Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold320
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: 2598547
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 12 of 17
Found at i:1708948 original size:22 final size:22
Alignment explanation
Indices: 1708903--1708949 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1708893 AAGTAATTTT
* *
1708903 AAATGTAATAAAAAAATAATTA
1 AAATATAATAAAAAAATAAATA
1708925 AAATATAAT-AAAAAATAACATA
1 AAATATAATAAAAAAATAA-ATA
1708947 AAA
1 AAA
1708950 AAATTAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (22 bp):
AAATATAATAAAAAAATAAATA
Found at i:1709034 original size:2 final size:2
Alignment explanation
Indices: 1709027--1709052 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1709017 ATAATAAAAT
1709027 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
1709053 ATACTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1710807 original size:19 final size:20
Alignment explanation
Indices: 1710770--1710810 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1710760 TTATTTTTCA
*
1710770 TTAAAATTCATTTTTAAAGT
1 TTAAAATTCATTTTCAAAGT
*
1710790 TTAATATTC-TTTTCAAAGT
1 TTAAAATTCATTTTCAAAGT
1710809 TT
1 TT
1710811 TTAAATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (20 bp):
TTAAAATTCATTTTCAAAGT
Found at i:1711639 original size:12 final size:11
Alignment explanation
Indices: 1711624--1711669 Score: 58
Period size: 12 Copynumber: 4.1 Consensus size: 11
1711614 GTTAAGTTAA
1711624 ATTTTAATAAAT
1 ATTTTAAT-AAT
1711636 ATTTTAATAAT
1 ATTTTAATAAT
*
1711647 -TTTTAATATT
1 ATTTTAATAAT
1711657 ATTTTAAATAAT
1 ATTTT-AATAAT
1711669 A
1 A
1711670 ATATGAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 9 0.30
11 7 0.23
12 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATTTTAATAAT
Found at i:1711652 original size:22 final size:22
Alignment explanation
Indices: 1711625--1711668 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1711615 TTAAGTTAAA
1711625 TTTTAATAAATATTTT-AATAAT
1 TTTTAAT-AATATTTTAAATAAT
*
1711647 TTTTAATATTATTTTAAATAAT
1 TTTTAATAATATTTTAAATAAT
1711669 AATATGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAATAATATTTTAAATAAT
Found at i:1713359 original size:16 final size:17
Alignment explanation
Indices: 1713340--1713404 Score: 51
Period size: 19 Copynumber: 3.5 Consensus size: 17
1713330 ATAATTTTAT
1713340 AATTAAATTAAATAA-A
1 AATTAAATTAAATAATA
1713356 AATTTTATTAATTAAATAATA
1 AA--TTA--AATTAAATAATA
* *
1713377 ATTTAAATTAAATAGATTC
1 AATTAAATTAAATA-A-TA
1713396 AATTAAATT
1 AATTAAATT
1713405 TAAAATATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
16 2 0.05
17 9 0.23
18 4 0.10
19 12 0.31
20 10 0.26
21 2 0.05
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
AATTAAATTAAATAATA
Found at i:1714815 original size:2 final size:2
Alignment explanation
Indices: 1714775--1714799 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1714765 ATGGGAAGTT
1714775 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 T
1714800 TATGTTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1715539 original size:2 final size:2
Alignment explanation
Indices: 1715532--1715568 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1715522 TCTCATTTCC
1715532 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
1715569 TACTAATTAC
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:1716301 original size:3 final size:3
Alignment explanation
Indices: 1716293--1716319 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1716283 ATTATCCATA
1716293 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1716320 GATGACAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1717896 original size:18 final size:19
Alignment explanation
Indices: 1717869--1717912 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1717859 AATATAATTT
*
1717869 TATATATAATT-AATAAAA
1 TATATTTAATTAAATAAAA
*
1717887 TATATTTAATTAAATAATA
1 TATATTTAATTAAATAAAA
1717906 TATATTT
1 TATATTT
1717913 TAACATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TATATTTAATTAAATAAAA
Found at i:1718021 original size:18 final size:17
Alignment explanation
Indices: 1717989--1718023 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1717979 TAAAAAATTT
*
1717989 AATTTTTTAACAATTAA
1 AATTTTTTAAAAATTAA
1718006 AATTTTTTACAAAATTAA
1 AATTTTTTA-AAAATTAA
1718024 TATATTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTTTTTAAAAATTAA
Found at i:1718251 original size:18 final size:19
Alignment explanation
Indices: 1718210--1718252 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
1718200 GTCCACTATG
1718210 CTTTTGTAACTTTTTTTTT
1 CTTTTGTAACTTTTTTTTT
*
1718229 C-TTTGT-ATTTTTTTTTT
1 CTTTTGTAACTTTTTTTTT
1718246 CTTTTGT
1 CTTTTGT
1718253 TTAGAAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 11 0.50
18 10 0.45
19 1 0.05
ACGTcount: A:0.07, C:0.09, G:0.07, T:0.77
Consensus pattern (19 bp):
CTTTTGTAACTTTTTTTTT
Found at i:1718452 original size:13 final size:15
Alignment explanation
Indices: 1718408--1718456 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 15
1718398 GTTATTAAAT
*
1718408 ATTTAAAAAGATTTAA
1 ATTTAAAAATA-TTAA
1718424 A--TAAAAATATTAA
1 ATTTAAAAATATTAA
1718437 ATTTAAAAA-ATT-A
1 ATTTAAAAATATTAA
1718450 ATTTAAA
1 ATTTAAA
1718457 TTAGGTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 13 0.43
14 10 0.33
15 6 0.20
16 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (15 bp):
ATTTAAAAATATTAA
Found at i:1719433 original size:19 final size:19
Alignment explanation
Indices: 1719404--1719479 Score: 100
Period size: 19 Copynumber: 3.8 Consensus size: 19
1719394 TAAAATAACT
1719404 TATTA-ATTTATATATTTA
1 TATTATATTTATATATTTA
1719422 TATTATATTTATATATTTTTA
1 TATTATATTTATATA--TTTA
1719443 TTAAATTATATTTATATATTTA
1 -T--ATTATATTTATATATTTA
1719465 TATTATATTTATATA
1 TATTATATTTATATA
1719480 AATTTTTATA
Statistics
Matches: 52, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.10
19 23 0.44
21 5 0.10
22 5 0.10
24 14 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTATATTTATATATTTA
Found at i:1719445 original size:37 final size:35
Alignment explanation
Indices: 1719403--1719510 Score: 101
Period size: 37 Copynumber: 2.9 Consensus size: 35
1719393 ATAAAATAAC
*
1719403 TTATTAATTTATATATTTATATTATATTTATATATTT
1 TTATTAATTTATATATTTATATT-TATAT-TATATTT
*
1719440 TTATTAAATTATAT-TTATATATTTATATTATATTT
1 TTATTAATTTATATATT-TATATTTATATTATATTT
* * * *
1719475 ATATAAATTTTTATATTTTAATAATTTAAATTATAT
1 TTATTAATTTATATA-TTT-AT-ATTTATATTATAT
1719511 AAATTTTAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
35 17 0.29
36 7 0.12
37 23 0.39
38 12 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (35 bp):
TTATTAATTTATATATTTATATTTATATTATATTT
Found at i:1719455 original size:24 final size:25
Alignment explanation
Indices: 1719414--1719478 Score: 89
Period size: 24 Copynumber: 2.6 Consensus size: 25
1719404 TATTAATTTA
1719414 TATATT-TATATTATATTTATATATT
1 TATATTATA-ATTATATTTATATATT
*
1719439 TTTATTA-AATTATATTTATATATT
1 TATATTATAATTATATTTATATATT
*
1719463 TATATTATATTTATAT
1 TATATTATAATTATAT
1719479 AAATTTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 22 0.63
25 13 0.37
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TATATTATAATTATATTTATATATT
Found at i:1719456 original size:43 final size:43
Alignment explanation
Indices: 1719405--1719488 Score: 143
Period size: 43 Copynumber: 1.9 Consensus size: 43
1719395 AAAATAACTT
1719405 ATTAATTTATATATTTATATTATATTTATAT-ATTTTTATTAA
1 ATTAATTTATATATTTATATTATATTTATATAATTTTTATTAA
1719447 ATTATATTTATATATTTATATTATATTTATATAAATTTTTAT
1 ATTA-ATTTATATATTTATATTATATTTATAT-AATTTTTAT
1719489 ATTTTAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
42 4 0.10
43 27 0.69
45 8 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (43 bp):
ATTAATTTATATATTTATATTATATTTATATAATTTTTATTAA
Found at i:1719479 original size:8 final size:8
Alignment explanation
Indices: 1719409--1719467 Score: 50
Period size: 8 Copynumber: 7.0 Consensus size: 8
1719399 TAACTTATTA
1719409 ATTTATAT
1 ATTTATAT
1719417 ATTTATATTAT
1 A-TT-TA-TAT
1719428 ATTTATAT
1 ATTTATAT
1719436 ATTT-T-T
1 ATTTATAT
*
1719442 ATTAAATTAT
1 ATT-TA-TAT
1719452 ATTTATAT
1 ATTTATAT
1719460 ATTTATAT
1 ATTTATAT
1719468 TATATTTATA
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
6 4 0.10
7 1 0.02
8 19 0.45
9 6 0.14
10 8 0.19
11 4 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
ATTTATAT
Found at i:1719489 original size:10 final size:10
Alignment explanation
Indices: 1719410--1719490 Score: 56
Period size: 10 Copynumber: 7.7 Consensus size: 10
1719400 AACTTATTAA
1719410 TTTATATATT
1 TTTATATATT
* *
1719420 TATAT-TATA
1 TTTATATATT
1719429 TTTATATATT
1 TTTATATATT
*
1719439 TTTATTAAATTATA
1 TTTA-T--A-TATT
1719453 TTTATATATT
1 TTTATATATT
*
1719463 TATATTATATT
1 TTTA-TATATT
* *
1719474 TATATAAATT
1 TTTATATATT
1719484 TTTATAT
1 TTTATAT
1719491 TTTAATAATT
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
9 7 0.13
10 27 0.49
11 12 0.22
13 2 0.04
14 7 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTATATATT
Found at i:1719494 original size:19 final size:19
Alignment explanation
Indices: 1719410--1719498 Score: 50
Period size: 19 Copynumber: 4.8 Consensus size: 19
1719400 AACTTATTAA
*
1719410 TTTATATATTTATATTATATT
1 TTTATAT-TTTATA-TAAATT
*
1719431 TATATATTTT-TATTAAA--
1 TTTATATTTTATA-TAAATT
1719448 -TTATA-TTTATAT--ATT
1 TTTATATTTTATATAAATT
*
1719463 TATATTATATTTATATAAATT
1 TTTA-TAT-TTTATATAAATT
1719484 TTTATATTTTA-ATAA
1 TTTATATTTTATATAA
1719499 TTTAAATTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 21
0.68 0.06 0.26
Matches are distributed among these distances:
13 1 0.02
15 4 0.07
16 8 0.15
17 2 0.04
18 4 0.07
19 17 0.31
20 6 0.11
21 12 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATATTTTATATAAATT
Found at i:1719649 original size:2 final size:2
Alignment explanation
Indices: 1719644--1719671 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1719634 ACACACACAA
1719644 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
1719672 TCCTCCGTAC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1723861 original size:70 final size:71
Alignment explanation
Indices: 1723747--1723881 Score: 177
Period size: 70 Copynumber: 1.9 Consensus size: 71
1723737 TAAAACTTGT
* **
1723747 GATTATAAAATTTTATCGTTGGTTATTATGGTTAGTTGAAAATAACAACTGCATG-AATACTTTC
1 GATTATAAAATTTTATCGTTGGTTATAATACTTAGTTGAAAATAACAACTGCATGAAAT-CTTTC
1723811 ATCTTTC
65 ATCTTTC
* * *
1723818 GATTAT-AAATTCTTGTCGTTGGTT-TAATACTTAGTTGAAAATAACGATTGCATGAAATCTTTC
1 GATTATAAAATT-TTATCGTTGGTTATAATACTTAGTTGAAAATAACAACTGCATGAAATCTTTC
1723881 A
65 A
1723882 CCCCTTCAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
70 36 0.64
71 20 0.36
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (71 bp):
GATTATAAAATTTTATCGTTGGTTATAATACTTAGTTGAAAATAACAACTGCATGAAATCTTTCA
TCTTTC
Found at i:1728995 original size:2 final size:2
Alignment explanation
Indices: 1728988--1729018 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1728978 TGCGGTTGAA
1728988 AT AT AT AT AT A- 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
1729019 TTCAAAAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1729799 original size:26 final size:27
Alignment explanation
Indices: 1729770--1729820 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
1729760 TTATATTATC
1729770 AAAATT-AATTATTTATA-ATTAATAAA
1 AAAATTAAATT-TTTATATATTAATAAA
*
1729796 AAAATTAAATTTTTTTATATTAATA
1 AAAATTAAATTTTTATATATTAATA
1729821 TTTTTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
AAAATTAAATTTTTATATATTAATAAA
Found at i:1729850 original size:21 final size:21
Alignment explanation
Indices: 1729808--1729850 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1729798 AATTAAATTT
**
1729808 TTTTATATTAATATTTTTATA
1 TTTTATATTAATATTTAAATA
1729829 TTTTATAATTAA-ATTTAAATA
1 TTTTAT-ATTAATATTTAAATA
1729850 T
1 T
1729851 AAATATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTATATTAATATTTAAATA
Found at i:1729861 original size:16 final size:17
Alignment explanation
Indices: 1729799--1729873 Score: 50
Period size: 16 Copynumber: 4.5 Consensus size: 17
1729789 TAATAAAAAA
*
1729799 ATTAAAT-TTTTT-TAT
1 ATTAAATATTTTTAAAT
*
1729814 ATT-AATATTTTTATAT
1 ATTAAATATTTTTAAAT
* **
1729830 TTTATAATTAAATTTAAAT
1 ATTA-AA-TATTTTTAAAT
*
1729849 A-TAAATATTTTTAATT
1 ATTAAATATTTTTAAAT
1729865 ATTAAATAT
1 ATTAAATAT
1729874 CAATTTAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
14 3 0.07
15 8 0.17
16 14 0.30
17 9 0.20
18 4 0.09
19 8 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTAAATATTTTTAAAT
Found at i:1729861 original size:35 final size:35
Alignment explanation
Indices: 1729812--1729888 Score: 97
Period size: 35 Copynumber: 2.2 Consensus size: 35
1729802 AAATTTTTTT
*
1729812 ATATTAATATTTTTATATT-TTATAAT-TAAATTTAA
1 ATATAAATATTTTTA-ATTATTA-AATATAAATTTAA
*
1729847 ATATAAATATTTTTAATTATTAAATATCAATTTAA
1 ATATAAATATTTTTAATTATTAAATATAAATTTAA
1729882 AT-TAAAT
1 ATATAAAT
1729889 CAATTATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
34 11 0.29
35 27 0.71
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (35 bp):
ATATAAATATTTTTAATTATTAAATATAAATTTAA
Found at i:1730401 original size:15 final size:15
Alignment explanation
Indices: 1730381--1730420 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1730371 ACAATCTTAC
*
1730381 AAAAAAATACGAAAA
1 AAAAAAATACCAAAA
*
1730396 AAAAAAAAACCAAAA
1 AAAAAAATACCAAAA
*
1730411 AAAAGAATAC
1 AAAAAAATAC
1730421 TGCAACCGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.80, C:0.10, G:0.05, T:0.05
Consensus pattern (15 bp):
AAAAAAATACCAAAA
Found at i:1734964 original size:14 final size:15
Alignment explanation
Indices: 1734936--1734977 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
1734926 TATTACGTAA
1734936 AATAATTTAAATTTT
1 AATAATTTAAATTTT
*
1734951 AATAA-TTAATTTTT
1 AATAATTTAAATTTT
1734965 AATTAAATTTAAA
1 AA-T-AATTTAAA
1734978 AATATATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.45
15 6 0.27
16 2 0.09
17 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATAATTTAAATTTT
Found at i:1735178 original size:21 final size:20
Alignment explanation
Indices: 1735145--1735183 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1735135 TAAAATTTTA
1735145 TTATATTTAAAATTATTAAAT
1 TTATATTTAAAA-TATTAAAT
* *
1735166 TTATTTTTTAAATATTAA
1 TTATATTTAAAATATTAA
1735184 TATATATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATATTTAAAATATTAAAT
Found at i:1735775 original size:18 final size:19
Alignment explanation
Indices: 1735737--1735781 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1735727 GAAAGGGAAA
*
1735737 TTTACAATAAATATTATAT
1 TTTAAAATAAATATTATAT
1735756 TTGTAAAATAAAT-TTA-AT
1 TT-TAAAATAAATATTATAT
1735774 TTTAAAAT
1 TTTAAAAT
1735782 CTTATTAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 6 0.25
18 4 0.17
19 5 0.21
20 9 0.38
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
TTTAAAATAAATATTATAT
Found at i:1736280 original size:21 final size:21
Alignment explanation
Indices: 1736256--1736296 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1736246 TATTAATATT
1736256 ATTATATAATATATAATATAA
1 ATTATATAATATATAATATAA
* *
1736277 ATTATATATTATATTATATA
1 ATTATATAATATATAATATA
1736297 TTTTTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTATATAATATATAATATAA
Found at i:1736297 original size:12 final size:12
Alignment explanation
Indices: 1736255--1736332 Score: 51
Period size: 12 Copynumber: 6.8 Consensus size: 12
1736245 TTATTAATAT
*
1736255 TATTATATAATA
1 TATTATATATTA
1736267 TA-TA-ATA-TA
1 TATTATATATTA
*
1736276 AATTATATATTA
1 TATTATATATTA
1736288 TATTATATATT-
1 TATTATATATTA
*
1736299 T-TTAAATATTTAA
1 TATTATATA-TT-A
*
1736312 TAATTTTAT-TTA
1 T-ATTATATATTA
1736324 TATTATATA
1 TATTATATA
1736333 CAATATATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
9 3 0.06
10 11 0.22
11 14 0.27
12 16 0.31
13 3 0.06
15 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATTATATATTA
Found at i:1736307 original size:33 final size:33
Alignment explanation
Indices: 1736230--1736307 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 33
1736220 TAATTTTAAG
1736230 TTTTTAAAATATAAATTATTAATATTATTATATA
1 TTTTT-AAATATAAATTATTAATATTATTATATA
* * *
1736264 -ATATATAATATAAATTATATATTA-TATTATATA
1 TTTTTA-AATATAAATTAT-TAATATTATTATATA
1736297 TTTTTAAATAT
1 TTTTTAAATAT
1736308 TTAATAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
32 1 0.03
33 28 0.78
34 7 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
TTTTTAAATATAAATTATTAATATTATTATATA
Found at i:1738034 original size:28 final size:27
Alignment explanation
Indices: 1738003--1738084 Score: 89
Period size: 24 Copynumber: 3.0 Consensus size: 27
1737993 TATAAACATG
1738003 ATATAAAAAATAATTAAAATACTATATA
1 ATATAAAAAATAATTAAAATA-TATATA
* *
1738031 ATATAAAAAATATAATTAAGATATAAAT-
1 ATAT-AAAAA-ATAATTAAAATATATATA
*
1738059 ATAT-AAAAAT-ATTAAAATTTATATA
1 ATATAAAAAATAATTAAAATATATATA
1738084 A
1 A
1738085 AATGAACTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
24 11 0.24
25 3 0.07
26 4 0.09
28 8 0.17
29 9 0.20
30 11 0.24
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (27 bp):
ATATAAAAAATAATTAAAATATATATA
Found at i:1738048 original size:30 final size:27
Alignment explanation
Indices: 1737993--1738067 Score: 78
Period size: 30 Copynumber: 2.6 Consensus size: 27
1737983 TAATATTATT
*
1737993 TATAAACATGATATAAAAAATAATTAAAA
1 TATAAATAT-ATA-AAAAAATAATTAAAA
* *
1738022 TACTATATAATATAAAAAATATAATTAAGA
1 TA-TAAAT-ATATAAAAAA-ATAATTAAAA
1738052 TATAAATATATAAAAA
1 TATAAATATATAAAAA
1738068 TATTAAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 9 0.23
29 11 0.28
30 17 0.44
31 2 0.05
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (27 bp):
TATAAATATATAAAAAAATAATTAAAA
Found at i:1738085 original size:28 final size:27
Alignment explanation
Indices: 1738003--1738085 Score: 75
Period size: 28 Copynumber: 3.0 Consensus size: 27
1737993 TATAAACATG
*
1738003 ATATAAAAAATAATTAAAATACTATAT-A
1 ATATAAAAAAT-ATTAAAAT-TTATATAA
*
1738031 ATATAAAAAATA-T--AATTAAGATATAA
1 ATATAAAAAATATTAAAATT--TATATAA
1738057 ATATATAAAAATATTAAAATTTATATAA
1 ATATA-AAAAATATTAAAATTTATATAA
1738085 A
1 A
1738086 ATGAACTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
24 3 0.07
25 4 0.09
26 7 0.16
27 8 0.18
28 19 0.42
30 4 0.09
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (27 bp):
ATATAAAAAATATTAAAATTTATATAA
Found at i:1738345 original size:16 final size:16
Alignment explanation
Indices: 1738307--1738350 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1738297 TATTGTTTTA
*
1738307 AATTAATT-AGATAAT
1 AATTAATTAAAATAAT
* *
1738322 AATAAATTAAAATATT
1 AATTAATTAAAATAAT
1738338 AATTAATTAAAAT
1 AATTAATTAAAAT
1738351 TTTTATAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
AATTAATTAAAATAAT
Found at i:1738481 original size:14 final size:15
Alignment explanation
Indices: 1738449--1738491 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
1738439 TTTTTAATAC
*
1738449 ATAAATATCTATATT
1 ATAAATATTTATATT
1738464 -TAAATATTTA-ATT
1 ATAAATATTTATATT
1738477 ATAAAATATTTATAT
1 AT-AAATATTTATAT
1738492 AATATATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 3 0.12
14 10 0.42
15 9 0.38
16 2 0.08
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
ATAAATATTTATATT
Found at i:1739291 original size:20 final size:19
Alignment explanation
Indices: 1739267--1739310 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1739257 TCATATTTTT
*
1739267 ATTTTGATAAAATTTAATA
1 ATTTTTATAAAATTTAATA
*
1739286 ATTTTTATTAAATTTAATA
1 ATTTTTATAAAATTTAATA
1739305 ATTTTT
1 ATTTTT
1739311 TATACGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
ATTTTTATAAAATTTAATA
Found at i:1739339 original size:15 final size:14
Alignment explanation
Indices: 1739317--1739384 Score: 55
Period size: 15 Copynumber: 4.5 Consensus size: 14
1739307 TTTTTATACG
1739317 ATATATAAATATAT
1 ATATATAAATATAT
*
1739331 ATATCATAAATTTAT
1 ATAT-ATAAATATAT
*
1739346 ATTTTATAAATTATTAAT
1 A-TATATAAA-TA-T-AT
*
1739364 ATATAAAAATATAT
1 ATATATAAATATAT
*
1739378 GTATATA
1 ATATATA
1739385 TACATAACAT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
14 11 0.26
15 16 0.38
16 5 0.12
17 7 0.17
18 3 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (14 bp):
ATATATAAATATAT
Found at i:1739421 original size:19 final size:19
Alignment explanation
Indices: 1739397--1739443 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1739387 CATAACATGG
1739397 ATTAAATTATAATAAAAAA
1 ATTAAATTATAATAAAAAA
* * *
1739416 ATTAAAATATAATATAAAT
1 ATTAAATTATAATAAAAAA
1739435 ATATAAATT
1 AT-TAAATT
1739444 TTTTCTTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTAAATTATAATAAAAAA
Found at i:1739719 original size:129 final size:129
Alignment explanation
Indices: 1739489--1739748 Score: 441
Period size: 129 Copynumber: 2.0 Consensus size: 129
1739479 TTAATCTTCA
* *
1739489 CCACAATTACCTTTAATTGATTAATTATTACAAAAAGTTATCAATTTCCCTCAATTTGCTACTGT
1 CCACAATTACCTCTAATTGATTAATTATTACAAAAAGTTATCAATTTCCCTCAATTTGCAACTGT
1739554 TGATAAAATTGAAGGATAACTTGAATTTATAAGATATCCAAATGTTTAAACTTTAAAGCATCCT
66 TGATAAAATTGAAGGATAACTTGAATTTATAAGATATCCAAATGTTTAAACTTTAAAGCATCCT
* *
1739618 CCACAATTACCTCTAATTGATTAATTATTACAAAAAGTTATCATTTTCCCTCAATTTGCAATTGT
1 CCACAATTACCTCTAATTGATTAATTATTACAAAAAGTTATCAATTTCCCTCAATTTGCAACTGT
* * *
1739683 CT-ATCAAATTGAAGGATAATTTGAATTTATAAGATATCCAAATGTTTAAACTTTGAAGCATCCT
66 -TGATAAAATTGAAGGATAACTTGAATTTATAAGATATCCAAATGTTTAAACTTTAAAGCATCCT
1739747 CC
1 CC
1739749 CCATCAATAA
Statistics
Matches: 123, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
129 122 0.99
130 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (129 bp):
CCACAATTACCTCTAATTGATTAATTATTACAAAAAGTTATCAATTTCCCTCAATTTGCAACTGT
TGATAAAATTGAAGGATAACTTGAATTTATAAGATATCCAAATGTTTAAACTTTAAAGCATCCT
Found at i:1740129 original size:32 final size:31
Alignment explanation
Indices: 1740048--1740129 Score: 78
Period size: 32 Copynumber: 2.6 Consensus size: 31
1740038 AATATAAATA
* * *
1740048 TATATTCAATGCATATT-TAAATATTATATT
1 TATATTAAATACATATTAAAAATATTATATT
* * *
1740078 TATA-TATAATTCTTTTTAAAAAGTATTATATT
1 TATATTA-AATACATATTAAAAA-TATTATATT
1740110 TATATTAAATACATATTAAA
1 TATATTAAATACATATTAAA
1740130 TAATCTAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
29 1 0.03
30 11 0.28
31 3 0.08
32 23 0.57
33 2 0.05
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (31 bp):
TATATTAAATACATATTAAAAATATTATATT
Found at i:1741976 original size:2 final size:2
Alignment explanation
Indices: 1741971--1741995 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1741961 GAGGACAGAT
1741971 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 T
1741996 CAAATCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1743473 original size:2 final size:2
Alignment explanation
Indices: 1743466--1743506 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1743456 GACAGAATTG
* *
1743466 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1743507 ACGATGCAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1743580 original size:37 final size:37
Alignment explanation
Indices: 1743530--1743602 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
1743520 GTGTTACTCT
1743530 ACACTGACCAAATCACAAGAAATTATATCATATAATA
1 ACACTGACCAAATCACAAGAAATTATATCATATAATA
*
1743567 ACACTGACGAAATCACAAGAAATTATATCATATAAT
1 ACACTGACCAAATCACAAGAAATTATATCATATAAT
1743603 TGAATCCTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.51, C:0.18, G:0.07, T:0.25
Consensus pattern (37 bp):
ACACTGACCAAATCACAAGAAATTATATCATATAATA
Found at i:1748069 original size:22 final size:21
Alignment explanation
Indices: 1748044--1748084 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1748034 TAATATTATT
1748044 TAATTATTTAAATTTAAAAATA
1 TAATT-TTTAAATTTAAAAATA
* *
1748066 TAATTTTTTATTTTAAAAA
1 TAATTTTTAAATTTAAAAA
1748085 GTAAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATTTTTAAATTTAAAAATA
Found at i:1748118 original size:20 final size:20
Alignment explanation
Indices: 1748095--1748167 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
1748085 GTAAAAAAAA
*
1748095 AATTTAATTTTATATAAATT
1 AATTTAAATTTATATAAATT
* *
1748115 AATTTATATTTTAAATAAA-T
1 AATTTA-AATTTATATAAATT
* *
1748135 AGTTTAAATTTATTTAAATT
1 AATTTAAATTTATATAAATT
*
1748155 TATTTAAATTTAT
1 AATTTAAATTTAT
1748168 TTATTTTTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 9 0.20
20 24 0.55
21 11 0.25
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (20 bp):
AATTTAAATTTATATAAATT
Found at i:1748152 original size:10 final size:10
Alignment explanation
Indices: 1748137--1748170 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
1748127 AAATAAATAG
1748137 TTTAAATTTA
1 TTTAAATTTA
1748147 TTTAAATTTA
1 TTTAAATTTA
1748157 TTTAAATTTA
1 TTTAAATTTA
1748167 TTTA
1 TTTA
1748171 TTTTTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTAAATTTA
Found at i:1748221 original size:15 final size:14
Alignment explanation
Indices: 1748195--1748230 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 14
1748185 ATAAGAATAT
1748195 ATTTTTAAAATTTA
1 ATTTTTAAAATTTA
1748209 ATTTTTAATAATTTA
1 ATTTTTAA-AATTTA
1748224 ATATTTT
1 AT-TTTT
1748231 TATATTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 8 0.40
16 4 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTTTTAAAATTTA
Found at i:1748284 original size:22 final size:23
Alignment explanation
Indices: 1748256--1748313 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
1748246 ATATTTACAT
1748256 AATAATATATATTT-TAAATAAA
1 AATAATATATATTTATAAATAAA
* *
1748278 AATAATAAATATTCTATAATTAAA
1 AATAATATATATT-TATAAATAAA
1748302 AATAA-AT-TATTT
1 AATAATATATATTT
1748314 CATATTTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 1 0.03
22 16 0.52
23 2 0.06
24 12 0.39
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AATAATATATATTTATAAATAAA
Found at i:1750384 original size:23 final size:22
Alignment explanation
Indices: 1750354--1750437 Score: 89
Period size: 22 Copynumber: 3.6 Consensus size: 22
1750344 TTTGGGGTGA
*
1750354 ATAAATAAATTTTTAAGGTTTTT
1 ATAAATAAATTTTTAA-TTTTTT
1750377 ATAAATAAAATTTTGTTAATTTTTT
1 ATAAAT-AAA-TTT-TTAATTTTTT
*
1750402 ATAAAT-AATTTTATTATTTTTT
1 ATAAATAAATTTT-TAATTTTTT
*
1750424 ATAAATTAATTTTT
1 ATAAATAAATTTTT
1750438 TATGAATAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
21 1 0.02
22 18 0.33
23 14 0.26
24 3 0.06
25 14 0.26
26 4 0.07
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (22 bp):
ATAAATAAATTTTTAATTTTTT
Found at i:1750423 original size:22 final size:21
Alignment explanation
Indices: 1750354--1750440 Score: 84
Period size: 23 Copynumber: 3.8 Consensus size: 21
1750344 TTTGGGGTGA
* *
1750354 ATAAATAAATTTTTAAGGTTTTT
1 ATAAAT-AATTTTTTA-TTTTTT
1750377 ATAAATAAAATTTTGTTAATTTTTT
1 ATAAAT--AATTTT-TT-ATTTTTT
1750402 ATAAATAATTTTATTATTTTTT
1 ATAAATAATTTT-TTATTTTTT
1750424 ATAAATTAATTTTTTAT
1 ATAAA-TAATTTTTTAT
1750441 GAATAATAGT
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
22 16 0.28
23 21 0.37
24 7 0.12
25 12 0.21
26 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
ATAAATAATTTTTTATTTTTT
Found at i:1750581 original size:19 final size:20
Alignment explanation
Indices: 1750553--1750594 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1750543 AATTAAGATG
1750553 TATTTAATTATTATAT-ATT
1 TATTTAATTATTATATAATT
* *
1750572 TATTTTATTATTTTATAATT
1 TATTTAATTATTATATAATT
1750592 TAT
1 TAT
1750595 ATTTGAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTAATTATTATATAATT
Found at i:1758283 original size:36 final size:36
Alignment explanation
Indices: 1758243--1758314 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
1758233 ATAATGACCT
1758243 TTTATCACAAAGGTGGCCTGGGTTTTGACCCAGGCC
1 TTTATCACAAAGGTGGCCTGGGTTTTGACCCAGGCC
*
1758279 TTTATCACAAAGGTGGCCTGGGTTTTGACCTAGGCC
1 TTTATCACAAAGGTGGCCTGGGTTTTGACCCAGGCC
1758315 ACTCAATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.29
Consensus pattern (36 bp):
TTTATCACAAAGGTGGCCTGGGTTTTGACCCAGGCC
Found at i:1758786 original size:3 final size:3
Alignment explanation
Indices: 1758778--1758834 Score: 68
Period size: 3 Copynumber: 20.3 Consensus size: 3
1758768 GTATTAGATG
*
1758778 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A AT- TTA AT- ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
1758822 ATA AAA ATA ATA A
1 ATA ATA ATA ATA A
1758835 AATTCCTTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 7 0.15
3 39 0.85
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1759183 original size:24 final size:20
Alignment explanation
Indices: 1759142--1759183 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1759132 AAATCCAAAT
1759142 ATAAATTATAAAATAATAAA
1 ATAAATTATAAAATAATAAA
* *
1759162 ATAAA-TATATAATAATTAA
1 ATAAATTATAAAATAATAAA
1759181 ATA
1 ATA
1759184 CATTTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAATTATAAAATAATAAA
Found at i:1761528 original size:15 final size:15
Alignment explanation
Indices: 1761503--1761624 Score: 51
Period size: 15 Copynumber: 8.8 Consensus size: 15
1761493 ACAAAATTTA
*
1761503 AATATTTAAATTTAAT
1 AATA-TTAAATATAAT
1761519 AATATTAAATATAAT
1 AATATTAAATATAAT
1761534 AA-ATTATACGATAT-A-
1 AATATTA-A--ATATAAT
*
1761549 AATA-T-AATATAAA
1 AATATTAAATATAAT
1761562 AAT-TTAAA-ATAA-
1 AATATTAAATATAAT
1761574 AAT-TTATAA-A-AAT
1 AATATTA-AATATAAT
1761587 AATA-T-AA-A-AAT
1 AATATTAAATATAAT
1761598 AATA-TAAATATAAT
1 AATATTAAATATAAT
*
1761612 AAATTTTAAATAT
1 -AATATTAAATAT
1761625 TGTAAGGTAT
Statistics
Matches: 88, Mismatches: 2, Indels: 32
0.72 0.02 0.26
Matches are distributed among these distances:
11 15 0.17
12 11 0.12
13 17 0.19
14 9 0.10
15 19 0.22
16 13 0.15
17 4 0.05
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.38
Consensus pattern (15 bp):
AATATTAAATATAAT
Found at i:1761560 original size:11 final size:11
Alignment explanation
Indices: 1761517--1761612 Score: 72
Period size: 11 Copynumber: 8.5 Consensus size: 11
1761507 TTTAAATTTA
1761517 ATAATATTAAAT
1 ATAATA-TAAAT
*
1761529 ATAATA-AATT
1 ATAATATAAAT
1761539 ATACGATATAAAT
1 ATA--ATATAAAT
1761552 ATAATATAAAAAT
1 ATAATAT--AAAT
* *
1761565 TTAAAATAAA-
1 ATAATATAAAT
* *
1761575 AT-TTATAAAA
1 ATAATATAAAT
*
1761585 ATAATATAAAA
1 ATAATATAAAT
1761596 ATAATATAAAT
1 ATAATATAAAT
1761607 ATAATA
1 ATAATA
1761613 AATTTTAAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
9 5 0.07
10 9 0.13
11 30 0.44
12 9 0.13
13 15 0.22
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:1763276 original size:30 final size:31
Alignment explanation
Indices: 1763242--1763309 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 31
1763232 GTTTCTATTG
**
1763242 ATTTTTTAAATTTTAA-AATATATTGATTAA
1 ATTTTTTAAATTTTAATAATATATAAATTAA
* **
1763272 A-TTTTTAATTTTTAATTTTATATAAATTAA
1 ATTTTTTAAATTTTAATAATATATAAATTAA
1763302 ATTTTTTA
1 ATTTTTTA
1763310 TTAATAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 13 0.42
30 12 0.39
31 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (31 bp):
ATTTTTTAAATTTTAATAATATATAAATTAA
Found at i:1765246 original size:12 final size:12
Alignment explanation
Indices: 1765229--1765255 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1765219 TAGCTCTGCA
1765229 TCTTCTTTCCTC
1 TCTTCTTTCCTC
1765241 TCTTCTTTCCTC
1 TCTTCTTTCCTC
1765253 TCT
1 TCT
1765256 CTCGCCATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (12 bp):
TCTTCTTTCCTC
Found at i:1766052 original size:30 final size:30
Alignment explanation
Indices: 1766018--1766075 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1766008 CAGGGAACTA
1766018 TAAAAAAATAAAA-TTATTATATTTATTTTT
1 TAAAAAAATAAAATTTATT-TATTTATTTTT
***
1766048 TAAAATTTTAAAATTTATTTATTTATTT
1 TAAAAAAATAAAATTTATTTATTTATTT
1766076 AATAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
TAAAAAAATAAAATTTATTTATTTATTTTT
Found at i:1767327 original size:19 final size:19
Alignment explanation
Indices: 1767296--1767375 Score: 51
Period size: 19 Copynumber: 4.3 Consensus size: 19
1767286 TTGATTCGTT
1767296 TTAAAAACT-TATTTTATTA
1 TTAAAAA-TATATTTTATTA
** *
1767315 TTAAAAATATATTGAAATA
1 TTAAAAATATATTTTATTA
*
1767334 TTAAAAA-ATTATTCTATGTA
1 TTAAAAATA-TATTTTAT-TA
* *
1767354 TT--ATATATATTTTATAA
1 TTAAAAATATATTTTATTA
1767371 TTAAA
1 TTAAA
1767376 TTTAAATAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
17 3 0.07
18 11 0.24
19 28 0.61
20 4 0.09
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (19 bp):
TTAAAAATATATTTTATTA
Found at i:1767807 original size:23 final size:23
Alignment explanation
Indices: 1767741--1767840 Score: 82
Period size: 23 Copynumber: 4.4 Consensus size: 23
1767731 TTATTATTAT
*
1767741 TATAA-ATTATAAAAAATATAAA
1 TATAATATGATAAAAAATATAAA
* * *
1767763 -ATAAGT-TGAGACACAATATAAA
1 TATAA-TATGATAAAAAATATAAA
* *
1767785 TACAATATGATAAGATAAT-TAAA
1 TATAATATGATAA-AAAATATAAA
* *
1767808 TATAGTGTGATAAAAAATATAAA
1 TATAATATGATAAAAAATATAAA
1767831 TATAATATGA
1 TATAATATGA
1767841 ATATATAAAC
Statistics
Matches: 58, Mismatches: 14, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
21 4 0.07
22 17 0.29
23 33 0.57
24 4 0.07
ACGTcount: A:0.58, C:0.03, G:0.09, T:0.30
Consensus pattern (23 bp):
TATAATATGATAAAAAATATAAA
Found at i:1768141 original size:13 final size:13
Alignment explanation
Indices: 1768123--1768184 Score: 62
Period size: 13 Copynumber: 5.0 Consensus size: 13
1768113 AATTTTTTTA
1768123 TTTTTCTCTTTCT
1 TTTTTCTCTTTCT
*
1768136 TTTTTCTTTTTC-
1 TTTTTCTCTTTCT
1768148 TTTTT-T-TTTC-
1 TTTTTCTCTTTCT
1768158 TTTTTCTACTTTCT
1 TTTTTCT-CTTTCT
1768172 TTTTATC-CTTTCT
1 TTTT-TCTCTTTCT
1768185 CTCTCCCATG
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
10 9 0.21
11 2 0.05
12 5 0.12
13 21 0.49
14 4 0.09
15 2 0.05
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTCTCTTTCT
Found at i:1768170 original size:29 final size:30
Alignment explanation
Indices: 1768118--1768175 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
1768108 CACATAATTT
**
1768118 TTTTATTTTTCTCTTTCTTTTTTCTTTTTC
1 TTTTATTTTTCTCTTTCTACTTTCTTTTTC
*
1768148 TTTT-TTTTTCTTTTTCTACTTTCTTTTT
1 TTTTATTTTTCTCTTTCTACTTTCTTTTT
1768176 ATCCTTTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (30 bp):
TTTTATTTTTCTCTTTCTACTTTCTTTTTC
Found at i:1768184 original size:36 final size:35
Alignment explanation
Indices: 1768115--1768184 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 35
1768105 AAACACATAA
*
1768115 TTTTTTTATTTTTCTCTTTCTTTTTTCTTTTTCTT
1 TTTTTTTATTTTTCTCTTTCTTTTTTCTCTTTCTT
*
1768150 TTTTTTTCTTTTTCTACTTTCTTTTTATC-CTTTCT
1 TTTTTTTATTTTTCT-CTTTCTTTTT-TCTCTTTCT
1768185 CTCTCCCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
35 14 0.45
36 15 0.48
37 2 0.06
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (35 bp):
TTTTTTTATTTTTCTCTTTCTTTTTTCTCTTTCTT
Found at i:1768446 original size:12 final size:12
Alignment explanation
Indices: 1768407--1768457 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
1768397 TGATTCCATA
1768407 ATATAAATATATT
1 ATATAAA-ATATT
*
1768420 ATA-AGAATA--
1 ATATAAAATATT
1768429 AT-TAAAATATT
1 ATATAAAATATT
1768440 ATATAAAATATT
1 ATATAAAATATT
1768452 ATATAA
1 ATATAA
1768458 TATAAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
9 7 0.22
11 5 0.16
12 17 0.53
13 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (12 bp):
ATATAAAATATT
Found at i:1768452 original size:20 final size:20
Alignment explanation
Indices: 1768406--1768478 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
1768396 TTGATTCCAT
*
1768406 AATA-TAAATATATTATAAG
1 AATATTAAATATATTATAAA
1768425 AATAATTAAA-ATATTATATAA
1 AAT-ATTAAATATATTATA-AA
*
1768446 AATATT--ATATAATAT-AA
1 AATATTAAATATATTATAAA
1768463 AATAATATAAATATAT
1 AAT-AT-TAAATATAT
1768479 AGAAATTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
17 5 0.12
18 3 0.07
19 10 0.23
20 12 0.28
21 13 0.30
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (20 bp):
AATATTAAATATATTATAAA
Found at i:1768543 original size:35 final size:35
Alignment explanation
Indices: 1768439--1768545 Score: 107
Period size: 35 Copynumber: 3.1 Consensus size: 35
1768429 ATTAAAATAT
* * *
1768439 TATATAAAATATTATAT-AATATAAAATAATATAAA
1 TATATAAAA-ATTATATAAATATATAATATTTTAAA
* * *
1768474 TATATAGAAATT-TATATAATGTAT-AT-TCTT-AA
1 TATATAAAAATTATATA-AATATATAATATTTTAAA
1768506 TATATAAAAATTATATAAATATATAATATTTTAAA
1 TATATAAAAATTATATAAATATATAATATTTTAAA
1768541 TATAT
1 TATAT
1768546 TTATAACACA
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
32 19 0.33
33 10 0.18
34 8 0.14
35 20 0.35
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (35 bp):
TATATAAAAATTATATAAATATATAATATTTTAAA
Found at i:1769626 original size:26 final size:26
Alignment explanation
Indices: 1769578--1769628 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1769568 ATTTGAATAA
*
1769578 ATATTTAATAAATAAAATTTATAATT
1 ATATTTAATAAATAAAATGTATAATT
*
1769604 ATATTTAAT-AATGAAGATGTATAAT
1 ATATTTAATAAAT-AAAATGTATAAT
1769629 AATTAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (26 bp):
ATATTTAATAAATAAAATGTATAATT
Found at i:1770588 original size:2 final size:2
Alignment explanation
Indices: 1770581--1770621 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1770571 TACTCTTCTC
1770581 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1770622 ATTGAAGTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1772651 original size:2 final size:2
Alignment explanation
Indices: 1772644--1772672 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1772634 TTTTTATGAA
1772644 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1772673 AATTTTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1773711 original size:2 final size:2
Alignment explanation
Indices: 1773704--1773729 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1773694 AACCTTCTTT
1773704 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
1773730 AAAGCATTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1774637 original size:2 final size:2
Alignment explanation
Indices: 1774630--1774658 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1774620 TTTAAAACAC
1774630 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 T
1774659 GGAGTAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1775621 original size:32 final size:32
Alignment explanation
Indices: 1775584--1775661 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
1775574 TTTAGATCGG
* * *
1775584 GTCATTTTGGGTTCGGGTCATTTCGGATTCGA
1 GTCATTTCGGGTTCGGGTCACTTCGAATTCGA
**
1775616 GTCATTTCAAGTTCGGGTCACTTCGAATTCGA
1 GTCATTTCGGGTTCGGGTCACTTCGAATTCGA
*
1775648 TTCATTTCGGGTTC
1 GTCATTTCGGGTTC
1775662 AAGTTATTTC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.15, C:0.19, G:0.26, T:0.40
Consensus pattern (32 bp):
GTCATTTCGGGTTCGGGTCACTTCGAATTCGA
Found at i:1775715 original size:16 final size:16
Alignment explanation
Indices: 1775584--1775715 Score: 88
Period size: 16 Copynumber: 8.2 Consensus size: 16
1775574 TTTAGATCGG
* *
1775584 GTCATTTTGGGTTCGG
1 GTCATTTCGGGTTCGA
*
1775600 GTCATTTCGGATTCGA
1 GTCATTTCGGGTTCGA
** *
1775616 GTCATTTCAAGTTCGG
1 GTCATTTCGGGTTCGA
* **
1775632 GTCACTTCGAATTCGA
1 GTCATTTCGGGTTCGA
* *
1775648 TTCATTTCGGGTTCAA
1 GTCATTTCGGGTTCGA
* *
1775664 GTTATTTCAGGTTCGAA
1 GTCATTTCGGGTTCG-A
* * *
1775681 TTGA-TTCGAGTTC-A
1 GTCATTTCGGGTTCGA
1775695 CGTCATTTCGGGTTCGA
1 -GTCATTTCGGGTTCGA
1775712 GTCA
1 GTCA
1775716 ATCGGGTTTA
Statistics
Matches: 85, Mismatches: 27, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
14 1 0.01
15 2 0.02
16 78 0.92
17 4 0.05
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (16 bp):
GTCATTTCGGGTTCGA
Found at i:1781401 original size:16 final size:16
Alignment explanation
Indices: 1781380--1781482 Score: 88
Period size: 16 Copynumber: 6.4 Consensus size: 16
1781370 TTATTCAGTT
1781380 ATTTCGGATTCGAGTC
1 ATTTCGGATTCGAGTC
1781396 ATTTCGGATTCGAGTC
1 ATTTCGGATTCGAGTC
* *
1781412 ATTTCGAGTTTGGA-TC
1 ATTTCG-GATTCGAGTC
*
1781428 ATTCTAGG-TTC-AGGTC
1 ATT-TCGGATTCGA-GTC
*
1781444 A-TTCTGAATTCGAGTC
1 ATTTC-GGATTCGAGTC
* *
1781460 ATTTTGGGTTCGAGTC
1 ATTTCGGATTCGAGTC
1781476 ATTTCGG
1 ATTTCGG
1781483 GTTCAGATTA
Statistics
Matches: 69, Mismatches: 10, Indels: 16
0.73 0.11 0.17
Matches are distributed among these distances:
14 2 0.03
15 4 0.06
16 53 0.77
17 10 0.14
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (16 bp):
ATTTCGGATTCGAGTC
Found at i:1783000 original size:23 final size:23
Alignment explanation
Indices: 1782971--1783014 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1782961 GATCTTTAAA
*
1782971 TTTAATTTGTA-ATCAAATAAATT
1 TTTAATTTATATAT-AAATAAATT
1782994 TTTAATTTATATATAAATAAA
1 TTTAATTTATATATAAATAAA
1783015 CTCTTAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTTAATTTATATATAAATAAATT
Found at i:1783021 original size:23 final size:23
Alignment explanation
Indices: 1782972--1783021 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1782962 ATCTTTAAAT
* * *
1782972 TTAATTTGTAATCAAATAAATTT
1 TTAATTTATAATCAAATAAACTC
1782995 TTAATTTATATAT-AAATAAACTC
1 TTAATTTATA-ATCAAATAAACTC
1783018 TTAA
1 TTAA
1783022 CATAAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (23 bp):
TTAATTTATAATCAAATAAACTC
Found at i:1790799 original size:27 final size:27
Alignment explanation
Indices: 1790741--1790808 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 27
1790731 AAATAAATTG
* *
1790741 ATTTTAATTAATAAAAATATTTTATTTA
1 ATTTTAATT-ATAAAAATAATTTATTAA
1790769 ATTTTAATTATAAAAATAATTT-TTAA
1 ATTTTAATTATAAAAATAATTTATTAA
*
1790795 TATTTAAATATATA
1 -ATTTTAAT-TATA
1790809 TTTAATGATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 3 0.09
27 19 0.54
28 13 0.37
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTTTAATTATAAAAATAATTTATTAA
Found at i:1792830 original size:30 final size:27
Alignment explanation
Indices: 1792794--1792860 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 27
1792784 TAATTTACAG
*
1792794 TTTTTATATTATAATTAAGTGTATTTTAAT
1 TTTTTATATTA-AATT-A-TATATTTTAAT
*
1792824 TTTTTATTATTAAATTATATATTTTTAT
1 TTTTTA-TATTAAATTATATATTTTAAT
1792852 TTTTTATAT
1 TTTTTATAT
1792861 ATTTAAAAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 3 0.09
28 15 0.44
29 1 0.03
30 10 0.29
31 5 0.15
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (27 bp):
TTTTTATATTAAATTATATATTTTAAT
Found at i:1793594 original size:21 final size:21
Alignment explanation
Indices: 1793550--1793590 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1793540 TAATTTGTTA
**
1793550 ATTTATATATTTTAAGTTAAT
1 ATTTATATATTTTAAAATAAT
1793571 ATTTATA-ATTTTAAAATAAT
1 ATTTATATATTTTAAAATAAT
1793591 TATTCTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
ATTTATATATTTTAAAATAAT
Found at i:1795759 original size:167 final size:167
Alignment explanation
Indices: 1795483--1795818 Score: 645
Period size: 167 Copynumber: 2.0 Consensus size: 167
1795473 ATGAGGAATA
1795483 AAGGATTGCTATAGATAATTTATGGTGTTCATGGAAATAGCAAATTGCAGGACGCCTGACATTCC
1 AAGGATTGCTATAGATAATTTATGGTGTTCATGGAAATAGCAAATTGCAGGACGCCTGACATTCC
*
1795548 CGTAAGCAAGCTTTTTATCATTGCCATCAAAGTTACAAGAGAAATATGCACATACGAAATGTAAA
66 CGTAAGCAAGCTTTTTACCATTGCCATCAAAGTTACAAGAGAAATATGCACATACGAAATGTAAA
*
1795613 GTTATATGTTTATATGGGCTTCCATGGATATTGATTT
131 CTTATATGTTTATATGGGCTTCCATGGATATTGATTT
1795650 AAGGATTGCTATAGATAATTTATGGTGTTCATGGAAATAGCAAATTGCAGGACGCCTGACATTCC
1 AAGGATTGCTATAGATAATTTATGGTGTTCATGGAAATAGCAAATTGCAGGACGCCTGACATTCC
*
1795715 CGTAAGCAAGCTTTTTACCATTGCCATCAAAGTTACAAGAGAAATATGCACATACGAATTGTAAA
66 CGTAAGCAAGCTTTTTACCATTGCCATCAAAGTTACAAGAGAAATATGCACATACGAAATGTAAA
1795780 CTTATATGTTTATATGGGCTTCCATGGATATTGATTT
131 CTTATATGTTTATATGGGCTTCCATGGATATTGATTT
1795817 AA
1 AA
1795819 CCATGCTTGA
Statistics
Matches: 166, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
167 166 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (167 bp):
AAGGATTGCTATAGATAATTTATGGTGTTCATGGAAATAGCAAATTGCAGGACGCCTGACATTCC
CGTAAGCAAGCTTTTTACCATTGCCATCAAAGTTACAAGAGAAATATGCACATACGAAATGTAAA
CTTATATGTTTATATGGGCTTCCATGGATATTGATTT
Found at i:1798203 original size:2 final size:2
Alignment explanation
Indices: 1798196--1798231 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1798186 TATCATGAAA
*
1798196 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1798232 CAGGAAAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1798813 original size:20 final size:20
Alignment explanation
Indices: 1798772--1798810 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1798762 TTAAAAATTT
1798772 TAATTATAAAATATAAAAAA
1 TAATTATAAAATATAAAAAA
1798792 TAATTATAAAAT-TAAAAAA
1 TAATTATAAAATATAAAAAA
1798811 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
TAATTATAAAATATAAAAAA
Found at i:1799832 original size:24 final size:24
Alignment explanation
Indices: 1799786--1799832 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1799776 ATCACATAAA
* *
1799786 AATATAAATATTTTAAATTTTTAT
1 AATATAAATATATTAAATATTTAT
1799810 AATATAAAT-TATTAATATATTTA
1 AATATAAATATATTAA-ATATTTA
1799833 ATTTATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AATATAAATATATTAAATATTTAT
Found at i:1799881 original size:41 final size:43
Alignment explanation
Indices: 1799816--1799896 Score: 105
Period size: 41 Copynumber: 1.9 Consensus size: 43
1799806 TTATAATATA
* *
1799816 AATTATTAATATATTTAATTTAT-AATA-AATATAAATATCAC
1 AATTATTAATATATATAATATATAAATATAATATAAATATCAC
*
1799857 AATTA-TAATATAATATAATATATAAATATGATATAAATAT
1 AATTATTAATAT-ATATAATATATAAATATAATATAAATAT
1799897 ATAAATTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 6 0.18
41 14 0.41
42 4 0.12
43 10 0.29
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (43 bp):
AATTATTAATATATATAATATATAAATATAATATAAATATCAC
Found at i:1799897 original size:19 final size:18
Alignment explanation
Indices: 1799863--1799902 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
1799853 TCACAATTAT
1799863 AATATAATATAATATATA
1 AATATAATATAATATATA
*
1799881 AATATGATATAAATATATA
1 AATATAATAT-AATATATA
1799900 AAT
1 AAT
1799903 TATTATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
AATATAATATAATATATA
Found at i:1799904 original size:43 final size:40
Alignment explanation
Indices: 1799811--1799910 Score: 103
Period size: 43 Copynumber: 2.4 Consensus size: 40
1799801 AATTTTTATA
* *
1799811 ATATAAATTATTAATATATTTAATTTATAATAAATATAAAT
1 ATATAAATTA-TAATATATATAATATATAATAAATATAAAT
* *
1799852 ATCA-CAATTATAATATAATATAATATATAAATATGATATAAAT
1 AT-ATAAATTATAATAT-ATATAATATAT-AATA-AATATAAAT
*
1799895 ATATAAATTATTATAT
1 ATATAAATTATAATAT
1799911 TTTTAGCATT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
40 6 0.12
41 16 0.33
42 6 0.12
43 20 0.42
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (40 bp):
ATATAAATTATAATATATATAATATATAATAAATATAAAT
Found at i:1802963 original size:22 final size:21
Alignment explanation
Indices: 1802935--1802976 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1802925 ATATTAAAAA
1802935 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
1802955 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
1802976 A
1 A
1802977 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:1803011 original size:21 final size:20
Alignment explanation
Indices: 1802973--1803017 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
1802963 TATAATTAAA
1802973 TTTAAATAAAAATATATTAT
1 TTTAAATAAAAATATATTAT
*
1802993 TTT-AATTAAAA-ATATTAT
1 TTTAAATAAAAATATATTAT
1803011 TTTAAAT
1 TTTAAAT
1803018 TTGATCGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 10 0.43
19 10 0.43
20 3 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAAATAAAAATATATTAT
Found at i:1803018 original size:19 final size:20
Alignment explanation
Indices: 1802973--1803018 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
1802963 TATAATTAAA
*
1802973 TTTAAATAAAAATATATTAT
1 TTTAAATTAAAATATATTAT
1802993 TTT-AATTAAAA-ATATTAT
1 TTTAAATTAAAATATATTAT
1803011 TTTAAATT
1 TTTAAATT
1803019 TGATCGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 10 0.42
19 11 0.46
20 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAAATTAAAATATATTAT
Found at i:1807880 original size:2 final size:2
Alignment explanation
Indices: 1807875--1807906 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1807865 AAAAGTGATA
1807875 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1807907 GAAATTACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1808168 original size:22 final size:22
Alignment explanation
Indices: 1808143--1808184 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1808133 TTAATAAAAT
1808143 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
1808165 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
1808185 AATAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:1809423 original size:30 final size:28
Alignment explanation
Indices: 1809389--1809460 Score: 76
Period size: 30 Copynumber: 2.6 Consensus size: 28
1809379 AAAAATTTAA
1809389 TTTAATTATTTTATTTTTTTATAATATAAT
1 TTTAATTATTTTATTTTTTTA-AA-ATAAT
* * *
1809419 TTTAAATATTTTA-TATTTTAAAATTAT
1 TTTAATTATTTTATTTTTTTAAAATAAT
*
1809446 TTTCATTA-TTTATTT
1 TTTAATTATTTTATTT
1809461 ATAAAAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
26 4 0.11
27 11 0.31
28 2 0.06
29 6 0.17
30 12 0.34
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (28 bp):
TTTAATTATTTTATTTTTTTAAAATAAT
Found at i:1815447 original size:17 final size:17
Alignment explanation
Indices: 1815425--1815457 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1815415 TTAAATATAA
1815425 TTAAAT-TATATTGTTAT
1 TTAAATATATA-TGTTAT
1815442 TTAAATATATATGTTA
1 TTAAATATATATGTTA
1815458 AATATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
TTAAATATATATGTTAT
Found at i:1815667 original size:24 final size:24
Alignment explanation
Indices: 1815635--1815685 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1815625 GATATTAATT
**
1815635 ATTATATTATTTTTATTTAAAATAA
1 ATTATATTATCATTATTTAAAA-AA
*
1815660 ATTA-ATTATCATTATTTTAAAAA
1 ATTATATTATCATTATTTAAAAAA
1815683 ATT
1 ATT
1815686 TAAAGATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 5 0.22
24 14 0.61
25 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTATATTATCATTATTTAAAAAA
Found at i:1815981 original size:21 final size:21
Alignment explanation
Indices: 1815947--1815986 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1815937 TATTATTAAA
1815947 TTAAAAATAAATTTAAAATAT
1 TTAAAAATAAATTTAAAATAT
* *
1815968 TTAAACATATATTTAAAAT
1 TTAAAAATAAATTTAAAAT
1815987 TAAATATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
TTAAAAATAAATTTAAAATAT
Found at i:1816468 original size:26 final size:24
Alignment explanation
Indices: 1816439--1816495 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 24
1816429 TATTATTATT
1816439 ATAAAATTAATATGAATTAATTA-AAA
1 ATAAAATT-ATATGAA-TAA-TACAAA
1816465 ATAAATAATTATATGAATAATACAAA
1 AT-AA-AATTATATGAATAATACAAA
1816491 ATAAA
1 ATAAA
1816496 TATAAAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
24 1 0.04
25 4 0.14
26 10 0.36
27 9 0.32
28 4 0.14
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.32
Consensus pattern (24 bp):
ATAAAATTATATGAATAATACAAA
Found at i:1819139 original size:2 final size:2
Alignment explanation
Indices: 1819094--1819120 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1819084 TCATCAAAGA
1819094 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1819121 AAGCCAAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1819139 original size:21 final size:21
Alignment explanation
Indices: 1819113--1819155 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1819103 TATATATATA
* *
1819113 TATATATAAAGCCAAAGCTTC
1 TATATAAAAAGCCAAAACTTC
1819134 TATATAAAAAGCCAAAACTTC
1 TATATAAAAAGCCAAAACTTC
1819155 T
1 T
1819156 TTCTAATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.19, G:0.07, T:0.28
Consensus pattern (21 bp):
TATATAAAAAGCCAAAACTTC
Found at i:1819345 original size:2 final size:2
Alignment explanation
Indices: 1819338--1819372 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1819328 GAATATCAGC
1819338 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1819373 AAGCCAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1819574 original size:230 final size:231
Alignment explanation
Indices: 1819134--1819597 Score: 686
Period size: 231 Copynumber: 2.0 Consensus size: 231
1819124 CCAAAGCTTC
* * * * **
1819134 TATATAAAAAGCCAAAACTTCTTTCTAATTTCTATTCTAAAGGGGGAAAATTAAAAGTAGGTTGG
1 TATATAAAAAGCCAAAACTTCTTTCTAATTTCCATTCCAAAGGGAGAAAATTAAAACTAGGTCAG
* *
1819199 GCAGAAAAATGGGTTTCTGTTCAAAATTGGAATTTGGAAGAGTTTCCAAGTACCGACAGAAACGA
66 GAAGAAAAATGGGTTTCTGTTCAAAATTGAAATTTGGAAGAGTTTCCAAGTACCGACAGAAACGA
* * *
1819264 CAAACAAAGCAAAATTTCATAAGTTTTCAATGCCAAAAATGTGAAATACTGGACGGCATACTTAG
131 AAAACAAAGCAAAATGTCATAAGTTTTCAATGCCAAAAATGTCAAATACTGGACGGCATACTTAG
1819329 AATATCAGCATATATATATATATATATATATATATA
196 AATATCAGCATATATATATATATATATATATATATA
* * *
1819365 TATATATAAAGCCAAAATTTCTTTCTAATTTCCATTCCAAAGGGAGAAAATTAAAACTGGGTCAG
1 TATATAAAAAGCCAAAACTTCTTTCTAATTTCCATTCCAAAGGGAGAAAATTAAAACTAGGTCAG
* * *
1819430 GAAGAAAAATTGGTTTC-GTTTCAAAATTGAAATTT-GATAGAGTTTCCAAGTTCTGACA-ATAA
66 GAAGAAAAATGGGTTTCTG-TTCAAAATTGAAATTTGGA-AGAGTTTCCAAGTACCGACAGA-AA
* *
1819492 -GAGAAAACAAAGTAAACTGTCATAAG-TTTCAATGCCAAAAATGTCAAATACTGGACGGCATAC
128 CGA-AAAACAAAGCAAAATGTCATAAGTTTTCAATGCCAAAAATGTCAAATACTGGACGGCATAC
1819555 TTAGAATATCAGCATATATATATATATATATATATATATA
192 TTAGAATATCAGCATATATATATATATATATATATATATA
1819595 TAT
1 TAT
1819598 CAACATAGAA
Statistics
Matches: 210, Mismatches: 19, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
230 85 0.40
231 125 0.60
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (231 bp):
TATATAAAAAGCCAAAACTTCTTTCTAATTTCCATTCCAAAGGGAGAAAATTAAAACTAGGTCAG
GAAGAAAAATGGGTTTCTGTTCAAAATTGAAATTTGGAAGAGTTTCCAAGTACCGACAGAAACGA
AAAACAAAGCAAAATGTCATAAGTTTTCAATGCCAAAAATGTCAAATACTGGACGGCATACTTAG
AATATCAGCATATATATATATATATATATATATATA
Found at i:1819575 original size:2 final size:2
Alignment explanation
Indices: 1819568--1819597 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1819558 GAATATCAGC
1819568 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
1819598 CAACATAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1820368 original size:21 final size:19
Alignment explanation
Indices: 1820331--1820376 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
1820321 ATAATTAATT
*
1820331 TTTTAAAATTTATTTTATA
1 TTTTAAAATTAATTTTATA
1820350 TTTTAAAATATAATATTTATA
1 TTTTAAAAT-TAAT-TTTATA
1820371 TATTTA
1 T-TTTA
1820377 TATTTAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 3 0.13
21 7 0.30
22 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAAAATTAATTTTATA
Found at i:1823440 original size:13 final size:13
Alignment explanation
Indices: 1823424--1823450 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1823414 AATTAAATTT
1823424 TTTAATATTTATA
1 TTTAATATTTATA
1823437 TTTAATATTTATA
1 TTTAATATTTATA
1823450 T
1 T
1823451 AAATACATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTAATATTTATA
Found at i:1823499 original size:23 final size:24
Alignment explanation
Indices: 1823469--1823513 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1823459 ATTAAAATAT
1823469 AAATATAAAAAA-TAATATTTTTA
1 AAATATAAAAAATTAATATTTTTA
*
1823492 AAATATAAAAAATTATTATTTT
1 AAATATAAAAAATTAATATTTT
1823514 ATACATCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATATAAAAAATTAATATTTTTA
Found at i:1824216 original size:2 final size:2
Alignment explanation
Indices: 1824209--1824239 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1824199 GACTTCTTTG
1824209 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1824240 GTGCTGATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1824381 original size:15 final size:15
Alignment explanation
Indices: 1824339--1824384 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
1824329 TTTATAAAAT
*
1824339 TTTTTATTTTATCTA
1 TTTTTATTTTATTTA
* *
1824354 ATTTTATATTATTTA
1 TTTTTATTTTATTTA
1824369 TTTTTATTTTATTTA
1 TTTTTATTTTATTTA
1824384 T
1 T
1824385 ATTATCTATC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTATTTTATTTA
Found at i:1824401 original size:24 final size:24
Alignment explanation
Indices: 1824356--1824401 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1824346 TTTATCTAAT
* * *
1824356 TTTATATTATTTATTTTTATTTTA
1 TTTATATTATCTATCTTAATTTTA
1824380 TTTATATTATCTATCTTAATTT
1 TTTATATTATCTATCTTAATTT
1824402 ATGAAGATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTATATTATCTATCTTAATTTTA
Found at i:1825863 original size:3 final size:3
Alignment explanation
Indices: 1825857--1825890 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1825847 TACCTCCTCC
* *
1825857 TCA TCA TCA TCA TCA TCA TCA TCA GCA TCT TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1825891 TATTATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.29, C:0.32, G:0.03, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:1826347 original size:2 final size:2
Alignment explanation
Indices: 1826342--1826377 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1826332 GTGTGTGTAC
1826342 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
1826378 GTACACACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1835076 original size:13 final size:13
Alignment explanation
Indices: 1835058--1835125 Score: 53
Period size: 13 Copynumber: 5.7 Consensus size: 13
1835048 TTACTTAACA
1835058 CACCTAACATTCT
1 CACCTAACATTCT
1835071 CACCTAACATAT-T
1 CACCTAACAT-TCT
1835084 -ACCTAACA----
1 CACCTAACATTCT
1835092 CACCTAACATTCT
1 CACCTAACATTCT
*
1835105 CACC-AA-ATACAT
1 CACCTAACATTC-T
1835117 CACCTAACA
1 CACCTAACA
1835126 AACCTAACAT
Statistics
Matches: 45, Mismatches: 1, Indels: 17
0.71 0.02 0.27
Matches are distributed among these distances:
9 8 0.18
11 3 0.07
12 15 0.33
13 17 0.38
14 2 0.04
ACGTcount: A:0.40, C:0.37, G:0.00, T:0.24
Consensus pattern (13 bp):
CACCTAACATTCT
Found at i:1835079 original size:34 final size:34
Alignment explanation
Indices: 1835036--1835168 Score: 167
Period size: 34 Copynumber: 3.9 Consensus size: 34
1835026 AATATCTTGT
*
1835036 TCACCTAACATATTACTTAACACACCTAACATTC
1 TCACCTAACATATTACCTAACACACCTAACATTC
1835070 TCACCTAACATATTACCTAACACACCTAACATTC
1 TCACCTAACATATTACCTAACACACCTAACATTC
* * * * *
1835104 TCACCAAATACATCACCTAACAAACCTAACATTC
1 TCACCTAACATATTACCTAACACACCTAACATTC
* * * * *
1835138 TCACCAAATACATCACCTAACACACCAAACA
1 TCACCTAACATATTACCTAACACACCTAACA
1835169 CACTTAACAA
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 91 1.00
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (34 bp):
TCACCTAACATATTACCTAACACACCTAACATTC
Found at i:1840166 original size:13 final size:13
Alignment explanation
Indices: 1840148--1840178 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1840138 ATTTTTTAAA
1840148 AAATATTTATATT
1 AAATATTTATATT
1840161 AAATATTTATATT
1 AAATATTTATATT
*
1840174 GAATA
1 AAATA
1840179 CATATTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (13 bp):
AAATATTTATATT
Found at i:1844825 original size:25 final size:26
Alignment explanation
Indices: 1844793--1844851 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
1844783 CTCTTTATAC
1844793 TATAAAAATTATATAATATAT-AAA-AA-
1 TATAAAAA-TA-AT-ATATATCAAATAAT
1844819 TATAAAAATAATATATATCAAATAAT
1 TATAAAAATAATATATATCAAATAAT
1844845 TATAAAA
1 TATAAAA
1844852 CATGCTAGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.20
24 5 0.17
25 4 0.13
26 15 0.50
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (26 bp):
TATAAAAATAATATATATCAAATAAT
Found at i:1844828 original size:18 final size:19
Alignment explanation
Indices: 1844793--1844833 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
1844783 CTCTTTATAC
*
1844793 TATAAAAATTATATAAT-A
1 TATAAAAATTATAAAATAA
1844811 TATAAAAA-TATAAAAATAA
1 TATAAAAATTAT-AAAATAA
1844830 TATA
1 TATA
1844834 TATCAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 3 0.15
18 12 0.60
19 5 0.25
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TATAAAAATTATAAAATAA
Found at i:1845650 original size:22 final size:21
Alignment explanation
Indices: 1845617--1845660 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1845607 CACTACTATC
* *
1845617 TCTACTTTTACCTTTCTTTTT
1 TCTACTTTTACCCTTCTCTTT
1845638 TCTACTATTTACCCTTCTCTTT
1 TCTACT-TTTACCCTTCTCTTT
1845660 T
1 T
1845661 ACCTTTCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.61
Consensus pattern (21 bp):
TCTACTTTTACCCTTCTCTTT
Done.