Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 2 of 318
Found at i:347951 original size:20 final size:20
Alignment explanation
Indices: 347925--347993 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
347915 TTTTTGAAAA
347925 TATTTTTAAAATTTTAAATAT
1 TATTTTT-AAATTTTAAATAT
347946 TATTTTTAAATTTTAAATAT
1 TATTTTTAAATTTTAAATAT
*
347966 TATTTTTAAATATTAAATA-
1 TATTTTTAAATTTTAAATAT
347985 TATTTTTAA
1 TATTTTTAA
347994 TAATATAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 9 0.19
20 31 0.66
21 7 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTTTTAAATTTTAAATAT
Found at i:347999 original size:54 final size:55
Alignment explanation
Indices: 347880--348000 Score: 142
Period size: 54 Copynumber: 2.2 Consensus size: 55
347870 ATTTAAAATG
* **
347880 TTTTATAATATATATTTTTAAATTTTACATATATATTTTTGAAAATATTTTTAAAA
1 TTTTATAATATATATTTTTAAATTTTAAATATATATTTTT-AAAATATTAATAAAA
* *
347936 TTTTA-AATAT-TATTTTTAAATTTTAAATAT-TATTTTT-AAATATTAAATATAT
1 TTTTATAATATATATTTTTAAATTTTAAATATATATTTTTAAAATATT-AATAAAA
347988 TTTTAATAATATA
1 TTTT-ATAATATA
348001 AAATATTTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
51 7 0.12
52 7 0.12
53 8 0.14
54 24 0.43
55 5 0.09
56 5 0.09
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (55 bp):
TTTTATAATATATATTTTTAAATTTTAAATATATATTTTTAAAATATTAATAAAA
Found at i:348005 original size:41 final size:41
Alignment explanation
Indices: 347925--348007 Score: 107
Period size: 41 Copynumber: 2.0 Consensus size: 41
347915 TTTTTGAAAA
* * *
347925 TATTTTTAAAATTTTAAATATTATTTTTAAATTTTAAATAT
1 TATTTTTAAAATATTAAATATTATTTTTAAATATAAAATAT
347966 TATTTTT-AAATATTAAATA-TATTTTTAATAATATAAAATAT
1 TATTTTTAAAATATTAAATATTATTTTT-A-AATATAAAATAT
348007 T
1 T
348008 TAAATATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 7 0.19
40 12 0.32
41 18 0.49
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (41 bp):
TATTTTTAAAATATTAAATATTATTTTTAAATATAAAATAT
Found at i:348061 original size:10 final size:10
Alignment explanation
Indices: 348048--348092 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
348038 TTATTATTAT
348048 TTTTATAATA
1 TTTTATAATA
348058 TTTTA-AATA
1 TTTTATAATA
348067 TTTT-TAATTTA
1 TTTTATAA--TA
348078 TTTTATAATA
1 TTTTATAATA
348088 TTTTA
1 TTTTA
348093 AAGATATCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 10 0.32
10 12 0.39
11 6 0.19
12 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTATAATA
Found at i:348070 original size:20 final size:19
Alignment explanation
Indices: 347922--348091 Score: 84
Period size: 20 Copynumber: 8.5 Consensus size: 19
347912 ATATTTTTGA
347922 AAATATTTTTAAA-ATTTT
1 AAATATTTTTAAATATTTT
*
347940 AAATATTATTTTTAAAT-TTTA
1 -AA-A-TATTTTTAAATATTTT
347961 AATATTATTTTTAAATA--TT
1 AA-A-TATTTTTAAATATTTT
* * *
347980 AAATATATTTTTAATAATAT
1 AAATAT-TTTTAAATATTTT
*
348000 AAA-ATATTTAAATATTTT
1 AAATATTTTTAAATATTTT
348018 AAAGATATGACTTTTCAAAT-TTATT
1 -AA-ATAT---TTTT-AAATATT-TT
*
348043 -ATTATTTTTATAATATTTT
1 AAATATTTTTA-AATATTTT
*
348062 AAATATTTTTAATTTATTTT
1 AAATATTTTTAA-ATATTTT
348082 ATAATATTTT
1 A-AATATTTT
348092 AAAGATATCA
Statistics
Matches: 119, Mismatches: 12, Indels: 38
0.70 0.07 0.22
Matches are distributed among these distances:
17 3 0.03
18 19 0.16
19 19 0.16
20 40 0.34
21 23 0.19
22 3 0.03
23 1 0.01
24 5 0.04
25 6 0.05
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (19 bp):
AAATATTTTTAAATATTTT
Found at i:348174 original size:21 final size:20
Alignment explanation
Indices: 348150--348230 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 20
348140 TAAATGTTTT
348150 ATATTATTAAAAAAATATTTA
1 ATATT-TTAAAAAAATATTTA
*
348171 ATATTTAAAAAATAATATTTA
1 ATATTTTAAAAA-AATATTTA
*
348192 CA-ATTTAAAAAAATAATATTTA
1 -ATATTT-TAAAAA-AATATTTA
*
348214 A-AATTT-AAAAAATATTT
1 ATATTTTAAAAAAATATTT
348231 TCAAAAATAT
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
18 7 0.13
19 4 0.07
20 6 0.11
21 21 0.39
22 16 0.30
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATTTTAAAAAAATATTTA
Found at i:348205 original size:22 final size:21
Alignment explanation
Indices: 348158--348225 Score: 95
Period size: 22 Copynumber: 3.2 Consensus size: 21
348148 TTATATTATT
348158 AAAAA-AATATTTAATATTT-A
1 AAAAATAATATTTAA-ATTTAA
348178 AAAAATAATATTTACAATTTAA
1 AAAAATAATATTTA-AATTTAA
348200 AAAAATAATATTTAAAATTTAA
1 AAAAATAATATTT-AAATTTAA
348222 AAAA
1 AAAA
348226 TATTTTCAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.11
21 12 0.27
22 26 0.59
23 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAAATAATATTTAAATTTAA
Found at i:348275 original size:25 final size:26
Alignment explanation
Indices: 348216--348279 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 26
348206 AATATTTAAA
348216 ATTTAAAAAATATTTTCAAAAATATAT
1 ATTT-AAAAATATTTTCAAAAATATAT
348243 ATTT-AAAAT-TTTT-AAAAATATAT
1 ATTTAAAAATATTTTCAAAAATATAT
348266 ATTATAAAAA-ATTT
1 ATT-TAAAAATATTT
348280 CAGATATACA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
23 13 0.38
24 5 0.15
25 12 0.35
27 4 0.12
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTTAAAAATATTTTCAAAAATATAT
Found at i:348415 original size:20 final size:21
Alignment explanation
Indices: 348377--348415 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
348367 AAGTTAAAAA
348377 AAAGTAAAAAAAGAAACAAAC
1 AAAGTAAAAAAAGAAACAAAC
*
348398 AAAGTAAATAAA-AAACAA
1 AAAGTAAAAAAAGAAACAA
348416 GCAGGGTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.77, C:0.08, G:0.08, T:0.08
Consensus pattern (21 bp):
AAAGTAAAAAAAGAAACAAAC
Found at i:353549 original size:31 final size:31
Alignment explanation
Indices: 353499--353557 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
353489 CAAAATGGTC
* *
353499 ATTGAGCTACTTGAGAGTTTTCATTTAAGTA
1 ATTGAACTACTTGAAAGTTTTCATTTAAGTA
* *
353530 ATTGAACTATTTGAAAGTTTTTATTTAA
1 ATTGAACTACTTGAAAGTTTTCATTTAA
353558 ATGACTAAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (31 bp):
ATTGAACTACTTGAAAGTTTTCATTTAAGTA
Found at i:359172 original size:30 final size:30
Alignment explanation
Indices: 359138--359200 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
359128 ACTTAACAAG
359138 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
359168 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
359198 CAA
1 CAA
359201 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:363549 original size:83 final size:85
Alignment explanation
Indices: 363384--363568 Score: 234
Period size: 83 Copynumber: 2.2 Consensus size: 85
363374 AAATAATTTT
* * *
363384 TTTTTCATTTTTAGAGGGGTTAAAGTGAAATTTTACTATATATATTAATTTATAATTTCTTTATT
1 TTTTTCATTTTTAGAGGGGTTAAAGTGAAATTTCAC-ATATATATTAATTAATAATTTCTCTATT
363449 TATAAGAGGATTGAATTGACAA
65 TATAAGAGGATTGAATTGA-AA
* * *
363471 TTTTTCA-TTTT-GAGGGGTTAAAGTGCAATTTCAC-TATATATTACTTAATAGTTTCTCTATTT
1 TTTTTCATTTTTAGAGGGGTTAAAGTGAAATTTCACATATATATTAATTAATAATTTCTCTATTT
*
363533 ATAAGATGGCTT-AATTGAAA
66 ATAAGA-GGATTGAATTGAAA
363553 TTTTTTTCATTTTTAG
1 --TTTTTCATTTTTAG
363569 GGAGGCCAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 11
0.83 0.07 0.11
Matches are distributed among these distances:
82 2 0.02
83 36 0.42
84 11 0.13
85 25 0.29
86 5 0.06
87 7 0.08
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.49
Consensus pattern (85 bp):
TTTTTCATTTTTAGAGGGGTTAAAGTGAAATTTCACATATATATTAATTAATAATTTCTCTATTT
ATAAGAGGATTGAATTGAAA
Found at i:363865 original size:30 final size:29
Alignment explanation
Indices: 363809--363865 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
363799 AATTTTTATC
* *
363809 AAATAAAGAAAGTGAAAATTATATTAAAA
1 AAATAAAGAAAGTGAAAATCAAATTAAAA
* *
363838 AAATAAAATAAAGTGAGAATCAAATTAA
1 AAAT-AAAGAAAGTGAAAATCAAATTAA
363866 CAAACTTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 4 0.17
30 19 0.83
ACGTcount: A:0.65, C:0.02, G:0.11, T:0.23
Consensus pattern (29 bp):
AAATAAAGAAAGTGAAAATCAAATTAAAA
Found at i:370486 original size:31 final size:31
Alignment explanation
Indices: 370450--370517 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
370440 TTAACAACCT
370450 AATGACTTAAATAAAAACTTT-TGAATAGTTC
1 AATGACTTAAATAAAAACTTTCT-AATAGTTC
** * *
370481 AATGACTTGGATGAAAACTTTCTAATAGTTT
1 AATGACTTAAATAAAAACTTTCTAATAGTTC
370512 AATGAC
1 AATGAC
370518 CATTTTGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.35
Consensus pattern (31 bp):
AATGACTTAAATAAAAACTTTCTAATAGTTC
Found at i:380726 original size:46 final size:46
Alignment explanation
Indices: 380676--380804 Score: 213
Period size: 46 Copynumber: 2.8 Consensus size: 46
380666 TGGTTGAGCA
*
380676 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
*
380722 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
380768 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
380805 GCGGGTTACA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:386676 original size:20 final size:19
Alignment explanation
Indices: 386642--386688 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
386632 TAAGCTGAAG
*
386642 TTTTTTATATATTCCTTTTGA
1 TTTTTT-TATATTCCATTT-A
*
386663 TTTTTTTATTTTCCATTTA
1 TTTTTTTATATTCCATTTA
386682 TTTTTTT
1 TTTTTTT
386689 GAATCAAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.33
20 10 0.42
21 6 0.25
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTTTTATATTCCATTTA
Found at i:398272 original size:18 final size:18
Alignment explanation
Indices: 398249--398288 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
398239 ATAATAAAAA
*
398249 AATTAATTAAT-AAATTAT
1 AATTAATT-ATGAAAATAT
398267 AATTAATTATGAAAATAT
1 AATTAATTATGAAAATAT
398285 AATT
1 AATT
398289 TTCTCAACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
AATTAATTATGAAAATAT
Found at i:399110 original size:30 final size:30
Alignment explanation
Indices: 399076--399133 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
399066 AAAAAATATA
**
399076 CTTAAATTATTAATCTCATGTCATTTTACC
1 CTTAAATTATTAATCTCATCCCATTTTACC
* *
399106 CTTAATTTATTAATTTCATCCCATTTTA
1 CTTAAATTATTAATCTCATCCCATTTTA
399134 TCCTCAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.19, G:0.02, T:0.50
Consensus pattern (30 bp):
CTTAAATTATTAATCTCATCCCATTTTACC
Found at i:399223 original size:2 final size:2
Alignment explanation
Indices: 399216--399250 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
399206 AATTTTGATA
399216 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
399251 AAATAAGGGT
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:405933 original size:5 final size:5
Alignment explanation
Indices: 405906--405946 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
405896 TGGAAACAGA
*
405906 AAAAA AAAAT AATAAT AATAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AA-AAT AA-AAT AAAAT AAAAT AAAAT AAAA
405947 GCACTTCATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
5 23 0.68
6 11 0.32
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:407338 original size:19 final size:19
Alignment explanation
Indices: 407326--407381 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
407316 AATTATTTAT
407326 AATTATTTTAATTTTTAAA
1 AATTATTTTAATTTTTAAA
*
407345 AATTATTTTAAATTACTTAAA
1 AATTATTTT-AATT-TTTAAA
*
407366 AGATTAATTTAATTTT
1 A-ATTATTTTAATTTT
407382 AAATTACTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 9 0.29
20 5 0.16
21 10 0.32
22 7 0.23
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
AATTATTTTAATTTTTAAA
Found at i:407381 original size:28 final size:28
Alignment explanation
Indices: 407349--407404 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
407339 TTTAAAAATT
*
407349 ATTTTAAATTACTTAAAAGATTAATTTA
1 ATTTTAAATTACTGAAAAGATTAATTTA
*
407377 ATTTTAAATTACTGAAAATATTAATTTA
1 ATTTTAAATTACTGAAAAGATTAATTTA
407405 CTCATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (28 bp):
ATTTTAAATTACTGAAAAGATTAATTTA
Found at i:407593 original size:48 final size:48
Alignment explanation
Indices: 407522--407616 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
407512 AAAAAAAAAG
407522 TATACGACATACGATATCATATGCTTTACTATTTACATATCTCTCTGA
1 TATACGACATACGATATCATATGCTTTACTATTTACATATCTCTCTGA
*
407570 TATACGATATACGATATCATATGCTTTACTATTTACATATCTCTCTG
1 TATACGACATACGATATCATATGCTTTACTATTTACATATCTCTCTG
407617 TTGGCATCAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (48 bp):
TATACGACATACGATATCATATGCTTTACTATTTACATATCTCTCTGA
Found at i:431913 original size:2 final size:2
Alignment explanation
Indices: 431906--431937 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
431896 ACTATGTATG
431906 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
431938 ACAAAAACAA
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:433368 original size:61 final size:61
Alignment explanation
Indices: 433273--433395 Score: 219
Period size: 61 Copynumber: 2.0 Consensus size: 61
433263 GGTAACAATG
* **
433273 AACACTTGATCAATTTGATCTAAGCTAAATTAAGTGGTACCATGCTCCCCTATAAGTTATA
1 AACACTTGATCAAGTTGATCTAAGCTAAATTAAGTGGTACCAAACTCCCCTATAAGTTATA
433334 AACACTTGATCAAGTTGATCTAAGCTAAATTAAGTGGTACCAAACTCCCCTATAAGTTATA
1 AACACTTGATCAAGTTGATCTAAGCTAAATTAAGTGGTACCAAACTCCCCTATAAGTTATA
433395 A
1 A
433396 GGGTTCAAAC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.31
Consensus pattern (61 bp):
AACACTTGATCAAGTTGATCTAAGCTAAATTAAGTGGTACCAAACTCCCCTATAAGTTATA
Found at i:437723 original size:25 final size:25
Alignment explanation
Indices: 437688--437744 Score: 105
Period size: 25 Copynumber: 2.2 Consensus size: 25
437678 CACACCCCAA
437688 ACAAGGTGGTTATTAGGGATATGCTT
1 ACAA-GTGGTTATTAGGGATATGCTT
437714 ACAAGTGGTTATTAGGGATATGCTT
1 ACAAGTGGTTATTAGGGATATGCTT
437739 ACAAGT
1 ACAAGT
437745 TATTCGAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 27 0.87
26 4 0.13
ACGTcount: A:0.30, C:0.09, G:0.28, T:0.33
Consensus pattern (25 bp):
ACAAGTGGTTATTAGGGATATGCTT
Found at i:442918 original size:4 final size:4
Alignment explanation
Indices: 442909--442959 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
442899 ACTTGCACAG
442909 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
442957 ACA
1 ACA
442960 ACGACGCCCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:447620 original size:2 final size:2
Alignment explanation
Indices: 447613--447638 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
447603 TTTCAAAGCG
447613 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
447639 AAAAAAAAAA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:448666 original size:97 final size:97
Alignment explanation
Indices: 448492--448683 Score: 305
Period size: 97 Copynumber: 2.0 Consensus size: 97
448482 AATACATATC
448492 CAAATATGTCTCAATCCCTATCAAACACTTATTTTTCCATTAAAAAATATCCATTTAAGATTCAA
1 CAAATATGTCTCAATCCCTATCAAACACTTATTTTTCCATTAAAAAATATCCATTTAAGATTCAA
* * * * *
448557 GCCTTTATTAAATACAATAATTTTTTTTATGG
66 ACCTCTACTAAATACAATAAATTATTTTATGG
* *
448589 CAAATATGTCTCAATCCCTATCAAACACTTATTTTTCTATT-AAAAATTTGCCATTTAAGATTCA
1 CAAATATGTCTCAATCCCTATCAAACACTTATTTTTCCATTAAAAAATAT-CCATTTAAGATTCA
448653 AACCTCTACTAAATACAATAAATTATTTTAT
65 AACCTCTACTAAATACAATAAATTATTTTAT
448684 AGACATTTTC
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
96 7 0.08
97 80 0.92
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (97 bp):
CAAATATGTCTCAATCCCTATCAAACACTTATTTTTCCATTAAAAAATATCCATTTAAGATTCAA
ACCTCTACTAAATACAATAAATTATTTTATGG
Found at i:449216 original size:15 final size:16
Alignment explanation
Indices: 449186--449218 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
449176 AAATAGTTAT
449186 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
449203 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
449218 A
1 A
449219 AAAATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:451870 original size:3 final size:3
Alignment explanation
Indices: 451862--451891 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
451852 AGGCCTTGAC
*
451862 GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
451892 CCTTGTTTGA
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:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:455002 original size:21 final size:21
Alignment explanation
Indices: 454942--455002 Score: 50
Period size: 21 Copynumber: 2.9 Consensus size: 21
454932 TTGCGGATTG
* * *
454942 TAACTTGGAGAGGTAGGGCTA
1 TAACTTGGTGAGGTAGGACCA
* * * *
454963 TAGCTAGGTGACGTGGGACCA
1 TAACTTGGTGAGGTAGGACCA
*
454984 TAACTTGGTGAGGTCGGAC
1 TAACTTGGTGAGGTAGGAC
455003 TGTACCCGGG
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.15, G:0.38, T:0.23
Consensus pattern (21 bp):
TAACTTGGTGAGGTAGGACCA
Found at i:455038 original size:21 final size:21
Alignment explanation
Indices: 455011--455192 Score: 105
Period size: 21 Copynumber: 8.7 Consensus size: 21
455001 ACTGTACCCG
* *
455011 GGAGAAGTGGGGCTATATGCT
1 GGAGAAGTAGGGCTATATGAT
* *
455032 GGGGAAGTAGGGCTGTATGAT
1 GGAGAAGTAGGGCTATATGAT
* * *
455053 GGAGATGTAGGGCTATAGGAG
1 GGAGAAGTAGGGCTATATGAT
* * * * * *
455074 GGTGAGGTTGGGCTGTAAGAA
1 GGAGAAGTAGGGCTATATGAT
* * * *
455095 GGAGATGTCGGACTGTATGAT
1 GGAGAAGTAGGGCTATATGAT
* * * *
455116 GGCGATGTTGGGCTGTATGAT
1 GGAGAAGTAGGGCTATATGAT
* *
455137 GGAGAAGTGGGGCTGTATGCA-
1 GGAGAAGTAGGGCTATATG-AT
* * *
455158 GGTGAAGTTGGGCTATATGCT
1 GGAGAAGTAGGGCTATATGAT
*
455179 GGTGAAGTAGGGCT
1 GGAGAAGTAGGGCT
455193 GTAGCTTGGT
Statistics
Matches: 127, Mismatches: 32, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
21 126 0.99
22 1 0.01
ACGTcount: A:0.23, C:0.08, G:0.45, T:0.25
Consensus pattern (21 bp):
GGAGAAGTAGGGCTATATGAT
Found at i:455057 original size:42 final size:42
Alignment explanation
Indices: 455011--455192 Score: 152
Period size: 42 Copynumber: 4.3 Consensus size: 42
455001 ACTGTACCCG
* * *
455011 GGAGAAGTGGGGCTATATGCTGGGGAAGTAGGGCTGTATGAT
1 GGAGAAGTAGGGCTATATGCAGGGGAAGTTGGGCTGTATGAT
* * * * *
455053 GGAGATGTAGGGCTATA-GGAGGGTGAGGTTGGGCTGTAAGAA
1 GGAGAAGTAGGGCTATATGCAGGG-GAAGTTGGGCTGTATGAT
* * * * * *
455095 GGAGATGTCGGACTGTATG-ATGGCGATGTTGGGCTGTATGAT
1 GGAGAAGTAGGGCTATATGCA-GGGGAAGTTGGGCTGTATGAT
* * * * *
455137 GGAGAAGTGGGGCTGTATGCAGGTGAAGTTGGGCTATATGCT
1 GGAGAAGTAGGGCTATATGCAGGGGAAGTTGGGCTGTATGAT
*
455179 GGTGAAGTAGGGCT
1 GGAGAAGTAGGGCT
455193 GTAGCTTGGT
Statistics
Matches: 112, Mismatches: 24, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
41 4 0.04
42 104 0.93
43 4 0.04
ACGTcount: A:0.23, C:0.08, G:0.45, T:0.25
Consensus pattern (42 bp):
GGAGAAGTAGGGCTATATGCAGGGGAAGTTGGGCTGTATGAT
Found at i:455245 original size:63 final size:63
Alignment explanation
Indices: 455178--455309 Score: 158
Period size: 63 Copynumber: 2.1 Consensus size: 63
455168 GGCTATATGC
* * * * *
455178 TGGTGAAGTAGGGCTGTAGCTTGGTGAAGTTGGACTATAGCTGGGAGATGT-GGGACTATAACT
1 TGGTGAAGTAGGACTGTAACTTGGAGAAGTAGGACTATAGCTGGGAGAGGTAGGG-CTATAACT
* * * * *
455241 TGGTGAAGTAGGACTGTAACTTGGAGACGTAGGGCTGTAGCTTGGAGAGGTAGGGCTATAGCT
1 TGGTGAAGTAGGACTGTAACTTGGAGAAGTAGGACTATAGCTGGGAGAGGTAGGGCTATAACT
455304 TGGTGA
1 TGGTGA
455310 GGTTGGAGAA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 55 0.95
64 3 0.05
ACGTcount: A:0.23, C:0.10, G:0.39, T:0.27
Consensus pattern (63 bp):
TGGTGAAGTAGGACTGTAACTTGGAGAAGTAGGACTATAGCTGGGAGAGGTAGGGCTATAACT
Found at i:455306 original size:42 final size:42
Alignment explanation
Indices: 455136--455306 Score: 150
Period size: 42 Copynumber: 4.1 Consensus size: 42
455126 GGCTGTATGA
* * * *
455136 TGGAGAAGTGGGGCTGTATGC-AGGTGAAGTTGGGCTATATGC-
1 TGGAGAAGTAGGGCTGTA-GCTTGGTGAAGTAGGACTATA-GCT
* *
455178 TGGTGAAGTAGGGCTGTAGCTTGGTGAAGTTGGACTATAGCT
1 TGGAGAAGTAGGGCTGTAGCTTGGTGAAGTAGGACTATAGCT
* * * * * *
455220 GGGAGATGT-GGGACTATAACTTGGTGAAGTAGGACTGTAACT
1 TGGAGAAGTAGGG-CTGTAGCTTGGTGAAGTAGGACTATAGCT
* * * *
455262 TGGAGACGTAGGGCTGTAGCTTGGAGAGGTAGGGCTATAGCT
1 TGGAGAAGTAGGGCTGTAGCTTGGTGAAGTAGGACTATAGCT
455304 TGG
1 TGG
455307 TGAGGTTGGA
Statistics
Matches: 104, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
41 7 0.07
42 94 0.90
43 3 0.03
ACGTcount: A:0.23, C:0.10, G:0.40, T:0.27
Consensus pattern (42 bp):
TGGAGAAGTAGGGCTGTAGCTTGGTGAAGTAGGACTATAGCT
Found at i:455312 original size:21 final size:21
Alignment explanation
Indices: 455158--455309 Score: 128
Period size: 21 Copynumber: 7.2 Consensus size: 21
455148 GCTGTATGCA
*
455158 GGTGAAGTTGGGCTATATGC-T
1 GGTGAAGTAGGGCTATA-GCTT
*
455179 GGTGAAGTAGGGCTGTAGCTT
1 GGTGAAGTAGGGCTATAGCTT
* * *
455200 GGTGAAGTTGGACTATAGCTG
1 GGTGAAGTAGGGCTATAGCTT
* * *
455221 GGAGATGT-GGGACTATAACTT
1 GGTGAAGTAGGG-CTATAGCTT
* * *
455242 GGTGAAGTAGGACTGTAACTT
1 GGTGAAGTAGGGCTATAGCTT
* * *
455263 GGAGACGTAGGGCTGTAGCTT
1 GGTGAAGTAGGGCTATAGCTT
* *
455284 GGAGAGGTAGGGCTATAGCTT
1 GGTGAAGTAGGGCTATAGCTT
455305 GGTGA
1 GGTGA
455310 GGTTGGAGAA
Statistics
Matches: 106, Mismatches: 22, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
20 4 0.04
21 100 0.94
22 2 0.02
ACGTcount: A:0.23, C:0.10, G:0.39, T:0.28
Consensus pattern (21 bp):
GGTGAAGTAGGGCTATAGCTT
Found at i:455402 original size:42 final size:43
Alignment explanation
Indices: 455356--455495 Score: 169
Period size: 42 Copynumber: 3.3 Consensus size: 43
455346 TGGACTTGTT
* * ** * * *
455356 GGGCTGTAACCTGGTGAACTAGGACTGTAAG-TAGGTGATGTG
1 GGGCTGTAACCAGGCGAGGTAGGACTGTAAGCCAGGAGATGTA
455398 GGGCTGTAACCAGGCGAGGTAGGACTGT-AGCCAGGAGATGTA
1 GGGCTGTAACCAGGCGAGGTAGGACTGTAAGCCAGGAGATGTA
*
455440 GGGCTGTAACCAGGCGAGGTAGGACTGT-AGCCAGGAGATGAA
1 GGGCTGTAACCAGGCGAGGTAGGACTGTAAGCCAGGAGATGTA
* *
455482 GGACTGTAGCCAGG
1 GGGCTGTAACCAGG
455496 AGATGATGGG
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
41 2 0.02
42 85 0.98
ACGTcount: A:0.26, C:0.16, G:0.40, T:0.19
Consensus pattern (43 bp):
GGGCTGTAACCAGGCGAGGTAGGACTGTAAGCCAGGAGATGTA
Found at i:455425 original size:21 final size:21
Alignment explanation
Indices: 455401--455498 Score: 124
Period size: 21 Copynumber: 4.7 Consensus size: 21
455391 TGATGTGGGG
* *
455401 CTGTAACCAGGCGAGGTAGGA
1 CTGTAGCCAGGAGAGGTAGGA
* *
455422 CTGTAGCCAGGAGATGTAGGG
1 CTGTAGCCAGGAGAGGTAGGA
* *
455443 CTGTAACCAGGCGAGGTAGGA
1 CTGTAGCCAGGAGAGGTAGGA
* *
455464 CTGTAGCCAGGAGATGAAGGA
1 CTGTAGCCAGGAGAGGTAGGA
455485 CTGTAGCCAGGAGA
1 CTGTAGCCAGGAGA
455499 TGATGGGCTG
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.29, C:0.17, G:0.39, T:0.15
Consensus pattern (21 bp):
CTGTAGCCAGGAGAGGTAGGA
Found at i:455499 original size:21 final size:21
Alignment explanation
Indices: 455418--455524 Score: 124
Period size: 21 Copynumber: 5.1 Consensus size: 21
455408 CAGGCGAGGT
*
455418 AGGACTGTAGCCAGGAGATGT
1 AGGACTGTAGCCAGGAGATGA
* * * * *
455439 AGGGCTGTAACCAGGCGAGGT
1 AGGACTGTAGCCAGGAGATGA
455460 AGGACTGTAGCCAGGAGATGA
1 AGGACTGTAGCCAGGAGATGA
455481 AGGACTGTAGCCAGGAGATGA
1 AGGACTGTAGCCAGGAGATGA
* * * *
455502 TGGGCTGTAACCAGGGGATGA
1 AGGACTGTAGCCAGGAGATGA
455523 AG
1 AG
455525 TGGGAGAGAA
Statistics
Matches: 72, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 72 1.00
ACGTcount: A:0.29, C:0.15, G:0.40, T:0.16
Consensus pattern (21 bp):
AGGACTGTAGCCAGGAGATGA
Found at i:455510 original size:42 final size:42
Alignment explanation
Indices: 455401--455524 Score: 142
Period size: 42 Copynumber: 3.0 Consensus size: 42
455391 TGATGTGGGG
* * * *
455401 CTGTAACCAGGCGAGGTAGGACTGTAGCCAGGAGATGTAGGG
1 CTGTAACCAGGAGAGATAGGACTGTAGCCAGGAGATGAAGGA
* *
455443 CTGTAACCAGGCGAGGTAGGACTGTAGCCAGGAGATGAAGGA
1 CTGTAACCAGGAGAGATAGGACTGTAGCCAGGAGATGAAGGA
* * * *
455485 CTGTAGCCAGGAGATGAT-GGGCTGTAACCAGGGGATGAAG
1 CTGTAACCAGGAGA-GATAGGACTGTAGCCAGGAGATGAAG
455525 TGGGAGAGAA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 71 0.97
43 2 0.03
ACGTcount: A:0.28, C:0.16, G:0.40, T:0.16
Consensus pattern (42 bp):
CTGTAACCAGGAGAGATAGGACTGTAGCCAGGAGATGAAGGA
Found at i:463438 original size:31 final size:31
Alignment explanation
Indices: 463383--463446 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
463373 CAAACTAGTC
** *
463383 ACTTAAATAAAAACTTTTGGATAATTCAATG
1 ACTTAAATAAAAACTTGCGAATAATTCAATG
* *
463414 ACTTAAATAAAAGCTTGCGAATAATTTAATG
1 ACTTAAATAAAAACTTGCGAATAATTCAATG
463445 AC
1 AC
463447 CATTTTATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (31 bp):
ACTTAAATAAAAACTTGCGAATAATTCAATG
Found at i:464088 original size:29 final size:29
Alignment explanation
Indices: 464051--464118 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 29
464041 CAAATTAAAT
464051 ACCCCACTAAACCGA-CCACTAACTCCATC
1 ACCCCACTAAACC-ATCCACTAACTCCATC
* *
464080 ACCCTACTAAACCATCCACTACCTCCATC
1 ACCCCACTAAACCATCCACTAACTCCATC
464109 ACCCCACTAA
1 ACCCCACTAA
464119 CTCCATCACC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 1 0.03
29 34 0.97
ACGTcount: A:0.34, C:0.49, G:0.01, T:0.16
Consensus pattern (29 bp):
ACCCCACTAAACCATCCACTAACTCCATC
Found at i:464117 original size:17 final size:17
Alignment explanation
Indices: 464066--464129 Score: 66
Period size: 17 Copynumber: 4.1 Consensus size: 17
464056 ACTAAACCGA
464066 CCACTAACTCCATCACC
1 CCACTAACTCCATCACC
* *
464083 CTACTAA-ACCAT----
1 CCACTAACTCCATCACC
*
464095 CCACTACCTCCATCACC
1 CCACTAACTCCATCACC
464112 CCACTAACTCCATCACC
1 CCACTAACTCCATCACC
464129 C
1 C
464130 TACTTGTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
12 5 0.14
13 4 0.11
16 4 0.11
17 23 0.64
ACGTcount: A:0.30, C:0.52, G:0.00, T:0.19
Consensus pattern (17 bp):
CCACTAACTCCATCACC
Found at i:464418 original size:21 final size:21
Alignment explanation
Indices: 464385--464435 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
464375 TATTATCCCC
**
464385 CATATTTAATGTTATCATCAA
1 CATATTTTTTGTTATCATCAA
* *
464406 CATATTTTTTGTTATTATCAT
1 CATATTTTTTGTTATCATCAA
*
464427 CATGTTTTT
1 CATATTTTT
464436 AATGTTATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.55
Consensus pattern (21 bp):
CATATTTTTTGTTATCATCAA
Found at i:464510 original size:18 final size:16
Alignment explanation
Indices: 464466--464512 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
464456 TAGCACAATG
464466 TTTATTACATTATTGTA
1 TTTATTA-ATTATTGTA
*
464483 TTTATT-ATTATTGTTGT
1 TTTATTAATTATTG-T-A
464500 TTTATTAATTATT
1 TTTATTAATTATT
464513 TCTATTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 7 0.27
16 1 0.04
17 12 0.46
18 6 0.23
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (16 bp):
TTTATTAATTATTGTA
Found at i:465831 original size:53 final size:53
Alignment explanation
Indices: 465750--465900 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
465740 CTTACACGGT
* *
465750 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
465805 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
465858 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
465901 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:467558 original size:126 final size:126
Alignment explanation
Indices: 467333--467576 Score: 425
Period size: 126 Copynumber: 1.9 Consensus size: 126
467323 CATTGATCTT
* * *
467333 CTCTCAAAATTTTTCAAAATAAAGGCAATGTTCTGTATTTAAAGAATTCGAAGAATCGTGCCCTA
1 CTCTCAAAAATTTTCAAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAAAAATCGTGCCCTA
*
467398 ACGTACTGGGTTTCGCTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAGTTCA
66 ACGTACTGGGTTTCACTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAGTTCA
*
467459 CTCTCAAAAATTTTCAAAATAAATGCAATGTTCGGTATTTAAAGAATTCGAAAAATCGTGCCCTA
1 CTCTCAAAAATTTTCAAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAAAAATCGTGCCCTA
* *
467524 ATGTACTGGGTTTCACTTTCTTTGTTTGTTTTGAATATTCGAATATCCTCTTA
66 ACGTACTGGGTTTCACTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTA
467577 AGGCTAAAAC
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 111 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (126 bp):
CTCTCAAAAATTTTCAAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAAAAATCGTGCCCTA
ACGTACTGGGTTTCACTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAGTTCA
Found at i:478927 original size:4 final size:4
Alignment explanation
Indices: 478918--478944 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
478908 TCAATTAATA
478918 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
478945 ACTAAAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:479305 original size:14 final size:14
Alignment explanation
Indices: 479280--479329 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
479270 GGTACGTACT
479280 ATTTTCTTATTATTA
1 ATTTT-TTATTATTA
*
479295 ATTTTTTATTA-CA
1 ATTTTTTATTATTA
*
479308 ATTTTTTATTTTTA
1 ATTTTTTATTATTA
*
479322 ATATTTTA
1 ATTTTTTA
479330 AAGAAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 11 0.37
14 14 0.47
15 5 0.17
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTTTATTATTA
Found at i:479312 original size:13 final size:14
Alignment explanation
Indices: 479280--479317 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
479270 GGTACGTACT
*
479280 ATTTTCTTATTATTA
1 ATTTT-TTATTATCA
479295 ATTTTTTATTA-CA
1 ATTTTTTATTATCA
479308 ATTTTTTATT
1 ATTTTTTATT
479318 TTTAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.50
14 6 0.27
15 5 0.23
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTTTATTATCA
Found at i:479712 original size:16 final size:17
Alignment explanation
Indices: 479673--479713 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
479663 AATTTATATG
479673 TATATATATTTTAAAATT
1 TATA-ATATTTTAAAATT
*
479691 TA-AATATTTT-AATTT
1 TATAATATTTTAAAATT
479706 TATAATAT
1 TATAATAT
479714 AAATATTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 6 0.29
16 12 0.57
17 1 0.05
18 2 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATAATATTTTAAAATT
Found at i:479726 original size:22 final size:22
Alignment explanation
Indices: 479680--479726 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
479670 ATGTATATAT
* **
479680 ATTTTAAAATTTAAATATTTTA
1 ATTTTAAAATATAAATATTCAA
*
479702 ATTTTATAATATAAATATTCAA
1 ATTTTAAAATATAAATATTCAA
479724 ATT
1 ATT
479727 ACTTATTACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTTAAAATATAAATATTCAA
Found at i:491586 original size:13 final size:13
Alignment explanation
Indices: 491570--491595 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
491560 AAAATGTACC
491570 AATAAAAGTATAT
1 AATAAAAGTATAT
491583 AATAAAAGTATAT
1 AATAAAAGTATAT
491596 TCTTTTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
AATAAAAGTATAT
Found at i:501987 original size:29 final size:29
Alignment explanation
Indices: 501955--502010 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
501945 TTCTAATTGC
* *
501955 ATCTCTAAATTTTGGAGATTATATCAATT
1 ATCTCTAAATTTTGAAGAATATATCAATT
501984 ATCTCTAAATTTTGAAGAATATATCAA
1 ATCTCTAAATTTTGAAGAATATATCAA
502011 CTAAGTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (29 bp):
ATCTCTAAATTTTGAAGAATATATCAATT
Found at i:502865 original size:15 final size:16
Alignment explanation
Indices: 502828--502865 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
502818 ATTTTTTTAA
*
502828 AAAATATATAAATTTTT
1 AAAAT-TATAAATTTTC
502845 AAAATTATAAA-TTTC
1 AAAATTATAAATTTTC
502860 AAAATT
1 AAAATT
502866 TTTATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 6 0.30
17 5 0.25
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAATTATAAATTTTC
Found at i:502906 original size:28 final size:27
Alignment explanation
Indices: 502839--502906 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
502829 AAATATATAA
* *
502839 ATTTTTAAAATTATAAATTTCAAAATT
1 ATTTTTAAAATTTTAAATTTAAAAATT
*
502866 -TTTATAAATATTTTGAAATTTAAAAATT
1 ATTTTTAAA-ATTTT-AAATTTAAAAATT
*
502894 ATTTTTTAAATTT
1 ATTTTTAAAATTT
502907 ATTTTGAGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
26 7 0.21
27 4 0.12
28 16 0.48
29 6 0.18
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (27 bp):
ATTTTTAAAATTTTAAATTTAAAAATT
Found at i:512491 original size:35 final size:35
Alignment explanation
Indices: 512452--512521 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
512442 AAATTTTGTG
512452 TAGATATATAATACTTTCAACATCATGGTAAAAAA
1 TAGATATATAATACTTTCAACATCATGGTAAAAAA
*
512487 TAGATATATAATACTTTCAACATTATGGTAAAAAA
1 TAGATATATAATACTTTCAACATCATGGTAAAAAA
512522 AGCCTAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.33
Consensus pattern (35 bp):
TAGATATATAATACTTTCAACATCATGGTAAAAAA
Found at i:513465 original size:27 final size:27
Alignment explanation
Indices: 513427--513482 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
513417 ACTCTGTTGA
513427 AAGTGCGAGTCCTTGTAAAGATGATTT
1 AAGTGCGAGTCCTTGTAAAGATGATTT
*
513454 AAGTGCGAGTCCTTGTAAAGATGGTTT
1 AAGTGCGAGTCCTTGTAAAGATGATTT
513481 AA
1 AA
513483 AGACACTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.32
Consensus pattern (27 bp):
AAGTGCGAGTCCTTGTAAAGATGATTT
Found at i:521537 original size:23 final size:20
Alignment explanation
Indices: 521476--521552 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 20
521466 TCTTTCATTT
*
521476 AATTTTAAA-TTAA-ATAAA
1 AATTTAAAATTTAATATAAA
*
521494 AATTTAAAATTTAATTCTAAA
1 AATTTAAAATTTAA-TATAAA
521515 AATATCTAAAATGTTAATAT-AA
1 AAT-T-TAAAAT-TTAATATAAA
*
521537 AATTGTAAATTTTAAT
1 AATT-TAAAATTTAAT
521553 TTTCTTTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
18 8 0.17
19 4 0.08
20 5 0.10
21 13 0.27
22 6 0.12
23 8 0.17
24 4 0.08
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
AATTTAAAATTTAATATAAA
Found at i:522839 original size:28 final size:28
Alignment explanation
Indices: 522791--522856 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
522781 TATTATCTTG
*
522791 GTATCT-AA-TTTTTTTTACCCAATTTA
1 GTATCTAAACTTTTTTTGACCCAATTTA
*
522817 GTATCTAAACTTTTTTTGGCCCAATTTA
1 GTATCTAAACTTTTTTTGACCCAATTTA
* *
522845 GCATCAAAACTT
1 GTATCTAAACTT
522857 GGCATTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 6 0.18
27 2 0.06
28 26 0.76
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (28 bp):
GTATCTAAACTTTTTTTGACCCAATTTA
Found at i:523055 original size:17 final size:17
Alignment explanation
Indices: 523030--523065 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
523020 TGAGTTATGC
523030 ATAAAAAAATAATATTAA
1 ATAAAAAAA-AATATTAA
*
523048 ATAAAAAAAAATTTTAA
1 ATAAAAAAAAATATTAA
523065 A
1 A
523066 AACCCCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAAAAAAAAATATTAA
Found at i:524572 original size:15 final size:15
Alignment explanation
Indices: 524552--524580 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
524542 GAAATAAAGG
524552 AAAGAAACAGAATGA
1 AAAGAAACAGAATGA
524567 AAAGAAACAGAATG
1 AAAGAAACAGAATG
524581 TGGAAACGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.07, G:0.21, T:0.07
Consensus pattern (15 bp):
AAAGAAACAGAATGA
Found at i:524591 original size:18 final size:15
Alignment explanation
Indices: 524550--524595 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
524540 ATGAAATAAA
524550 GGAAAGAAACAGAAT
1 GGAAAGAAACAGAAT
*
524565 GAAAAGAAACAGAATGT
1 GGAAAGAAACAGAA--T
524582 GGAAACGAAACAGA
1 GGAAA-GAAACAGA
524596 GAAGAAACAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 13 0.50
17 5 0.19
18 8 0.31
ACGTcount: A:0.59, C:0.09, G:0.26, T:0.07
Consensus pattern (15 bp):
GGAAAGAAACAGAAT
Found at i:525368 original size:15 final size:15
Alignment explanation
Indices: 525320--525370 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
525310 TTTATCAAAT
*
525320 TTATTTTGATTGAAA
1 TTATATTGATTGAAA
* * *
525335 TCATTTTGATTGAAT
1 TTATATTGATTGAAA
525350 TTATATTGATTGAAA
1 TTATATTGATTGAAA
525365 TTATAT
1 TTATAT
525371 ATATATATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:525373 original size:2 final size:2
Alignment explanation
Indices: 525366--525402 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
525356 TGATTGAAAT
525366 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
525403 GATCTATGTA
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:525797 original size:23 final size:23
Alignment explanation
Indices: 525767--525810 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
525757 GCTTTATCGA
*
525767 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTTATGTGTCGTATT
*
525790 TCAGGCACCTTGTGTGTCGTA
1 TCAGGCACCTTATGTGTCGTA
525811 CTCTAATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (23 bp):
TCAGGCACCTTATGTGTCGTATT
Found at i:526121 original size:17 final size:17
Alignment explanation
Indices: 526099--526131 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
526089 TATTGTTAAG
526099 AAGTAAAGTGTGAATAC
1 AAGTAAAGTGTGAATAC
*
526116 AAGTAAATTGTGAATA
1 AAGTAAAGTGTGAATA
526132 TATTGTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.21, T:0.27
Consensus pattern (17 bp):
AAGTAAAGTGTGAATAC
Found at i:528645 original size:24 final size:24
Alignment explanation
Indices: 528618--528663 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
528608 CAAATAATTT
* *
528618 AAATATATCATTTGAAAATAAAGA
1 AAATATATAATATGAAAATAAAGA
*
528642 AAATATATAATATGTAAATAAA
1 AAATATATAATATGAAAATAAA
528664 TATATAAATA
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:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (24 bp):
AAATATATAATATGAAAATAAAGA
Found at i:535129 original size:32 final size:32
Alignment explanation
Indices: 535093--535161 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
535083 GCTTTTTACA
* *
535093 TGTTGCGACGG-AATACGTTTTTTTTCGTGACT
1 TGTTGCGA-GGAAATACGCTTTTTCTCGTGACT
*
535125 TGTTGCGAGGAAATATGCTTTTTCTCGTGACT
1 TGTTGCGAGGAAATACGCTTTTTCTCGTGACT
535157 TGTTG
1 TGTTG
535162 TGAAATGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 2 0.06
32 31 0.94
ACGTcount: A:0.16, C:0.14, G:0.26, T:0.43
Consensus pattern (32 bp):
TGTTGCGAGGAAATACGCTTTTTCTCGTGACT
Found at i:535964 original size:34 final size:34
Alignment explanation
Indices: 535916--535980 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
535906 CTGAGAGTTC
535916 AATCCTCATATTCGGTATAAAACAATTTTAATTT
1 AATCCTCATATTCGGTATAAAACAATTTTAATTT
* *
535950 AATCCTCATTTTCGGTATAAAACAGTTTTAA
1 AATCCTCATATTCGGTATAAAACAATTTTAA
535981 AACTCATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (34 bp):
AATCCTCATATTCGGTATAAAACAATTTTAATTT
Found at i:536284 original size:31 final size:31
Alignment explanation
Indices: 536200--536284 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
536190 TGCTTATAGT
*
536200 TAAATTACTTTTTTTATTAAAA--AAATGAG
1 TAAATTAATTTTTTTATTAAAATTAAATGAG
**
536229 TAAATTAATTATTATACATT-AAATTAAA-GAG
1 TAAATTAATT-TT-TTTATTAAAATTAAATGAG
536260 TAAATTAATTTTTTTAGTTAAAATT
1 TAAATTAATTTTTTTA-TTAAAATT
536285 TTTGTCTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
29 11 0.24
30 9 0.20
31 22 0.49
32 3 0.07
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (31 bp):
TAAATTAATTTTTTTATTAAAATTAAATGAG
Found at i:547424 original size:20 final size:21
Alignment explanation
Indices: 547382--547425 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
547372 ATAATTTTTT
*
547382 ATTTAATTTGAATAAATTTAA
1 ATTTAATTTGAATAAAATTAA
*
547403 ATTTTATTTGAA-AAAATTAA
1 ATTTAATTTGAATAAAATTAA
547423 ATT
1 ATT
547426 AAATGATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (21 bp):
ATTTAATTTGAATAAAATTAA
Found at i:548835 original size:16 final size:16
Alignment explanation
Indices: 548814--548848 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
548804 TATAAATCTA
*
548814 TTTGTATTTACCTCTC
1 TTTGTATCTACCTCTC
548830 TTTGTATCTACCTCTC
1 TTTGTATCTACCTCTC
548846 TTT
1 TTT
548849 CTAGTGTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.11, C:0.26, G:0.06, T:0.57
Consensus pattern (16 bp):
TTTGTATCTACCTCTC
Found at i:550949 original size:14 final size:16
Alignment explanation
Indices: 550925--550956 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
550915 GGGAAAGTTG
550925 AAAAATGTAAAA-GAA
1 AAAAATGTAAAACGAA
550940 AAAAAT-TAAAACGAA
1 AAAAATGTAAAACGAA
550955 AA
1 AA
550957 GATAGAAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.75, C:0.03, G:0.09, T:0.12
Consensus pattern (16 bp):
AAAAATGTAAAACGAA
Found at i:552340 original size:2 final size:2
Alignment explanation
Indices: 552333--552358 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
552323 GTATTTGGCA
552333 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
552359 GCTACATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:555263 original size:3 final size:3
Alignment explanation
Indices: 555255--555280 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
555245 CCTGCAAGTA
555255 GCT GCT GCT GCT GCT GCT GCT GCT GC
1 GCT GCT GCT GCT GCT GCT GCT GCT GC
555281 CCATTGCTGT
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:0.00, C:0.35, G:0.35, T:0.31
Consensus pattern (3 bp):
GCT
Found at i:559951 original size:24 final size:24
Alignment explanation
Indices: 559924--559971 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
559914 TAATAATATT
559924 TGTAATAAATTCTTGAAAATAAAA
1 TGTAATAAATTCTTGAAAATAAAA
559948 TGTAATAAATTCTTGAAAATAAAA
1 TGTAATAAATTCTTGAAAATAAAA
559972 ATATAAGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.33
Consensus pattern (24 bp):
TGTAATAAATTCTTGAAAATAAAA
Found at i:568594 original size:6 final size:6
Alignment explanation
Indices: 568583--568610 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
568573 ACAAAACCCA
568583 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
568611 TCCCAAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:572143 original size:7 final size:7
Alignment explanation
Indices: 572131--572160 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
572121 ACGTAAAAAT
572131 ATAATTA
1 ATAATTA
572138 ATAATTA
1 ATAATTA
572145 ATAATTA
1 ATAATTA
572152 ATAATTA
1 ATAATTA
572159 AT
1 AT
572161 GAAATTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATAATTA
Found at i:577514 original size:39 final size:39
Alignment explanation
Indices: 577447--577664 Score: 286
Period size: 39 Copynumber: 5.7 Consensus size: 39
577437 ACAAAGCATG
* * *
577447 CGGGACTTTAAGCCCGGATATAATACCAGCAC-AAAGCCTG
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
*
577487 CGGGACTTTAACCCGGATATAACACCAGCACGAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTT
*
577527 CGGGGCTTAGCCC-----TAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
577561 CGGGACTTCGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* * *
577600 CAGGACTTAGCCCGAATATAACACCAACACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
577639 CGGGACTTAGCCCGGATATAACACCA
1 CGGGACTTAGCCCGGATATAACACCA
577665 TTATAAAGTC
Statistics
Matches: 158, Mismatches: 14, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
34 32 0.20
39 106 0.67
40 20 0.13
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.18
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:577575 original size:73 final size:74
Alignment explanation
Indices: 577466--577664 Score: 267
Period size: 73 Copynumber: 2.6 Consensus size: 74
577456 AAGCCCGGAT
* * * * *
577466 ATAATACCAGCAC-AAAGCCTGCGGGACTTTAACCCGGATATAACACCAGCACGAATGCCTTCGG
1 ATAACACCAGCACGAATGCCTTCGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTTCAG
*
577530 GGCTTAGCCC
65 GACTTAGCCC
*
577540 -TAACACCAGCACGAATGCCTTCGGGACTTCGCCCGGATATAACACCAGCACGAATGCCTTCAGG
1 ATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTCAGG
577604 ACTTAGCCC
66 ACTTAGCCC
*
577613 GAATATAACACCAACACGAATGCCTTCGGGACTTAGCCCGGATATAACACCA
1 ----ATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACACCA
577665 TTATAAAGTC
Statistics
Matches: 110, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
73 53 0.48
74 12 0.11
78 45 0.41
ACGTcount: A:0.31, C:0.32, G:0.20, T:0.18
Consensus pattern (74 bp):
ATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTCAGG
ACTTAGCCC
Found at i:577770 original size:28 final size:28
Alignment explanation
Indices: 577737--577818 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
577727 ATTTAATCAT
* *
577737 TCAATATTTTGCACACTAAGTGTCATTC
1 TCAATATTTCGCACACTAAGTGCCATTC
* *
577765 TCAATATCTCGCACATTAAGTGCCATTC
1 TCAATATTTCGCACACTAAGTGCCATTC
* * *
577793 TCAATATTTCGTACACTGAGTACCAT
1 TCAATATTTCGCACACTAAGTGCCAT
577819 ATTTGATTGC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.35
Consensus pattern (28 bp):
TCAATATTTCGCACACTAAGTGCCATTC
Found at i:578765 original size:13 final size:14
Alignment explanation
Indices: 578747--578780 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
578737 AGATGACACA
578747 TTTATTC-TTTTAT
1 TTTATTCATTTTAT
578760 TTTATTCATTTTAT
1 TTTATTCATTTTAT
578774 TATTATT
1 T-TTATT
578781 TTTAACCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 7 0.37
15 5 0.26
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTCATTTTAT
Found at i:581517 original size:25 final size:26
Alignment explanation
Indices: 581480--581539 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
581470 TTTAAGTCGA
* *
581480 TATATATTTTAAT-TTTTAATTTT-AT
1 TATATATTATAATAATTT-ATTTTAAT
581505 TATATATTATAATAATTTATTTTAAT
1 TATATATTATAATAATTTATTTTAAT
581531 TATA-ATTAT
1 TATATATTAT
581540 TTGAATGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 22 0.71
26 9 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TATATATTATAATAATTTATTTTAAT
Found at i:581534 original size:19 final size:20
Alignment explanation
Indices: 581500--581541 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
581490 AATTTTTAAT
581500 TTTATTATATATTATAATAA
1 TTTATTATATATTATAATAA
* *
581520 TTTATTTTA-ATTATAATTA
1 TTTATTATATATTATAATAA
581539 TTT
1 TTT
581542 GAATGAATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATTATATATTATAATAA
Found at i:584570 original size:17 final size:16
Alignment explanation
Indices: 584543--584579 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
584533 ATTTATTATA
*
584543 TAAAAATTATTTTAAT
1 TAAAAATTATTTCAAT
584559 TAAAATATTATTTCAAT
1 TAAAA-ATTATTTCAAT
584576 TAAA
1 TAAA
584580 TGTCTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAAAATTATTTCAAT
Found at i:588086 original size:19 final size:19
Alignment explanation
Indices: 588062--588098 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
588052 ATTAAAAATT
588062 AACTTAATTAAAAAATTTG
1 AACTTAATTAAAAAATTTG
*
588081 AACTTAATTATAAAATTT
1 AACTTAATTAAAAAATTT
588099 AAGGTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (19 bp):
AACTTAATTAAAAAATTTG
Found at i:588762 original size:11 final size:11
Alignment explanation
Indices: 588748--588774 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
588738 AAATCTGTTC
588748 AAATTATTAAT
1 AAATTATTAAT
588759 AAATTATTAAT
1 AAATTATTAAT
588770 AAATT
1 AAATT
588775 CAACTCTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AAATTATTAAT
Found at i:591526 original size:4 final size:4
Alignment explanation
Indices: 591517--591553 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
591507 TTAAGACTTC
* *
591517 ATGT ATGT ATGT AGGT ATGC ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
591554 GGTCTTGCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.27, C:0.03, G:0.27, T:0.43
Consensus pattern (4 bp):
ATGT
Found at i:591655 original size:4 final size:4
Alignment explanation
Indices: 591646--591695 Score: 100
Period size: 4 Copynumber: 12.5 Consensus size: 4
591636 TAAAACTTCA
591646 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
591694 TA
1 TA
591696 CCTGCAAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:593745 original size:3 final size:3
Alignment explanation
Indices: 593739--593775 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
593729 ATTTTCTGCT
593739 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
593776 ACATAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:600831 original size:24 final size:23
Alignment explanation
Indices: 600786--600831 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
600776 TTATATTAAA
*
600786 ATTAAAAATAAAATGTAAATATG
1 ATTAAAAATAAAATATAAATATG
*
600809 ATTAAAAATAAAAATATATATAT
1 ATTAAAAAT-AAAATATAAATAT
600832 TTAGTATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (23 bp):
ATTAAAAATAAAATATAAATATG
Found at i:605785 original size:280 final size:282
Alignment explanation
Indices: 604978--605838 Score: 739
Period size: 280 Copynumber: 3.0 Consensus size: 282
604968 GGAATGTTGC
* * * * * * *
604978 TTGAAAATGAAACCTAGCTTGTGCTAAAGCTGCATGTAAATTTAAACTGGAGACTGGAACAAAAA
1 TTGAAAATGAAACCTAACTTGTACCAAAGCTCCATGTAAATTTACACTGGAGAATGGAACAAAGA
* * * * * *
605043 ATCATGCAAGTTATATAAT-GGGA-ATCATTTAACAGATTATGAAGCTTATATCTTCAATGAGT-
66 ATCATGCAACTTATATAATAGGAATATCATTTAA-TGATCATGAAGCTTACATCTTC--TGACTG
* * *** * * * *
605105 TTTTTATTCATTAGTAACAGTGAAAGAGTCCCTCTTTCACTTCGATTTGTTCTTGCTGCACATTG
128 TCTTT-TT-ATTAGCAACAGTGAAAGAGGGACACTCTAACTTCAATTTGTTCTTGCTGCACATTG
* * ** ** ** **
605170 GTTCTAGGCCTGCTTGTGTTCTTTCACTACAGTTTAGCTTCTTCCT-TTGTATT-AGCTAGAAT-
191 GTTCTAGGCCTGCTTGTGTTCTTTCACTACTGGTTAGCTTCTTTGTATTGGCTTCCCCT-GTGTG
* ** * * *
605232 CT-AGTGGAA-TTGCATTTTGCCCATGGTGAAATGTT
255 CTCA-T-AAACTAACACTTTG-TC-T--TGTAA---T
* * *
605267 GCTTGAACATGAAACCTAACTTGTACCAAAGCTGCATGTAAATTTACTCTGGAGAATGGAACAAA
1 --TTGAAAATGAAACCTAACTTGTACCAAAGCTCCATGTAAATTTACACTGGAGAATGGAACAAA
*
605332 GAATCATGCAAGTTATATAATAGGAAATATCATTTAATGGATCATGAAGCTTACATCTTCTGACT
64 GAATCATGCAACTTATATAATAGG-AATATCATTTAAT-GATCATGAAGCTTACATCTTCTGACT
* * * *
605397 TTCTTTTTAATTAGTAACATTGAAAGAGGGACACTTTAACTTCAATTTGTTCTTGCTGCACATTG
127 GTCTTTTT-ATTAGCAACAGTGAAAGAGGGACACTCTAACTTCAATTTGTTCTTGCTGCACATTG
* *
605462 GTTCTAGGTCTGCTTGTGTTCTTTCACTAGTGGTTAGCTTCTTTGTATTGGCTTCCCCTGTGTGC
191 GTTCTAGGCCTGCTTGTGTTCTTTCACTACTGGTTAGCTTCTTTGTATTGGCTTCCCCTGTGTGC
605527 TCATAAACTAACAC-TTGCTCTTGTAAT
256 TCATAAACTAACACTTTG-TCTTGTAAT
* * * * *
605554 TTGAAAATGAAACCTAGCTTGTACTAAAGCTCCATGTTAATTTGCACTGGAGAATTGAACAAAGA
1 TTGAAAATGAAACCTAACTTGTACCAAAGCTCCATGTAAATTTACACTGGAGAATGGAACAAAGA
*
605619 ATCATGCAACTTATATAAT-GG-A-ATCATTTAAT-ATACTGTGAAGCTTACATCTT-TGA-TGA
66 ATCATGCAACTTATATAATAGGAATATCATTTAATGAT-C-ATGAAGCTTACATCTTCTGACT--
* * * ** *
605678 GTGTATTTT-TTAGCAACAGTGAAGGAGGGACAAC-CTCACTTGTATTTGTTCTTGTTGCACATT
127 GTCT-TTTTATTAGCAACAGTGAAAGAGGGAC-ACTCTAACTTCAATTTGTTCTTGCTGCACATT
* ** ** * *
605741 TGTTCTCTGCCTGCTTGTGTTCTTTTGCTACTGTTTAGCTTCTTTGTATTGGCTTCCCCTTTGTG
190 GGTTCTAGGCCTGCTTGTGTTCTTTCACTACTGGTTAGCTTCTTTGTATTGGCTTCCCCTGTGTG
* *
605806 GTCATAAACTGACACTTTGTCTTGTAAT
255 CTCATAAACTAACACTTTGTCTTGTAAT
605834 TTGAA
1 TTGAA
605839 GATTAAGAGA
Statistics
Matches: 482, Mismatches: 71, Indels: 45
0.81 0.12 0.08
Matches are distributed among these distances:
279 3 0.01
280 130 0.27
281 32 0.07
282 5 0.01
284 2 0.00
285 75 0.16
287 1 0.00
290 4 0.01
291 76 0.16
292 98 0.20
293 19 0.04
294 36 0.07
295 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.38
Consensus pattern (282 bp):
TTGAAAATGAAACCTAACTTGTACCAAAGCTCCATGTAAATTTACACTGGAGAATGGAACAAAGA
ATCATGCAACTTATATAATAGGAATATCATTTAATGATCATGAAGCTTACATCTTCTGACTGTCT
TTTTATTAGCAACAGTGAAAGAGGGACACTCTAACTTCAATTTGTTCTTGCTGCACATTGGTTCT
AGGCCTGCTTGTGTTCTTTCACTACTGGTTAGCTTCTTTGTATTGGCTTCCCCTGTGTGCTCATA
AACTAACACTTTGTCTTGTAAT
Found at i:605907 original size:21 final size:22
Alignment explanation
Indices: 605864--605926 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
605854 AGAGAAGGCC
*
605864 AAGAAGGA-AAGGAAGAAAGAA
1 AAGAAGGAGAAGAAAGAAAGAA
605885 AAGAAGGAGAAGAAAG--AGAA
1 AAGAAGGAGAAGAAAGAAAGAA
605905 AA-AACGGGAGAAGAAAGAAAGA
1 AAGAA--GGAGAAGAAAGAAAGA
605927 GATAAGTCTC
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
19 2 0.06
20 6 0.17
21 19 0.53
22 6 0.17
23 3 0.08
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (22 bp):
AAGAAGGAGAAGAAAGAAAGAA
Found at i:610203 original size:102 final size:101
Alignment explanation
Indices: 610014--610206 Score: 296
Period size: 102 Copynumber: 1.9 Consensus size: 101
610004 CCTTTCAAGA
** *
610014 CCCCCTATCCGGTAGCTACATTGGTCTTAATAAACCCGAAGTTTAGCCAAATTAGACCCTTACGA
1 CCCCCTATCCGGTAGCTACATTGAACTTAATAAACCCGAAGTTTAGCCAAATTAGACCCTTAAGA
***
610079 AAGCAAGCTCTCCTAGTGGTATTTTCAATCAAGACT
66 AAGCAAGCTCTCCTACCAGTATTTTCAATCAAGACT
* * *
610115 CCCCCTATCTGGTAGCTACATTGAACTTAACTAAACCCGGAGTTTAGCCGAATTAGACCCTTAAG
1 CCCCCTATCCGGTAGCTACATTGAACTTAA-TAAACCCGAAGTTTAGCCAAATTAGACCCTTAAG
610180 AAAGCAAGCTCTCCTACCAGTATTTTC
65 AAAGCAAGCTCTCCTACCAGTATTTTC
610207 TCCACTCAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
101 27 0.33
102 55 0.67
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (101 bp):
CCCCCTATCCGGTAGCTACATTGAACTTAATAAACCCGAAGTTTAGCCAAATTAGACCCTTAAGA
AAGCAAGCTCTCCTACCAGTATTTTCAATCAAGACT
Found at i:611006 original size:15 final size:15
Alignment explanation
Indices: 610980--611014 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
610970 TTTCTTCTTC
610980 TTTTTTTATTTTTAA
1 TTTTTTTATTTTTAA
610995 TGTTTTTT-TTTTTAA
1 T-TTTTTTATTTTTAA
611010 TTTTT
1 TTTTT
611015 AATGAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.21
15 9 0.47
16 6 0.32
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTTTTTATTTTTAA
Found at i:616036 original size:30 final size:31
Alignment explanation
Indices: 615990--616049 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
615980 AACACCACAA
*
615990 ATTAAATTGTAATTTTTA-TATTTTTTAAAAT
1 ATTAAATTGAAATTTTTATTA-TTTTTAAAAT
616021 ATTAAATT-AAATTTTTATTATTTTTAAAA
1 ATTAAATTGAAATTTTTATTATTTTTAAAA
616050 GGGTTAAAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (31 bp):
ATTAAATTGAAATTTTTATTATTTTTAAAAT
Found at i:617076 original size:20 final size:22
Alignment explanation
Indices: 617053--617097 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
617043 CTAAAATTCT
617053 TAAAA-TAAAAAATAA-AAGAA
1 TAAAATTAAAAAATAAGAAGAA
*
617073 TAAAATTTCAAAAATAAGAAGAA
1 TAAAA-TTAAAAAATAAGAAGAA
617096 TA
1 TA
617098 TATAGATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
22 9 0.43
23 7 0.33
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (22 bp):
TAAAATTAAAAAATAAGAAGAA
Found at i:617804 original size:21 final size:23
Alignment explanation
Indices: 617761--617804 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
617751 ACTATATTTG
*
617761 TAATCACTCAACTATACTTTTTT
1 TAATCACCCAACTATACTTTTTT
617784 TAATCACCCAACTA-A-TTTTTT
1 TAATCACCCAACTATACTTTTTT
617805 AATGTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 1 0.05
23 13 0.65
ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45
Consensus pattern (23 bp):
TAATCACCCAACTATACTTTTTT
Found at i:618662 original size:23 final size:23
Alignment explanation
Indices: 618617--618661 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
618607 TATATACGAA
*
618617 TAAAAGATAATATTTGATAAAAT
1 TAAAAGATAATATTTAATAAAAT
*
618640 TAAATGATAATATTTCAATAAA
1 TAAAAGATAATATTT-AATAAA
618662 TATATTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (23 bp):
TAAAAGATAATATTTAATAAAAT
Found at i:619621 original size:31 final size:32
Alignment explanation
Indices: 619580--619649 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
619570 TATAAAATGA
* * *
619580 TCACTAAACTATTTGAAAGTTTTCA-TTTAAG
1 TCACTGAACTATTTAAAAATTTTCATTTTAAG
*
619611 TCACTGAACTATTTAAAAATTTTTATTTTTAAG
1 TCACTGAACTATTTAAAAATTTTCA-TTTTAAG
619644 TCACTG
1 TCACTG
619650 GGTTGTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 21 0.64
33 12 0.36
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (32 bp):
TCACTGAACTATTTAAAAATTTTCATTTTAAG
Found at i:620123 original size:18 final size:18
Alignment explanation
Indices: 620100--620134 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
620090 TATAAATTAC
620100 ATAATATATAAA-ATTAAT
1 ATAATATA-AAATATTAAT
620118 ATAATATAAAATATTAA
1 ATAATATAAAATATTAA
620135 AAATTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAATATAAAATATTAAT
Found at i:621475 original size:4 final size:4
Alignment explanation
Indices: 621468--621497 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
621458 AGGCAGGAAG
621468 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
621498 GGTCATGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:633019 original size:77 final size:76
Alignment explanation
Indices: 632870--633012 Score: 173
Period size: 77 Copynumber: 1.9 Consensus size: 76
632860 TCTAATGAGT
* *
632870 AAGACACTAAAGGGATAAACCAATGATATTATAAAAGTAGAAAAACCAAATTATGCTAAATTATA
1 AAGACACTAAAGGGATAAACCAATGAAATTATAAAAGTAGAAAAA-CAAATTATGCTAAATTAGA
632935 GACACTAAATTA
65 GACACTAAATTA
* * * * *
632947 AAGATACTAAAGGGATTAACTAATGAAATTATAAAGGTAGAGGAAAA-GAATTATTGC-AAATTA
1 AAGACACTAAAGGGATAAACCAATGAAATTATAAAAGTAGA--AAAACAAATTA-TGCTAAATTA
633010 GAG
63 GAG
633013 GGACTAATTC
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
77 49 0.88
78 3 0.05
79 4 0.07
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (76 bp):
AAGACACTAAAGGGATAAACCAATGAAATTATAAAAGTAGAAAAACAAATTATGCTAAATTAGAG
ACACTAAATTA
Found at i:633251 original size:146 final size:146
Alignment explanation
Indices: 633025--633379 Score: 563
Period size: 146 Copynumber: 2.4 Consensus size: 146
633015 ACTAATTCCA
* * * * * * *
633025 AAATTAGAGCATAATAGAAGGG-CCAAAATCAAAATTTGA-CC-CTGGTTTTAACCATGGATGAC
1 AAATTTGAGCATAACAG-AGGGACCAAAATCAGAATTTGACCCTCTAGTTTCAGCCATGGATGAG
* *
633087 CAAACTACTATTTGATTGGAATTCTAACGATATTTTGATTAACTAAAGGAAAAGAATCATGCCAA
65 CAAAATACTATTTGATTGGAATTCTAACGATATTTTGATCAACTAAAGGAAAAGAATCATGCCAA
*
633152 ATTATAAACACAATCCC
130 ATTATAAACACAACCCC
*
633169 AAATTTGAGCATAACAGAGGGACCAAAACCAGAATTTGACCCTCTAGTTTCAGCCATGGATGAGC
1 AAATTTGAGCATAACAGAGGGACCAAAATCAGAATTTGACCCTCTAGTTTCAGCCATGGATGAGC
633234 AAAATACTATTTGATTGGAATTCTAACGATATTTTGATCAACTAAAGGAAAAGAATCATGCCAAA
66 AAAATACTATTTGATTGGAATTCTAACGATATTTTGATCAACTAAAGGAAAAGAATCATGCCAAA
*
633299 TTATAAGCACAACCCC
131 TTATAAACACAACCCC
*
633315 AAAGTTGAGCATAACAGAGGGACCAAAATCAGAATTTGACCCTCTAGTTTCAGCCATGGATGAGC
1 AAATTTGAGCATAACAGAGGGACCAAAATCAGAATTTGACCCTCTAGTTTCAGCCATGGATGAGC
633380 TGAGAAAAAG
Statistics
Matches: 194, Mismatches: 14, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
143 4 0.02
144 30 0.15
145 2 0.01
146 158 0.81
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (146 bp):
AAATTTGAGCATAACAGAGGGACCAAAATCAGAATTTGACCCTCTAGTTTCAGCCATGGATGAGC
AAAATACTATTTGATTGGAATTCTAACGATATTTTGATCAACTAAAGGAAAAGAATCATGCCAAA
TTATAAACACAACCCC
Found at i:644861 original size:66 final size:65
Alignment explanation
Indices: 644753--644923 Score: 207
Period size: 66 Copynumber: 2.6 Consensus size: 65
644743 AGGAGGAGAA
* * ** *
644753 GGATCTGAGTAACCGTTATGGCCGCTAACGGAATATTCAAAAGACGGTGCGGTTGGCGCAAAAGA
1 GGATCTGAGTAACCGTTATGG-TGCTAACGGAATATTGAAAAGACGCAGCCGTTGGCGCAAAAGA
644818 C
65 C
* *
644819 GGATCTGAGTAACCGTTATGGTGACTAACGGAATATTGAAAAGACTCAGCCGTTGGTGCAAAAGA
1 GGATCTGAGTAACCGTTATGGTG-CTAACGGAATATTGAAAAGACGCAGCCGTTGGCGCAAAAGA
644884 C
65 C
* *** *
644885 GGAGCTGAGTGGTCGTTACGGTGTCTAACGGAATATTGA
1 GGATCTGAGTAACCGTTATGGTG-CTAACGGAATATTGA
644924 GGATAGTCCG
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
65 1 0.01
66 90 0.99
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (65 bp):
GGATCTGAGTAACCGTTATGGTGCTAACGGAATATTGAAAAGACGCAGCCGTTGGCGCAAAAGAC
Found at i:650174 original size:77 final size:77
Alignment explanation
Indices: 650038--650183 Score: 193
Period size: 77 Copynumber: 1.9 Consensus size: 77
650028 TCATAGAAGG
* * * *
650038 GCTTCTCAAATATCGTATAACAGATTTTAAATTATGTTTTTATTTCTTTATTTTCTTTTCAAGCA
1 GCTTCTCAAATATCGTATAACAGATTTCAAATTATGTCTTTATTACTTTATTTTATTTTCAAGCA
650103 ATATATATACGA
66 ATATATATACGA
* * * * * * *
650115 GCTTCTTAAATGTCTTATATCAGGTTTCAAATTATGTCTTTCTTACTTTCTTTTATTTTCAAGCA
1 GCTTCTCAAATATCGTATAACAGATTTCAAATTATGTCTTTATTACTTTATTTTATTTTCAAGCA
650180 ATAT
66 ATAT
650184 CTAATTCAAC
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
77 58 1.00
ACGTcount: A:0.28, C:0.14, G:0.08, T:0.49
Consensus pattern (77 bp):
GCTTCTCAAATATCGTATAACAGATTTCAAATTATGTCTTTATTACTTTATTTTATTTTCAAGCA
ATATATATACGA
Found at i:650698 original size:2 final size:2
Alignment explanation
Indices: 650691--650722 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
650681 CAATCTTCAA
650691 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
650723 GTTCACCAGA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:656090 original size:22 final size:21
Alignment explanation
Indices: 656043--656090 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
656033 AGGGTCTTAT
* **
656043 TTAAAAAAAAAAAACCTAAGG
1 TTAAAAAAAAAAAAACTAAAA
*
656064 GTAAAAAAAGAAAAAACTAAAA
1 TTAAAAAAA-AAAAAACTAAAA
656086 TTAAA
1 TTAAA
656091 TTAAAAATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.15
Consensus pattern (21 bp):
TTAAAAAAAAAAAAACTAAAA
Found at i:668196 original size:164 final size:164
Alignment explanation
Indices: 667866--668481 Score: 698
Period size: 164 Copynumber: 3.8 Consensus size: 164
667856 ACATATGCAA
* * * * * * *
667866 TTCTCTACATTTATT-AGTGAGTACTCGAAACTTCTTC-ATCACACGAGTATGACAGACACCTTA
1 TTCT-TACATTTATTGA-TGAGTACTCGAAACTT-GTCGGTTACATGAGCATGACAGAGACTTTA
* * * **
667929 GCTCCAGTATCATGTGGCCTTAGGCTC--AA----CGTCCTTACGTCAACTTATGTCTAAGTTAT
63 GCTCCGGTATCATGTGGCCTTAAGCTCAAAACTTCCGTCCTTACATCAACGAATGTCTAAGTTAT
* *
667988 ATGTATAAGCAACTTTTTCTAATGTGTAACGTTGATT
128 ATGTATATGCAACTTTTTCTAATGTGTAACGCTGATT
668025 TTCTTACATTTATTGATGAGTACTCGAAACTTGTCGGTTACATGAGCATGACAGAGACTTTAGCT
1 TTCTTACATTTATTGATGAGTACTCGAAACTTGTCGGTTACATGAGCATGACAGAGACTTTAGCT
*
668090 CCGGTATCATGTGGCCTTAAGCTCAAAACTTCCGTCCTTACATCAACGAATGTCTAAGTTTTATG
66 CCGGTATCATGTGGCCTTAAGCTCAAAACTTCCGTCCTTACATCAACGAATGTCTAAGTTATATG
*
668155 TATATGCAACTTTTTCTAATGTGTAACACTGATT
131 TATATGCAACTTTTTCTAATGTGTAACGCTGATT
* *
668189 TTCTTACATTTATTGACGAGTACTCGAAACTTGTCCGTTACATGAGCATGACAGAGACTTTAGCT
1 TTCTTACATTTATTGATGAGTACTCGAAACTTGTCGGTTACATGAGCATGACAGAGACTTTAGCT
* * * * *
668254 CCGGTATCATGTGGCCTTAGGCTCAAAACTTCCATCCTTACGTCAAGGTATGTCTAAGTTATATG
66 CCGGTATCATGTGGCCTTAAGCTCAAAACTTCCGTCCTTACATCAACGAATGTCTAAGTTATATG
* *
668319 TACATGCAACTTTTTCTAATGTGTAACGCTGACT
131 TATATGCAACTTTTTCTAATGTGTAACGCTGATT
* * * * * * * *
668353 TTCCTACCTTTATTAAAGAGTACCCGAAACTTGTCCGTCCGTTGCATGAGGATGGA-AGAGATTT
1 TTCTTACATTTATTGATGAGTACTCGAAACTTGT-CG---GTTACATGAGCAT-GACAGAGACTT
* * * * * *
668417 TAGCTCCGGCATCTTGCCGTCC-T-AGACTCAAAACTTACGTCTTTACATCAAC-ATATGTCTAA
61 TAGCTCCGGTATCATG-TGGCCTTAAG-CTCAAAACTTCCGTCCTTACATCAACGA-ATGTCTAA
668479 GTT
123 GTT
668482 GTCAACTTTA
Statistics
Matches: 394, Mismatches: 47, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
157 2 0.01
158 71 0.18
159 5 0.01
160 2 0.01
164 242 0.61
165 1 0.00
167 1 0.00
168 65 0.16
169 5 0.01
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (164 bp):
TTCTTACATTTATTGATGAGTACTCGAAACTTGTCGGTTACATGAGCATGACAGAGACTTTAGCT
CCGGTATCATGTGGCCTTAAGCTCAAAACTTCCGTCCTTACATCAACGAATGTCTAAGTTATATG
TATATGCAACTTTTTCTAATGTGTAACGCTGATT
Found at i:672947 original size:28 final size:30
Alignment explanation
Indices: 672892--672952 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 30
672882 TGGCAAAATT
*
672892 AAACTTATTATATAATTTTTTTATTTCTATAA
1 AAACTTATTATATAA--TTTTTAATTCTATAA
672924 AAACTTATTATAT-A-TTTTAATTCTATAA
1 AAACTTATTATATAATTTTTAATTCTATAA
672952 A
1 A
672953 TATTTTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 14 0.50
31 1 0.04
32 13 0.46
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (30 bp):
AAACTTATTATATAATTTTTAATTCTATAA
Found at i:678885 original size:28 final size:30
Alignment explanation
Indices: 678853--678911 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
678843 TAGTGACAAA
678853 AAAAAATTAAATT-A-AATAATTGGGTAATC
1 AAAAAA-TAAATTCACAATAATTGGGTAATC
*
678882 AAAAAATAAATTCACTAATAGTTGGGTAAT
1 AAAAAATAAATTCAC-AATAATTGGGTAAT
678912 TATTAGTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 6 0.23
29 7 0.27
31 13 0.50
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.31
Consensus pattern (30 bp):
AAAAAATAAATTCACAATAATTGGGTAATC
Found at i:680376 original size:31 final size:33
Alignment explanation
Indices: 680338--680418 Score: 103
Period size: 38 Copynumber: 2.4 Consensus size: 33
680328 TAACAAAAAA
680338 ACTAATTTACTC-TT-TGATCTAATGTATAGAC
1 ACTAATTTACTCTTTATGATCTAATGTATAGAC
680369 ACTAATTTACTCATTTTTAAGTGATCTAATGTATAGAC
1 ACTAATTTACTC---TTT-A-TGATCTAATGTATAGAC
680407 ACTAATTTACTC
1 ACTAATTTACTC
680419 ATTTTTAAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
31 12 0.28
35 2 0.05
38 29 0.67
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (33 bp):
ACTAATTTACTCTTTATGATCTAATGTATAGAC
Found at i:680403 original size:38 final size:38
Alignment explanation
Indices: 680352--680428 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
680342 ATTTACTCTT
680352 TGATCTAATGTATAGACACTAATTTACTCATTTTTAAG
1 TGATCTAATGTATAGACACTAATTTACTCATTTTTAAG
680390 TGATCTAATGTATAGACACTAATTTACTCATTTTTAAG
1 TGATCTAATGTATAGACACTAATTTACTCATTTTTAAG
680428 T
1 T
680429 AAAAAGAACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (38 bp):
TGATCTAATGTATAGACACTAATTTACTCATTTTTAAG
Found at i:682877 original size:2 final size:2
Alignment explanation
Indices: 682870--682901 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
682860 TTTTGGCCCT
682870 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
682902 CCTTTACTAA
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:693373 original size:6 final size:6
Alignment explanation
Indices: 693362--693396 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
693352 GATACAAGAT
693362 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTA
693397 TTATTGGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:694158 original size:71 final size:71
Alignment explanation
Indices: 694009--694151 Score: 223
Period size: 71 Copynumber: 2.0 Consensus size: 71
693999 GGTCTATTCG
* * *
694009 ATCGATACCTTGAGGACTTCTACTGAAACAAGTAAAGTCAATAGCCAAAGTTCAGCATCTCCTGC
1 ATCGATACCTTGAGGACTTATACCGAAACAAGTAAAGTCAATAGCCAAAGTTCAGCATCCCCTGC
694074 ACTTCT
66 ACTTCT
* * **
694080 ATCGATACCTTGAGGACTTATACCGAAACAAGTCAAGTCAATGGTTAAAGTTCAGCATCCCCTGC
1 ATCGATACCTTGAGGACTTATACCGAAACAAGTAAAGTCAATAGCCAAAGTTCAGCATCCCCTGC
694145 ACTTCT
66 ACTTCT
694151 A
1 A
694152 CTGATACTCT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (71 bp):
ATCGATACCTTGAGGACTTATACCGAAACAAGTAAAGTCAATAGCCAAAGTTCAGCATCCCCTGC
ACTTCT
Found at i:707074 original size:16 final size:16
Alignment explanation
Indices: 707055--707095 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 16
707045 CCCGCTTTTT
707055 AAGTTACTTTTAGTAC
1 AAGTTACTTTTAGTAC
707071 AAG----TTTTAGTAC
1 AAGTTACTTTTAGTAC
707083 AAGTTACTTTTAG
1 AAGTTACTTTTAG
707096 CCACAAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 8
0.72 0.00 0.28
Matches are distributed among these distances:
12 12 0.57
16 9 0.43
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.44
Consensus pattern (16 bp):
AAGTTACTTTTAGTAC
Found at i:710941 original size:10 final size:11
Alignment explanation
Indices: 710904--710934 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
710894 CTATAAACAA
710904 ATATTATATAT
1 ATATTATATAT
710915 ATATATATATAT
1 ATAT-TATATAT
710927 ATATTATA
1 ATATTATA
710935 CATTATTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATATTATATAT
Done.