Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 77 of 91
Found at i:28245211 original size:2 final size:2
Alignment explanation
Indices: 28245204--28245243 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
28245194 GCATAAAATA
28245204 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
28245244 AACACATCAG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:28263641 original size:6 final size:6
Alignment explanation
Indices: 28263630--28263661 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
28263620 TGAGAGAGAC
28263630 TGAGCT TGAGCT TGAGCT TGAGCT TGAGCT TG
1 TGAGCT TGAGCT TGAGCT TGAGCT TGAGCT TG
28263662 CGCGCGTGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.16, G:0.34, T:0.34
Consensus pattern (6 bp):
TGAGCT
Found at i:28274579 original size:27 final size:27
Alignment explanation
Indices: 28274492--28274667 Score: 181
Period size: 27 Copynumber: 6.4 Consensus size: 27
28274482 TTATCATGGT
*
28274492 ATGTAACAATTAAATTTTTCAATATAAC
1 ATGTAACAATTAAA-TTTTCAACATAAC
* * * * *
28274520 GTGTAACAACTATATTTTTTAACATGAC
1 ATGTAACAATTA-AATTTTCAACATAAC
* * *
28274548 ATGTAATAACTAAATTTTTAACATAAC
1 ATGTAACAATTAAATTTTCAACATAAC
* * * *
28274575 GTGTAATAATTAAATTTTCAACATGAT
1 ATGTAACAATTAAATTTTCAACATAAC
* *
28274602 ATGTAACAATTAAAATTTCAACATGAC
1 ATGTAACAATTAAATTTTCAACATAAC
*
28274629 ATGTAACAATTAAAATTTCAACATAAC
1 ATGTAACAATTAAATTTTCAACATAAC
*
28274656 ATGTAATAATTA
1 ATGTAACAATTA
28274668 TTTCCAATAT
Statistics
Matches: 126, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
27 95 0.75
28 30 0.24
29 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (27 bp):
ATGTAACAATTAAATTTTCAACATAAC
Found at i:28274625 original size:54 final size:54
Alignment explanation
Indices: 28274492--28274716 Score: 202
Period size: 54 Copynumber: 4.1 Consensus size: 54
28274482 TTATCATGGT
* * * *
28274492 ATGTAACAATTAAATTTTTCAATATAACGTGTAACAACTATATTTTTTAACATGAC
1 ATGTAACAATTAAA-TTTTCAACATAACGTGTAACAATTA-AATTTTCAACATGAC
* * * * *
28274548 ATGTAATAACTAAATTTTTAACATAACGTGTAATAATTAAATTTTCAACATGAT
1 ATGTAACAATTAAATTTTCAACATAACGTGTAACAATTAAATTTTCAACATGAC
* * * * *
28274602 ATGTAACAATTAAAATTTCAACATGACATGTAACAATTAAAATTTCAACATAAC
1 ATGTAACAATTAAATTTTCAACATAACGTGTAACAATTAAATTTTCAACATGAC
* * * ** * * *
28274656 ATGTAATAATT--ATTTCCAATATAGTGTATAACAATTAAATTTTAGAATATGAC
1 ATGTAACAATTAAATTTTCAACATAACGTGTAACAATTAAATTTT-CAACATGAC
*
28274709 GTGTAACA
1 ATGTAACA
28274717 CTATATTTTT
Statistics
Matches: 134, Mismatches: 34, Indels: 5
0.77 0.20 0.03
Matches are distributed among these distances:
52 23 0.17
53 12 0.09
54 66 0.49
55 21 0.16
56 12 0.09
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (54 bp):
ATGTAACAATTAAATTTTCAACATAACGTGTAACAATTAAATTTTCAACATGAC
Found at i:28283676 original size:21 final size:20
Alignment explanation
Indices: 28283631--28283676 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
28283621 ACGTAAAGGG
*
28283631 TACA-AAATTAATATAAGAA
1 TACATAAATTAATATAAAAA
28283650 TACATAAATATAATATGAAAAA
1 TACATAAAT-TAATAT-AAAAA
28283672 T-CATA
1 TACATA
28283677 CGGACAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 4 0.17
20 4 0.17
21 10 0.43
22 5 0.22
ACGTcount: A:0.61, C:0.07, G:0.04, T:0.28
Consensus pattern (20 bp):
TACATAAATTAATATAAAAA
Found at i:28287772 original size:29 final size:29
Alignment explanation
Indices: 28287740--28287795 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
28287730 TATTTAAAAA
**
28287740 TTTTAAATAAAATTTTATTTTTTTATTAC
1 TTTTAAATAAAATTTTATACTTTTATTAC
* *
28287769 TTTTAATTAAATTTTTATACTTTTATT
1 TTTTAAATAAAATTTTATACTTTTATT
28287796 TTGAAATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (29 bp):
TTTTAAATAAAATTTTATACTTTTATTAC
Found at i:28293075 original size:22 final size:22
Alignment explanation
Indices: 28293047--28293092 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
28293037 GGTAAAGAAT
28293047 ATGAGAAATGTTAAAATTTTTC
1 ATGAGAAATGTTAAAATTTTTC
28293069 ATGAGAAATGTTAAAATTTTTC
1 ATGAGAAATGTTAAAATTTTTC
28293091 AT
1 AT
28293093 AAAAAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.41
Consensus pattern (22 bp):
ATGAGAAATGTTAAAATTTTTC
Found at i:28293099 original size:22 final size:22
Alignment explanation
Indices: 28293052--28293100 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
28293042 AGAATATGAG
* *
28293052 AAATGTTAAAATTTTTCATGAG
1 AAATGTTAAAATTTTTCATAAA
28293074 AAATGTTAAAATTTTTCATAAA
1 AAATGTTAAAATTTTTCATAAA
28293096 AAATG
1 AAATG
28293101 AATAGTGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.39
Consensus pattern (22 bp):
AAATGTTAAAATTTTTCATAAA
Found at i:28296527 original size:25 final size:25
Alignment explanation
Indices: 28296499--28296553 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
28296489 ATTTCTCTTG
28296499 TAAAAAACAATATACTATAACCAAT
1 TAAAAAACAATATACTATAACCAAT
***
28296524 TAAAATTTAATATACTATAACCAAT
1 TAAAAAACAATATACTATAACCAAT
*
28296549 CAAAA
1 TAAAA
28296554 TTTAATTAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (25 bp):
TAAAAAACAATATACTATAACCAAT
Found at i:28296554 original size:25 final size:25
Alignment explanation
Indices: 28296507--28296559 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
28296497 TGTAAAAAAC
*
28296507 AATATACTATAACCAATTAAAATTT
1 AATATACTATAACCAATCAAAATTT
28296532 AATATACTATAACCAATCAAAATTT
1 AATATACTATAACCAATCAAAATTT
28296557 AAT
1 AAT
28296560 TAAGACTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (25 bp):
AATATACTATAACCAATCAAAATTT
Found at i:28297644 original size:81 final size:82
Alignment explanation
Indices: 28297390--28297720 Score: 481
Period size: 82 Copynumber: 4.1 Consensus size: 82
28297380 ACCTATTGGT
* *
28297390 AGATAATATTTATATTTTTGACCAATCAAAAAATTAGTTATTGGTCATCTAATTTATCTCTAAAT
1 AGATAATATTCATATTTTTGACCAATCAAAAAATTAGTTATTGGTCATCCAATTTATCTCTAAAT
*
28297455 AAATCAAAATAATATAG
66 AAATCAAAATAATTTAG
*
28297472 AGATAATATTCATATTTTTGACCAATCAAAAAATTAGTTATTGGTCATCCAATTTATCTATAAAT
1 AGATAATATTCATATTTTTGACCAATCAAAAAATTAGTTATTGGTCATCCAATTTATCTCTAAAT
28297537 AAATCAAAATAATTTAG
66 AAATCAAAATAATTTAG
* * *
28297554 AAATAATATTCATATTTTTTATCAATCAAAAAATTAGTTATTGGTCATCCAA-TTATCTCTAAAT
1 AGATAATATTCATATTTTTGACCAATCAAAAAATTAGTTATTGGTCATCCAATTTATCTCTAAAT
* *
28297618 AATTCAAGATAATTTAG
66 AAATCAAAATAATTTAG
* * **
28297635 AGATTATATTCATATTTTTTACCAATC-AAAAATTAGTTATTGGTCATTTTAATTTATCTCT-AA
1 AGATAATATTCATATTTTTGACCAATCAAAAAATTAGTTATTGGTCA-TCCAATTTATCTCTAAA
* * *
28297698 T-AATTATACTAATTTAG
65 TAAATCAAAATAATTTAG
28297715 AGATAA
1 AGATAA
28297721 AAGTCAAATT
Statistics
Matches: 226, Mismatches: 21, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
80 35 0.15
81 56 0.25
82 135 0.60
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (82 bp):
AGATAATATTCATATTTTTGACCAATCAAAAAATTAGTTATTGGTCATCCAATTTATCTCTAAAT
AAATCAAAATAATTTAG
Found at i:28298001 original size:18 final size:18
Alignment explanation
Indices: 28297978--28298021 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
28297968 GGAAGCAATT
28297978 GAAGATTGGGAGGCATTC
1 GAAGATTGGGAGGCATTC
28297996 GAAGATTGGGAGGCATTC
1 GAAGATTGGGAGGCATTC
28298014 GAAGATTG
1 GAAGATTG
28298022 AGAGCATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.30, C:0.09, G:0.39, T:0.23
Consensus pattern (18 bp):
GAAGATTGGGAGGCATTC
Found at i:28298112 original size:25 final size:24
Alignment explanation
Indices: 28298082--28298280 Score: 194
Period size: 25 Copynumber: 8.8 Consensus size: 24
28298072 AACGGCAACA
*
28298082 AAGTTCATGATCAAGATATCAAGCG
1 AAGTTCGTGATCAAGATATC-AGCG
28298107 AAGTTCGTGATCAAGATA-CA--G
1 AAGTTCGTGATCAAGATATCAGCG
*
28298128 -TGTTCGTGATCAAGCA-A-CAGCG
1 AAGTTCGTGATCAAG-ATATCAGCG
28298150 AAGTTCGTGATCAAGATATCAAGCG
1 AAGTTCGTGATCAAGATATC-AGCG
*
28298175 AAGTTCATGATCAAGATAT-A--G
1 AAGTTCGTGATCAAGATATCAGCG
*
28298196 -TGTTCGTGATCAAGATA-CA--G
1 AAGTTCGTGATCAAGATATCAGCG
* * *
28298216 -TGTTCGTGATCAAG-CAGCAGCG
1 AAGTTCGTGATCAAGATATCAGCG
28298238 AAGTTCGTGATCAAGATATCAAGCG
1 AAGTTCGTGATCAAGATATC-AGCG
28298263 AAGTTCGTGATCAAGATA
1 AAGTTCGTGATCAAGATA
28298281 CAGTGTTCGT
Statistics
Matches: 150, Mismatches: 10, Indels: 28
0.80 0.05 0.15
Matches are distributed among these distances:
19 1 0.01
20 49 0.33
21 3 0.02
22 3 0.02
23 29 0.19
24 4 0.03
25 61 0.41
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (24 bp):
AAGTTCGTGATCAAGATATCAGCG
Found at i:28298134 original size:20 final size:22
Alignment explanation
Indices: 28298082--28298299 Score: 168
Period size: 20 Copynumber: 9.8 Consensus size: 22
28298072 AACGGCAACA
*
28298082 AAGTTCATGATCAAGATATCAAGCG
1 AAGTTCGTGATCAAGATA-C-A-CG
28298107 AAGTTCGTGATCAAGATACA-G
1 AAGTTCGTGATCAAGATACACG
*
28298128 -TGTTCGTGATCAAGCA-ACAGCG
1 AAGTTCGTGATCAAG-ATACA-CG
28298150 AAGTTCGTGATCAAGATATCAAGCG
1 AAGTTCGTGATCAAGATA-C-A-CG
* *
28298175 AAGTTCATGATCAAGATATA-G
1 AAGTTCGTGATCAAGATACACG
*
28298196 -TGTTCGTGATCAAGATACA-G
1 AAGTTCGTGATCAAGATACACG
* *
28298216 -TGTTCGTGATCAAGCA-GCAGCG
1 AAGTTCGTGATCAAG-ATACA-CG
28298238 AAGTTCGTGATCAAGATATCAAGCG
1 AAGTTCGTGATCAAGATA-C-A-CG
28298263 AAGTTCGTGATCAAGATACA-G
1 AAGTTCGTGATCAAGATACACG
* *
28298284 -TGTTCGTGATCTAGAT
1 AAGTTCGTGATCAAGAT
28298300 TAAGTCATCT
Statistics
Matches: 166, Mismatches: 13, Indels: 33
0.78 0.06 0.16
Matches are distributed among these distances:
20 63 0.38
21 5 0.03
22 4 0.02
23 30 0.18
24 4 0.02
25 60 0.36
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.26
Consensus pattern (22 bp):
AAGTTCGTGATCAAGATACACG
Found at i:28298153 original size:43 final size:43
Alignment explanation
Indices: 28298103--28298255 Score: 179
Period size: 43 Copynumber: 3.5 Consensus size: 43
28298093 CAAGATATCA
28298103 AGCGAAGTTCGTGATCAAGATACAGTGTTCGTGATCAAGCAAC
1 AGCGAAGTTCGTGATCAAGATACAGTGTTCGTGATCAAGCAAC
* * *
28298146 AGCGAAGTTCGTGATCAAGATATCAAGCGAAGTTCATGATCAAG-ATAT
1 AGCGAAGTTCGTGATCAAGATA-C-A--G-TGTTCGTGATCAAGCA-AC
* *
28298194 A--G-TGTTCGTGATCAAGATACAGTGTTCGTGATCAAGCAGC
1 AGCGAAGTTCGTGATCAAGATACAGTGTTCGTGATCAAGCAAC
28298234 AGCGAAGTTCGTGATCAAGATA
1 AGCGAAGTTCGTGATCAAGATA
28298256 TCAAGCGAAG
Statistics
Matches: 91, Mismatches: 9, Indels: 20
0.76 0.08 0.17
Matches are distributed among these distances:
40 13 0.14
41 2 0.02
42 1 0.01
43 39 0.43
44 2 0.02
45 17 0.19
46 1 0.01
47 2 0.02
48 14 0.15
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (43 bp):
AGCGAAGTTCGTGATCAAGATACAGTGTTCGTGATCAAGCAAC
Found at i:28298161 original size:68 final size:66
Alignment explanation
Indices: 28298082--28298299 Score: 248
Period size: 68 Copynumber: 3.3 Consensus size: 66
28298072 AACGGCAACA
*
28298082 AAGTTCATGATCAAGATATCAAGCGAAGTTCGTGATCAAGATACAGTGTTCGTGATCAAGCA-AC
1 AAGTTCGTGATCAAGATATCAAGCGAAGTTCGTGATCAAGATACAGTGTTCGTGATCAAG-ATAC
28298146 AGCG
65 A--G
* *
28298150 AAGTTCGTGATCAAGATATCAAGCGAAGTTCATGATCAAGATATAGTGTTCGTGATCAAGATACA
1 AAGTTCGTGATCAAGATATCAAGCGAAGTTCGTGATCAAGATACAGTGTTCGTGATCAAGATACA
28298215 G
66 G
* * * *
28298216 -TGTTCGTGATCAAG-CAGC-AGCGAAGTTCGTGATCAAGATATCAAGCGAAGTTCGTGATCAAG
1 AAGTTCGTGATCAAGATATCAAGCGAAGTTCGTGATCAAGATA-C-A--G-TGTTCGTGATCAAG
28298278 ATACAG
61 ATACAG
* *
28298284 -TGTTCGTGATCTAGAT
1 AAGTTCGTGATCAAGAT
28298300 TAAGTCATCT
Statistics
Matches: 132, Mismatches: 11, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
63 21 0.16
64 2 0.02
65 14 0.11
66 1 0.01
67 2 0.02
68 92 0.70
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.26
Consensus pattern (66 bp):
AAGTTCGTGATCAAGATATCAAGCGAAGTTCGTGATCAAGATACAGTGTTCGTGATCAAGATACA
G
Found at i:28298237 original size:88 final size:88
Alignment explanation
Indices: 28298109--28298299 Score: 346
Period size: 88 Copynumber: 2.2 Consensus size: 88
28298099 ATCAAGCGAA
28298109 GTTCGTGATCAAGATACAGTGTTCGTGATCAAGCAACAGCGAAGTTCGTGATCAAGATATCAAGC
1 GTTCGTGATCAAGATACAGTGTTCGTGATCAAGCAACAGCGAAGTTCGTGATCAAGATATCAAGC
*
28298174 GAAGTTCATGATCAAGATATAGT
66 GAAGTTCATGATCAAGATACAGT
*
28298197 GTTCGTGATCAAGATACAGTGTTCGTGATCAAGCAGCAGCGAAGTTCGTGATCAAGATATCAAGC
1 GTTCGTGATCAAGATACAGTGTTCGTGATCAAGCAACAGCGAAGTTCGTGATCAAGATATCAAGC
*
28298262 GAAGTTCGTGATCAAGATACAGT
66 GAAGTTCATGATCAAGATACAGT
*
28298285 GTTCGTGATCTAGAT
1 GTTCGTGATCAAGAT
28298300 TAAGTCATCT
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 99 1.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (88 bp):
GTTCGTGATCAAGATACAGTGTTCGTGATCAAGCAACAGCGAAGTTCGTGATCAAGATATCAAGC
GAAGTTCATGATCAAGATACAGT
Found at i:28298335 original size:49 final size:49
Alignment explanation
Indices: 28298282--28298502 Score: 343
Period size: 49 Copynumber: 4.5 Consensus size: 49
28298272 ATCAAGATAC
* * *
28298282 AGTGTTCGTGATCTAGATTAAGTCATCTAGACCCTTGAAGCGAAGATCA
1 AGTGTTCGTGATCAAGATTAAGTCGTCAAGACCCTTGAAGCGAAGATCA
** *
28298331 AGTGTTCGTGATCAAGATTAACCCGTCAAGACCTTTGAAGCGAAGATCA
1 AGTGTTCGTGATCAAGATTAAGTCGTCAAGACCCTTGAAGCGAAGATCA
28298380 AGTGTTCGTGATCAAGATTAAGTCGTCAAGACCCTTGAAGCGAAGATCA
1 AGTGTTCGTGATCAAGATTAAGTCGTCAAGACCCTTGAAGCGAAGATCA
*
28298429 AGTGTTCGTGATCAAGATTAAGTCGTCAAGACCCTTAAAGCGAAGATCA
1 AGTGTTCGTGATCAAGATTAAGTCGTCAAGACCCTTGAAGCGAAGATCA
* *
28298478 AGCAAGTTCGTGATCAAGACTAAGT
1 AG--TGTTCGTGATCAAGATTAAGT
28298503 TCAAGTTCGT
Statistics
Matches: 158, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
49 139 0.88
51 19 0.12
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (49 bp):
AGTGTTCGTGATCAAGATTAAGTCGTCAAGACCCTTGAAGCGAAGATCA
Found at i:28299502 original size:9 final size:8
Alignment explanation
Indices: 28299468--28299518 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
28299458 AAAAATTTTA
*
28299468 TTATTTTT
1 TTATATTT
* *
28299476 TTCTACTT
1 TTATATTT
28299484 TT-TATTT
1 TTATATTT
28299491 TTATATTAT
1 TTATATT-T
28299500 TTATTATTT
1 TTA-TATTT
28299509 TTATATTT
1 TTATATTT
28299517 TT
1 TT
28299519 TATGTTTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 6 0.17
8 18 0.50
9 8 0.22
10 4 0.11
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (8 bp):
TTATATTT
Found at i:28299506 original size:18 final size:18
Alignment explanation
Indices: 28299464--28299521 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
28299454 GGACAAAAAT
28299464 TTTATTATTTTT-T-TCTA
1 TTTATTATTTTTATAT-TA
28299481 CTTT-TTATTTTTATATTA
1 -TTTATTATTTTTATATTA
*
28299499 TTTATTATTTTTATATTT
1 TTTATTATTTTTATATTA
28299517 TTTAT
1 TTTAT
28299522 GTTTTGATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
17 11 0.31
18 24 0.67
19 1 0.03
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTATTATTTTTATATTA
Found at i:28299515 original size:15 final size:16
Alignment explanation
Indices: 28299464--28299551 Score: 63
Period size: 18 Copynumber: 5.2 Consensus size: 16
28299454 GGACAAAAAT
*
28299464 TTTATTATTTTTTTCTA
1 TTTATTATTTTTAT-TA
28299481 CTTT-TTATTTTTATATTA
1 -TTTATTA-TTTT-TATTA
28299499 TTTATTATTTTTA-TA
1 TTTATTATTTTTATTA
*
28299514 TTTTTTATGTTTTGATTA
1 TTTATTAT-TTTT-ATTA
* *
28299532 TCATATTATTATTATTA
1 T-TTATTATTTTTATTA
28299549 TTT
1 TTT
28299552 TTTGTAAGCA
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
15 9 0.16
16 7 0.12
17 16 0.28
18 18 0.32
19 7 0.12
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTATTATTTTTATTA
Found at i:28300073 original size:19 final size:19
Alignment explanation
Indices: 28300051--28300088 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
28300041 ATATCATTTA
*
28300051 TATTTT-TTTATTTATTATT
1 TATTTTATTAATTT-TTATT
28300070 TATTTTATTAATTTTTATT
1 TATTTTATTAATTTTTATT
28300089 ATATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
TATTTTATTAATTTTTATT
Found at i:28301444 original size:11 final size:10
Alignment explanation
Indices: 28301411--28301457 Score: 58
Period size: 11 Copynumber: 4.5 Consensus size: 10
28301401 TACCTCTCTC
28301411 TTTTTTTCAT
1 TTTTTTTCAT
*
28301421 TTTTTCTTTAT
1 TTTTT-TTCAT
28301432 TTTTTTGTCAT
1 TTTTTT-TCAT
*
28301443 TTTTATTCAT
1 TTTTTTTCAT
28301453 TTTTT
1 TTTTT
28301458 GTTTATGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
10 14 0.45
11 17 0.55
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTTTTTCAT
Found at i:28301454 original size:21 final size:21
Alignment explanation
Indices: 28301411--28301457 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
28301401 TACCTCTCTC
* *
28301411 TTTTTTTCATTTTTTCTTTAT
1 TTTTTTTCATTTTTTATTCAT
28301432 TTTTTTGTCA-TTTTTATTCAT
1 TTTTTT-TCATTTTTTATTCAT
28301453 TTTTT
1 TTTTT
28301458 GTTTATGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTTTTCATTTTTTATTCAT
Found at i:28302530 original size:30 final size:30
Alignment explanation
Indices: 28302496--28302562 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
28302486 AAATTTTTTG
* *
28302496 TTGGAAAGGCATTTTCCACGGAGAATTCCA
1 TTGGAAAAGCATTTCCCACGGAGAATTCCA
* *
28302526 TTGGAAAAGCATTTCCCACGGAGAATTTCG
1 TTGGAAAAGCATTTCCCACGGAGAATTCCA
28302556 TTGGAAA
1 TTGGAAA
28302563 TTCTCAATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (30 bp):
TTGGAAAAGCATTTCCCACGGAGAATTCCA
Found at i:28304633 original size:3 final size:3
Alignment explanation
Indices: 28304616--28304682 Score: 116
Period size: 3 Copynumber: 21.7 Consensus size: 3
28304606 ACTTATTATG
28304616 TAA TGAA TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28304663 TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
28304683 TNNNNNNNNN
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
3 56 0.90
4 6 0.10
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:28314808 original size:15 final size:15
Alignment explanation
Indices: 28314788--28314819 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
28314778 ATCGGGTTCC
28314788 CGGACCCGCACGTTA
1 CGGACCCGCACGTTA
28314803 CGGACCCGCACGTTA
1 CGGACCCGCACGTTA
28314818 CG
1 CG
28314820 ACAGTTCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.41, G:0.28, T:0.12
Consensus pattern (15 bp):
CGGACCCGCACGTTA
Found at i:28317261 original size:2 final size:2
Alignment explanation
Indices: 28317254--28317287 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28317244 CAAATTCTCC
28317254 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
28317288 CACTATCTCT
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):
TA
Found at i:28322496 original size:54 final size:55
Alignment explanation
Indices: 28322380--28322536 Score: 142
Period size: 54 Copynumber: 2.9 Consensus size: 55
28322370 AAAGGCGATC
** * * *
28322380 TCCAAGTCCCTA-CCGAAGAGAGAGGGGTAGCCCTGATTATGGCCGTGGCTCTAG
1 TCCAAGTCCCTATAGGAAGAGAGAGGGGGAGCCCTGATTATGGCCGGGGCTCCAG
** * *
28322434 TCGTAGTCCTTATAGGAAG-GAGAGGGGGAGCCCTGATTATGGTCGGGGC-CGCAG
1 TCCAAGTCCCTATAGGAAGAGAGAGGGGGAGCCCTGATTATGGCCGGGGCTC-CAG
* * * ** *
28322488 TCCAAGTCCCTATAAG-AGAGATAGAGCTAGCCCTGAATATGGCCGGGGC
1 TCCAAGTCCCTATAGGAAGAGAGAGGGGGAGCCCTGATTATGGCCGGGGC
28322537 ACTAGCCGTA
Statistics
Matches: 81, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
53 3 0.04
54 74 0.91
55 4 0.05
ACGTcount: A:0.24, C:0.23, G:0.34, T:0.20
Consensus pattern (55 bp):
TCCAAGTCCCTATAGGAAGAGAGAGGGGGAGCCCTGATTATGGCCGGGGCTCCAG
Found at i:28322763 original size:54 final size:54
Alignment explanation
Indices: 28322705--28322813 Score: 141
Period size: 54 Copynumber: 2.0 Consensus size: 54
28322695 TAGCCCTAGT
* * *
28322705 CATAGTCCATAT-AGAAGAGAAAG-GCCTAGCTCTGATAATGGTCGTGGACCCAGC
1 CATAGCCCATATGA-AAGAGAAAGAG-CTAGCCCTGAAAATGGTCGTGGACCCAGC
* *
28322759 CATAGCCCATATGAAAGAGATAGAGCTAGCCCTGAAAATGGTCGTGGTCCCAGC
1 CATAGCCCATATGAAAGAGAAAGAGCTAGCCCTGAAAATGGTCGTGGACCCAGC
28322813 C
1 C
28322814 CAAGTTCTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
54 46 0.96
55 2 0.04
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (54 bp):
CATAGCCCATATGAAAGAGAAAGAGCTAGCCCTGAAAATGGTCGTGGACCCAGC
Found at i:28324091 original size:3 final size:3
Alignment explanation
Indices: 28324083--28324108 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28324073 AAGCAAACGA
28324083 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
28324109 CAGATTGAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28325682 original size:2 final size:2
Alignment explanation
Indices: 28325677--28325771 Score: 127
Period size: 2 Copynumber: 47.0 Consensus size: 2
28325667 ACACACACAC
28325677 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT NAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
* * * * * *
28325720 AC AC AC AC AC AC 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
28325762 AT AT AT AT AT
1 AT AT AT AT AT
28325772 TGCTAGTTAG
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
2 88 0.98
3 2 0.02
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:28326275 original size:34 final size:37
Alignment explanation
Indices: 28326209--28326278 Score: 119
Period size: 34 Copynumber: 2.0 Consensus size: 37
28326199 TTAAATTATA
28326209 AAAAACAAATATCTCAAATATATCAACTTAAATAACT
1 AAAAACAAATATCTCAAATATATCAACTTAAATAACT
28326246 AAAAACAAATATC-CAAATA-A-CAACTTAAATAAC
1 AAAAACAAATATCTCAAATATATCAACTTAAATAAC
28326279 ATTACAAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
34 13 0.39
35 1 0.03
36 6 0.18
37 13 0.39
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (37 bp):
AAAAACAAATATCTCAAATATATCAACTTAAATAACT
Found at i:28326452 original size:16 final size:16
Alignment explanation
Indices: 28326420--28326456 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28326410 GGTATATATA
28326420 TTAT-AATTAATAATT
1 TTATAAATTAATAATT
28326435 TTATAAATT-ATAATTT
1 TTATAAATTAATAA-TT
28326451 TTATAA
1 TTATAA
28326457 CGTTAATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATAAATTAATAATT
Found at i:28326522 original size:2 final size:2
Alignment explanation
Indices: 28326515--28326546 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28326505 GTAGTAAAAG
28326515 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
28326547 ATAATAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28334909 original size:2 final size:2
Alignment explanation
Indices: 28334898--28334927 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
28334888 GACCATATGC
28334898 AT AT -T 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 A
28334928 AGTTGGCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28337201 original size:3 final size:3
Alignment explanation
Indices: 28337189--28337218 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
28337179 CATCATCATC
*
28337189 ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28337219 TTCTGACTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:28351586 original size:2 final size:2
Alignment explanation
Indices: 28351509--28351569 Score: 108
Period size: 2 Copynumber: 31.5 Consensus size: 2
28351499 AGCCCNTATC
28351509 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA -A 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
28351549 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
28351570 TCAGTTTATG
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 55 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28351623 original size:45 final size:46
Alignment explanation
Indices: 28351572--28351666 Score: 129
Period size: 51 Copynumber: 2.0 Consensus size: 46
28351562 ATATATATTC
*
28351572 AGTTTATG-AATATATGATTTATAAAATAAAAGAAAATTAATTTTG
1 AGTTTATGAAATATATGATTTATAAAATAAAAGAAAACTAATTTTG
28351617 AGTTTATGACAAATAATATATGATTTATAAAATAAAAGAAAACTAATTTT
1 AGTTTATG----A-AATATATGATTTATAAAATAAAAGAAAACTAATTTT
28351667 CATTACATAA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
45 8 0.19
51 35 0.81
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (46 bp):
AGTTTATGAAATATATGATTTATAAAATAAAAGAAAACTAATTTTG
Found at i:28356392 original size:2 final size:2
Alignment explanation
Indices: 28356385--28356427 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
28356375 ATGTATAAAG
28356385 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
28356427 A
1 A
28356428 AAAGTTAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28366520 original size:1 final size:1
Alignment explanation
Indices: 28366516--28366566 Score: 102
Period size: 1 Copynumber: 51.0 Consensus size: 1
28366506 ATTATAATTT
28366516 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
28366567 TTAATAATAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:28368098 original size:30 final size:30
Alignment explanation
Indices: 28368063--28368166 Score: 122
Period size: 30 Copynumber: 3.5 Consensus size: 30
28368053 AATCATTAAT
* *
28368063 TATAAGAGTTTATTTGATTCAAAATAAAAA
1 TATAAGAATTTATTTGACTCAAAATAAAAA
28368093 TATAAGAATTTATTTGACTCAAAATAAAAA
1 TATAAGAATTTATTTGACTCAAAATAAAAA
* * **
28368123 TATAAAAATTTGA-TTGAAT-GTAATAAAAA
1 TATAAGAATTT-ATTTGACTCAAAATAAAAA
*
28368152 TATAAAAATTTATTT
1 TATAAGAATTTATTT
28368167 AAATTTTTAT
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
28 1 0.02
29 21 0.32
30 43 0.65
31 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.38
Consensus pattern (30 bp):
TATAAGAATTTATTTGACTCAAAATAAAAA
Found at i:28390765 original size:1 final size:1
Alignment explanation
Indices: 28390759--28390788 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
28390749 TCACCAGAGC
28390759 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
28390789 ATAAAATGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:28399729 original size:16 final size:17
Alignment explanation
Indices: 28399708--28399740 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28399698 TATCTTAGTG
28399708 CTAATAT-TTTATACAA
1 CTAATATATTTATACAA
28399724 CTAATATATTTATACAA
1 CTAATATATTTATACAA
28399741 ATCCATCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (17 bp):
CTAATATATTTATACAA
Found at i:28427170 original size:25 final size:26
Alignment explanation
Indices: 28427141--28427202 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
28427131 ATAATGTTTC
28427141 ATAATATA-AAATATTATGA-ATATAT
1 ATAATATATAAATATTAT-ATATATAT
*
28427166 ATAATTGTATAAATATTATATATATAT
1 ATAA-TATATAAATATTATATATATAT
28427193 ATACATATAT
1 ATA-ATATAT
28427203 TTAATTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
25 4 0.13
26 4 0.13
27 22 0.71
28 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (26 bp):
ATAATATATAAATATTATATATATAT
Found at i:28427481 original size:188 final size:192
Alignment explanation
Indices: 28427189--28427577 Score: 570
Period size: 188 Copynumber: 2.0 Consensus size: 192
28427179 TATTATATAT
*
28427189 ATATATACATATATTTAATTTATACATAAGTACCACTATAATTTATAAAAAAAAACTTTATTTAT
1 ATATATACATATATTTAATTTATACATAAGTACCACTATAACTTAT--AAAAAAACTTTATTTAT
* *
28427254 ATGAGTACACTTAATAACTTTATTAGTTATCATCTTAGTTTTTATAACATATTATTTATAATTAG
64 ATAAGTACACTTAATAACTTTATTAGTTATCACCTTAGTTTTTATAACATATTATTTATAATTAG
* *
28427319 TTATTATTTATACAAACTTTGATAT-AAAA-T-ATTATAACATATAAGTTGTGTCATTAATTTC
129 TTATTATTTATACAAACTTTAATATAAAAATTAATTATAACACATAAGTTGTGTCATTAATTTC
** * * * *
28427380 ATATATACATATATTTAATTTATACATAAGTATTACTATAACTTAT-AATAGATTTTGTTTATAT
1 ATATATACATATATTTAATTTATACATAAGTACCACTATAACTTATAAAAAAACTTTATTTATAT
* *
28427444 AATTACACTTAATAACTTTATTAGTTATCACCTTAGTTTTTATAATATATTATTTATAATTAGTT
66 AAGTACACTTAATAACTTTATTAGTTATCACCTTAGTTTTTATAACATATTATTTATAATTAGTT
*
28427509 TTTATTTATACAAACTTTAATATAAAAATTAAAACATTATAACACATAAGTTGTGTCATTAATTT
131 ATTATTTATACAAACTTTAATATAAAAATT---A-ATTATAACACATAAGTTGTGTCATTAATTT
28427574 C
192 C
28427575 ATA
1 ATA
28427578 CATATAATAA
Statistics
Matches: 177, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
188 96 0.54
189 4 0.02
190 1 0.01
191 43 0.24
195 33 0.19
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.46
Consensus pattern (192 bp):
ATATATACATATATTTAATTTATACATAAGTACCACTATAACTTATAAAAAAACTTTATTTATAT
AAGTACACTTAATAACTTTATTAGTTATCACCTTAGTTTTTATAACATATTATTTATAATTAGTT
ATTATTTATACAAACTTTAATATAAAAATTAATTATAACACATAAGTTGTGTCATTAATTTC
Found at i:28427624 original size:21 final size:19
Alignment explanation
Indices: 28427591--28427635 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
28427581 ATAATAAAGT
*
28427591 AATATATTTTTTATATATA
1 AATATATTTTTTATACATA
*
28427610 CATATATTTAATTTATACATA
1 AATATATTT--TTTATACATA
28427631 AATAT
1 AATAT
28427636 TACTATAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 8 0.38
21 13 0.62
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (19 bp):
AATATATTTTTTATACATA
Found at i:28430235 original size:31 final size:32
Alignment explanation
Indices: 28430190--28430249 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
28430180 AATCATTAAT
*
28430190 TAAAAGGACTTATTTGACTTAAAATAAAAATG
1 TAAAAGGACTTATTTGACTCAAAATAAAAATG
*
28430222 TAAAAGG-CTTATTTGTCTCAAAATAAAA
1 TAAAAGGACTTATTTGACTCAAAATAAAA
28430250 GTACATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 19 0.73
32 7 0.27
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (32 bp):
TAAAAGGACTTATTTGACTCAAAATAAAAATG
Found at i:28432263 original size:15 final size:15
Alignment explanation
Indices: 28432243--28432272 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28432233 AAGCAAATCA
28432243 AAAAAAAAAAAAAGG
1 AAAAAAAAAAAAAGG
*
28432258 AAAAAAAAAGAAAGG
1 AAAAAAAAAAAAAGG
28432273 GAAGAGTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAGG
Found at i:28433025 original size:2 final size:2
Alignment explanation
Indices: 28433018--28433068 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
28433008 CCCAACAGTT
28433018 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28433059 A- AG A- AG AG AG
1 AG AG AG AG AG AG
28433069 GATCTGATGC
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28443323 original size:2 final size:2
Alignment explanation
Indices: 28443316--28443358 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
28443306 CCCTATATTA
28443316 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
28443358 A
1 A
28443359 ATAAATAAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28465819 original size:20 final size:21
Alignment explanation
Indices: 28465794--28465834 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
28465784 CTTGTCAAGA
*
28465794 CATGAATTTC-AGTGTTAAGG
1 CATGAATTACAAGTGTTAAGG
28465814 CATGAATTACAAGTGTTAAGG
1 CATGAATTACAAGTGTTAAGG
28465835 AAGTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (21 bp):
CATGAATTACAAGTGTTAAGG
Found at i:28474564 original size:82 final size:83
Alignment explanation
Indices: 28474457--28474608 Score: 200
Period size: 82 Copynumber: 1.8 Consensus size: 83
28474447 AAGGTTTTAC
* * *
28474457 TTTTCAAAATAAATTCCCATCTCATCATTTC-TTCATCGTAATACTATAAAAACATCCATATTCA
1 TTTTCAAAATAAATTCCCATCTCATCATTTCGTT-ATCATAAGACTATAAAAACATCCACATTCA
28474521 TTAATTGTATAAACTCTAA
65 TTAATTGTATAAACTCTAA
* * * * * *
28474540 TTTTTAAAA-AAATTTCCATCTCATCCTTTCGTTATCATAAGATTATAAAAATATCTACATTCAT
1 TTTTCAAAATAAATTCCCATCTCATCATTTCGTTATCATAAGACTATAAAAACATCCACATTCAT
28474604 TAATT
66 TAATT
28474609 ACACAAATAA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
82 49 0.83
83 10 0.17
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.41
Consensus pattern (83 bp):
TTTTCAAAATAAATTCCCATCTCATCATTTCGTTATCATAAGACTATAAAAACATCCACATTCAT
TAATTGTATAAACTCTAA
Found at i:28481119 original size:16 final size:17
Alignment explanation
Indices: 28481100--28481140 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
28481090 TAGAAATTTT
28481100 AAAA-AAATGAAAAATA
1 AAAAGAAATGAAAAATA
* *
28481116 AAAATAGA-GAAAAATA
1 AAAAGAAATGAAAAATA
28481132 AAAAGAAAT
1 AAAAGAAAT
28481141 TAAATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (17 bp):
AAAAGAAATGAAAAATA
Found at i:28486226 original size:24 final size:24
Alignment explanation
Indices: 28486191--28486240 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
28486181 CCCAAGATGC
28486191 CAAAAAAAATCTTCCAGGTTTTGG
1 CAAAAAAAATCTTCCAGGTTTTGG
*
28486215 CAAAAAATATCTTCCAGGTTTTGG
1 CAAAAAAAATCTTCCAGGTTTTGG
28486239 CA
1 CA
28486241 CTTAACAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (24 bp):
CAAAAAAAATCTTCCAGGTTTTGG
Found at i:28505194 original size:36 final size:36
Alignment explanation
Indices: 28505154--28505242 Score: 133
Period size: 36 Copynumber: 2.4 Consensus size: 36
28505144 GCAAAATTCG
28505154 AATCTTATCCTCCTAAACCGACGACAGCAAGACCCA
1 AATCTTATCCTCCTAAACCGACGACAGCAAGACCCA
* *
28505190 AATCTTATCCCCCTAAACCGACGACAGCAAGATCCA
1 AATCTTATCCTCCTAAACCGACGACAGCAAGACCCA
**
28505226 TCTCTTATCCTCTCTAA
1 AATCTTATCCTC-CTAA
28505243 CCAGCAGCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 43 0.91
37 4 0.09
ACGTcount: A:0.33, C:0.36, G:0.09, T:0.22
Consensus pattern (36 bp):
AATCTTATCCTCCTAAACCGACGACAGCAAGACCCA
Found at i:28505837 original size:24 final size:23
Alignment explanation
Indices: 28505810--28505890 Score: 65
Period size: 24 Copynumber: 3.3 Consensus size: 23
28505800 ATTCCTTCCC
* *
28505810 TTTTTTTTAATTCATTATTTATTTT
1 TTTTTTTTTATTTATTATTTA--TT
*
28505835 TTTATTATATTTTTTTATTATTTATT
1 TTT-TT-T-TTTATTTATTATTTATT
28505861 TTTTTATTTTATTTATT-TTATATT
1 TTTTT-TTTTATTTATTATT-TATT
28505885 TTTTTT
1 TTTTTT
28505891 GAAATAGGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
23 3 0.06
24 18 0.38
25 7 0.15
26 7 0.15
27 1 0.02
28 12 0.25
ACGTcount: A:0.20, C:0.01, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTTTTTTATTTATTATTTATT
Found at i:28505845 original size:17 final size:16
Alignment explanation
Indices: 28505824--28505879 Score: 75
Period size: 13 Copynumber: 3.7 Consensus size: 16
28505814 TTTTAATTCA
28505824 TTATTTATTTTTTTA-
1 TTATTTATTTTTTTAT
28505839 TTA--TATTTTTTTA-
1 TTATTTATTTTTTTAT
28505852 TTATTTATTTTTTTATT
1 TTATTTATTTTTTTA-T
28505869 TTATTTATTTT
1 TTATTTATTTT
28505880 ATATTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
13 13 0.35
15 13 0.35
17 11 0.30
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (16 bp):
TTATTTATTTTTTTAT
Found at i:28505856 original size:28 final size:29
Alignment explanation
Indices: 28505823--28505890 Score: 106
Period size: 28 Copynumber: 2.4 Consensus size: 29
28505813 TTTTTAATTC
28505823 ATTATTTATTTTTTTATTATATTT-TTTT
1 ATTATTTATTTTTTTATTATATTTATTTT
*
28505851 ATTATTTATTTTTTTATTTTATTTATTTT
1 ATTATTTATTTTTTTATTATATTTATTTT
28505880 A-TATTT-TTTTT
1 ATTATTTATTTTT
28505891 GAAATAGGTG
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
27 5 0.13
28 28 0.74
29 5 0.13
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (29 bp):
ATTATTTATTTTTTTATTATATTTATTTT
Found at i:28505887 original size:17 final size:16
Alignment explanation
Indices: 28505824--28505879 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 16
28505814 TTTTAATTCA
*
28505824 TTATTTATTTTTTTA-
1 TTATTTTTTTTTTTAT
*
28505839 TTATATTTTTTTATTAT
1 TTAT-TTTTTTTTTTAT
28505856 TTATTTTTTTATTTTAT
1 TTATTTTTTT-TTTTAT
28505873 TTATTTT
1 TTATTTT
28505880 ATATTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.11
16 15 0.43
17 16 0.46
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (16 bp):
TTATTTTTTTTTTTAT
Found at i:28506699 original size:15 final size:18
Alignment explanation
Indices: 28506665--28506760 Score: 64
Period size: 15 Copynumber: 5.6 Consensus size: 18
28506655 TTTTTTAAAT
28506665 ATTAATAATATATAATTA
1 ATTAATAATATATAATTA
28506683 ATTAA-AATAT-TAA-TA
1 ATTAATAATATATAATTA
*
28506698 ATTAATAATTTA-AATATCA
1 ATTAATAATATATAAT-T-A
** *
28506717 ATATTTTAATATA-ATTTA
1 AT-TAATAATATATAATTA
*
28506735 ATTACTAATAT-T--TTA
1 ATTAATAATATATAATTA
28506750 ATTAATAATAT
1 ATTAATAATAT
28506761 TTTATTTATN
Statistics
Matches: 63, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
15 20 0.32
16 9 0.14
17 12 0.19
18 9 0.14
19 4 0.06
20 9 0.14
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTAATAATATATAATTA
Found at i:28506744 original size:25 final size:25
Alignment explanation
Indices: 28506702--28506755 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
28506692 TTAATAATTA
28506702 ATAATTTAAATATCAATATTTTAAT
1 ATAATTTAAATATCAATATTTTAAT
*
28506727 ATAATTTAATTA-CTAATATTTTAAT
1 ATAATTTAAATATC-AATATTTTAAT
28506752 -TAAT
1 ATAAT
28506756 AATATTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (25 bp):
ATAATTTAAATATCAATATTTTAAT
Found at i:28506858 original size:25 final size:24
Alignment explanation
Indices: 28506826--28506901 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 24
28506816 TTTATACTCA
28506826 TTAAAAATTAAATATATTAATAAT
1 TTAAAAATTAAATATATTAATAAT
*
28506850 TTAATAAA-TAAA-ACATTAATAAT
1 TTAA-AAATTAAATATATTAATAAT
* *
28506873 TTAAAATATATTAATAT-TTAATATT
1 TTAAAA-AT-TAAATATATTAATAAT
28506898 TTAA
1 TTAA
28506902 TCATGTTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
22 2 0.05
23 15 0.35
24 8 0.19
25 17 0.40
26 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (24 bp):
TTAAAAATTAAATATATTAATAAT
Found at i:28506965 original size:28 final size:28
Alignment explanation
Indices: 28506909--28506965 Score: 64
Period size: 28 Copynumber: 2.0 Consensus size: 28
28506899 TAATCATGTT
* *
28506909 AATATTAATAATGTTTAAATTATATATA
1 AATATTAATAATGTTTAAATTACAAATA
28506937 AATATTAAT-AT-TTTAAATTTTACAAATA
1 AATATTAATAATGTTTAAA--TTACAAATA
28506965 A
1 A
28506966 TTTTTTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 6 0.24
27 2 0.08
28 17 0.68
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (28 bp):
AATATTAATAATGTTTAAATTACAAATA
Found at i:28510320 original size:35 final size:35
Alignment explanation
Indices: 28510277--28510505 Score: 226
Period size: 35 Copynumber: 6.5 Consensus size: 35
28510267 GTTAAGCTGT
*
28510277 GCCTAATTAACTAAATTGTTTAATTGAA-TCATTGG
1 GCCTAATTAATTAAATTGTTTAATT-AAGTCATTGG
*
28510312 GCCTAATTAATTAAATTATTTAATTAAGTCATTGG
1 GCCTAATTAATTAAATTGTTTAATTAAGTCATTGG
* * *** *
28510347 GCTTAATTAGTTAAATTAAATAATTAAGTTATTGG
1 GCCTAATTAATTAAATTGTTTAATTAAGTCATTGG
* * * * *
28510382 GTCTAATTGATTGAATTTGTTTAATTAAGCCATTAG
1 GCCTAATTAATT-AAATTGTTTAATTAAGTCATTGG
* * * ** *
28510418 GCCTACTTGATTAAAATTGTTTAATTAAATTGTTAG
1 GCCTAATTAATT-AAATTGTTTAATTAAGTCATTGG
* *
28510454 GCTTAATTAATTAAATTGTTTAATTAAGTTATTGG
1 GCCTAATTAATTAAATTGTTTAATTAAGTCATTGG
*
28510489 GCCTAATTGATTAAATT
1 GCCTAATTAATTAAATT
28510506 AAACAATTAA
Statistics
Matches: 158, Mismatches: 34, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
34 2 0.01
35 103 0.65
36 53 0.34
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (35 bp):
GCCTAATTAATTAAATTGTTTAATTAAGTCATTGG
Found at i:28510460 original size:107 final size:106
Alignment explanation
Indices: 28510277--28510505 Score: 273
Period size: 107 Copynumber: 2.2 Consensus size: 106
28510267 GTTAAGCTGT
* * * * *
28510277 GCCTAATTAACTAAA-TTGTTTAATTGAATCATTGGGCCTAATTAATTAAATTATTTAATTAAGT
1 GCCTAATTGATTAAATTTGTTTAATTGAACCATTAGGCCTAATTAATTAAATTATTTAATTAAAT
* *
28510341 CATTGGGCTTAATTAGTTAAATTAAATAATTAAGTTATTGG
66 CATTAGGCTTAATTAATTAAATTAAATAATTAAGTTATTGG
* * * * *
28510382 GTCTAATTGATTGAATTTGTTTAATT-AAGCCATTAGGCCTACTTGATTAAAATTGTTTAATTAA
1 GCCTAATTGATTAAATTTGTTTAATTGAA-CCATTAGGCCTAATTAATT-AAATTATTTAATTAA
** ***
28510446 ATTGTTAGGCTTAATTAATTAAATTGTTTAATTAAGTTATTGG
64 ATCATTAGGCTTAATTAATTAAATTAAATAATTAAGTTATTGG
28510489 GCCTAATTGATTAAATT
1 GCCTAATTGATTAAATT
28510506 AAACAATTAA
Statistics
Matches: 102, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
105 13 0.13
106 25 0.25
107 64 0.63
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (106 bp):
GCCTAATTGATTAAATTTGTTTAATTGAACCATTAGGCCTAATTAATTAAATTATTTAATTAAAT
CATTAGGCTTAATTAATTAAATTAAATAATTAAGTTATTGG
Found at i:28517057 original size:35 final size:35
Alignment explanation
Indices: 28516987--28517235 Score: 236
Period size: 35 Copynumber: 7.1 Consensus size: 35
28516977 CACTTGATTA
* *
28516987 AAATTGTTTAATTAAG-C--TGTGCCTAATTAACT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
28517019 AAATTGTTTAATTGAA-TCATTGGGCCTAATTAATT
1 AAATTGTTTAATT-AAGTCATTGGGCCTAATTAATT
* *
28517054 AAATTGTTTAATTAAGTCATTTGGCCTCATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
**** * *
28517089 AAATTAAACAATTAAGTTATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* ** * *
28517124 GAATTTGTTTAATTAAGTCATTAAGCCTACTTGATT
1 -AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* ** * *
28517160 AAAATTGTTTAATTAAATTGTCGGGCTTAATTAATT
1 -AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* * *
28517196 AAATTTTTTAATTAAGTTATTGGGCTTAATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
28517231 AAATT
1 AAATT
28517236 AAACAATTAA
Statistics
Matches: 175, Mismatches: 36, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
32 13 0.07
33 3 0.02
34 2 0.01
35 106 0.61
36 51 0.29
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.44
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
Found at i:28520132 original size:163 final size:162
Alignment explanation
Indices: 28519857--28520189 Score: 497
Period size: 163 Copynumber: 2.0 Consensus size: 162
28519847 TATATCTCCT
* *
28519857 ACCAAAACCGCACTTAAGTCTGTCCGTAAACATCATAATAACGTAGACCGCCACACATAATGAGG
1 ACCAAAACCGCACTTAAGTCTATCCGTAAACAGCATAATAACGTAGACCGCCACACATAATGAGG
* *
28519922 TACACATCTCGCTCAAGCCACTTAAGCCTACAAACTGGAATCTCATGCACACCTCACGATCCATA
66 TACACATCTCGCTCAAGCCACTTAAGCCTACAAACTGGAACCTCATGCACACCGCACGATCCATA
* * *
28519987 TCCAGCTGACCGAATTTCGTGGTACACGTCCA
131 TACAGCGGACCGAATTTCATGGTACACGTCCA
* * *
28520019 ACCAAAACCGCACTTAAGTTTATCCGTAAGCCAGCATAATAACGTAGACCGCCACTCATAATGAG
1 ACCAAAACCGCACTTAAGTCTATCCGTAA-ACAGCATAATAACGTAGACCGCCACACATAATGAG
* * *
28520084 GTCCACATCTCGTTCAAGCCACTTAAG-CTGACAAATTGGAACCTCATGCACACCGCACGATCCA
65 GTACACATCTCGCTCAAGCCACTTAAGCCT-ACAAACTGGAACCTCATGCACACCGCACGATCCA
* *
28520148 TATACAGCGGACCGAATTTCATGGTATATGTCCA
129 TATACAGCGGACCGAATTTCATGGTACACGTCCA
*
28520182 ATCAAAAC
1 ACCAAAAC
28520190 ATGGGCCAAA
Statistics
Matches: 153, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
162 29 0.19
163 124 0.81
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.21
Consensus pattern (162 bp):
ACCAAAACCGCACTTAAGTCTATCCGTAAACAGCATAATAACGTAGACCGCCACACATAATGAGG
TACACATCTCGCTCAAGCCACTTAAGCCTACAAACTGGAACCTCATGCACACCGCACGATCCATA
TACAGCGGACCGAATTTCATGGTACACGTCCA
Found at i:28528574 original size:60 final size:60
Alignment explanation
Indices: 28528422--28528601 Score: 281
Period size: 62 Copynumber: 3.0 Consensus size: 60
28528412 NNNNNNNNNT
*
28528422 AATTGAAATTCCTAGACTTGACCTAGGCTCGACCTATCTCACAAAATAGGTTCGATTTAAAA
1 AATTGAAATTCCTAGACTTGACCTAGGCTCGACCTATCTCAC-AAACAGGTTCGATTT-AAA
*
28528484 AATTGAAATTCCTAGACTTGACCTAGGCTCGACCCATCTCACAAACAGGTTCGATTTAAA
1 AATTGAAATTCCTAGACTTGACCTAGGCTCGACCTATCTCACAAACAGGTTCGATTTAAA
* * * *
28528544 AATTAAAATTCTTAGACTTAATCTAGGCTCGACCTATCTCA-AAACAGGTTCGATTTAA
1 AATTGAAATTCCTAGACTTGACCTAGGCTCGACCTATCTCACAAACAGGTTCGATTTAA
28528602 TTCACAAATG
Statistics
Matches: 111, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
59 17 0.15
60 39 0.35
61 14 0.13
62 41 0.37
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (60 bp):
AATTGAAATTCCTAGACTTGACCTAGGCTCGACCTATCTCACAAACAGGTTCGATTTAAA
Found at i:28531097 original size:35 final size:35
Alignment explanation
Indices: 28531027--28531275 Score: 236
Period size: 35 Copynumber: 7.1 Consensus size: 35
28531017 CACTTGATTA
* *
28531027 AAATTGTTTAATTAAG-C--TGTGCCTAATTAACT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
28531059 AAATTGTTTAATTGAA-TCATTGGGCCTAATTAATT
1 AAATTGTTTAATT-AAGTCATTGGGCCTAATTAATT
* * *
28531094 AAATTATTTAATTAAGTCATTGGGCTTAATTAGTT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
**** * * *
28531129 AAATTAAACAATTAAGTTATTGGGTCTAATTGATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* * * *
28531164 GAATTTGTTTAATTAAGTCATTAGGCCTACTTGATT
1 -AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* ** * *
28531200 AAAATTGTTTAATTAAATTGTTAGGCTTAATTAATT
1 -AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* *
28531236 AAATTGTTTAATTAAGTTATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
28531271 AAATT
1 AAATT
28531276 AAATAATTAA
Statistics
Matches: 176, Mismatches: 35, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
32 13 0.07
33 3 0.02
34 2 0.01
35 104 0.59
36 54 0.31
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
Found at i:28531198 original size:36 final size:36
Alignment explanation
Indices: 28531020--28531296 Score: 196
Period size: 35 Copynumber: 7.9 Consensus size: 36
28531010 TCTCAAGCAC
* *
28531020 TTGATTAAAATTGTTTAATTAAGCT-GT--GCCTAA
1 TTGATTAAAATTGTTTAATTAAGTTATTAGGCCTAA
* * * *
28531053 TTAACT-AAATTGTTTAATTGAA-TCATTGGGCCTAA
1 TTGATTAAAATTGTTTAATT-AAGTTATTAGGCCTAA
* * * * *
28531088 TTAATT-AAATTATTTAATTAAGTCATTGGGCTTAA
1 TTGATTAAAATTGTTTAATTAAGTTATTAGGCCTAA
**** * *
28531123 TT-AGTT-AAATTAAACAATTAAGTTATTGGGTCTAA
1 TTGA-TTAAAATTGTTTAATTAAGTTATTAGGCCTAA
* * * *
28531158 TTGATTGAATTTGTTTAATTAAGTCATTAGGCCTAC
1 TTGATTAAAATTGTTTAATTAAGTTATTAGGCCTAA
* * *
28531194 TTGATTAAAATTGTTTAATTAAATTGTTAGGCTTAA
1 TTGATTAAAATTGTTTAATTAAGTTATTAGGCCTAA
* *
28531230 TTAATT-AAATTGTTTAATTAAGTTATTGGGCCTAA
1 TTGATTAAAATTGTTTAATTAAGTTATTAGGCCTAA
***
28531265 TTGATT-AAATTAAATAATTAAGTTAATTAGGC
1 TTGATTAAAATTGTTTAATTAAGTT-ATTAGGC
28531297 TTCTTAAGGA
Statistics
Matches: 195, Mismatches: 40, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
32 13 0.07
33 7 0.04
34 3 0.02
35 111 0.57
36 61 0.31
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (36 bp):
TTGATTAAAATTGTTTAATTAAGTTATTAGGCCTAA
Found at i:28531238 original size:107 final size:106
Alignment explanation
Indices: 28531047--28531275 Score: 273
Period size: 107 Copynumber: 2.2 Consensus size: 106
28531037 ATTAAGCTGT
* * * *
28531047 GCCTAATTAACTAAA-TTGTTTAATTGAATCATTGGGCCTAATTAATTAAATTATTTAATTAAGT
1 GCCTAATTGATTAAATTTGTTTAATTGAATCATTAGGCCTAATTAATTAAATTATTTAATTAAAT
* *
28531111 CATTGGGCTTAATTAGTTAAATTAAACAATTAAGTTATTGG
66 CATTAGGCTTAATTAATTAAATTAAACAATTAAGTTATTGG
* * * * *
28531152 GTCTAATTGATTGAATTTGTTTAATT-AAGTCATTAGGCCTACTTGATTAAAATTGTTTAATTAA
1 GCCTAATTGATTAAATTTGTTTAATTGAA-TCATTAGGCCTAATTAATT-AAATTATTTAATTAA
** ****
28531216 ATTGTTAGGCTTAATTAATTAAATTGTTTAATTAAGTTATTGG
64 ATCATTAGGCTTAATTAATTAAATTAAACAATTAAGTTATTGG
28531259 GCCTAATTGATTAAATT
1 GCCTAATTGATTAAATT
28531276 AAATAATTAA
Statistics
Matches: 102, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
105 13 0.13
106 26 0.25
107 63 0.62
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (106 bp):
GCCTAATTGATTAAATTTGTTTAATTGAATCATTAGGCCTAATTAATTAAATTATTTAATTAAAT
CATTAGGCTTAATTAATTAAATTAAACAATTAAGTTATTGG
Found at i:28531295 original size:71 final size:70
Alignment explanation
Indices: 28531085--28531298 Score: 243
Period size: 71 Copynumber: 3.0 Consensus size: 70
28531075 TCATTGGGCC
* * *
28531085 TAATTAATTAAATTATTTAATTAAGTCATTGGGCTTAATT-AGTTAAATTAAACAATTAAGTTAT
1 TAATTAATTAAATTGTTTAATTAAGTCATTGGGCCTAATTGA-TTAAATTAAATAATTAAGTTAT
*
28531149 T-GGGT
65 TAGGCT
* * * * *** *
28531154 CTAATTGATTGAATTTGTTTAATTAAGTCATTAGGCCTACTTGATTAAAATTGTTTAATTAAATT
1 -TAATTAATT-AAATTGTTTAATTAAGTCATTGGGCCTAATTGATT-AAATTAAATAATTAAGTT
*
28531219 GTTAGGCT
63 ATTAGGCT
*
28531227 TAATTAATTAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTAAATAATTAAGTTAAT
1 TAATTAATTAAATTGTTTAATTAAGTCATTGGGCCTAATTGATTAAATTAAATAATTAAGTT-AT
28531292 TAGGCT
65 TAGGCT
28531298 T
1 T
28531299 CTTAAGGACT
Statistics
Matches: 116, Mismatches: 23, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
70 22 0.19
71 67 0.58
72 24 0.21
73 3 0.03
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (70 bp):
TAATTAATTAAATTGTTTAATTAAGTCATTGGGCCTAATTGATTAAATTAAATAATTAAGTTATT
AGGCT
Found at i:28537599 original size:35 final size:35
Alignment explanation
Indices: 28537529--28537773 Score: 246
Period size: 35 Copynumber: 7.0 Consensus size: 35
28537519 CACTTGATTA
* *
28537529 AAATTGTTTAATTAA---ATTGTGCCTAATTAACT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
28537561 AAATTGTTTAATTGAA-TCATTGGGCCTAATTAATT
1 AAATTGTTTAATT-AAGTCATTGGGCCTAATTAATT
* *
28537596 AAATTGTTTAATTAAGTCATTTGGCCTCATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
**** * *
28537631 AAATTAAACAATTAAGTTATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* ** * *
28537666 GAATTTGTTTAATTAAGTCATTAAGCCTACTTGATT
1 -AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* ** *
28537702 AAAATTGTTTAATTAAATTGTTGGGCTTAATTAATT
1 -AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* *
28537738 AAATTGTTTAATTAAGTTATTGGGCTTAATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
28537773 A
1 A
28537774 GATTAAACAA
Statistics
Matches: 175, Mismatches: 33, Indels: 7
0.81 0.15 0.03
Matches are distributed among these distances:
32 13 0.07
33 2 0.01
34 2 0.01
35 106 0.61
36 52 0.30
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.44
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
Found at i:28537741 original size:107 final size:106
Alignment explanation
Indices: 28537564--28537768 Score: 250
Period size: 107 Copynumber: 1.9 Consensus size: 106
28537554 ATTAACTAAA
** * * *
28537564 TTGTTTAATTGAATCATTGGGCCTAATTAATTAAATTGTTTAATTAAGTCATTTGGCCTCATTAA
1 TTGTTTAATTGAATCATTAAGCCTAATTAATTAAATTGTTTAATTAAATCATTGGGCCTAATTAA
28537629 TTAAATTAAACAATTAAGTTATTGGGCCTAATTGATTGAAT
66 TTAAATTAAACAATTAAGTTATTGGGCCTAATTGATTGAAT
* * ** *
28537670 TTGTTTAATT-AAGTCATTAAGCCTACTTGATTAAAATTGTTTAATTAAATTGTTGGGCTTAATT
1 TTGTTTAATTGAA-TCATTAAGCCTAATTAATT-AAATTGTTTAATTAAATCATTGGGCCTAATT
**** *
28537734 AATTAAATTGTTTAATTAAGTTATTGGGCTTAATT
64 AATTAAATTAAACAATTAAGTTATTGGGCCTAATT
28537769 AATTAGATTA
Statistics
Matches: 82, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
105 2 0.02
106 25 0.30
107 55 0.67
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (106 bp):
TTGTTTAATTGAATCATTAAGCCTAATTAATTAAATTGTTTAATTAAATCATTGGGCCTAATTAA
TTAAATTAAACAATTAAGTTATTGGGCCTAATTGATTGAAT
Found at i:28537768 original size:18 final size:17
Alignment explanation
Indices: 28537710--28537773 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 17
28537700 TTAAAATTGT
*
28537710 TTAATTAAATTGTTGGGC
1 TTAATT-AATTATTGGGC
*
28537728 TTAATTAATTAAATT--GT
1 TTAATTAATT--ATTGGGC
28537745 TTAATTAAGTTATTGGGC
1 TTAATTAA-TTATTGGGC
28537763 TTAATTAATTA
1 TTAATTAATTA
28537774 GATTAAACAA
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
16 3 0.08
17 16 0.42
18 17 0.45
19 2 0.05
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48
Consensus pattern (17 bp):
TTAATTAATTATTGGGC
Found at i:28537786 original size:35 final size:35
Alignment explanation
Indices: 28537579--28537796 Score: 112
Period size: 35 Copynumber: 6.1 Consensus size: 35
28537569 TAATTGAATC
* **** *
28537579 ATTGGGCCTAATTAATTAAATTGTTTAATTAAGTC
1 ATTGGGCTTAATTAATTAAATTAAACAATTAAGTT
* * *
28537614 ATTTGGCCTCATTAATTAAATTAAACAATTAAGTT
1 ATTGGGCTTAATTAATTAAATTAAACAATTAAGTT
* * * **** *
28537649 ATTGGGCCTAATTGATTGAATTTGTTTAATTAAGTC
1 ATTGGGCTTAATTAATT-AAATTAAACAATTAAGTT
** * * * **** *
28537685 ATTAAGCCTACTTGATTAAAATTGTTTAATTAAATT
1 ATTGGGCTTAATTAATT-AAATTAAACAATTAAGTT
* ****
28537721 GTTGGGCTTAATTAATTAAATTGTTTAATTAAGTT
1 ATTGGGCTTAATTAATTAAATTAAACAATTAAGTT
*
28537756 ATTGGGCTTAATTAATTAGATTAAACAATTAAGTT
1 ATTGGGCTTAATTAATTAAATTAAACAATTAAGTT
28537791 AATTGG
1 -ATTGG
28537797 ACTTCTTAAG
Statistics
Matches: 145, Mismatches: 36, Indels: 3
0.79 0.20 0.02
Matches are distributed among these distances:
35 88 0.61
36 57 0.39
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.43
Consensus pattern (35 bp):
ATTGGGCTTAATTAATTAAATTAAACAATTAAGTT
Found at i:28543208 original size:855 final size:852
Alignment explanation
Indices: 28541517--28543223 Score: 3310
Period size: 855 Copynumber: 2.0 Consensus size: 852
28541507 CGCCGTTCGG
28541517 AAGAGAGAAGGGCCGGCGAGATGCACAGAGAGAAATGGGAGTTGAGATGGAAAAAGGTTGCTTTT
1 AAGAGAGAAGGGCCGGCGAGATGCACAGAGAGAAATGGGAGTTGAGATGGAAAAAGGTTGCTTTT
28541582 ATAGTTAGGATTTTTGGGGTTAGGGGGAGGGGAGAATTGAGAGAAAATAAAAAGGAAAGTGTTGA
66 ATAGTTAGGATTTTTGGGGTTAGGGGGAGGGGAGAATTGAGAGAAAATAAAAAGGAAAGTGTTGA
28541647 GCTGACCAGCCCAAGCTCGACCAACTGAGGATTGCAGGCCTTAACGGGCTCATCCAGACTAAGCC
131 GCTGACCAGCCCAAGCTCGACCAACTGAGGATTGCAGGCCTTAACGGGCTCATCCAGACTAAGCC
28541712 CATTGGAGATTTATTTTCCTAGCCCATGTTTCATTGCTTATTTAATTTTTATTATTTTATGTGTA
196 CATTGGAGATTTATTTTCCTAGCCCATGTTTCATTGCTTATTTAATTTTTATTATTTTATGTGTA
28541777 TAATTCAATTTATGAAATTGATAAAAATAGTAATTAAAAAATAAACACGTGATAAAGTTAAATTC
261 TAATTCAATTTATGAAATTGATAAAAATAGTAATTAAAAAATAAACACGTGATAAAGTTAAATTC
28541842 CTACGCAAATAAATTTAATATTAAAAATATTAATTAATTAGGAAAATAATTTTCTTAAATTTTTC
326 CTACGCAAATAAATTTAATATTAAAAATATTAATTAATTAGGAAAATAATTTTCTTAAATTTTTC
*
28541907 AATTGAAAATGATTATGGAGCCTTATCAAAAGTGTTGGAGGGCTTCCTAAAGGTTATTTTCGCAA
391 AAGTGAAAATGATTATGGAGCCTTATCAAAAGTGTTGGAGGGCTTCCTAAAGGTTATTTTCGCAA
28541972 AGAAAATTATAAATAAATTATTACACATGAAAAATCAAAACAAATGCATAGTAAATAAAATTCTG
456 AGAAAATTATAAATAAATTATTACACATGAAAAATCAAAACAAATGCATAGTAAATAAAATTCTG
28542037 AAAAATTTGCAAATTGCATGATATTTATTTGCCTGCACCATTTGCATTTTACTTTTAGTTACACA
521 AAAAATTTGCAAATTGCATGATATTTATTTGCCTGCACCATTTGCATTTTACTTTTAGTTACACA
28542102 AGCAAGTGAAATTCTAACCAATCATAAAATTTCAAAGAAAGTTATGCGTGACATTTTCTTGAAAA
586 AGCAAGTGAAATTCTAACCAATCATAAAATTTCAAAGAAAGTTATGCGTGACATTTTCTTGAAAA
28542167 TTCCTATGTAAGAAAAAAAATTCTTAAATTTTATCAAATGTAGTGGAAATTTTAGAAAACTTTCA
651 TTCCTATGTAAGAAAAAAAATTCTTAAATTTTATCAAATGTAGTGGAAATTTTAGAAAACTTTCA
28542232 ATATTGAAGACTTTTATTTATTTCTAAGAGAAATAAAAAATATAAAAATATAAAAAGGGTATAAA
716 ATATTGAAGACTTTTATTTATTTCTAAGAGAAATAAAAAATATAAAAATATAAAAAGGGTATAAA
28542297 TTTTTTTAAAAAAATTAGAAAACAAACAAAAAGAAACAAGGAGTAAAAGATTTAATCTAAATTTT
781 TTTTTTTAAAAAAATTAGAAAACAAACAAAAAGAAACAAGGAGTAAAAGATTTAATCTAAATTTT
28542362 CTTTTTA
846 CTTTTTA
*
28542369 NAAGAGAGAAGGGCCGGCGAG-TGCACAGGGAGAAATGGGAGTTGTGAGATGGAAAAAGGTTGCT
1 -AAGAGAGAAGGGCCGGCGAGATGCACAGAGAGAAATGGGAG-T-TGAGATGGAAAAAGGTTGCT
28542433 TTTATAGTTAGGATTTTTGGGGTTAGGGGGAGGGGAGAATTGAGAGAAAATAAAAAGGAAAGTGT
63 TTTATAGTTAGGATTTTTGGGGTTAGGGGGAGGGGAGAATTGAGAGAAAATAAAAAGGAAAGTGT
28542498 TGAGCTGACCAGCCCAAGCTCGACCAACTGAGGATTGCAGGCCTTAACGGGCTCATCCAGACTAA
128 TGAGCTGACCAGCCCAAGCTCGACCAACTGAGGATTGCAGGCCTTAACGGGCTCATCCAGACTAA
28542563 GCCCATTGGAGATTTATTTTCCTAGCCCATGTTTCATTGCTTATTTAATTTTTATTATTTTATGT
193 GCCCATTGGAGATTTATTTTCCTAGCCCATGTTTCATTGCTTATTTAATTTTTATTATTTTATGT
28542628 GTATAATTCAATTTATGAAATTGATAAAAATAGTAATTAAAAAATAAACACGTGATAAAGTTAAA
258 GTATAATTCAATTTATGAAATTGATAAAAATAGTAATTAAAAAATAAACACGTGATAAAGTTAAA
28542693 TTCCTACGCAAATAAATTTAATATTTAAAAATATTAATTAATTAGGAAAATAATTTTCTTAAATT
323 TTCCTACGCAAATAAATTTAATA-TTAAAAATATTAATTAATTAGGAAAATAATTTTCTTAAATT
28542758 TTTCAAGTGAAAATGATTATGGAGCCTTATCAAAAGTGTTGGAGGGCTTCCTAAAGGTTATTTTC
387 TTTCAAGTGAAAATGATTATGGAGCCTTATCAAAAGTGTTGGAGGGCTTCCTAAAGGTTATTTTC
28542823 GCAAAGAAAATTATAAATAAATTATTACACATGAAAAATCAAAACAAATGCATAGTAAATAAAAT
452 GCAAAGAAAATTATAAATAAATTATTACACATGAAAAATCAAAACAAATGCATAGTAAATAAAAT
28542888 TCTGAAAAATTTGCAAATTGCATGATATTTATTTGCCTGCACCATTTGCATTTTACTTTTAGTTA
517 TCTGAAAAATTTGCAAATTGCATGATATTTATTTGCCTGCACCATTTGCATTTTACTTTTAGTTA
28542953 CACAAGCAAGTGAAATTCTAACCAATCATAAAATTTCAAAGAAAGTTATGCGTGACATTTTCTTG
582 CACAAGCAAGTGAAATTCTAACCAATCATAAAATTTCAAAGAAAGTTATGCGTGACATTTTCTTG
* *
28543018 AAAATTCCTATGTGAGAAAAAAAATTCTTAAATTTTATCAAATGTAGTGGAAATTTTAGAAAATT
647 AAAATTCCTATGTAAGAAAAAAAATTCTTAAATTTTATCAAATGTAGTGGAAATTTTAGAAAACT
28543083 TTCAATATTAGAAGACTTTTATTTATTTCTAAGAGAAATAAAAAATATAAAAATATAAAAAGGGT
712 TTCAATATT-GAAGACTTTTATTTATTTCTAAGAGAAATAAAAAATATAAAAATATAAAAAGGGT
*
28543148 AT-AATTTTTTTAAAAAAATTAGAAAACAAACAAAAAGAAACAAGGAGTAAGAGATTTAATCTAA
776 ATAAATTTTTTTAAAAAAATTAGAAAACAAACAAAAAGAAACAAGGAGTAAAAGATTTAATCTAA
28543212 ATTTTCTTTTTA
841 ATTTTCTTTTTA
28543224 TAAAATATCA
Statistics
Matches: 845, Mismatches: 5, Indels: 6
0.99 0.01 0.01
Matches are distributed among these distances:
852 19 0.02
853 21 0.02
854 303 0.36
855 445 0.53
856 57 0.07
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.32
Consensus pattern (852 bp):
AAGAGAGAAGGGCCGGCGAGATGCACAGAGAGAAATGGGAGTTGAGATGGAAAAAGGTTGCTTTT
ATAGTTAGGATTTTTGGGGTTAGGGGGAGGGGAGAATTGAGAGAAAATAAAAAGGAAAGTGTTGA
GCTGACCAGCCCAAGCTCGACCAACTGAGGATTGCAGGCCTTAACGGGCTCATCCAGACTAAGCC
CATTGGAGATTTATTTTCCTAGCCCATGTTTCATTGCTTATTTAATTTTTATTATTTTATGTGTA
TAATTCAATTTATGAAATTGATAAAAATAGTAATTAAAAAATAAACACGTGATAAAGTTAAATTC
CTACGCAAATAAATTTAATATTAAAAATATTAATTAATTAGGAAAATAATTTTCTTAAATTTTTC
AAGTGAAAATGATTATGGAGCCTTATCAAAAGTGTTGGAGGGCTTCCTAAAGGTTATTTTCGCAA
AGAAAATTATAAATAAATTATTACACATGAAAAATCAAAACAAATGCATAGTAAATAAAATTCTG
AAAAATTTGCAAATTGCATGATATTTATTTGCCTGCACCATTTGCATTTTACTTTTAGTTACACA
AGCAAGTGAAATTCTAACCAATCATAAAATTTCAAAGAAAGTTATGCGTGACATTTTCTTGAAAA
TTCCTATGTAAGAAAAAAAATTCTTAAATTTTATCAAATGTAGTGGAAATTTTAGAAAACTTTCA
ATATTGAAGACTTTTATTTATTTCTAAGAGAAATAAAAAATATAAAAATATAAAAAGGGTATAAA
TTTTTTTAAAAAAATTAGAAAACAAACAAAAAGAAACAAGGAGTAAAAGATTTAATCTAAATTTT
CTTTTTA
Found at i:28544308 original size:6 final size:6
Alignment explanation
Indices: 28544297--28544325 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
28544287 CATCTAAGAT
28544297 ATATAG ATATAG ATATAG ATATAG ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATA
28544326 TAGCACTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:28548958 original size:33 final size:33
Alignment explanation
Indices: 28548916--28549028 Score: 154
Period size: 33 Copynumber: 3.3 Consensus size: 33
28548906 AAGAAAAACA
*
28548916 AGGAGAGAGGCCGACGGAAGGTTGAGATCTGAG
1 AGGAGAGAGGCCGACGGAAGGGTGAGATCTGAG
*
28548949 AGGAGAGAGGCCGACCGAAGGGTGAGATCTGAGAGGAG
1 AGGAGAGAGGCCGACGGAAGGGTGAGATCT-----GAG
*
28548987 AGGAGAGAGGTCGACGGAAGGGTGAGATCTGAG
1 AGGAGAGAGGCCGACGGAAGGGTGAGATCTGAG
28549020 AGGAGAGAG
1 AGGAGAGAG
28549029 AAGGCCGACG
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
33 40 0.56
38 31 0.44
ACGTcount: A:0.32, C:0.11, G:0.48, T:0.10
Consensus pattern (33 bp):
AGGAGAGAGGCCGACGGAAGGGTGAGATCTGAG
Found at i:28548988 original size:38 final size:38
Alignment explanation
Indices: 28548946--28549037 Score: 152
Period size: 38 Copynumber: 2.5 Consensus size: 38
28548936 GTTGAGATCT
28548946 GAGAGGAGAGAGGCCGACCGAAGGGTGAGATCTGAGAG
1 GAGAGGAGAGAGGCCGACCGAAGGGTGAGATCTGAGAG
* *
28548984 GAGAGGAGAGAGGTCGACGGAAGGGTGAGATCTGAGAG
1 GAGAGGAGAGAGGCCGACCGAAGGGTGAGATCTGAGAG
28549022 GAGA-GAGA-AGGCCGAC
1 GAGAGGAGAGAGGCCGAC
28549038 GGGAAGAGAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
36 7 0.14
37 4 0.08
38 40 0.78
ACGTcount: A:0.33, C:0.12, G:0.48, T:0.08
Consensus pattern (38 bp):
GAGAGGAGAGAGGCCGACCGAAGGGTGAGATCTGAGAG
Found at i:28559651 original size:163 final size:162
Alignment explanation
Indices: 28559376--28559706 Score: 502
Period size: 163 Copynumber: 2.0 Consensus size: 162
28559366 TATATCTCCT
* *
28559376 ACCAAAACCGCACTTAAGTCTGTCCGTAAACATCATAATAACGTAGACCGCCACACATAATGAGG
1 ACCAAAACCGCACTTAAGTCTATCCGTAAACAGCATAATAACGTAGACCGCCACACATAATGAGG
*
28559441 TACACATCTCGCTCAAGCCACTTAAGCCTACAAACTGGAATCTCATGCACACCTCACGATCCATA
66 TACACATCTCGCTCAAGCCACTTAAGCCTACAAACTGGAACCTCATGCACACCTCACGATCCATA
* *
28559506 TCCAGCTGACCGAATTTCGTGGTACACGTCCA
131 TACAGCAGACCGAATTTCGTGGTACACGTCCA
* * *
28559538 ACCAAAACCGCACTTAAGTTTATCCGTAAGCCAGCATAATAACGTAGACCGCCACTCATAATGAG
1 ACCAAAACCGCACTTAAGTCTATCCGTAA-ACAGCATAATAACGTAGACCGCCACACATAATGAG
* * *
28559603 GTCCACATCTCGTTCAAGCCACTTAAG-CTGACAAATTGGAACCTCATGCACACCTCACGATCCA
65 GTACACATCTCGCTCAAGCCACTTAAGCCT-ACAAACTGGAACCTCATGCACACCTCACGATCCA
* * *
28559667 TATACAGCAGACCGAATTTTGTGGTATATGTCCA
129 TATACAGCAGACCGAATTTCGTGGTACACGTCCA
*
28559701 ATCAAA
1 ACCAAA
28559707 GACGAAACTA
Statistics
Matches: 152, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
162 29 0.19
163 123 0.81
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.22
Consensus pattern (162 bp):
ACCAAAACCGCACTTAAGTCTATCCGTAAACAGCATAATAACGTAGACCGCCACACATAATGAGG
TACACATCTCGCTCAAGCCACTTAAGCCTACAAACTGGAACCTCATGCACACCTCACGATCCATA
TACAGCAGACCGAATTTCGTGGTACACGTCCA
Found at i:28565685 original size:8 final size:8
Alignment explanation
Indices: 28565672--28565743 Score: 74
Period size: 8 Copynumber: 8.8 Consensus size: 8
28565662 ATTCATCATC
28565672 ATTTTTTT
1 ATTTTTTT
28565680 ATTTTTTT
1 ATTTTTTT
28565688 ATTATTTTT
1 ATT-TTTTT
* *
28565697 ATCTATTT
1 ATTTTTTT
* *
28565705 -TTTATTA
1 ATTTTTTT
28565712 ATTTTTTT
1 ATTTTTTT
28565720 AATTTTTTT
1 -ATTTTTTT
28565729 AATTTTTTT
1 -ATTTTTTT
28565738 ATTTTT
1 ATTTTT
28565744 GAGCTTTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
7 5 0.09
8 26 0.47
9 24 0.44
ACGTcount: A:0.19, C:0.01, G:0.00, T:0.79
Consensus pattern (8 bp):
ATTTTTTT
Found at i:28565686 original size:10 final size:10
Alignment explanation
Indices: 28565673--28565773 Score: 67
Period size: 10 Copynumber: 9.5 Consensus size: 10
28565663 TTCATCATCA
28565673 TTTTTTTATT
1 TTTTTTTATT
28565683 TTTTTATTATT
1 TTTTT-TTATT
* *
28565694 TTTATCTATT
1 TTTTTTTATT
* *
28565704 TTTTATTAAT
1 TTTTTTTATT
*
28565714 TTTTTTAATT
1 TTTTTTTATT
*
28565724 TTTTTAATTTTT
1 TTTTT--TTATT
*
28565736 TTATTTTTGAGCT
1 TT-TTTTT-A-TT
*
28565749 TTTTTTTCTT
1 TTTTTTTATT
28565759 TTTTTTTATT
1 TTTTTTTATT
*
28565769 CTTTT
1 TTTTT
28565774 GAAGTAGGTG
Statistics
Matches: 68, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
10 41 0.60
11 11 0.16
12 10 0.15
13 6 0.09
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:28565687 original size:9 final size:9
Alignment explanation
Indices: 28565673--28565743 Score: 70
Period size: 9 Copynumber: 7.4 Consensus size: 9
28565663 TTCATCATCA
28565673 TTTTTTTATT
1 TTTTTTTA-T
28565683 TTTTTATTAT
1 TTTTT-TTAT
*
28565693 TTTTATCTAT
1 TTTT-TTTAT
*
28565703 TTTTTATTAA
1 TTTTT-TTAT
*
28565713 TTTTTTTAA
1 TTTTTTTAT
*
28565722 TTTTTTTAA
1 TTTTTTTAT
28565731 TTTTTTTAT
1 TTTTTTTAT
28565740 TTTT
1 TTTT
28565744 GAGCTTTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
9 26 0.48
10 24 0.44
11 4 0.07
ACGTcount: A:0.18, C:0.01, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:28566105 original size:59 final size:59
Alignment explanation
Indices: 28566045--28566693 Score: 685
Period size: 59 Copynumber: 10.6 Consensus size: 59
28566035 TCTATATTTG
* * *
28566045 ATCTAGACTCGACCTATCTC-CAAACAGGTTCGACTTAAAAATTGAAATTCCTAGACTTG
1 ATCTAGGCTCGACCTATCTCAC-AACAGGTTCGATTTAAAAATTGAAATTCCTAGACTTA
* *
28566104 ATCTAGGCTCGACCTATCTCACAACAGGTTCGACTTAAAGAATTGAAATTCCTAGACTTG
1 ATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAA-AATTGAAATTCCTAGACTTA
* * *
28566164 A-CTTAGGCTCGACCTATCTCACAAAACAGGTTCAATTTTAAAAAATGAAATTCCTAAACTTA
1 ATC-TAGGCTCGACCTATCTCAC--AACAGGTTCGA-TTTAAAAATTGAAATTCCTAGACTTA
* * * * * *
28566226 ATATAAGCTCGACTTATTTCACAACAGGTTCGATTTAAAAATTAAAATTCCTAGACTTT
1 ATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTGAAATTCCTAGACTTA
* * ** *
28566285 ATCTAGGATCAACCTATCTCACAACAGGTTTAATTT-AAAATTGAAATTCCTAAACTTA
1 ATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTGAAATTCCTAGACTTA
* *
28566343 ATCTAGGCTTGACCTATCTCACAACAGGTTCGATTTAAACAAAATTGAAATTCCTAAACTTA
1 ATCTAGGCTCGACCTATCTCACAACAGGTTCGATTT--A-AAAATTGAAATTCCTAGACTTA
* * * *
28566405 ATTTAGGCTCGACCTATCTCAAAACAAAACAGGCTCGATTTTAAAAAAAAAATTAAAATTCTTAG
1 ATCTAGGCTCGACCTATCTC---AC--AACAGGTTCGA-TTT-----AAAAATTGAAATTCCTAG
*
28566470 ACTTG
55 ACTTA
* * * * *
28566475 A-CTTAGGCTCGACCCATCTCACAAATAGGTTTGATTTAAAAATTAAAATTCCTAGACTTG
1 ATC-TAGGCTCGACCTATCTCAC-AACAGGTTCGATTTAAAAATTGAAATTCCTAGACTTA
28566535 ATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTGAAATTCCTAGACTTA
1 ATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTGAAATTCCTAGACTTA
* * *
28566594 ATCTAGGTTTGACCTATCTCACAACAGGTTCGATTTAAACAAAATTGAAATTCCTAAACTTA
1 ATCTAGGCTCGACCTATCTCACAACAGGTTCGATTT--A-AAAATTGAAATTCCTAGACTTA
* * * * * *
28566656 ATTTAGGTTAGACCTATATCAAAACAGGTTCGACTTAA
1 ATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAA
28566694 TTCATAAATG
Statistics
Matches: 508, Mismatches: 57, Indels: 50
0.83 0.09 0.08
Matches are distributed among these distances:
58 50 0.10
59 155 0.31
60 93 0.18
61 2 0.00
62 136 0.27
63 5 0.01
65 5 0.01
66 9 0.02
67 12 0.02
68 3 0.01
70 35 0.07
71 3 0.01
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (59 bp):
ATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTGAAATTCCTAGACTTA
Found at i:28580430 original size:22 final size:23
Alignment explanation
Indices: 28580387--28580430 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
28580377 TATATCTAAA
* *
28580387 TTACATTATCTTTTTAATAAATC
1 TTACATTATCTATTTAAAAAATC
28580410 TTACATTAT-TATTTAAAAAAT
1 TTACATTATCTATTTAAAAAAT
28580431 ATTCACATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (23 bp):
TTACATTATCTATTTAAAAAATC
Found at i:28580438 original size:23 final size:23
Alignment explanation
Indices: 28580386--28580438 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
28580376 ATATATCTAA
* *
28580386 ATTACATTATCTTTTTAATAAAT
1 ATTACATTATCTATTTAAAAAAT
*
28580409 CTTACATTAT-TATTTAAAAAAT
1 ATTACATTATCTATTTAAAAAAT
28580431 ATTCACAT
1 ATT-ACAT
28580439 ATAGATGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTACATTATCTATTTAAAAAAT
Found at i:28585597 original size:119 final size:121
Alignment explanation
Indices: 28585390--28585622 Score: 362
Period size: 119 Copynumber: 1.9 Consensus size: 121
28585380 AAAAGGCTCT
* **
28585390 ATTAAGTCTTCACCTAATCCTTCAAAAGAAAAAAACAAAATAAAGTCATTCCCAAAGGTTCACGT
1 ATTAAGTCGTCACCTAATCCTTCAAAAG-AAAAAACAAAATAAAGTCAACCCCAAAGGTTCACGT
*
28585455 CTCTTTTCACCTCCCCTGCAAGCAATCTCTTTGCAGTACAAATAAAGGATAGGCTTG
65 CTCTTTTCACCTCCCATGCAAGCAATCTCTTTGCAGTACAAATAAAGGATAGGCTTG
* * *
28585512 ATTAAGTCGTCACCTAATCCTTCAAAAG-AAAAATATAA-AAGGTCAACCCCAAAGGTTCACGTC
1 ATTAAGTCGTCACCTAATCCTTCAAAAGAAAAAACAAAATAAAGTCAACCCCAAAGGTTCACGTC
* *
28585575 TCTTTTCACCTCCTATGCAAGCAATCTCTTTGCAGTATAAATAAAGGA
66 TCTTTTCACCTCCCATGCAAGCAATCTCTTTGCAGTACAAATAAAGGA
28585623 ACTCAATAAA
Statistics
Matches: 102, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
119 67 0.66
120 8 0.08
122 27 0.26
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.27
Consensus pattern (121 bp):
ATTAAGTCGTCACCTAATCCTTCAAAAGAAAAAACAAAATAAAGTCAACCCCAAAGGTTCACGTC
TCTTTTCACCTCCCATGCAAGCAATCTCTTTGCAGTACAAATAAAGGATAGGCTTG
Found at i:28590902 original size:18 final size:19
Alignment explanation
Indices: 28590879--28590921 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
28590869 ATGTTTTTTC
* *
28590879 TTTTTTCTTTTCTTTC-CT
1 TTTTTTCCTTTCTCTCTCT
28590897 TTTTTTCCTTTCTCTCTCT
1 TTTTTTCCTTTCTCTCTCT
28590916 TTTTTT
1 TTTTTT
28590922 AATAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTTCCTTTCTCTCTCT
Found at i:28590907 original size:19 final size:18
Alignment explanation
Indices: 28590879--28590921 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
28590869 ATGTTTTTTC
*
28590879 TTTTTTCTTT-TCTTTCCT
1 TTTTTTCTTTCTCTCT-CT
28590897 TTTTTTCCTTTCTCTCTCT
1 TTTTTT-CTTTCTCTCTCT
28590916 TTTTTT
1 TTTTTT
28590922 AATAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 6 0.27
19 12 0.55
20 4 0.18
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTTCTTTCTCTCTCT
Found at i:28591195 original size:42 final size:42
Alignment explanation
Indices: 28591136--28591220 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
28591126 AAAGACTAAG
28591136 AAAGAAAGAGCTTCCCCTATTCCCTCTCCTCCCCTCTCCCAT
1 AAAGAAAGAGCTTCCCCTATTCCCTCTCCTCCCCTCTCCCAT
28591178 AAAGAAAGAGCTTCCCCTATTCCCTCTCCTCCCCTCTCCCAT
1 AAAGAAAGAGCTTCCCCTATTCCCTCTCCTCCCCTCTCCCAT
28591220 A
1 A
28591221 GTCAAGAGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.22, C:0.45, G:0.07, T:0.26
Consensus pattern (42 bp):
AAAGAAAGAGCTTCCCCTATTCCCTCTCCTCCCCTCTCCCAT
Found at i:28591581 original size:9 final size:9
Alignment explanation
Indices: 28591567--28591616 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
28591557 TTTTCTAATC
28591567 TTTTTTCTT
1 TTTTTTCTT
28591576 TTTTTTCATT
1 TTTTTTC-TT
**
28591586 TTTCCTCTT
1 TTTTTTCTT
28591595 TTTTTTCTCT
1 TTTTTTCT-T
*
28591605 TTTTCTCTT
1 TTTTTTCTT
28591614 TTT
1 TTT
28591617 AGTTTTCCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
9 19 0.56
10 15 0.44
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:28591594 original size:19 final size:19
Alignment explanation
Indices: 28591572--28591616 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
28591562 TAATCTTTTT
28591572 TCTTTTTTTTCAT-TTTTCC
1 TCTTTTTTTTC-TCTTTTCC
*
28591591 TCTTTTTTTTCTCTTTTTC
1 TCTTTTTTTTCTCTTTTCC
28591610 TCTTTTT
1 TCTTTTT
28591617 AGTTTTCCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (19 bp):
TCTTTTTTTTCTCTTTTCC
Found at i:28599109 original size:163 final size:162
Alignment explanation
Indices: 28598806--28599293 Score: 638
Period size: 163 Copynumber: 3.0 Consensus size: 162
28598796 AAAAGCAGAC
* * * * * *
28598806 CGAATTTAGTGGTATATGTCCTACCAAAACCGCACTTAAGTCTGTCCGCAAACATCATAATGACG
1 CGAATTTCGTGGTATATGTCCAACTAAAACCGCACTTAAGTCTATCCGCAATCATCATAATAACG
* * * * ** **
28598871 TAGACCGCCACGCATAATGAGGTACACATCTATTTCAAGTCACTTTCGCGAACAAACTGGAACCT
66 TAGACCGCCACTCATAATGAGGTCCACATCTAGTTCAAGCCACTTAAGCTTACAAACTGGAACCT
* *
28598936 CATCCACACCTCACGATCCATATCCAGTTGAT
131 CATGCACACCTCACGATCCATATCCAGATGAT
* * * *
28598968 CGAATTTCGAGGTATTTGTCCAACTAAAACCGCACTTAAGTCTATCCGCAAGTCATCAAAATAAG
1 CGAATTTCGTGGTATATGTCCAACTAAAACCGCACTTAAGTCTATCCGCAA-TCATCATAATAAC
* * * * *
28599033 GTAGACCGTCACTCACAATGTGGTCCACATCTCGTTCAAGCCACTTAAGCTTACAAATTGGAACC
65 GTAGACCGCCACTCATAATGAGGTCCACATCTAGTTCAAGCCACTTAAGCTTACAAACTGGAACC
** *
28599098 TCATGCACACCTCACGATCCATATCCAGCGGAC
130 TCATGCACACCTCACGATCCATATCCAGATGAT
*
28599131 CGAATTTCGTGGTATATGTCCAA-TCAAAACCGCACTTAAGTCTATCCGTAAATCATCATAATAA
1 CGAATTTCGTGGTATATGTCCAACT-AAAACCGCACTTAAGTCTATCCG-CAATCATCATAATAA
* *
28599195 CGTAGACCGCCACTCTTAATGAGGTCCACATCTAGTTCAAGCCACTTAAG-TGTACATACTGGAA
64 CGTAGACCGCCACTCATAATGAGGTCCACATCTAGTTCAAGCCACTTAAGCT-TACAAACTGGAA
*
28599259 CCTCATGCACACCTCACGATCCATAGCCAGATGAT
128 CCTCATGCACACCTCACGATCCATATCCAGATGAT
28599294 TCAAAACCGC
Statistics
Matches: 279, Mismatches: 43, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
162 47 0.17
163 230 0.82
164 2 0.01
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.25
Consensus pattern (162 bp):
CGAATTTCGTGGTATATGTCCAACTAAAACCGCACTTAAGTCTATCCGCAATCATCATAATAACG
TAGACCGCCACTCATAATGAGGTCCACATCTAGTTCAAGCCACTTAAGCTTACAAACTGGAACCT
CATGCACACCTCACGATCCATATCCAGATGAT
Found at i:28600460 original size:58 final size:59
Alignment explanation
Indices: 28600389--28600505 Score: 200
Period size: 58 Copynumber: 2.0 Consensus size: 59
28600379 ATTATCTATA
28600389 AAATCATAAGACTTTCATATAAAATCAAAATA-TTTTATTGAATTACATACATTGATAG
1 AAATCATAAGACTTTCATATAAAATCAAAATATTTTTATTGAATTACATACATTGATAG
* * *
28600447 AAATCATAGGACTTTCATATAAAATCAGAATATTTTTATTGAATTACATATATTGATAG
1 AAATCATAAGACTTTCATATAAAATCAAAATATTTTTATTGAATTACATACATTGATAG
28600506 TCGGTGATGC
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
58 30 0.55
59 25 0.45
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (59 bp):
AAATCATAAGACTTTCATATAAAATCAAAATATTTTTATTGAATTACATACATTGATAG
Found at i:28609553 original size:119 final size:121
Alignment explanation
Indices: 28609396--28609634 Score: 297
Period size: 122 Copynumber: 2.0 Consensus size: 121
28609386 CAGGTCAAAA
* * * * *
28609396 AGGCTTGATAAGTCGTCACCTAATCCTTCAAAAG-AAAA-AAAATAAAA-GTCATTCCCGAAGGT
1 AGGCTTGAAAAGTCGTCACCCAATCCTTCAAAAGAAAAATAAAATAAAAGGCCATCCCCAAAGGT
* * * * * *
28609458 ACACGTC-TCTTTTCACCTCCTATGCACGTAATCTCTTTGCGCTATAAATAAAGGAC
66 ACACATCGT-TTTTAACCTCCTATGCAAGCAATCTCCTTACGCTATAAATAAAGGAC
*
28609514 AGGCTTGACAAAGTGGTCACCCAATCCTTCAAAAGAAAAATAAAATAAAAGGCCATCCCCAAAGG
1 AGGCTTGA-AAAGTCGTCACCCAATCCTTCAAAAGAAAAATAAAATAAAAGGCCATCCCCAAAGG
* * *
28609579 TTCGCATCGTTTTTAACCTCCTATGCAAGCAATCTCCTTACGGTATAAATAAAGGA
65 TACACATCGTTTTTAACCTCCTATGCAAGCAATCTCCTTACGCTATAAATAAAGGA
28609635 ACTCAATAAA
Statistics
Matches: 101, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
118 8 0.08
119 23 0.23
120 4 0.04
121 9 0.09
122 56 0.55
123 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.25
Consensus pattern (121 bp):
AGGCTTGAAAAGTCGTCACCCAATCCTTCAAAAGAAAAATAAAATAAAAGGCCATCCCCAAAGGT
ACACATCGTTTTTAACCTCCTATGCAAGCAATCTCCTTACGCTATAAATAAAGGAC
Found at i:28612743 original size:11 final size:11
Alignment explanation
Indices: 28612710--28612749 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
28612700 AAGTATATAT
28612710 AAAAATAAAAA
1 AAAAATAAAAA
* *
28612721 AAGAATTTAAAA
1 AA-AAATAAAAA
28612733 AAAAATAAAAA
1 AAAAATAAAAA
28612744 AAAAAT
1 AAAAAT
28612750 CCNNNNNNNN
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:28626909 original size:27 final size:28
Alignment explanation
Indices: 28626874--28626932 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 28
28626864 TGGAGCAATG
*
28626874 TTTTTTCTTTTATCTTTTCT-TCTCTTT
1 TTTTTTCTTTTATCCTTTCTCTCTCTTT
*
28626901 TTTTTTCTTTTTTCCTTTCTCTCTCTTT
1 TTTTTTCTTTTATCCTTTCTCTCTCTTT
28626929 TTTT
1 TTTT
28626933 AATAAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (28 bp):
TTTTTTCTTTTATCCTTTCTCTCTCTTT
Found at i:28626918 original size:28 final size:27
Alignment explanation
Indices: 28626874--28626932 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 27
28626864 TGGAGCAATG
28626874 TTTTTTCTTTTATCTTT-TCTTCTCTTT
1 TTTTTTCTTTTATCTTTCTC-TCTCTTT
*
28626901 TTTTTTCTTTTTTCCTTTCTCTCTCTTT
1 TTTTTTCTTTTAT-CTTTCTCTCTCTTT
28626929 TTTT
1 TTTT
28626933 AATAAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 12 0.41
28 15 0.52
29 2 0.07
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (27 bp):
TTTTTTCTTTTATCTTTCTCTCTCTTT
Found at i:28649245 original size:27 final size:27
Alignment explanation
Indices: 28649215--28649266 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
28649205 TAACGTGTCA
* *
28649215 GCCATTTGGATATTGTTTGATGTATCG
1 GCCATTTGGAAATTGTTTGAAGTATCG
28649242 GCCATTTGGAAATTGTTTGAAGTAT
1 GCCATTTGGAAATTGTTTGAAGTAT
28649267 TAGCCCCACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (27 bp):
GCCATTTGGAAATTGTTTGAAGTATCG
Found at i:28667362 original size:205 final size:205
Alignment explanation
Indices: 28666993--28667369 Score: 528
Period size: 205 Copynumber: 1.8 Consensus size: 205
28666983 CTCCCACCAG
* * * *
28666993 CATCATATTGTATTTCCTCCAACATAATCCAGATACTCTTTAATTATAACCAACTACGACATTAC
1 CATCATATTGCATTTCCTCCAACATAATCAAGATACTCTTAAATTATAACAAACTACGACATTAC
***
28667058 CAAGAAGCCATTCCATGGAAAGTAAGACTCTGGCTACAAGGGAAACACCTAGCACACCAAATAAC
66 CAAGAAGCCATTCCATGGAAAGTAAGAC-CTGAAAACAAGGGAAACACCTAGCACACCAAATAAC
*
28667123 TCTCAATTGGTCGAAATCATGCACCAAAGATTACGCATTGAATGACATATGAATTGACTTAAAAG
130 TCTCAATTGGTCGAAAGCATGCACCAAAGATTACGCATTGAATGACATATGAATTGACTTAAAAG
28667188 AATGAAATTTC
195 AATGAAATTTC
* **
28667199 CATCATCTTGCATTTCCTCTGACATAATCAAGATACTCTTCAAATTATAA-AAGACTACGACATT
1 CATCATATTGCATTTCCTCCAACATAATCAAGATACTCTT-AAATTATAACAA-ACTACGACATT
*
28667263 ACCAAGAAGCCATTCCATGG-AAGTTAAGA-CTGAAAACAAGGGAAATACCTAGCACACCAAATA
64 ACCAAGAAGCCATTCCATGGAAAG-TAAGACCTGAAAACAAGGGAAACACCTAGCACACCAAATA
* * * * *
28667326 TCTGTCAATTGGTTGACAGCATTG-GCCAAAGATTACGCATTGAA
128 ACTCTCAATTGGTCGAAAGCA-TGCACCAAAGATTACGCATTGAA
28667370 CTATCTTGTT
Statistics
Matches: 150, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
205 65 0.43
206 41 0.27
207 44 0.29
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.25
Consensus pattern (205 bp):
CATCATATTGCATTTCCTCCAACATAATCAAGATACTCTTAAATTATAACAAACTACGACATTAC
CAAGAAGCCATTCCATGGAAAGTAAGACCTGAAAACAAGGGAAACACCTAGCACACCAAATAACT
CTCAATTGGTCGAAAGCATGCACCAAAGATTACGCATTGAATGACATATGAATTGACTTAAAAGA
ATGAAATTTC
Found at i:28668502 original size:9 final size:9
Alignment explanation
Indices: 28668480--28668516 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
28668470 TACTTTCTTG
28668480 CAACAATTTT
1 CAAC-ATTTT
28668490 -AACATTTT
1 CAACATTTT
28668498 CAACATTTT
1 CAACATTTT
28668507 CAACATTTT
1 CAACATTTT
28668516 C
1 C
28668517 CTTGCACAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 5 0.19
9 21 0.81
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (9 bp):
CAACATTTT
Found at i:28668788 original size:26 final size:28
Alignment explanation
Indices: 28668741--28668799 Score: 86
Period size: 26 Copynumber: 2.2 Consensus size: 28
28668731 GAAGATAAGA
28668741 GAATAGAAAGAAAAAAATAAAAAAAAAA
1 GAATAGAAAGAAAAAAATAAAAAAAAAA
*
28668769 GAATA-AGAGAAAAAAA-AAAAAAAAAA
1 GAATAGAAAGAAAAAAATAAAAAAAAAA
*
28668795 CAATA
1 GAATA
28668800 TATCATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 14 0.48
27 10 0.34
28 5 0.17
ACGTcount: A:0.81, C:0.02, G:0.10, T:0.07
Consensus pattern (28 bp):
GAATAGAAAGAAAAAAATAAAAAAAAAA
Found at i:28669374 original size:74 final size:75
Alignment explanation
Indices: 28669296--28669452 Score: 219
Period size: 74 Copynumber: 2.1 Consensus size: 75
28669286 TAAATTTTTT
* * * *
28669296 TTTATAAATT-GAATAAATCTTACTAATAATTATAATAAAAATTATTTAAATGATCATCATTTGA
1 TTTATAAATTGGAATAAATCCTACTAATAATTATAACAAAAAATATTTAAATGATCATCATTTAA
*
28669360 TAAATATACA
66 TAAATACACA
**
28669370 TTTAT-AATTGGTTTAAATCCTACTAATAATTATAACAAAAAATATTTAAATGATCATCATTTAA
1 TTTATAAATTGGAATAAATCCTACTAATAATTATAACAAAAAATATTTAAATGATCATCATTTAA
* *
28669434 TGAATACATA
66 TAAATACACA
28669444 TTTATAAAT
1 TTTATAAAT
28669453 ATATATTTTA
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
73 4 0.06
74 65 0.90
75 3 0.04
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (75 bp):
TTTATAAATTGGAATAAATCCTACTAATAATTATAACAAAAAATATTTAAATGATCATCATTTAA
TAAATACACA
Found at i:28670658 original size:29 final size:29
Alignment explanation
Indices: 28670626--28670687 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
28670616 AATAATGTTA
*
28670626 TTTAGATATATTTAAATAAAA-TTTTATTT
1 TTTA-ATATATTTAAATAAAATTTTTAATT
* *
28670655 TTTATTATATTTAATTAAAATTTTTAATT
1 TTTAATATATTTAAATAAAATTTTTAATT
28670684 TTTA
1 TTTA
28670688 TTCTGAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (29 bp):
TTTAATATATTTAAATAAAATTTTTAATT
Found at i:28670668 original size:28 final size:29
Alignment explanation
Indices: 28670632--28670689 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
28670622 GTTATTTAGA
*
28670632 TATATTTAAATAAAA-TTTTATTTTTTAT
1 TATATTTAAATAAAATTTTTAATTTTTAT
*
28670660 TATATTTAATTAAAATTTTTAATTTTTAT
1 TATATTTAAATAAAATTTTTAATTTTTAT
28670689 T
1 T
28670690 CTGAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
TATATTTAAATAAAATTTTTAATTTTTAT
Found at i:28690181 original size:19 final size:21
Alignment explanation
Indices: 28690142--28690188 Score: 71
Period size: 19 Copynumber: 2.3 Consensus size: 21
28690132 ATAAATATGA
*
28690142 TATTTTAAAAAGTTCTTAAAT
1 TATTTTTAAAAGTTCTTAAAT
28690163 TATTTTTAAAA-TT-TTAAAT
1 TATTTTTAAAAGTTCTTAAAT
28690182 TATTTTT
1 TATTTTT
28690189 TATTTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 13 0.52
20 2 0.08
21 10 0.40
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TATTTTTAAAAGTTCTTAAAT
Found at i:28712000 original size:2 final size:2
Alignment explanation
Indices: 28711995--28712031 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
28711985 TTATGATGTT
28711995 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28712032 GGATGTGATA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28724161 original size:21 final size:20
Alignment explanation
Indices: 28724128--28724169 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
28724118 ATATTTAAGT
28724128 TTATAATACTAAA-TATTAAA
1 TTATAATACTAAAGTA-TAAA
*
28724148 TTATGATACATAAAGTATAAA
1 TTATAATAC-TAAAGTATAAA
28724169 T
1 T
28724170 AGTTCAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 8 0.42
21 9 0.47
22 2 0.11
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (20 bp):
TTATAATACTAAAGTATAAA
Found at i:28724422 original size:15 final size:16
Alignment explanation
Indices: 28724391--28724425 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28724381 ATAATTTTTT
*
28724391 AATTTTTAAAAATTAA
1 AATTATTAAAAATTAA
28724407 AATTATTAAAAA-TAA
1 AATTATTAAAAATTAA
28724422 AATT
1 AATT
28724426 CACGTAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTATTAAAAATTAA
Found at i:28724690 original size:19 final size:20
Alignment explanation
Indices: 28724663--28724705 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
28724653 ATTAAATAAA
*
28724663 ATTTGTAAAGTTAT-TTTATT
1 ATTTGTAAA-TTATATTAATT
28724683 ATTT-TAAATTATATTAATT
1 ATTTGTAAATTATATTAATT
28724702 ATTT
1 ATTT
28724706 AATAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 13 0.62
20 4 0.19
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
ATTTGTAAATTATATTAATT
Found at i:28726258 original size:18 final size:17
Alignment explanation
Indices: 28726232--28726265 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
28726222 AAAAGTTATT
28726232 ATAAAAATTTTATAAAAA
1 ATAAAAATTTT-TAAAAA
*
28726250 ATAATAATTTTTAAAA
1 ATAAAAATTTTTAAAA
28726266 TTAAGTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAAAAATTTTTAAAAA
Found at i:28727896 original size:51 final size:52
Alignment explanation
Indices: 28727801--28727898 Score: 121
Period size: 51 Copynumber: 1.9 Consensus size: 52
28727791 NNNNNNNNNN
*
28727801 GATTGAAAATATTAATAATTGGTAATTTAATTTATAATTTAAATATTATTAT
1 GATTGAAAATATTAATAATTGGTAATTTAATTTATAATTAAAATATTATTAT
* * *
28727853 GATT-AAAATATTAATACTT-TTAA-TTAATTTTTAAATTCAAAATATT
1 GATTGAAAATATTAATAATTGGTAATTTAATTTAT-AATT-AAAATATT
28727899 TTGTAATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
49 8 0.20
50 7 0.17
51 21 0.52
52 4 0.10
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (52 bp):
GATTGAAAATATTAATAATTGGTAATTTAATTTATAATTAAAATATTATTAT
Found at i:28730689 original size:28 final size:29
Alignment explanation
Indices: 28730635--28730694 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
28730625 TTTATAATTA
* * * *
28730635 AAAAAAAATTAAACTTTACTT-TTTAAAT
1 AAAAAAAATTAAACATTAATTAATAAAAT
*
28730663 AAAAAAAATTATACATTAATTAATAAAAT
1 AAAAAAAATTAAACATTAATTAATAAAAT
28730692 AAA
1 AAA
28730695 TATTTAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (29 bp):
AAAAAAAATTAAACATTAATTAATAAAAT
Found at i:28753554 original size:2 final size:2
Alignment explanation
Indices: 28753547--28753574 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28753537 TTATTCTCAA
28753547 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
28753575 TTGAGATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28761431 original size:12 final size:12
Alignment explanation
Indices: 28761414--28761517 Score: 111
Period size: 12 Copynumber: 8.7 Consensus size: 12
28761404 TCATTTTTTC
*
28761414 TCTTCCTTCTTT
1 TCTTCTTTCTTT
*
28761426 TCTTCCTTCTTT
1 TCTTCTTTCTTT
* *
28761438 TCCTCTTTCTTC
1 TCTTCTTTCTTT
*
28761450 TCTTCTTTCTTC
1 TCTTCTTTCTTT
*
28761462 TCCTCTTT-TTT
1 TCTTCTTTCTTT
*
28761473 CTCCTCTTTCTTT
1 -TCTTCTTTCTTT
*
28761486 TCCTCTTTCTTT
1 TCTTCTTTCTTT
*
28761498 TCTTCTTTCTTC
1 TCTTCTTTCTTT
28761510 TCTTCTTT
1 TCTTCTTT
28761518 GGCAGGTCCA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
11 2 0.02
12 77 0.94
13 3 0.04
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (12 bp):
TCTTCTTTCTTT
Found at i:28761453 original size:24 final size:24
Alignment explanation
Indices: 28761411--28761517 Score: 124
Period size: 24 Copynumber: 4.5 Consensus size: 24
28761401 TTTTCATTTT
* * * *
28761411 TTCTCTTCCTTCTTTTCTTCCTTC
1 TTCTCCTCTTTCTTCTCTTCTTTC
*
28761435 TTTTCCTCTTTCTTCTCTTCTTTC
1 TTCTCCTCTTTCTTCTCTTCTTTC
* *
28761459 TTCTCCTCTTTTTTCTCCTCTTTC
1 TTCTCCTCTTTCTTCTCTTCTTTC
* *
28761483 TTTTCCTCTTTCTTTTCTTCTTTC
1 TTCTCCTCTTTCTTCTCTTCTTTC
*
28761507 TTCTCTTCTTT
1 TTCTCCTCTTT
28761518 GGCAGGTCCA
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (24 bp):
TTCTCCTCTTTCTTCTCTTCTTTC
Found at i:28764412 original size:18 final size:20
Alignment explanation
Indices: 28764389--28764435 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
28764379 TAAAAAATTA
28764389 TTTAAAAAAAA-T-CTTATT
1 TTTAAAAAAAATTACTTATT
*
28764407 TTTAAAAAAAATTACTTTTT
1 TTTAAAAAAAATTACTTATT
28764427 TTTAAAAAA
1 TTTAAAAAA
28764436 CTTCTCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 11 0.42
19 1 0.04
20 14 0.54
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAAAAAAAATTACTTATT
Found at i:28775442 original size:40 final size:40
Alignment explanation
Indices: 28775387--28775467 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
28775377 GAGAGAGAAG
*
28775387 AGGCACCATGTTGCTCAGAAATTACTCAGTAGACCAGACC
1 AGGCACCATGTTGCTCAGAAATTACTCAGCAGACCAGACC
*
28775427 AGGCACGATGTTGCTCAGAAATTACTCAGCAGACCAGACC
1 AGGCACCATGTTGCTCAGAAATTACTCAGCAGACCAGACC
28775467 A
1 A
28775468 TCATCACATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (40 bp):
AGGCACCATGTTGCTCAGAAATTACTCAGCAGACCAGACC
Done.