Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397257.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_95.0, 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: 12062019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 103452 characters in sequence are not A, C, G, or T
File 13 of 26
Found at i:4706042 original size:10 final size:10
Alignment explanation
Indices: 4706027--4706051 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4706017 TCTTAGATCA
4706027 AAATAAACAT
1 AAATAAACAT
4706037 AAATAAACAT
1 AAATAAACAT
4706047 AAATA
1 AAATA
4706052 TTTAATGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (10 bp):
AAATAAACAT
Found at i:4718152 original size:37 final size:37
Alignment explanation
Indices: 4718111--4718199 Score: 97
Period size: 39 Copynumber: 2.4 Consensus size: 37
4718101 CAATCAACGA
*
4718111 AATCAAATCACGCATAGTATCAAAGTAACTAACAGAG
1 AATCAAATCACGCACAGTATCAAAGTAACTAACAGAG
* * ** *
4718148 AATCAAATCTCACACACGGTATTGAAGTAACTAGCAGAG
1 AATCAAA--TCACGCACAGTATCAAAGTAACTAACAGAG
*
4718187 AGTCAAATCACGC
1 AATCAAATCACGC
4718200 TCAATGTTGA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
37 12 0.29
39 30 0.71
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.19
Consensus pattern (37 bp):
AATCAAATCACGCACAGTATCAAAGTAACTAACAGAG
Found at i:4719131 original size:19 final size:20
Alignment explanation
Indices: 4719086--4719132 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
4719076 TTTAGTTTCA
4719086 TTTAGTTTTAATCCTTGATT
1 TTTAGTTTTAATCCTTGATT
* *
4719106 ATCAGTTTTAAT-CTTG-TT
1 TTTAGTTTTAATCCTTGATT
4719124 GTTTAGTTT
1 -TTTAGTTT
4719133 GATCTATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 2 0.09
19 10 0.45
20 10 0.45
ACGTcount: A:0.19, C:0.09, G:0.13, T:0.60
Consensus pattern (20 bp):
TTTAGTTTTAATCCTTGATT
Found at i:4726116 original size:22 final size:22
Alignment explanation
Indices: 4726070--4726117 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
4726060 AATATGAAAA
*
4726070 AATTAAAATACATTTTTTTATT
1 AATTAAAATACATTTTATTATT
4726092 AATTAAAA-A-ATTATTATTATAT
1 AATTAAAATACATT-TTATTAT-T
4726114 AATT
1 AATT
4726118 TTTTTGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 3 0.13
21 7 0.30
22 13 0.57
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
AATTAAAATACATTTTATTATT
Found at i:4727678 original size:27 final size:26
Alignment explanation
Indices: 4727614--4727681 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 26
4727604 TGAAATAAAA
*
4727614 AATAA-TTTTAA-ATATGAAAATAAT
1 AATAATTTTTAATTTATGAAAATAAT
** *
4727638 AATTTTTTTATAATTTATGAAAAGTATT
1 AATAATTTT-TAATTTATGAAAA-TAAT
4727666 AATAATTTTTAATTTA
1 AATAATTTTTAATTTA
4727682 AATTTTAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
24 3 0.09
25 3 0.09
26 3 0.09
27 15 0.44
28 10 0.29
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (26 bp):
AATAATTTTTAATTTATGAAAATAAT
Found at i:4727790 original size:24 final size:23
Alignment explanation
Indices: 4727738--4727791 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
4727728 ATTAAAATTT
*
4727738 TAATTTAATTTTTGAAATTTGAA
1 TAATTAAATTTTTGAAATTTGAA
4727761 -ATATTAAATTATTTGAAATATT-AA
1 TA-ATTAAATT-TTTGAAAT-TTGAA
4727785 TAATTAA
1 TAATTAA
4727792 TAAGTAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
22 1 0.04
23 7 0.27
24 15 0.58
25 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (23 bp):
TAATTAAATTTTTGAAATTTGAA
Found at i:4738532 original size:79 final size:80
Alignment explanation
Indices: 4738395--4738566 Score: 283
Period size: 79 Copynumber: 2.2 Consensus size: 80
4738385 ATTTGAGATT
* *
4738395 ATTTGGAGATAATATTTAAATTGGACTAATTAAAAAATTAGTTATTGGTCATCCAATTTATCTAT
1 ATTTGGAGATAATATTTAAATTGGACCAATTAAAAAATTAGTTATTGGTAATCCAATTTATCTAT
4738460 AAATAAATCAAAATA
66 AAATAAATCAAAATA
* * * *
4738475 ATTTAGAGATAATATTTAAATTGGACCAA-TCAAATATTAGTTATTGGTAATCCAATTTATCTCT
1 ATTTGGAGATAATATTTAAATTGGACCAATTAAAAAATTAGTTATTGGTAATCCAATTTATCTAT
4738539 AAATAAATCAAAATA
66 AAATAAATCAAAATA
4738554 ATTTGGAGATAAT
1 ATTTGGAGATAAT
4738567 CTTCATATTT
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
79 58 0.68
80 27 0.32
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.37
Consensus pattern (80 bp):
ATTTGGAGATAATATTTAAATTGGACCAATTAAAAAATTAGTTATTGGTAATCCAATTTATCTAT
AAATAAATCAAAATA
Found at i:4738620 original size:81 final size:79
Alignment explanation
Indices: 4738395--4738644 Score: 281
Period size: 79 Copynumber: 3.2 Consensus size: 79
4738385 ATTTGAGATT
* * * * *
4738395 ATTTGGAGATAATATTTAAATTGGACTAATTAAAAAATTAGTTATTGGTCATCCAATTTATCTAT
1 ATTTAGAGATAATATTTAAATTGGACCAA-TCAAAATTTAGTTATTGGTCATCCAATTTATCTCT
4738460 AAATAAATCAAAATA
65 AAATAAATCAAAATA
*
4738475 ATTTAGAGATAATATTTAAATTGGACCAATC-AAATATTAGTTATTGGTAATCCAATTTATCTCT
1 ATTTAGAGATAATATTTAAATTGGACCAATCAAAAT-TTAGTTATTGGTCATCCAATTTATCTCT
4738539 AAATAAATCAAAATA
65 AAATAAATCAAAATA
* * ** * * ** *
4738554 ATTTGGAGATAATCTTCATATTTTTGACCAATCAAAATTTAATTATTGGTCATTTAAATTATCTC
1 ATTTAGAGATAATATT--TAAATTGGACCAATCAAAATTTAGTTATTGGTCATCCAATTTATCTC
* * *
4738619 T-AAT-AATTATATTA
64 TAAATAAATCAAAATA
4738633 ATTTAGAGATAA
1 ATTTAGAGATAA
4738645 AAATCAAATT
Statistics
Matches: 146, Mismatches: 20, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
78 3 0.02
79 74 0.51
80 30 0.21
81 35 0.24
82 4 0.03
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (79 bp):
ATTTAGAGATAATATTTAAATTGGACCAATCAAAATTTAGTTATTGGTCATCCAATTTATCTCTA
AATAAATCAAAATA
Found at i:4738918 original size:18 final size:18
Alignment explanation
Indices: 4738895--4738939 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
4738885 TCATTCATTC
4738895 GGAAGCATTTAAAGATTG
1 GGAAGCATTTAAAGATTG
*
4738913 GGAAGCATTTGAAGATTG
1 GGAAGCATTTAAAGATTG
*
4738931 AG-AGCATTT
1 GGAAGCATTT
4738940 CAGAGATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.36, C:0.07, G:0.29, T:0.29
Consensus pattern (18 bp):
GGAAGCATTTAAAGATTG
Found at i:4739005 original size:22 final size:22
Alignment explanation
Indices: 4738980--4739269 Score: 562
Period size: 22 Copynumber: 13.1 Consensus size: 22
4738970 AGTAAAGATT
4738980 AAGCGACAGCGAAGTTCGTGTC
1 AAGCGACAGCGAAGTTCGTGTC
4739002 AAGCGACAGCGAAGTTCGTGTC
1 AAGCGACAGCGAAGTTCGTGTC
4739024 AAGCGACAGCGAAGTTCGTGTC
1 AAGCGACAGCGAAGTTCGTGTC
4739046 AAGCGACAGCGAAGTTCGTGTC
1 AAGCGACAGCGAAGTTCGTGTC
4739068 AAGCGACAGCGAAGTTCGTGTC
1 AAGCGACAGCGAAGTTCGTGTC
4739090 AAGCGACAGCGAAGTTCGTGTC
1 AAGCGACAGCGAAGTTCGTGTC
4739112 AAGCGACAGCGAAGTTCGTGTC
1 AAGCGACAGCGAAGTTCGTGTC
4739134 AAGCGACAGCGAAGTTCGTGTC
1 AAGCGACAGCGAAGTTCGTGTC
4739156 AAGCGACAGCGAAGTTCGTGTC
1 AAGCGACAGCGAAGTTCGTGTC
4739178 AAGCGACAGCGAAGTTCGTGTC
1 AAGCGACAGCGAAGTTCGTGTC
4739200 AAGCGACAGCGAAGTTCGTGTC
1 AAGCGACAGCGAAGTTCGTGTC
4739222 AAGCGACAGCGAAGTTCGTGTC
1 AAGCGACAGCGAAGTTCGTGTC
*
4739244 AAGCGACAACGAAGTTCGTGATC
1 AAGCGACAGCGAAGTTCGTG-TC
4739267 AAG
1 AAG
4739270 ATATCAAGTG
Statistics
Matches: 266, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
22 261 0.98
23 5 0.02
ACGTcount: A:0.28, C:0.22, G:0.31, T:0.18
Consensus pattern (22 bp):
AAGCGACAGCGAAGTTCGTGTC
Found at i:4739385 original size:61 final size:63
Alignment explanation
Indices: 4739284--4739411 Score: 206
Period size: 61 Copynumber: 2.1 Consensus size: 63
4739274 CAAGTGTTCG
* * * *
4739284 TAATCAAGACAAAGTCCAAGTTCGTGACTCTTGAAAAAAAAGTGAAAAAATTCATCAGAAAAT
1 TAATCAAGACAAAGTCCAAGTTCATAACTCTTGAAAAAAAAGTGAAAAAATTAATCAAAAAAT
4739347 TAATC-AG-CAAAGTCCAAGTTCATAACTCTTGAAAAAAAAGTGAAAAAATTAATCAAAAAAT
1 TAATCAAGACAAAGTCCAAGTTCATAACTCTTGAAAAAAAAGTGAAAAAATTAATCAAAAAAT
4739408 TAAT
1 TAAT
4739412 TAGAGGAATT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
61 54 0.89
62 2 0.03
63 5 0.08
ACGTcount: A:0.52, C:0.13, G:0.12, T:0.23
Consensus pattern (63 bp):
TAATCAAGACAAAGTCCAAGTTCATAACTCTTGAAAAAAAAGTGAAAAAATTAATCAAAAAAT
Found at i:4744148 original size:30 final size:30
Alignment explanation
Indices: 4744107--4744935 Score: 522
Period size: 30 Copynumber: 27.8 Consensus size: 30
4744097 TGGTGGTGGT
*
4744107 GGTGACTTGTACATGTATGGTGGAGGAGGA
1 GGTGACTTGTACATGTATGGAGGAGGAGGA
* ** *
4744137 GGTGACGTGTACACATATGGAGGAGGAGGT
1 GGTGACTTGTACATGTATGGAGGAGGAGGA
*
4744167 GGTGACTTGTACATGTATGGTGGAGGAGGA
1 GGTGACTTGTACATGTATGGAGGAGGAGGA
* ** *
4744197 GGTGACGTGTACACATATGGAGGAGGAGGT
1 GGTGACTTGTACATGTATGGAGGAGGAGGA
* *
4744227 GGTGACTTGTACATGTATGGTGGAGGTGGA
1 GGTGACTTGTACATGTATGGAGGAGGAGGA
*
4744257 GGTGACTTGTAAATGTATGGAGGAGGAGGA
1 GGTGACTTGTACATGTATGGAGGAGGAGGA
* * ** *
4744287 GGTGATTTATACACATATGGTGGAGG-GTG-
1 GGTGACTTGTACATGTATGGAGGAGGAG-GA
* * * *
4744316 GTGTGGCGATTCGTACTTGTATGGAGGAGGTGGT
1 G-GTGAC--TT-GTACATGTATGGAGGAGGAGGA
* * *
4744350 GGTGATTTGTAC-TCATATGGAGGAGGA-GT
1 GGTGACTTGTACAT-GTATGGAGGAGGAGGA
* * * * *
4744379 GGTGACTTATAAATGTATGGAGGTGGTGGT
1 GGTGACTTGTACATGTATGGAGGAGGAGGA
* *
4744409 GGTGACTTGTAC-TCATATGGAGGAGGAGGT
1 GGTGACTTGTACAT-GTATGGAGGAGGAGGA
* * * *
4744439 GGTGACTTATTTAAATGTATGGAGG-GGTGGT
1 GGTGAC-T-TGTACATGTATGGAGGAGGAGGA
*
4744470 GGTGA-TTGTACCA--TATGGAGGAGGAGGT
1 GGTGACTTGTA-CATGTATGGAGGAGGAGGA
* * * *
4744498 GGTGAC-T-TATATGTATGGA-GTGGTGGTG
1 GGTGACTTGTACATGTATGGAGGAGGAGG-A
* * *
4744526 GGTGATTTGTAC-T-CATAGGAGGAGGAGGT
1 GGTGACTTGTACATGTAT-GGAGGAGGAGGA
* * * * *
4744555 GGTGACTTATAAATGTATGGAGGTGGTGGT
1 GGTGACTTGTACATGTATGGAGGAGGAGGA
**
4744585 GGTGACTTGTACACATATGGAGGAGGAGGA
1 GGTGACTTGTACATGTATGGAGGAGGAGGA
* * ** * * *
4744615 GGTGATTTGTATACATACGGAGGAGGTGGT
1 GGTGACTTGTACATGTATGGAGGAGGAGGA
* * * *
4744645 GGCGACTTATACATGTATGGAGGAGGTGGT
1 GGTGACTTGTACATGTATGGAGGAGGAGGA
* ** *
4744675 GGTGAATTGTACACATATGGAGGAGGTGGA
1 GGTGACTTGTACATGTATGGAGGAGGAGGA
** * * *
4744705 GGTGACTCATACTTGTATGGAGGAGGTGGT
1 GGTGACTTGTACATGTATGGAGGAGGAGGA
* ** *
4744735 GGTGAATTGTACACATAT---GGAGGTGGA
1 GGTGACTTGTACATGTATGGAGGAGGAGGA
** * * * * *
4744762 GGTGACTCATACTTATATGGAGGTGGTGGT
1 GGTGACTTGTACATGTATGGAGGAGGAGGA
* * *
4744792 GGTGACTTGTAAATATATGGAGGTGGAGGA
1 GGTGACTTGTACATGTATGGAGGAGGAGGA
* * *
4744822 GGTGACTTGTAAATATATGGAGGTGGAGGA
1 GGTGACTTGTACATGTATGGAGGAGGAGGA
* * ** * *
4744852 GGCGACTTGTATACATATGGAGGTGGAGGT
1 GGTGACTTGTACATGTATGGAGGAGGAGGA
** * * *
4744882 GGTGACTCATACTTATATGGAGGAGGTGGA
1 GGTGACTTGTACATGTATGGAGGAGGAGGA
* *
4744912 GGTGACATGTACATGTACGGAGGA
1 GGTGACTTGTACATGTATGGAGGA
4744936 AAATTCGGCG
Statistics
Matches: 624, Mismatches: 146, Indels: 58
0.75 0.18 0.07
Matches are distributed among these distances:
26 1 0.00
27 36 0.06
28 27 0.04
29 41 0.07
30 471 0.75
31 15 0.02
32 13 0.02
33 18 0.03
34 2 0.00
ACGTcount: A:0.24, C:0.07, G:0.41, T:0.28
Consensus pattern (30 bp):
GGTGACTTGTACATGTATGGAGGAGGAGGA
Found at i:4744165 original size:27 final size:27
Alignment explanation
Indices: 4744127--4744227 Score: 121
Period size: 27 Copynumber: 3.5 Consensus size: 27
4744117 ACATGTATGG
4744127 TGGAGGAGGAGGTGACGTGTACACATA
1 TGGAGGAGGAGGTGACGTGTACACATA
* * *
4744154 TGGAGGAGGAGGTGGTGACTTGTACATGTATGG
1 TGGAGGAGGA---GGTGACGTGTACA--CAT-A
4744187 TGGAGGAGGAGGTGACGTGTACACATA
1 TGGAGGAGGAGGTGACGTGTACACATA
4744214 TGGAGGAGGAGGTG
1 TGGAGGAGGAGGTG
4744228 GTGACTTGTA
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
27 24 0.39
28 2 0.03
30 24 0.39
32 2 0.03
33 10 0.16
ACGTcount: A:0.26, C:0.08, G:0.46, T:0.21
Consensus pattern (27 bp):
TGGAGGAGGAGGTGACGTGTACACATA
Found at i:4744169 original size:60 final size:60
Alignment explanation
Indices: 4744101--4744935 Score: 656
Period size: 60 Copynumber: 14.0 Consensus size: 60
4744091 GTAATATGGT
* * * * *
4744101 GGTGGTGGTGACTTGTACATGTATGGTGGAGGAGGAGGTGACGTGTACACATATGGAGGA
1 GGTGGTGGTGACTTGTACATATATGGAGGAGGAGGTGGTGACTTGTACATATATGGAGGA
* * * * * *
4744161 GGAGGTGGTGACTTGTACATGTATGGTGGAGGAGGAGGTGACGTGTACACATATGGAGGA
1 GGTGGTGGTGACTTGTACATATATGGAGGAGGAGGTGGTGACTTGTACATATATGGAGGA
* * * * * * *
4744221 GGAGGTGGTGACTTGTACATGTATGGTGGAGGTGGAGGTGACTTGTAAATGTATGGAGGA
1 GGTGGTGGTGACTTGTACATATATGGAGGAGGAGGTGGTGACTTGTACATATATGGAGGA
* * * * * * * * * *
4744281 GGAGGAGGTGATTTATACACATATGGTGGAGGGTGGT-GTGGCGATTCGTACTTGTATGGAGGA
1 GGTGGTGGTGACTTGTACATATATGGAGGA-GGAGGTGGTGAC--TT-GTACATATATGGAGGA
* * * * *
4744344 GGTGGTGGTGATTTGTAC-TCATATGGAGGAGGA-GTGGTGACTTATAAATGTATGGAGGT
1 GGTGGTGGTGACTTGTACAT-ATATGGAGGAGGAGGTGGTGACTTGTACATATATGGAGGA
* * *
4744403 GGTGGTGGTGACTTGTAC-TCATATGGAGGAGGAGGTGGTGACTTATTTAAATGTATGGAGG-
1 GGTGGTGGTGACTTGTACAT-ATATGGAGGAGGAGGTGGTGAC-T-TGTACATATATGGAGGA
* * * *
4744464 GGTGGTGGTGA-TTGTAC-CATATGGAGGAGGAGGTGGTGAC-T-TATATGTATGGA-GT
1 GGTGGTGGTGACTTGTACATATATGGAGGAGGAGGTGGTGACTTGTACATATATGGAGGA
* * * * *
4744519 GGTGGTGGGTGATTTGTAC-TCATA-GGAGGAGGAGGTGGTGACTTATAAATGTATGGAGGT
1 GGTGGT-GGTGACTTGTACAT-ATATGGAGGAGGAGGTGGTGACTTGTACATATATGGAGGA
* * * * * *
4744579 GGTGGTGGTGACTTGTACACATATGGAGGAGGAGGAGGTGATTTGTATACATACGGAGGA
1 GGTGGTGGTGACTTGTACATATATGGAGGAGGAGGTGGTGACTTGTACATATATGGAGGA
* * * * * *
4744639 GGTGGTGGCGACTTATACATGTATGGAGGAGGTGGTGGTGAATTGTACACATATGGAGGA
1 GGTGGTGGTGACTTGTACATATATGGAGGAGGAGGTGGTGACTTGTACATATATGGAGGA
* ** * * * * *
4744699 GGTGGAGGTGACTCATACTTGTATGGAGGAGGTGGTGGTGAATTGTACACATAT---GGA
1 GGTGGTGGTGACTTGTACATATATGGAGGAGGAGGTGGTGACTTGTACATATATGGAGGA
* ** * * * * *
4744756 GGTGGAGGTGACTCATACTTATATGGAGGTGGTGGTGGTGACTTGTAAATATATGGAGGT
1 GGTGGTGGTGACTTGTACATATATGGAGGAGGAGGTGGTGACTTGTACATATATGGAGGA
* * * * * * * * *
4744816 GGAGGAGGTGACTTGTAAATATATGGAGGTGGAGGAGGCGACTTGTATACATATGGAGGT
1 GGTGGTGGTGACTTGTACATATATGGAGGAGGAGGTGGTGACTTGTACATATATGGAGGA
* ** * * * * * *
4744876 GGAGGTGGTGACTCATACTTATATGGAGGAGGTGGAGGTGACATGTACATGTACGGAGGA
1 GGTGGTGGTGACTTGTACATATATGGAGGAGGAGGTGGTGACTTGTACATATATGGAGGA
4744936 AAATTCGGCG
Statistics
Matches: 669, Mismatches: 85, Indels: 42
0.84 0.11 0.05
Matches are distributed among these distances:
54 1 0.00
55 17 0.03
56 6 0.01
57 76 0.11
58 4 0.01
59 91 0.14
60 394 0.59
61 19 0.03
62 23 0.03
63 38 0.06
ACGTcount: A:0.24, C:0.07, G:0.41, T:0.28
Consensus pattern (60 bp):
GGTGGTGGTGACTTGTACATATATGGAGGAGGAGGTGGTGACTTGTACATATATGGAGGA
Found at i:4744216 original size:90 final size:90
Alignment explanation
Indices: 4744104--4744935 Score: 648
Period size: 90 Copynumber: 9.3 Consensus size: 90
4744094 ATATGGTGGT
* * * * *
4744104 GGTGGTGACTTGTACATGTATGGTGGAGGAGGAGGTGACGTGTACACATATGGAGGAGGAGGTGG
1 GGTGGTGACTTGTACATATATGGAGGAGGAGGTGGTGACTTGTACACATATGGAGGAGGTGGTGG
* *
4744169 TGACTTGTACATGTATGGTGGAGGA
66 TGACTTGTACATATATGGAGGAGGA
* * * ** * *
4744194 GGAGGTGACGTGTACACATATGGAGGAGGAGGTGGTGACTTGTACATGTATGGTGGAGGTGGAGG
1 GGTGGTGACTTGTACATATATGGAGGAGGAGGTGGTGACTTGTACACATATGGAGGAGGTGGTGG
* *
4744259 TGACTTGTAAATGTATGGAGGAGGA
66 TGACTTGTACATATATGGAGGAGGA
* * * * * * * ***
4744284 GGAGGTGATTTATACACATATGGTGGAGGGTGGT-GTGGCGATTCGTACTTGTATGGAGGAGGTG
1 GGTGGTGACTTGTACATATATGGAGGA-GGAGGTGGTGAC--TT-GTACACATATGGAGGAGGTG
*
4744348 GTGGTGATTTGTAC-TCATATGGAGGAGGA
62 GTGGTGACTTGTACAT-ATATGGAGGAGGA
* * * * * * *
4744377 -GTGGTGACTTATAAATGTATGGAGGTGGTGGTGGTGACTTGTACTCATATGGAGGAGGAGGTGG
1 GGTGGTGACTTGTACATATATGGAGGAGGAGGTGGTGACTTGTACACATATGGAGGAGGTGGTGG
* * * *
4744441 TGACTTATTTAAATGTATGGAGG-GGT
66 TGAC-T-TGTACATATATGGAGGAGGA
* * ** *
4744467 GGTGGTGA-TTGTAC-CATATGGAGGAGGAGGTGGTGAC-T-TATATGTATGGA-GTGGTGGTGG
1 GGTGGTGACTTGTACATATATGGAGGAGGAGGTGGTGACTTGTACACATATGGAGGAGGTGGT-G
*
4744527 GTGATTTGTAC-TCATA-GGAGGAGGA
65 GTGACTTGTACAT-ATATGGAGGAGGA
* * * * * * *
4744552 GGTGGTGACTTATAAATGTATGGAGGTGGTGGTGGTGACTTGTACACATATGGAGGAGGAGGAGG
1 GGTGGTGACTTGTACATATATGGAGGAGGAGGTGGTGACTTGTACACATATGGAGGAGGTGGTGG
* * * * *
4744617 TGATTTGTATACATACGGAGGAGGT
66 TGACTTGTACATATATGGAGGAGGA
* * * * * *
4744642 GGTGGCGACTTATACATGTATGGAGGAGGTGGTGGTGAATTGTACACATATGGAGGAGGTGGAGG
1 GGTGGTGACTTGTACATATATGGAGGAGGAGGTGGTGACTTGTACACATATGGAGGAGGTGGTGG
** * * *
4744707 TGACTCATACTTGTATGGAGGAGGT
66 TGACTTGTACATATATGGAGGAGGA
* * * ** ** *
4744732 GGTGGTGAATTGTACACATATGGAGGTGGA---GGTGACTCATACTTATATGGAGGTGGTGGTGG
1 GGTGGTGACTTGTACATATATGGAGGAGGAGGTGGTGACTTGTACACATATGGAGGAGGTGGTGG
* *
4744794 TGACTTGTAAATATATGGAGGTGGA
66 TGACTTGTACATATATGGAGGAGGA
* * * * * * * *
4744819 GGAGGTGACTTGTAAATATATGGAGGTGGAGGAGGCGACTTGTATACATATGGAGGTGGAGGTGG
1 GGTGGTGACTTGTACATATATGGAGGAGGAGGTGGTGACTTGTACACATATGGAGGAGGTGGTGG
** * *
4744884 TGACTCATACTTATATGGAGGAGGT
66 TGACTTGTACATATATGGAGGAGGA
* * * *
4744909 GGAGGTGACATGTACATGTACGGAGGA
1 GGTGGTGACTTGTACATATATGGAGGA
4744936 AAATTCGGCG
Statistics
Matches: 589, Mismatches: 130, Indels: 46
0.77 0.17 0.06
Matches are distributed among these distances:
84 6 0.01
85 15 0.03
86 11 0.02
87 101 0.17
88 2 0.00
89 66 0.11
90 291 0.49
91 29 0.05
92 27 0.05
93 41 0.07
ACGTcount: A:0.24, C:0.07, G:0.41, T:0.28
Consensus pattern (90 bp):
GGTGGTGACTTGTACATATATGGAGGAGGAGGTGGTGACTTGTACACATATGGAGGAGGTGGTGG
TGACTTGTACATATATGGAGGAGGA
Found at i:4757892 original size:14 final size:14
Alignment explanation
Indices: 4757855--4757893 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
4757845 AAGCATATAT
* *
4757855 GAAAATGTACAAGA
1 GAAAAGGTAAAAGA
4757869 GAATAAGGTAAAAGA
1 GAA-AAGGTAAAAGA
4757884 GAAAAGGTAA
1 GAAAAGGTAA
4757894 GAGGGAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.59, C:0.03, G:0.26, T:0.13
Consensus pattern (14 bp):
GAAAAGGTAAAAGA
Found at i:4759929 original size:36 final size:36
Alignment explanation
Indices: 4759834--4759946 Score: 106
Period size: 36 Copynumber: 3.2 Consensus size: 36
4759824 GTGGTGATGA
* * * *
4759834 AGATGGTGGAGGAGGAGACTTGTAGACATATGG-TG
1 AGATGGTGGAGGTGGAGATTTGTAGACATAAGGAGG
* * * *
4759869 -G-TGGAGGTGGTGGTGATTTATAGACATAAGGAGG
1 AGATGGTGGAGGTGGAGATTTGTAGACATAAGGAGG
* *
4759903 AGATGGTGGAGGTGGGGATTTGTAGACATAGGGAGG
1 AGATGGTGGAGGTGGAGATTTGTAGACATAAGGAGG
*
4759939 AGGTGGTG
1 AGATGGTG
4759947 ATGGAGATGG
Statistics
Matches: 61, Mismatches: 14, Indels: 5
0.76 0.17 0.06
Matches are distributed among these distances:
33 23 0.38
34 2 0.03
35 1 0.02
36 35 0.57
ACGTcount: A:0.26, C:0.04, G:0.47, T:0.24
Consensus pattern (36 bp):
AGATGGTGGAGGTGGAGATTTGTAGACATAAGGAGG
Found at i:4759953 original size:48 final size:48
Alignment explanation
Indices: 4759901--4759992 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
4759891 GACATAAGGA
* * *
4759901 GGAGATGGTGGAGGTGGGGATTTGTAGACATAGGGAGGAGGTGGTGAT
1 GGAGATGGTGGAGGTGGAGACTTGTAGACATAAGGAGGAGGTGGTGAT
* *
4759949 GGAGATGGTGGGGGTGGAGACTTGTAGATATAAGGAGGAGGTGG
1 GGAGATGGTGGAGGTGGAGACTTGTAGACATAAGGAGGAGGTGG
4759993 GGACTTGTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.24, C:0.02, G:0.52, T:0.22
Consensus pattern (48 bp):
GGAGATGGTGGAGGTGGAGACTTGTAGACATAAGGAGGAGGTGGTGAT
Found at i:4759960 original size:42 final size:41
Alignment explanation
Indices: 4759863--4759961 Score: 100
Period size: 36 Copynumber: 2.5 Consensus size: 41
4759853 TTGTAGACAT
* *
4759863 ATGGTGGTGGAGGTGGTGGTGATTTATAGACATAAGGAGGAG
1 ATGGT-GTGGAGATGGTGGGGATTTATAGACATAAGGAGGAG
* *
4759905 AT-G-GT-G-GA-GGTGGGGATTTGTAGACATAGGGAGGAG
1 ATGGTGTGGAGATGGTGGGGATTTATAGACATAAGGAGGAG
*
4759941 GTGGTGATGGAGATGGTGGGG
1 ATGGTG-TGGAGATGGTGGGG
4759962 GTGGAGACTT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
36 26 0.57
37 2 0.04
38 2 0.04
39 3 0.07
40 1 0.02
41 3 0.07
42 9 0.20
ACGTcount: A:0.23, C:0.02, G:0.51, T:0.24
Consensus pattern (41 bp):
ATGGTGTGGAGATGGTGGGGATTTATAGACATAAGGAGGAG
Found at i:4759989 original size:75 final size:75
Alignment explanation
Indices: 4759910--4760067 Score: 210
Period size: 75 Copynumber: 2.1 Consensus size: 75
4759900 AGGAGATGGT
* * * * *
4759910 GGAGGTGGGGATTTGTAGACATAGGGAGGAG-GTGGTGATGGAGATGGTGGGGGTGGAGACTTGT
1 GGAGGTGGGGACTTGTAGACATAAGGAGGAGAG-GGTAAGGGAGATGGTGGAGGTGGAGACTTGT
* *
4759974 AGATATAAGGA
65 AAACATAAGGA
* * *
4759985 GGAGGTGGGGACTTGTAGACATAAGGTGGTGAGGGTAAGGGAGATGGTGGAGGTGGGGACTTGTA
1 GGAGGTGGGGACTTGTAGACATAAGGAGGAGAGGGTAAGGGAGATGGTGGAGGTGGAGACTTGTA
4760050 AACATAAGGA
66 AACATAAGGA
4760060 GGAGGTGG
1 GGAGGTGG
4760068 TGNNNNNNNN
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
75 71 0.99
76 1 0.01
ACGTcount: A:0.26, C:0.04, G:0.49, T:0.21
Consensus pattern (75 bp):
GGAGGTGGGGACTTGTAGACATAAGGAGGAGAGGGTAAGGGAGATGGTGGAGGTGGAGACTTGTA
AACATAAGGA
Found at i:4767078 original size:2 final size:2
Alignment explanation
Indices: 4767071--4767109 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4767061 AGAAGAAACA
4767071 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
4767110 TTATTCCTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4781973 original size:18 final size:20
Alignment explanation
Indices: 4781952--4781990 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
4781942 CCACTGTTAT
*
4781952 TTTCTTTTTCT-G-ATTTTG
1 TTTCATTTTCTCGAATTTTG
4781970 TTTCATTTTCTCGAATTTTG
1 TTTCATTTTCTCGAATTTTG
4781990 T
1 T
4781991 ATTTGGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 1 0.06
20 7 0.39
ACGTcount: A:0.10, C:0.13, G:0.10, T:0.67
Consensus pattern (20 bp):
TTTCATTTTCTCGAATTTTG
Found at i:4786424 original size:2 final size:2
Alignment explanation
Indices: 4786412--4786442 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4786402 ATATTTATTC
*
4786412 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4786443 CTAAACACTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4786696 original size:16 final size:15
Alignment explanation
Indices: 4786672--4786742 Score: 63
Period size: 15 Copynumber: 4.5 Consensus size: 15
4786662 TTAAAATTTT
*
4786672 TATATAATTAAAAATA
1 TATAAAATTAAAAA-A
4786688 TATAAAATTAAATTAAA
1 TATAAAATTAAA--AAA
4786705 T-TAAAAATTAAAAAA
1 TAT-AAAATTAAAAAA
* *
4786720 CACAAAATTAAAAAA
1 TATAAAATTAAAAAA
4786735 TATTAAAA
1 TA-TAAAA
4786743 AAAAAAGAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
15 16 0.36
16 16 0.36
17 11 0.24
18 2 0.04
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TATAAAATTAAAAAA
Found at i:4786740 original size:32 final size:33
Alignment explanation
Indices: 4786677--4786743 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
4786667 ATTTTTATAT
* * *
4786677 AATTAAAAATATATAAAATTAAATTAAATTAAA
1 AATTAAAAATACACAAAATTAAATAAAATTAAA
4786710 AATTAAAAA-ACACAAAATTAAA-AAATATTAAA
1 AATTAAAAATACACAAAATTAAATAAA-ATTAAA
4786742 AA
1 AA
4786744 AAAAAGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 2 0.07
32 19 0.63
33 9 0.30
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (33 bp):
AATTAAAAATACACAAAATTAAATAAAATTAAA
Found at i:4790240 original size:180 final size:180
Alignment explanation
Indices: 4789933--4790293 Score: 641
Period size: 180 Copynumber: 2.0 Consensus size: 180
4789923 GCATTGAGAT
*
4789933 ACTTTGACTTTACCATAACGGATACCAAACCAATTATGGATTAAGTACATGAATTACAAATTTTG
1 ACTTTGACTTTACCACAACGGATACCAAACCAATTATGGATTAAGTACATGAATTACAAATTTTG
* * *
4789998 GCCTCTAAATTAAGTTAACTGGAAATAAAAATCCCTGGCTCACTTTAAGTGGGAGCAATTCTGTC
66 GCCTCTAAATTAAGTGAACTGGAAATAAAAATCCCTGACTCACTTCAAGTGGGAGCAATTCTGTC
*
4790063 CAAACTTTCACTTTCTTGGAATGGATATAGGAAGAAAATTTTGCATTCTC
131 CAAACTTTCACTTTCTTGGAATGGATATAGGAAGAAAAATTTGCATTCTC
* *
4790113 ACTTTGACTTTACTACAATGGATACCAAACCAATTATGGATTAAGTACATGAATTACAAATTTTG
1 ACTTTGACTTTACCACAACGGATACCAAACCAATTATGGATTAAGTACATGAATTACAAATTTTG
* *
4790178 GCCTCTAAATTAAGTGAACTGGAAATAAAAATGCCTGACTCACTTCAAGTGGGAGTAATTCTGTC
66 GCCTCTAAATTAAGTGAACTGGAAATAAAAATCCCTGACTCACTTCAAGTGGGAGCAATTCTGTC
4790243 CAAACTTTCACTTTCTTGGAATGGATATAGGAAGAAAAATTTGCATTCTC
131 CAAACTTTCACTTTCTTGGAATGGATATAGGAAGAAAAATTTGCATTCTC
4790293 A
1 A
4790294 AAAAAGTTTT
Statistics
Matches: 172, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
180 172 1.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (180 bp):
ACTTTGACTTTACCACAACGGATACCAAACCAATTATGGATTAAGTACATGAATTACAAATTTTG
GCCTCTAAATTAAGTGAACTGGAAATAAAAATCCCTGACTCACTTCAAGTGGGAGCAATTCTGTC
CAAACTTTCACTTTCTTGGAATGGATATAGGAAGAAAAATTTGCATTCTC
Found at i:4792200 original size:32 final size:32
Alignment explanation
Indices: 4792161--4792224 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
4792151 GATAGACAAT
*
4792161 AATCAAATGAAGTATTGAGGGACATCATAATC
1 AATCAAATGAAGTATTAAGGGACATCATAATC
4792193 AATCAAATGAAGTATTAAGGGACATCATAATC
1 AATCAAATGAAGTATTAAGGGACATCATAATC
4792225 TTAAGTCTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.25
Consensus pattern (32 bp):
AATCAAATGAAGTATTAAGGGACATCATAATC
Found at i:4794694 original size:20 final size:20
Alignment explanation
Indices: 4794671--4794709 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
4794661 ATTTTCTTTG
4794671 TTTTTTGGTTGT-TTTTTCTA
1 TTTTTTGGTT-TCTTTTTCTA
4794691 TTTTTTGGTTTCTTTTTCT
1 TTTTTTGGTTTCTTTTTCT
4794710 TTAGATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.03, C:0.08, G:0.13, T:0.77
Consensus pattern (20 bp):
TTTTTTGGTTTCTTTTTCTA
Found at i:4795449 original size:8 final size:8
Alignment explanation
Indices: 4795436--4795464 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
4795426 TAATAATAGT
4795436 AAAATTAA
1 AAAATTAA
4795444 AAAATTAA
1 AAAATTAA
4795452 AAAATTAA
1 AAAATTAA
4795460 AAAAT
1 AAAAT
4795465 AGTGCTTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATTAA
Found at i:4797699 original size:25 final size:27
Alignment explanation
Indices: 4797666--4797719 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 27
4797656 TGGCTTAAAT
4797666 ATGAATGATAAA-TTATGATCAA-AGA
1 ATGAATGATAAACTTATGATCAATAGA
*
4797691 ATGAGTGATAAAGCTTATGATCAATAGA
1 ATGAATGATAAA-CTTATGATCAATAGA
4797719 A
1 A
4797720 AAAATATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 11 0.44
27 10 0.40
28 4 0.16
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.28
Consensus pattern (27 bp):
ATGAATGATAAACTTATGATCAATAGA
Found at i:4799188 original size:18 final size:17
Alignment explanation
Indices: 4799165--4799201 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
4799155 AAGAATAAGT
4799165 AGAGAATTAAAGAGTAAA
1 AGAGAATTAAAGAG-AAA
*
4799183 AGAGAATTCAAGAGAAA
1 AGAGAATTAAAGAGAAA
4799200 AG
1 AG
4799202 TTAGAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.59, C:0.03, G:0.24, T:0.14
Consensus pattern (17 bp):
AGAGAATTAAAGAGAAA
Found at i:4803459 original size:30 final size:29
Alignment explanation
Indices: 4803404--4803460 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
4803394 CTATTATTCA
* * *
4803404 TTTATTTTATTTAATTAATTTTTTATATT
1 TTTATTTTAATTAAATAAATTTTTATATT
4803433 TTTATTTTAAATTAAATAAATTTTTATA
1 TTTATTTT-AATTAAATAAATTTTTATA
4803461 ATTAATAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (29 bp):
TTTATTTTAATTAAATAAATTTTTATATT
Found at i:4828314 original size:5 final size:5
Alignment explanation
Indices: 4828290--4828332 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
4828280 TATCCTAGCA
* *
4828290 TTTAT GTTTA- TTTGT TTTAT TTTAT TTTAT TTCAT TTTAT TTT
1 TTTAT -TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
4828333 GGTTTCTTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
4 3 0.09
5 25 0.78
6 4 0.12
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:4828468 original size:4 final size:4
Alignment explanation
Indices: 4828456--4828490 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
4828446 TCCTAAATAA
*
4828456 AAAT AAAAT AAAT AAAC AAAT AAAT AAAT AAAT AA
1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
4828491 GGCGGTTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:4832444 original size:26 final size:26
Alignment explanation
Indices: 4832389--4832445 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
4832379 GTCTTTTCTC
*
4832389 TTTTCTCCTTACTCTTGAACTTGTTCA
1 TTTTCTCCTTACTCTTG-ACTTGTGCA
*
4832416 TTTTCTCTTTACTCTTTG-CTTGTGCA
1 TTTTCTCCTTACTC-TTGACTTGTGCA
4832442 TTTT
1 TTTT
4832446 ACTTGGCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 11 0.41
27 13 0.48
28 3 0.11
ACGTcount: A:0.11, C:0.23, G:0.09, T:0.58
Consensus pattern (26 bp):
TTTTCTCCTTACTCTTGACTTGTGCA
Found at i:4835371 original size:15 final size:15
Alignment explanation
Indices: 4835351--4835381 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4835341 AATCATGTTG
4835351 AGTTGTTTTAATTTA
1 AGTTGTTTTAATTTA
*
4835366 AGTTGTTTTATTTTA
1 AGTTGTTTTAATTTA
4835381 A
1 A
4835382 TTTTATGTTA
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:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (15 bp):
AGTTGTTTTAATTTA
Found at i:4838204 original size:30 final size:29
Alignment explanation
Indices: 4838148--4838204 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
4838138 TTCTTTCTTC
* *
4838148 TTTAATTTTAATAAAAAAAGTTTTATTTT
1 TTTAATTTCAATAAAAAAAGTCTTATTTT
4838177 TTTAATTTCAATAAAAAAAGATCTTATT
1 TTTAATTTCAATAAAAAAAG-TCTTATT
4838205 GAAATATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (29 bp):
TTTAATTTCAATAAAAAAAGTCTTATTTT
Found at i:4840096 original size:17 final size:17
Alignment explanation
Indices: 4840070--4840102 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4840060 ATTAGAATGA
*
4840070 TGGCAGCTGTTGCCATG
1 TGGCAACTGTTGCCATG
4840087 TGGCAACTGTTGCCAT
1 TGGCAACTGTTGCCAT
4840103 TGCAAAGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.24, G:0.30, T:0.30
Consensus pattern (17 bp):
TGGCAACTGTTGCCATG
Found at i:4844274 original size:23 final size:23
Alignment explanation
Indices: 4844248--4844295 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
4844238 ATATGACAAG
4844248 GACCAACACCAAAGTCAGAAGAA
1 GACCAACACCAAAGTCAGAAGAA
4844271 GACCAACACCAAAGTCAGAAGAA
1 GACCAACACCAAAGTCAGAAGAA
4844294 GA
1 GA
4844296 TATAACACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.25, G:0.19, T:0.04
Consensus pattern (23 bp):
GACCAACACCAAAGTCAGAAGAA
Found at i:4866218 original size:14 final size:14
Alignment explanation
Indices: 4866195--4866234 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
4866185 TTTTTTTATT
4866195 TGTC-TTGCTCCAC
1 TGTCTTTGCTCCAC
*
4866208 TGTCTTTGCTCCAT
1 TGTCTTTGCTCCAC
4866222 TGTCTTTGCTCCA
1 TGTCTTTGCTCCA
4866235 GAGACCAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 4 0.16
14 21 0.84
ACGTcount: A:0.07, C:0.33, G:0.15, T:0.45
Consensus pattern (14 bp):
TGTCTTTGCTCCAC
Found at i:4877335 original size:30 final size:31
Alignment explanation
Indices: 4877301--4877360 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
4877291 GGGTGACGTT
4877301 GTAA-TTATGAACAAG-TTGAAGGATCAAATG
1 GTAATTTATGAA-AAGTTTGAAGGATCAAATG
*
4877331 GTAATTTATGAAATGTTTGAAGGATCAAAT
1 GTAATTTATGAAAAGTTTGAAGGATCAAAT
4877361 TATAAAAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 6 0.22
31 21 0.78
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.32
Consensus pattern (31 bp):
GTAATTTATGAAAAGTTTGAAGGATCAAATG
Found at i:4884558 original size:20 final size:20
Alignment explanation
Indices: 4884515--4884555 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
4884505 TGTTAAGTGA
4884515 TTAATTTAAATTATTTTAGT
1 TTAATTTAAATTATTTTAGT
*
4884535 TTAATTTATATTATTTT-GT
1 TTAATTTAAATTATTTTAGT
4884554 TT
1 TT
4884556 TAAATTACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (20 bp):
TTAATTTAAATTATTTTAGT
Found at i:4886487 original size:29 final size:28
Alignment explanation
Indices: 4886454--4886508 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
4886444 TAGTGGTAAG
* *
4886454 GTTATACCTTCATAGCAAAAGGTAGAACA
1 GTTATACCTCCATA-AAAAAGGTAGAACA
4886483 GTTATACCTCCATAAAAAAGGTAGAA
1 GTTATACCTCCATAAAAAAGGTAGAA
4886509 AGATTGTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (28 bp):
GTTATACCTCCATAAAAAAGGTAGAACA
Found at i:4890222 original size:18 final size:17
Alignment explanation
Indices: 4890190--4890224 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
4890180 ATATTTATTT
*
4890190 CCTAGCTTTCGAAAATA
1 CCTAGCTTTCAAAAATA
4890207 CCTAGCTTTTCAAAAATA
1 CCTAGC-TTTCAAAAATA
4890225 ACCAAATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.31
Consensus pattern (17 bp):
CCTAGCTTTCAAAAATA
Found at i:4898184 original size:69 final size:69
Alignment explanation
Indices: 4898073--4898210 Score: 222
Period size: 69 Copynumber: 2.0 Consensus size: 69
4898063 GATAGAAGAG
* * * *
4898073 TACTTAGATTAAATTTGACATGATTGTGCTTAGAAGATTGTTGAACACCATCATTAATAGAATTA
1 TACTTAGATCAAATTCGACATGATTGGGCTTAGAAGATTGTTGAACACCATCACTAATAGAATTA
4898138 TGTT
66 TGTT
* *
4898142 TACTTAGATCAAATTCGACATGATTGGGCTTAGAAGATTGTTGAATACCATCACTAGTAGAATTA
1 TACTTAGATCAAATTCGACATGATTGGGCTTAGAAGATTGTTGAACACCATCACTAATAGAATTA
4898207 TGTT
66 TGTT
4898211 ATTGTTGGCT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (69 bp):
TACTTAGATCAAATTCGACATGATTGGGCTTAGAAGATTGTTGAACACCATCACTAATAGAATTA
TGTT
Found at i:4898714 original size:41 final size:41
Alignment explanation
Indices: 4898636--4898716 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
4898626 TTAATTTGGA
* * * * *
4898636 TTGAAATTTACTTATAATTGAAACCGATATGAGTTGTTTTG
1 TTGAAAATTACTTACAATTGAAACCGAGATAAATTGTTTTG
*
4898677 TTGAAAATTACTTACAATTGAAACCTAGATAAATTGTTTT
1 TTGAAAATTACTTACAATTGAAACCGAGATAAATTGTTTT
4898717 TAGAAAGTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.42
Consensus pattern (41 bp):
TTGAAAATTACTTACAATTGAAACCGAGATAAATTGTTTTG
Found at i:4906215 original size:15 final size:15
Alignment explanation
Indices: 4906173--4906218 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
4906163 ATTTGGTATT
4906173 TTACTGAAAATGTGA
1 TTACTGAAAATGTGA
* *
4906188 TTA-TTAGATATGTGA
1 TTACTGA-AAATGTGA
4906203 TTACTGAAAATGTGA
1 TTACTGAAAATGTGA
4906218 T
1 T
4906219 CGTTGTGAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 2 0.08
15 21 0.84
16 2 0.08
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (15 bp):
TTACTGAAAATGTGA
Found at i:4906576 original size:14 final size:14
Alignment explanation
Indices: 4906557--4906605 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
4906547 TTTGAAAAAA
4906557 TTAAATTATTTAAT
1 TTAAATTATTTAAT
* *
4906571 TTAAATTTTTTATAA
1 TTAAATTATTTA-AT
* *
4906586 ATAAATTAGTTAAT
1 TTAAATTATTTAAT
4906600 TTAAAT
1 TTAAAT
4906606 AACTAATTAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 17 0.63
15 10 0.37
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (14 bp):
TTAAATTATTTAAT
Found at i:4906703 original size:6 final size:6
Alignment explanation
Indices: 4906666--4906710 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
4906656 TCTAGGTTCA
* *
4906666 TTTTTC TTTTAC TTTTTC TTGTTC --TTTC -TTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
4906711 CTTGCACTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 3 0.09
5 4 0.12
6 26 0.79
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:4914376 original size:10 final size:9
Alignment explanation
Indices: 4914351--4914378 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
4914341 GTAGCTCTCA
4914351 AAATTTTTT
1 AAATTTTTT
4914360 AAATTTTTT
1 AAATTTTTT
4914369 AAATTTTTT
1 AAATTTTTT
4914378 A
1 A
4914379 TTTGTTAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
AAATTTTTT
Found at i:4914511 original size:16 final size:16
Alignment explanation
Indices: 4914486--4914518 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4914476 TATCTACACC
4914486 TCTTTCTCTCTCTCTT
1 TCTTTCTCTCTCTCTT
*
4914502 TCTTTTTCTCTCTCTT
1 TCTTTCTCTCTCTCTT
4914518 T
1 T
4914519 TATCTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (16 bp):
TCTTTCTCTCTCTCTT
Found at i:4914511 original size:18 final size:19
Alignment explanation
Indices: 4914488--4914527 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
4914478 TCTACACCTC
4914488 TTTCTCTCTCTCTT-TCTT
1 TTTCTCTCTCTCTTATCTT
*
4914506 TTTCTCTCTCTTTTATCTT
1 TTTCTCTCTCTCTTATCTT
4914525 TTT
1 TTT
4914528 ATTTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTCTCTCTCTCTTATCTT
Found at i:4915201 original size:23 final size:21
Alignment explanation
Indices: 4915155--4915202 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
4915145 TTTAAAAATT
*
4915155 ATATAAAAATAAAAATTTGAA
1 ATATAAAAATAAAAATTTCAA
4915176 ATATAAATAATTAAAAA-TTCATA
1 ATATAAA-AA-TAAAAATTTCA-A
4915199 ATAT
1 ATAT
4915203 TAACTATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 7 0.30
22 5 0.22
23 11 0.48
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
ATATAAAAATAAAAATTTCAA
Found at i:4919010 original size:38 final size:38
Alignment explanation
Indices: 4918946--4919026 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 38
4918936 GATAACAAAA
* *
4918946 TTTCATATTACAAGTAGAAATAGCATTTAACTACAATG
1 TTTCATATTACAAGCAAAAATAGCATTTAACTACAATG
* * *
4918984 TTTCATATTATAAGCAAAAATTGCATTTAACTATAATG
1 TTTCATATTACAAGCAAAAATAGCATTTAACTACAATG
4919022 TTTCA
1 TTTCA
4919027 AGATTTTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (38 bp):
TTTCATATTACAAGCAAAAATAGCATTTAACTACAATG
Found at i:4919291 original size:29 final size:29
Alignment explanation
Indices: 4919244--4919320 Score: 127
Period size: 29 Copynumber: 2.7 Consensus size: 29
4919234 ATAAATTTTA
* *
4919244 TGACATGTCAATATCACATTAACATCGTC
1 TGACATGTCAACATAACATTAACATCGTC
*
4919273 TGACATGTCAACATTACATTAACATCGTC
1 TGACATGTCAACATAACATTAACATCGTC
4919302 TGACATGTCAACATAACAT
1 TGACATGTCAACATAACAT
4919321 CAATGTCACT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.30
Consensus pattern (29 bp):
TGACATGTCAACATAACATTAACATCGTC
Found at i:4919880 original size:30 final size:30
Alignment explanation
Indices: 4919844--4919940 Score: 110
Period size: 30 Copynumber: 3.3 Consensus size: 30
4919834 AATCATTAAT
*
4919844 TATAAAAACTTATTTGACTT-AAAATAAAAA
1 TATAAAAACTTATTT-AATTCAAAATAAAAA
*
4919874 TATAAAATCTTATTTAATTCAAAATAAAAA
1 TATAAAAACTTATTTAATTCAAAATAAAAA
* * *
4919904 TATAAAAAGTTGA-TTAA-ACATAATAAAAA
1 TATAAAAACTT-ATTTAATTCAAAATAAAAA
4919933 TATAAAAA
1 TATAAAAA
4919941 AAATTTTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
29 21 0.36
30 37 0.63
31 1 0.02
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (30 bp):
TATAAAAACTTATTTAATTCAAAATAAAAA
Found at i:4930707 original size:3 final size:3
Alignment explanation
Indices: 4930699--4930741 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
4930689 CGTCATCAGA
* *
4930699 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC CTC ATC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
4930742 ACCTCAAGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:4931365 original size:32 final size:31
Alignment explanation
Indices: 4931306--4931366 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
4931296 TTACGTCAAA
4931306 ATTTTTTTTATATTAATTTTAAATTAAAATT
1 ATTTTTTTTATATTAATTTTAAATTAAAATT
* * * *
4931337 ATTTTTATTTTTATTATTTTTTATTTAAAA
1 ATTTTT-TTTATATTAATTTTAAATTAAAA
4931367 ATTAAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 6 0.24
32 19 0.76
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (31 bp):
ATTTTTTTTATATTAATTTTAAATTAAAATT
Found at i:4945604 original size:3 final size:3
Alignment explanation
Indices: 4945598--4945637 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
4945588 TGTTATTATT
*
4945598 ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4945638 AGACCTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4954652 original size:22 final size:24
Alignment explanation
Indices: 4954620--4954663 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
4954610 CAGCTTGCAA
4954620 ATTACCAAT-GGA-TTATTGACCG
1 ATTACCAATGGGATTTATTGACCG
*
4954642 ATTACCGATGGGATTTATTGAC
1 ATTACCAATGGGATTTATTGAC
4954664 GAAAGTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 3 0.16
24 8 0.42
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (24 bp):
ATTACCAATGGGATTTATTGACCG
Found at i:4955171 original size:22 final size:20
Alignment explanation
Indices: 4955138--4955204 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
4955128 CAGGTTTGTC
*
4955138 TTTTGCTCTCTTTCTCGTAT
1 TTTTGCTCTCTTTCTCATAT
4955158 TTTTGACTACTCTTTCTCATA-
1 TTTTG-CT-CTCTTTCTCATAT
* * *
4955179 TTTTGTTTTTTTTTCTCATAT
1 TTTTG-CTCTCTTTCTCATAT
4955200 TTTTG
1 TTTTG
4955205 TGATATTTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 15 0.38
21 13 0.33
22 11 0.28
ACGTcount: A:0.10, C:0.18, G:0.07, T:0.64
Consensus pattern (20 bp):
TTTTGCTCTCTTTCTCATAT
Found at i:4960228 original size:7 final size:7
Alignment explanation
Indices: 4960208--4960251 Score: 63
Period size: 7 Copynumber: 6.3 Consensus size: 7
4960198 ATTTATATTT
4960208 AAAT-TA
1 AAATATA
*
4960214 AAAAATA
1 AAATATA
4960221 AAATATA
1 AAATATA
4960228 AAATTATA
1 AAA-TATA
4960236 AAATATA
1 AAATATA
4960243 AAATATA
1 AAATATA
4960250 AA
1 AA
4960252 TAATTAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
6 3 0.09
7 24 0.71
8 7 0.21
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAATATA
Found at i:4960238 original size:15 final size:14
Alignment explanation
Indices: 4960208--4960251 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 14
4960198 ATTTATATTT
*
4960208 AAAT-TAAAAAATA
1 AAATATAAAATATA
4960221 AAATATAAAATTATA
1 AAATATAAAA-TATA
4960236 AAATATAAAATATA
1 AAATATAAAATATA
4960250 AA
1 AA
4960252 TAATTAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 4 0.14
14 11 0.39
15 13 0.46
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAATATAAAATATA
Found at i:4960252 original size:21 final size:21
Alignment explanation
Indices: 4960207--4960271 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
4960197 TATTTATATT
4960207 TAAATTA-AAAA-ATAAAATA
1 TAAATTATAAAATATAAAATA
4960226 TAAAATTATAAAATATAAAATA
1 T-AAATTATAAAATATAAAATA
* * **
4960248 TAAATAATTAAATACGAAATA
1 TAAATTATAAAATATAAAATA
4960269 TAA
1 TAA
4960272 GATTTCACAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 6 0.15
21 23 0.59
22 9 0.23
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (21 bp):
TAAATTATAAAATATAAAATA
Found at i:4960259 original size:22 final size:21
Alignment explanation
Indices: 4960208--4960259 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
4960198 ATTTATATTT
4960208 AAATTAAAAAATAAAATAT-A
1 AAATTAAAAAATAAAATATAA
4960228 AAATTATAAAATATAAAATATAA
1 AAATTA-AAAA-ATAAAATATAA
4960251 ATAATTAAA
1 A-AATTAAA
4960260 TACGAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.21
21 4 0.14
22 9 0.32
23 4 0.14
24 5 0.18
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATTAAAAAATAAAATATAA
Found at i:4972441 original size:3 final size:3
Alignment explanation
Indices: 4972433--4972457 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4972423 ATGTAAGATT
4972433 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
4972458 AATACTCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4980718 original size:2 final size:2
Alignment explanation
Indices: 4980713--4980751 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
4980703 ACATCAAAAT
* *
4980713 TA TA TA TA TA TA TA TA CA TA TA TA CA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4980752 GTGACTCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:4981913 original size:15 final size:15
Alignment explanation
Indices: 4981890--4981920 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4981880 TCATCTTTGT
4981890 TTTTATTATTATTAG
1 TTTTATTATTATTAG
*
4981905 TTTTGTTATTATTAG
1 TTTTATTATTATTAG
4981920 T
1 T
4981921 CTTCATGTGA
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:0.23, C:0.00, G:0.10, T:0.68
Consensus pattern (15 bp):
TTTTATTATTATTAG
Found at i:4984261 original size:224 final size:224
Alignment explanation
Indices: 4983799--4984246 Score: 851
Period size: 224 Copynumber: 2.0 Consensus size: 224
4983789 AAGTCTTTTA
*
4983799 TCAAAAGGTCTACATTTGGTATGTCAATCTTACTCCTAGTTTTATACAATCATGGATTCAAATGT
1 TCAAAAGGTCTACATTTGGTATGTCAATCTTACTCATAGTTTTATACAATCATGGATTCAAATGT
*
4983864 GTAGGATGTTTAGGAAAACTTTTTCTCTACCCAAGAAAAAGTAATTCTTGTTTAATTGGGAAGAG
66 GTAGGATGTTTAGGAAAACTTTTTCTCTACCCAAGAAAAAGTAATTCTTGTTTAATTCGGAAGAG
*
4983929 AGCATCATAATTTAAAGGAAGATATCATGGAATACATCTAACGCTTTAAAGAAATGATGCTGGAC
131 AGCATCATAATTTAAAAGAAGATATCATGGAATACATCTAACGCTTTAAAGAAATGATGCTGGAC
4983994 ATATAAGATTCTTATGATGAGAAAGAGCT
196 ATATAAGATTCTTATGATGAGAAAGAGCT
*
4984023 TCAAAAGGTCTACATTTGGTATGTCAATCTTCCTCATAGTTTTATACAATCATGGATTCAAATGT
1 TCAAAAGGTCTACATTTGGTATGTCAATCTTACTCATAGTTTTATACAATCATGGATTCAAATGT
4984088 GTAGGATGTTTAGGAAAACTTTTTCTCTACCCAAGAAAAAGTAATTCTTGTTTAATTCGGAAGAG
66 GTAGGATGTTTAGGAAAACTTTTTCTCTACCCAAGAAAAAGTAATTCTTGTTTAATTCGGAAGAG
*
4984153 AGCATCATAATTTAAAAGAAGATGTCATGGAATACATCTAACGCTTTAAAGAAATGATGCTGGAC
131 AGCATCATAATTTAAAAGAAGATATCATGGAATACATCTAACGCTTTAAAGAAATGATGCTGGAC
4984218 ATATAAGATTCTTATGATGAGAAAGAGCT
196 ATATAAGATTCTTATGATGAGAAAGAGCT
4984247 AGTCAAAGTC
Statistics
Matches: 219, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
224 219 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (224 bp):
TCAAAAGGTCTACATTTGGTATGTCAATCTTACTCATAGTTTTATACAATCATGGATTCAAATGT
GTAGGATGTTTAGGAAAACTTTTTCTCTACCCAAGAAAAAGTAATTCTTGTTTAATTCGGAAGAG
AGCATCATAATTTAAAAGAAGATATCATGGAATACATCTAACGCTTTAAAGAAATGATGCTGGAC
ATATAAGATTCTTATGATGAGAAAGAGCT
Found at i:4985052 original size:105 final size:105
Alignment explanation
Indices: 4984880--4985071 Score: 278
Period size: 105 Copynumber: 1.8 Consensus size: 105
4984870 CTTTATCCCT
* * *
4984880 CTTACTTTGGCTGTAATGTTATTGTTGCACTTGATCGCAAGCTTTATTGCTCATTATATGACAAT
1 CTTACTTTGGCTATAACGTTATTGTTGCACTTGATCGCAAGCTTTATTGCTCATTATATAACAAT
*
4984945 ATAATTCATCACTTATATTTCACCCGCATTTTTTAGCGCG
66 ATAATTCATCACTCATATTTCACCCGCATTTTTTAGCGCG
* * * * * *
4984985 CTTACTTTGGCTATAACGTTATTGTTGCA-TTTAGTCGTAAGCTTTATTGCTTATTTTTTAACCA
1 CTTACTTTGGCTATAACGTTATTGTTGCACTTGA-TCGCAAGCTTTATTGCTCATTATATAACAA
4985049 TATAATTCATCACTCATATTTCA
65 TATAATTCATCACTCATATTTCA
4985072 GCCACAAGCT
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
104 3 0.04
105 73 0.96
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.44
Consensus pattern (105 bp):
CTTACTTTGGCTATAACGTTATTGTTGCACTTGATCGCAAGCTTTATTGCTCATTATATAACAAT
ATAATTCATCACTCATATTTCACCCGCATTTTTTAGCGCG
Found at i:4986958 original size:27 final size:27
Alignment explanation
Indices: 4986928--4986994 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
4986918 CAGAAGCGCT
*
4986928 TAAGGGAGTTCCAAACATGGAGGTGCC
1 TAAGGGAGTTCCAAACATGGAAGTGCC
* * *
4986955 TAA-GGAGTTTCAAGCGTGGAAGTGCC
1 TAAGGGAGTTCCAAACATGGAAGTGCC
* *
4986981 TAGGGGTGTTCCAA
1 TAAGGGAGTTCCAA
4986995 TCACGAAATG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
26 21 0.66
27 11 0.34
ACGTcount: A:0.27, C:0.16, G:0.34, T:0.22
Consensus pattern (27 bp):
TAAGGGAGTTCCAAACATGGAAGTGCC
Found at i:4992037 original size:27 final size:28
Alignment explanation
Indices: 4991992--4992044 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
4991982 AGAGGCAATA
*
4991992 AGTGAAATAAAAAGGTGGGG-GCCAACG
1 AGTGAAATAAAAAGATGGGGAGCCAACG
4992019 AGTGAAATAAATAA-ATGGGGAGCCAA
1 AGTGAAATAAA-AAGATGGGGAGCCAA
4992045 AAAATCCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.45, C:0.09, G:0.32, T:0.13
Consensus pattern (28 bp):
AGTGAAATAAAAAGATGGGGAGCCAACG
Found at i:5000112 original size:2 final size:2
Alignment explanation
Indices: 5000105--5000131 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5000095 GAGAATTTAT
5000105 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5000132 TTCATTGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5002131 original size:39 final size:39
Alignment explanation
Indices: 5002088--5002175 Score: 113
Period size: 39 Copynumber: 2.3 Consensus size: 39
5002078 CTATTTTAGT
**
5002088 TTATTCATATGATGAAGGTCAATTTATGAATGATTTGGC
1 TTATTCATATGATGAACATCAATTTATGAATGATTTGGC
** * *
5002127 TTATTCATATGATGAACATTGATTTATGAATGTTTTGGT
1 TTATTCATATGATGAACATCAATTTATGAATGATTTGGC
*
5002166 TTATTTATAT
1 TTATTCATAT
5002176 AACGAATATC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.30, C:0.06, G:0.17, T:0.48
Consensus pattern (39 bp):
TTATTCATATGATGAACATCAATTTATGAATGATTTGGC
Found at i:5002190 original size:39 final size:39
Alignment explanation
Indices: 5002109--5002192 Score: 105
Period size: 39 Copynumber: 2.2 Consensus size: 39
5002099 ATGAAGGTCA
* * *
5002109 ATTTATGAATGATTTGGCTTATTCATATGATGAACATTG
1 ATTTATGAATGATTTGGCTTATTCATATAACGAACATCG
* * * *
5002148 ATTTATGAATGTTTTGGTTTATTTATATAACGAATATCG
1 ATTTATGAATGATTTGGCTTATTCATATAACGAACATCG
5002187 ATTTAT
1 ATTTAT
5002193 AAATAAAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (39 bp):
ATTTATGAATGATTTGGCTTATTCATATAACGAACATCG
Found at i:5003344 original size:40 final size:39
Alignment explanation
Indices: 5003204--5003359 Score: 125
Period size: 39 Copynumber: 4.0 Consensus size: 39
5003194 ATTTCATCCT
* * * * * * *
5003204 ATTCATAAATTAATATCCGTCATATAAATAAATCACAAC
1 ATTCATAAATCAATATTCATCATATGAATAAATAAAAAA
* * * * * *
5003243 ATTCATTAATCATTCTTCATCCTATGAATAAATTAAAAC
1 ATTCATAAATCAATATTCATCATATGAATAAATAAAAAA
** *
5003282 ATTTGTAAATCAATATTTATCATATGAATAAATAAAAAAA
1 ATTCATAAATCAATATTCATCATATGAATAAAT-AAAAAA
* *
5003322 ATTCATAAATCAACT-TTCATCATATAAATAAATCAAAA
1 ATTCATAAATCAA-TATTCATCATATGAATAAATAAAAA
5003360 TAGAAAATAA
Statistics
Matches: 91, Mismatches: 24, Indels: 4
0.76 0.20 0.03
Matches are distributed among these distances:
39 59 0.65
40 31 0.34
41 1 0.01
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (39 bp):
ATTCATAAATCAATATTCATCATATGAATAAATAAAAAA
Found at i:5013288 original size:61 final size:61
Alignment explanation
Indices: 5013193--5013313 Score: 215
Period size: 61 Copynumber: 2.0 Consensus size: 61
5013183 ATCAAAAAGC
*
5013193 AAGGTCCCAATAGAATATTATGATTCACTTCTAAGCCCCAGTCTCACCCTTTTCTAGCAGA
1 AAGGTCCCAATAGAATATTATGATTCACTTCTAAGCCCCAGTCTAACCCTTTTCTAGCAGA
* *
5013254 AAGGTCCCAATTGAATATTATGATTCACTTCTAAGCCCCAGTCTAACCCTTTTCTTGCAG
1 AAGGTCCCAATAGAATATTATGATTCACTTCTAAGCCCCAGTCTAACCCTTTTCTAGCAG
5013314 TTCTTGTTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.31
Consensus pattern (61 bp):
AAGGTCCCAATAGAATATTATGATTCACTTCTAAGCCCCAGTCTAACCCTTTTCTAGCAGA
Found at i:5016830 original size:27 final size:27
Alignment explanation
Indices: 5016792--5016847 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
5016782 CCCAAGAAGA
5016792 AAGAAAAAAAATTTAAATTTATATTCT
1 AAGAAAAAAAATTTAAATTTATATTCT
5016819 AAGAAAAAAAATTTAAATTTATATTCT
1 AAGAAAAAAAATTTAAATTTATATTCT
5016846 AA
1 AA
5016848 AAAGAGGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (27 bp):
AAGAAAAAAAATTTAAATTTATATTCT
Found at i:5020178 original size:16 final size:16
Alignment explanation
Indices: 5020159--5020192 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5020149 ATATAAATTT
5020159 TAAAATTAATAAAAAA
1 TAAAATTAATAAAAAA
* *
5020175 TAAAATTATTCAAAAA
1 TAAAATTAATAAAAAA
5020191 TA
1 TA
5020193 TTATCATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAAATTAATAAAAAA
Found at i:5022564 original size:9 final size:9
Alignment explanation
Indices: 5022550--5022580 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
5022540 TTTCATCTAG
5022550 AATTTGTCA
1 AATTTGTCA
5022559 AATTTGTCA
1 AATTTGTCA
5022568 AATTTGT-A
1 AATTTGTCA
5022576 AATTT
1 AATTT
5022581 TAAATTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 6 0.27
9 16 0.73
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (9 bp):
AATTTGTCA
Found at i:5022592 original size:22 final size:22
Alignment explanation
Indices: 5022558--5022616 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
5022548 AGAATTTGTC
*
5022558 AAATTTGTCAAATTTGTAAATTTT
1 AAATTTGTCAAATTT-T-AATGTT
5022582 AAA-TT-TCAAATTTTAATGTT
1 AAATTTGTCAAATTTTAATGTT
5022602 AAATTTGTCAAATTT
1 AAATTTGTCAAATTT
5022617 CAAAACTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 8 0.25
21 3 0.09
22 16 0.50
23 2 0.06
24 3 0.09
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (22 bp):
AAATTTGTCAAATTTTAATGTT
Found at i:5022593 original size:52 final size:52
Alignment explanation
Indices: 5022550--5022649 Score: 125
Period size: 52 Copynumber: 1.9 Consensus size: 52
5022540 TTTCATCTAG
*
5022550 AATTTGTCAAATTTGTC-AAA-TTTGTAAATTTTAAATTTCAAATTTTAATGTTA
1 AATTTGTCAAA-TT-TCAAAACTTTG-AAATTTTAAATTTCAAATTTTAATGCTA
* *
5022603 AATTTGTCAAATTTCAAAACTTTGAAATTTTACATTTC-ATTTTTAAT
1 AATTTGTCAAATTTCAAAACTTTGAAATTTTAAATTTCAAATTTTAAT
5022650 TTTCATCTAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
51 10 0.23
52 18 0.42
53 15 0.35
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (52 bp):
AATTTGTCAAATTTCAAAACTTTGAAATTTTAAATTTCAAATTTTAATGCTA
Found at i:5034828 original size:21 final size:21
Alignment explanation
Indices: 5034798--5034852 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
5034788 AAAAATATAA
* *
5034798 TAATAGTTTAATATTAAACCT
1 TAATATTTTAATACTAAACCT
* *
5034819 TAATGTTTTAATACTAAATCT
1 TAATATTTTAATACTAAACCT
5034840 TAATATTTTAATA
1 TAATATTTTAATA
5034853 ATAGCATAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (21 bp):
TAATATTTTAATACTAAACCT
Found at i:5035669 original size:27 final size:28
Alignment explanation
Indices: 5035630--5035685 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
5035620 GATTATTTAT
* *
5035630 TTTATTTTTAAATATTAATAATTTATAA
1 TTTATTTTAAAATATTAATAATTGATAA
*
5035658 TTTA-TTTAAAATGTTAATAATTGATAA
1 TTTATTTTAAAATATTAATAATTGATAA
5035685 T
1 T
5035686 ATAAATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (28 bp):
TTTATTTTAAAATATTAATAATTGATAA
Found at i:5035748 original size:28 final size:26
Alignment explanation
Indices: 5035703--5035761 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 26
5035693 TTATTATTTT
* *
5035703 TATTTATAATTTAATTATTATTTTAAAA
1 TATTAATAATTTAATTA-TAATTT-AAA
* *
5035731 TATTAATATTTTATTTATAATTTAAA
1 TATTAATAATTTAATTATAATTTAAA
5035757 TATTA
1 TATTA
5035762 TTGTGATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 8 0.30
27 5 0.19
28 14 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TATTAATAATTTAATTATAATTTAAA
Found at i:5035775 original size:43 final size:40
Alignment explanation
Indices: 5035688--5035763 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 40
5035678 TTGATAATAT
* *
5035688 AAATATTATTATTTTTATTTATAATTTAATTATTATTTTA
1 AAATATTAATATTTTTATTTATAATTTAAATATTATTTTA
5035728 AAATATTAATA-TTTTATTTATAATTTAAATATTATT
1 AAATATTAATATTTTTATTTATAATTTAAATATTATT
5035764 GTGATTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 24 0.71
40 10 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (40 bp):
AAATATTAATATTTTTATTTATAATTTAAATATTATTTTA
Found at i:5035781 original size:43 final size:39
Alignment explanation
Indices: 5035700--5035781 Score: 110
Period size: 39 Copynumber: 2.0 Consensus size: 39
5035690 ATATTATTAT
* *
5035700 TTTTATTTATAATTTAATTATTATTTTAAAATATTAATA
1 TTTTATTTATAATTTAAATATTATTTTAAAATAGTAATA
5035739 TTTTATTTATAATTTAAATATTATTGTGATTAAAATAGTAATA
1 TTTTATTTATAATTTAAATATTA-T-T--TTAAAATAGTAATA
5035782 ATCTTAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
39 22 0.59
40 1 0.03
41 1 0.03
43 13 0.35
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (39 bp):
TTTTATTTATAATTTAAATATTATTTTAAAATAGTAATA
Found at i:5041304 original size:19 final size:20
Alignment explanation
Indices: 5041260--5041305 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
5041250 TAAATTTTAC
*
5041260 TTCTTTTTTTTTTCTTGATT
1 TTCTTTTTATTTTCTTGATT
5041280 TCTCTTTTTATTTT-TT-ATGT
1 T-TCTTTTTATTTTCTTGAT-T
5041300 TTCTTT
1 TTCTTT
5041306 GATCCATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 7 0.30
20 5 0.22
21 11 0.48
ACGTcount: A:0.07, C:0.11, G:0.04, T:0.78
Consensus pattern (20 bp):
TTCTTTTTATTTTCTTGATT
Found at i:5047645 original size:26 final size:28
Alignment explanation
Indices: 5047589--5047645 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 28
5047579 AAATTTAGAT
* *
5047589 AATTATTTATTTTTATTATTTTCAATTA
1 AATTATTTATATTTATTATTTTCAATCA
*
5047617 AATT-TTTATATTT-TTATTTTGAATCA
1 AATTATTTATATTTATTATTTTCAATCA
5047643 AAT
1 AAT
5047646 AAATCTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 14 0.54
27 8 0.31
28 4 0.15
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (28 bp):
AATTATTTATATTTATTATTTTCAATCA
Found at i:5052074 original size:2 final size:2
Alignment explanation
Indices: 5052057--5052092 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
5052047 TCTTTTTCTT
5052057 TA TA T- TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5052093 ATGATAACAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5053455 original size:2 final size:2
Alignment explanation
Indices: 5053440--5053480 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
5053430 TGCAGAAAGA
* * *
5053440 AT AT AT AC AG AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5053481 CGTAGAGATG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:5053495 original size:3 final size:3
Alignment explanation
Indices: 5053487--5053520 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5053477 TATACGTAGA
5053487 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
5053521 GGGGTGGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:5055070 original size:7 final size:7
Alignment explanation
Indices: 5055060--5055089 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
5055050 TAAAGTCTAA
5055060 ACTAGTT
1 ACTAGTT
5055067 ACTAGTT
1 ACTAGTT
5055074 ACTAGTT
1 ACTAGTT
5055081 ACTAGTT
1 ACTAGTT
5055088 AC
1 AC
5055090 ACCCATCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (7 bp):
ACTAGTT
Found at i:5055693 original size:26 final size:26
Alignment explanation
Indices: 5055664--5055717 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
5055654 TACTCAAAAA
5055664 GAAAGATCAAAAGTTACATTCATGTT
1 GAAAGATCAAAAGTTACATTCATGTT
5055690 GAAAGATCAAAAGTTACATTCATGTT
1 GAAAGATCAAAAGTTACATTCATGTT
5055716 GA
1 GA
5055718 TCCTTTATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.30
Consensus pattern (26 bp):
GAAAGATCAAAAGTTACATTCATGTT
Found at i:5061074 original size:2 final size:2
Alignment explanation
Indices: 5061067--5061110 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
5061057 ACATACATAC
5061067 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5061109 AT
1 AT
5061111 GCTGCAGGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5061730 original size:17 final size:16
Alignment explanation
Indices: 5061691--5061731 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
5061681 ATATTAATAT
5061691 ATAAA-TTATTTTTTG
1 ATAAATTTATTTTTTG
5061706 ATAAATTTATTTTTTG
1 ATAAATTTATTTTTTG
5061722 ATAATATTTA
1 ATAA-ATTTA
5061732 AATATTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 5 0.21
16 14 0.58
17 5 0.21
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (16 bp):
ATAAATTTATTTTTTG
Found at i:5061740 original size:24 final size:24
Alignment explanation
Indices: 5061707--5061764 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
5061697 TATTTTTTGA
** *
5061707 TAAAT-TTATTTTTTGATAATATT
1 TAAATATTATTTTTAAAAAATATT
5061730 TAAATATTATTTTTAAAAAATATT
1 TAAATATTATTTTTAAAAAATATT
5061754 TAAATATTATT
1 TAAATATTATT
5061765 AAAAAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
23 5 0.16
24 26 0.84
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
TAAATATTATTTTTAAAAAATATT
Found at i:5064272 original size:17 final size:16
Alignment explanation
Indices: 5064233--5064273 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
5064223 ATATTAATAT
*
5064233 ATAAA-TTATTTTTTG
1 ATAAATTTACTTTTTG
5064248 ATAAATTTACTTTTTG
1 ATAAATTTACTTTTTG
5064264 ATAATATTTA
1 ATAA-ATTTA
5064274 AATATTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.22
16 13 0.57
17 5 0.22
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (16 bp):
ATAAATTTACTTTTTG
Found at i:5077878 original size:18 final size:18
Alignment explanation
Indices: 5077848--5077885 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
5077838 AAATGAAAGT
5077848 AAAAAAAAAAAGAG-GAG
1 AAAAAAAAAAAGAGAGAG
*
5077865 AAAAAAAAGGAAGAGAGAG
1 AAAAAAAA-AAAGAGAGAG
5077884 AA
1 AA
5077886 CCAAATTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 5 0.28
19 5 0.28
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAGAGAGAG
Found at i:5078107 original size:132 final size:132
Alignment explanation
Indices: 5077870--5078262 Score: 680
Period size: 132 Copynumber: 3.0 Consensus size: 132
5077860 AGGAGAAAAA
* *
5077870 AAAGGAAGAGAGAGAACCAAATTGCTGAAACTAAATGAAAACTGTATTATGTTTGAAGCTCATAA
1 AAAGGAAGAGAGAGAACCAAATTGCTGAAACTAAATGAAAACTGTATTATGTTTGAAGTTCACAA
* *
5077935 GTAGGTTCTTGGAGACTCTATATTTGGTGCTAAATTATGTGATCTTTACGTAGATGGACAGTTTT
66 GTAGGTACTTGGAGACCCTATATTTGGTGCTAAATTATGTGATCTTTACGTAGATGGACAGTTTT
5078000 GC
131 GC
* *
5078002 AAAGGAAGAGAGAGAACCAAGTTGCTGAAACTAAATGAAAACTCTATTATGTTTGAAGTTCACAA
1 AAAGGAAGAGAGAGAACCAAATTGCTGAAACTAAATGAAAACTGTATTATGTTTGAAGTTCACAA
* *
5078067 GTAGGTACTAGGAGACCCTATATTTGGTGCTAAATTATGTGATCTTTATGTAGATGGACAGTTTT
66 GTAGGTACTTGGAGACCCTATATTTGGTGCTAAATTATGTGATCTTTACGTAGATGGACAGTTTT
5078132 GC
131 GC
*
5078134 AAAGGAAGAGAGAGAACCAAATTGCTGAAACTAAATGCAAACTGTATTATGTTTGAAGTTCACAA
1 AAAGGAAGAGAGAGAACCAAATTGCTGAAACTAAATGAAAACTGTATTATGTTTGAAGTTCACAA
*
5078199 GTAGGTACTTGGAGACCCTATATTTGGTGCTAAATTCA-GTGATCTTTACTTAGATGGACAGTTT
66 GTAGGTACTTGGAGACCCTATATTTGGTGCTAAATT-ATGTGATCTTTACGTAGATGGACAGTTT
5078263 AGCAGGACAG
Statistics
Matches: 246, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
132 245 1.00
133 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (132 bp):
AAAGGAAGAGAGAGAACCAAATTGCTGAAACTAAATGAAAACTGTATTATGTTTGAAGTTCACAA
GTAGGTACTTGGAGACCCTATATTTGGTGCTAAATTATGTGATCTTTACGTAGATGGACAGTTTT
GC
Found at i:5078773 original size:187 final size:187
Alignment explanation
Indices: 5078455--5078819 Score: 493
Period size: 187 Copynumber: 2.0 Consensus size: 187
5078445 CAATGTCATG
* * *
5078455 TTTTTCTGTTGTACTTTGGAAGGATTTCCTTTTCTTATCTTTGATGAGTTGGTGGTTTCTTTCCA
1 TTTTTCTATTGTACTTCGGAAGGATTGCCTTTTCTTATCTTTGATGAGTTGGTGGTTTCTTTCCA
* * * * * *
5078520 TCCATTGCTCTGCCCTTTTTTCTTGCAATTCTTCCTTTCTTTTTGTTGACTTGATGTCTGGGGAG
66 TCCATTGCTCTACCCTGTTTTCTTGCAATTCTTCATTTCTTTGTGTGGACCTGATGTCTGGGGAG
* *
5078585 TTGACATGGGATGCCAGTGG-AAGGGGAAATCTGACCAAAGCATGATTTCTGTTGTGT
131 TTGACATGGGATGCAAG-GGAAAGGGAAAATCTGACCAAAGCATGATTTCTGTTGTGT
5078642 TTTTTCTATTGTACTTCGGAAGTG-TTGCCTTTTCTTATC-TTGATGAGTTGGTGGTTTCTTTCC
1 TTTTTCTATTGTACTTCGGAAG-GATTGCCTTTTCTTATCTTTGATGAGTTGGTGGTTTCTTTCC
* * ** * * * *
5078705 GTCCATTGCTTTTACCCTGTTTTCTTGCTTTTCTTCATTTCTTTGTGTGGTCCTGGTGTTTTGGG
65 ATCCATTGC-TCTACCCTGTTTTCTTGCAATTCTTCATTTCTTTGTGTGGACCTGATGTCTGGGG
**
5078770 AGTTGACATGGGATGCAAGGGAAAGGGAAAATCTGACTGAAGCATGATTT
129 AGTTGACATGGGATGCAAGGGAAAGGGAAAATCTGACCAAAGCATGATTT
5078820 TATTTATGTT
Statistics
Matches: 154, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
186 34 0.22
187 119 0.77
188 1 0.01
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (187 bp):
TTTTTCTATTGTACTTCGGAAGGATTGCCTTTTCTTATCTTTGATGAGTTGGTGGTTTCTTTCCA
TCCATTGCTCTACCCTGTTTTCTTGCAATTCTTCATTTCTTTGTGTGGACCTGATGTCTGGGGAG
TTGACATGGGATGCAAGGGAAAGGGAAAATCTGACCAAAGCATGATTTCTGTTGTGT
Found at i:5085087 original size:35 final size:34
Alignment explanation
Indices: 5085026--5085100 Score: 80
Period size: 35 Copynumber: 2.2 Consensus size: 34
5085016 TTTTTTTTTG
*
5085026 GTTTTTTCCCCTCTATGCTTTGTTTTTCTACCAA
1 GTTTTTTCCCCTCTATGCTTTATTTTTCTACCAA
* * * *
5085060 CGTTTTTTTCCCT-TTTGCTTTAATTTTTTTTCCAA
1 -GTTTTTTCCCCTCTATGCTTT-ATTTTTCTACCAA
5085095 GTTTTT
1 GTTTTT
5085101 CTTTCAGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
34 13 0.38
35 21 0.62
ACGTcount: A:0.11, C:0.21, G:0.08, T:0.60
Consensus pattern (34 bp):
GTTTTTTCCCCTCTATGCTTTATTTTTCTACCAA
Found at i:5086532 original size:11 final size:11
Alignment explanation
Indices: 5086516--5086547 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
5086506 ATTAAATATG
5086516 ATTATGAATAC
1 ATTATGAATAC
5086527 ATTATGAATAC
1 ATTATGAATAC
*
5086538 ATTATTAATA
1 ATTATGAATA
5086548 TTAATTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (11 bp):
ATTATGAATAC
Found at i:5088776 original size:16 final size:15
Alignment explanation
Indices: 5088742--5088790 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 15
5088732 AATTATAAGT
*
5088742 ATTATTAATTTAATTA
1 ATTATTAATTTAA-AA
5088758 ATTATTAATTATAAAA
1 ATTATTAATT-TAAAA
5088774 ATTTATTTAATTTAAAA
1 A-TTA-TTAATTTAAAA
5088791 TAAAAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 12 0.41
17 11 0.38
18 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTATTAATTTAAAA
Found at i:5088803 original size:30 final size:29
Alignment explanation
Indices: 5088767--5088844 Score: 104
Period size: 30 Copynumber: 2.7 Consensus size: 29
5088757 AATTATTAAT
*
5088767 TATAAAAATTTATTTAATTTAAAATAAAAA
1 TATAAAAATTTATTTAA-ATAAAATAAAAA
* *
5088797 TATAAAAATTTTAATTAAATATAATAAAAA
1 TATAAAAA-TTTATTTAAATAAAATAAAAA
5088827 -ATAAAAATTTATTTAAAT
1 TATAAAAATTTATTTAAAT
5088845 TTTTATAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 10 0.23
29 7 0.16
30 18 0.42
31 8 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
TATAAAAATTTATTTAAATAAAATAAAAA
Found at i:5088806 original size:21 final size:22
Alignment explanation
Indices: 5088782--5088826 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
5088772 AAATTTATTT
5088782 AATTTAAAATAAAAAT-ATAAA
1 AATTTAAAATAAAAATAATAAA
* * *
5088803 AATTTTAATTAAATATAATAAA
1 AATTTAAAATAAAAATAATAAA
5088825 AA
1 AA
5088827 ATAAAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AATTTAAAATAAAAATAATAAA
Found at i:5089448 original size:11 final size:11
Alignment explanation
Indices: 5089416--5089468 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
5089406 TAAATCTTAA
5089416 TTTTTAATT-T
1 TTTTTAATTAT
*
5089426 TATTTTTA-TAT
1 T-TTTTAATTAT
5089437 TTTTTAATTAT
1 TTTTTAATTAT
* *
5089448 TATTTATTTAT
1 TTTTTAATTAT
5089459 TTTTTAATTA
1 TTTTTAATTA
5089469 CTACCTTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
10 7 0.21
11 27 0.79
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTAATTAT
Found at i:5089450 original size:22 final size:22
Alignment explanation
Indices: 5089416--5089468 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
5089406 TAAATCTTAA
5089416 TTTTTAATT-TTATTT-TTATAT
1 TTTTTAATTATTATTTATT-TAT
5089437 TTTTTAATTATTATTTATTTAT
1 TTTTTAATTATTATTTATTTAT
5089459 TTTTTAATTA
1 TTTTTAATTA
5089469 CTACCTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.30
22 19 0.63
23 2 0.07
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTTAATTATTATTTATTTAT
Found at i:5090968 original size:22 final size:22
Alignment explanation
Indices: 5090943--5091008 Score: 114
Period size: 22 Copynumber: 3.0 Consensus size: 22
5090933 CGTCGGTTAC
*
5090943 CATAACCGACAGTTGCGGTTGG
1 CATAACCGACAGTTGCGGTCGG
5090965 CATAACCGACAGTTGCGGTCGG
1 CATAACCGACAGTTGCGGTCGG
*
5090987 CATAACCGACAATTGCGGTCGG
1 CATAACCGACAGTTGCGGTCGG
5091009 TTGCCCAGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.24, C:0.26, G:0.30, T:0.20
Consensus pattern (22 bp):
CATAACCGACAGTTGCGGTCGG
Found at i:5092516 original size:3 final size:3
Alignment explanation
Indices: 5092508--5092537 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5092498 ATTGTTTTAT
5092508 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5092538 AAAAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5098489 original size:64 final size:64
Alignment explanation
Indices: 5098388--5098515 Score: 159
Period size: 64 Copynumber: 2.0 Consensus size: 64
5098378 ACCATAATAC
* *
5098388 TATAAAAATATCAATATTTATCAATTATATAAAACAT-CCAAAACATATATTTATGTGTATTCAT
1 TATAAAAATATCAATATTTATCAATTATATAAAACATCCCAAAAC-TATACTTATATGTATTCAT
* * * * * * *
5098452 TATAAAAATATTAATATTTATTAGTTCTGTAACACATCCCAAATCTATACTTATATGTATTCAT
1 TATAAAAATATCAATATTTATCAATTATATAAAACATCCCAAAACTATACTTATATGTATTCAT
5098516 AAAATGACAA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
64 48 0.89
65 6 0.11
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (64 bp):
TATAAAAATATCAATATTTATCAATTATATAAAACATCCCAAAACTATACTTATATGTATTCAT
Found at i:5098903 original size:14 final size:16
Alignment explanation
Indices: 5098884--5098917 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
5098874 ATAAGTCTTG
5098884 AAAATATTTT-C-TAA
1 AAAATATTTTACATAA
5098898 AAAATATTTTACATAA
1 AAAATATTTTACATAA
5098914 AAAA
1 AAAA
5098918 ATATGGACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
15 1 0.06
16 7 0.39
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATATTTTACATAA
Found at i:5100077 original size:81 final size:78
Alignment explanation
Indices: 5099961--5100197 Score: 273
Period size: 77 Copynumber: 3.0 Consensus size: 78
5099951 AGTAATGGAA
* * *
5099961 GGGATTGCACAATAGATAATTTGGAAATTGAAAAAAAACAAGCTATAGTTTCTTTGAATGGTTTC
1 GGGATTGCACAATAGACAA-TTGGAAATTGGAAAAAAA-AAGCT-TAGTTTCTTTGAATGGTTTT
*
5100026 CTCTTTCATATCACAG
63 CTCTTTCATATCAAAG
*
5100042 GGGATTGTACAATAGACAAGTTGGAAATTGGAAAAAAAAAG-TT-GTTTC-TTGAAATGGTTTTC
1 GGGATTGCACAATAGACAA-TTGGAAATTGGAAAAAAAAAGCTTAGTTTCTTTG-AATGGTTTTC
*
5100104 TTTTTCATATCAAAG
64 TCTTTCATATCAAAG
* * * * *
5100119 GGAATTGCACAATAGACAATTTGACACTTGGAAAAAAAAAGCTGTAGTTGCTTTTATATGGTTTT
1 GGGATTGCACAATAGACAATTGGA-AATTGGAAAAAAAAAGCT-TAGTTTCTTTGA-ATGGTTTT
*
5100184 TTCTTTCATATCAA
63 CTCTTTCATATCAA
5100198 CAATTCAACA
Statistics
Matches: 134, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
76 7 0.05
77 59 0.44
78 2 0.01
79 2 0.01
80 8 0.06
81 56 0.42
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35
Consensus pattern (78 bp):
GGGATTGCACAATAGACAATTGGAAATTGGAAAAAAAAAGCTTAGTTTCTTTGAATGGTTTTCTC
TTTCATATCAAAG
Found at i:5100131 original size:77 final size:78
Alignment explanation
Indices: 5099959--5100197 Score: 261
Period size: 81 Copynumber: 3.0 Consensus size: 78
5099949 CAAGTAATGG
* *
5099959 AAGGGATTGCACAATAGATAATTTGGAAATTGAAAAAAAACAAGCTATAGTTTCTTTGAATGGTT
1 AAGGGATTGCACAATAGACAA-TTGGAAATTGGAAAAAAA-AAGCTATAGTTTCTTTGAATGGTT
5100024 TCCTCTTTCATATCA
64 TCCTCTTTCATATCA
* *
5100039 CAGGGGATTGTACAATAGACAAGTTGGAAATTGGAAAAAAAAAG-T-T-GTTTC-TTGAAATGGT
1 -AAGGGATTGCACAATAGACAA-TTGGAAATTGGAAAAAAAAAGCTATAGTTTCTTTG-AATGGT
* *
5100100 TTTCTTTTTCATATCA
63 TTCCTCTTTCATATCA
* * * * *
5100116 AAGGGAATTGCACAATAGACAATTTGACACTTGGAAAAAAAAAGCTGTAGTTGCTTTTATATGGT
1 AAGGG-ATTGCACAATAGACAATTGGA-AATTGGAAAAAAAAAGCTATAGTTTCTTTGA-ATGGT
**
5100181 TTTTTCTTTCATATCA
63 TTCCTCTTTCATATCA
5100197 A
1 A
5100198 CAATTCAACA
Statistics
Matches: 135, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
76 11 0.08
77 55 0.41
78 2 0.01
79 2 0.01
80 8 0.06
81 57 0.42
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (78 bp):
AAGGGATTGCACAATAGACAATTGGAAATTGGAAAAAAAAAGCTATAGTTTCTTTGAATGGTTTC
CTCTTTCATATCA
Found at i:5100706 original size:89 final size:90
Alignment explanation
Indices: 5100542--5100719 Score: 252
Period size: 89 Copynumber: 2.0 Consensus size: 90
5100532 TTCCCAGTTG
* * *
5100542 TAAGAACAATTTGGTGAACATTGTGCAAACGCCGTGCAATTGAGTCTTGTTATTTGAAACATGTG
1 TAAGAACAATTTGGTGAACATCGTGCAAACGCCATGCAATTAAGTCTTGTTATTTGAAACATGTG
*
5100607 TACTTTAATGGTATGTCTGTAGATA
66 TACTTTAATGGCATGTCTGTAGATA
* * * *
5100632 TAAGAAC-TTTTGGTGAACGTCGTGCAAATGCCATGCAATTAAGTCTTGTTATTTGGAACATGTG
1 TAAGAACAATTTGGTGAACATCGTGCAAACGCCATGCAATTAAGTCTTGTTATTTGAAACATGTG
*
5100696 TA-TTTCAATGGCATGTTTGTAGAT
66 TACTTT-AATGGCATGTCTGTAGAT
5100720 TGGACTTAAT
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
88 3 0.04
89 68 0.87
90 7 0.09
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (90 bp):
TAAGAACAATTTGGTGAACATCGTGCAAACGCCATGCAATTAAGTCTTGTTATTTGAAACATGTG
TACTTTAATGGCATGTCTGTAGATA
Found at i:5108646 original size:38 final size:38
Alignment explanation
Indices: 5108591--5108665 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
5108581 AAGCTTTAGA
**
5108591 AGTGTTTTTCCTTTTTTCCATCTTTGATGGCAATTAAT
1 AGTGTTTTTCCCCTTTTCCATCTTTGATGGCAATTAAT
5108629 AGTGTTTTTCCCCTTTTCCATCTTTGATGGCAATTAA
1 AGTGTTTTTCCCCTTTTCCATCTTTGATGGCAATTAA
5108666 GTTCAGACTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.49
Consensus pattern (38 bp):
AGTGTTTTTCCCCTTTTCCATCTTTGATGGCAATTAAT
Found at i:5115016 original size:162 final size:161
Alignment explanation
Indices: 5114736--5115026 Score: 492
Period size: 162 Copynumber: 1.8 Consensus size: 161
5114726 GAAGAACAAC
*
5114736 TTGGTATCGCCTAGCATTCTTGGTGAGTTCCTCTCCCCATCTTTTCTTCCTTTCTACTAAGGAGA
1 TTGGTATCGCCTAGCATTCTTGGTGAGTTCCTCTCCCCATCTTTTCTTCCTTCCTACTAAGGAGA
* * * * * *
5114801 TGAGATGCCACACTTTTTTTGTTGTTTCCATAGTATTAACGTTTATGAGAATTTCTCCTCTCTTT
66 TGAGATGCCACACTTTTTCTGTTGTTTCCATAGAACTAACCTTCATCAGAATTTCTCCTCTCTTT
5114866 ATAGTCCTTTATCAGTACTTTTCCATCATGA
131 ATAGTCCTTTATCAGTACTTTTCCATCATGA
5114897 TTGGTATCGCCTAGCATTCTTGGTGAGTTCCTCTCCCCATCTTTTCTTCCCTTCCTACTAAGGAG
1 TTGGTATCGCCTAGCATTCTTGGTGAGTTCCTCTCCCCATCTTTTCTT-CCTTCCTACTAAGGAG
* *
5114962 ATGAGATGTCACACTTTTTCTGTTGTTTCCATAGAACTAACCTTCATCAGAATTTCTCTTCTCTT
65 ATGAGATGCCACACTTTTTCTGTTGTTTCCATAGAACTAACCTTCATCAGAATTTCTCCTCTCTT
5115027 CCATCATGAT
Statistics
Matches: 120, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
161 48 0.40
162 72 0.60
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.42
Consensus pattern (161 bp):
TTGGTATCGCCTAGCATTCTTGGTGAGTTCCTCTCCCCATCTTTTCTTCCTTCCTACTAAGGAGA
TGAGATGCCACACTTTTTCTGTTGTTTCCATAGAACTAACCTTCATCAGAATTTCTCCTCTCTTT
ATAGTCCTTTATCAGTACTTTTCCATCATGA
Found at i:5115790 original size:107 final size:107
Alignment explanation
Indices: 5115603--5115817 Score: 385
Period size: 107 Copynumber: 2.0 Consensus size: 107
5115593 ATTTTCAACA
*
5115603 TTGACTGAAATTAAACTTTGATATGATAAAAAAGTTGAGTCATGTAGTGGTCATAAGAAAACAAG
1 TTGACTGAAATTAAACTTTGATATGAAAAAAAAGTTGAGTCATGTAGTGGTCATAAGAAAACAAG
* * *
5115668 GTACAGATTGTCAAAATTAATTACATGTTTTGTGTGTTTCTG
66 GTACAGATTGGCAAAATTAATTACATGTGTTCTGTGTTTCTG
*
5115710 TTGACTGAGATTAAACTTTGATATGAAAAAAAAGTTGAGTCATGTAGTGGTCATAAGAAAACAAG
1 TTGACTGAAATTAAACTTTGATATGAAAAAAAAGTTGAGTCATGTAGTGGTCATAAGAAAACAAG
5115775 GTACAGATTGGCAAAATTAATTACATGTGTTCTGTGTTTCTG
66 GTACAGATTGGCAAAATTAATTACATGTGTTCTGTGTTTCTG
5115817 T
1 T
5115818 AGTCTTGTAA
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 103 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.34
Consensus pattern (107 bp):
TTGACTGAAATTAAACTTTGATATGAAAAAAAAGTTGAGTCATGTAGTGGTCATAAGAAAACAAG
GTACAGATTGGCAAAATTAATTACATGTGTTCTGTGTTTCTG
Found at i:5126814 original size:2 final size:2
Alignment explanation
Indices: 5126807--5126837 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5126797 GCATTTGCTT
5126807 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5126838 TTCACCCTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5127528 original size:95 final size:96
Alignment explanation
Indices: 5127355--5127607 Score: 345
Period size: 95 Copynumber: 2.7 Consensus size: 96
5127345 ATAAAGAAAG
** ** *
5127355 AATTAGTCTTTGATTGAATCGGATTCAAT-CTTTGTACCTATATTCTGTAATGTTGA-TTTATCC
1 AATTAGTCTTTGATTGAATCAAATTCAATCCTTT-TACCTATATTCTGTAACATTCATTTTATCC
* *
5127418 TAATCTTTCAGAATATTTTATAAAGTTATAAA
65 TAATCTTCCAAAATATTTTATAAAGTTATAAA
* *
5127450 AGTTAGT-TTTCGATTGAATCAAATTCAATCCTTTTACTTATATTCTGTAACATTCATTTTA-CC
1 AATTAGTCTTT-GATTGAATCAAATTCAATCCTTTTACCTATATTCTGTAACATTCATTTTATCC
*
5127513 TAGTCTTCCAAAATATTTTATAAAGTTATAAA
65 TAATCTTCCAAAATATTTTATAAAGTTATAAA
*
5127545 AATTAGTCTTTGATTGAAAT-AAATTCAATCCTTTTACCTATATTCTGTAACAATCATTTTATC
1 AATTAGTCTTTGATTG-AATCAAATTCAATCCTTTTACCTATATTCTGTAACATTCATTTTATC
5127608 TGATTTTTTA
Statistics
Matches: 139, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
94 3 0.02
95 121 0.87
96 15 0.11
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.45
Consensus pattern (96 bp):
AATTAGTCTTTGATTGAATCAAATTCAATCCTTTTACCTATATTCTGTAACATTCATTTTATCCT
AATCTTCCAAAATATTTTATAAAGTTATAAA
Done.