Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 133 of 279
Found at i:42823655 original size:16 final size:15
Alignment explanation
Indices: 42823634--42823677 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
42823624 TAAAACAAAA
*
42823634 TAAAATATTTAAATTT
1 TAAAAT-TTTAAAATT
42823650 TAAAATTTTAAAATT
1 TAAAATTTTAAAATT
*
42823665 TATAA-TTTAAAAT
1 TAAAATTTTAAAAT
42823678 CTATATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 8 0.31
15 12 0.46
16 6 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAAATTTTAAAATT
Found at i:42823673 original size:14 final size:14
Alignment explanation
Indices: 42823640--42823686 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
42823630 AAAATAAAAT
* *
42823640 ATTTAAATTTTAAA
1 ATTTAAAATTTATA
42823654 ATTTTAAAATTTATA
1 A-TTTAAAATTTATA
*
42823669 ATTTAAAATCTAT-
1 ATTTAAAATTTATA
42823682 ATTTA
1 ATTTA
42823687 TCAAACAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 5 0.17
14 12 0.41
15 12 0.41
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTTAAAATTTATA
Found at i:42823765 original size:15 final size:15
Alignment explanation
Indices: 42823742--42823783 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
42823732 ATAATTTAAA
*
42823742 TTCAGTACTTAAAAT
1 TTCAATACTTAAAAT
*
42823757 TTCAATACTTAATAT
1 TTCAATACTTAAAAT
*
42823772 TTCAACACTTAA
1 TTCAATACTTAA
42823784 TTTGTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.40
Consensus pattern (15 bp):
TTCAATACTTAAAAT
Found at i:42871247 original size:27 final size:27
Alignment explanation
Indices: 42871214--42871287 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
42871204 GAGGGCATGT
** *
42871214 CACAGGCGGCACCGGTGGTGGGGGTGC
1 CACAGGCGGCACCAATGGAGGGGGTGC
* * *
42871241 CAGAGGCGGCACCAATGGAGGGGTTGT
1 CACAGGCGGCACCAATGGAGGGGGTGC
42871268 CACAGGCGGCACCAATGGAG
1 CACAGGCGGCACCAATGGAG
42871288 AAGAAAAGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.20, C:0.24, G:0.45, T:0.11
Consensus pattern (27 bp):
CACAGGCGGCACCAATGGAGGGGGTGC
Found at i:42871320 original size:14 final size:14
Alignment explanation
Indices: 42871285--42871313 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
42871275 GGCACCAATG
42871285 GAGAAGAA-AAGAA
1 GAGAAGAAGAAGAA
42871298 GAGAAGAAGAAGAA
1 GAGAAGAAGAAGAA
42871312 GA
1 GA
42871314 ACAGAAGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (14 bp):
GAGAAGAAGAAGAA
Found at i:42872017 original size:6 final size:6
Alignment explanation
Indices: 42872008--42872032 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
42871998 TATTTTTGTT
42872008 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
42872033 AATATTATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:42872040 original size:20 final size:20
Alignment explanation
Indices: 42871998--42872040 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
42871988 TGGGATAGCC
* * * *
42871998 TATTTTTGTTTTTTTATTTT
1 TATTTTTATTTTTATAATAT
42872018 TATTTTTATTTTTATAATAT
1 TATTTTTATTTTTATAATAT
42872038 TAT
1 TAT
42872041 GGTAAAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (20 bp):
TATTTTTATTTTTATAATAT
Found at i:42872653 original size:24 final size:24
Alignment explanation
Indices: 42872617--42872662 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
42872607 GAGAGAATTT
*
42872617 TTATTTTATTTAATATCAATATAA
1 TTATTTTATTTAAGATCAATATAA
*
42872641 TTATATTTA-TTAAGATTAATAT
1 TTAT-TTTATTTAAGATCAATAT
42872663 TAATATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
TTATTTTATTTAAGATCAATATAA
Found at i:42873830 original size:5 final size:5
Alignment explanation
Indices: 42873822--42873848 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
42873812 CCCCGCCCCC
42873822 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
42873849 GCCACCAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:42891468 original size:15 final size:15
Alignment explanation
Indices: 42891450--42891488 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
42891440 TTATATAATC
*
42891450 AATATATTTATATTA
1 AATATATTTAAATTA
*
42891465 AATATATTAAAATTA
1 AATATATTTAAATTA
*
42891480 AATAAATTT
1 AATATATTT
42891489 TTGGTCAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATATTTAAATTA
Found at i:42898209 original size:13 final size:12
Alignment explanation
Indices: 42898187--42898222 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
42898177 GTTCAGCCCG
42898187 TATTAATTTTTTA
1 TATT-ATTTTTTA
42898200 TATTATTTTTTA
1 TATTATTTTTTA
*
42898212 TATAATTTTTT
1 TATTATTTTTT
42898223 TAAAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTATTTTTTA
Found at i:42898496 original size:20 final size:21
Alignment explanation
Indices: 42898460--42898502 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
42898450 AAGATAGTGA
*
42898460 AAAAAATAACAAGAAAATAAC
1 AAAAAATAACAAGAAAAAAAC
42898481 AAAAAA-AAC-AGTAAAAAAAC
1 AAAAAATAACAAG-AAAAAAAC
42898501 AA
1 AA
42898503 TAATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 12 0.60
21 6 0.30
ACGTcount: A:0.79, C:0.09, G:0.05, T:0.07
Consensus pattern (21 bp):
AAAAAATAACAAGAAAAAAAC
Found at i:42900733 original size:22 final size:21
Alignment explanation
Indices: 42900707--42900804 Score: 67
Period size: 21 Copynumber: 4.8 Consensus size: 21
42900697 TTGTTAACTA
42900707 TTTACAATTTTTTAATAATTAT
1 TTTACAA-TTTTTAATAATTAT
*
42900729 TTTACGATTTTTAATAA-T-T
1 TTTACAATTTTTAATAATTAT
* ** * *
42900748 TTTAAAAAATTAAATAA-TGT
1 TTTACAATTTTTAATAATTAT
* * *
42900768 TTTATAACTTTTAATAATTTT
1 TTTACAATTTTTAATAATTAT
* *
42900789 TTTAAAATTTTAAATA
1 TTTACAATTTTTAATA
42900805 TTTTAAAAAA
Statistics
Matches: 60, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
19 14 0.23
20 15 0.25
21 25 0.42
22 6 0.10
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTACAATTTTTAATAATTAT
Found at i:42900750 original size:10 final size:10
Alignment explanation
Indices: 42900715--42900789 Score: 55
Period size: 10 Copynumber: 7.5 Consensus size: 10
42900705 TATTTACAAT
42900715 TTTTTAATAA
1 TTTTTAATAA
* **
42900725 TTATTTTACGA
1 TT-TTTAATAA
42900736 TTTTTAATAA
1 TTTTTAATAA
42900746 TTTTTAA-AA
1 TTTTTAATAA
** *
42900755 AATTAAATAA
1 TTTTTAATAA
42900765 TGTTTT-ATAA
1 T-TTTTAATAA
*
42900775 CTTTTAATAA
1 TTTTTAATAA
42900785 TTTTT
1 TTTTT
42900790 TTAAAATTTT
Statistics
Matches: 47, Mismatches: 14, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
9 10 0.21
10 28 0.60
11 9 0.19
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:42900783 original size:20 final size:19
Alignment explanation
Indices: 42900737--42900827 Score: 76
Period size: 20 Copynumber: 4.6 Consensus size: 19
42900727 ATTTTACGAT
42900737 TTTTAATAATTTTTAAAAA
1 TTTTAATAATTTTTAAAAA
* * * *
42900756 ATTAAATAATGTTTTATAAC
1 TTTTAATAAT-TTTTAAAAA
*
42900776 TTTTAATAATTTTTTTAAAA
1 TTTTAATAA-TTTTTAAAAA
*
42900796 TTTTAA-ATATTTTAAAAAAA
1 TTTTAATA-ATTTT-TAAAAA
42900816 TATTTAATAATT
1 T-TTTAATAATT
42900828 ATTACAATAT
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
19 13 0.24
20 32 0.58
21 9 0.16
22 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (19 bp):
TTTTAATAATTTTTAAAAA
Found at i:42916288 original size:16 final size:15
Alignment explanation
Indices: 42916262--42916321 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
42916252 GAGCAAAGGT
42916262 AAATATAATATTATAAA
1 AAAT-TAATATTA-AAA
42916279 AAATTAATA-TAAATA
1 AAATTAATATTAAA-A
*
42916294 AAATTAACATTAAAA
1 AAATTAATATTAAAA
42916309 TAAATTAAT-TTAA
1 -AAATTAATATTAA
42916322 CAATATATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 2 0.05
15 16 0.42
16 16 0.42
17 4 0.11
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
AAATTAATATTAAAA
Found at i:42916305 original size:21 final size:21
Alignment explanation
Indices: 42916281--42916338 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
42916271 ATTATAAAAA
42916281 ATTAATATAAATAAAATTAAC
1 ATTAATATAAATAAAATTAAC
* * *
42916302 ATTAAAATAAATTAATTTAAC
1 ATTAATATAAATAAAATTAAC
*
42916323 AATATATAATAAATAA
1 ATTA-AT-ATAAATAA
42916339 CTTATAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
21 21 0.72
22 1 0.03
23 7 0.24
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (21 bp):
ATTAATATAAATAAAATTAAC
Found at i:42916355 original size:23 final size:23
Alignment explanation
Indices: 42916307--42916368 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
42916297 TTAACATTAA
*
42916307 AATAAATTAATTTAACAATATAT
1 AATAAATTAATTTAAAAATATAT
42916330 AATAAA-TAACTTATAAAAATAT-T
1 AATAAATTAA-TT-TAAAAATATAT
42916353 AATAACATT-ATTTAAA
1 AATAA-ATTAATTTAAA
42916369 TTACAATACA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
22 7 0.21
23 16 0.47
24 10 0.29
25 1 0.03
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (23 bp):
AATAAATTAATTTAAAAATATAT
Found at i:42933748 original size:13 final size:13
Alignment explanation
Indices: 42933730--42933756 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42933720 ACAAATATCA
42933730 TACTTGTTTTGAG
1 TACTTGTTTTGAG
42933743 TACTTGTTTTGAG
1 TACTTGTTTTGAG
42933756 T
1 T
42933757 GTCTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.22, T:0.56
Consensus pattern (13 bp):
TACTTGTTTTGAG
Found at i:42955602 original size:20 final size:20
Alignment explanation
Indices: 42955574--42955612 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
42955564 CGACCACGAG
42955574 CCTACCCACACGGGCGTGTC
1 CCTACCCACACGGGCGTGTC
*
42955594 CCTATCCACACGGGCGTGT
1 CCTACCCACACGGGCGTGT
42955613 GGCCCTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.41, G:0.26, T:0.18
Consensus pattern (20 bp):
CCTACCCACACGGGCGTGTC
Found at i:42957512 original size:42 final size:42
Alignment explanation
Indices: 42957444--42957607 Score: 186
Period size: 42 Copynumber: 3.7 Consensus size: 42
42957434 CTTCGTTTAC
** *
42957444 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACAT-A
* * *
42957487 T-GATGCCATAGCCCAGCTATAGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATA
42957528 TCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC---AT--C-T-TCACATA
*
42957577 TCGATGCTATAGCCCAGCTATGGTCTTACAC
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC
42957608 GAATCACATA
Statistics
Matches: 103, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
41 2 0.02
42 61 0.59
43 1 0.01
45 2 0.02
48 1 0.01
49 36 0.35
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATA
Found at i:42957589 original size:49 final size:48
Alignment explanation
Indices: 42957514--42957650 Score: 179
Period size: 49 Copynumber: 2.9 Consensus size: 48
42957504 TATAGTCTTA
*
42957514 CACATATTCATATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAAT
1 CACATA-TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACG-AAT
*
42957564 CACATATCACATATCGATGCTATAGCCCAGCTATGGTCTTACACGAAT
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGAAT
* * * * *
42957612 CACATATCTCA-CT-GATGTCATATCCCAGATATGGTCTTA
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTA
42957651 TACAGCAGCA
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
46 22 0.28
47 1 0.01
48 13 0.16
49 37 0.47
50 6 0.08
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (48 bp):
CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGAAT
Found at i:42957754 original size:31 final size:31
Alignment explanation
Indices: 42957719--42957867 Score: 190
Period size: 31 Copynumber: 4.8 Consensus size: 31
42957709 CTTGTCACTT
* *
42957719 GTAGCCAAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * * * *
42957750 GTAGCCGGAGTTATCATTTTTCACTGGTCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
42957781 GTAGCCGGAGCTACCACTTTTCACTGATCTG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
42957812 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
42957843 GCAGCCGAAGCTATCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
42957868 TGTCATTTGT
Statistics
Matches: 100, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 100 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:42957943 original size:50 final size:50
Alignment explanation
Indices: 42957845--42958019 Score: 287
Period size: 50 Copynumber: 3.5 Consensus size: 50
42957835 CTGATCAGGC
*
42957845 AGCCGAAGCTATCACTTTTCACTTGTCATTTGTCCTTGATCAGATAAGTGT
1 AGCCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGTGT
* * *
42957896 AGCTGAAGCTATCACTTATCACTTTCACTTGTCCTTTATCAGATAAGTGT
1 AGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGTGT
*
42957946 AGCCGAAGCTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGTGT
1 AGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGTGT
*
42957996 AGCCGAAGCTATTACTTATCACTT
1 AGCCGAAGCTATCACTTATCACTT
42958020 GTTGCCATGG
Statistics
Matches: 116, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 94 0.81
51 22 0.19
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (50 bp):
AGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGTGT
Found at i:42958521 original size:21 final size:22
Alignment explanation
Indices: 42958494--42958550 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
42958484 ATATATTAAA
42958494 TTATTATTATTATTTATTATAG
1 TTATTATTATTATTTATTATAG
* *
42958516 TT-TTA-TATTTAATTATTATTG
1 TTATTATTA-TTATTTATTATAG
*
42958537 TTATTGTTATTATT
1 TTATTATTATTATT
42958551 ATTTAAATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
20 2 0.07
21 16 0.57
22 8 0.29
23 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (22 bp):
TTATTATTATTATTTATTATAG
Found at i:42958745 original size:15 final size:15
Alignment explanation
Indices: 42958725--42958753 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
42958715 GAAATAAAAG
42958725 AAAGAAACAGAATGA
1 AAAGAAACAGAATGA
42958740 AAAGAAACAGAATG
1 AAAGAAACAGAATG
42958754 TGGAAACGAA
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:0.66, C:0.07, G:0.21, T:0.07
Consensus pattern (15 bp):
AAAGAAACAGAATGA
Found at i:42959178 original size:23 final size:21
Alignment explanation
Indices: 42959131--42959171 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
42959121 TTTGGTTAAA
42959131 AATTGAATAGAAATGAAGTATG
1 AATTGAATAGAAA-GAAGTATG
42959153 AATTGAGATAGAAA-AAGTA
1 AATTGA-ATAGAAAGAAGTA
42959172 AGTGAATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (21 bp):
AATTGAATAGAAAGAAGTATG
Found at i:42959549 original size:15 final size:15
Alignment explanation
Indices: 42959501--42959550 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
42959491 TTTATCAAAT
42959501 TTATATTGATTGAAA
1 TTATATTGATTGAAA
* * *
42959516 TCATTTTGATTGAAT
1 TTATATTGATTGAAA
42959531 TTATATTGATTGAAA
1 TTATATTGATTGAAA
42959546 TTATA
1 TTATA
42959551 ATATATATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:42959781 original size:18 final size:18
Alignment explanation
Indices: 42959758--42959792 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
42959748 TTGAATTGAA
42959758 TGAAAATGTATGAAAATG
1 TGAAAATGTATGAAAATG
*
42959776 TGAAAATGTGTGAAAAT
1 TGAAAATGTATGAAAAT
42959793 ATGTGATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.23, T:0.29
Consensus pattern (18 bp):
TGAAAATGTATGAAAATG
Found at i:42960087 original size:23 final size:23
Alignment explanation
Indices: 42960059--42960116 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
42960049 ATATTCCGGG
*
42960059 TGTGTTTGGGTTGGATATTCTGA
1 TGTGTTTGGGTTGAATATTCTGA
*
42960082 TGTGTTTGGGTTGAATATTCTGG
1 TGTGTTTGGGTTGAATATTCTGA
42960105 TGTGTTTGGGTT
1 TGTGTTTGGGTT
42960117 TGGGTTGGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.10, C:0.03, G:0.36, T:0.50
Consensus pattern (23 bp):
TGTGTTTGGGTTGAATATTCTGA
Found at i:42960128 original size:29 final size:29
Alignment explanation
Indices: 42960085--42960143 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
42960075 ATTCTGATGT
42960085 GTTTGGGTTGAATATTCTGGTGTGTTTGG
1 GTTTGGGTTGAATATTCTGGTGTGTTTGG
*
42960114 GTTTGGGTTGGATATTCTGGTGTGTTTGG
1 GTTTGGGTTGAATATTCTGGTGTGTTTGG
42960143 G
1 G
42960144 AGGAATCGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.08, C:0.03, G:0.41, T:0.47
Consensus pattern (29 bp):
GTTTGGGTTGAATATTCTGGTGTGTTTGG
Found at i:42960269 original size:18 final size:19
Alignment explanation
Indices: 42960248--42960288 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
42960238 AATGAAATGA
42960248 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
42960266 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
42960285 GAAA
1 GAAA
42960289 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:42968699 original size:40 final size:40
Alignment explanation
Indices: 42968655--42968741 Score: 111
Period size: 40 Copynumber: 2.2 Consensus size: 40
42968645 AATTCATTAC
* * * *
42968655 TTCAGTAATTTCACAGTTCAGTGCAGTACACATAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
* **
42968695 TTCAGTAACTTCACAATTCAATTCAGTATTCAAAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
42968735 TTCAGTA
1 TTCAGTA
42968742 TTCCATAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (40 bp):
TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
Found at i:42969554 original size:14 final size:13
Alignment explanation
Indices: 42969517--42969568 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
42969507 TTCTTCTTTA
* *
42969517 CTTTGTTTTGTTT
1 CTTTATTTTATTT
42969530 CTTTATTTTATTT
1 CTTTATTTTATTT
*
42969543 CATTTCTTTTATTAT
1 C-TTTATTTTATT-T
42969558 -TTTATTTTATT
1 CTTTATTTTATT
42969569 AACTTAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 22 0.67
14 10 0.30
15 1 0.03
ACGTcount: A:0.13, C:0.08, G:0.04, T:0.75
Consensus pattern (13 bp):
CTTTATTTTATTT
Found at i:42969615 original size:19 final size:19
Alignment explanation
Indices: 42969572--42969624 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
42969562 TTTTATTAAC
42969572 TTAATAAT-AATA-ATTAT
1 TTAATAATAAATATATTAT
* *
42969589 TATTATAATAAATATCTTAT
1 T-TAATAATAAATATATTAT
*
42969609 TTAATAACAAATATAT
1 TTAATAATAAATATAT
42969625 ATATATTACA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 1 0.04
18 6 0.21
19 16 0.57
20 5 0.18
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAATAATAAATATATTAT
Found at i:42969867 original size:20 final size:20
Alignment explanation
Indices: 42969842--42969902 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
42969832 TTATTTTTAA
*
42969842 TAATAATAATAATCATAATT
1 TAATAATAATAATAATAATT
*
42969862 TAATAAT-ATAAATTATAATT
1 TAATAATAAT-AATAATAATT
*
42969882 TGATAGAATAATAATAATAAT
1 T-A-ATAATAATAATAATAAT
42969903 GATAAATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 2 0.06
20 17 0.50
21 1 0.03
22 12 0.35
23 2 0.06
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (20 bp):
TAATAATAATAATAATAATT
Found at i:42970054 original size:25 final size:27
Alignment explanation
Indices: 42970020--42970081 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 27
42970010 TGGCTTTAAT
*
42970020 TTAATTTAATTCATAATATGATATTTATAA
1 TTAA-TTAATTAATAATAT-AT-TTTATAA
42970050 TTAATTAATTTAATAATATATTTTATAA
1 TTAATTAA-TTAATAATATATTTTATAA
42970078 TTAA
1 TTAA
42970082 ATTATATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 11 0.37
29 6 0.20
30 13 0.43
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (27 bp):
TTAATTAATTAATAATATATTTTATAA
Found at i:42970092 original size:24 final size:23
Alignment explanation
Indices: 42970051--42970105 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
42970041 TATTTATAAT
* **
42970051 TAATTAATTTAATAATATATTTTA
1 TAATTAAATTAATAATAT-TTACA
42970075 TAATTAAATT-ATATATATTTACA
1 TAATTAAATTAATA-ATATTTACA
42970098 TAATTAAA
1 TAATTAAA
42970106 ATCTAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATTAAATTAATAATATTTACA
Found at i:42973557 original size:19 final size:18
Alignment explanation
Indices: 42973522--42973583 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
42973512 TAAAATTGGT
* *
42973522 TATACTTAACATTTTTAA
1 TATATTTAAAATTTTTAA
42973540 TATATTTAAAATTTTTTAA
1 TATATTTAAAA-TTTTTAA
* *
42973559 GT-TTTTTAAAATTTTAAA
1 -TATATTTAAAATTTTTAA
42973577 TATATTT
1 TATATTT
42973584 CCCTAAACCC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
17 1 0.03
18 19 0.53
19 15 0.42
20 1 0.03
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (18 bp):
TATATTTAAAATTTTTAA
Found at i:42975105 original size:9 final size:9
Alignment explanation
Indices: 42975091--42975124 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
42975081 CAATAAGATG
42975091 AAAGTAAAA
1 AAAGTAAAA
42975100 AAAGTAAAA
1 AAAGTAAAA
42975109 AAAG-AAAA
1 AAAGTAAAA
42975117 GAAAGTAA
1 -AAAGTAA
42975125 CAGCAGGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.17
9 17 0.74
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (9 bp):
AAAGTAAAA
Found at i:42975455 original size:11 final size:11
Alignment explanation
Indices: 42975441--42975465 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42975431 TAAAAAAACC
42975441 AAAAGAAAAAG
1 AAAAGAAAAAG
42975452 AAAAGAAAAAG
1 AAAAGAAAAAG
42975463 AAA
1 AAA
42975466 GTTTAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:42982062 original size:13 final size:13
Alignment explanation
Indices: 42982046--42982078 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
42982036 ATGTTAAATT
42982046 AATAAATTTAAAA
1 AATAAATTTAAAA
42982059 AATAAATTTAAAA
1 AATAAATTTAAAA
42982072 AATAAAT
1 AATAAAT
42982079 ATCTAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AATAAATTTAAAA
Found at i:42987329 original size:21 final size:22
Alignment explanation
Indices: 42987305--42987355 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 22
42987295 AATCTAAAGC
42987305 CTAGA-GCACAATCAACTATAG
1 CTAGACGCACAATCAACTATAG
*
42987326 CTAGAATCCTCACAATCAACTATAG
1 CTAG-A--CGCACAATCAACTATAG
42987351 CTAGA
1 CTAGA
42987356 ATCCTCACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.16
22 1 0.04
24 1 0.04
25 19 0.76
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.22
Consensus pattern (22 bp):
CTAGACGCACAATCAACTATAG
Found at i:42987345 original size:25 final size:25
Alignment explanation
Indices: 42987311--42987371 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
42987301 AAGCCTAGAG
42987311 CACAATCAACTATAGCTAGAATCCT
1 CACAATCAACTATAGCTAGAATCCT
42987336 CACAATCAACTATAGCTAGAATCCT
1 CACAATCAACTATAGCTAGAATCCT
42987361 CACAATCAACT
1 CACAATCAACT
42987372 TGTCTCCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.41, C:0.30, G:0.07, T:0.23
Consensus pattern (25 bp):
CACAATCAACTATAGCTAGAATCCT
Found at i:42990024 original size:3 final size:3
Alignment explanation
Indices: 42990016--42990042 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
42990006 CCACTTTGAT
42990016 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
42990043 TCTGAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:42991901 original size:4 final size:4
Alignment explanation
Indices: 42991892--42991916 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
42991882 GAAGAAGAAG
42991892 AAGA AAGA AAGA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA A
42991917 CAAATCTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:42997982 original size:18 final size:18
Alignment explanation
Indices: 42997952--42997990 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
42997942 TTAAAACTTG
42997952 AAAAATGAATAATTA-AA
1 AAAAATGAATAATTATAA
*
42997969 AAAAATTAATTAATTATAA
1 AAAAATGAA-TAATTATAA
42997988 AAA
1 AAA
42997991 GTGTATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 6 0.32
19 5 0.26
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAAATGAATAATTATAA
Found at i:43007952 original size:20 final size:20
Alignment explanation
Indices: 43007923--43007990 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
43007913 AAAAATATAT
*
43007923 CAAATTTTCATAATCCGCAA
1 CAAATCTTCATAATCCGCAA
*
43007943 CAAATCTTCATTATCCG-ATTGCA
1 CAAATCTTCATAATCCGCA----A
*
43007966 CCAATCTTCATAATCCGCAA
1 CAAATCTTCATAATCCGCAA
43007986 CAAAT
1 CAAAT
43007991 TGATGCCTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
19 1 0.03
20 20 0.53
23 16 0.42
24 1 0.03
ACGTcount: A:0.37, C:0.28, G:0.06, T:0.29
Consensus pattern (20 bp):
CAAATCTTCATAATCCGCAA
Found at i:43012953 original size:21 final size:22
Alignment explanation
Indices: 43012927--43012968 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
43012917 ATCCTAGTCA
43012927 AGATTTAC-TCTT-AACTTTTAC
1 AGATTT-CTTCTTAAACTTTTAC
43012948 AGATTTCTTCTTAAACTTTTA
1 AGATTTCTTCTTAAACTTTTA
43012969 TTCAGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.05
21 10 0.53
22 8 0.42
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.50
Consensus pattern (22 bp):
AGATTTCTTCTTAAACTTTTAC
Found at i:43013744 original size:105 final size:105
Alignment explanation
Indices: 43013626--43013835 Score: 411
Period size: 105 Copynumber: 2.0 Consensus size: 105
43013616 AACAAATTAA
43013626 ACCAATAATTACATTTAGTTATGAACATATATATATTATATTGATGTTAAATCATGGCATTGCCT
1 ACCAATAATTACATTTAGTTATGAACATATATATATTATATTGATGTTAAATCATGGCATTGCCT
43013691 CTGTATAATGGTTTTAATATTATAAGTAAGGTTAATTTAT
66 CTGTATAATGGTTTTAATATTATAAGTAAGGTTAATTTAT
*
43013731 ACCAATAATTACATTTAGTTATGAACATATATATATTATATTGATGTTAAATCATGGCATTGTCT
1 ACCAATAATTACATTTAGTTATGAACATATATATATTATATTGATGTTAAATCATGGCATTGCCT
43013796 CTGTATAATGGTTTTAATATTATAAGTAAGGTTAATTTAT
66 CTGTATAATGGTTTTAATATTATAAGTAAGGTTAATTTAT
43013836 GAGGTGAAGA
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 104 1.00
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.43
Consensus pattern (105 bp):
ACCAATAATTACATTTAGTTATGAACATATATATATTATATTGATGTTAAATCATGGCATTGCCT
CTGTATAATGGTTTTAATATTATAAGTAAGGTTAATTTAT
Found at i:43013934 original size:43 final size:43
Alignment explanation
Indices: 43013873--43013959 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
43013863 TTCTGTTCAC
43013873 ATTCTCCATTGATTTTGTAGAATGTTATAAGAATTTACTAAAA
1 ATTCTCCATTGATTTTGTAGAATGTTATAAGAATTTACTAAAA
*
43013916 ATTCTCCATTGATTTTGTAGGATGTTATAAGAATTTACTAAAA
1 ATTCTCCATTGATTTTGTAGAATGTTATAAGAATTTACTAAAA
43013959 A
1 A
43013960 ATTACATATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (43 bp):
ATTCTCCATTGATTTTGTAGAATGTTATAAGAATTTACTAAAA
Found at i:43025723 original size:27 final size:25
Alignment explanation
Indices: 43025658--43025724 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 25
43025648 ATTTATTTAT
*
43025658 TATTTATAATGTTAATCATTTAAATA
1 TATTTATAAT-TTAATAATTTAAATA
43025684 TGATTTATTAATTTAATAATTTAAAACTA
1 T-ATTTA-TAATTTAATAATTT-AAA-TA
*
43025713 TATTTACAATTT
1 TATTTATAATTT
43025725 TAACAGTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
26 1 0.03
27 19 0.54
28 12 0.34
29 3 0.09
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (25 bp):
TATTTATAATTTAATAATTTAAATA
Found at i:43028782 original size:13 final size:13
Alignment explanation
Indices: 43028764--43028788 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43028754 AATAAATATC
43028764 ATTTTAATTTTTA
1 ATTTTAATTTTTA
43028777 ATTTTAATTTTT
1 ATTTTAATTTTT
43028789 CACTCCTTTT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTAATTTTTA
Found at i:43029108 original size:65 final size:65
Alignment explanation
Indices: 43028999--43029121 Score: 192
Period size: 65 Copynumber: 1.9 Consensus size: 65
43028989 TGTATTCTCC
* * * *
43028999 AACTGATCTAGTAGTCCCTCTACTGTTTCTAGGCAATTCTCAGCAATTTCGAGTTCTGCACTCTT
1 AACTAATCTAATAGTCCCTCTACTGTTTCTAAGCAATACTCAGCAATTTCGAGTTCTGCACTCTT
* *
43029064 AACTAATCTAATAGTCTCTCTACTGTTTCTAAGCAATACTCAGCAATTTCGGGTTCTG
1 AACTAATCTAATAGTCCCTCTACTGTTTCTAAGCAATACTCAGCAATTTCGAGTTCTG
43029122 TGCCTTTCAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 52 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (65 bp):
AACTAATCTAATAGTCCCTCTACTGTTTCTAAGCAATACTCAGCAATTTCGAGTTCTGCACTCTT
Found at i:43037995 original size:31 final size:31
Alignment explanation
Indices: 43037957--43038019 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
43037947 TACAGATTGT
43037957 AAATGGCAAAAGAATTGACCTTCCCTTGAGA
1 AAATGGCAAAAGAATTGACCTTCCCTTGAGA
43037988 AAATGGCAAAAGAATTGACCTTCCCTTGAGA
1 AAATGGCAAAAGAATTGACCTTCCCTTGAGA
43038019 A
1 A
43038020 TAATAACAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (31 bp):
AAATGGCAAAAGAATTGACCTTCCCTTGAGA
Found at i:43050918 original size:47 final size:50
Alignment explanation
Indices: 43050796--43050975 Score: 202
Period size: 47 Copynumber: 3.8 Consensus size: 50
43050786 TGTAACCCGC
* * *
43050796 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C-GTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTCACAT
*
43050842 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-AGTTCACAT
* * *
43050892 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTCACAT
*
43050936 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
43050976 TCAACCATCC
Statistics
Matches: 114, Mismatches: 8, Indels: 20
0.80 0.06 0.14
Matches are distributed among these distances:
43 3 0.03
44 4 0.04
45 1 0.01
46 37 0.32
47 58 0.51
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (50 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTCACAT
Found at i:43050964 original size:94 final size:93
Alignment explanation
Indices: 43050804--43050975 Score: 308
Period size: 94 Copynumber: 1.8 Consensus size: 93
43050794 GCCCATAAGT
*
43050804 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
43050869 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
43050897 GAACTCGGACTCAACTCAACGAGTTCGGACATTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGGAC-GTTCGCATCCATAAGTGAACTCGGACTCAACTCA
43050962 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
43050976 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
93 28 0.37
94 47 0.63
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:43051428 original size:30 final size:30
Alignment explanation
Indices: 43051394--43051453 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
43051384 CCTTAATACG
43051394 AACTTTGGCAAAATTAC-CATTTTGCCCCTA
1 AACTTTGGCAAAATTACAC-TTTTGCCCCTA
* *
43051424 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
43051454 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.28, C:0.27, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:43052278 original size:6 final size:6
Alignment explanation
Indices: 43052267--43052291 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
43052257 ATATTACAAG
43052267 AACAGT AACAGT AACAGT AACAGT A
1 AACAGT AACAGT AACAGT AACAGT A
43052292 CGGTACACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:43052336 original size:47 final size:47
Alignment explanation
Indices: 43052279--43052385 Score: 178
Period size: 47 Copynumber: 2.3 Consensus size: 47
43052269 CAGTAACAGT
* *
43052279 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATTCGG
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
* *
43052326 AACAGTAACAGTACGGTACACGGAGTACCTCATTGGAACAAATCCGA
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
43052373 AACAGTAACAGTA
1 AACAGTAACAGTA
43052386 ATGGTAGCAG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 56 1.00
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (47 bp):
AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
Found at i:43053507 original size:20 final size:18
Alignment explanation
Indices: 43053471--43053515 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
43053461 AAACCTTGAA
43053471 TTTTCCCTTTCTTCTTTC
1 TTTTCCCTTTCTTCTTTC
43053489 TTTTCTCCTTTCTTTCTTTC
1 TTTTC-CCTTTC-TTCTTTC
43053509 -TTTCCCT
1 TTTTCCCT
43053516 GCTTTTCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 10 0.40
20 7 0.28
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTCCCTTTCTTCTTTC
Found at i:43053735 original size:16 final size:15
Alignment explanation
Indices: 43053703--43053737 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
43053693 TTTTTATTAT
*
43053703 ATAATATATTATTTA
1 ATAATATATTATATA
43053718 ATAATATACTTATATA
1 ATAATATA-TTATATA
43053734 ATAA
1 ATAA
43053738 GTAAATATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
ATAATATATTATATA
Found at i:43073375 original size:74 final size:74
Alignment explanation
Indices: 43073254--43073398 Score: 281
Period size: 74 Copynumber: 2.0 Consensus size: 74
43073244 CTTCAGTCAA
43073254 AGTTTAGAGATGACATTGAAAATGGAGAAACAATCAAAGTCTGTTATCCTATTCAGCCATTCTAG
1 AGTTTAGAGATGACATTGAAAATGGAGAAACAATCAAAGTCTGTTATCCTATTCAGCCATTCTAG
43073319 GTCATTCAG
66 GTCATTCAG
*
43073328 AGTTTAGAGATGACATTGAAAATGGAGAAACAATCAAAGTCTGTTATCCTATTCAGCCATTCTTG
1 AGTTTAGAGATGACATTGAAAATGGAGAAACAATCAAAGTCTGTTATCCTATTCAGCCATTCTAG
43073393 GTCATT
66 GTCATT
43073399 ATAAGGGTAC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (74 bp):
AGTTTAGAGATGACATTGAAAATGGAGAAACAATCAAAGTCTGTTATCCTATTCAGCCATTCTAG
GTCATTCAG
Found at i:43076473 original size:18 final size:18
Alignment explanation
Indices: 43076450--43076484 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43076440 TGTAATATCA
* *
43076450 ATTAATTTTTTTATTTTT
1 ATTAATTATTATATTTTT
43076468 ATTAATTATTATATTTT
1 ATTAATTATTATATTTT
43076485 AATTCCATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTAATTATTATATTTTT
Found at i:43082885 original size:19 final size:17
Alignment explanation
Indices: 43082863--43082898 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
43082853 ATGAAAATTT
43082863 AAAATTTATAAAATATTAA
1 AAAATTTA-AAAA-ATTAA
43082882 AAAATTTAAAAAATTAA
1 AAAATTTAAAAAATTAA
43082899 GATTAAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 4 0.24
19 8 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTTAAAAAATTAA
Found at i:43082893 original size:10 final size:9
Alignment explanation
Indices: 43082863--43082896 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
43082853 ATGAAAATTT
*
43082863 AAAATTTAT
1 AAAATTTAA
43082872 AAAATATTAA
1 AAAAT-TTAA
43082882 AAAATTTAA
1 AAAATTTAA
43082891 AAAATT
1 AAAATT
43082897 AAGATTAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAATTTAA
Found at i:43083230 original size:14 final size:16
Alignment explanation
Indices: 43083202--43083234 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
43083192 TTACGGTAAT
43083202 AAAAATATAATATTTA
1 AAAAATATAATATTTA
43083218 AAAAAT-TAA-ATTTA
1 AAAAATATAATATTTA
43083232 AAA
1 AAA
43083235 TTTTATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 3 0.18
16 6 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAATATAATATTTA
Found at i:43083576 original size:85 final size:85
Alignment explanation
Indices: 43083433--43083597 Score: 330
Period size: 85 Copynumber: 1.9 Consensus size: 85
43083423 CCAGAATCAA
43083433 TGGTATGATAATGATAGCAGAAAGGAAATATAAATTGAATTAAAACAGCCATGAGTACGGACATT
1 TGGTATGATAATGATAGCAGAAAGGAAATATAAATTGAATTAAAACAGCCATGAGTACGGACATT
43083498 ATTAGTCCCAAAAACGATTC
66 ATTAGTCCCAAAAACGATTC
43083518 TGGTATGATAATGATAGCAGAAAGGAAATATAAATTGAATTAAAACAGCCATGAGTACGGACATT
1 TGGTATGATAATGATAGCAGAAAGGAAATATAAATTGAATTAAAACAGCCATGAGTACGGACATT
43083583 ATTAGTCCCAAAAAC
66 ATTAGTCCCAAAAAC
43083598 ACGAGGGCCA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 80 1.00
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (85 bp):
TGGTATGATAATGATAGCAGAAAGGAAATATAAATTGAATTAAAACAGCCATGAGTACGGACATT
ATTAGTCCCAAAAACGATTC
Found at i:43091593 original size:18 final size:19
Alignment explanation
Indices: 43091572--43091610 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
43091562 ATTTTGGATT
*
43091572 TTTTATAAA-TATTTTAAA
1 TTTTAAAAATTATTTTAAA
*
43091590 TTTTAAAAATTATTTTGAA
1 TTTTAAAAATTATTTTAAA
43091609 TT
1 TT
43091611 ATTTTGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTTAAAAATTATTTTAAA
Found at i:43099990 original size:11 final size:11
Alignment explanation
Indices: 43099976--43100020 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
43099966 AGATAAATAT
43099976 TATTTTATTAA
1 TATTTTATTAA
*
43099987 TATTTTAATATGA
1 TATTTT-AT-TAA
*
43100000 TATTTTATTAT
1 TATTTTATTAA
43100011 TATTTTATTA
1 TATTTTATTA
43100021 GTTTATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 17 0.59
12 4 0.14
13 8 0.28
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:43100089 original size:3 final size:3
Alignment explanation
Indices: 43100081--43100114 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
43100071 AACTAAAGTG
43100081 AGA AGA AGA AGA AGA AGA AGA AGA AGA A-A AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
43100115 TTTTCATTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:43101408 original size:62 final size:62
Alignment explanation
Indices: 43101341--43102281 Score: 1785
Period size: 62 Copynumber: 15.2 Consensus size: 62
43101331 TCATTGTATG
43101341 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
1 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
43101403 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
1 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
43101465 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
1 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
43101527 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
1 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
43101589 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
1 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
43101651 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
1 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
43101713 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
1 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
43101775 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
1 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
43101837 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
1 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
43101899 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
1 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
43101961 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
1 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
43102023 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
1 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
*** * * * *
43102085 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATAGAATGTTCATTGTATG-
1 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATA-TCGGTTGAATGAAAGA
43102147 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
1 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
*
43102209 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATCTCGGTTGAATGAAAGA
1 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
43102271 AAAATTCGATG
1 AAAATT-GATG
43102282 GATCTCTGAA
Statistics
Matches: 861, Mismatches: 15, Indels: 5
0.98 0.02 0.01
Matches are distributed among these distances:
61 8 0.01
62 841 0.98
63 12 0.01
ACGTcount: A:0.50, C:0.03, G:0.21, T:0.26
Consensus pattern (62 bp):
AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
Found at i:43102656 original size:46 final size:46
Alignment explanation
Indices: 43102586--43102900 Score: 398
Period size: 46 Copynumber: 6.8 Consensus size: 46
43102576 GCTCTCTGAA
* * *
43102586 ATGAAATGTGTAAGACCATTGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
43102632 ATGAAATGTGTAAGACCAGGGTTGAAAGATGCCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * **
43102678 ATGAAATGTGTAAGACCATGGTTGAAAGATACTATGCCAATGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
43102724 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAGCGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
43102770 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
43102816 ATGAAAAGAATAAGACCCTGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
43102862 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
43102901 TCAATGTCAA
Statistics
Matches: 240, Mismatches: 28, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 1 0.00
46 239 1.00
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:43105865 original size:11 final size:11
Alignment explanation
Indices: 43105851--43105895 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
43105841 AGATAAATAT
43105851 TATTTTATTAA
1 TATTTTATTAA
*
43105862 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
43105875 TATTTTATTAT
1 TATTTTATTAA
43105886 TATTTTATTA
1 TATTTTATTA
43105896 GTATATGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:43107550 original size:21 final size:21
Alignment explanation
Indices: 43107526--43107597 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 21
43107516 CTCTCTGAAA
43107526 TGAAATGTGTAAGACCATGGT
1 TGAAATGTGTAAGACCATGGT
* *
43107547 TGAAA-G-ATACCATGACAACATGAT
1 TGAAATGTGTA--A-GAC--CATGGT
43107571 ATGAAATGTGTAAGACCATGGT
1 -TGAAATGTGTAAGACCATGGT
43107593 TGAAA
1 TGAAA
43107598 GATACCATGG
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 11 0.28
22 8 0.21
24 8 0.21
25 6 0.15
26 1 0.03
27 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (21 bp):
TGAAATGTGTAAGACCATGGT
Found at i:43107577 original size:46 final size:46
Alignment explanation
Indices: 43107525--43107885 Score: 474
Period size: 46 Copynumber: 7.8 Consensus size: 46
43107515 GCTCTCTGAA
** * * *
43107525 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
**
43107571 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
** * *
43107617 ATGAAAAAAATAAGACCATGGTTGAGAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
** *
43107663 GGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCTGA-GTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGC-AACGTGAC
43107709 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* * *
43107755 ATGAAATGAATAAGATCATGGTTGAAAGAGACCATGACAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* *
43107801 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* * * * *
43107847 A-GAAAATGAGTAAGATCATAGTTGAAAGAAACTATGGCA
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCA
43107886 TCAATGTCAA
Statistics
Matches: 279, Mismatches: 33, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
45 2 0.01
46 276 0.99
47 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
Found at i:43117387 original size:46 final size:46
Alignment explanation
Indices: 43117335--43117512 Score: 286
Period size: 46 Copynumber: 3.9 Consensus size: 46
43117325 GTGCTCTCTA
*
43117335 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTG
1 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
43117381 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
*
43117427 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
1 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
* * * * *
43117473 ACA-GAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
43117513 TCATGTCAAA
Statistics
Matches: 125, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
45 33 0.26
46 92 0.74
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
Found at i:43117533 original size:45 final size:45
Alignment explanation
Indices: 43117347--43117535 Score: 146
Period size: 46 Copynumber: 4.2 Consensus size: 45
43117337 ATGAAATGTG
* * * * * ***
43117347 TAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATGTG
1 TAAGACCATAGTTGAAAGACACCATGGCAACATGACA-GAAATAAA
* * * * ***
43117393 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTG
1 TAAGACCATAGTTGAAAGACACCATGGCAACATGACA-GAAATAAA
* * * *
43117439 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAATGAG
1 TAAGACCATAGTTGAAAGACACCATGGCAACATGACAGAAATAAA
* * *
43117484 TAAGACCATAGTTGAAAGACACTATGGCATCATGTCA-AAGATAAA
1 TAAGACCATAGTTGAAAGACACCATGGCAACATGACAGAA-ATAAA
43117529 TAAGACC
1 TAAGACC
43117536 GTGGATGGGA
Statistics
Matches: 131, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
44 2 0.02
45 49 0.37
46 80 0.61
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.22
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACCATGGCAACATGACAGAAATAAA
Found at i:43118754 original size:43 final size:41
Alignment explanation
Indices: 43118677--43118756 Score: 99
Period size: 43 Copynumber: 1.9 Consensus size: 41
43118667 TGGTAGAATG
43118677 TACATGTTGAGTCATCGTTTCTGGGCAACCCGGGGTGGTTA
1 TACATGTTGAGTCATCGTTTCTGGGCAACCCGGGGTGGTTA
* * *
43118718 TACATGTTTAGAGTCATTGTTGTC-GGGCCACTCGGGGTG
1 TACATG-TT-GAGTCATCGTT-TCTGGGCAACCCGGGGTG
43118757 ACAAATCTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 6 0.18
42 2 0.06
43 23 0.70
44 2 0.06
ACGTcount: A:0.16, C:0.19, G:0.33, T:0.33
Consensus pattern (41 bp):
TACATGTTGAGTCATCGTTTCTGGGCAACCCGGGGTGGTTA
Found at i:43121381 original size:18 final size:18
Alignment explanation
Indices: 43121360--43121402 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
43121350 GAACAATTAT
* * *
43121360 TTATTCAGTAACAGTCAG
1 TTATTCAGCAACAATCAA
*
43121378 TTATTCGGCAACAATCAA
1 TTATTCAGCAACAATCAA
43121396 TTATTCA
1 TTATTCA
43121403 ATAATAACTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATTCAGCAACAATCAA
Found at i:43121568 original size:18 final size:18
Alignment explanation
Indices: 43121445--43121609 Score: 113
Period size: 18 Copynumber: 9.2 Consensus size: 18
43121435 ATTGGCTATC
43121445 CAGTAACAGTCAATTATT
1 CAGTAACAGTCAATTATT
* *
43121463 TAGTAA-AATCAGA-TATT
1 CAGTAACAGTCA-ATTATT
* * *
43121480 CAGTAGCAATTAAGTTATT
1 CAGTAACAGTCAA-TTATT
* * *
43121499 CAGTGACAATCAGTTATT
1 CAGTAACAGTCAATTATT
* *
43121517 CAGTAA-TGATCATTTATT
1 CAGTAACAG-TCAATTATT
*
43121535 CAGTAATA-TCCAATTATT
1 CAGTAACAGT-CAATTATT
* *
43121553 CAGTAACAGTCTATTATC
1 CAGTAACAGTCAATTATT
** *
43121571 CAGTTTCGGTCAATTATT
1 CAGTAACAGTCAATTATT
*
43121589 CAGTAACAGTAAATTATT
1 CAGTAACAGTCAATTATT
43121607 CAG
1 CAG
43121610 AAATAATCAG
Statistics
Matches: 112, Mismatches: 27, Indels: 16
0.72 0.17 0.10
Matches are distributed among these distances:
17 14 0.12
18 84 0.75
19 14 0.12
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (18 bp):
CAGTAACAGTCAATTATT
Found at i:43121624 original size:36 final size:36
Alignment explanation
Indices: 43121445--43121624 Score: 134
Period size: 36 Copynumber: 5.0 Consensus size: 36
43121435 ATTGGCTATC
* *
43121445 CAGTAACAGTCAATTATTTAGTAA-AATCAGATATT
1 CAGTAACAGTCAATTATTCAGTAATAATCAGTTATT
* * * * *
43121480 CAGTAGCAATTAAGTTATTCAGTGACAATCAGTTATT
1 CAGTAACAGTCAA-TTATTCAGTAATAATCAGTTATT
* * *
43121517 CAGTAA-TGATCATTTATTCAGTAAT-ATCCAATTATT
1 CAGTAACAG-TCAATTATTCAGTAATAAT-CAGTTATT
* * * ** *
43121553 CAGTAACAGTCTATTATCCAGT-TTCGGTCAATTATT
1 CAGTAACAGTCAATTATTCAGTAAT-AATCAGTTATT
* *
43121589 CAGTAACAGTAAATTATTCAGAAATAATCAGTTATT
1 CAGTAACAGTCAATTATTCAGTAATAATCAGTTATT
43121625 TTATATATTT
Statistics
Matches: 109, Mismatches: 28, Indels: 15
0.72 0.18 0.10
Matches are distributed among these distances:
35 13 0.12
36 76 0.70
37 20 0.18
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (36 bp):
CAGTAACAGTCAATTATTCAGTAATAATCAGTTATT
Found at i:43123964 original size:31 final size:31
Alignment explanation
Indices: 43123916--43123977 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
43123906 TCTTCTACGG
* *
43123916 AATGCCGTTACCGATACTCGGTAGTATTTCA
1 AATGCCGATACCAATACTCGGTAGTATTTCA
43123947 AATGCCGATACCAATACTCGGTAGTATTTCA
1 AATGCCGATACCAATACTCGGTAGTATTTCA
43123978 CATTTTCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (31 bp):
AATGCCGATACCAATACTCGGTAGTATTTCA
Found at i:43125300 original size:45 final size:44
Alignment explanation
Indices: 43125191--43125303 Score: 127
Period size: 45 Copynumber: 2.5 Consensus size: 44
43125181 AAATTCTGAA
* * *
43125191 CAGTAACAGTAACAGTAACAATATTCAACACACAAAGTGCTGAAT
1 CAGTAACAGTAA-TGTAACAGTATTCAACACACAAAGTGCCGAAT
* * * *
43125236 CAATAACGGTAAATATAACAGTATTCGACACACAAAGTGCCGAAT
1 CAGTAACAGT-AATGTAACAGTATTCAACACACAAAGTGCCGAAT
*
43125281 CGGTAACAGTAATGGTAACAGTA
1 CAGTAACAGTAAT-GTAACAGTA
43125304 ACAGTAGTCG
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
44 3 0.05
45 50 0.91
46 2 0.04
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (44 bp):
CAGTAACAGTAATGTAACAGTATTCAACACACAAAGTGCCGAAT
Found at i:43125306 original size:51 final size:48
Alignment explanation
Indices: 43125189--43125326 Score: 124
Period size: 45 Copynumber: 2.9 Consensus size: 48
43125179 ACAAATTCTG
* * * *
43125189 AACAGTAACAGTAACAGTAACAATATTCAACACACAAAGTGCTGAATC
1 AACAGTAACGGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
*
43125237 -A-A-TAACGGTAA-ATATAACAGTATTCGACACACAAAGTGCCGAATC
1 AACAGTAACGGTAACA-GTAACAGTATTCGACACACAAAGTGCCGAATC
* * * *
43125282 GGTAACAGTAATGGTAACAGTAACAGTAGTCGGCACA-TAAGTGCC
1 ---AACAGTAACGGTAACAGTAACAGTATTCGACACACAAAGTGCC
43125327 TAATGAGTAA
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
44 1 0.01
45 36 0.50
46 1 0.01
47 1 0.01
49 1 0.01
50 8 0.11
51 23 0.32
52 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.20
Consensus pattern (48 bp):
AACAGTAACGGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
Found at i:43125687 original size:72 final size:72
Alignment explanation
Indices: 43125611--43125837 Score: 202
Period size: 72 Copynumber: 3.1 Consensus size: 72
43125601 TTTAATACAA
43125611 TTCAATTTACTTTTCATTTTCATATAATTAAATTCCACAATAAACACATGTTCATAATTATTTCA
1 TTCAATTTACTTTTCATTTTCATATAATTAAATTCCACAATAAACACATGTTCATAATTATTTCA
43125676 CCATATT
66 CCATATT
* * ** *
43125683 TTCAAATCCTCATACATTTTCATTCAATTCA-AT-ATATATATATCTCA-ATTATTCACATTAAT
1 TTC-AAT--T--TAC-TTTTCATT---TTCATATAAT-TAAAT-TC-CACAATAAACACA-T-GT
*
43125745 TCATAATT-TAAT-A-CA-A--
52 TCATAATTAT-TTCACCATATT
43125761 TTCAATTTACTTTTCATTTTCATATAATTAAATTCCACAATAAACACATGTTCATAATTATTTCA
1 TTCAATTTACTTTTCATTTTCATATAATTAAATTCCACAATAAACACATGTTCATAATTATTTCA
43125826 CCATATT
66 CCATATT
43125833 TTCAA
1 TTCAA
43125838 ATCAAATCAT
Statistics
Matches: 119, Mismatches: 12, Indels: 48
0.66 0.07 0.27
Matches are distributed among these distances:
67 10 0.08
68 5 0.04
69 15 0.13
70 7 0.06
71 2 0.02
72 16 0.13
73 6 0.05
75 2 0.02
77 6 0.05
78 11 0.09
79 2 0.02
80 7 0.06
81 15 0.13
82 5 0.04
83 10 0.08
ACGTcount: A:0.37, C:0.18, G:0.01, T:0.44
Consensus pattern (72 bp):
TTCAATTTACTTTTCATTTTCATATAATTAAATTCCACAATAAACACATGTTCATAATTATTTCA
CCATATT
Found at i:43125712 original size:150 final size:150
Alignment explanation
Indices: 43125530--43125840 Score: 606
Period size: 150 Copynumber: 2.1 Consensus size: 150
43125520 ATATTCACAC
43125530 ATTTTCACAAT-CTCATACATTTTCATTCAATTCAATATATATATATCTCAATTATTCACATTAA
1 ATTTTCA-AATCCTCATACATTTTCATTCAATTCAATATATATATATCTCAATTATTCACATTAA
43125594 TTCATAATTTAATACAATTCAATTTACTTTTCATTTTCATATAATTAAATTCCACAATAAACACA
65 TTCATAATTTAATACAATTCAATTTACTTTTCATTTTCATATAATTAAATTCCACAATAAACACA
43125659 TGTTCATAATTATTTCACCAT
130 TGTTCATAATTATTTCACCAT
43125680 ATTTTCAAATCCTCATACATTTTCATTCAATTCAATATATATATATCTCAATTATTCACATTAAT
1 ATTTTCAAATCCTCATACATTTTCATTCAATTCAATATATATATATCTCAATTATTCACATTAAT
43125745 TCATAATTTAATACAATTCAATTTACTTTTCATTTTCATATAATTAAATTCCACAATAAACACAT
66 TCATAATTTAATACAATTCAATTTACTTTTCATTTTCATATAATTAAATTCCACAATAAACACAT
43125810 GTTCATAATTATTTCACCAT
131 GTTCATAATTATTTCACCAT
43125830 ATTTTCAAATC
1 ATTTTCAAATC
43125841 AAATCATTTT
Statistics
Matches: 160, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
149 3 0.02
150 157 0.98
ACGTcount: A:0.38, C:0.18, G:0.01, T:0.43
Consensus pattern (150 bp):
ATTTTCAAATCCTCATACATTTTCATTCAATTCAATATATATATATCTCAATTATTCACATTAAT
TCATAATTTAATACAATTCAATTTACTTTTCATTTTCATATAATTAAATTCCACAATAAACACAT
GTTCATAATTATTTCACCAT
Found at i:43126565 original size:16 final size:15
Alignment explanation
Indices: 43126539--43126568 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
43126529 ATTTATTTCA
43126539 TAATATAATTAATAT
1 TAATATAATTAATAT
43126554 TAATATTAATTAATA
1 TAATA-TAATTAATA
43126569 ATTATAGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATATAATTAATAT
Found at i:43126579 original size:16 final size:16
Alignment explanation
Indices: 43126539--43126579 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
43126529 ATTTATTTCA
43126539 TAATA-TAATTAATAT
1 TAATAGTAATTAATAT
*
43126554 TAATATTAATTAATAAT
1 TAATAGTAATTAAT-AT
43126571 T-ATAGTAAT
1 TAATAGTAAT
43126580 GATTTAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 15 0.65
17 3 0.13
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
TAATAGTAATTAATAT
Found at i:43142663 original size:5 final size:5
Alignment explanation
Indices: 43142653--43142684 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
43142643 TGAAAAGGAT
43142653 AGATG AGATG AGATG AGATG AGATG AGATG AG
1 AGATG AGATG AGATG AGATG AGATG AGATG AG
43142685 GGAAATAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.41, T:0.19
Consensus pattern (5 bp):
AGATG
Found at i:43144045 original size:29 final size:29
Alignment explanation
Indices: 43144003--43144069 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
43143993 CCCTAAAATG
43144003 GAAGGAATTTGAAACCAAAGTTGTTATTT
1 GAAGGAATTTGAAACCAAAGTTGTTATTT
43144032 GAAGGAATTTGAAACCAAAGTTGTTATTT
1 GAAGGAATTTGAAACCAAAGTTGTTATTT
43144061 GAAGGAATT
1 GAAGGAATT
43144070 AATATTAGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (29 bp):
GAAGGAATTTGAAACCAAAGTTGTTATTT
Found at i:43147771 original size:21 final size:21
Alignment explanation
Indices: 43147745--43147786 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
43147735 ATAACATATA
43147745 AATTTATTATAAAAATATAAT
1 AATTTATTATAAAAATATAAT
43147766 AATTTATTATAAAAATATAAT
1 AATTTATTATAAAAATATAAT
43147787 TTTTACTCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTTATTATAAAAATATAAT
Found at i:43149757 original size:475 final size:475
Alignment explanation
Indices: 43148867--43149816 Score: 1900
Period size: 475 Copynumber: 2.0 Consensus size: 475
43148857 CTTTAGGAAT
43148867 CAAGATTCAGGACCAGAGTAGCAAACTGTCGCCTTAATGTTGGCGGTATTTAGTTGGAGCCATAG
1 CAAGATTCAGGACCAGAGTAGCAAACTGTCGCCTTAATGTTGGCGGTATTTAGTTGGAGCCATAG
43148932 CTTCAGCTTGTCCCCGACCAACTTACCAAATAGACTATAGATTCATAAAGAGAAGGGCAAATGAT
66 CTTCAGCTTGTCCCCGACCAACTTACCAAATAGACTATAGATTCATAAAGAGAAGGGCAAATGAT
43148997 CCCGTGTGGATCTATATAATTTGGCACATCTTTATCATACGGCTGTGCTAGAAACGACATATCAG
131 CCCGTGTGGATCTATATAATTTGGCACATCTTTATCATACGGCTGTGCTAGAAACGACATATCAG
43149062 TAATAAAGATTAGTGGCTGTAGGATACAGCTGCCTGCTTCTGCAGTAGATAACATACGCAACTGA
196 TAATAAAGATTAGTGGCTGTAGGATACAGCTGCCTGCTTCTGCAGTAGATAACATACGCAACTGA
43149127 CGCAAGCCTTAGTATTATGATATTATCCCATACTCAGATTAATTCCCATCACCAGTTGCCGAACT
261 CGCAAGCCTTAGTATTATGATATTATCCCATACTCAGATTAATTCCCATCACCAGTTGCCGAACT
43149192 GCCATTCTCCTATAAATGATTCTATCAGGATGGATTACCGCGTAAAATCTAATCTAGCCATGGAA
326 GCCATTCTCCTATAAATGATTCTATCAGGATGGATTACCGCGTAAAATCTAATCTAGCCATGGAA
43149257 GCCTCACTGTTCTGCTACATTGTCTTCTTTCTCTTCCTCTATTTTCTTACCAGAAGGTTGCTCCA
391 GCCTCACTGTTCTGCTACATTGTCTTCTTTCTCTTCCTCTATTTTCTTACCAGAAGGTTGCTCCA
43149322 AAACAAAGGTCTCCCACCAA
456 AAACAAAGGTCTCCCACCAA
43149342 CAAGATTCAGGACCAGAGTAGCAAACTGTCGCCTTAATGTTGGCGGTATTTAGTTGGAGCCATAG
1 CAAGATTCAGGACCAGAGTAGCAAACTGTCGCCTTAATGTTGGCGGTATTTAGTTGGAGCCATAG
43149407 CTTCAGCTTGTCCCCGACCAACTTACCAAATAGACTATAGATTCATAAAGAGAAGGGCAAATGAT
66 CTTCAGCTTGTCCCCGACCAACTTACCAAATAGACTATAGATTCATAAAGAGAAGGGCAAATGAT
43149472 CCCGTGTGGATCTATATAATTTGGCACATCTTTATCATACGGCTGTGCTAGAAACGACATATCAG
131 CCCGTGTGGATCTATATAATTTGGCACATCTTTATCATACGGCTGTGCTAGAAACGACATATCAG
43149537 TAATAAAGATTAGTGGCTGTAGGATACAGCTGCCTGCTTCTGCAGTAGATAACATACGCAACTGA
196 TAATAAAGATTAGTGGCTGTAGGATACAGCTGCCTGCTTCTGCAGTAGATAACATACGCAACTGA
43149602 CGCAAGCCTTAGTATTATGATATTATCCCATACTCAGATTAATTCCCATCACCAGTTGCCGAACT
261 CGCAAGCCTTAGTATTATGATATTATCCCATACTCAGATTAATTCCCATCACCAGTTGCCGAACT
43149667 GCCATTCTCCTATAAATGATTCTATCAGGATGGATTACCGCGTAAAATCTAATCTAGCCATGGAA
326 GCCATTCTCCTATAAATGATTCTATCAGGATGGATTACCGCGTAAAATCTAATCTAGCCATGGAA
43149732 GCCTCACTGTTCTGCTACATTGTCTTCTTTCTCTTCCTCTATTTTCTTACCAGAAGGTTGCTCCA
391 GCCTCACTGTTCTGCTACATTGTCTTCTTTCTCTTCCTCTATTTTCTTACCAGAAGGTTGCTCCA
43149797 AAACAAAGGTCTCCCACCAA
456 AAACAAAGGTCTCCCACCAA
43149817 GCCCTGCTCT
Statistics
Matches: 475, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
475 475 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (475 bp):
CAAGATTCAGGACCAGAGTAGCAAACTGTCGCCTTAATGTTGGCGGTATTTAGTTGGAGCCATAG
CTTCAGCTTGTCCCCGACCAACTTACCAAATAGACTATAGATTCATAAAGAGAAGGGCAAATGAT
CCCGTGTGGATCTATATAATTTGGCACATCTTTATCATACGGCTGTGCTAGAAACGACATATCAG
TAATAAAGATTAGTGGCTGTAGGATACAGCTGCCTGCTTCTGCAGTAGATAACATACGCAACTGA
CGCAAGCCTTAGTATTATGATATTATCCCATACTCAGATTAATTCCCATCACCAGTTGCCGAACT
GCCATTCTCCTATAAATGATTCTATCAGGATGGATTACCGCGTAAAATCTAATCTAGCCATGGAA
GCCTCACTGTTCTGCTACATTGTCTTCTTTCTCTTCCTCTATTTTCTTACCAGAAGGTTGCTCCA
AAACAAAGGTCTCCCACCAA
Found at i:43152598 original size:15 final size:15
Alignment explanation
Indices: 43152578--43152685 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
43152568 TTTATGGAAA
*
43152578 ATCAAAGATATGGGT
1 ATCAAATATATGGGT
* **
43152593 ATCAAATA-ATAGAA
1 ATCAAATATATGGGT
*
43152607 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
**
43152623 ATCAAATAT-TGGAA
1 ATCAAATATATGGGT
43152637 AGTCAAATATATGGGT
1 A-TCAAATATATGGGT
**
43152653 ATCAAATAT-TGGAA
1 ATCAAATATATGGGT
*
43152667 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
43152683 ATC
1 ATC
43152686 GAGATATTGG
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 12 0.17
15 45 0.65
16 12 0.17
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.27
Consensus pattern (15 bp):
ATCAAATATATGGGT
Found at i:43152615 original size:30 final size:30
Alignment explanation
Indices: 43152572--43152695 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
43152562 TCCATATTTA
* *
43152572 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
43152602 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
43152632 TGGAAAGTCAAATATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
43152662 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
43152693 TGG
1 TGG
43152696 CATAATAAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
30 78 0.91
31 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.27
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:43156073 original size:15 final size:15
Alignment explanation
Indices: 43156053--43156160 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
43156043 TTTATGGAAA
43156053 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
43156068 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
43156082 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
43156098 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
43156112 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
43156128 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
43156142 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
43156158 ATC
1 ATC
43156161 GAGATATTGG
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 13 0.19
15 43 0.62
16 13 0.19
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:43156082 original size:30 final size:30
Alignment explanation
Indices: 43156046--43156160 Score: 203
Period size: 30 Copynumber: 3.8 Consensus size: 30
43156036 ATCCATATTT
*
43156046 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
43156076 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
43156106 TTGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
43156136 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
43156161 GAGATATTGG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 83 1.00
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:43184758 original size:22 final size:21
Alignment explanation
Indices: 43184722--43184762 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
43184712 CACGATCAAC
43184722 AAATATATTAATATATAAACA
1 AAATATATTAATATATAAACA
*
43184743 AAATATAATTATTATATAAA
1 AAATAT-ATTAATATATAAA
43184763 TAAATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AAATATATTAATATATAAACA
Found at i:43184767 original size:21 final size:21
Alignment explanation
Indices: 43184722--43184786 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 21
43184712 CACGATCAAC
* *
43184722 AAATAT-ATTAATATATAAACA
1 AAATATAATTATTATATAAA-T
43184743 AAATATAATTATTATATAAAT
1 AAATATAATTATTATATAAAT
* *
43184764 AAATTTAA--ATGATATAAAT
1 AAATATAATTATTATATAAAT
43184783 AAAT
1 AAAT
43184787 GAAAGTATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 14 0.36
21 13 0.33
22 12 0.31
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
AAATATAATTATTATATAAAT
Found at i:43188540 original size:7 final size:7
Alignment explanation
Indices: 43188528--43188553 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
43188518 GATTCTTGCC
43188528 CTCAACT
1 CTCAACT
43188535 CTCAACT
1 CTCAACT
43188542 CTCAACT
1 CTCAACT
43188549 CTCAA
1 CTCAA
43188554 ATTACTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.42, G:0.00, T:0.27
Consensus pattern (7 bp):
CTCAACT
Found at i:43188971 original size:17 final size:18
Alignment explanation
Indices: 43188941--43188974 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
43188931 ATAGTAGTTA
*
43188941 AATATAATTTTATTTTTC
1 AATATAATTATATTTTTC
43188959 AATA-AATTATATTTTT
1 AATATAATTATATTTTT
43188975 ATAATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
AATATAATTATATTTTTC
Found at i:43194938 original size:13 final size:12
Alignment explanation
Indices: 43194920--43194972 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
43194910 TTTACTTCTT
43194920 TTTTTAATAAAAA
1 TTTTTAA-AAAAA
**
43194933 TTTTTAAAAAGG
1 TTTTTAAAAAAA
43194945 TTTTTAAAAAAA
1 TTTTTAAAAAAA
*
43194957 TTTATT-TAAAAA
1 TTT-TTAAAAAAA
43194969 TTTT
1 TTTT
43194973 AAATGTTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
11 1 0.03
12 24 0.71
13 9 0.26
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (12 bp):
TTTTTAAAAAAA
Found at i:43195013 original size:19 final size:21
Alignment explanation
Indices: 43194982--43195040 Score: 86
Period size: 20 Copynumber: 2.8 Consensus size: 21
43194972 TAAATGTTTA
43194982 AATATTATTAAAAAT-ATATTT
1 AATATT-TTAAAAATAATATTT
43195003 AATA-TTTAAAAATAATATTT
1 AATATTTTAAAAATAATATTT
43195023 AATATTTTAAAAAATAAT
1 AATATTTT-AAAAATAAT
43195041 TTCAAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.23
20 11 0.31
21 7 0.20
22 9 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATATTTTAAAAATAATATTT
Found at i:43195014 original size:20 final size:20
Alignment explanation
Indices: 43194982--43195035 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 20
43194972 TAAATGTTTA
43194982 AATATTATTAAAAATATATTT
1 AATATT-TTAAAAATATATTT
43195003 AATA-TTTAAAAATAATATTT
1 AATATTTTAAAAAT-ATATTT
43195023 AATATTTTAAAAA
1 AATATTTTAAAAA
43195036 ATAATTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.26
20 11 0.35
21 12 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATTTTAAAAATATATTT
Found at i:43195057 original size:15 final size:14
Alignment explanation
Indices: 43195024--43195061 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
43195014 ATAATATTTA
*
43195024 ATATTTTAAAAAAT
1 ATATTTCAAAAAAT
43195038 A-ATTTCAAAAATAT
1 ATATTTCAAAAA-AT
43195052 ATATTTCAAA
1 ATATTTCAAA
43195062 TTTAAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 9 0.43
14 4 0.19
15 8 0.38
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATTTCAAAAAAT
Found at i:43195067 original size:55 final size:55
Alignment explanation
Indices: 43194991--43195290 Score: 134
Period size: 55 Copynumber: 5.6 Consensus size: 55
43194981 AAATATTATT
43194991 AAAA-ATATATTT-AATATTTAAAAATAATATTTAATATTTTAAAAAATAATTTCA
1 AAAATATATATTTCAA-ATTTAAAAATAATATTTAATATTTTAAAAAATAATTTCA
* * ** *
43195045 AAAATATATATTTCAAATTTAAAAGTATATTTTTGAAATTATTTT---ATTTTATTT-A
1 AAAATATATATTTCAAATTTAAAAATA-ATATTT--AA-TATTTTAAAAAATAATTTCA
* ** * ** * *
43195100 AAAATATAT-TTTTAAAAATATATTTAAAATTTAA-AATTTAGAAAAATTAATTTCA
1 AAAATATATATTTCAAATTTAAAAATAATATTTAATATTTTA-AAAAA-TAATTTCA
* * * * *
43195155 AAAATATAT-TTTTAAA---ATATATAAGA---CATATTTTCAAAAAAATAATATTC-
1 AAAATATATATTTCAAATTTAAAAATAATATTTAATATTTT--AAAAAATAAT-TTCA
**** * *
43195205 AAAAT-T-TAAAAAATAATTTAAAAATAATATTTAATATTTTAGAAAATAGTTTCA
1 AAAATATATATTTCA-AATTTAAAAATAATATTTAATATTTTAAAAAATAATTTCA
* *
43195259 AAAGTATATATTTCAAATTTAAAAGT-ATATTT
1 AAAATATATATTTCAAATTTAAAAATAATATTT
43195291 TTGAAATTAT
Statistics
Matches: 182, Mismatches: 37, Indels: 54
0.67 0.14 0.20
Matches are distributed among these distances:
48 1 0.01
49 7 0.04
50 15 0.08
51 10 0.05
52 9 0.05
53 15 0.08
54 38 0.21
55 56 0.31
56 23 0.13
58 2 0.01
59 6 0.03
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (55 bp):
AAAATATATATTTCAAATTTAAAAATAATATTTAATATTTTAAAAAATAATTTCA
Found at i:43195073 original size:21 final size:22
Alignment explanation
Indices: 43195038--43195084 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
43195028 TTTAAAAAAT
43195038 AATTTCAAAAATATATATTTCA
1 AATTTCAAAAATATATATTTCA
* * *
43195060 AATTT-AAAAGTATATTTTTGA
1 AATTTCAAAAATATATATTTCA
43195081 AATT
1 AATT
43195085 ATTTTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (22 bp):
AATTTCAAAAATATATATTTCA
Found at i:43195115 original size:14 final size:14
Alignment explanation
Indices: 43195096--43195176 Score: 62
Period size: 13 Copynumber: 5.9 Consensus size: 14
43195086 TTTTATTTTA
43195096 TTTAAAAATATATT
1 TTTAAAAATATATT
43195110 TTTAAAAATATA--
1 TTTAAAAATATATT
* *
43195122 TTTAAAATTTAAAATT
1 TTTAAAA-AT-ATATT
** *
43195138 TAGAAAAAT-TAAT
1 TTTAAAAATATATT
*
43195151 TTCAAAAATATATT
1 TTTAAAAATATATT
43195165 TTT-AAAATATAT
1 TTTAAAAATATAT
43195177 AAGACATATT
Statistics
Matches: 51, Mismatches: 11, Indels: 11
0.70 0.15 0.15
Matches are distributed among these distances:
12 7 0.14
13 19 0.37
14 19 0.37
15 1 0.02
16 5 0.10
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (14 bp):
TTTAAAAATATATT
Found at i:43195215 original size:21 final size:20
Alignment explanation
Indices: 43195191--43195229 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
43195181 CATATTTTCA
*
43195191 AAAAAATAATATTCAAAATTT
1 AAAAAATAAT-TTAAAAATTT
43195212 AAAAAATAATTTAAAAAT
1 AAAAAATAATTTAAAAAT
43195230 AATATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAAATAATTTAAAAATTT
Found at i:43195233 original size:32 final size:33
Alignment explanation
Indices: 43195132--43195282 Score: 108
Period size: 32 Copynumber: 4.3 Consensus size: 33
43195122 TTTAAAATTT
* *
43195132 AAAATTTAGAAAAATTAATTTCAAAAATATATTTTT
1 AAAATTTA-AAAAA-TAATTTCAAAAATA-ATATTC
* * *
43195168 AAAATATATAAGACATATTTTCAAAAAAATAATATTC
1 AAAAT-T-TAAAAAATAATTTC--AAAAATAATATTC
*
43195205 AAAATTTAAAAAATAATTT-AAAAATAATATTT
1 AAAATTTAAAAAATAATTTCAAAAATAATATTC
* * * *
43195237 AATATTTTAGAAAATAGTTTCAAAAGTATATATTTC
1 AA-AATTTAAAAAATAATTTCAAAAATA-ATA-TTC
43195273 -AAATTTAAAA
1 AAAATTTAAAA
43195283 GTATATTTTT
Statistics
Matches: 91, Mismatches: 16, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
32 14 0.15
33 14 0.15
34 13 0.14
35 14 0.15
36 14 0.15
37 13 0.14
38 9 0.10
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (33 bp):
AAAATTTAAAAAATAATTTCAAAAATAATATTC
Found at i:43195284 original size:21 final size:21
Alignment explanation
Indices: 43195258--43195298 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
43195248 AAATAGTTTC
43195258 AAAAGTATATATTTCAAATTT
1 AAAAGTATATATTTCAAATTT
* *
43195279 AAAAGTATATTTTTGAAATT
1 AAAAGTATATATTTCAAATT
43195299 ATTTTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (21 bp):
AAAAGTATATATTTCAAATTT
Found at i:43195329 original size:14 final size:14
Alignment explanation
Indices: 43195310--43195390 Score: 62
Period size: 13 Copynumber: 5.9 Consensus size: 14
43195300 TTTTATTTTA
43195310 TTTAAAAATATATT
1 TTTAAAAATATATT
43195324 TTTAAAAATATA--
1 TTTAAAAATATATT
* *
43195336 TTTAAAATTTAAAATT
1 TTTAAAA-AT-ATATT
** *
43195352 TAGAAAAAT-TAAT
1 TTTAAAAATATATT
*
43195365 TTCAAAAATATATT
1 TTTAAAAATATATT
43195379 TTT-AAAATATAT
1 TTTAAAAATATAT
43195391 AAGACATATT
Statistics
Matches: 51, Mismatches: 11, Indels: 11
0.70 0.15 0.15
Matches are distributed among these distances:
12 7 0.14
13 19 0.37
14 19 0.37
15 1 0.02
16 5 0.10
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (14 bp):
TTTAAAAATATATT
Found at i:43195365 original size:214 final size:214
Alignment explanation
Indices: 43195006--43195466 Score: 886
Period size: 214 Copynumber: 2.2 Consensus size: 214
43194996 TATATTTAAT
43195006 ATTTAAAAATAATATTTAATATTTTAAAAAATAATTTCAAAAATATATATTTCAAATTTAAAAGT
1 ATTTAAAAATAATATTTAATATTTTAAAAAATAATTTCAAAAATATATATTTCAAATTTAAAAGT
43195071 ATATTTTTGAAATTATTTTATTTTATTTAAAAATATATTTTTAAAAATATATTTAAAATTTAAAA
66 ATATTTTTGAAATTATTTTATTTTATTTAAAAATATATTTTTAAAAATATATTTAAAATTTAAAA
43195136 TTTAGAAAAATTAATTTCAAAAATATATTTTTAAAATATATAAGACATATTTTCAAAAAAATAAT
131 TTTAGAAAAATTAATTTCAAAAATATATTTTTAAAATATATAAGACATATTTTCAAAAAAATAAT
43195201 ATTCAAAATTTAAAAAATA
196 ATTCAAAATTTAAAAAATA
* * *
43195220 ATTTAAAAATAATATTTAATATTTTAGAAAATAGTTTCAAAAGTATATATTTCAAATTTAAAAGT
1 ATTTAAAAATAATATTTAATATTTTAAAAAATAATTTCAAAAATATATATTTCAAATTTAAAAGT
43195285 ATATTTTTGAAATTATTTTATTTTATTTAAAAATATATTTTTAAAAATATATTTAAAATTTAAAA
66 ATATTTTTGAAATTATTTTATTTTATTTAAAAATATATTTTTAAAAATATATTTAAAATTTAAAA
43195350 TTTAGAAAAATTAATTTCAAAAATATATTTTTAAAATATATAAGACATATTTTCAAAAAAATAAT
131 TTTAGAAAAATTAATTTCAAAAATATATTTTTAAAATATATAAGACATATTTTCAAAAAAATAAT
43195415 ATTCAAAATTTAAAAAATA
196 ATTCAAAATTTAAAAAATA
*
43195434 ATTTAAAAATAATATTTAAAATTTTAAAAAATA
1 ATTTAAAAATAATATTTAATATTTTAAAAAATA
43195467 TATTATAAAA
Statistics
Matches: 242, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
214 242 1.00
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (214 bp):
ATTTAAAAATAATATTTAATATTTTAAAAAATAATTTCAAAAATATATATTTCAAATTTAAAAGT
ATATTTTTGAAATTATTTTATTTTATTTAAAAATATATTTTTAAAAATATATTTAAAATTTAAAA
TTTAGAAAAATTAATTTCAAAAATATATTTTTAAAATATATAAGACATATTTTCAAAAAAATAAT
ATTCAAAATTTAAAAAATA
Found at i:43195429 original size:21 final size:20
Alignment explanation
Indices: 43195405--43195443 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
43195395 CATATTTTCA
*
43195405 AAAAAATAATATTCAAAATTT
1 AAAAAATAAT-TTAAAAATTT
43195426 AAAAAATAATTTAAAAAT
1 AAAAAATAATTTAAAAAT
43195444 AATATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAAATAATTTAAAAATTT
Found at i:43195447 original size:32 final size:35
Alignment explanation
Indices: 43195406--43195476 Score: 112
Period size: 32 Copynumber: 2.1 Consensus size: 35
43195396 ATATTTTCAA
43195406 AAAAATAATATTCAAAA-TTTAAAAAATA-ATT-T
1 AAAAATAATATTCAAAATTTTAAAAAATATATTAT
*
43195438 AAAAATAATATTTAAAATTTTAAAAAATATATTAT
1 AAAAATAATATTCAAAATTTTAAAAAATATATTAT
43195473 AAAA
1 AAAA
43195477 CATTTCAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
32 16 0.46
33 11 0.31
34 3 0.09
35 5 0.14
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (35 bp):
AAAAATAATATTCAAAATTTTAAAAAATATATTAT
Found at i:43195597 original size:20 final size:21
Alignment explanation
Indices: 43195564--43195619 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
43195554 ATAAAACTCA
*
43195564 AAAAAAGAAAAAAAATTAAAG
1 AAAAAAGAACAAAAATTAAAG
* *
43195585 AAAAAAG-ACAAAAGTTAAAT
1 AAAAAAGAACAAAAATTAAAG
*
43195605 AAAAAAGTACAAAAA
1 AAAAAAGAACAAAAA
43195620 AAAAAGTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.77, C:0.04, G:0.09, T:0.11
Consensus pattern (21 bp):
AAAAAAGAACAAAAATTAAAG
Found at i:43196036 original size:23 final size:20
Alignment explanation
Indices: 43196004--43196052 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 20
43195994 AAGGGTTAGA
43196004 AAAATAGAAAGATAGAAAATAT
1 AAAATAGAAAGA-AGAAAA-AT
*
43196026 ATAAATGGAAAGAAGAAAAAT
1 A-AAATAGAAAGAAGAAAAAT
43196047 AAAATA
1 AAAATA
43196053 TAATTTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 4 0.17
21 3 0.12
22 7 0.29
23 10 0.42
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.16
Consensus pattern (20 bp):
AAAATAGAAAGAAGAAAAAT
Found at i:43207201 original size:28 final size:29
Alignment explanation
Indices: 43207170--43207247 Score: 70
Period size: 28 Copynumber: 2.7 Consensus size: 29
43207160 TATTATTATT
*
43207170 TATATAAATATATAAATTA-ATTATAAAG
1 TATATAAATAAATAAATTACATTATAAAG
* * *
43207198 TATATTATTAAATTAATTACATTATAAA-
1 TATATAAATAAATAAATTACATTATAAAG
*
43207226 TATTATATTAAGAAATAAATTA
1 TA-TATA--AATAAATAAATTA
43207248 AATAAAGACA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
28 17 0.45
29 11 0.29
31 10 0.26
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (29 bp):
TATATAAATAAATAAATTACATTATAAAG
Found at i:43207247 original size:31 final size:28
Alignment explanation
Indices: 43207181--43207248 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
43207171 ATATAAATAT
**
43207181 ATAAATTAATTATAAAGTATATTATTAA
1 ATAAATTAATTATAAAGTATATTAAGAA
* *
43207209 ATTAATTACATTATAAATATTATATTAAGAA
1 ATAAATTA-ATTAT-AA-AGTATATTAAGAA
43207240 ATAAATTAA
1 ATAAATTAA
43207249 ATAAAGACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.22
29 5 0.16
30 3 0.09
31 17 0.53
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (28 bp):
ATAAATTAATTATAAAGTATATTAAGAA
Found at i:43207470 original size:11 final size:11
Alignment explanation
Indices: 43207454--43207479 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
43207444 AGAAAGAGAC
43207454 GAAACAGGGGA
1 GAAACAGGGGA
43207465 GAAACAGGGGA
1 GAAACAGGGGA
43207476 GAAA
1 GAAA
43207480 GAAAGAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Done.