAAATTAATAAAT
5472272 ATAAATTTTTT
1 AT-AATTTTTT
5472283 TTAAAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.21
21 7 0.24
22 14 0.48
23 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATAATTTTTTAAAATTAATAAAT
Found at i:5479912 original size:122 final size:122
Alignment explanation
Indices: 5479770--5480028 Score: 500
Period size: 122 Copynumber: 2.1 Consensus size: 122
5479760 AATACGTTTA
5479770 AATGATAAATTAAATGAATAATAAATAAATTATGAATTATACAAAACATAATAACACAATTCATT
1 AATGATAAATTAAATGAATAATAAATAAATTATGAATTATACAAAACATAATAACACAATTCATT
5479835 TAATGGATTAAACAAATTTGATACATTTAAGATACAAAATTTTGATATTTTAATTAT
66 TAATGGATTAAACAAATTTGATACATTTAAGATACAAAATTTTGATATTTTAATTAT
5479892 AATGATAAATTAAATGAATAATAAATAAATTATGAATTATACAAAACATAATAACACAATTCATT
1 AATGATAAATTAAATGAATAATAAATAAATTATGAATTATACAAAACATAATAACACAATTCATT
5479957 TAATGGATTAAACAAATTTGATACATTTAAGATACAAAATTTTGATATTTTAATTAT
66 TAATGGATTAAACAAATTTGATACATTTAAGATACAAAATTTTGATATTTTAATTAT
*
5480014 AATAATATAATTAAA
1 AATGATA-AATTAAA
5480029 ATACGAATAT
Statistics
Matches: 135, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
122 128 0.95
123 7 0.05
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (122 bp):
AATGATAAATTAAATGAATAATAAATAAATTATGAATTATACAAAACATAATAACACAATTCATT
TAATGGATTAAACAAATTTGATACATTTAAGATACAAAATTTTGATATTTTAATTAT
Found at i:5495373 original size:6 final size:6
Alignment explanation
Indices: 5495358--5495390 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
5495348 CATCACCTTA
5495358 AAAAAG AAAAA- AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
5495391 TCCATAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:5495373 original size:11 final size:11
Alignment explanation
Indices: 5495357--5495390 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
5495347 CCATCACCTT
5495357 AAAAAAGAAAA
1 AAAAAAGAAAA
5495368 AAAAAAGAAAA
1 AAAAAAGAAAA
5495379 AGAAAAAGAAAA
1 A-AAAAAGAAAA
5495391 TCCATAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:5497812 original size:26 final size:26
Alignment explanation
Indices: 5497776--5497839 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
5497766 TTCCTCATTT
*
5497776 ATCGTATGAACACATCAATGTTGCAA
1 ATCGTATGAACACATCAATGATGCAA
5497802 ATCGTATGAACACATCAATGATGCAA
1 ATCGTATGAACACATCAATGATGCAA
*
5497828 ATTGTATGAACA
1 ATCGTATGAACA
5497840 TGCTGAATAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.27
Consensus pattern (26 bp):
ATCGTATGAACACATCAATGATGCAA
Found at i:5507105 original size:32 final size:34
Alignment explanation
Indices: 5507069--5507151 Score: 98
Period size: 34 Copynumber: 2.5 Consensus size: 34
5507059 TTTTAATGTC
* *
5507069 ATATATTTTATTTTTA-TT-TTTATTATAATCTT
1 ATATATTTTATTTTTATTTCTTTAATATAATATT
*
5507101 ATATATTTTATTTTCATTTCTTTAATATAATATT
1 ATATATTTTATTTTTATTTCTTTAATATAATATT
* *
5507135 TTATATTATATATTTTA
1 ATATATTTTAT-TTTTA
5507152 ATTTAATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
32 15 0.36
33 2 0.05
34 21 0.50
35 4 0.10
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (34 bp):
ATATATTTTATTTTTATTTCTTTAATATAATATT
Found at i:5507204 original size:21 final size:22
Alignment explanation
Indices: 5507180--5507228 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
5507170 TATTACATAA
*
5507180 ATTTTAAAT-TTTTTATATTTT
1 ATTTTAAATATTTTTATATTAT
*
5507201 ATTTT-ATTATTTTTATATTAT
1 ATTTTAAATATTTTTATATTAT
5507222 ATATTTA
1 AT-TTTA
5507229 TTTTAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 2 0.09
21 18 0.78
22 3 0.13
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
ATTTTAAATATTTTTATATTAT
Found at i:5507211 original size:13 final size:12
Alignment explanation
Indices: 5507190--5507233 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
5507180 ATTTTAAATT
5507190 TTTTATATTTTA
1 TTTTATATTTTA
5507202 TTTTATTATTTTTA
1 TTTTA-TA-TTTTA
*
5507216 TATTATATATTTA
1 TTTTATAT-TTTA
5507229 TTTTA
1 TTTTA
5507234 ATTATAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 6 0.22
13 12 0.44
14 9 0.33
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTATATTTTA
Found at i:5507546 original size:36 final size:36
Alignment explanation
Indices: 5507499--5507573 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
5507489 TAAGATCATT
5507499 AATAATTAGAATATTTGGTCTAATCTAACAAAAGGA
1 AATAATTAGAATATTTGGTCTAATCTAACAAAAGGA
5507535 AATAATTAGAATATTTGGTCTAATCTAACAAAAGGA
1 AATAATTAGAATATTTGGTCTAATCTAACAAAAGGA
5507571 AAT
1 AAT
5507574 TTTGGGATGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.48, C:0.08, G:0.13, T:0.31
Consensus pattern (36 bp):
AATAATTAGAATATTTGGTCTAATCTAACAAAAGGA
Found at i:5512284 original size:35 final size:35
Alignment explanation
Indices: 5512236--5512330 Score: 158
Period size: 35 Copynumber: 2.7 Consensus size: 35
5512226 AAAAAGGTAG
5512236 ATTTTATTT-AAAAAAATTATATATTAATAATATTT
1 ATTTT-TTTAAAAAAAATTATATATTAATAATATTT
5512271 ATTTTTTTAAAAAAAATTATATATTAATAATATTT
1 ATTTTTTTAAAAAAAATTATATATTAATAATATTT
*
5512306 A-TTTTTTAAAAAAAATTAAATATTA
1 ATTTTTTTAAAAAAAATTATATATTA
5512331 TCAAAAAATA
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
34 26 0.45
35 32 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
ATTTTTTTAAAAAAAATTATATATTAATAATATTT
Found at i:5512558 original size:17 final size:18
Alignment explanation
Indices: 5512536--5512575 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
5512526 TTAATTAGGC
5512536 TTTAATTGTAAG-TAA-TT
1 TTTAATT-TAAGTTAAGTT
5512553 TTTAATTTAAGTTAAGTT
1 TTTAATTTAAGTTAAGTT
5512571 TTTAA
1 TTTAA
5512576 ATATTTTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.19
17 10 0.48
18 7 0.33
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (18 bp):
TTTAATTTAAGTTAAGTT
Found at i:5512898 original size:14 final size:16
Alignment explanation
Indices: 5512870--5512901 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
5512860 ATTTTATGAA
5512870 TTTTAATATATTTATT
1 TTTTAATATATTTATT
5512886 TTTTAAT-TA-TTATT
1 TTTTAATATATTTATT
5512900 TT
1 TT
5512902 AATCATGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTAATATATTTATT
Found at i:5513788 original size:97 final size:97
Alignment explanation
Indices: 5513671--5513966 Score: 504
Period size: 97 Copynumber: 3.1 Consensus size: 97
5513661 GGCAACGCTC
*
5513671 TCATT-GCCGTTGGCCACCCTGTCTACCTTGATCCGTTAGGGCGCTAGGCGTGAGTCGGATGAGA
1 TCATTAGCCGTTGGCCACCCTGTCTACCTTGATCCGTTAGGGCGCTTGGCGTGAGTCGGATGAGA
* *
5513735 TCTGGTTGACTCTGATACCGCTTGTCATGGGG
66 TCTGGTTGACTCTGATACCACTTGTCACGGGG
5513767 TCATTAGCCGTTGGCCACCCTGTCTACCTTGATCCGTTAGGGCGCTTGGCGTGAGTCGGATGAGA
1 TCATTAGCCGTTGGCCACCCTGTCTACCTTGATCCGTTAGGGCGCTTGGCGTGAGTCGGATGAGA
*
5513832 TCTGGTTGACTCTGATACTACTTGTCACGGGG
66 TCTGGTTGACTCTGATACCACTTGTCACGGGG
* * * *
5513864 TCATTAGCCGTTGGCCACCCTGCCTACCTCGATCCGTTAGGGCGCTTGGCGTAAGTGGGATGAGA
1 TCATTAGCCGTTGGCCACCCTGTCTACCTTGATCCGTTAGGGCGCTTGGCGTGAGTCGGATGAGA
*
5513929 TCTGGTTGATTCTGATACCACTTGTCACGGGG
66 TCTGGTTGACTCTGATACCACTTGTCACGGGG
5513961 TCATTA
1 TCATTA
5513967 CCCTCTCCCC
Statistics
Matches: 189, Mismatches: 10, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
96 5 0.03
97 184 0.97
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.29
Consensus pattern (97 bp):
TCATTAGCCGTTGGCCACCCTGTCTACCTTGATCCGTTAGGGCGCTTGGCGTGAGTCGGATGAGA
TCTGGTTGACTCTGATACCACTTGTCACGGGG
Found at i:5514283 original size:213 final size:213
Alignment explanation
Indices: 5513909--5514305 Score: 510
Period size: 213 Copynumber: 1.9 Consensus size: 213
5513899 GTTAGGGCGC
* * * * *
5513909 TTGGCGTAAGTGGGATGAGATCTGGTTGATTCTGATACCACTTGTCACGGGGTCATTACCCTCTC
1 TTGGCGTAAGTCGGATGAGATCCGATTGACTCTGATACCACTTGTCACGAGGTCATTACCCTCTC
* **
5513974 CCCAAAAGACGTGCTTGTTGAGGTGTGTAGCACACCCGTTTATAAGGAACCCAAGACCTTCCACT
66 CCCAAAAGACGTGCTTGTTGAGGTGTGAAGCACACCCACTTATAAGGAACCCAAGACCTTCCACT
* * *
5514039 CTTGTCCGATGTGGGATAGAGGCATCCTTTGTGACACTCTCTCCCACTCGATTCTGGTAACTCCC
131 CCTATCCGATGTGGGATAGAGGCACCCTTTGTGACACTCTCTCCCACTCGATTCTGGTAACTCCC
5514104 TCCGGTCTATTGGGACGT
196 TCCGGTCTATTGGGACGT
* * * * * *
5514122 TTGGCGTGAGTCGGATGAGGTCCGATTGACTCTGATATCACTTGTCACGAGGTTATTACCCTTTT
1 TTGGCGTAAGTCGGATGAGATCCGATTGACTCTGATACCACTTGTCACGAGGTCATTACCCTCTC
* * * * * * * **
5514187 CTCAAAAGACGAAT-C-TGTTGGGGTGTGAAGGACACCTACTTATAAGGAGCCTAGGACCTTCTG
66 CCCAAAAGACG--TGCTTGTTGAGGTGTGAAGCACACCCACTTATAAGGAACCCAAGACCTTCCA
* *
5514250 TTCCTATCCGATGTGGGATAGAGGCACCCTTTGTGACATTCTCTCCCACTCGATTC
129 CTCCTATCCGATGTGGGATAGAGGCACCCTTTGTGACACTCTCTCCCACTCGATTC
5514306 CAGCAACGCC
Statistics
Matches: 154, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
213 152 0.99
214 1 0.01
215 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.30
Consensus pattern (213 bp):
TTGGCGTAAGTCGGATGAGATCCGATTGACTCTGATACCACTTGTCACGAGGTCATTACCCTCTC
CCCAAAAGACGTGCTTGTTGAGGTGTGAAGCACACCCACTTATAAGGAACCCAAGACCTTCCACT
CCTATCCGATGTGGGATAGAGGCACCCTTTGTGACACTCTCTCCCACTCGATTCTGGTAACTCCC
TCCGGTCTATTGGGACGT
Found at i:5519881 original size:23 final size:23
Alignment explanation
Indices: 5519855--5519910 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
5519845 TTTAAAAAAT
**
5519855 TTTAATAAATATTTTTTATTATA
1 TTTAATAAATATTTTACATTATA
*
5519878 TTTAATTAAA-ATTTTACATTTTA
1 TTTAA-TAAATATTTTACATTATA
*
5519901 TTTAAAAAAT
1 TTTAATAAAT
5519911 TATATAACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 3 0.11
23 20 0.74
24 4 0.15
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTAATAAATATTTTACATTATA
Found at i:5520050 original size:25 final size:26
Alignment explanation
Indices: 5520020--5520077 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 26
5520010 CTATATTAAT
* *
5520020 TATAAAATTTTATTTAAT-TAAAAAA
1 TATAAAATTTAATTAAATATAAAAAA
5520045 TATAAAATTTAATTAAATATAAAAAA
1 TATAAAATTTAATTAAATATAAAAAA
5520071 TATAAAA
1 TATAAAA
5520078 AAATTTCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 16 0.53
26 14 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
TATAAAATTTAATTAAATATAAAAAA
Found at i:5520060 original size:24 final size:27
Alignment explanation
Indices: 5520020--5520077 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 27
5520010 CTATATTAAT
*
5520020 TATAAAATTTT-ATTTAAT-TAAAAAA
1 TATAAAATTTTAATTAAATATAAAAAA
5520045 TATAAAA-TTTAATTAAATATAAAAAA
1 TATAAAATTTTAATTAAATATAAAAAA
5520071 TATAAAA
1 TATAAAA
5520078 AAATTTCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 3 0.10
25 13 0.43
26 14 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
TATAAAATTTTAATTAAATATAAAAAA
Found at i:5520133 original size:21 final size:21
Alignment explanation
Indices: 5520092--5520135 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5520082 TTCAATTTGA
**
5520092 TTGAAGAGTTGAAAATTTTTT
1 TTGAAGAGTTGAAAAAATTTT
5520113 TTGAAGAGTTGAAAAAATTTT
1 TTGAAGAGTTGAAAAAATTTT
5520134 TT
1 TT
5520136 AAAACATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (21 bp):
TTGAAGAGTTGAAAAAATTTT
Found at i:5527180 original size:24 final size:24
Alignment explanation
Indices: 5527159--5527223 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
5527149 GACCCAAATC
* *
5527159 AGGCTCTTCCTTAACTTTCAAAAA
1 AGGCTCCTCCTTCACTTTCAAAAA
* *
5527183 AGGCTCGTCCTTCACTTTTAAAAA
1 AGGCTCCTCCTTCACTTTCAAAAA
5527207 AGGCTCCTCCTTCACTT
1 AGGCTCCTCCTTCACTT
5527224 GGGTATTAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (24 bp):
AGGCTCCTCCTTCACTTTCAAAAA
Found at i:5536935 original size:99 final size:99
Alignment explanation
Indices: 5536752--5536936 Score: 234
Period size: 99 Copynumber: 1.9 Consensus size: 99
5536742 GAGGTTGAGA
* * *
5536752 TGGTGATGGTGCTCAAGCTAAATGTAAATATTAAGGTGATAATGACAGCAGTCAAAGAGCGATGG
1 TGGTGATGGTGCTCAAGCTAAATGAAAATATTAAGGTGATAATGACAGCAATCAAAGAGCGATAG
** *
5536817 TGTTATGAAAGATACCAGGGTGTTTTGATGGAGG
66 TGTTACAAAAGATAACAGGGTGTTTTGATGGAGG
* *
5536851 TGGTGATGGTGCTCAAGC-AAATTGAAAATATTATGGTGGTAATGACAGCAAT-AGAAGA-CTGA
1 TGGTGATGGTGCTCAAGCTAAA-TGAAAATATTAAGGTGATAATGACAGCAATCA-AAGAGC-GA
5536913 TAGTGTTAACAAAAG-TAACAGGGT
63 TAGTGTT-ACAAAAGATAACAGGGT
5536937 ATTACTGTGA
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
98 5 0.07
99 64 0.86
100 5 0.07
ACGTcount: A:0.35, C:0.09, G:0.29, T:0.26
Consensus pattern (99 bp):
TGGTGATGGTGCTCAAGCTAAATGAAAATATTAAGGTGATAATGACAGCAATCAAAGAGCGATAG
TGTTACAAAAGATAACAGGGTGTTTTGATGGAGG
Found at i:5543523 original size:14 final size:16
Alignment explanation
Indices: 5543484--5543530 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
5543474 ATAAATTGCA
*
5543484 AATTCATTATTTTTTG
1 AATTCTTTATTTTTTG
5543500 AATTCTTTATTTTTTG
1 AATTCTTTATTTTTTG
*
5543516 AA-TC-TTATTATTTG
1 AATTCTTTATTTTTTG
5543530 A
1 A
5543531 TAATATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 10 0.34
15 2 0.07
16 17 0.59
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (16 bp):
AATTCTTTATTTTTTG
Found at i:5551778 original size:35 final size:33
Alignment explanation
Indices: 5551720--5551785 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 33
5551710 GTTCTAAGGG
5551720 GAAGAAAGAGAAAACAAGGGTTCTATAAGGAGA
1 GAAGAAAGAGAAAACAAGGGTTCTATAAGGAGA
* * *
5551753 GAAGAAAGCACGACAACGAGGGTTCTATGAGGA
1 GAAGAAAG-A-GAAAACAAGGGTTCTATAAGGA
5551786 AACTCATAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 8 0.29
34 1 0.04
35 19 0.68
ACGTcount: A:0.45, C:0.11, G:0.32, T:0.12
Consensus pattern (33 bp):
GAAGAAAGAGAAAACAAGGGTTCTATAAGGAGA
Found at i:5561908 original size:31 final size:31
Alignment explanation
Indices: 5561870--5561943 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 31
5561860 AATTTTTTAA
* * *
5561870 ATATTTTTATATTAT-ATTTAATTAAGTTATT
1 ATATTTTTATATTATGAATTAAATAAATT-TT
5561901 ATATTTTTAT-TT-TGAATTAAATAAATTTT
1 ATATTTTTATATTATGAATTAAATAAATTTT
*
5561930 ATATTTTTAAATTA
1 ATATTTTTATATTA
5561944 AATAAATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
29 12 0.33
30 14 0.39
31 10 0.28
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (31 bp):
ATATTTTTATATTATGAATTAAATAAATTTT
Found at i:5561936 original size:23 final size:23
Alignment explanation
Indices: 5561903--5561956 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 23
5561893 AAGTTATTAT
*
5561903 ATTTTTA-TTTTGAATTAAATAA
1 ATTTTTATTTTTAAATTAAATAA
5561925 ATTTTATATTTTTAAATTAAATAA
1 ATTTT-TATTTTTAAATTAAATAA
5561949 ATTTTTAT
1 ATTTTTAT
5561957 AATTAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 5 0.17
23 5 0.17
24 19 0.66
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
ATTTTTATTTTTAAATTAAATAA
Found at i:5581530 original size:21 final size:22
Alignment explanation
Indices: 5581497--5581537 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5581487 CCGGCTGAGG
* *
5581497 TGTCTCCTGCGTCTG-CGTATC
1 TGTCGCCTCCGTCTGACGTATC
5581518 TGTCGCCTCCGTCTGACGTA
1 TGTCGCCTCCGTCTGACGTA
5581538 GAAGTGCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.07, C:0.34, G:0.24, T:0.34
Consensus pattern (22 bp):
TGTCGCCTCCGTCTGACGTATC
Found at i:5584140 original size:31 final size:30
Alignment explanation
Indices: 5584096--5584157 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
5584086 TAATAAAATG
* *
5584096 TTTTTAAATATGACGTGTAATAATAATTTTT
1 TTTTTAAACATGACATGTAATAA-AATTTTT
* *
5584127 TTTTTCAACATGACATGTAATAAACTTTTT
1 TTTTTAAACATGACATGTAATAAAATTTTT
5584157 T
1 T
5584158 AACTATAGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (30 bp):
TTTTTAAACATGACATGTAATAAAATTTTT
Found at i:5584352 original size:76 final size:78
Alignment explanation
Indices: 5584169--5584352 Score: 185
Period size: 76 Copynumber: 2.4 Consensus size: 78
5584159 ACTATAGTGT
* * * * * *
5584169 GTAACATATTTTTGTGCATGGCATGTAATAATAGTATTTTTTTTTTCAATATAACATATAAGAAT
1 GTAATATATTTTTGTACATGGCGTGTAACAATAGTATTTTTTTTTTCAATATAACATATAACAAC
* * * **
5584234 TTAATCATGGTGT
66 CTAACCATGATAC
* ** * * *
5584247 GTAACT-TGTTTTTGTACATGATGTATAACAATAGTA-TTTTTTTTT-AATATAACATGTATCAA
1 GTAA-TATATTTTTGTACATGGCGTGTAACAATAGTATTTTTTTTTTCAATATAACATATAACAA
5584309 CCTAACCATGATAC
65 CCTAACCATGATAC
5584323 GTAATATATTTTTGTACATGGCGTGTAACA
1 GTAATATATTTTTGTACATGGCGTGTAACA
5584353 TCATAGCTTA
Statistics
Matches: 83, Mismatches: 21, Indels: 6
0.75 0.19 0.05
Matches are distributed among these distances:
75 1 0.01
76 46 0.55
77 9 0.11
78 27 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (78 bp):
GTAATATATTTTTGTACATGGCGTGTAACAATAGTATTTTTTTTTTCAATATAACATATAACAAC
CTAACCATGATAC
Found at i:5584463 original size:13 final size:13
Alignment explanation
Indices: 5584419--5584466 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 13
5584409 AAATTATAAA
5584419 AAAAATTATTTTT
1 AAAAATTATTTTT
*
5584432 GAAAACATCTTACTTTT
1 -AAAA-A--TTATTTTT
5584449 AAAAATTATTTTT
1 AAAAATTATTTTT
5584462 AAAAA
1 AAAAA
5584467 CACCCATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 12 0.41
14 4 0.14
15 2 0.07
16 4 0.14
17 7 0.24
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (13 bp):
AAAAATTATTTTT
Found at i:5590052 original size:15 final size:15
Alignment explanation
Indices: 5590032--5590087 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
5590022 NNNNNNNCAG
5590032 GTAATGTGATTGCAA
1 GTAATGTGATTGCAA
* *
5590047 GTAATGTTATTACAA
1 GTAATGTGATTGCAA
5590062 GTAATGTGATTGCAA
1 GTAATGTGATTGCAA
*
5590077 GCAATGTGATT
1 GTAATGTGATT
5590088 ACAGGAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (15 bp):
GTAATGTGATTGCAA
Found at i:5590068 original size:30 final size:30
Alignment explanation
Indices: 5590032--5590090 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
5590022 NNNNNNNCAG
* *
5590032 GTAATGTGATTGCAAGTAATGTTATTACAA
1 GTAATGTGATTGCAAGCAATGTGATTACAA
5590062 GTAATGTGATTGCAAGCAATGTGATTACA
1 GTAATGTGATTGCAAGCAATGTGATTACA
5590091 GGAAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (30 bp):
GTAATGTGATTGCAAGCAATGTGATTACAA
Found at i:5590387 original size:23 final size:21
Alignment explanation
Indices: 5590313--5590493 Score: 106
Period size: 22 Copynumber: 8.3 Consensus size: 21
5590303 TCATATATTT
*
5590313 TATTTTTTA-TTTATTATTAAA
1 TATTTTATATTTTATTATT-AA
*
5590334 TATTTTATATTTTATTTTTAA
1 TATTTTATATTTTATTATTAA
5590355 TATATTTATATTTTTATTATTAA
1 TAT-TTTATA-TTTTATTATTAA
* *
5590378 T-TTTTATATAATATCATTTCTTAA
1 TATTTTATAT--T-TTA-TTATTAA
* * * **
5590402 TATATTTTTAATGTCATATATTTT
1 TAT-TTTAT-ATTTTAT-TATTAA
5590426 TATTTTAT-TTATTATTA-TAA
1 TATTTTATATT-TTATTATTAA
*
5590446 TA-TTTATATTTTATTTTTAA
1 TATTTTATATTTTATTATTAA
5590466 TATATTTATA-TTTATATATTAA
1 TAT-TTTATATTTTAT-TATTAA
5590488 T-TTTTA
1 TATTTTA
5590494 ATATATCATA
Statistics
Matches: 126, Mismatches: 17, Indels: 35
0.71 0.10 0.20
Matches are distributed among these distances:
19 10 0.08
20 15 0.12
21 28 0.22
22 31 0.25
23 19 0.15
24 16 0.13
25 1 0.01
26 4 0.03
27 2 0.02
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.65
Consensus pattern (21 bp):
TATTTTATATTTTATTATTAA
Found at i:5590475 original size:6 final size:6
Alignment explanation
Indices: 5590418--5590482 Score: 55
Period size: 6 Copynumber: 10.8 Consensus size: 6
5590408 TTTAATGTCA
* * *
5590418 TATATT TTTATT T-TATT TATTATT ATAATATT TATATT T-TATT TTTA-A
1 TATATT TATATT TATATT TA-TATT -T-ATATT TATATT TATATT TATATT
5590466 TATATT TATATT TATAT
1 TATATT TATATT TATAT
5590483 ATTAATTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
5 13 0.27
6 25 0.51
7 5 0.10
8 5 0.10
9 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATATT
Found at i:5590475 original size:31 final size:29
Alignment explanation
Indices: 5590300--5590608 Score: 178
Period size: 29 Copynumber: 10.9 Consensus size: 29
5590290 TATATTTTTA
*
5590300 ATATCATATATTT-TATTTT-TTATTT-AT
1 ATATTATATATTTATATTTTATT-TTTAAT
*
5590327 -TATTAAATATTTTATATTTTATTTTTAAT
1 ATATTATATA-TTTATATTTTATTTTTAAT
*
5590356 ATATT-TATATTTTTATTATTAATTTTT-AT
1 ATATTATATATTTATATT-TT-ATTTTTAAT
* * *
5590385 ATA--ATATCATTTCTTAATATATTTTTAAT
1 ATATTATAT-ATTT-ATATTTTATTTTTAAT
*
5590414 GTCA-TATAT-TTT-TATTTTA--TTT-AT
1 AT-ATTATATATTTATATTTTATTTTTAAT
5590438 -TATTATAATATTTATATTTTATTTTTAAT
1 ATATTAT-ATATTTATATTTTATTTTTAAT
*
5590467 ATATT-TATATTTATATATTAATTTTTAAT
1 ATATTATATATTTATAT-TTTATTTTTAAT
* *
5590496 ATATCATAT-TTTA-A-TATATTTTTAAT
1 ATATTATATATTTATATTTTATTTTTAAT
* *
5590522 GTCA-TATAT-TTTAT-TTTTATTTATTATT
1 AT-ATTATATATTTATATTTTATTT-TTAAT
*
5590550 ATAATTTATATATTTAT-TTTCATTCTTTAAT
1 AT-A-TTATATATTTATATTTTATT-TTTAAT
*
5590581 ATATTTTTTATATTATATATTTTATTTT
1 ATA--TTATATATT-TATATTTTATTTT
5590609 AACTTGTTTA
Statistics
Matches: 225, Mismatches: 23, Indels: 63
0.72 0.07 0.20
Matches are distributed among these distances:
22 1 0.00
23 4 0.02
24 4 0.02
25 6 0.03
26 33 0.15
27 15 0.07
28 45 0.20
29 47 0.21
30 28 0.12
31 30 0.13
32 6 0.03
33 6 0.03
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (29 bp):
ATATTATATATTTATATTTTATTTTTAAT
Found at i:5590497 original size:15 final size:15
Alignment explanation
Indices: 5590458--5590515 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
5590448 TTTATATTTT
*
5590458 ATTTTTAATATATTT
1 ATTTTTAATATATTA
*
5590473 ATATTT-ATATATTA
1 ATTTTTAATATATTA
*
5590487 ATTTTTAATATA-TC
1 ATTTTTAATATATTA
5590501 ATATTTTAATATATT
1 AT-TTTTAATATATT
5590516 TTTAATGTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 15 0.42
15 20 0.56
16 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTTAATATATTA
Found at i:5590530 original size:26 final size:25
Alignment explanation
Indices: 5590286--5590534 Score: 135
Period size: 26 Copynumber: 9.1 Consensus size: 25
5590276 ATATCATTTC
5590286 TTAATATATTTTTAATATCATATATT
1 TTAATATATTTTTAATAT-ATATATT
* * * *
5590312 TT-ATTTTTTATTTATTATTAAATATT
1 TTAATATATT-TTTAATA-TATATATT
*
5590338 TTATATTTTATTTTTAATATATTTATATTT
1 TTA-A-TATATTTTTAATATA--TATA-TT
*
5590368 TTATTATTAATTTTT-ATATAATATCATTT
1 TTAATA-T-ATTTTTAATAT-ATAT-A-TT
*
5590397 CTTAATATATTTTTAATGTCATATATTT
1 -TTAATATATTTTTAATAT-ATATA-TT
* * *
5590425 TTATTTTATTTATTATTATA-ATATT
1 TTAATATATTT-TTAATATATATATT
* * *
5590450 TATATTTTATTTTTAATATATTTATAT
1 T-TAATATATTTTTAATATATATAT-T
5590477 TTATATATTAATTTTTAATATATCATATT
1 TTA-ATA-T-ATTTTTAATATAT-ATATT
*
5590506 TTAATATATTTTTAATGTCATATATT
1 TTAATATATTTTTAATAT-ATATATT
5590532 TTA
1 TTA
5590535 TTTTTATTTA
Statistics
Matches: 178, Mismatches: 22, Indels: 46
0.72 0.09 0.19
Matches are distributed among these distances:
25 15 0.08
26 52 0.29
27 19 0.11
28 30 0.17
29 42 0.24
30 20 0.11
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (25 bp):
TTAATATATTTTTAATATATATATT
Done.