Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397265.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_146.0, 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: 8065533
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 116430 characters in sequence are not A, C, G, or T
File 10 of 18
Found at i:4187960 original size:30 final size:30
Alignment explanation
Indices: 4187867--4187963 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
4187857 TATAGGAACC
* *
4187867 AAATTAAACAAAATTGTAAAGTACATA-GACT
1 AAATTAAAAAAAATT-TATAGTACA-AGGACT
* * * * * *
4187898 AAATTGAACAAAACTCTATACTATAGGGACT
1 AAATT-AAAAAAAATTTATAGTACAAGGACT
4187929 AAATTAAAAAAAATTTATAGTACAAGGACT
1 AAATTAAAAAAAATTTATAGTACAAGGACT
4187959 AAATT
1 AAATT
4187964 GAACAAAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 5
0.72 0.20 0.07
Matches are distributed among these distances:
30 24 0.48
31 20 0.40
32 6 0.12
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.27
Consensus pattern (30 bp):
AAATTAAAAAAAATTTATAGTACAAGGACT
Found at i:4190852 original size:13 final size:14
Alignment explanation
Indices: 4190829--4190862 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
4190819 CTTTTGTTAA
*
4190829 AGAACAAAATTTTT
1 AGAAAAAAATTTTT
4190843 A-AAAAAAATTTTT
1 AGAAAAAAATTTTT
4190856 AGAAAAA
1 AGAAAAA
4190863 GCTCTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (14 bp):
AGAAAAAAATTTTT
Found at i:4197322 original size:17 final size:18
Alignment explanation
Indices: 4197297--4197336 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
4197287 AGCAACCAAA
*
4197297 ATAATAATAATAATT-AT
1 ATAAAAATAATAATTAAT
*
4197314 ATAAAAATAGTAATTAAT
1 ATAAAAATAATAATTAAT
4197332 ATAAA
1 ATAAA
4197337 GTTATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
ATAAAAATAATAATTAAT
Found at i:4207429 original size:30 final size:29
Alignment explanation
Indices: 4207389--4207489 Score: 98
Period size: 28 Copynumber: 3.4 Consensus size: 29
4207379 TTTAGTATAT
* *
4207389 AATTACGACAAAAATATTTTATCTTATCTA
1 AATTAAGACAAAAATATTTT-TCTTGTCTA
*
4207419 AATTGAGAC--AAATATGTTTTCTTGTCTA
1 AATTAAGACAAAAATAT-TTTTCTTGTCTA
* * *
4207447 TATTAAGATAAAACATATTTTTTTTGTCTTA
1 AATTAAGACAAAA-ATATTTTTCTTGTC-TA
4207478 AATTAAGACAAA
1 AATTAAGACAAA
4207490 CATANNNNNN
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
28 20 0.35
29 3 0.05
30 18 0.32
31 16 0.28
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.42
Consensus pattern (29 bp):
AATTAAGACAAAAATATTTTTCTTGTCTA
Found at i:4207491 original size:30 final size:29
Alignment explanation
Indices: 4207389--4207493 Score: 97
Period size: 30 Copynumber: 3.6 Consensus size: 29
4207379 TTTAGTATAT
* * *
4207389 AATTACGACAAAAATATTTTATCTTATCTA
1 AATTAAGACAAACATATTTT-TCTTGTCTA
*
4207419 AATTGAGAC-AA-ATATGTTTTCTTGTCTA
1 AATTAAGACAAACATAT-TTTTCTTGTCTA
* * *
4207447 TATTAAGATAAAACATATTTTTTTTGTCTTA
1 AATTAAGA-CAAACATATTTTTCTTGTC-TA
4207478 AATTAAGACAAACATA
1 AATTAAGACAAACATA
4207494 NNNNNNNNNN
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
28 18 0.30
29 5 0.08
30 25 0.41
31 13 0.21
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (29 bp):
AATTAAGACAAACATATTTTTCTTGTCTA
Found at i:4217858 original size:18 final size:18
Alignment explanation
Indices: 4217835--4217880 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
4217825 CCAACAAGCC
4217835 AACAACAAGCAAGTAATA
1 AACAACAAGCAAGTAATA
4217853 AACAACAAGCAAGTAATA
1 AACAACAAGCAAGTAATA
4217871 AACAACAAGC
1 AACAACAAGC
4217881 TCATTGAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.61, C:0.20, G:0.11, T:0.09
Consensus pattern (18 bp):
AACAACAAGCAAGTAATA
Found at i:4219221 original size:3 final size:3
Alignment explanation
Indices: 4219213--4219241 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4219203 GACCGTTAAA
4219213 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
4219242 AGTAATGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:4219492 original size:28 final size:28
Alignment explanation
Indices: 4219456--4219533 Score: 138
Period size: 28 Copynumber: 2.8 Consensus size: 28
4219446 AAGAAAAATC
* *
4219456 AATTAAATTTTTATAATTTTATAAATTT
1 AATTTAATTTTTATATTTTTATAAATTT
4219484 AATTTAATTTTTATATTTTTATAAATTT
1 AATTTAATTTTTATATTTTTATAAATTT
4219512 AATTTAATTTTTATATTTTTAT
1 AATTTAATTTTTATATTTTTAT
4219534 TTTAAATTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
AATTTAATTTTTATATTTTTATAAATTT
Found at i:4219537 original size:20 final size:20
Alignment explanation
Indices: 4219492--4219538 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
4219482 TTAATTTAAT
4219492 TTTTATATTTTTATAAATTTA
1 TTTTA-ATTTTTATAAATTTA
* **
4219513 ATTTAATTTTTATATTTTTA
1 TTTTAATTTTTATAAATTTA
4219533 TTTTAA
1 TTTTAA
4219539 ATTAAATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTAATTTTTATAAATTTA
Found at i:4225431 original size:45 final size:44
Alignment explanation
Indices: 4225381--4225587 Score: 220
Period size: 45 Copynumber: 4.6 Consensus size: 44
4225371 CACGTCAGGA
* * *
4225381 TGTTACACACTATGTACAAAAACATGTTACACGCTATGGTTAGGT
1 TGTTACAC-CTATGTACAAAAACATGTTACACGCCATAGTTAAGT
* * *
4225426 TGTTACACGTCATGTACAAAAACGTGTGACACGCCATAGTTAAGT
1 TGTTACACCT-ATGTACAAAAACATGTTACACGCCATAGTTAAGT
* * * *
4225471 TGTTACACGTCATGTACAAAAACGTGTTACACGCCATAATTAGGT
1 TGTTACACCT-ATGTACAAAAACATGTTACACGCCATAGTTAAGT
* * * *
4225516 TGTTACACGCTATGTACAAAAATATGTGACACGTCATGGTTAAGT
1 TGTTACAC-CTATGTACAAAAACATGTTACACGCCATAGTTAAGT
*
4225561 TGTTACACTCCATGTAC--AAACATGTTA
1 TGTTACAC-CTATGTACAAAAACATGTTA
4225588 TATGTCATGT
Statistics
Matches: 139, Mismatches: 21, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
43 8 0.06
44 1 0.01
45 129 0.93
46 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (44 bp):
TGTTACACCTATGTACAAAAACATGTTACACGCCATAGTTAAGT
Found at i:4225499 original size:24 final size:24
Alignment explanation
Indices: 4225426--4225503 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 24
4225416 ATGGTTAGGT
4225426 TGTTACACGTCATGTACAAAAACG
1 TGTTACACGTCATGTACAAAAACG
* * *
4225450 TGTGACACGCCATAGT----TAA-G
1 TGTTACACGTCAT-GTACAAAAACG
4225470 TTGTTACACGTCATGTACAAAAACG
1 -TGTTACACGTCATGTACAAAAACG
4225495 TGTTACACG
1 TGTTACACG
4225504 CCATAATTAG
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
20 3 0.07
21 13 0.32
24 22 0.54
25 3 0.07
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (24 bp):
TGTTACACGTCATGTACAAAAACG
Found at i:4225534 original size:90 final size:90
Alignment explanation
Indices: 4225381--4225587 Score: 278
Period size: 90 Copynumber: 2.3 Consensus size: 90
4225371 CACGTCAGGA
* * * **
4225381 TGTTACACACTATGTACAAAAACATGTTACACGCTATGGTTAGGTTGTTACACGTCATGTACAAA
1 TGTTACACTCCATGTACAAAAACATGTTACACGCCATAATTAGGTTGTTACACGTCATGTACAAA
*
4225446 AACGTGTGACACGCCATAGTTAAGT
66 AACATGTGACACGCCATAGTTAAGT
*
4225471 TGTTACACGT-CATGTACAAAAACGTGTTACACGCCATAATTAGGTTGTTACACG-CTATGTACA
1 TGTTACAC-TCCATGTACAAAAACATGTTACACGCCATAATTAGGTTGTTACACGTC-ATGTACA
* * *
4225534 AAAATATGTGACACGTCATGGTTAAGT
64 AAAACATGTGACACGCCATAGTTAAGT
4225561 TGTTACACTCCATGTAC--AAACATGTTA
1 TGTTACACTCCATGTACAAAAACATGTTA
4225588 TATGTCATGT
Statistics
Matches: 103, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
88 9 0.09
89 2 0.02
90 92 0.89
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (90 bp):
TGTTACACTCCATGTACAAAAACATGTTACACGCCATAATTAGGTTGTTACACGTCATGTACAAA
AACATGTGACACGCCATAGTTAAGT
Found at i:4225620 original size:52 final size:54
Alignment explanation
Indices: 4225559--4225661 Score: 138
Period size: 52 Copynumber: 1.9 Consensus size: 54
4225549 TCATGGTTAA
* * *
4225559 GTTGTTACACTCCATGTAC-AAACATGTTATATGTCAT-GTTAAAAAAAATACT
1 GTTGTTACACGCCATGTACAAAACATGTTACATGCCATGGTTAAAAAAAATACT
* *
4225611 GTTGTTACACGCTATGTACAAAAACATGTTACATGCCATGGTTTAAAAAAA
1 GTTGTTACACGCCATGTAC-AAAACATGTTACATGCCATGGTTAAAAAAAA
4225662 GTTATTACAC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
52 17 0.40
54 16 0.37
55 10 0.23
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (54 bp):
GTTGTTACACGCCATGTACAAAACATGTTACATGCCATGGTTAAAAAAAATACT
Found at i:4225697 original size:30 final size:29
Alignment explanation
Indices: 4225662--4225754 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 29
4225652 TTTAAAAAAA
4225662 GTTATTACACGTCATATTGAAAAAAATATT
1 GTTATTACACGTCATATT-AAAAAAATATT
** *
4225692 GTTATTACACACCATGTTAAAAAAATATT
1 GTTATTACACGTCATATTAAAAAAATATT
* * * * *
4225721 GCTGTTACATGTCATATTCAAAAACATTTT
1 GTTATTACACGTCATATT-AAAAAAATATT
4225751 GTTA
1 GTTA
4225755 CACTTTAATG
Statistics
Matches: 49, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
29 23 0.47
30 26 0.53
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.38
Consensus pattern (29 bp):
GTTATTACACGTCATATTAAAAAAATATT
Found at i:4225743 original size:29 final size:29
Alignment explanation
Indices: 4225664--4225744 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
4225654 TAAAAAAAGT
*
4225664 TATTACACGTCATATTGAAAAAAATATTGT
1 TATTACACGTCATATT-AAAAAAATATTGC
** *
4225694 TATTACACACCATGTTAAAAAAATATTGC
1 TATTACACGTCATATTAAAAAAATATTGC
* * *
4225723 TGTTACATGTCATATTCAAAAA
1 TATTACACGTCATATTAAAAAA
4225745 CATTTTGTTA
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 28 0.68
30 13 0.32
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.35
Consensus pattern (29 bp):
TATTACACGTCATATTAAAAAAATATTGC
Found at i:4227859 original size:18 final size:18
Alignment explanation
Indices: 4227838--4227876 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4227828 CATGTGGAGC
4227838 AACTAATTTA-AGTAGAAT
1 AACTAATTTACA-TAGAAT
*
4227856 AACTACTTTACATAGAAT
1 AACTAATTTACATAGAAT
4227874 AAC
1 AAC
4227877 CACTTCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.31
Consensus pattern (18 bp):
AACTAATTTACATAGAAT
Found at i:4227888 original size:18 final size:18
Alignment explanation
Indices: 4227850--4227889 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4227840 CTAATTTAAG
* *
4227850 TAGAATAACTACTTTACA
1 TAGAATAACCACTTCACA
*
4227868 TAGAATAACCACTTCATA
1 TAGAATAACCACTTCACA
4227886 TAGA
1 TAGA
4227890 TGACAGTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.30
Consensus pattern (18 bp):
TAGAATAACCACTTCACA
Found at i:4234061 original size:26 final size:26
Alignment explanation
Indices: 4234029--4234078 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
4234019 AATGTATCGC
* *
4234029 TACATTTTGGAATGTATCGATACAAA
1 TACATTTTGAAATGTATCCATACAAA
4234055 TACATTTTGAAATGTATCCATACA
1 TACATTTTGAAATGTATCCATACA
4234079 TTTTGGGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (26 bp):
TACATTTTGAAATGTATCCATACAAA
Found at i:4234265 original size:21 final size:21
Alignment explanation
Indices: 4234224--4234306 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
4234214 TGCAAGGGAG
* * *
4234224 GTTTAAAACCAATT-AATCAA
1 GTTTAAAAACTATTCAAACAA
4234244 GTTTAAAAACTATTCAAACAA
1 GTTTAAAAACTATTCAAACAA
* * *
4234265 GTTCAAAAATTATTCAAGCAA
1 GTTTAAAAACTATTCAAACAA
*
4234286 -TTTCAAAACTCATTCAAACAA
1 GTTTAAAAACT-ATTCAAACAA
4234307 TTTTTAGAAC
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
20 19 0.37
21 32 0.63
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.29
Consensus pattern (21 bp):
GTTTAAAAACTATTCAAACAA
Found at i:4234392 original size:21 final size:22
Alignment explanation
Indices: 4234366--4234442 Score: 115
Period size: 21 Copynumber: 3.6 Consensus size: 22
4234356 AAATAAGCTT
4234366 AAAAACT-ATTCAAACAAGTTC
1 AAAAACTCATTCAAACAAGTTC
*
4234387 AAAAACTCATTCAAACAACTTC
1 AAAAACTCATTCAAACAAGTTC
4234409 AAAAA-TCATTCAAACAAGTTC
1 AAAAACTCATTCAAACAAGTTC
*
4234430 AAAGA-TCATTCAA
1 AAAAACTCATTCAA
4234443 GTAATTTTGA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
21 34 0.65
22 18 0.35
ACGTcount: A:0.52, C:0.21, G:0.04, T:0.23
Consensus pattern (22 bp):
AAAAACTCATTCAAACAAGTTC
Found at i:4242332 original size:22 final size:19
Alignment explanation
Indices: 4242286--4242323 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
4242276 CAACAAAAGA
*
4242286 TTAT-AAATATAATAATAT
1 TTATCAAATATAATAAAAT
4242304 TTATCAAATATAATAAAAT
1 TTATCAAATATAATAAAAT
4242323 T
1 T
4242324 CAATATCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
TTATCAAATATAATAAAAT
Found at i:4250575 original size:32 final size:33
Alignment explanation
Indices: 4250501--4250586 Score: 113
Period size: 32 Copynumber: 2.6 Consensus size: 33
4250491 AAAAGAAATT
* **
4250501 AAAAT-AAAATATATAATATAAAAAATTATGTTAA
1 AAAATGAAAATA-A-AATATATAAAATTATAATAA
4250535 AAAATGAAAATAAAATATATAAAATTATAAT-A
1 AAAATGAAAATAAAATATATAAAATTATAATAA
4250567 AAAATGAAAATAAAATATAT
1 AAAATGAAAATAAAATATAT
4250587 GATACTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
32 21 0.44
33 15 0.31
34 6 0.12
35 6 0.12
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.29
Consensus pattern (33 bp):
AAAATGAAAATAAAATATATAAAATTATAATAA
Found at i:4250588 original size:15 final size:15
Alignment explanation
Indices: 4250538--4250602 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 15
4250528 ATGTTAAAAA
4250538 ATGAAAATAAAATAT
1 ATGAAAATAAAATAT
* *
4250553 AT-AAAATTATAATAAAA
1 ATGAAAA-TA-AA-ATAT
4250570 ATGAAAATAAAATAT
1 ATGAAAATAAAATAT
* *
4250585 ATGATACTAAAAATAT
1 ATGAAAAT-AAAATAT
4250601 AT
1 AT
4250603 TTAAGAAATC
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
14 4 0.10
15 12 0.31
16 13 0.33
17 6 0.15
18 4 0.10
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (15 bp):
ATGAAAATAAAATAT
Found at i:4250627 original size:16 final size:15
Alignment explanation
Indices: 4250578--4250627 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
4250568 AAATGAAAAT
*
4250578 AAAATATATGATACTA
1 AAAATATATTATA-TA
4250594 AAAATATATT-TA-A
1 AAAATATATTATATA
*
4250607 GAAATCATATTATATA
1 AAAAT-ATATTATATA
4250623 AAAAT
1 AAAAT
4250628 TAATACTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 5 0.18
14 5 0.18
15 4 0.14
16 14 0.50
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (15 bp):
AAAATATATTATATA
Found at i:4250829 original size:15 final size:15
Alignment explanation
Indices: 4250805--4250859 Score: 83
Period size: 15 Copynumber: 3.7 Consensus size: 15
4250795 CTTTCTTTTC
* *
4250805 AATCACATTACTTGT
1 AATCATATTACCTGT
4250820 AATCATATTACCTGT
1 AATCATATTACCTGT
*
4250835 AATCATATTACCTAT
1 AATCATATTACCTGT
4250850 AATCATATTA
1 AATCATATTA
4250860 TATTATAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (15 bp):
AATCATATTACCTGT
Found at i:4254769 original size:68 final size:68
Alignment explanation
Indices: 4254642--4254958 Score: 280
Period size: 68 Copynumber: 4.7 Consensus size: 68
4254632 CATGTTTGGT
* * * ** * * * * *
4254642 ATGATGAATGCCATAAGATTATGTGTACAATGTAAATTTCATATACCATATGAGATGATTAAATA
1 ATGATGAATGCTATAAGATTGTGTATATGATGTAAATTCCATATACTACAAGAGTTGATTAAATA
4254707 TGC
66 TGC
* * * * * * * *
4254710 ATGGTGTATACTGTAAGATTGTGTATATGATGTAAATTCCATATACTATATGAGGTGATTAAGTA
1 ATGATGAATGCTATAAGATTGTGTATATGATGTAAATTCCATATACTACAAGAGTTGATTAAATA
4254775 TGC
66 TGC
* * * * *
4254778 ATGATAAATGCCATGAGATTGTGTATATAATGTATATTCCATATACTACAAGAGTTGATTAAGA-
1 ATGATGAATGCTATAAGATTGTGTATATGATGTAAATTCCATATACTACAAGAGTTGATTAA-AT
*
4254842 AAGC
65 ATGC
* * *
4254846 ATGATGAATGCTATGAA-ATTATGTATATGATGCATATTCCATATACTACAAGAGTTGATTAAGA
1 ATGATGAATGCTAT-AAGATTGTGTATATGATGTAAATTCCATATACTACAAGAGTTGATTAA-A
*
4254910 -AAGC
64 TATGC
* * * * **
4254914 ATGATGAAGGCCATGAGATTATGTATATGATGTATTTTCCATATA
1 ATGATGAATGCTATAAGATTGTGTATATGATGTAAATTCCATATA
4254959 GCTTATAAGA
Statistics
Matches: 208, Mismatches: 38, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
67 1 0.00
68 206 0.99
69 1 0.00
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (68 bp):
ATGATGAATGCTATAAGATTGTGTATATGATGTAAATTCCATATACTACAAGAGTTGATTAAATA
TGC
Found at i:4254848 original size:136 final size:136
Alignment explanation
Indices: 4254642--4254958 Score: 359
Period size: 136 Copynumber: 2.3 Consensus size: 136
4254632 CATGTTTGGT
* * * * * * *
4254642 ATGATGAATGCCATAAGATTATGTGTACAATGTAAATTTCATATACCATATGAGATGATTAAATA
1 ATGATGAATGCCATGAGATTATGTATATAATGTATATTCCATATACCACAAGAGATGATTAAATA
* * * * * * * *
4254707 TGCATGGTGTATACTGT-AAGATTGTGTATATGATGTAAATTCCATATACTATATGAGGTGATTA
66 AGCATGATGAATACTATGAA-ATTATGTATATGATGCAAATTCCATATACTACAAGAGGTGATTA
* *
4254771 AGTATGC
130 AGAAAGC
* * * *
4254778 ATGATAAATGCCATGAGATTGTGTATATAATGTATATTCCATATACTACAAGAGTTGATTAAGA-
1 ATGATGAATGCCATGAGATTATGTATATAATGTATATTCCATATACCACAAGAGATGATTAA-AT
* * *
4254842 AAGCATGATGAATGCTATGAAATTATGTATATGATGCATATTCCATATACTACAAGAGTTGATTA
65 AAGCATGATGAATACTATGAAATTATGTATATGATGCAAATTCCATATACTACAAGAGGTGATTA
4254907 AGAAAGC
130 AGAAAGC
* * *
4254914 ATGATGAAGGCCATGAGATTATGTATATGATGTATTTTCCATATA
1 ATGATGAATGCCATGAGATTATGTATATAATGTATATTCCATATA
4254959 GCTTATAAGA
Statistics
Matches: 150, Mismatches: 29, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
136 147 0.98
137 3 0.02
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (136 bp):
ATGATGAATGCCATGAGATTATGTATATAATGTATATTCCATATACCACAAGAGATGATTAAATA
AGCATGATGAATACTATGAAATTATGTATATGATGCAAATTCCATATACTACAAGAGGTGATTAA
GAAAGC
Found at i:4258108 original size:2 final size:2
Alignment explanation
Indices: 4258097--4258128 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4258087 GTTTTTATCA
4258097 AT AT -T 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
4258129 AGTGGCTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4268316 original size:20 final size:20
Alignment explanation
Indices: 4268293--4268340 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
4268283 TTAGAATTAG
* *
4268293 ACAGAAGAAATTGGAGAGGA
1 ACAGAAGAAATTGAAGAGAA
**
4268313 ACAGTGGAAATTGAAGAGAA
1 ACAGAAGAAATTGAAGAGAA
4268333 ACAGAAGA
1 ACAGAAGA
4268341 TGTAGGGTGA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.06, G:0.31, T:0.10
Consensus pattern (20 bp):
ACAGAAGAAATTGAAGAGAA
Found at i:4269300 original size:40 final size:41
Alignment explanation
Indices: 4269242--4269321 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 41
4269232 TTGTGAAAAA
* *
4269242 CACTAATCGTGGCGAGGTTAG-AAACCCTACTAAGGTGAAC
1 CACTAATCGTGGCAAGGTTAGAAAACCCCACTAAGGTGAAC
* *
4269282 CACTAATCTTGGCAAGGTTAGAAAACCCCACTGAGGTGAA
1 CACTAATCGTGGCAAGGTTAGAAAACCCCACTAAGGTGAA
4269322 GAATAGCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
40 19 0.54
41 16 0.46
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.20
Consensus pattern (41 bp):
CACTAATCGTGGCAAGGTTAGAAAACCCCACTAAGGTGAAC
Found at i:4272355 original size:58 final size:58
Alignment explanation
Indices: 4272256--4272370 Score: 169
Period size: 58 Copynumber: 2.0 Consensus size: 58
4272246 TTGTGGTTCG
* * *
4272256 TATTTTATTGTTAGTGGTAGTTTTCCATTTCTTGTTGTTGGAGGTTGTGTCTTCACCC
1 TATTTTATTGTCAGTGGTAGTTTTCCATTTCATGTTGTTGGAGGTTGTGTCTCCACCC
* *
4272314 TATTTTATTGTCAGTGGTAGTTTTCTATTTCATGATT-TTGGAGGTTTTGTCTCCACC
1 TATTTTATTGTCAGTGGTAGTTTTCCATTTCATG-TTGTTGGAGGTTGTGTCTCCACC
4272371 TTTCCACTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 49 0.96
59 2 0.04
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.51
Consensus pattern (58 bp):
TATTTTATTGTCAGTGGTAGTTTTCCATTTCATGTTGTTGGAGGTTGTGTCTCCACCC
Found at i:4274934 original size:29 final size:28
Alignment explanation
Indices: 4274877--4274954 Score: 93
Period size: 29 Copynumber: 2.8 Consensus size: 28
4274867 NNNNNNNNNN
* *
4274877 TGTCTTAATTAAGACAAACATATTCTTT
1 TGTCTAAATTAAGACAAACATATTATTT
*
4274905 TGTCTAAATTTAGACCAAACATATTATTT
1 TGTCTAAATTAAGA-CAAACATATTATTT
* * *
4274934 TGTTTAAATTAGGATAAACAT
1 TGTCTAAATTAAGACAAACAT
4274955 GTTAAAATTG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 18 0.43
29 24 0.57
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (28 bp):
TGTCTAAATTAAGACAAACATATTATTT
Found at i:4278096 original size:58 final size:57
Alignment explanation
Indices: 4278023--4278138 Score: 162
Period size: 58 Copynumber: 2.0 Consensus size: 57
4278013 CATTGTGGTT
* *
4278023 CCTATTTATTCTTAGTGGTAGTTTTCCATTTCTTG-TTGTTGAAGGTTGTGTCTCCAC
1 CCTATTTATTCTTAGTGGTAGTTTTCCATTTCATGATT-TTGAAGGTTGTGTCTACAC
* * *
4278080 CCTATTTTATTGTTAGTGGTAGTTTTCTATTTCATGATTTTGGAGGTTGTGTCTACAC
1 CCTA-TTTATTCTTAGTGGTAGTTTTCCATTTCATGATTTTGAAGGTTGTGTCTACAC
4278138 C
1 C
4278139 TTTCCACTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
57 4 0.08
58 46 0.88
59 2 0.04
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.49
Consensus pattern (57 bp):
CCTATTTATTCTTAGTGGTAGTTTTCCATTTCATGATTTTGAAGGTTGTGTCTACAC
Found at i:4281798 original size:33 final size:32
Alignment explanation
Indices: 4281736--4281801 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 32
4281726 TAGTTGTTAG
4281736 CATATCATAATTAATGATAATATTGTATATTAA
1 CATATCATAATT-ATGATAATATTGTATATTAA
4281769 CATATCATAA-T-TGATAATGATGTGATATATTAA
1 CATATCATAATTATGATAAT-AT-TG-TATATTAA
4281802 TTTGACATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
30 7 0.23
31 2 0.07
32 3 0.10
33 18 0.60
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (32 bp):
CATATCATAATTATGATAATATTGTATATTAA
Found at i:4281958 original size:29 final size:29
Alignment explanation
Indices: 4281911--4281972 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
4281901 CTGATTATAA
* *
4281911 AAATTTAATAAAAATATAAAAATTTAATT
1 AAATCTAATAAAAATATAAAAACTTAATT
*
4281940 AAATCTAAT-AAAATAATAAAAACTTACTT
1 AAATCTAATAAAAAT-ATAAAAACTTAATT
4281969 AAAT
1 AAAT
4281973 ATTTTTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 5 0.17
29 24 0.83
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (29 bp):
AAATCTAATAAAAATATAAAAACTTAATT
Found at i:4286113 original size:1 final size:1
Alignment explanation
Indices: 4286107--4286131 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
4286097 AACAAATCCA
4286107 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
4286132 AAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:4299374 original size:5 final size:5
Alignment explanation
Indices: 4299364--4299397 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
4299354 AAACCTACAA
* *
4299364 GAGAG GAGAG GAGAG GAGAG GAGAA GAGAA GAGA
1 GAGAG GAGAG GAGAG GAGAG GAGAG GAGAG GAGA
4299398 AAAGAAAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (5 bp):
GAGAG
Found at i:4305463 original size:38 final size:41
Alignment explanation
Indices: 4305412--4305488 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
4305402 TATTGTTAGT
4305412 TGTTGGAATTTTAA-A-T-TTGTTGTTGGAATTTCTTGAAA
1 TGTTGGAATTTTAAGATTATTGTTGTTGGAATTTCTTGAAA
4305450 TGTTGGAATTTTAAGATTATTGTTGTTGGAATTTCTTGA
1 TGTTGGAATTTTAAGATTATTGTTGTTGGAATTTCTTGA
4305489 TCATTGAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
38 14 0.39
39 1 0.03
40 1 0.03
41 20 0.56
ACGTcount: A:0.25, C:0.03, G:0.22, T:0.51
Consensus pattern (41 bp):
TGTTGGAATTTTAAGATTATTGTTGTTGGAATTTCTTGAAA
Found at i:4305494 original size:23 final size:22
Alignment explanation
Indices: 4305410--4305494 Score: 58
Period size: 23 Copynumber: 4.0 Consensus size: 22
4305400 ACTATTGTTA
**
4305410 GTTGTTGGAATTT-TAAAT-TT
1 GTTGTTGGAATTTCTTGATATT
4305430 GTTGTTGGAATTTCTTGA-A--
1 GTTGTTGGAATTTCTTGATATT
* *
4305449 -ATGTTGGAATTT-TAAGATTATT
1 GTTGTTGGAATTTCT-TGA-TATT
4305471 GTTGTTGGAATTTCTTGATCATT
1 GTTGTTGGAATTTCTTGAT-ATT
4305494 G
1 G
4305495 AAACGGTAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 17
0.68 0.08 0.24
Matches are distributed among these distances:
17 1 0.02
18 13 0.27
20 14 0.29
21 2 0.04
22 1 0.02
23 17 0.35
24 1 0.02
ACGTcount: A:0.24, C:0.04, G:0.22, T:0.51
Consensus pattern (22 bp):
GTTGTTGGAATTTCTTGATATT
Found at i:4305548 original size:22 final size:22
Alignment explanation
Indices: 4305520--4305575 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
4305510 TTTTAAATTG
*
4305520 GTTGAATTTGTTTTAAAATGTT
1 GTTGAATTTGTTTTAAAATATT
*
4305542 GTTGAATTTG-CTTAAAATATT
1 GTTGAATTTGTTTTAAAATATT
*
4305563 GTTAAATGTTGTT
1 GTTGAAT-TTGTT
4305576 GAATTTGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.29, C:0.02, G:0.18, T:0.52
Consensus pattern (22 bp):
GTTGAATTTGTTTTAAAATATT
Found at i:4305569 original size:52 final size:49
Alignment explanation
Indices: 4305512--4305617 Score: 133
Period size: 52 Copynumber: 2.1 Consensus size: 49
4305502 AGATTGAATT
* *
4305512 TTAAAT-TGGTTGAATTTGTTTTAAAATGTTGTTGAATTTGCTTAAAATATTG
1 TTAAATGTGGTTGAATTTG-TTCAAAATGCTGTTGAATTT-CTT-AAATA-TG
* *
4305564 TTAAATGTTGTTGAATTTGTTCAAAATGCTGTTGAATTTCTTGAATATG
1 TTAAATGTGGTTGAATTTGTTCAAAATGCTGTTGAATTTCTTAAATATG
4305613 TTAAA
1 TTAAA
4305618 AGTTATATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
49 7 0.14
50 4 0.08
51 3 0.06
52 24 0.49
53 11 0.22
ACGTcount: A:0.31, C:0.04, G:0.17, T:0.48
Consensus pattern (49 bp):
TTAAATGTGGTTGAATTTGTTCAAAATGCTGTTGAATTTCTTAAATATG
Found at i:4307823 original size:7 final size:7
Alignment explanation
Indices: 4307811--4307838 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
4307801 ATTGGTAGAA
4307811 GCTTTAG
1 GCTTTAG
4307818 GCTTTAG
1 GCTTTAG
4307825 GCTTTAG
1 GCTTTAG
4307832 GCTTTAG
1 GCTTTAG
4307839 ACTGTAGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (7 bp):
GCTTTAG
Found at i:4309090 original size:4 final size:4
Alignment explanation
Indices: 4309081--4309109 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
4309071 GAAAAAAGCT
4309081 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
4309110 CCGTAGCCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:4309373 original size:5 final size:5
Alignment explanation
Indices: 4309363--4309388 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4309353 CCTCTTCTCC
4309363 TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT T
4309389 CTCTCTGGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:4313868 original size:25 final size:21
Alignment explanation
Indices: 4313840--4313891 Score: 50
Period size: 23 Copynumber: 2.2 Consensus size: 21
4313830 TTTAAAAATA
4313840 TTATAAAATAGAATAATTTATATTT
1 TTATAAAATA-AA-AA--TATATTT
4313865 TTATTTAAAATAAAAATATATTT
1 TTA--TAAAATAAAAATATATTT
4313888 TTAT
1 TTAT
4313892 GAATTCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
21 1 0.04
23 10 0.40
25 5 0.20
26 2 0.08
27 7 0.28
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TTATAAAATAAAAATATATTT
Found at i:4314106 original size:25 final size:25
Alignment explanation
Indices: 4314058--4314107 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
4314048 TTTACGCTTG
*
4314058 AAATTTTAAAAACAGAAATAATTTT
1 AAATTTTAAAAACAGAAAAAATTTT
*
4314083 AAATTTTAAAAA-ATAAAAACATTTT
1 AAATTTTAAAAACAGAAAAA-ATTTT
4314108 TTTATTCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (25 bp):
AAATTTTAAAAACAGAAAAAATTTT
Found at i:4315051 original size:2 final size:2
Alignment explanation
Indices: 4315044--4315075 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4315034 TGAAAGTTAA
4315044 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
4315076 TGAAAAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4322982 original size:29 final size:28
Alignment explanation
Indices: 4322940--4322994 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
4322930 GCCCAAAACC
4322940 CTTTTATTTGCCTTTTTCTTATTCTTTCT
1 CTTTTATTTGCCTTTTTCTTA-TCTTTCT
* *
4322969 CTTTTCTTTGCCTTTTTTTTATCTTT
1 CTTTTATTTGCCTTTTTCTTATCTTT
4322995 AAAATACACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.05, C:0.20, G:0.04, T:0.71
Consensus pattern (28 bp):
CTTTTATTTGCCTTTTTCTTATCTTTCT
Found at i:4323133 original size:20 final size:24
Alignment explanation
Indices: 4323108--4323156 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 24
4323098 TTTTATTTTT
4323108 TTTCTTCTTC-CT-C-TCTCT-TC
1 TTTCTTCTTCACTCCTTCTCTCTC
*
4323128 TTTCTTTTTCACTCCTTCTCTCTC
1 TTTCTTCTTCACTCCTTCTCTCTC
4323152 TTTCT
1 TTTCT
4323157 CTGACAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 9 0.38
21 2 0.08
22 1 0.04
23 5 0.21
24 7 0.29
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTCTTCTTCACTCCTTCTCTCTC
Found at i:4332809 original size:23 final size:23
Alignment explanation
Indices: 4332782--4332837 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
4332772 TAGGGTTGAA
*
4332782 CATTACATGACTAGTTGATATGT
1 CATTACATGACTAGTTGATAAGT
* *
4332805 CATTACGTGACTGGTTGATAAGT
1 CATTACATGACTAGTTGATAAGT
*
4332828 CATTGCATGA
1 CATTACATGA
4332838 ATATGGTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (23 bp):
CATTACATGACTAGTTGATAAGT
Found at i:4333247 original size:171 final size:171
Alignment explanation
Indices: 4332962--4333279 Score: 582
Period size: 171 Copynumber: 1.9 Consensus size: 171
4332952 ATTTCTTGTA
*
4332962 TGAAATTGACGTGTGATAACTGCATGAAATTTATCTATGTGGCATTGCATGACTAACATTACGTT
1 TGAAATTGACGTGTGATAACTGCATGAAATTTATCTACGTGGCATTGCATGACTAACATTACGTT
*
4333027 CATTCTGTATTATTTTAGGTCAACTATATTGCTTTAATATATATATGTTGATTTACTTAATAATC
66 CATTCTGTATTATTTTAGGTCAACTATAATGCTTTAATATATATATGTTGATTTACTTAATAATC
4333092 CATGCTCGACACATGCAGTTGACGTGTGTCTATTTCAGGTC
131 CATGCTCGACACATGCAGTTGACGTGTGTCTATTTCAGGTC
* **
4333133 TGAAATTGATGTGTGATAACTGCATGAAATTTATCTACGTGGCATTGCATGACTAACATTGTGTT
1 TGAAATTGACGTGTGATAACTGCATGAAATTTATCTACGTGGCATTGCATGACTAACATTACGTT
*
4333198 CATTCTGTATTATTTTAGGTCAACTATAATGCTTTAATATGTATATGTTGATTTACTTAATAATC
66 CATTCTGTATTATTTTAGGTCAACTATAATGCTTTAATATATATATGTTGATTTACTTAATAATC
4333263 CATGCTCGACACATGCA
131 CATGCTCGACACATGCA
4333280 TTAATTATTC
Statistics
Matches: 141, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
171 141 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.40
Consensus pattern (171 bp):
TGAAATTGACGTGTGATAACTGCATGAAATTTATCTACGTGGCATTGCATGACTAACATTACGTT
CATTCTGTATTATTTTAGGTCAACTATAATGCTTTAATATATATATGTTGATTTACTTAATAATC
CATGCTCGACACATGCAGTTGACGTGTGTCTATTTCAGGTC
Found at i:4334880 original size:22 final size:21
Alignment explanation
Indices: 4334835--4334881 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4334825 CATGATTGGG
* * *
4334835 TTTTAGGCATTTGTGACTTGT
1 TTTTAGGCATTCGTGACATAT
4334856 TTTTAGGCATTACGTGACATAT
1 TTTTAGGCATT-CGTGACATAT
4334878 TTTT
1 TTTT
4334882 TCATTTTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.19, C:0.11, G:0.19, T:0.51
Consensus pattern (21 bp):
TTTTAGGCATTCGTGACATAT
Found at i:4338644 original size:23 final size:23
Alignment explanation
Indices: 4338618--4338677 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
4338608 TAAAAAATTA
4338618 TCACATAATACCTTATCAACCAG
1 TCACATAATACCTTATCAACCAG
* * *
4338641 TCACGTAATTCCTTATCAACTAG
1 TCACATAATACCTTATCAACCAG
* *
4338664 TCACACAATGCCTT
1 TCACATAATACCTT
4338678 TATGCTATAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (23 bp):
TCACATAATACCTTATCAACCAG
Found at i:4340319 original size:23 final size:22
Alignment explanation
Indices: 4340293--4340340 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
4340283 ATGCCGTACA
4340293 AACCAGTCC-CACAATGCCTTATC
1 AACCAG-CCACACAATGCC-TATC
*
4340316 AACCAGCCACATAATGCCTATC
1 AACCAGCCACACAATGCCTATC
4340338 AAC
1 AAC
4340341 TAATCATGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.35, C:0.38, G:0.08, T:0.19
Consensus pattern (22 bp):
AACCAGCCACACAATGCCTATC
Found at i:4340363 original size:22 final size:22
Alignment explanation
Indices: 4340252--4340494 Score: 155
Period size: 22 Copynumber: 10.9 Consensus size: 22
4340242 CCAATCAAGC
* *
4340252 AGTCATGCAATACCTAAAAACT
1 AGTCACGCAATGCCTAAAAACT
* * *
4340274 AGTAACGCAATGCCGTACAAACC
1 AGTCACGCAATGCC-TAAAAACT
* * ** *
4340297 AGTCCCACAATGCCTTATCAACC
1 AGTCACGCAATGCC-TAAAAACT
* ** **
4340320 AGCCACATAATGCCTATCAACT
1 AGTCACGCAATGCCTAAAAACT
* *
4340342 AATCATGCAATGCCTAAAAACT
1 AGTCACGCAATGCCTAAAAACT
* * *
4340364 AGTCACACAATGCCTAAAACCC
1 AGTCACGCAATGCCTAAAAACT
* *
4340386 AGTCACGTAATGCCCTAAAAACC
1 AGTCACGCAATG-CCTAAAAACT
* * * *
4340409 AATGATGCAATACCTTAAAAACT
1 AGTCACGCAATGCC-TAAAAACT
*
4340432 AGTCACGTAATGCCTAAAAA-T
1 AGTCACGCAATGCCTAAAAACT
* * **
4340453 CGATCACGCAATGCTTATCAACT
1 AG-TCACGCAATGCCTAAAAACT
4340476 AGTCACGCAATGCCTAAAA
1 AGTCACGCAATGCCTAAAA
4340495 TTCAATCAAG
Statistics
Matches: 166, Mismatches: 50, Indels: 10
0.73 0.22 0.04
Matches are distributed among these distances:
21 2 0.01
22 96 0.58
23 68 0.41
ACGTcount: A:0.40, C:0.28, G:0.12, T:0.21
Consensus pattern (22 bp):
AGTCACGCAATGCCTAAAAACT
Found at i:4340417 original size:67 final size:66
Alignment explanation
Indices: 4340280--4340450 Score: 173
Period size: 67 Copynumber: 2.5 Consensus size: 66
4340270 AACTAGTAAC
* * * * ** *
4340280 GCAATGCCGTACAAACCAGTCCCACAATGCCTTATCAACCAGCCACATAATGCCTATCAACTAAT
1 GCAATGCCGTAAAAACTAGTCACACAATGCC-TA-AAACCAGCCACATAATGCCTAAAAACCAAT
4340345 CAT
64 CAT
* *
4340348 GCAATGCC-TAAAAACTAGTCACACAATGCCTAAAACCCAGTCACGTAATGCCCTAAAAACCAAT
1 GCAATGCCGTAAAAACTAGTCACACAATGCCTAAAA-CCAGCCACATAATG-CCTAAAAACCAAT
*
4340412 GAT
64 CAT
* * **
4340415 GCAATACCTTAAAAACTAGTCACGTAATGCCTAAAA
1 GCAATGCCGTAAAAACTAGTCACACAATGCCTAAAA
4340451 ATCGATCACG
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
65 2 0.02
66 14 0.16
67 38 0.44
68 33 0.38
ACGTcount: A:0.40, C:0.29, G:0.11, T:0.20
Consensus pattern (66 bp):
GCAATGCCGTAAAAACTAGTCACACAATGCCTAAAACCAGCCACATAATGCCTAAAAACCAATCA
T
Found at i:4340508 original size:44 final size:45
Alignment explanation
Indices: 4340386--4340533 Score: 145
Period size: 44 Copynumber: 3.3 Consensus size: 45
4340376 CCTAAAACCC
* * * * * **
4340386 AGTCACGTAATGCCCTAAAAACCAATGATGCAATACCTTAAAAACT
1 AGTCACGCAATG-CCTAAAAATCAATCAAGCAATACTTTATCAACT
* * * *
4340432 AGTCACGTAATGCCTAAAAATCGATCACGCAATGC-TTATCAACT
1 AGTCACGCAATGCCTAAAAATCAATCAAGCAATACTTTATCAACT
* * *
4340476 AGTCACGCAATGCCTAAAATTCAATCAAGCAATACTTTATTAACC
1 AGTCACGCAATGCCTAAAAATCAATCAAGCAATACTTTATCAACT
*
4340521 AGTCGCGCAATGC
1 AGTCACGCAATGC
4340534 TTAAGTCATG
Statistics
Matches: 86, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
44 37 0.43
45 37 0.43
46 12 0.14
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.24
Consensus pattern (45 bp):
AGTCACGCAATGCCTAAAAATCAATCAAGCAATACTTTATCAACT
Found at i:4349197 original size:21 final size:21
Alignment explanation
Indices: 4349156--4349210 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
4349146 ATTAAAAATA
* *
4349156 AAAATATTTTATTTAATTTTTT
1 AAAATAATTTATATAA-TTTTT
4349178 AAAATAATTTATAT-ATTTTT
1 AAAATAATTTATATAATTTTT
*
4349198 AAAATTA-TTATAT
1 AAAATAATTTATAT
4349211 CTAAAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.20
20 11 0.37
21 1 0.03
22 12 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AAAATAATTTATATAATTTTT
Found at i:4349491 original size:14 final size:15
Alignment explanation
Indices: 4349472--4349505 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
4349462 ATAAAAAATG
4349472 TTAAAATTTATAA-A
1 TTAAAATTTATAACA
*
4349486 TTAAAATTTTTAACA
1 TTAAAATTTATAACA
4349501 TTAAA
1 TTAAA
4349506 TTAAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
TTAAAATTTATAACA
Found at i:4351005 original size:29 final size:29
Alignment explanation
Indices: 4350937--4351007 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
4350927 ATTTTTATTT
* *
4350937 AAAAT-AAAAATATATTTAATATAAAATA
1 AAAATAAAAAATTTATTAAATATAAAATA
*
4350965 AAAATATAAAAATTTAATTAAATATAATA-A
1 AAAATA-AAAAATTT-ATTAAATATAAAATA
4350995 AAAATAAAAAATT
1 AAAATAAAAAATT
4351008 ATTGTAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 5 0.14
29 7 0.19
30 14 0.38
31 11 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (29 bp):
AAAATAAAAAATTTATTAAATATAAAATA
Found at i:4351015 original size:29 final size:28
Alignment explanation
Indices: 4350937--4351017 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 28
4350927 ATTTTTATTT
4350937 AAAAT-AAAAATATATTTAATATAAAATAA
1 AAAATAAAAAAT-TATTTAA-ATAAAATAA
* * *
4350966 AAATATAAAAATTTAATTAAATATAATAA
1 AAA-ATAAAAAATTATTTAAATAAAATAA
4350995 AAAATAAAAAATTATTGTAAATA
1 AAAATAAAAAATTATT-TAAATA
4351018 GTATTATGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 11 0.25
29 20 0.45
30 8 0.18
31 5 0.11
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (28 bp):
AAAATAAAAAATTATTTAAATAAAATAA
Found at i:4357801 original size:6 final size:6
Alignment explanation
Indices: 4357790--4357815 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4357780 AGGATGTTAA
4357790 AGTCCC AGTCCC AGTCCC AGTCCC AG
1 AGTCCC AGTCCC AGTCCC AGTCCC AG
4357816 CATGATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.46, G:0.19, T:0.15
Consensus pattern (6 bp):
AGTCCC
Found at i:4358324 original size:17 final size:17
Alignment explanation
Indices: 4358302--4358335 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4358292 ACATAACATG
4358302 TAACAAATAAATTTTTA
1 TAACAAATAAATTTTTA
4358319 TAACAAATAAATTTTTA
1 TAACAAATAAATTTTTA
4358336 ACATGTGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
TAACAAATAAATTTTTA
Found at i:4362183 original size:2 final size:2
Alignment explanation
Indices: 4362176--4362200 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4362166 AATATTATTC
4362176 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 A
4362201 ATTAACATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4363476 original size:19 final size:19
Alignment explanation
Indices: 4363437--4363476 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4363427 GGCATAATTC
* *
4363437 TTAAAAAAATTTGAATTAT
1 TTAAAAAAATTTAAATAAT
*
4363456 TTAAGAAAATTTAAATAAT
1 TTAAAAAAATTTAAATAAT
4363475 TT
1 TT
4363477 TTTATTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
TTAAAAAAATTTAAATAAT
Found at i:4365060 original size:24 final size:25
Alignment explanation
Indices: 4365032--4365080 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
4365022 ATGAACTTGA
4365032 GAAATGAAGC-TTTTCTCTTCTCTT
1 GAAATGAAGCATTTTCTCTTCTCTT
* *
4365056 GAAATGAAGCATTTTTTCTTTTCTT
1 GAAATGAAGCATTTTCTCTTCTCTT
4365081 TTTCTTAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.22, C:0.16, G:0.12, T:0.49
Consensus pattern (25 bp):
GAAATGAAGCATTTTCTCTTCTCTT
Found at i:4366533 original size:23 final size:21
Alignment explanation
Indices: 4366502--4366561 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 21
4366492 TGATGATGGG
*
4366502 AAAATAAAATAATATGTTAATA
1 AAAATAAAATAATATGAT-ATA
4366524 ATAAATAAAA-AATAATGATATA
1 A-AAATAAAATAAT-ATGATATA
4366546 AATAATAAAATAATAT
1 AA-AATAAAATAATAT
4366562 TAATGGATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 1 0.03
22 17 0.52
23 15 0.45
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (21 bp):
AAAATAAAATAATATGATATA
Found at i:4370720 original size:77 final size:77
Alignment explanation
Indices: 4370639--4370802 Score: 206
Period size: 77 Copynumber: 2.1 Consensus size: 77
4370629 TGAATTTCCC
* * * * **
4370639 AAATTAAAATGCTATCTTTAATTTTAGTAATTTC-TTTTAAAGTATTAAACAATTTCCTT-TTCT
1 AAATTAAAATGCTATCCTTAATTTTAGGAA-TTCACTTTAAAGAAAGAAAC-ATTTCCTTATTCT
*
4370702 TTATGAATCACTTA
64 TTATGAATCACCTA
* * *
4370716 AAATTCAAATTCTATCCTTAATTTTAGGAATTCACTTTAAAGAAAGAAACATTTTCTTATTCTTT
1 AAATTAAAATGCTATCCTTAATTTTAGGAATTCACTTTAAAGAAAGAAACATTTCCTTATTCTTT
4370781 ATGAATCACCTA
66 ATGAATCACCTA
4370793 AAATTAAAAT
1 AAATTAAAAT
4370803 AGATGGCATA
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
76 10 0.14
77 64 0.86
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.43
Consensus pattern (77 bp):
AAATTAAAATGCTATCCTTAATTTTAGGAATTCACTTTAAAGAAAGAAACATTTCCTTATTCTTT
ATGAATCACCTA
Found at i:4381234 original size:30 final size:32
Alignment explanation
Indices: 4381195--4381267 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 32
4381185 ATCCTCAACT
* * *
4381195 TCTTTTTTATCTTCAT-T-TCTTTCCATGTCA
1 TCTTCTTTATCTTCATATCTCCTTCCATGCCA
*
4381225 TCTTCTTTATCTTCATCATCTCCTTGCATGCCA
1 TCTTCTTTATCTTCAT-ATCTCCTTCCATGCCA
4381258 TCTTCTTTAT
1 TCTTCTTTAT
4381268 TCTTAATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 15 0.42
32 1 0.03
33 20 0.56
ACGTcount: A:0.14, C:0.27, G:0.04, T:0.55
Consensus pattern (32 bp):
TCTTCTTTATCTTCATATCTCCTTCCATGCCA
Found at i:4383699 original size:20 final size:20
Alignment explanation
Indices: 4383674--4383712 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4383664 CCAAACTAAG
* *
4383674 AACAATAAGAAACAAATAAA
1 AACAATAACAAAAAAATAAA
4383694 AACAATAACAAAAAAATAA
1 AACAATAACAAAAAAATAA
4383713 CTTTAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.77, C:0.10, G:0.03, T:0.10
Consensus pattern (20 bp):
AACAATAACAAAAAAATAAA
Found at i:4386483 original size:25 final size:24
Alignment explanation
Indices: 4386455--4386513 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
4386445 TAAATTCTTC
*
4386455 AAAAGAAAACAAAGAAAAATGAAAA
1 AAAAGAAAACAAACAAAAA-GAAAA
*
4386480 AAAA-ATAAACAAACCAAAAGAAAA
1 AAAAGA-AAACAAACAAAAAGAAAA
4386504 AAAGAGAAAA
1 AAA-AGAAAA
4386514 ACTTGCAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 9 0.31
25 19 0.66
26 1 0.03
ACGTcount: A:0.80, C:0.07, G:0.10, T:0.03
Consensus pattern (24 bp):
AAAAGAAAACAAACAAAAAGAAAA
Found at i:4400022 original size:33 final size:31
Alignment explanation
Indices: 4399985--4400157 Score: 108
Period size: 33 Copynumber: 5.5 Consensus size: 31
4399975 TTTTAATATC
4399985 ATATATTTTATTTTCATTTCTTATTATAATTTT
1 ATATATTTTATTTT-ATTT-TTATTATAATTTT
*
4400018 ATATATTTTATATTTTATTTTTAATATAATTTT
1 ATATA-TTT-TATTTTATTTTTATTATAATTTT
* * *
4400051 TTATATTATATATTTTATTTTAATTTTAA-TTT
1 ATATATT-T-TATTTTATTTTTATTATAATTTT
** * *
4400083 ATATTATATAAATTTTA-ATTTCTTAT-A--TT
1 ATA-TAT-TTTATTTTATTTTTATTATAATTTT
* * *
4400112 -T-TATTTTATTTTAATTTTTAATTTTTATATT
1 ATATATTTTATTTT-ATTTTT-ATTATAATTTT
4400143 ATATATTTTATTTTA
1 ATATATTTTATTTTA
4400158 ATATTTTTTA
Statistics
Matches: 110, Mismatches: 17, Indels: 27
0.71 0.11 0.18
Matches are distributed among these distances:
25 6 0.05
26 4 0.04
27 3 0.03
28 4 0.04
29 3 0.03
30 1 0.01
31 7 0.06
32 15 0.14
33 53 0.48
34 8 0.07
35 6 0.05
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (31 bp):
ATATATTTTATTTTATTTTTATTATAATTTT
Found at i:4400031 original size:7 final size:7
Alignment explanation
Indices: 4400019--4400172 Score: 84
Period size: 7 Copynumber: 23.3 Consensus size: 7
4400009 TATAATTTTA
4400019 TATATTT
1 TATATTT
4400026 TATATTT
1 TATATTT
4400033 TAT-TTT
1 TATATTT
*
4400039 TA-ATAT
1 TATATTT
* *
4400045 AATTTTT
1 TATATTT
*
4400052 TATATTA
1 TATATTT
4400059 TATA-TT
1 TATATTT
4400065 T-TATTT
1 TATATTT
4400071 TA-ATTT
1 TATATTT
4400077 TA-A-TT
1 TATATTT
4400082 TATATTAT
1 TATATT-T
*
4400090 ATAAATTT
1 -TATATTT
4400098 TA-ATTT
1 TATATTT
4400104 CT-TATATT
1 -TATAT-TT
4400112 T-TATTT
1 TATATTT
4400118 TAT-TTT
1 TATATTT
*
4400124 AAT-TTT
1 TATATTT
4400130 TA-ATTTT
1 TATA-TTT
*
4400137 TATATTA
1 TATATTT
4400144 TATATTT
1 TATATTT
4400151 TAT-TTT
1 TATATTT
*
4400157 AATATTT
1 TATATTT
*
4400164 TTTATTT
1 TATATTT
4400171 TA
1 TA
4400173 ATTATAACAT
Statistics
Matches: 114, Mismatches: 17, Indels: 32
0.70 0.10 0.20
Matches are distributed among these distances:
5 6 0.05
6 42 0.37
7 56 0.49
8 5 0.04
9 5 0.04
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (7 bp):
TATATTT
Found at i:4400057 original size:26 final size:27
Alignment explanation
Indices: 4399945--4400169 Score: 84
Period size: 30 Copynumber: 8.4 Consensus size: 27
4399935 TTATTGTTAA
*
4399945 TTTTTATATAATATCATCTCTTAA-ATATAT
1 TTTTTATATTATAT-AT-T-TTAATATA-AT
* * * * *
4399975 TTTTAATATCATATATTTTATTTTCA-
1 TTTTTATATTATATATTTTAATATAAT
*
4400001 TTTCT-TATTATA-ATTTT-ATAT-A-
1 TTTTTATATTATATATTTTAATATAAT
*
4400023 -TTTTATATTTTAT-TTTTAATATAAT
1 TTTTTATATTATATATTTTAATATAAT
* *
4400048 TTTTTATATTATATATTTTATTTTAATT
1 TTTTTATATTATATATTTTAATATAA-T
**
4400076 TTAATTTATATTATATAAATTTTAAT-TTCT
1 TT--TTTATATTATAT--ATTTTAATATAAT
*
4400106 TATATTT-TATT-T-TATTTTAATTTTTAA-
1 T-T-TTTATATTATATATTTTAA--TATAAT
* *
4400133 TTTTTATATTATATATTTTATTTTAAT
1 TTTTTATATTATATATTTTAATATAAT
4400160 ATTTTT-TATT
1 -TTTTTATATT
4400170 TTAATTATAA
Statistics
Matches: 152, Mismatches: 21, Indels: 47
0.69 0.10 0.21
Matches are distributed among these distances:
21 3 0.02
22 11 0.07
23 6 0.04
24 6 0.04
25 16 0.11
26 25 0.16
27 21 0.14
28 19 0.12
29 6 0.04
30 30 0.20
31 2 0.01
32 7 0.05
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTTTATATTATATATTTTAATATAAT
Found at i:4400085 original size:73 final size:70
Alignment explanation
Indices: 4399968--4400103 Score: 175
Period size: 73 Copynumber: 1.9 Consensus size: 70
4399958 TCATCTCTTA
* * * *
4399968 AATATATTTTTAATATCATATATTTTATTTTCATTTCTTATTATAATTTTATATATTTTATATTT
1 AATATATTTTTAATATCATATATTTTATTTTAATTTCTAATTAT-ATTATATAAATTTTA-ATTT
4400033 TATTTTT
64 TATTTTT
* *
4400040 AATATAATTTTTTATATTATATATTTTATTTTAATTT-TAATTTATATTATATAAATTTTAATTT
1 AATAT-ATTTTTAATATCATATATTTTATTTTAATTTCTAA-TTATATTATATAAATTTTAATTT
4400104 CTTATATTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
71 4 0.07
72 20 0.36
73 32 0.57
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (70 bp):
AATATATTTTTAATATCATATATTTTATTTTAATTTCTAATTATATTATATAAATTTTAATTTTA
TTTTT
Found at i:4400118 original size:5 final size:5
Alignment explanation
Indices: 4400061--4400172 Score: 57
Period size: 5 Copynumber: 21.4 Consensus size: 5
4400051 TTATATTATA
* * * * * * *
4400061 TATTT TATTT TAATTT TAATT TATAT TATATA AATTT TAATT TCTTA TATTT
1 TATTT TATTT T-ATTT TATTT TATTT TAT-TT TATTT TATTT TATTT TATTT
* * *
4400113 TATTT TATTT TAATTTT TAATTTT TATAT TA-TA TATTT TATTT TAATAT
1 TATTT TATTT T-A-TTT T-A-TTT TATTT TATTT TATTT TATTT T-ATTT
4400162 T-TTT TATTT TA
1 TATTT TATTT TA
4400173 ATTATAACAT
Statistics
Matches: 80, Mismatches: 20, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
4 5 0.06
5 51 0.64
6 13 0.16
7 11 0.14
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (5 bp):
TATTT
Found at i:4400167 original size:53 final size:51
Alignment explanation
Indices: 4400052--4400172 Score: 145
Period size: 53 Copynumber: 2.3 Consensus size: 51
4400042 TATAATTTTT
**
4400052 TATATTATATATTTTATTTTAATTTTAATTTATATTATATAAATTTTAATTTCT
1 TATATT-T-TATTTTATTTTAATTTTAATTTATATTATAT-AATTTTAATTTAA
*
4400106 TATATTTTATTTTATTTTAATTTTTAATTTTTATATTATAT-ATTTTATTTTAA
1 TATATTTTATTTTATTTTAA-TTTTAA--TTTATATTATATAATTTTAATTTAA
*
4400159 TATTTTTTATTTTA
1 TATATTTTATTTTA
4400173 ATTATAACAT
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
52 13 0.22
53 29 0.48
54 6 0.10
55 12 0.20
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (51 bp):
TATATTTTATTTTATTTTAATTTTAATTTATATTATATAATTTTAATTTAA
Found at i:4402493 original size:20 final size:21
Alignment explanation
Indices: 4402462--4402503 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
4402452 ATGGATAAAG
4402462 AAATATTTCATACAT-TATTTA
1 AAATATTTCATA-ATGTATTTA
4402483 AAATA-TTCATAATGTATTTA
1 AAATATTTCATAATGTATTTA
4402503 A
1 A
4402504 TATGAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 2 0.10
20 13 0.65
21 5 0.25
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (21 bp):
AAATATTTCATAATGTATTTA
Found at i:4406341 original size:6 final size:6
Alignment explanation
Indices: 4406330--4406369 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
4406320 ATATTTTAGA
* *
4406330 TTAGTT TTAGTT ATTAGTT TTAATT TTAATT TTAGTT TTA
1 TTAGTT TTAGTT -TTAGTT TTAGTT TTAGTT TTAGTT TTA
4406370 ATTATTTAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (6 bp):
TTAGTT
Found at i:4406345 original size:13 final size:13
Alignment explanation
Indices: 4406329--4406366 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
4406319 TATATTTTAG
4406329 ATTAGTTTTAGTT
1 ATTAGTTTTAGTT
*
4406342 ATTAGTTTTAATT
1 ATTAGTTTTAGTT
*
4406355 -TTAATTTTAGTT
1 ATTAGTTTTAGTT
4406367 TTAATTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (13 bp):
ATTAGTTTTAGTT
Found at i:4408691 original size:15 final size:15
Alignment explanation
Indices: 4408671--4408701 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4408661 CGATTCATGA
4408671 TTAACTTGTACAAAG
1 TTAACTTGTACAAAG
*
4408686 TTAACTTGTATAAAG
1 TTAACTTGTACAAAG
4408701 T
1 T
4408702 CTTTGACCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (15 bp):
TTAACTTGTACAAAG
Found at i:4415464 original size:28 final size:28
Alignment explanation
Indices: 4415430--4415675 Score: 251
Period size: 28 Copynumber: 8.6 Consensus size: 28
4415420 GACAGTTTTT
*
4415430 ACATGTTTGTCTTAATTTAAACAACAAA
1 ACATGTTTGTCTTAATTTAAACAAGAAA
* * * * *
4415458 ATATGTTTATCTTAAATTAGATAAGAAA
1 ACATGTTTGTCTTAATTTAAACAAGAAA
4415486 ACATGTTTGTCTTAATTTAAACAAG-AA
1 ACATGTTTGTCTTAATTTAAACAAGAAA
* * *
4415513 ATATGTTTGTATTAATTTAAGATAAGAAA
1 ACATGTTTGTCTTAATTTAA-ACAAGAAA
*
4415542 ACATGTTTTGTCTTAATTTAGACAAGAAA
1 ACATG-TTTGTCTTAATTTAAACAAGAAA
* *
4415571 ACATGTTTGTCATAATTTAAGAAAAGAAAA
1 ACATGTTTGTCTTAATTTAA-ACAAG-AAA
* * *
4415601 ATATGTTTTGTCTTAATTTAGACAAAAAA
1 ACATG-TTTGTCTTAATTTAAACAAGAAA
* * * *
4415630 ACATGTTTGTCTCACTTTAGACAAGATA
1 ACATGTTTGTCTTAATTTAAACAAGAAA
*
4415658 ACATGTTTTATCTTAATT
1 ACATG-TTTGTCTTAATT
4415676 AAATATAAGA
Statistics
Matches: 177, Mismatches: 34, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
27 20 0.11
28 83 0.47
29 38 0.21
30 23 0.13
31 13 0.07
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (28 bp):
ACATGTTTGTCTTAATTTAAACAAGAAA
Found at i:4415631 original size:59 final size:58
Alignment explanation
Indices: 4415430--4415675 Score: 272
Period size: 59 Copynumber: 4.3 Consensus size: 58
4415420 GACAGTTTTT
* * * * *
4415430 ACATG-TTTGTCTTAATTTAAACAACAAAATATGTTTATCTTAAATT-AGATAAGAAA
1 ACATGTTTTGTCTTAATTTAAACAAAAAAACATGTTTGTCATAATTTAAGATAAGAAA
* *
4415486 ACATG-TTTGTCTTAATTTAAAC-AAGAAATATGTTTGT-ATTAATTTAAGATAAGAAA
1 ACATGTTTTGTCTTAATTTAAACAAAAAAACATGTTTGTCA-TAATTTAAGATAAGAAA
* * *
4415542 ACATGTTTTGTCTTAATTTAGACAAGAAAACATGTTTGTCATAATTTAAGAAAAGAAAA
1 ACATGTTTTGTCTTAATTTAAACAAAAAAACATGTTTGTCATAATTTAAGATAAG-AAA
* * * * *
4415601 ATATGTTTTGTCTTAATTTAGACAAAAAAACATGTTTGTC-TCACTTT-AGACAAGATA
1 ACATGTTTTGTCTTAATTTAAACAAAAAAACATGTTTGTCAT-AATTTAAGATAAGAAA
*
4415658 ACATGTTTTATCTTAATT
1 ACATGTTTTGTCTTAATT
4415676 AAATATAAGA
Statistics
Matches: 166, Mismatches: 17, Indels: 13
0.85 0.09 0.07
Matches are distributed among these distances:
55 17 0.10
56 37 0.22
57 34 0.20
58 32 0.19
59 46 0.28
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (58 bp):
ACATGTTTTGTCTTAATTTAAACAAAAAAACATGTTTGTCATAATTTAAGATAAGAAA
Found at i:4418985 original size:18 final size:20
Alignment explanation
Indices: 4418945--4418997 Score: 53
Period size: 21 Copynumber: 2.9 Consensus size: 20
4418935 TTTGCTAATA
*
4418945 TATTATTTTTAATTATTAGTT
1 TATTAGTTTTAATTATTA-TT
4418966 TATTAGTTTTAATT-TT-TT
1 TATTAGTTTTAATTATTATT
4418984 TA--A-TTTTAATTATT
1 TATTAGTTTTAATTATT
4418998 TAGATAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 8 0.27
16 3 0.10
18 4 0.13
20 2 0.07
21 13 0.43
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (20 bp):
TATTAGTTTTAATTATTATT
Found at i:4420782 original size:22 final size:22
Alignment explanation
Indices: 4420737--4420795 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
4420727 TAAAGAATTA
*
4420737 AATTAGTTAATTT-AAATAACT
1 AATTAATTAATTTAAAATAACT
**
4420758 AATTAATTAATTTAAAATAGTT
1 AATTAATTAATTTAAAATAACT
*
4420780 AATCAATTAATGTTAA
1 AATTAATTAAT-TTAA
4420796 TGACACATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 12 0.38
22 16 0.50
23 4 0.12
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.42
Consensus pattern (22 bp):
AATTAATTAATTTAAAATAACT
Found at i:4435485 original size:2 final size:2
Alignment explanation
Indices: 4435478--4435508 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4435468 TACTTCTTGT
4435478 TC TC TC TC 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
4435509 GATTTTTCCC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4436110 original size:15 final size:15
Alignment explanation
Indices: 4436090--4436118 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4436080 GGCATTGATA
4436090 TTATTGTTATTATTG
1 TTATTGTTATTATTG
4436105 TTATTGTTATTATT
1 TTATTGTTATTATT
4436119 ACTGTAATAA
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:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (15 bp):
TTATTGTTATTATTG
Found at i:4437679 original size:2 final size:2
Alignment explanation
Indices: 4437672--4437697 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4437662 TTAGGGATTA
4437672 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
4437698 TGGGTGCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4438308 original size:437 final size:444
Alignment explanation
Indices: 4437455--4438342 Score: 1438
Period size: 437 Copynumber: 2.0 Consensus size: 444
4437445 CTAATTTTAT
4437455 TTTTCATTCTTACTTTGTCTGTCCTTCCTCACCCTTGTTTTGCATCAATTAGGGAGACTGATGAA
1 TTTTCATTCTTACTTTGTCTGTCCTTCCTCACCCTTGTTTTGCATCAATTAGGGAGACTGATGAA
* *
4437520 GAACAAGATCATGTTTATTGGAATTAAATTATGTAGGGATTATTTATTTTTAACAGTGTTTCTGC
66 GAACAAGATCATGTTTATTGGAAATAAATTATGTAGAGATTATTTATTTTTAACAGTGTTTCTGC
4437585 CCTTTGTCTTATTTTTCTCTATCTCTCTTTGCCTCTTCTTCCCTGCCCCTGTTTTGCATCAATTA
131 CCTTTGTCTTATTTTTCTCTATCTCTCTTTGCCTCTTCTTCCCTGCCCCTGTTTTGCATCAATTA
*
4437650 GGGAGAGAATGATTAGGGATTAATATATATATATATATATATATATATTGGGTGCATTTGTAATT
196 GGGAGAGAATGATTA-GG---AAGATATATATATATATATATATATATTGGGTGCATTTGTAATT
4437715 TTCAGTATTTAGAGAAGTTCTACCGCATTTAGGTTACATTTGGTATTTTGTGTTTATGTTAGGGT
257 TTCAGTATTTAGAGAAGTTCTACCGCATTTAGGTTACATTTGGTATTTTGTGTTTATGTTAGGGT
* * * *
4437780 TACCGATTAGTCTACTACCATGTATGATCTTTTAGTTTCTGGTAGGTTTTAATAATGGATTATTG
322 TACAGATTAGTCTACTACCATCTATGATCTTTTAGCTTCTGGTAGCTTTTAATAATGGATTATTG
*
4437845 AGATTTTCCCTCTTGGTTCGGTCTTTTCTTTCTCCACTTTTCTGTATTTCTCTGAGAA
387 AGATTTTCCCTCTTGGTTCGGTCTTTTCTTTCTCCACTTTGCTGTATTTCTCTGAGAA
* * *
4437903 TTTTCATTCTTACTTTGTCTGTCCTTCCTCTCCCTTGTTTTGCATCGATTAGGGAGACTGATGCA
1 TTTTCATTCTTACTTTGTCTGTCCTTCCTCACCCTTGTTTTGCATCAATTAGGGAGACTGATGAA
*
4437968 GAACAAGATCATGTTTATTGGAAATAAATTATGTAGAGATTATTTATTTTTAACGGTGTTTCTGC
66 GAACAAGATCATGTTTATTGGAAATAAATTATGTAGAGATTATTTATTTTTAACAGTGTTTCTGC
* *
4438033 CCTTTATGTCTTATTTTTCTCTATCTCTCTTTGTCTCTTCTTCCCCTG-CCTTGTTTTGCATCAA
131 CC-TT-TGTCTTATTTTTCTCTATCTCTCTTTGCCTCTTCTT-CCCTGCCCCTGTTTTGCATCAA
4438097 TTAGGGAGAGAATGATT-GG-AGAT-TA-ATATATAT-T-T-T-T-TTGGGTGCATTTGTAATTT
193 TTAGGGAGAGAATGATTAGGAAGATATATATATATATATATATATATTGGGTGCATTTGTAATTT
* * * *
4438153 TCAGTGTTTAGAGAATTTTTACCGCATTTAGGTTATATTTGGTATTTTGTGTTTATGTTAGGGTT
258 TCAGTATTTAGAGAAGTTCTACCGCATTTAGGTTACATTTGGTATTTTGTGTTTATGTTAGGGTT
* *
4438218 ACAGATTAGTCTA-TACCATCTATGATATTTTTAGCTTCTGGTAGCTTTTATTAATGGATTATTG
323 ACAGATTAGTCTACTACCATCTATGAT-CTTTTAGCTTCTGGTAGCTTTTAATAATGGATTATTG
*
4438282 AGATTTTCCCTCTTGGTTCTGTCTTTTCTTTCTCCACTTTGCTGTATTTCTCTGAGAA
387 AGATTTTCCCTCTTGGTTCGGTCTTTTCTTTCTCCACTTTGCTGTATTTCTCTGAGAA
4438340 TTT
1 TTT
4438343 CTTTTAACCT
Statistics
Matches: 415, Mismatches: 21, Indels: 19
0.91 0.05 0.04
Matches are distributed among these distances:
436 12 0.03
437 184 0.44
438 1 0.00
439 1 0.00
440 1 0.00
441 1 0.00
442 8 0.02
443 2 0.00
444 3 0.01
448 128 0.31
449 2 0.00
450 67 0.16
451 5 0.01
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.46
Consensus pattern (444 bp):
TTTTCATTCTTACTTTGTCTGTCCTTCCTCACCCTTGTTTTGCATCAATTAGGGAGACTGATGAA
GAACAAGATCATGTTTATTGGAAATAAATTATGTAGAGATTATTTATTTTTAACAGTGTTTCTGC
CCTTTGTCTTATTTTTCTCTATCTCTCTTTGCCTCTTCTTCCCTGCCCCTGTTTTGCATCAATTA
GGGAGAGAATGATTAGGAAGATATATATATATATATATATATATTGGGTGCATTTGTAATTTTCA
GTATTTAGAGAAGTTCTACCGCATTTAGGTTACATTTGGTATTTTGTGTTTATGTTAGGGTTACA
GATTAGTCTACTACCATCTATGATCTTTTAGCTTCTGGTAGCTTTTAATAATGGATTATTGAGAT
TTTCCCTCTTGGTTCGGTCTTTTCTTTCTCCACTTTGCTGTATTTCTCTGAGAA
Found at i:4438846 original size:64 final size:64
Alignment explanation
Indices: 4438757--4438884 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 64
4438747 AAATTGTGAG
* *
4438757 GGTTGTTCCTTATGGTCAAATAGGTACATTTAAATAGAACAAAGCGCATTGGGTAAACTGACCA
1 GGTTGTTCCTCATGGTCAAATAGGTACATTTAAATAGAACAAAGCACATTGGGTAAACTGACCA
4438821 GGTTGTTCCTCATGGTCAAATAGGTACATTTAAATAGAACAAAGCACATTGGGTAAACTGACCA
1 GGTTGTTCCTCATGGTCAAATAGGTACATTTAAATAGAACAAAGCACATTGGGTAAACTGACCA
4438885 ATTGTAAAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.27
Consensus pattern (64 bp):
GGTTGTTCCTCATGGTCAAATAGGTACATTTAAATAGAACAAAGCACATTGGGTAAACTGACCA
Found at i:4445558 original size:50 final size:50
Alignment explanation
Indices: 4445455--4445560 Score: 124
Period size: 50 Copynumber: 2.1 Consensus size: 50
4445445 GTAAAGTATG
* * * *
4445455 TGATTGTTAAAAAATAATTTTACAGCGTTTGGTATTATATGGAAATGTGA
1 TGATTGCTAAAAAATAATTTTACAGCGTTTGGTATAAAATGGAAATGTAA
* * * *
4445505 TGATTGCTAGAAAATAGTTTTATAGTGTTTGGTATAAAATGCGAAA-GTAA
1 TGATTGCTAAAAAATAATTTTACAGCGTTTGGTATAAAATG-GAAATGTAA
4445555 TGATTG
1 TGATTG
4445561 TAAGGAATGT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 43 0.91
51 4 0.09
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.39
Consensus pattern (50 bp):
TGATTGCTAAAAAATAATTTTACAGCGTTTGGTATAAAATGGAAATGTAA
Found at i:4446010 original size:19 final size:19
Alignment explanation
Indices: 4445982--4446036 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
4445972 TAGAACTATA
* *
4445982 CTTTTCTTTTTTCTTTCTT
1 CTTTTTTTTTTTCTTACTT
4446001 CTTTTTTTTTTT-TGTACTT
1 CTTTTTTTTTTTCT-TACTT
**
4446020 CCATTTTTTTTTCTTAC
1 CTTTTTTTTTTTCTTAC
4446037 CTTCCTCGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 1 0.03
19 28 0.93
20 1 0.03
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (19 bp):
CTTTTTTTTTTTCTTACTT
Found at i:4449775 original size:18 final size:17
Alignment explanation
Indices: 4449743--4449777 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
4449733 NNNNNNNNGG
*
4449743 AAGTAAGAGAAAAACAA
1 AAGTAAGACAAAAACAA
4449760 AAGTAGAGACAAAAACAA
1 AAGTA-AGACAAAAACAA
4449778 CGAATCAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.69, C:0.09, G:0.17, T:0.06
Consensus pattern (17 bp):
AAGTAAGACAAAAACAA
Found at i:4454526 original size:36 final size:36
Alignment explanation
Indices: 4454471--4454561 Score: 92
Period size: 36 Copynumber: 2.5 Consensus size: 36
4454461 AAGTTAGGCC
* * * * * *
4454471 TGATCTTGTGAAAAAGCATGTTATGAAGGTTATGCT
1 TGATCTTATTAAAAGGCATGTTATAAAAGTTATACT
*
4454507 TGATCTTATTAAAAGGCATGTTGTAAAAGTTATACT
1 TGATCTTATTAAAAGGCATGTTATAAAAGTTATACT
* *
4454543 TGACCCTATTGAAAAGGCA
1 TGATCTTATT-AAAAGGCA
4454562 AGTAGATAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
36 37 0.82
37 8 0.18
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (36 bp):
TGATCTTATTAAAAGGCATGTTATAAAAGTTATACT
Found at i:4455567 original size:209 final size:210
Alignment explanation
Indices: 4455206--4455604 Score: 613
Period size: 209 Copynumber: 1.9 Consensus size: 210
4455196 TGGCAAATAC
* * *
4455206 TTCACTCTTTTTATTGATAATTGTACTAGGATGTACTTGGTGTACATTATCAAATCTAAAAGTGA
1 TTCACTCTCTTTATTGACAATTATACTAGGATGTACTTGGTGTACATTATCAAATCTAAAAGTGA
* *
4455271 GGTCTTTGTTATGTTCAAGAGGTTCAAGTTTCTTGTTAAGAACCAAAGTGGCCTGAACATAAAAA
66 GGTCTTTGTTATGTTCAAAAGGTTCAAGTTTCTTGTTAAGAACCAAAGTGGCCTAAACATAAAAA
* *
4455336 TCCTGAGATCTGACAATGGCACTAAATATTCATTTACTCAATTTAATGAGTTTTGTAGCACTGAA
131 TCCTAAGATCTGACAATGGCACTAAATATACATTTACTCAATTTAATGAGTTTTGTAGCACTGAA
4455401 TATACTTCTACTCAA
196 TATACTTCTACTCAA
* * *
4455416 TTCACTCTCTTTATTGACAATTATACTAGGATGT-GTTGAGTGTACTTTATCAAATGT-AAAGTG
1 TTCACTCTCTTTATTGACAATTATACTAGGATGTACTTG-GTGTACATTATCAAATCTAAAAGTG
* * * * *
4455479 AGGTCTTTGTTGTGTTCAAAAGGTTCAAGTTTCTTGTTGAGAACCAAGGTGGCTTAAACATTAAA
65 AGGTCTTTGTTATGTTCAAAAGGTTCAAGTTTCTTGTTAAGAACCAAAGTGGCCTAAACATAAAA
* * *
4455544 ATCTTAAGATTTGACAATGGCACTAAATATACCTTTACTCAATTTAATGAGTTTTGTAGCA
130 ATCCTAAGATCTGACAATGGCACTAAATATACATTTACTCAATTTAATGAGTTTTGTAGCA
4455605 TTCTATGCAT
Statistics
Matches: 170, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
209 123 0.72
210 47 0.28
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Consensus pattern (210 bp):
TTCACTCTCTTTATTGACAATTATACTAGGATGTACTTGGTGTACATTATCAAATCTAAAAGTGA
GGTCTTTGTTATGTTCAAAAGGTTCAAGTTTCTTGTTAAGAACCAAAGTGGCCTAAACATAAAAA
TCCTAAGATCTGACAATGGCACTAAATATACATTTACTCAATTTAATGAGTTTTGTAGCACTGAA
TATACTTCTACTCAA
Found at i:4457623 original size:3 final size:3
Alignment explanation
Indices: 4457615--4457643 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4457605 AAAATAAATC
4457615 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4457644 GATGTATTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4468700 original size:7 final size:7
Alignment explanation
Indices: 4468675--4468712 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
4468665 CACTTCATTC
4468675 TTTTTCT
1 TTTTTCT
*
4468682 TCTCTT-T
1 T-TTTTCT
4468689 TTTTTCT
1 TTTTTCT
4468696 TTTTTCT
1 TTTTTCT
4468703 TTTTTCT
1 TTTTTCT
4468710 TTT
1 TTT
4468713 AAATATCACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 3 0.11
7 21 0.78
8 3 0.11
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:4480342 original size:26 final size:26
Alignment explanation
Indices: 4480288--4480343 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 26
4480278 GTCAATCAGC
*
4480288 TTTTAGATTTAATTTAATTATTATTAT
1 TTTTAGATTTAATTTAATTA-TATCAT
4480315 TTTTAG-TTTAACTTTTAATTA-ATCAT
1 TTTTAGATTTAA--TTTAATTATATCAT
4480341 TTT
1 TTT
4480344 AATTCAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 12 0.46
27 6 0.23
28 8 0.31
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (26 bp):
TTTTAGATTTAATTTAATTATATCAT
Found at i:4484394 original size:63 final size:63
Alignment explanation
Indices: 4484291--4484440 Score: 185
Period size: 63 Copynumber: 2.4 Consensus size: 63
4484281 GAATAGCTCA
* ** * *
4484291 TTAATCGGTT-AAGACGATCTTTAACCAATTAAAGCCTTTTGTCTTGCAGTCTGCTTCATTGTG
1 TTAATCGGTTAAAGAGGA-CTTTAACCAATTAAAGCCTTTTGTCTCACAATCTGCTTCATAGTG
* * * * *
4484354 TTAATTGGTTAAAGAGGACTTTAACCAATTAAATCTTTTTGTCTCATAATCTGTTTCATAGTG
1 TTAATCGGTTAAAGAGGACTTTAACCAATTAAAGCCTTTTGTCTCACAATCTGCTTCATAGTG
*
4484417 TTAATCGGTTAAAGGGGACTTTAA
1 TTAATCGGTTAAAGAGGACTTTAA
4484441 TTGCTCTTTA
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
63 68 0.92
64 6 0.08
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (63 bp):
TTAATCGGTTAAAGAGGACTTTAACCAATTAAAGCCTTTTGTCTCACAATCTGCTTCATAGTG
Found at i:4487141 original size:2 final size:2
Alignment explanation
Indices: 4487134--4487171 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
4487124 TAGATTATTG
* *
4487134 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4487172 TTTACTGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4491843 original size:25 final size:26
Alignment explanation
Indices: 4491815--4491871 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
4491805 ATTAAATAAA
*
4491815 TATTTGTAATTAAT-AATAAT-TTATT
1 TATTTATAATTAATCAA-AATATTATT
*
4491840 TATTTATTATTAATCAAAATATTATT
1 TATTTATAATTAATCAAAATATTATT
4491866 T-TTTAT
1 TATTTAT
4491872 TTTATAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 20 0.71
26 8 0.29
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (26 bp):
TATTTATAATTAATCAAAATATTATT
Found at i:4491872 original size:25 final size:25
Alignment explanation
Indices: 4491823--4491872 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
4491813 AATATTTGTA
4491823 ATTAATAATAATTTATTTATTTATT
1 ATTAATAATAATTTATTTATTTATT
4491848 ATTAATCAA-AATATTATTT-TTTATT
1 ATTAAT-AATAAT-TTATTTATTTATT
4491873 TTATAACTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTAATAATAATTTATTTATTTATT
Found at i:4501330 original size:13 final size:14
Alignment explanation
Indices: 4501312--4501340 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4501302 TAAAAGATAG
4501312 AAAAG-AAAAGAGA
1 AAAAGAAAAAGAGA
4501325 AAAAGAAAAAGAGA
1 AAAAGAAAAAGAGA
4501339 AA
1 AA
4501341 TAGATGTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAGAGA
Found at i:4507288 original size:24 final size:23
Alignment explanation
Indices: 4507234--4507279 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
4507224 CTGAATAATA
*
4507234 AAAATTGAA-TTAAAAATAAAAC
1 AAAATTAAACTTAAAAATAAAAC
4507256 AAAATTAAACTTAAAAACTAAAAC
1 AAAATTAAACTTAAAAA-TAAAAC
4507280 TAATCTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.38
23 7 0.33
24 6 0.29
ACGTcount: A:0.67, C:0.09, G:0.02, T:0.22
Consensus pattern (23 bp):
AAAATTAAACTTAAAAATAAAAC
Found at i:4512411 original size:43 final size:42
Alignment explanation
Indices: 4512348--4512432 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 42
4512338 ATCTTTCAAT
*
4512348 TAAAAAAAAAAATCTTATGTGTACTCTACCAACATGCCAAAA
1 TAAAAAAAAAAATCTCATGTGTACTCTACCAACATGCCAAAA
* * *
4512390 TAAAAAAAAAATTTCTCATGTGTACTTTACCAACATGCTAAAA
1 TAAAAAAAAAA-ATCTCATGTGTACTCTACCAACATGCCAAAA
4512433 GGGACATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
42 11 0.29
43 27 0.71
ACGTcount: A:0.48, C:0.18, G:0.07, T:0.27
Consensus pattern (42 bp):
TAAAAAAAAAAATCTCATGTGTACTCTACCAACATGCCAAAA
Found at i:4512905 original size:30 final size:29
Alignment explanation
Indices: 4512841--4512911 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
4512831 TTTAAAAATT
* *
4512841 TAATTTTTT-TATTTTTTATTACATTTAA
1 TAATTTTTTATATTTTTTATTAAATTAAA
*
4512869 TCAATTTTTTATATTTTTATTTTAAATTAAA
1 T-AATTTTTTATATTTTT-TATTAAATTAAA
*
4512900 TAATTTATTATA
1 TAATTTTTTATA
4512912 ATTAATATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 8 0.22
30 17 0.47
31 10 0.28
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (29 bp):
TAATTTTTTATATTTTTTATTAAATTAAA
Found at i:4514290 original size:28 final size:29
Alignment explanation
Indices: 4514228--4514284 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
4514218 ATAATTAATT
*
4514228 ATAAAAATATAAAAATTTAATTAAATATA
1 ATAAAAATATAAAAAATTAATTAAATATA
*
4514257 ATAAAAA-ATAAAAAATTATTTAAATATA
1 ATAAAAATATAAAAAATTAATTAAATATA
4514285 TCAAAATTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (29 bp):
ATAAAAATATAAAAAATTAATTAAATATA
Found at i:4515110 original size:2 final size:2
Alignment explanation
Indices: 4515103--4515136 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4515093 GCGAAACTAA
4515103 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4515137 ACTGATTTAT
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:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4522233 original size:23 final size:23
Alignment explanation
Indices: 4522202--4522245 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
4522192 TCTGATGTAT
* *
4522202 TCTATTTGACATAGAGGGAGTCC
1 TCTAGTTGACAAAGAGGGAGTCC
*
4522225 TCTAGTTGACAAAGATGGAGT
1 TCTAGTTGACAAAGAGGGAGT
4522246 AATAAATCAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (23 bp):
TCTAGTTGACAAAGAGGGAGTCC
Found at i:4522294 original size:21 final size:22
Alignment explanation
Indices: 4522268--4522314 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 22
4522258 TACACTGCAC
4522268 TTTTCTCTGGAGAATCTAGCA-
1 TTTTCTCTGGAGAATCTAGCAG
4522289 TTTTCTCTGGAGAATCTAGCAG
1 TTTTCTCTGGAGAATCTAGCAG
4522311 TTTT
1 TTTT
4522315 TACCTTGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (22 bp):
TTTTCTCTGGAGAATCTAGCAG
Found at i:4523673 original size:25 final size:25
Alignment explanation
Indices: 4523607--4523676 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
4523597 AAGAAAATAA
* *
4523607 AATCCCTACAATTATGATGAATCCC
1 AATCCCTATAATTATGGTGAATCCC
4523632 AATCCCTATAATTATGGTGAATCCC
1 AATCCCTATAATTATGGTGAATCCC
4523657 AATCCCTATAATTATGGTGA
1 AATCCCTATAATTATGGTGA
4523677 TTAATAAAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.31
Consensus pattern (25 bp):
AATCCCTATAATTATGGTGAATCCC
Found at i:4531354 original size:19 final size:18
Alignment explanation
Indices: 4531332--4531390 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
4531322 CAAAATAGAA
4531332 AAATTATATAAAAAATATG
1 AAATTAT-TAAAAAATATG
* *
4531351 AAATT-TTATAAAATAGTT
1 AAATTATTAAAAAATA-TG
4531369 AAATTATGTAAAAAATATG
1 AAATTAT-TAAAAAATATG
4531388 AAA
1 AAA
4531391 GCTACTACCT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 8 0.24
18 7 0.21
19 10 0.30
20 8 0.24
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (18 bp):
AAATTATTAAAAAATATG
Found at i:4531466 original size:229 final size:226
Alignment explanation
Indices: 4531120--4531552 Score: 726
Period size: 227 Copynumber: 1.9 Consensus size: 226
4531110 TTTATATTTT
4531120 TGAAATTTTAAAAAATAGCTAAATTATGTAAAAAAAAAATGAAAACTACCTTTCAGTGCATGAAA
1 TGAAATTTTAAAAAATAGCTAAATTATGT-AAAAAAAAATGAAAACTACCTTTCAGTGCATGAAA
*
4531185 TTTGTAATGTTTATATTGTTGAAAACAAAAATAATTCAAGAAAAAATTTTAATAATATTTTTATT
65 TTTGTAATGTTTATATTGTTGAAAACAAAAATAATTCAAGAAAAAATTTTAATAATATTTTCA-T
*
4531250 TAATGTGAAACTTTTCTTTATCTAGATTATTTTTAAACTTTATATAATTTCCATCATTAACAAAT
129 TAATGTGAAACTTTT-TTTATCTAGATTATCTTTAAACTTTATATAATTTCCATCATTAACAAAT
4531315 TTGATCACAAAATAGAAAAATTATATAAAAAATA
193 TTGATCACAAAATAGAAAAATTATATAAAAAATA
* * * *
4531349 TGAAATTTTATAAAATAGTTAAATTATGT-AAAAAATATGAAAGCTACTACCTTTTAGTGCATGA
1 TGAAATTTTAAAAAATAGCTAAATTATGTAAAAAAAAATGAAA---ACTACCTTTCAGTGCATGA
4531413 AATTTGTAATGTTTATATTGTTG-AAACAAAAATAATTCAAGAAAAAATTTTAATAATATTTTCA
63 AATTTGTAATGTTTATATTGTTGAAAACAAAAATAATTCAAGAAAAAATTTTAATAATATTTTCA
* *
4531477 TTAATTTTAAACTTTTTTTATCTAGATTATCTTTAAACTTTATATAATTTCCATCATTAACAAAT
128 TTAATGTGAAACTTTTTTTATCTAGATTATCTTTAAACTTTATATAATTTCCATCATTAACAAAT
4531542 TTGATCACAAA
193 TTGATCACAAA
4531553 GGATATTTTC
Statistics
Matches: 193, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
227 71 0.37
228 14 0.07
229 67 0.35
230 41 0.21
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (226 bp):
TGAAATTTTAAAAAATAGCTAAATTATGTAAAAAAAAATGAAAACTACCTTTCAGTGCATGAAAT
TTGTAATGTTTATATTGTTGAAAACAAAAATAATTCAAGAAAAAATTTTAATAATATTTTCATTA
ATGTGAAACTTTTTTTATCTAGATTATCTTTAAACTTTATATAATTTCCATCATTAACAAATTTG
ATCACAAAATAGAAAAATTATATAAAAAATA
Found at i:4532852 original size:2 final size:2
Alignment explanation
Indices: 4532847--4532891 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
4532837 TAAATATTCA
* * *
4532847 AT AT AT AT AT AT AT -T AT AC AT AT AT AC AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4532888 AT AT
1 AT AT
4532892 TATTATCGCT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4538885 original size:21 final size:22
Alignment explanation
Indices: 4538850--4538891 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
4538840 GAACCATTAC
*
4538850 TTTAATGACATTTTTCAAACCT
1 TTTAATGACAATTTTCAAACCT
*
4538872 TTTAATG-CAATTTTCTAACC
1 TTTAATGACAATTTTCAAACC
4538892 ATAAGTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.45
Consensus pattern (22 bp):
TTTAATGACAATTTTCAAACCT
Found at i:4545781 original size:10 final size:10
Alignment explanation
Indices: 4545746--4545794 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
4545736 ATAATGGCAT
*
4545746 AATATCTAAA
1 AATATTTAAA
* *
4545756 AAAATTTTAA
1 AATATTTAAA
*
4545766 ATTATTTAAA
1 AATATTTAAA
4545776 AATATTTAATA
1 AATATTTAA-A
4545787 AATATTTA
1 AATATTTA
4545795 TATTTTTATT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
10 22 0.71
11 9 0.29
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (10 bp):
AATATTTAAA
Found at i:4546826 original size:33 final size:33
Alignment explanation
Indices: 4546738--4546828 Score: 119
Period size: 33 Copynumber: 2.8 Consensus size: 33
4546728 ACTAATTTGG
* * * * *
4546738 CATACTAACATATTATAATTGACGAAAATGTAG
1 CATACTAATATATCATAATTGATGAAAATATAA
4546771 CATACTAATATATCATAATTGATGAAAATATAA
1 CATACTAATATATCATAATTGATGAAAATATAA
* *
4546804 CATGCTGATATATCATAATTGATGA
1 CATACTAATATATCATAATTGATGA
4546829 TGATGTGATA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (33 bp):
CATACTAATATATCATAATTGATGAAAATATAA
Found at i:4547443 original size:20 final size:20
Alignment explanation
Indices: 4547415--4547455 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
4547405 GTGATAATTA
*
4547415 GTCACAATGATATTAACGTG
1 GTCAAAATGATATTAACGTG
*
4547435 GTCAAAATGATATTAATGTG
1 GTCAAAATGATATTAACGTG
4547455 G
1 G
4547456 CATGTTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.32
Consensus pattern (20 bp):
GTCAAAATGATATTAACGTG
Found at i:4550090 original size:2 final size:2
Alignment explanation
Indices: 4550083--4550113 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4550073 AGGTAATTTA
4550083 TC TC TC TC 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
4550114 GTATGTATAC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4552447 original size:295 final size:296
Alignment explanation
Indices: 4551865--4552454 Score: 1075
Period size: 295 Copynumber: 2.0 Consensus size: 296
4551855 CGGGTACAGT
4551865 TCCTAAACAGCTCTATAATATCTCGTCCATGATTCATTTTTCCATAGCTGATAGGGCCAGATTTC
1 TCCTAAACAGCTCTATAATATCTCGTCCATGATTCATTTTTCCATAGCTGATAGGGCCAGATTTC
*
4551930 ACCTGACTTAGGCTTGACCCTCCCTATTCTTGGGCAAAACAAGTTTTCAGGGCCTATTCTAGCAT
66 ACCTGACTTAGGCTTGACCCTCCCTAATCTTGGGCAAAACAAGTTTTCAGGGCCTATTCTAGCAT
4551995 CAATAGCCAATTCCTCAGGACTCGTTCTACTTGATAATATACGGGTATGAATGGCATGAAGAATT
131 CAATAGCCAATTCCTCAGGACTCGTTCTACTTGATAATATACGGGTATGAATGGCATGAAGAATT
4552060 TGGGAAGCCTTTAAATTTTGGCAGCAACCCCCTTGACTTAAGTTTTCTACTTCCTTGACTAATTG
196 TGGGAAGCCTTTAAATTTTGGCAGCAACCCCCTTGACTTAAGTTTTCTACTTCCTTGACTAATTG
4552125 CACCAATCTAAGCCCTGTAAGTTCCCTAAAATCACA
261 CACCAATCTAAGCCCTGTAAGTTCCCTAAAATCACA
4552161 TCCTAAACAGCTCTATAAATAT-TCGTCCATGATTCATTTTTCACATAGCTGA-ATGGGCCAGAT
1 TCCTAAACAGCTCTAT-AATATCTCGTCCATGATTCATTTTTC-CATAGCTGATA-GGGCCAGAT
4552224 TTCACCTGACTTAGGCTTGACCCTCCCTAATC-TGGGCAAAACAAGTTTTCA-GGCCTATTCTAG
63 TTCACCTGACTTAGGCTTGACCCTCCCTAATCTTGGGCAAAACAAGTTTTCAGGGCCTATTCTAG
4552287 CATCAATAGCCAATTCCTCAGGACTCGTTCTACTTGATAATATACGGGTATGAATGGCATGAAGA
128 CATCAATAGCCAATTCCTCAGGACTCGTTCTACTTGATAATATACGGGTATGAATGGCATGAAGA
4552352 ATTT-GGAAGCC-TTAAATTTTGGCAGCAACCCCCTTGACTTAAGTTTTCTACTTCCTTGACTAA
193 ATTTGGGAAGCCTTTAAATTTTGGCAGCAACCCCCTTGACTTAAGTTTTCTACTTCCTTGACTAA
*
4552415 TTGCACCAATCTAAGCCTCTTGTAATTTCCCTAAAATCAC
258 TTGCACCAATCTAAGCC-C-TGTAAGTTCCCTAAAATCAC
4552455 CTGAGAGGTG
Statistics
Matches: 287, Mismatches: 2, Indels: 11
0.96 0.01 0.04
Matches are distributed among these distances:
293 69 0.24
294 8 0.03
295 100 0.35
296 56 0.20
297 54 0.19
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.32
Consensus pattern (296 bp):
TCCTAAACAGCTCTATAATATCTCGTCCATGATTCATTTTTCCATAGCTGATAGGGCCAGATTTC
ACCTGACTTAGGCTTGACCCTCCCTAATCTTGGGCAAAACAAGTTTTCAGGGCCTATTCTAGCAT
CAATAGCCAATTCCTCAGGACTCGTTCTACTTGATAATATACGGGTATGAATGGCATGAAGAATT
TGGGAAGCCTTTAAATTTTGGCAGCAACCCCCTTGACTTAAGTTTTCTACTTCCTTGACTAATTG
CACCAATCTAAGCCCTGTAAGTTCCCTAAAATCACA
Done.