Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009014.1 Hibiscus syriacus cultivar Beakdansim tig00112402_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3470424
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 13
Found at i:3207612 original size:2 final size:2
Alignment explanation
Indices: 3207605--3207638 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3207595 CTCAAGAATA
3207605 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
3207639 CAAATGTAAG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3214876 original size:21 final size:22
Alignment explanation
Indices: 3214834--3214876 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
3214824 TTAATCATTG
* *
3214834 TATTATTAGGGTTTAGATTTTA
1 TATTATTAAGGTTTAGAGTTTA
*
3214856 TATT-TTAAGGTTTAGGGTTTA
1 TATTATTAAGGTTTAGAGTTTA
3214877 AAATCATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (22 bp):
TATTATTAAGGTTTAGAGTTTA
Found at i:3231474 original size:15 final size:14
Alignment explanation
Indices: 3231442--3231491 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
3231432 AAGTCAACGG
* *
3231442 GTTGACTCGGACGA
1 GTTGACTCAGATGA
3231456 GTTGACTCAGATTGA
1 GTTGACTCAGA-TGA
*
3231471 GTTGAATCAGATGA
1 GTTGACTCAGATGA
3231485 GTTGACT
1 GTTGACT
3231492 TGGTGAATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (14 bp):
GTTGACTCAGATGA
Found at i:3249663 original size:12 final size:13
Alignment explanation
Indices: 3249635--3249666 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3249625 TTAATTATAG
3249635 TTTTATTAAATTA
1 TTTTATTAAATTA
3249648 TTTTATTAAA-TA
1 TTTTATTAAATTA
3249660 TTTTATT
1 TTTTATT
3249667 TATTGAGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTTATTAAATTA
Found at i:3250328 original size:31 final size:31
Alignment explanation
Indices: 3250293--3250356 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
3250283 TTTTTTTTCT
* *
3250293 TTAAAAAGTCAACTATGTGTTTGTATAATAA
1 TTAAAAAGTAAACTATGCGTTTGTATAATAA
3250324 TTAAAAAGTAAACTATGCGTTTGTATAATAA
1 TTAAAAAGTAAACTATGCGTTTGTATAATAA
3250355 TT
1 TT
3250357 TTTCTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (31 bp):
TTAAAAAGTAAACTATGCGTTTGTATAATAA
Found at i:3250445 original size:22 final size:25
Alignment explanation
Indices: 3250420--3250471 Score: 74
Period size: 22 Copynumber: 2.2 Consensus size: 25
3250410 GTTCAACATA
3250420 TAAAAATAATT-AA-AATTTT-AAT
1 TAAAAATAATTAAACAATTTTAAAT
*
3250442 TAAAAATATTTAAACAATTTTAAAT
1 TAAAAATAATTAAACAATTTTAAAT
3250467 TAAAA
1 TAAAA
3250472 GTAAAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 10 0.38
23 2 0.08
24 6 0.23
25 8 0.31
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
TAAAAATAATTAAACAATTTTAAAT
Found at i:3252906 original size:18 final size:18
Alignment explanation
Indices: 3252883--3252953 Score: 97
Period size: 18 Copynumber: 3.8 Consensus size: 18
3252873 TCAGTATTTA
3252883 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
*
3252901 TCCCGAAGGACCACTTATTA
1 TCCCGAAGGACCAC-TA-TG
* *
3252921 TTCCGAAGAACCACTATG
1 TCCCGAAGGACCACTATG
3252939 TCCCGAAGGACCACT
1 TCCCGAAGGACCACT
3252954 GTATATCCCT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 28 0.62
19 4 0.09
20 13 0.29
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:3252927 original size:38 final size:38
Alignment explanation
Indices: 3252880--3252962 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 38
3252870 CGTTCAGTAT
*
3252880 TTATCCCGAAGGACCACTATGTCCCGAAGGACCACTTA
1 TTATCCCGAAGAACCACTATGTCCCGAAGGACCACTTA
*
3252918 TTATTCCGAAGAACCACTATGTCCCGAAGGACCACTGTA
1 TTATCCCGAAGAACCACTATGTCCCGAAGGACCACT-TA
3252957 -TATCCC
1 TTATCCC
3252963 TCGACTCTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 39 0.95
39 2 0.05
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (38 bp):
TTATCCCGAAGAACCACTATGTCCCGAAGGACCACTTA
Found at i:3258863 original size:18 final size:18
Alignment explanation
Indices: 3258840--3258912 Score: 85
Period size: 18 Copynumber: 3.9 Consensus size: 18
3258830 GTTCAGTATT
3258840 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
3258858 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
** *
3258877 TTGGT-CCGAAAAACAACTA
1 -T-GTCCCGAAGGACCACTA
3258896 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
3258913 GTATATCCCT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
17 2 0.04
18 28 0.62
19 2 0.04
20 11 0.24
21 2 0.04
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:3259063 original size:21 final size:20
Alignment explanation
Indices: 3259016--3259070 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
3259006 CTATCACTTC
3259016 TCATATAACACATAATTTATT
1 TCATAT-ACACATAATTTATT
*
3259037 TCATATACACATGATTCT-TT
1 TCATATACACATAATT-TATT
*
3259057 TCAATATTCACATA
1 TC-ATATACACATA
3259071 CCTGTATCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.38, C:0.18, G:0.02, T:0.42
Consensus pattern (20 bp):
TCATATACACATAATTTATT
Found at i:3268742 original size:13 final size:13
Alignment explanation
Indices: 3268724--3268748 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3268714 CAACCCGACC
3268724 CGACCCGTTGACT
1 CGACCCGTTGACT
3268737 CGACCCGTTGAC
1 CGACCCGTTGAC
3268749 CCGTTGACCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.40, G:0.24, T:0.20
Consensus pattern (13 bp):
CGACCCGTTGACT
Found at i:3275955 original size:13 final size:13
Alignment explanation
Indices: 3275934--3275987 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 13
3275924 GTTACAACCC
*
3275934 GACCTGACCTGTT
1 GACCCGACCTGTT
*
3275947 GACCCGACC---C
1 GACCCGACCTGTT
*
3275957 GACCCAACCTGTT
1 GACCCGACCTGTT
*
3275970 GACCCGACCCGTT
1 GACCCGACCTGTT
3275983 GACCC
1 GACCC
3275988 AGGTGCTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
10 8 0.25
13 24 0.75
ACGTcount: A:0.19, C:0.44, G:0.20, T:0.17
Consensus pattern (13 bp):
GACCCGACCTGTT
Found at i:3275957 original size:23 final size:23
Alignment explanation
Indices: 3275930--3275980 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
3275920 ACCGGTTACA
**
3275930 ACCCGACCTGACCTGTTGACCCG
1 ACCCGACCCAACCTGTTGACCCG
3275953 ACCCGACCCAACCTGTTGACCCG
1 ACCCGACCCAACCTGTTGACCCG
3275976 ACCCG
1 ACCCG
3275981 TTGACCCAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.20, C:0.47, G:0.20, T:0.14
Consensus pattern (23 bp):
ACCCGACCCAACCTGTTGACCCG
Found at i:3276031 original size:29 final size:29
Alignment explanation
Indices: 3275989--3276047 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
3275979 CGTTGACCCA
3275989 GGTGCTATTCTGGTAATTATTTGGAAAAG
1 GGTGCTATTCTGGTAATTATTTGGAAAAG
*
3276018 GGTGCTATTCTGGTAATTATTTTGAAAAG
1 GGTGCTATTCTGGTAATTATTTGGAAAAG
3276047 G
1 G
3276048 TGTTTTTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.27, C:0.07, G:0.27, T:0.39
Consensus pattern (29 bp):
GGTGCTATTCTGGTAATTATTTGGAAAAG
Found at i:3276095 original size:26 final size:27
Alignment explanation
Indices: 3276062--3276121 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
3276052 TTTTTCGTAA
*
3276062 TTTA-AAAAAAATAATTTCGTAATT-T
1 TTTAGAAAAAAATAATTTAGTAATTAT
** *
3276087 TTTAGAAAATGATATTTTAGTAATTAT
1 TTTAGAAAAAAATAATTTAGTAATTAT
3276114 TTT-GAAAA
1 TTTAGAAAA
3276122 TGGTGATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 4 0.14
26 21 0.72
27 4 0.14
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (27 bp):
TTTAGAAAAAAATAATTTAGTAATTAT
Found at i:3276122 original size:26 final size:25
Alignment explanation
Indices: 3276080--3276154 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 25
3276070 AAATAATTTC
3276080 GTAATTTTTTAGAAAATGATATTTTA
1 GTAATTTTTT-GAAAATGATATTTTA
*
3276106 GTAATTATTTTGAAAATGGTGATATTTTG
1 GTAATT-TTTTGAAAA---TGATATTTTA
3276135 GTAATTTTTTTGAAAATGAT
1 GTAA-TTTTTTGAAAATGAT
3276155 GTTATTTTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
26 15 0.35
27 4 0.09
29 22 0.51
30 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (25 bp):
GTAATTTTTTGAAAATGATATTTTA
Found at i:3276128 original size:29 final size:29
Alignment explanation
Indices: 3276095--3276167 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
3276085 TTTTTAGAAA
3276095 ATGATATTTTAGTAATTATTTTGAAAATG
1 ATGATATTTTAGTAATTATTTTGAAAATG
* * *
3276124 GTGATATTTTGGTAATTTTTTTGAAAATG
1 ATGATATTTTAGTAATTATTTTGAAAATG
* *
3276153 ATGTTATTTTTGTAA
1 ATGATATTTTAGTAA
3276168 AATGGTTGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (29 bp):
ATGATATTTTAGTAATTATTTTGAAAATG
Found at i:3278180 original size:129 final size:127
Alignment explanation
Indices: 3277952--3278187 Score: 348
Period size: 129 Copynumber: 1.8 Consensus size: 127
3277942 AAATTGAGGT
* * * *
3277952 ATTAGATTGTAATAACCCTGAAGATCCAATCCATCTACATATCTGATGAGTAATGGTGCATCCTA
1 ATTAGATTGTAACAACCCTGAAGATCCAATCCATCCACATATATGATGAGTAATGGAGCATCCTA
* *
3278017 ATTAGGAAGAGATAATTTTATCCATCATGAAGCTCTTTTTCATCCTAATGAGCAAGTGGGGC
66 ATTAGGAAGAGATAATTTCATCCATCATGAAGCTCTATTTCATCCTAATGAGCAAGTGGGGC
* *
3278079 ATTAGATTGTAACAACCC-GAAGATCCAGTCGAGCATCCACATATATGATGAGTAATGGAGCATT
1 ATTAGATTGTAACAACCCTGAAGATCCAATC---CATCCACATATATGATGAGTAATGGAGCATC
* *
3278143 CTAATTAGGAAGAGATCATTTCATTCATCATGAAGCTCTATTTCA
63 CTAATTAGGAAGAGATAATTTCATCCATCATGAAGCTCTATTTCA
3278188 CTTGCAGTGT
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
126 11 0.11
127 17 0.18
129 68 0.71
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (127 bp):
ATTAGATTGTAACAACCCTGAAGATCCAATCCATCCACATATATGATGAGTAATGGAGCATCCTA
ATTAGGAAGAGATAATTTCATCCATCATGAAGCTCTATTTCATCCTAATGAGCAAGTGGGGC
Found at i:3279322 original size:33 final size:34
Alignment explanation
Indices: 3279285--3279409 Score: 91
Period size: 35 Copynumber: 3.7 Consensus size: 34
3279275 TAAATTCACA
* * * *
3279285 AAAAATATAGAGATAAAGAG-GAGAGAAGAAAAT
1 AAAAATATAGAGATAAAAAGAGAAAAAAGAAAAG
*
3279318 AAAAA-AGA-AGATAAAAAGAGAAAAAAGAAAAG
1 AAAAATATAGAGATAAAAAGAGAAAAAAGAAAAG
3279350 AGAAAATATAGA-A-AAAGAAGAAGAAAAAAGAGAAA-
1 A-AAAATATAGAGATAAA-AAG-AGAAAAAAGA-AAAG
* * *
3279385 AAAAAGAAAAGAGAGAAAAAGAGAA
1 AAAAA-TATAGAGATAAAAAGAGAA
3279410 GAGAAAAGAT
Statistics
Matches: 74, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
31 9 0.12
32 13 0.18
33 12 0.16
34 10 0.14
35 20 0.27
36 7 0.09
37 3 0.04
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.06
Consensus pattern (34 bp):
AAAAATATAGAGATAAAAAGAGAAAAAAGAAAAG
Found at i:3279331 original size:12 final size:12
Alignment explanation
Indices: 3279310--3279394 Score: 64
Period size: 12 Copynumber: 6.6 Consensus size: 12
3279300 AAGAGGAGAG
3279310 AAGAAAATAAAA
1 AAGAAAATAAAA
*
3279322 AAGAAGATAAAA
1 AAGAAAATAAAA
*
3279334 AGAGAAAAAAGAAA
1 A-AGAAAATA-AAA
3279348 AGAGAAAATATAGAAA
1 A-AG-AAA-ATA-AAA
*
3279364 AAGAAGAAGAAAA
1 AAGAA-AATAAAA
*
3279377 AAGAGAA-AAAA
1 AAGAAAATAAAA
3279388 AAGAAAA
1 AAGAAAA
3279395 GAGAGAAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
11 10 0.16
12 14 0.23
13 13 0.21
14 11 0.18
15 6 0.10
16 7 0.11
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.05
Consensus pattern (12 bp):
AAGAAAATAAAA
Found at i:3279345 original size:42 final size:44
Alignment explanation
Indices: 3279306--3279459 Score: 134
Period size: 42 Copynumber: 3.7 Consensus size: 44
3279296 GATAAAGAGG
*
3279306 AGAGAAGAAAATA-AAAAAGAAG-A-TAAAAAGAGAAAAAAGAAA
1 AGAGAA-AAAATAGAAAAAGAAGAAGAAAAAAGAGAAAAAAGAAA
*
3279348 AGAGAAAATATAGAAAAAGAAGAAGAAAAAAGAG---AAA-AAA
1 AGAGAAAAAATAGAAAAAGAAGAAGAAAAAAGAGAAAAAAGAAA
* * * *
3279388 A-AGAAAAGAGAGAAAAAG-AGAAGAGAAAAGATAGAAAAAGAAGA
1 AGAGAAAAAATAGAAAAAGAAGAAGAAAAAAGAGA-AAAAAGAA-A
*
3279432 AGAG-AAAAATA-AAAAAGATGAA-AAAAAA
1 AGAGAAAAAATAGAAAAAGAAGAAGAAAAAA
3279460 TAAAGAAAAT
Statistics
Matches: 91, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
38 12 0.13
39 15 0.16
40 4 0.04
41 8 0.09
42 18 0.20
43 14 0.15
44 18 0.20
45 2 0.02
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.05
Consensus pattern (44 bp):
AGAGAAAAAATAGAAAAAGAAGAAGAAAAAAGAGAAAAAAGAAA
Found at i:3279415 original size:31 final size:30
Alignment explanation
Indices: 3279331--3279425 Score: 106
Period size: 30 Copynumber: 3.1 Consensus size: 30
3279321 AAAGAAGATA
*
3279331 AAAAGAGA-AAAAAGAAAAGAGAAAATATAG
1 AAAAGAGAGAAAAAG-AAAGAGAAAAAATAG
*
3279361 AAAA-AGAAGAAGAAA-AAAGAGAAAAAAAAG
1 AAAAGAG-AGAA-AAAGAAAGAGAAAAAATAG
*
3279391 AAAAGAGAGAAAAAGAGAAGAGAAAAGATAG
1 AAAAGAGAGAAAAAGA-AAGAGAAAAAATAG
3279422 AAAA
1 AAAA
3279426 AGAAGAAGAG
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
29 5 0.09
30 27 0.49
31 20 0.36
32 3 0.05
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (30 bp):
AAAAGAGAGAAAAAGAAAGAGAAAAAATAG
Found at i:3279455 original size:61 final size:61
Alignment explanation
Indices: 3279299--3279457 Score: 203
Period size: 61 Copynumber: 2.5 Consensus size: 61
3279289 ATATAGAGAT
* *
3279299 AAAGAGGAGAGAAGAAAATAAAAAAGAAGATAAAAAGAGAAAAAAGAAAAGAGAAAATATAGAA
1 AAAGAAGA-AGAA-AAAATAAAAAAGAAGA-AAAAAGAGAAAAAAGAAAAGAGAAAAGATAGAA
* * * *
3279363 AAAGAAGAAGAAAAAAGAGAAAAAAAAGAAAAGAGAG-AAAAAGAGAAGAGAAAAGATAGAA
1 AAAGAAGAAGAAAAAATA-AAAAAGAAGAAAAAAGAGAAAAAAGAAAAGAGAAAAGATAGAA
*
3279424 AAAGAAGAAGAGAAAAATAAAAAAGATGAAAAAA
1 AAAGAAGAAGA-AAAAATAAAAAAGAAGAAAAAA
3279458 AATAAAGAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
61 45 0.54
62 18 0.22
63 13 0.16
64 7 0.08
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (61 bp):
AAAGAAGAAGAAAAAATAAAAAAGAAGAAAAAAGAGAAAAAAGAAAAGAGAAAAGATAGAA
Found at i:3279456 original size:16 final size:15
Alignment explanation
Indices: 3279413--3279465 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
3279403 AAGAGAAGAG
*
3279413 AAAAGATAGAAAAAGA
1 AAAAGAT-GAAAAAAA
*
3279429 AGAAGA-GAAAAATAA
1 AAAAGATGAAAAA-AA
3279444 AAAAGATGAAAAAAA
1 AAAAGATGAAAAAAA
3279459 ATAAAGA
1 A-AAAGA
3279466 AAATAAATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 6 0.19
15 9 0.29
16 16 0.52
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (15 bp):
AAAAGATGAAAAAAA
Found at i:3279466 original size:29 final size:29
Alignment explanation
Indices: 3279413--3279481 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
3279403 AAGAGAAGAG
*
3279413 AAAAGATAGAAAAAGAAGAAGAGAAAAATAA
1 AAAAGAT-GAAAAAAAAGAAGAG-AAAATAA
*
3279444 AAAAGATGAAAAAAAATAA-AGAAAATAA
1 AAAAGATGAAAAAAAAGAAGAGAAAATAA
*
3279472 ATCAAGATGA
1 A-AAAGATGA
3279482 GTGACTCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 8 0.24
29 9 0.26
30 10 0.29
31 7 0.21
ACGTcount: A:0.72, C:0.01, G:0.16, T:0.10
Consensus pattern (29 bp):
AAAAGATGAAAAAAAAGAAGAGAAAATAA
Found at i:3280593 original size:44 final size:44
Alignment explanation
Indices: 3280506--3280638 Score: 158
Period size: 44 Copynumber: 3.0 Consensus size: 44
3280496 AATGATGGAG
* * * * * * *
3280506 CAAGAAATGATGAATATTGGGGGCACTTTTGAGGGCTCGTATCAT
1 CAAGAAATAATAAATGTT-GGGGCATTTTTGAAGGCCCATATCAT
* * *
3280551 CCATAAATAATAAATGTTGGGGCATTTTTGAAGGCCCATATCAA
1 CAAGAAATAATAAATGTTGGGGCATTTTTGAAGGCCCATATCAT
*
3280595 CAAGAAATGATAAATGTTGGGGCATTTTTGAAGGCCCATATCAT
1 CAAGAAATAATAAATGTTGGGGCATTTTTGAAGGCCCATATCAT
3280639 TTAGGAATAC
Statistics
Matches: 74, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
44 61 0.82
45 13 0.18
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.29
Consensus pattern (44 bp):
CAAGAAATAATAAATGTTGGGGCATTTTTGAAGGCCCATATCAT
Found at i:3282290 original size:17 final size:17
Alignment explanation
Indices: 3282268--3282302 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3282258 TTAGAGATAT
*
3282268 TTAAGTGCATTATTTCA
1 TTAAGTACATTATTTCA
3282285 TTAAGTACATTATTTCA
1 TTAAGTACATTATTTCA
3282302 T
1 T
3282303 ACCTGCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (17 bp):
TTAAGTACATTATTTCA
Found at i:3282659 original size:41 final size:42
Alignment explanation
Indices: 3282565--3282672 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
3282555 TCCAAAATTG
* * * * *
3282565 GTAAGTCCTCCGGGCCAT-CAGTAAGTCTTTCGAGCATGATGA
1 GTAAATCCTTCGGGCCATCCA-TAAGCCTTTCGAGCAAGAGGA
* *
3282607 GTAAATCCTTCGGGTCATCTATAAGCCTTTCGAGCAAGAGGA
1 GTAAATCCTTCGGGCCATCCATAAGCCTTTCGAGCAAGAGGA
*
3282649 -TAAATTCTTCGGGCCATCCATAAG
1 GTAAATCCTTCGGGCCATCCATAAG
3282673 ACGTTCGGGT
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 21 0.38
42 33 0.60
43 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (42 bp):
GTAAATCCTTCGGGCCATCCATAAGCCTTTCGAGCAAGAGGA
Found at i:3283642 original size:268 final size:266
Alignment explanation
Indices: 3283013--3283662 Score: 695
Period size: 268 Copynumber: 2.4 Consensus size: 266
3283003 AATCGAATTC
* * * * *
3283013 GATTCAATCTTCCCTGAAG-AACAGTAGAATGAATCAACGTCTCTATATCTAATTTTCCCTCAAG
1 GATTCAATCTTCCCTG-AGTAACAGTGGAATGAATCAACGTCCCCATATATGATTTT-CCTCAAG
* * * *
3283077 AATAAGCGGGACAGATTCATATCTTTT-TAGATTTGATATTCCCTGAGTAACAGTGAAACAAGCC
64 AAGAAGCGGAACAGA-TCAT-TCTTTTCAAGATTTGATATTCCCTGAGTAACAGCGAAACAAGCC
* *
3283141 TGCCTCGATTCAATCTTTCCTGAAGAACAGTGGAATGAATCAATGTCCCCAGATCTGATTTTCCC
127 TGCCTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCC
* * *
3283206 TCAAGAAAAAGTAGAACATAACCATCTCTTTCAAGATTTGATATTCCATGAGTAATATTCGAACA
192 TCAAGAAAAAGCAGAACATAACCATCTCTTTCAAGATTTGATATTCCATGAGTAACATGCGAACA
*
3283271 AGTCTGCCTT
257 AGTCTACCTT
* * * * * * *
3283281 AATTCAATATTCCATTG-GTAAAATTGGAATGAATCAACATCCCCATATATGATTTTACCT-AAA
1 GATTCAATCTTCC-CTGAGTAACAGTGGAATGAATCAACGTCCCCATATATGATTTT-CCTCAAG
** ** * * *
3283344 AATGAAATGGAACAGATCCCTATATTTCAAGATTTGATATTCTCC-GAGTAACAGCGGAACAAGT
64 AA-GAAGCGGAACAGATCATTCT-TTTCAAGATTTGATATTC-CCTGAGTAACAGCGAAACAAGC
* * * *
3283408 CTGCCTCGATTCAATCTTCCCTG-AGTAATAGTGGAATTAATCAACGTCCTCAGATTTGATTTTC
126 CTGCCTCGATTCAATCTTCCCTGAAG-AACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTC
* * * * *
3283472 CCTCAAGAACAAGCGGAACA-AATCCCTTTCTTTCAAGATTTGATATTCCCTGAGTAACA-GCGG
190 CCTCAAGAAAAAGCAGAACATAA-CCATCTCTTTCAAGATTTGATATTCCATGAGTAACATGC-G
*
3283535 AATAAGTCTACCTT
253 AACAAGTCTACCTT
* * * *
3283549 GATTCAATCTTTCGTGAGTAACAGTGGAATTAATCAACGTCCCCATATATGATTTTCCTTCAGGA
1 GATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACGTCCCCATATATGATTTTCC-TCAAGA
* * * *
3283614 AGAAGCGAAACATATCATTCTCTTTCAAGATTTAATATTCCTTGAGTAA
65 AGAAGCGGAACAGATCATTCT-TTTCAAGATTTGATATTCCCTGAGTAA
3283663 TAGTAGAATA
Statistics
Matches: 309, Mismatches: 60, Indels: 26
0.78 0.15 0.07
Matches are distributed among these distances:
266 2 0.01
267 20 0.06
268 280 0.91
269 7 0.02
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (266 bp):
GATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACGTCCCCATATATGATTTTCCTCAAGAA
GAAGCGGAACAGATCATTCTTTTCAAGATTTGATATTCCCTGAGTAACAGCGAAACAAGCCTGCC
TCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAA
GAAAAAGCAGAACATAACCATCTCTTTCAAGATTTGATATTCCATGAGTAACATGCGAACAAGTC
TACCTT
Found at i:3283673 original size:134 final size:134
Alignment explanation
Indices: 3283011--3283662 Score: 620
Period size: 134 Copynumber: 4.9 Consensus size: 134
3283001 CAAATCGAAT
* * * * *
3283011 TCGATTCAATCTTCCCTGAAG-AACAGTAGAATGAATCAACGTCTCTATATCTAATTTTCCCTCA
1 TCGATTCAATCTTCCCTG-AGTAACAGTGGAATGAATCAACGTCCCCATATATGATTTTCCCTCA
* * * *
3283075 AGAATAAGCGGGACAGATTCATATCT-TTT-TAGATTTGATATTCCCTGAGTAACAGTGAAACAA
65 AGAAGAAGCGGAACAGA-TCAT-TCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
*
3283138 GCCTGCC
128 GTCTGCC
* * * *
3283145 TCGATTCAATCTTTCCTGAAG-AACAGTGGAATGAATCAATGTCCCCAGATCTGATTTTCCCTCA
1 TCGATTCAATCTTCCCTG-AGTAACAGTGGAATGAATCAACGTCCCCATATATGATTTTCCCTCA
* ** * * * * * *
3283209 AGAAAAAGTAGAACATAACCA-TCTCTTTCAAGATTTGATATTCCATGAGTAATATTCGAACAAG
65 AGAAGAAGCGGAACA-GATCATTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
3283273 TCTGCC
129 TCTGCC
** * * * * * *
3283279 TTAATTCAATATTCCATTG-GTAAAATTGGAATGAATCAACATCCCCATATATGATTTTACCT-A
1 TCGATTCAATCTTCC-CTGAGTAACAGTGGAATGAATCAACGTCCCCATATATGATTTTCCCTCA
* ** ** * * *
3283342 AAAATGAAATGGAACAGATCCCTATATTTCAAGATTTGATATTCTCC-GAGTAACAGCGGAACAA
65 AGAA-GAAGCGGAACAGATCATTCTCTTTCAAGATTTGATATTC-CCTGAGTAACAGTGGAACAA
3283406 GTCTGCC
128 GTCTGCC
* * * * *
3283413 TCGATTCAATCTTCCCTGAGTAATAGTGGAATTAATCAACGTCCTCAGATTTGATTTTCCCTCAA
1 TCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACGTCCCCATATATGATTTTCCCTCAA
* * * * *
3283478 GAACAAGCGGAACAAATCCCTT-TCTTTCAAGATTTGATATTCCCTGAGTAACAGCGGAATAAGT
66 GAAGAAGCGGAACAGAT-CATTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
*
3283542 CTACC
130 CTGCC
* * * * * *
3283547 TTGATTCAATCTTTCGTGAGTAACAGTGGAATTAATCAACGTCCCCATATATGATTTTCCTTCAG
1 TCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACGTCCCCATATATGATTTTCCCTCAA
* * * *
3283612 GAAGAAGCGAAACATATCATTCTCTTTCAAGATTTAATATTCCTTGAGTAA
66 GAAGAAGCGGAACAGATCATTCTCTTTCAAGATTTGATATTCCCTGAGTAA
3283663 TAGTAGAATA
Statistics
Matches: 423, Mismatches: 82, Indels: 26
0.80 0.15 0.05
Matches are distributed among these distances:
132 3 0.01
133 17 0.04
134 392 0.93
135 11 0.03
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (134 bp):
TCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACGTCCCCATATATGATTTTCCCTCAA
GAAGAAGCGGAACAGATCATTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTC
TGCC
Found at i:3283832 original size:228 final size:227
Alignment explanation
Indices: 3283415--3283844 Score: 556
Period size: 228 Copynumber: 1.9 Consensus size: 227
3283405 AGTCTGCCTC
* * * * * *
3283415 GATTCAATCTTCCCTGAGTAATAGTGGAATTAATCAACGTCCTCAGATTTGATTTTCCCTCAAGA
1 GATTCAATATTCCCTGAGTAATAGTAGAATAAATCAACATCCCCAGATATGATTTTCCCTCAAGA
* ** * *
3283480 ACAAGCGGAACAAATCCCTTTCTTTCAAGATTTGATATTCCCTGAGTAACAGCGGAATAAGTCTA
66 ACAAGCGAAACAAATCCCTCACTTTCAAGATTTGATATTCCCTGAGTAAAAGCGGAACAAGTCTA
** * ** * * * *
3283545 CCTTGATTCAATCTTTCGTGAGTAACAGTGGAATTAATCAACGTCCCCATATATGATTTTCCTTC
131 CCACGATTCAATCTTCCCCGAGGAACAGTGGAATGAATCAACGTCCCCAGATATGATTTTCCCTC
*
3283610 AGGAAGAAGCGAAACATATCATTCTCTTTCAA
196 AAGAAGAAGCGAAACATATCATTCTCTTTCAA
* * *
3283642 GATTTAATATTCCTTGAGTAATAGTAGAATAAATCAACATCCCCAGATATGATTTTCTCTCAAGA
1 GATTCAATATTCCCTGAGTAATAGTAGAATAAATCAACATCCCCAGATATGATTTTCCCTCAAGA
* * * * *
3283707 AGAAGCGAAATAGATCCCTCACTTTTCAATATTTGATATTCCCTGAG-AATAAGTGGAACAAGTC
66 ACAAGCGAAACAAATCCCTCAC-TTTCAAGATTTGATATTCCCTGAGTAA-AAGCGGAACAAGTC
* *
3283771 TGCCACGATTCAATCTTCCCCGAGGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCC
129 TACCACGATTCAATCTTCCCCGAGGAACAGTGGAATGAATCAACGTCCCCAGATATGATTTTCCC
3283836 TCAAGAAGA
194 TCAAGAAGA
3283845 TTGAAAACAT
Statistics
Matches: 170, Mismatches: 31, Indels: 3
0.83 0.15 0.01
Matches are distributed among these distances:
227 74 0.44
228 96 0.56
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.30
Consensus pattern (227 bp):
GATTCAATATTCCCTGAGTAATAGTAGAATAAATCAACATCCCCAGATATGATTTTCCCTCAAGA
ACAAGCGAAACAAATCCCTCACTTTCAAGATTTGATATTCCCTGAGTAAAAGCGGAACAAGTCTA
CCACGATTCAATCTTCCCCGAGGAACAGTGGAATGAATCAACGTCCCCAGATATGATTTTCCCTC
AAGAAGAAGCGAAACATATCATTCTCTTTCAA
Found at i:3292604 original size:2 final size:2
Alignment explanation
Indices: 3292592--3292637 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
3292582 TTATATCTTT
3292592 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3292634 TA TA
1 TA TA
3292638 AAAAGGGGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3293923 original size:2 final size:2
Alignment explanation
Indices: 3293914--3293959 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
3293904 AATTGTTTTT
3293914 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3293955 TA TA T
1 TA TA T
3293960 CTAAAAATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3294274 original size:15 final size:14
Alignment explanation
Indices: 3294250--3294281 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
3294240 TCATTTTTTA
3294250 TTTTTTAAAATTAT
1 TTTTTTAAAATTAT
3294264 TTTTCTTAAAATTAT
1 TTTT-TTAAAATTAT
3294279 TTT
1 TTT
3294282 AAAGGTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTTTAAAATTAT
Found at i:3296338 original size:64 final size:65
Alignment explanation
Indices: 3296246--3296377 Score: 214
Period size: 64 Copynumber: 2.0 Consensus size: 65
3296236 CATTCAAAAA
**
3296246 AATATTATATATGAATTATATCAATTTAAACTAT-A-AAAAATATAAATGTAAAAATAAAAAATA
1 AATATTATATATGAATTATATCAATTTAAACTATAACAAAAATATAAAAATAAAAAT-AAAAATA
3296309 T
65 T
*
3296310 AATATTATATATGAATTATATCAATTTAAACTATAACAAAAATATAAAAATACAAATAAAAATAT
1 AATATTATATATGAATTATATCAATTTAAACTATAACAAAAATATAAAAATAAAAATAAAAATAT
3296375 AAT
1 AAT
3296378 TATAATAAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
64 34 0.54
65 12 0.19
66 17 0.27
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (65 bp):
AATATTATATATGAATTATATCAATTTAAACTATAACAAAAATATAAAAATAAAAATAAAAATAT
Found at i:3296757 original size:2 final size:2
Alignment explanation
Indices: 3296750--3296786 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3296740 TGAACCCTTA
3296750 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3296787 ATCTTAGCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3297586 original size:32 final size:33
Alignment explanation
Indices: 3297496--3297595 Score: 96
Period size: 36 Copynumber: 3.0 Consensus size: 33
3297486 GCAATGAATG
3297496 AATAGAAGAGATGTTGGTTTCTTTATTTTT-AA
1 AATAGAAGAGATGTTGGTTTCTTTATTTTTAAA
* * ** **
3297528 TATTGATTATGTATAGTTGAACTTCTTT-TTTTTAAA
1 AATAGAAGA-G-AT-GTTG-GTTTCTTTATTTTTAAA
3297564 AATAGAAGAGATGTTGGTTTCTTTATTTTTAA
1 AATAGAAGAGATGTTGGTTTCTTTATTTTTAA
3297596 TATTGATTAT
Statistics
Matches: 50, Mismatches: 12, Indels: 11
0.68 0.16 0.15
Matches are distributed among these distances:
32 11 0.22
33 12 0.24
34 4 0.08
35 10 0.20
36 13 0.26
ACGTcount: A:0.30, C:0.04, G:0.16, T:0.50
Consensus pattern (33 bp):
AATAGAAGAGATGTTGGTTTCTTTATTTTTAAA
Found at i:3297605 original size:68 final size:67
Alignment explanation
Indices: 3297496--3297624 Score: 249
Period size: 68 Copynumber: 1.9 Consensus size: 67
3297486 GCAATGAATG
3297496 AATAGAAGAGATGTTGGTTTCTTTATTTTTAATATTGATTATGTATAGTTGAACTTCTTTTTTTT
1 AATAGAAGAGATGTTGGTTTCTTTATTTTTAATATTGATTATGTATAGTTGAACTT-TTTTTTTT
3297561 AAA
65 AAA
3297564 AATAGAAGAGATGTTGGTTTCTTTATTTTTAATATTGATTATGTATAGTTGAACTTTTTTT
1 AATAGAAGAGATGTTGGTTTCTTTATTTTTAATATTGATTATGTATAGTTGAACTTTTTTT
3297625 AAAAAGAATG
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
67 5 0.08
68 56 0.92
ACGTcount: A:0.29, C:0.04, G:0.16, T:0.52
Consensus pattern (67 bp):
AATAGAAGAGATGTTGGTTTCTTTATTTTTAATATTGATTATGTATAGTTGAACTTTTTTTTTTA
AA
Found at i:3299522 original size:2 final size:2
Alignment explanation
Indices: 3299515--3299554 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3299505 CCATTATGGA
3299515 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
3299555 TAAATACAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3301714 original size:43 final size:43
Alignment explanation
Indices: 3301650--3301909 Score: 195
Period size: 43 Copynumber: 6.4 Consensus size: 43
3301640 AAGAATAATT
*
3301650 CATATGGGTGCATTATTGGCATGAAAGGATGCATAGCTGAAATG
1 CATATGGGTGCATTATCGGCATGAAAGGATGCATAG-TGAAATG
3301694 CATATGGGTG-ATTATCGGCAT-AAA--A--CA-A-T--AATG
1 CATATGGGTGCATTATCGGCATGAAAGGATGCATAGTGAAATG
* *
3301727 CATATGGGTGCATTATTGGCATTAAAGGATGCCATAGCTGAAATG
1 CATATGGGTGCATTATCGGCATGAAAGGATG-CATAG-TGAAATG
*
3301772 CATATGGGTGCATTATCGACAT-AAA--A-G-A-A-T--AATG
1 CATATGGGTGCATTATCGGCATGAAAGGATGCATAGTGAAATG
* * * * *
3301806 CTTATGCGTGTATTATCGGCATGAAAGGATGCCAAAAG-AATAATG
1 CATATGGGTGCATTATCGGCATGAAAGGATG-C-ATAGTGA-AATG
* *
3301851 CATAT-GG-GCATTATTGGCATGAAAGGATGCAATAACTGAAATG
1 CATATGGGTGCATTATCGGCATGAAAGGATGC-AT-AGTGAAATG
3301894 CATATGGGTGCATTAT
1 CATATGGGTGCATTAT
3301910 TGACATAAAA
Statistics
Matches: 173, Mismatches: 15, Indels: 55
0.71 0.06 0.23
Matches are distributed among these distances:
33 14 0.08
34 32 0.18
35 7 0.04
36 1 0.01
37 3 0.02
38 4 0.02
39 1 0.01
40 3 0.02
41 3 0.02
42 8 0.05
43 41 0.24
44 17 0.10
45 39 0.23
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (43 bp):
CATATGGGTGCATTATCGGCATGAAAGGATGCATAGTGAAATG
Found at i:3301774 original size:45 final size:44
Alignment explanation
Indices: 3301723--3301942 Score: 169
Period size: 45 Copynumber: 5.2 Consensus size: 44
3301713 ATAAAACAAT
*
3301723 AATGCATATGGGTGCATTATTGGCATTAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATA-CTGA
* *
3301768 AATGCATATGGGTGCATTATCGACAT-AAA--A-G--A-A-T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATACTGA
* * * * **
3301802 AATGCTTATGCGTGTATTATCGGCATGAAAGGATGCCA-AAAGAA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATACTG-A
*
3301846 TAATGCATAT-GG-GCATTATTGGCATGAAAGGATGCAATAACTGA
1 -AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAT-ACTGA
* * * * *
3301890 AATGCATATGGGTGCATTATTGACATAAAAGTATACTATACTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAC-TGA
3301935 AATGCATA
1 AATGCATA
3301943 ATGGTGTATT
Statistics
Matches: 140, Mismatches: 19, Indels: 32
0.73 0.10 0.17
Matches are distributed among these distances:
34 22 0.16
35 3 0.02
36 1 0.01
37 1 0.01
38 2 0.01
39 1 0.01
40 2 0.01
41 1 0.01
42 1 0.01
43 31 0.22
44 9 0.06
45 66 0.47
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (44 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATACTGA
Found at i:3301821 original size:34 final size:34
Alignment explanation
Indices: 3301768--3301832 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
3301758 CCATAGCTGA
*
3301768 AATGCATATGGGTGCATTATCGACATAAAAGAAT
1 AATGCATATGCGTGCATTATCGACATAAAAGAAT
* * * *
3301802 AATGCTTATGCGTGTATTATCGGCATGAAAG
1 AATGCATATGCGTGCATTATCGACATAAAAG
3301833 GATGCCAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.29
Consensus pattern (34 bp):
AATGCATATGCGTGCATTATCGACATAAAAGAAT
Found at i:3301827 original size:79 final size:79
Alignment explanation
Indices: 3301559--3301839 Score: 449
Period size: 79 Copynumber: 3.6 Consensus size: 79
3301549 ATGAATGAAC
* *
3301559 AAAAGAATAATGCATATGGGTGCATTATTGGCATTAAAGGATGCCATAACTGAAATGCATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGG
*
3301624 TGCATTGTCGACAT
66 TGCATTATCGACAT
*
3301638 AAAAGAATAATTCATATGGGTGCATTATTGGCATGAAAGGATG-CATAGCTGAAATGCATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGG
*
3301702 TG-ATTATCGGCAT
66 TGCATTATCGACAT
* *
3301715 AAAACAATAATGCATATGGGTGCATTATTGGCATTAAAGGATGCCATAGCTGAAATGCATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGG
3301780 TGCATTATCGACAT
66 TGCATTATCGACAT
* * * *
3301794 AAAAGAATAATGCTTATGCGTGTATTATCGGCATGAAAGGATGCCA
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA
3301840 AAAGAATAAT
Statistics
Matches: 185, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
77 49 0.26
78 45 0.24
79 91 0.49
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (79 bp):
AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGG
TGCATTATCGACAT
Found at i:3301864 original size:156 final size:155
Alignment explanation
Indices: 3301559--3301870 Score: 466
Period size: 156 Copynumber: 2.0 Consensus size: 155
3301549 ATGAATGAAC
*
3301559 AAAAGAATAATGCATATGGGTGCATTATTGGCATTAAAGGATGCCATAACTGAAATGCATATGGG
1 AAAACAATAATGCATATGGGTGCATTATTGGCATTAAAGGATGCCATAACTGAAATGCATATGGG
* * * * * *
3301624 TGCATTGTCGACATAAAAGAATAATTCATATGGGTGCATTATTGGCATGAAAGGATGCATAGCTG
66 TGCATTATCGACATAAAAGAATAATGCATATGCGTGCATTATCGGCATGAAAGGATGCAAAGAT-
*
3301689 AAATGCATATGGGTGATTATCGGCAT
130 AAATGCATATGGGTCATTATCGGCAT
*
3301715 AAAACAATAATGCATATGGGTGCATTATTGGCATTAAAGGATGCCATAGCTGAAATGCATATGGG
1 AAAACAATAATGCATATGGGTGCATTATTGGCATTAAAGGATGCCATAACTGAAATGCATATGGG
* *
3301780 TGCATTATCGACATAAAAGAATAATGCTTATGCGTGTATTATCGGCATGAAAGGATGCCAAAAGA
66 TGCATTATCGACATAAAAGAATAATGCATATGCGTGCATTATCGGCATGAAAGGATG-C-AAAGA
*
3301845 -ATAATGCATATGGG-CATTATTGGCAT
129 TA-AATGCATATGGGTCATTATCGGCAT
3301871 GAAAGGATGC
Statistics
Matches: 141, Mismatches: 12, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
156 125 0.89
157 13 0.09
158 3 0.02
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (155 bp):
AAAACAATAATGCATATGGGTGCATTATTGGCATTAAAGGATGCCATAACTGAAATGCATATGGG
TGCATTATCGACATAAAAGAATAATGCATATGCGTGCATTATCGGCATGAAAGGATGCAAAGATA
AATGCATATGGGTCATTATCGGCAT
Found at i:3309840 original size:5 final size:5
Alignment explanation
Indices: 3309830--3309861 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
3309820 AAAATAACTA
3309830 AAAAT AAAAT AAAAT -AAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
3309862 CATTCATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:3309850 original size:14 final size:14
Alignment explanation
Indices: 3309831--3309861 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3309821 AAATAACTAA
3309831 AAATAAAATAAAAT
1 AAATAAAATAAAAT
3309845 AAATAAAATAAAAT
1 AAATAAAATAAAAT
3309859 AAA
1 AAA
3309862 CATTCATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:3344579 original size:83 final size:84
Alignment explanation
Indices: 3344421--3344585 Score: 278
Period size: 83 Copynumber: 2.0 Consensus size: 84
3344411 AGTTATTTAC
* * *
3344421 TTATCTTCCTTAGAGTCGCCAATGTATATGTATTTTAAGAAAAAATTATTAGATGGATCCGACTC
1 TTATATTCCTTAGAGTCGCCAATATATATGTATTTTAAGAAAAAATTATTAGATGGATCCAACTC
3344486 ATCACATCATTCATGGTAT
66 ATCACATCATTCATGGTAT
*
3344505 TTATATTCCTTAGAGTCGTCAATATATATGTATTTTAAG-AAAAATTATTAGATGGATCCAACTC
1 TTATATTCCTTAGAGTCGCCAATATATATGTATTTTAAGAAAAAATTATTAGATGGATCCAACTC
*
3344569 ATCACGTCATTCATGGT
66 ATCACATCATTCATGGT
3344586 CTAATCAATA
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
83 40 0.53
84 36 0.47
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (84 bp):
TTATATTCCTTAGAGTCGCCAATATATATGTATTTTAAGAAAAAATTATTAGATGGATCCAACTC
ATCACATCATTCATGGTAT
Found at i:3344803 original size:21 final size:22
Alignment explanation
Indices: 3344778--3344818 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3344768 AGATAAATTT
*
3344778 ATAAAAAATTTA-AAAATAAAA
1 ATAAAAAATTAATAAAATAAAA
*
3344799 ATAAAATATTAATAAAATAA
1 ATAAAAAATTAATAAAATAA
3344819 TATTTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (22 bp):
ATAAAAAATTAATAAAATAAAA
Found at i:3345521 original size:20 final size:20
Alignment explanation
Indices: 3345496--3345544 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
3345486 TAGTGGAAGT
*
3345496 ATCGATACTCCTGAGTCAAC
1 ATCGATACTCATGAGTCAAC
* **
3345516 ATCGATACTGATGAGTCAGT
1 ATCGATACTCATGAGTCAAC
3345536 ATCGATACT
1 ATCGATACT
3345545 ACCTCAGTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (20 bp):
ATCGATACTCATGAGTCAAC
Found at i:3360807 original size:20 final size:20
Alignment explanation
Indices: 3360784--3360831 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
3360774 TTCATTGTTT
3360784 GAAACTTTTGTAAGAATTTG
1 GAAACTTTTGTAAGAATTTG
* ** *
3360804 GAAACTTTTTTAAGGGTTTT
1 GAAACTTTTGTAAGAATTTG
3360824 GAAACTTT
1 GAAACTTT
3360832 ATCCCTTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (20 bp):
GAAACTTTTGTAAGAATTTG
Found at i:3363900 original size:63 final size:63
Alignment explanation
Indices: 3363822--3363944 Score: 246
Period size: 63 Copynumber: 2.0 Consensus size: 63
3363812 ACTAGGAGTG
3363822 CTTAATGAGTTGAACAGGTCGTGAGCTGCTCAAACTCGACTTGATTAACGCTCGACTTGGGAC
1 CTTAATGAGTTGAACAGGTCGTGAGCTGCTCAAACTCGACTTGATTAACGCTCGACTTGGGAC
3363885 CTTAATGAGTTGAACAGGTCGTGAGCTGCTCAAACTCGACTTGATTAACGCTCGACTTGG
1 CTTAATGAGTTGAACAGGTCGTGAGCTGCTCAAACTCGACTTGATTAACGCTCGACTTGG
3363945 TTGATTCGAC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (63 bp):
CTTAATGAGTTGAACAGGTCGTGAGCTGCTCAAACTCGACTTGATTAACGCTCGACTTGGGAC
Found at i:3367378 original size:20 final size:20
Alignment explanation
Indices: 3367330--3367382 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
3367320 TAATACAAAA
* *
3367330 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
3367350 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
3367370 TCGCAACGCGATT
1 TCGCAACGCGATT
3367383 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:3367974 original size:20 final size:19
Alignment explanation
Indices: 3367934--3367979 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
3367924 GCAACGAGAT
*
3367934 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
3367953 AATTCGCAACGCGAAACCAA
1 AA-TCGCAACGCGAAACAAA
3367973 AATCGCA
1 AATCGCA
3367980 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.48, C:0.26, G:0.15, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:3367997 original size:19 final size:19
Alignment explanation
Indices: 3367975--3368144 Score: 215
Period size: 19 Copynumber: 9.1 Consensus size: 19
3367965 GAAACCAAAA
*
3367975 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3367994 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3368013 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3368032 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3368051 TCGCAGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
3368071 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
3368087 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
3368104 TCACGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
3368123 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
3368143 TC
1 TC
3368145 AACCAAAAGA
Statistics
Matches: 134, Mismatches: 10, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
14 10 0.07
15 1 0.01
16 1 0.01
17 1 0.01
19 85 0.63
20 36 0.27
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3368071 original size:39 final size:38
Alignment explanation
Indices: 3367975--3368144 Score: 215
Period size: 39 Copynumber: 4.6 Consensus size: 38
3367965 GAAACCAAAA
*
3367975 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
3368013 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
3368051 TCGCAGTTGCGATTTTCATTTCGCGTTGCGATTGTC---
1 TCGC-GTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* ** * *
3368087 T-G-GTCGCGATAGTCATTTCACGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
3368123 ATCTCGTTGCGATTTTCATTTC
1 -TCGCGTTGCGATTTTCATTTC
3368145 AACCAAAAGA
Statistics
Matches: 114, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
33 26 0.23
35 1 0.01
36 1 0.01
37 1 0.01
38 41 0.36
39 44 0.39
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.45
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:3368137 original size:72 final size:75
Alignment explanation
Indices: 3367975--3368144 Score: 215
Period size: 72 Copynumber: 2.3 Consensus size: 75
3367965 GAAACCAAAA
* * ** *
3367975 TCGCA-TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTT
1 TCGCAGTTGCGATTTTCATTTCGCGTTGCGATTGTC--TTCGCGTCGCGATAGTCATTTCACGTT
*
3368039 GCGATTTTCATT
64 GCGATTCTCATT
3368051 TCGCAGTTGCGATTTTCATTTCGCGTTGCGATTGTC-T-G-GTCGCGATAGTCATTTCACGTTGC
1 TCGCAGTTGCGATTTTCATTTCGCGTTGCGATTGTCTTCGCGTCGCGATAGTCATTTCACGTTGC
3368113 GATTCTCATT
66 GATTCTCATT
*
3368123 ATCTC-GTTGCGATTTTCATTTC
1 -TCGCAGTTGCGATTTTCATTTC
3368145 AACCAAAAGA
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
72 46 0.54
73 4 0.05
74 1 0.01
76 5 0.06
77 29 0.34
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.45
Consensus pattern (75 bp):
TCGCAGTTGCGATTTTCATTTCGCGTTGCGATTGTCTTCGCGTCGCGATAGTCATTTCACGTTGC
GATTCTCATT
Found at i:3370204 original size:42 final size:42
Alignment explanation
Indices: 3370144--3370266 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
3370134 GCCCGACTCA
* * *
3370144 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
3370186 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
3370228 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
3370267 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:3370224 original size:21 final size:21
Alignment explanation
Indices: 3370200--3370266 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3370190 TCATTCCTCG
3370200 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
3370221 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
3370242 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
3370263 AGAG
1 AGAG
3370267 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:3371648 original size:14 final size:14
Alignment explanation
Indices: 3371629--3371664 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3371619 TTTGTTTAAT
3371629 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
3371643 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
3371657 TGATTTGT
1 TGATTTGT
3371665 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:3371869 original size:33 final size:32
Alignment explanation
Indices: 3371827--3371953 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
3371817 ATTAAATTCG
3371827 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
3371860 CGTTGCGATTTTCATTTCGCATTGCAAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGC--GATTCCT
3371893 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
3371926 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
3371954 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:3371907 original size:66 final size:66
Alignment explanation
Indices: 3371820--3371950 Score: 244
Period size: 66 Copynumber: 2.0 Consensus size: 66
3371810 ACGCGAAATT
*
3371820 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
3371885 A
66 A
*
3371886 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
3371951 GATAGTAATT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
A
Found at i:3375924 original size:16 final size:16
Alignment explanation
Indices: 3375890--3375924 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3375880 AAAAAATTTT
*
3375890 AAATTGAGAAAATATA
1 AAATTGAGAAAATAAA
*
3375906 AAATTTAGAAAATAAA
1 AAATTGAGAAAATAAA
3375922 AAA
1 AAA
3375925 ATATTCGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (16 bp):
AAATTGAGAAAATAAA
Found at i:3377307 original size:25 final size:26
Alignment explanation
Indices: 3377279--3377335 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
3377269 TATTTAACCT
*
3377279 TTTTTTTAATTTC-ATAATTTTTTTA
1 TTTTTTTAATTTCTATAATTGTTTTA
*
3377304 TTTTTTTATTTTCTTATAATTGTTTTA
1 TTTTTTTAATTTC-TATAATTGTTTTA
3377331 TTTTT
1 TTTTT
3377336 AAATATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 12 0.43
27 16 0.57
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (26 bp):
TTTTTTTAATTTCTATAATTGTTTTA
Found at i:3378464 original size:16 final size:17
Alignment explanation
Indices: 3378427--3378464 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3378417 AAAATTTAAA
3378427 TAAA-TTTAATTTTCTT
1 TAAATTTTAATTTTCTT
*
3378443 TTAATTTTAATTTT-TT
1 TAAATTTTAATTTTCTT
3378459 TAAATT
1 TAAATT
3378465 ATCCTGATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TAAATTTTAATTTTCTT
Found at i:3394583 original size:22 final size:21
Alignment explanation
Indices: 3394523--3394726 Score: 160
Period size: 22 Copynumber: 9.0 Consensus size: 21
3394513 ATATGATAGT
*
3394523 ATATAATATATAGTTTTGTCAAA
1 ATAT-ATATATAGTTTT-TGAAA
* *
3394546 AAATATATAT-GGTTTTGAAA
1 ATATATATATAGTTTTTGAAA
*
3394566 ATATATAGTATAGTTTTTAAAA
1 ATATATA-TATAGTTTTTGAAA
* *
3394588 ACATATGGTATAGTTTTTGAAA
1 ATATAT-ATATAGTTTTTGAAA
* *
3394610 ACATATTATATAGTTTTAGAAAAA
1 ATATA-TATATAGTTTTTG--AAA
3394634 CATATAATATATAGTTTTTGAAA
1 -ATAT-ATATATAGTTTTTGAAA
*
3394657 ATATATAGTATAGTTTTTAAAA
1 ATATATA-TATAGTTTTTGAAA
*
3394679 ACCTATTGTTATATAG-TTTTGAAAA
1 A--TA-T-ATATATAGTTTTTG-AAA
3394704 ATATAGTATATAGTTTTTGAAA
1 ATATA-TATATAGTTTTTGAAA
3394726 A
1 A
3394727 ACATATGTAA
Statistics
Matches: 148, Mismatches: 17, Indels: 33
0.75 0.09 0.17
Matches are distributed among these distances:
20 10 0.07
21 10 0.07
22 77 0.52
23 14 0.09
24 9 0.06
25 25 0.17
26 3 0.02
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (21 bp):
ATATATATATAGTTTTTGAAA
Found at i:3394654 original size:47 final size:46
Alignment explanation
Indices: 3394547--3394796 Score: 201
Period size: 47 Copynumber: 5.3 Consensus size: 46
3394537 TTTGTCAAAA
* * *
3394547 AATATATATGGTTTTGAAAATATA-TAGTATAGTTTTTAAAAACATAT
1 AATATATA-GTTTTTGAAAACATATTA-TATAGTTTTGAAAAACATAT
**
3394594 --GGTATAGTTTTTGAAAACATATTATATAGTTTTAGAAAAACATAT
1 AATATATAGTTTTTGAAAACATATTATATAGTTTT-GAAAAACATAT
* * *
3394639 AATATATAGTTTTTGAAAATATA-TAGTATAGTTTTTAAAAACCTATT
1 AATATATAGTTTTTGAAAACATATTA-TATAGTTTTGAAAAACATA-T
**
3394686 GTTATATAG-TTTTGAAAA-ATATAGTATATAGTTTTTGAAAAACATATGT
1 AATATATAGTTTTTGAAAACATAT--TATATAG-TTTTGAAAAACATA--T
* *
3394735 AATATATA-TATATTGAAAACATATTATATGAG-TTTGAAAATATAATAT
1 AATATATAGT-TTTTGAAAACATATTATAT-AGTTTTGAAAA-A-CATAT
*
3394783 ATTATATAGTTTTT
1 AATATATAGTTTTT
3394797 AATATATATA
Statistics
Matches: 164, Mismatches: 21, Indels: 35
0.75 0.10 0.16
Matches are distributed among these distances:
44 22 0.13
45 19 0.12
46 19 0.12
47 40 0.24
48 33 0.20
49 14 0.09
50 13 0.08
51 4 0.02
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (46 bp):
AATATATAGTTTTTGAAAACATATTATATAGTTTTGAAAAACATAT
Found at i:3394803 original size:26 final size:25
Alignment explanation
Indices: 3394755--3394808 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
3394745 TATTGAAAAC
3394755 ATATTATATGAGTTTGAAAATATAAT
1 ATATTATATGAGTTTGAAAATAT-AT
* *
3394781 ATATTATAT-AGTTTTTAATATATAT
1 ATATTATATGAG-TTTGAAAATATAT
3394806 ATA
1 ATA
3394809 AGTTAGGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (25 bp):
ATATTATATGAGTTTGAAAATATAT
Found at i:3394825 original size:3 final size:3
Alignment explanation
Indices: 3394817--3394845 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3394807 TAAGTTAGGT
3394817 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3394846 TATTTTCTTT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3396083 original size:18 final size:18
Alignment explanation
Indices: 3396060--3396099 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3396050 AAAATTTTCT
3396060 TTTATTCTT-TTTTATTTA
1 TTTATTCTTATTTTA-TTA
*
3396078 TTTATTTTTATTTTATTA
1 TTTATTCTTATTTTATTA
3396096 TTTA
1 TTTA
3396100 ACATTCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTATTCTTATTTTATTA
Found at i:3398401 original size:22 final size:23
Alignment explanation
Indices: 3398360--3398404 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
3398350 GATAATTTAT
* *
3398360 TTTGACCATAGTTGATCGTTGAC
1 TTTGACCAGAGTTGACCGTTGAC
3398383 TTTGACCAGA-TTGACCGTTGAC
1 TTTGACCAGAGTTGACCGTTGAC
3398405 AATTGACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (23 bp):
TTTGACCAGAGTTGACCGTTGAC
Found at i:3398410 original size:23 final size:23
Alignment explanation
Indices: 3398361--3398411 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
3398351 ATAATTTATT
* * *
3398361 TTGACCATAGTTGATCGTTGACT
1 TTGACCAGAGTTGACCGTTGACA
3398384 TTGACCAGA-TTGACCGTTGACAA
1 TTGACCAGAGTTGACCGTTGAC-A
3398407 TTGAC
1 TTGAC
3398412 TTTGACCCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (23 bp):
TTGACCAGAGTTGACCGTTGACA
Found at i:3402414 original size:22 final size:22
Alignment explanation
Indices: 3402354--3402414 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
3402344 TATGTTTTTG
*
3402354 AAACTATATCATATAT-TTTTAA
1 AAACTATA-AATATATATTTTAA
* * *
3402376 AAAATAT-TATATAATATTTTCA
1 AAACTATAAATAT-ATATTTTAA
3402398 AAACTATAAATATATAT
1 AAACTATAAATATATAT
3402415 ATATATATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 4 0.13
21 2 0.06
22 21 0.68
23 4 0.13
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.43
Consensus pattern (22 bp):
AAACTATAAATATATATTTTAA
Found at i:3402425 original size:78 final size:73
Alignment explanation
Indices: 3402364--3402499 Score: 181
Period size: 73 Copynumber: 1.9 Consensus size: 73
3402354 AAACTATATC
* * * *
3402364 ATATAT-TTTTA-AAAAATATTATA-TA-ATATTTTCAAAACTATAAATATATATATATATATAT
1 ATATATATTTTATTAAAATATTATACTATATAATAT-AAAACAAT-AATATATATATATATATAT
3402425 GTTTTTGAAA
64 GTTTTTGAAA
*
3402435 ATATATATTTTATTAAAATATTATACTATATAATATAACACAATAATATATATATATATATATGT
1 ATATATATTTTATTAAAATATTATACTATATAATATAAAACAATAATATATATATATATATATGT
3402500 ATACAAATGT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
71 6 0.11
72 5 0.09
73 32 0.57
74 8 0.14
75 5 0.09
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (73 bp):
ATATATATTTTATTAAAATATTATACTATATAATATAAAACAATAATATATATATATATATATGT
TTTTGAAA
Found at i:3402438 original size:18 final size:17
Alignment explanation
Indices: 3402417--3402455 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
3402407 ATATATATAT
3402417 ATATATATGTTT-TTGAAA
1 ATATATAT-TTTATT-AAA
3402435 ATATATATTTTATTAAA
1 ATATATATTTTATTAAA
3402452 ATAT
1 ATAT
3402456 TATACTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
ATATATATTTTATTAAA
Found at i:3409442 original size:12 final size:11
Alignment explanation
Indices: 3409425--3409521 Score: 65
Period size: 12 Copynumber: 8.6 Consensus size: 11
3409415 TCTTTTTGAA
3409425 AATATATATAGT
1 AATATATATA-T
* *
3409437 AATATAGTTTTT
1 AATATA-TATAT
3409449 AATATATATAT
1 AATATATATAT
3409460 ATATATATATAT
1 A-ATATATATAT
* *
3409472 ATAAAAATATAT
1 A-ATATATATAT
*
3409484 AAGTATATGTAT
1 AA-TATATATAT
*
3409496 -ATATTTA-AT
1 AATATATATAT
*
3409505 TAT-TATATAT
1 AATATATATAT
3409515 AATATAT
1 AATATAT
3409522 TATTATATTA
Statistics
Matches: 66, Mismatches: 13, Indels: 13
0.72 0.14 0.14
Matches are distributed among these distances:
9 5 0.08
10 10 0.15
11 9 0.14
12 40 0.61
13 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.47
Consensus pattern (11 bp):
AATATATATAT
Found at i:3409455 original size:26 final size:27
Alignment explanation
Indices: 3409417--3409468 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
3409407 ATTATATTTC
3409417 TTTTTGAAAATATATATAGTA-ATATAG
1 TTTTTGAAAATATATATA-TATATATAG
*
3409444 TTTTT-AATATATATATATATATATA
1 TTTTTGAAAATATATATATATATATA
3409469 TATATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 2 0.09
26 16 0.70
27 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (27 bp):
TTTTTGAAAATATATATATATATATAG
Found at i:3409457 original size:2 final size:2
Alignment explanation
Indices: 3409450--3409529 Score: 66
Period size: 2 Copynumber: 43.0 Consensus size: 2
3409440 ATAGTTTTTA
* *
3409450 AT AT AT AT AT AT AT AT AT AT AT AT AA AA AT AT AT A- AGT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* *
3409492 GT AT AT AT TT A- AT -T AT -T AT AT AT A- AT AT AT -T AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3409528 AT
1 AT
3409530 TATTACTTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
1 7 0.11
2 56 0.88
3 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3409513 original size:15 final size:17
Alignment explanation
Indices: 3409429--3409529 Score: 60
Period size: 14 Copynumber: 6.3 Consensus size: 17
3409419 TTTGAAAATA
*
3409429 TATATAGTAATATAGTTTT
1 TATATA-TAATATA-TTAT
3409448 TA-ATAT-ATATA-TA-
1 TATATATAATATATTAT
* *
3409461 TATATAT-ATATATAAA
1 TATATATAATATATTAT
*
3409477 AATATATAAGTATATGTA-
1 TATATATAA-TATAT-TAT
3409495 TATAT-T--TA-ATTAT
1 TATATATAATATATTAT
3409508 TATATATAATATATTAT
1 TATATATAATATATTAT
3409525 TATAT
1 TATAT
3409530 TATTACTTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 24
0.69 0.05 0.25
Matches are distributed among these distances:
12 2 0.03
13 9 0.14
14 13 0.20
15 1 0.02
16 13 0.20
17 13 0.20
18 12 0.18
19 3 0.05
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TATATATAATATATTAT
Found at i:3409515 original size:17 final size:18
Alignment explanation
Indices: 3409493--3409533 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3409483 TAAGTATATG
3409493 TATATATTTA-ATTATTA
1 TATATATTTATATTATTA
*
3409510 TATATA-ATATATTATTA
1 TATATATTTATATTATTA
3409527 TAT-TATT
1 TATATATT
3409534 ACTTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATATATTTATATTATTA
Found at i:3414373 original size:59 final size:59
Alignment explanation
Indices: 3414246--3414374 Score: 159
Period size: 59 Copynumber: 2.2 Consensus size: 59
3414236 CGTAATGCAA
* * * * *
3414246 TCCCGAGTTTGACACATAAGGTCGTGTCCACCATCTATACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
* * * ** *
3414305 TCCCAAATATGACACATAAGGTTGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
3414364 TCCCGAATATG
1 TCCCGAATATG
3414375 CAGCCTGCTG
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:3418080 original size:23 final size:22
Alignment explanation
Indices: 3418044--3418111 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
3418034 CATCTTATAT
3418044 GACACTTCGATGTATTTCTACGC
1 GACACTTCG-TGTATTTCTACGC
* * *
3418067 GGCACTTCAGTGTAATTCTACGT
1 GACACTTC-GTGTATTTCTACGC
*
3418090 GACACTTCGGTGTATTTATACG
1 GACACTTC-GTGTATTTCTACG
3418112 AGTTGTGGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
23 36 0.97
24 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (22 bp):
GACACTTCGTGTATTTCTACGC
Found at i:3422605 original size:73 final size:70
Alignment explanation
Indices: 3422495--3422921 Score: 374
Period size: 73 Copynumber: 5.9 Consensus size: 70
3422485 AAAACTTTTC
* * *
3422495 GTTTATCTGTAAACAAAAATTTCATCTTCCTTGAGATATTTTCCCTTGAAATGTTTTAGTCTCAC
1 GTTTCTCT-TAAACGAAAATTTCATCTCCCTTGAGATATTTTCCCTTGAAAT-TTTT-GTCTCAC
* *
3422560 TGGAGAGA
63 TCGAGACA
* * *
3422568 GTTTCTCTTGAAACGAAAATTTCACCTCCCTTAAGATATTTTCCCTTG-AATTTTTTTCTCACTC
1 GTTTCTCTT-AAACGAAAATTTCATCTCCCTTGAGATATTTTCCCTTGAAATTTTTGTCTCACTC
3422632 GAGACA
65 GAGACA
* * * * *
3422638 ATTTCTCTTAAA-GAAAATTTTTTATCTCTCTTGAGAGATATTTTCTCTTGAAAATTTTCCGTCT
1 GTTTCTCTTAAACGAAAA--TTTCATCTCCCTT--GAGATATTTTCCCTTG-AAATTTT-TGTCT
*
3422702 CGCTCGAGACA
60 CACTCGAGACA
* * * * * * *
3422713 GTTTCTATTGAAATGAAAATTACATCTCTCTTGAGATATTTTCCCTTGAAAATTTCGTCTCACTT
1 GTTTCTCTT-AAACGAAAATTTCATCTCCCTTGAGATATTTTCCCTTGAAATTTTTGTCTCACTC
*
3422778 GTGACA
65 GAGACA
* * *
3422784 ATTTCTCTCTAAAC-ATAAATTTCATCTCCCTTGAGATATTTTTTCCTTGAAATTTATTTTCTCA
1 GTTTCTCT-TAAACGA-AAATTTCATCTCCCTTGAGATA-TTTTCCCTTGAAATTT-TTGTCTCA
**
3422848 CTCGAGATG
62 CTCGAGACA
* * * * * * *
3422857 GTTTCCCTCAAATCCAAAATTTCATCTCACTTGAGATATTTTCTCTTGAAAAATTTCGTCTCACT
1 GTTTCTCTTAAA-CGAAAATTTCATCTCCCTTGAGATATTTTCCCTTG-AAATTTTTGTCTCACT
3422922 TAAGACATTT
Statistics
Matches: 289, Mismatches: 48, Indels: 35
0.78 0.13 0.09
Matches are distributed among these distances:
68 5 0.02
69 3 0.01
70 31 0.11
71 46 0.16
72 58 0.20
73 100 0.35
74 7 0.02
75 31 0.11
76 3 0.01
77 5 0.02
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (70 bp):
GTTTCTCTTAAACGAAAATTTCATCTCCCTTGAGATATTTTCCCTTGAAATTTTTGTCTCACTCG
AGACA
Found at i:3422883 original size:144 final size:141
Alignment explanation
Indices: 3422504--3422933 Score: 429
Period size: 145 Copynumber: 3.0 Consensus size: 141
3422494 CGTTTATCTG
* * *
3422504 TAAACAAAAATTTCATCTTCCTTGAGATA-TTTTCCCTTGAAATGTTTTAGTCTCACTGGAGAGA
1 TAAAC-AAAATTTCATCTCCCTTGAGATATTTTTTCCTTGAAAT-TTTT-GTCTCACTCGAGAG-
* * * * **
3422568 GTTTCTCTTGAAA-CGAAAATTTCACCTCCCTTAAGATATTTTCCCTTG-AATTTTTTTCTCACT
62 GTTTCTCTTGAAATCGAAAATTTCATCTCACTTGAGATATTTTCCCTTGAAAATTTCGTCTCACT
*
3422631 CGAGACAATTTCTCT
127 TGAGACAATTTCTCT
* * * * * * *
3422646 TAAAGAAAATTTTTTATCTCTCTTGAGAGATATTTTCTCTTGAAAATTTTCCGTCTCGCTCGAGA
1 TAAACAAAA--TTTCATCTCCCTTGAGATATTTTTTC-CTTG-AAATTTT-TGTCTCACTCGAGA
* * * *
3422711 CAGTTTCTATTGAAAT-GAAAATTACATCTCTCTTGAGATATTTTCCCTTGAAAATTTCGTCTCA
61 -GGTTTCTCTTGAAATCGAAAATTTCATCTCACTTGAGATATTTTCCCTTGAAAATTTCGTCTCA
*
3422775 CTTGTGACAATTTCTCT
125 CTTGAGACAATTTCTCT
*
3422792 CTAAACATAAATTTCATCTCCCTTGAGATATTTTTTCCTTGAAATTTATTTTCTCACTCGAGATG
1 -TAAACA-AAATTTCATCTCCCTTGAGATATTTTTTCCTTGAAATTT-TTGTCTCACTCGAGA-G
* * * *
3422857 GTTTC-CCTCAAATCCAAAATTTCATCTCACTTGAGATATTTTCTCTTGAAAAATTTCGTCTCAC
62 GTTTCTCTTGAAATCGAAAATTTCATCTCACTTGAGATATTTTCCCTTG-AAAATTTCGTCTCAC
* *
3422921 TTAAGACATTTTC
126 TTGAGACAATTTC
3422934 CTAGCATAAC
Statistics
Matches: 233, Mismatches: 41, Indels: 25
0.78 0.14 0.08
Matches are distributed among these distances:
141 4 0.02
142 4 0.02
143 20 0.09
144 56 0.24
145 90 0.39
146 51 0.22
147 5 0.02
148 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (141 bp):
TAAACAAAATTTCATCTCCCTTGAGATATTTTTTCCTTGAAATTTTTGTCTCACTCGAGAGGTTT
CTCTTGAAATCGAAAATTTCATCTCACTTGAGATATTTTCCCTTGAAAATTTCGTCTCACTTGAG
ACAATTTCTCT
Found at i:3423775 original size:3 final size:3
Alignment explanation
Indices: 3423767--3423810 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
3423757 TATTTTACGG
*
3423767 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTGA TTA ATA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA T
3423811 ATTTCTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3423946 original size:14 final size:14
Alignment explanation
Indices: 3423927--3423956 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3423917 ATATATATAA
3423927 TATATTATTACTAT
1 TATATTATTACTAT
*
3423941 TATATTATTATTAT
1 TATATTATTACTAT
3423955 TA
1 TA
3423957 CTTTTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (14 bp):
TATATTATTACTAT
Found at i:3423949 original size:3 final size:3
Alignment explanation
Indices: 3423929--3423978 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
3423919 ATATATAATA
*
3423929 TAT TAT TAC TAT TA- TAT TAT TAT TAT TACT T-T TAT T-T TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
3423971 TAT TAT TA
1 TAT TAT TA
3423979 ATTTATTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 8 0.20
3 30 0.75
4 2 0.05
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:3423954 original size:20 final size:19
Alignment explanation
Indices: 3423922--3423975 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
3423912 GATTGATATA
*
3423922 TATAATATATTATTACTAT
1 TATATTATATTATTACTAT
*
3423941 TATATTATTATTATTACTTT
1 TATATTA-TATTATTACTAT
*
3423961 TATTTTATATTATTA
1 TATATTATATTATTA
3423976 TTAATTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (19 bp):
TATATTATATTATTACTAT
Found at i:3426308 original size:5 final size:5
Alignment explanation
Indices: 3426281--3426319 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
3426271 ATTTTAAACA
*
3426281 AAATT AAATT GAATT GAAA-T AAATT AAATT AAATT AAAT
1 AAATT AAATT AAATT -AAATT AAATT AAATT AAATT AAAT
3426320 AAAGACTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 3 0.10
5 25 0.83
6 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:3428727 original size:16 final size:17
Alignment explanation
Indices: 3428696--3428728 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3428686 AAGCTCCTCT
*
3428696 ATTTTCTCTTTTTCTTC
1 ATTTTCTCTATTTCTTC
3428713 ATTTTCTC-ATTTCTTC
1 ATTTTCTCTATTTCTTC
3428729 TCTCTCTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTCTCTATTTCTTC
Found at i:3429774 original size:18 final size:19
Alignment explanation
Indices: 3429740--3429776 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3429730 CACGGAATGT
3429740 AAGATTACATGTGGGAATAA
1 AAGATTACA-GTGGGAATAA
3429760 AAGATTACA-TGGGAATA
1 AAGATTACAGTGGGAATA
3429777 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.24
Consensus pattern (19 bp):
AAGATTACAGTGGGAATAA
Found at i:3431435 original size:36 final size:36
Alignment explanation
Indices: 3431395--3431488 Score: 163
Period size: 36 Copynumber: 2.6 Consensus size: 36
3431385 TCCGATATGG
3431395 TGTATAACATCGTATAAATTTTGAGGTCAAATACCT
1 TGTATAACATCGTATAAATTTTGAGGTCAAATACCT
3431431 TGTATAACATCGTA-AAATTTTTGAGGTCAAATACCT
1 TGTATAACATCGTATAAA-TTTTGAGGTCAAATACCT
*
3431467 TGTATAACATCGTATAATTTTT
1 TGTATAACATCGTATAAATTTT
3431489 ATCCTATTCT
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
35 3 0.05
36 50 0.91
37 2 0.04
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (36 bp):
TGTATAACATCGTATAAATTTTGAGGTCAAATACCT
Found at i:3433354 original size:23 final size:21
Alignment explanation
Indices: 3433313--3433359 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
3433303 ACTTGACCTG
*
3433313 AAATTAAAAAAAAATAAAAAT
1 AAATTAAAAAAAAAGAAAAAT
3433334 AAATTAATAAACAAAAGAAAAAT
1 AAATTAA-AAA-AAAAGAAAAAT
3433357 AAA
1 AAA
3433360 ACTATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.30
22 3 0.13
23 13 0.57
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (21 bp):
AAATTAAAAAAAAAGAAAAAT
Found at i:3433366 original size:23 final size:23
Alignment explanation
Indices: 3433323--3433367 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3433313 AAATTAAAAA
* *
3433323 AAAATAAAAATAAATTAATAAAC
1 AAAAGAAAAATAAACTAATAAAC
3433346 AAAAGAAAAATAAAACT-ATAAA
1 AAAAGAAAAAT-AAACTAATAAA
3433368 TAATAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (23 bp):
AAAAGAAAAATAAACTAATAAAC
Found at i:3433372 original size:30 final size:28
Alignment explanation
Indices: 3433318--3433373 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 28
3433308 ACCTGAAATT
3433318 AAAAAAAAATAAAAATAAATTAATAAAC
1 AAAAAAAAATAAAAATAAATTAATAAAC
3433346 AAAAGAAAAATAAAACTATAAA-TAATAA
1 AAAA-AAAAATAAAA--ATAAATTAATAA
3433374 TATATATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 4 0.16
29 10 0.40
30 6 0.24
31 5 0.20
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.18
Consensus pattern (28 bp):
AAAAAAAAATAAAAATAAATTAATAAAC
Found at i:3433405 original size:2 final size:2
Alignment explanation
Indices: 3433398--3433480 Score: 90
Period size: 2 Copynumber: 45.0 Consensus size: 2
3433388 TTTCAAAAAT
3433398 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
3433440 -A AA TA T- TA TA -A TA CA TA -A TA TA -A TA T- TG TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3433475 TA TA TA
1 TA TA TA
3433481 CACACAAATG
Statistics
Matches: 70, Mismatches: 4, Indels: 14
0.80 0.05 0.16
Matches are distributed among these distances:
1 7 0.10
2 63 0.90
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3436617 original size:2 final size:2
Alignment explanation
Indices: 3436610--3436643 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3436600 TTACAGGAGA
3436610 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
3436644 TGAGTTGAGT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3447942 original size:20 final size:20
Alignment explanation
Indices: 3447917--3447993 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
3447907 TTTGTTGTAC
*
3447917 AAAGGATTGATCCCTTTTCA
1 AAAGGATCGATCCCTTTTCA
* *
3447937 AAAGGATTGATCCTTTTTCA
1 AAAGGATCGATCCCTTTTCA
3447957 AAAGGATCGATCCCTTTTCA
1 AAAGGATCGATCCCTTTTCA
3447977 AAAGGATCGATCCCTTT
1 AAAGGATCGATCCCTTT
3447994 GGGAAAAGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.34
Consensus pattern (20 bp):
AAAGGATCGATCCCTTTTCA
Found at i:3455130 original size:5 final size:5
Alignment explanation
Indices: 3455030--3455128 Score: 135
Period size: 5 Copynumber: 19.8 Consensus size: 5
3455020 GTTTGTCTGT
* * * *
3455030 TATGT TATGT TATGT TATGC TATGA TATGC TATGC TATGC TATGC TATGC
1 TATGC TATGC TATGC TATGC TATGC TATGC TATGC TATGC TATGC TATGC
* * *
3455080 TATGC TATGC TATGC TATGC TATGC TATGC TATGT TATGT TATGT TATG
1 TATGC TATGC TATGC TATGC TATGC TATGC TATGC TATGC TATGC TATG
3455129 TTGATATTCG
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 90 1.00
ACGTcount: A:0.21, C:0.12, G:0.20, T:0.46
Consensus pattern (5 bp):
TATGC
Found at i:3457470 original size:18 final size:18
Alignment explanation
Indices: 3457443--3457490 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
3457433 TTTTTCAGTC
* *
3457443 TTCTTTCTCTCTCTCCGA
1 TTCTTCCTCTCTCCCCGA
3457461 TTCTTCCTCTCTCCCCGA
1 TTCTTCCTCTCTCCCCGA
3457479 TTCTTCCTCTCT
1 TTCTTCCTCTCT
3457491 TTTTTCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.04, C:0.44, G:0.04, T:0.48
Consensus pattern (18 bp):
TTCTTCCTCTCTCCCCGA
Found at i:3458739 original size:3 final size:3
Alignment explanation
Indices: 3458725--3458761 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
3458715 TTTTTGTCTC
*
3458725 ATT ATT -TT ATT ATT ATT ATT ATT -TT AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3458762 TAATAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:3458747 original size:17 final size:17
Alignment explanation
Indices: 3458725--3458761 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
3458715 TTTTTGTCTC
*
3458725 ATTATTTTATTATTATT
1 ATTATTTTAATATTATT
3458742 ATTATTTTAATATTATT
1 ATTATTTTAATATTATT
3458759 ATT
1 ATT
3458762 TAATAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTATTTTAATATTATT
Found at i:3458770 original size:17 final size:14
Alignment explanation
Indices: 3458725--3458766 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3458715 TTTTTGTCTC
*
3458725 ATTATT-TTATTATT
1 ATTATTATT-TTAAT
3458739 ATTATTATTTTAAT
1 ATTATTATTTTAAT
3458753 ATTATTA-TTTAAT
1 ATTATTATTTTAAT
3458766 A
1 A
3458767 AATAATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 7 0.27
14 17 0.65
15 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTATTATTTTAAT
Found at i:3460081 original size:2 final size:2
Alignment explanation
Indices: 3460076--3460149 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
3460066 AATCACACAC
3460076 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
3460118 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
3460150 TAGATTAAAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3460354 original size:91 final size:91
Alignment explanation
Indices: 3460182--3460364 Score: 221
Period size: 91 Copynumber: 2.0 Consensus size: 91
3460172 TTATCTTTCA
* * * *
3460182 ATATTAAGAAATGACAGTCTTAAAATAACTAGATGTCCATTTTTTGATATATTTAATAAATATCA
1 ATATTAAGAAATGACAGTCTTAAAACAACTAGAAGTCCATTTTCTGATATATTTAATAAATATAA
*
3460247 TACTTTTATAAAATATATATATTAAT
66 TACTTTTATAAAATATATAAATTAAT
* *
3460273 ATATTAAGAAATGACAGTCTTAAAGCACCTAGAAGT-CATTTTCTGATAT-TTCTAAATAAATA-
1 ATATTAAGAAATGACAGTCTTAAAACAACTAGAAGTCCATTTTCTGATATATT-T-AATAAATAT
* *
3460335 AATATCTTATT-TTATATATATAAATTAAT
64 AATA-CTT-TTATAAAATATATAAATTAAT
3460364 A
1 A
3460365 GATTTTCTTA
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
89 2 0.03
90 16 0.20
91 59 0.75
92 2 0.03
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (91 bp):
ATATTAAGAAATGACAGTCTTAAAACAACTAGAAGTCCATTTTCTGATATATTTAATAAATATAA
TACTTTTATAAAATATATAAATTAAT
Found at i:3462377 original size:43 final size:43
Alignment explanation
Indices: 3462308--3462391 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
3462298 TTGGCTTCAG
3462308 AGTTAGGAGGGAAAGTTATCTCCTATATGTAAAGTTTTGTTGA
1 AGTTAGGAGGGAAAGTTATCTCCTATATGTAAAGTTTTGTTGA
** *
3462351 AGTTAGGATTGAAAGTTGTC-CTCTATATGTAAAGTTTTGTT
1 AGTTAGGAGGGAAAGTTATCTC-CTATATGTAAAGTTTTGTT
3462392 TGATGCATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 1 0.03
43 36 0.97
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (43 bp):
AGTTAGGAGGGAAAGTTATCTCCTATATGTAAAGTTTTGTTGA
Found at i:3462570 original size:20 final size:19
Alignment explanation
Indices: 3462547--3462585 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
3462537 TTTTATTGTA
3462547 ACATTCACATATTTACATTT
1 ACATTCACAT-TTTACATTT
*
3462567 ACATTTACATTTTACATTT
1 ACATTCACATTTTACATTT
3462586 TTTCATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (19 bp):
ACATTCACATTTTACATTT
Found at i:3462574 original size:12 final size:13
Alignment explanation
Indices: 3462557--3462585 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3462547 ACATTCACAT
3462557 ATTTACA-TTTAC
1 ATTTACATTTTAC
3462569 ATTTACATTTTAC
1 ATTTACATTTTAC
3462582 ATTT
1 ATTT
3462586 TTTCATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTTACATTTTAC
Found at i:3465377 original size:9 final size:9
Alignment explanation
Indices: 3465363--3465419 Score: 64
Period size: 9 Copynumber: 6.6 Consensus size: 9
3465353 TTATACTTGA
3465363 AAAAAAAAG
1 AAAAAAAAG
3465372 -AAAAAAAG
1 AAAAAAAAG
**
3465380 GGAAAAAAG
1 AAAAAAAAG
3465389 AAAAAAAA-
1 AAAAAAAAG
*
3465397 AAAAAAAGG
1 AAAAAAAAG
*
3465406 AAAAAAAGG
1 AAAAAAAAG
3465415 AAAAA
1 AAAAA
3465420 CTTGAATCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
8 15 0.36
9 27 0.64
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:3465385 original size:17 final size:16
Alignment explanation
Indices: 3465365--3465419 Score: 74
Period size: 17 Copynumber: 3.3 Consensus size: 16
3465355 ATACTTGAAA
3465365 AAAAAAGAAAAAAAGGG
1 AAAAAAGAAAAAAA-GG
**
3465382 AAAAAAGAAAAAAAAA
1 AAAAAAGAAAAAAAGG
3465398 AAAAAAGGAAAAAAAGG
1 AAAAAA-GAAAAAAAGG
3465415 AAAAA
1 AAAAA
3465420 CTTGAATCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 6 0.18
17 27 0.82
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAAAGG
Found at i:3465386 original size:20 final size:20
Alignment explanation
Indices: 3465361--3465398 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3465351 AATTATACTT
3465361 GAAAAAA-AAAGAAAAAAAGG
1 GAAAAAAGAAA-AAAAAAAGG
3465381 GAAAAAAGAAAAAAAAAA
1 GAAAAAAGAAAAAAAAAA
3465399 AAAAAGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (20 bp):
GAAAAAAGAAAAAAAAAAGG
Found at i:3465392 original size:24 final size:24
Alignment explanation
Indices: 3465363--3465411 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
3465353 TTATACTTGA
3465363 AAAAAAAAGAAAAAAAGGGAAAAAAG
1 AAAAAAAA-AAAAAAA-GGAAAAAAG
3465389 AAAAAAAAAAAAAAAGGAAAAAA
1 AAAAAAAAAAAAAAAGGAAAAAA
3465412 AGGAAAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 8 0.35
25 7 0.30
26 8 0.35
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAAAAAAAGGAAAAAAG
Found at i:3465392 original size:25 final size:25
Alignment explanation
Indices: 3465363--3465419 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 25
3465353 TTATACTTGA
*
3465363 AAAAAAAAGAAAAAAAGGGAAAAAAG
1 AAAAAAAA-AAAAAAAGGAAAAAAAG
3465389 AAAAAAAAAAAAAAAGGAAAAAAAG
1 AAAAAAAAAAAAAAAGGAAAAAAAG
*
3465414 GAAAAA
1 AAAAAA
3465420 CTTGAATCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 21 0.72
26 8 0.28
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (25 bp):
AAAAAAAAAAAAAAAGGAAAAAAAG
Done.