Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold712.1
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: 793842
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 2523 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:328489 original size:15 final size:16
Alignment explanation
Indices: 328459--328491 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
328449 TGGTTAATTA
328459 ATTTTATAATTATTTT
1 ATTTTATAATTATTTT
*
328475 ATTTT-TAATTTTTTT
1 ATTTTATAATTATTTT
328490 AT
1 AT
328492 ATCCATATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
ATTTTATAATTATTTT
Found at i:330348 original size:24 final size:24
Alignment explanation
Indices: 330321--330372 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
330311 TTAGTAAGTC
*
330321 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
330345 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
330369 AAAT
1 AAAT
330373 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:332317 original size:24 final size:24
Alignment explanation
Indices: 332290--332341 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
332280 TTAGTAAGTC
*
332290 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
332314 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
332338 AAAT
1 AAAT
332342 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:333952 original size:16 final size:16
Alignment explanation
Indices: 333931--333967 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
333921 CTACAATAAC
* *
333931 AATTAATTAATTTTTA
1 AATTAATTAATATTAA
333947 AATTAATTAATATTAA
1 AATTAATTAATATTAA
333963 AATTA
1 AATTA
333968 CTCTTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTAATTAATATTAA
Found at i:337768 original size:3 final size:3
Alignment explanation
Indices: 337760--337786 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
337750 CAGTGCATCA
337760 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
337787 TGTCACTTTC
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:338529 original size:31 final size:30
Alignment explanation
Indices: 338493--338571 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
338483 TCTATTGGTA
338493 GTAAAATTTTAAATTAATCCCTTCTTAAAA-TT
1 GTAAAATTTTAAATTAAT-CC-T-TTAAAAGTT
* *
338525 -TAAAATTCATAACTTAATCCTTTAAAAGTT
1 GTAAAATT-TTAAATTAATCCTTTAAAAGTT
*
338555 GTAAAATTTTACATTAA
1 GTAAAATTTTAAATTAA
338572 AATAATAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
29 6 0.15
30 9 0.23
31 16 0.41
32 8 0.21
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (30 bp):
GTAAAATTTTAAATTAATCCTTTAAAAGTT
Found at i:345784 original size:31 final size:31
Alignment explanation
Indices: 345744--345809 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
345734 AAAATCTCAA
* *
345744 AATTTGAAAAGTACAATGG-CTAAAATTGACC
1 AATTCGAAAAGCACAA-GGACTAAAATTGACC
* *
345775 AATTCGAAAAGCATAAGGACTAAAATTGATC
1 AATTCGAAAAGCACAAGGACTAAAATTGACC
345806 AATT
1 AATT
345810 AATGTATAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (31 bp):
AATTCGAAAAGCACAAGGACTAAAATTGACC
Found at i:346107 original size:51 final size:51
Alignment explanation
Indices: 346026--346142 Score: 139
Period size: 51 Copynumber: 2.3 Consensus size: 51
346016 TTAGGTATAA
* * *
346026 TAACAAATTTAGCTCTCAAAATTTACACATTTTGTCAA-TTTGATCTTGATT
1 TAACAAATTTAGCTCACAAAATTTACACATTCTATCAATTTTG-TCTTGATT
* * *
346077 TAACAAATTTAGC-CAACAATATTTATACATTCTATTAATTTTGTCTTGATT
1 TAACAAATTTAGCTC-ACAAAATTTACACATTCTATCAATTTTGTCTTGATT
*
346128 TAGCAAATTTAGCTC
1 TAACAAATTTAGCTC
346143 GTGATATTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
50 1 0.02
51 50 0.89
52 5 0.09
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (51 bp):
TAACAAATTTAGCTCACAAAATTTACACATTCTATCAATTTTGTCTTGATT
Found at i:353957 original size:72 final size:73
Alignment explanation
Indices: 353831--353986 Score: 174
Period size: 72 Copynumber: 2.2 Consensus size: 73
353821 AGAATCAACC
* * * * * * * **
353831 GAAGGCCAATGTGTGAGGTCTCATCCCTTTGAGGGATTGGCAAAGTTGTTAGGTCTTGT-CCCTT
1 GAAGACCAAGGTGTGAGGTATCATCCCATTGAGGAATTGGCAAAGATGTAAGGTCTCATCCCCTT
*
353895 TTGCCCTT
66 ATGCCCTT
*
353903 G-AGACCAAGGTGTGAGGTATCATCTTCATTGAGGAATTGGCTAAA-ATGTAAGGTCTCATCCCC
1 GAAGACCAAGGTGTGAGGTATCATC-CCATTGAGGAATTGGC-AAAGATGTAAGGTCTCATCCCC
353966 TTATGCCCTT
64 TTATGCCCTT
353976 GAAGACCAAGG
1 GAAGACCAAGG
353987 CGAGAGGTCT
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
71 20 0.29
72 24 0.35
73 16 0.23
74 9 0.13
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (73 bp):
GAAGACCAAGGTGTGAGGTATCATCCCATTGAGGAATTGGCAAAGATGTAAGGTCTCATCCCCTT
ATGCCCTT
Found at i:354397 original size:19 final size:19
Alignment explanation
Indices: 354373--354415 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
354363 GTTGCTCACC
354373 CTCTTCATAACAAAATTAT
1 CTCTTCATAACAAAATTAT
354392 CTCTTCATAACAAAATTAT
1 CTCTTCATAACAAAATTAT
354411 CTCTT
1 CTCTT
354416 TAGGCTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (19 bp):
CTCTTCATAACAAAATTAT
Found at i:358866 original size:122 final size:121
Alignment explanation
Indices: 358648--358948 Score: 390
Period size: 122 Copynumber: 2.5 Consensus size: 121
358638 TACAACAACG
* *
358648 ACCTAATGACTTAAATAAAAACTTTTGAATAGTTTAGTGACTATTTTGTAACTTTTTGAAGTTAC
1 ACCTAATGAATTAAATAAAAACTTTTGAATAGTTTAGTGAC-ATTTTGTAACTTTTTGAAGCTAC
*
358713 AAATAACGATTTTAACTTTCTGCGAAGAGAGAAGGCTATACAACAATAATTTTAACA
65 AAATAACAATTTTAACTTTCTGCGAAGAGAGAAGGCTATACAACAATAATTTTAACA
** * *
358770 ACCTAATGAATTAAATAAAAACTTTAAAATAGTTTAATGATCATTTTGTAACTTTTTGAAGCTGC
1 ACCTAATGAATTAAATAAAAACTTTTGAATAGTTTAGTGA-CATTTTGTAACTTTTTGAAGCTAC
* * * * *
358835 AAATAATAATTTTAACTTTTTGC-AGATAGAGAAGGCTATACAATAATGATTTTAACA
65 AAATAACAATTTTAACTTTCTGCGA-AGAGAGAAGGCTATACAACAATAATTTTAACA
* * ***
358892 GCTTAAT-AATTTAAATAAATTTTTTTGAATAGTTTAGTGACCATTTTGTAACTTTTT
1 ACCTAATGAA-TTAAATAAAAACTTTTGAATAGTTTAGTGA-CATTTTGTAACTTTTT
358949 AAAGTTGAAT
Statistics
Matches: 155, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
121 3 0.02
122 151 0.97
123 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (121 bp):
ACCTAATGAATTAAATAAAAACTTTTGAATAGTTTAGTGACATTTTGTAACTTTTTGAAGCTACA
AATAACAATTTTAACTTTCTGCGAAGAGAGAAGGCTATACAACAATAATTTTAACA
Found at i:365714 original size:30 final size:30
Alignment explanation
Indices: 365675--365749 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 30
365665 TTAAATTAAT
* *
365675 AATAGTAAAATTATACTTTAACCTCTCAAA
1 AATAATAAAATTATAATTTAACCTCTCAAA
* * * *
365705 AATGATAAAAATT-TAATTTAAGCTTTTAAA
1 AATAAT-AAAATTATAATTTAACCTCTCAAA
*
365735 AATAATAAAAATATA
1 AATAATAAAATTATA
365750 GACGATTAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
29 5 0.14
30 24 0.69
31 6 0.17
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (30 bp):
AATAATAAAATTATAATTTAACCTCTCAAA
Found at i:366124 original size:18 final size:17
Alignment explanation
Indices: 366096--366129 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
366086 TTTTTTTTCT
*
366096 TTTTAAATTTAGTTTAA
1 TTTTAAATTTAATTTAA
366113 TTTTAAATTTTAATTTA
1 TTTTAAA-TTTAATTTA
366130 CTACTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTTAAATTTAATTTAA
Found at i:371486 original size:23 final size:23
Alignment explanation
Indices: 371455--371505 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
371445 ACCTACTTCC
* *
371455 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
371478 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
371501 TTACA
1 TTACA
371506 TTTCTCCCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:385520 original size:5 final size:5
Alignment explanation
Indices: 385510--385548 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
385500 ATATGGTAAA
385510 AAAAT AAAAT AAAAT AAAAT AAAAT ATTAAA- AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT A--AAAT AAAAT AAA
385549 CATGTGAGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 3 0.10
5 24 0.77
6 1 0.03
7 3 0.10
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:385530 original size:15 final size:15
Alignment explanation
Indices: 385506--385548 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
385496 TATAATATGG
385506 TAAAAAAATAAAATA
1 TAAAAAAATAAAATA
385521 -AAATAAAATAAAATA
1 TAAA-AAAATAAAATA
385536 TTAAAAAAATAAA
1 -TAAAAAAATAAA
385549 CATGTGAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.12
15 11 0.44
16 8 0.32
17 3 0.12
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAAAAAATAAAATA
Found at i:387656 original size:13 final size:14
Alignment explanation
Indices: 387628--387656 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
387618 AAATAATTTT
387628 AATATTTATCCTAA
1 AATATTTATCCTAA
387642 AATATTTAT-CTAA
1 AATATTTATCCTAA
387655 AA
1 AA
387657 CGAATTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (14 bp):
AATATTTATCCTAA
Found at i:398514 original size:40 final size:40
Alignment explanation
Indices: 398444--398519 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
398434 ATATCAACAC
* * *
398444 TTATATGCACGAAATTAACAAAATTGAATAATCCAACAAT
1 TTATATGCACGAAATTAACAAAAATAAATAACCCAACAAT
*
398484 TTATATGCAAC-AAATTAATAAAAATAAATAACCCAA
1 TTATATGC-ACGAAATTAACAAAAATAAATAACCCAA
398520 AGGCAAAGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 29 0.94
41 2 0.06
ACGTcount: A:0.54, C:0.14, G:0.05, T:0.26
Consensus pattern (40 bp):
TTATATGCACGAAATTAACAAAAATAAATAACCCAACAAT
Found at i:401518 original size:28 final size:28
Alignment explanation
Indices: 401462--401544 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
401452 CACAGGAATA
*
401462 AGTTGCTCACACAAGCTAACAGTATATTAG
1 AGTTCCTCACACAAGCTAACA-T-TATTAG
* * *
401492 GGTTCCTCACACAAGTTGACATTATTAG
1 AGTTCCTCACACAAGCTAACATTATTAG
* *
401520 AGTTGCTCACGCAAGCTAACATTAT
1 AGTTCCTCACACAAGCTAACATTAT
401545 ATTGAGGTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
28 26 0.59
29 1 0.02
30 17 0.39
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.29
Consensus pattern (28 bp):
AGTTCCTCACACAAGCTAACATTATTAG
Found at i:402634 original size:18 final size:18
Alignment explanation
Indices: 402608--402642 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
402598 TTGTCAGGCT
*
402608 ATCTACCCAAGTTTGAAA
1 ATCTACCCAAATTTGAAA
*
402626 ATCTGCCCAAATTTGAA
1 ATCTACCCAAATTTGAA
402643 GGGTTCCAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (18 bp):
ATCTACCCAAATTTGAAA
Found at i:403158 original size:14 final size:14
Alignment explanation
Indices: 403127--403166 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
403117 TATGAAATTT
*
403127 AATTAAATATTTAAA
1 AATTAAA-ATTAAAA
403142 AATTAAAATTAAAA
1 AATTAAAATTAAAA
*
403156 AATAAAAATTA
1 AATTAAAATTA
403167 CCTCCTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATTAAAATTAAAA
Found at i:414921 original size:10 final size:10
Alignment explanation
Indices: 414906--415017 Score: 57
Period size: 10 Copynumber: 10.7 Consensus size: 10
414896 TTTATATATA
*
414906 TTTTTAGATT
1 TTTTTAAATT
414916 TTTTTAAA-T
1 TTTTTAAATT
* *
414925 TTATTATATT
1 TTTTTAAATT
*
414935 TTTTAAAATAT
1 TTTTTAAAT-T
*
414946 AAATTTTGAAATT
1 ---TTTTTAAATT
*
414959 TTTATAAATT
1 TTTTTAAATT
414969 TTTTTAAA-T
1 TTTTTAAATT
* *
414978 TTTATAAATA
1 TTTTTAAATT
**
414988 TTTTTATTTT
1 TTTTTAAATT
414998 ATTTTTATAATT
1 -TTTTTA-AATT
415010 TTTGTTAA
1 TTT-TTAA
415018 GAGATAGATC
Statistics
Matches: 75, Mismatches: 18, Indels: 17
0.68 0.16 0.15
Matches are distributed among these distances:
9 15 0.20
10 35 0.47
11 11 0.15
12 5 0.07
13 1 0.01
14 8 0.11
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (10 bp):
TTTTTAAATT
Found at i:414980 original size:19 final size:18
Alignment explanation
Indices: 414913--414993 Score: 62
Period size: 18 Copynumber: 4.5 Consensus size: 18
414903 ATATTTTTAG
*
414913 ATTTTTTTAAATTTAT-T
1 ATTTTTTTAAATTTATAA
*
414930 ATATTTTTTAAA-ATATAA
1 AT-TTTTTTAAATTTATAA
*
414948 A--TTTTGAAATTTTTATAA
1 ATTTTTTTAAA--TTTATAA
414966 ATTTTTTTAAATTTTATAA
1 ATTTTTTTAAA-TTTATAA
*
414985 ATATTTTTA
1 ATTTTTTTA
414994 TTTTATTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
15 7 0.14
17 5 0.10
18 16 0.31
19 16 0.31
20 7 0.14
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (18 bp):
ATTTTTTTAAATTTATAA
Found at i:414988 original size:43 final size:43
Alignment explanation
Indices: 414899--414985 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
414889 AACTTTCTTT
* * * * * *
414899 ATATATATTTTTAGATTTTTTTAAATTTATTATATTTTTTAAA
1 ATATAAATTTTGAAATTTTTATAAATTTATTAAATTTTATAAA
*
414942 ATATAAATTTTGAAATTTTTATAAATTTTTTTAAATTTTATAAA
1 ATATAAATTTTGAAATTTTTATAAA-TTTATTAAATTTTATAAA
414986 TATTTTTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 21 0.58
44 15 0.42
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (43 bp):
ATATAAATTTTGAAATTTTTATAAATTTATTAAATTTTATAAA
Found at i:417131 original size:29 final size:28
Alignment explanation
Indices: 417084--417162 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 28
417074 GTGAATGTTT
* * *
417084 TCAATTTAGTCTTTATATTTTAATTTGA
1 TCAATTTAGTTTTTGTATTTTAAATTGA
*
417112 TCATATTTAGTTTTTGTATTTTTAAATTGG
1 TCA-ATTTAGTTTTTGTA-TTTTAAATTGA
*
417142 TCAATTTTAGTTTATGTATTT
1 TCAA-TTTAGTTTTTGTATTT
417163 AAAAAAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
28 3 0.07
29 16 0.37
30 24 0.56
ACGTcount: A:0.25, C:0.05, G:0.10, T:0.59
Consensus pattern (28 bp):
TCAATTTAGTTTTTGTATTTTAAATTGA
Found at i:423711 original size:27 final size:29
Alignment explanation
Indices: 423655--423712 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
423645 TAAATAAGAA
* * *
423655 AATATAAAATTTTAAAAATTATAATTTTT
1 AATATAAAATTATAAAAATGATAATCTTT
423684 AATA-AAAATTATAAAAATGA-AATCTTT
1 AATATAAAATTATAAAAATGATAATCTTT
423711 AA
1 AA
423713 AATTCAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 8 0.31
28 14 0.54
29 4 0.15
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (29 bp):
AATATAAAATTATAAAAATGATAATCTTT
Found at i:424003 original size:16 final size:17
Alignment explanation
Indices: 423982--424019 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
423972 TAAACATTAA
423982 TATTTATATA-AT-TTTT
1 TATTTA-ATACATATTTT
423998 TATTTAATACATATTTT
1 TATTTAATACATATTTT
424015 TATTT
1 TATTT
424020 TCGTAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 3 0.15
16 8 0.40
17 9 0.45
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTAATACATATTTT
Found at i:426771 original size:16 final size:18
Alignment explanation
Indices: 426740--426777 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
426730 AAAATTCACG
426740 AAATTGAAACATTAAAAA
1 AAATTGAAACATTAAAAA
*
426758 AAATT-AAA-ATTAAAAC
1 AAATTGAAACATTAAAAA
426774 AAAT
1 AAAT
426778 CTTCACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
17 3 0.16
18 5 0.26
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (18 bp):
AAATTGAAACATTAAAAA
Found at i:442684 original size:2 final size:2
Alignment explanation
Indices: 442679--442710 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
442669 TGTTGTGCAA
442679 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
442711 TCCTTGTTTT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:444308 original size:316 final size:313
Alignment explanation
Indices: 443734--444359 Score: 1189
Period size: 316 Copynumber: 2.0 Consensus size: 313
443724 TTCATACGAA
443734 CTTACCAGGCTAAATTGCAGAAATACCAAAATTTAGGGACATTTTGGTAATTTTCTATTTTCATC
1 CTTACCAGGCTAAATTGCAGAAATACCAAAATTTAGGGACATTTTGGTAATTTTCTATTTTCATC
443799 AAATATTCACCCAATCTTGATCTAAATTAATATTTCATTCAATTTATTAATTTAAATAATAAAAC
66 AAATATTCACCCAATCTTGATCTAAATTAATATTTCATTCAATTTATTAATTTAAATAATAAAAC
443864 AATTCATTTCATGAAATTTGGTCACTTTTTGACATTTTTACAAATTTACCCTTAAAGTTTCACAT
131 AATTCATTTCATGAAATTTGGTCACTTTTTGACATTTTTACAAATTTACCCTTAAAGTTTCACAT
443929 TTGTTCAATTTAGTCCCTAAACTTAAAACATGTAAATTAGCTATTTTTAAAATAATATCATATTA
196 TTGTTCAATTTAGTCCCTAAACTTAAAACATGTAAATTAGCTATTTTTAAAATAATATCATATTA
443994 GATGAATATTCACATATATTTTTCCTCCTCCTCCTCTCCATTCCACATCCTTGATT
261 GATGAATATTCACATATA-TTTT--TCCTCCTCCTCTCCATTCCACATCCTTGATT
444050 CTTACCAGGCTAAATTGCAGAAATACCAAAATTTAGGGACATTTTGGTAATTTTCTATTTTCATC
1 CTTACCAGGCTAAATTGCAGAAATACCAAAATTTAGGGACATTTTGGTAATTTTCTATTTTCATC
444115 AAATATTCACCCAATCTTGATCTAAATTAATATTTCATTCAATTTATTAATTTAAATAATAAAAC
66 AAATATTCACCCAATCTTGATCTAAATTAATATTTCATTCAATTTATTAATTTAAATAATAAAAC
* *
444180 AATTCATTTCATGAAATTTGGTCACTTTTTGACATTTTTGCAAATTTACCCTTAAAGTTTCATAT
131 AATTCATTTCATGAAATTTGGTCACTTTTTGACATTTTTACAAATTTACCCTTAAAGTTTCACAT
*
444245 TTGTTCAATTTAGTCCCTAAACTTAAAACATGTAAATTAGCTATTTTTAAAATAATCTCATATTA
196 TTGTTCAATTTAGTCCCTAAACTTAAAACATGTAAATTAGCTATTTTTAAAATAATATCATATTA
*
444310 GCTGAATATTCACATATATTTTTCCTCCTCCTCTCCATTCCACATCCTTG
261 GATGAATATTCACATATATTTTTCCTCCTCCTCTCCATTCCACATCCTTG
444360 GTATATACAT
Statistics
Matches: 306, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
313 28 0.09
315 4 0.01
316 274 0.90
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (313 bp):
CTTACCAGGCTAAATTGCAGAAATACCAAAATTTAGGGACATTTTGGTAATTTTCTATTTTCATC
AAATATTCACCCAATCTTGATCTAAATTAATATTTCATTCAATTTATTAATTTAAATAATAAAAC
AATTCATTTCATGAAATTTGGTCACTTTTTGACATTTTTACAAATTTACCCTTAAAGTTTCACAT
TTGTTCAATTTAGTCCCTAAACTTAAAACATGTAAATTAGCTATTTTTAAAATAATATCATATTA
GATGAATATTCACATATATTTTTCCTCCTCCTCTCCATTCCACATCCTTGATT
Found at i:447326 original size:47 final size:47
Alignment explanation
Indices: 447258--447398 Score: 176
Period size: 47 Copynumber: 3.0 Consensus size: 47
447248 TTCGTTTTCT
** *
447258 CGATGCCATAGACCA-ACTATGGTCTTACATGGAATCACATATCACAC
1 CGATGCCATATCCCAGA-TATGGTCTTACACGGAATCACATATCACAC
* * * *
447305 CGATGTCATATCCCAGATATGGTCTTACACAGTAGCACATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTACACGGAATCACATATCACAC
* *
447352 TGATGCCATATCCCAGATATGATCTTACACGGAAATCACATATCACA
1 CGATGCCATATCCCAGATATGGTCTTACACGG-AATCACATATCACA
447399 TATTGCCATG
Statistics
Matches: 79, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
47 66 0.84
48 13 0.16
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (47 bp):
CGATGCCATATCCCAGATATGGTCTTACACGGAATCACATATCACAC
Found at i:459409 original size:20 final size:20
Alignment explanation
Indices: 459371--459409 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
459361 TGAACCAAAA
*
459371 TTTTAATATTTTTTATAATT
1 TTTTAATATTTATTATAATT
459391 TTTTAATGATTTATT-TAAT
1 TTTTAAT-ATTTATTATAAT
459410 CAAATCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTTAATATTTATTATAATT
Found at i:465413 original size:31 final size:31
Alignment explanation
Indices: 465378--465436 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
465368 CAATCCAATA
*
465378 ACTTAAATAAAAACTTTCGAATAATTTAATG
1 ACTTAAATAAAAACTTTCAAATAATTTAATG
* * *
465409 ACTTAAATGAGAACTTTTAAATAATTTA
1 ACTTAAATAAAAACTTTCAAATAATTTA
465437 CTGATCATTT
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:0.47, C:0.08, G:0.07, T:0.37
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAATAATTTAATG
Found at i:466094 original size:17 final size:18
Alignment explanation
Indices: 466074--466109 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
466064 GAGAGAAAGG
*
466074 AGAAGAAG-AGAAGGAAA
1 AGAAGAAGAAGAAAGAAA
466091 AGAAGAAGAAGAAAGAAA
1 AGAAGAAGAAGAAAGAAA
466109 A
1 A
466110 AAAAAAGGTA
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:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (18 bp):
AGAAGAAGAAGAAAGAAA
Found at i:466104 original size:14 final size:14
Alignment explanation
Indices: 466058--466101 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
466048 TAGAGAAAAA
466058 AAAAGAGAGAGAAAGG
1 AAAAGA-AGAG-AAGG
*
466074 AGAAGAAGAGAAGG
1 AAAAGAAGAGAAGG
466088 AAAAGAAGAAGAAG
1 AAAAGAAG-AGAAG
466102 AAAGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 11 0.44
15 9 0.36
16 5 0.20
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAGAAGG
Found at i:466111 original size:20 final size:20
Alignment explanation
Indices: 466060--466110 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
466050 GAGAAAAAAA
* *
466060 AAGAG-AGAGAAAGGAGAAG
1 AAGAGAAGAAAAAGAAGAAG
*
466079 AAGAGAAGGAAAAGAAGAAG
1 AAGAGAAGAAAAAGAAGAAG
466099 AAGA-AAGAAAAA
1 AAGAGAAGAAAAA
466111 AAAAAGGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (20 bp):
AAGAGAAGAAAAAGAAGAAG
Found at i:466317 original size:41 final size:38
Alignment explanation
Indices: 466266--466457 Score: 115
Period size: 41 Copynumber: 4.7 Consensus size: 38
466256 TATAGTTTAG
* * *
466266 ATTAGAATTTTGTATGAATATTTTAAATTTTTTGTATGAAT
1 ATTATAATTTTGTATGAATATTGT-AA--TGTTGTATGAAT
*
466307 ATTATAATTTTTTATGAATATTGTAATGTTGTATGAAT
1 ATTATAATTTTGTATGAATATTGTAATGTTGTATGAAT
* * *
466345 ATTGTAATTATTTTAT-AATTAAATTTGTATTTATAGTT-T-TG--G
1 ATTATAATT-TTGTATGAA-T--A-TTGTA---AT-GTTGTATGAAT
*
466387 ATTAGTAATTTTTTGTATGAATATTGTAATTTTGTATGAAT
1 ATTA-TAA--TTTTGTATGAATATTGTAATGTTGTATGAAT
466428 ATTATAAATTTTTTGTATGAATATTGTAAT
1 ATTAT-AA--TTTTGTATGAATATTGTAAT
466458 ATTATAGTTT
Statistics
Matches: 123, Mismatches: 10, Indels: 36
0.73 0.06 0.21
Matches are distributed among these distances:
37 2 0.02
38 24 0.20
39 9 0.07
40 3 0.02
41 55 0.45
42 9 0.07
43 3 0.02
44 8 0.07
45 7 0.06
46 3 0.02
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (38 bp):
ATTATAATTTTGTATGAATATTGTAATGTTGTATGAAT
Found at i:466474 original size:27 final size:24
Alignment explanation
Indices: 466416--466651 Score: 190
Period size: 27 Copynumber: 9.8 Consensus size: 24
466406 AATATTGTAA
*
466416 TTTTGTATGAATATTATAA-A-TT
1 TTTTGTATGAATATTGTAATATTT
466438 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGTAATATT-T
*
466463 AGTTTTGTATGAATATTG-CA-ATTT
1 --TTTTGTATGAATATTGTAATATTT
*
466487 TTTTGCATGAATATTGT-A-A-TT
1 TTTTGTATGAATATTGTAATATTT
* ** * *
466508 TTGTACATGAATATTATAATTTTGT
1 TTTTGTATGAATATTGTAATATT-T
466533 AATTTTGTATGAATA-T-T-ATATTT
1 --TTTTGTATGAATATTGTAATATTT
*
466556 TTTTGTATGAATGTTGTAATATTAT
1 TTTTGTATGAATATTGTAATATT-T
*
466581 AATTTTGTATGAATATTG-CA-ATTT
1 --TTTTGTATGAATATTGTAATATTT
466605 TTTTGTATGAATATTGTAATATTGT
1 TTTTGTATGAATATTGTAATATT-T
466630 AATTTTGTATGAATATTGTAAT
1 --TTTTGTATGAATATTGTAAT
466652 GTGAGGATAT
Statistics
Matches: 176, Mismatches: 15, Indels: 41
0.76 0.06 0.18
Matches are distributed among these distances:
21 28 0.16
22 53 0.30
23 4 0.02
24 16 0.09
25 11 0.06
26 3 0.02
27 61 0.35
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (24 bp):
TTTTGTATGAATATTGTAATATTT
Found at i:466512 original size:41 final size:40
Alignment explanation
Indices: 466273--466699 Score: 198
Period size: 49 Copynumber: 9.5 Consensus size: 40
466263 TAGATTAGAA
* *
466273 TTTTGTATGAATATTTTAAATTTTTTGTATGAATATTATAA-T
1 TTTTGTATGAATATTGT-AA--TTTTGTATGAATATTGTAATT
*
466315 TTTT-TATGAATATTGTAATGTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATT
* * * * *
466354 ATTTTATAATTAA-ATTTGT-ATTTATAGTTTTGGAT-TAGTAATT
1 -TTTTGT-ATGAATA-TTGTAATTT-T-G-TATGAATATTGTAATT
*
466397 TTTTGTATGAATATTGTAATTTTGTATGAATATTATAAATT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTGT-AATT
*
466438 TTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTGCAATTT
1 TTTTGTATGAATATTG------TA-A-TTTTGTATGAATATTGTAA-TT
* *
466487 TTTTGCATGAATATTGTAATTTTGTACATGAATATTATAATTTTGT
1 TTTTGTATGAATATTGTAATTTTGT--ATGAATATTGTAA---T-T
* * *
466533 AATTTTGTATGAATATTATATTTTTTTGTATGAATGTTGTAATATTAT
1 --TTTTGTATGAATATTGTA--ATTTTGTATGAATATTGT-A-A-T-T
*
466581 AATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTGT
1 --TTTTGTATGAATATTGTAA---TTTTGTATGAATATTGT-A-A-T-T
* *
466630 AATTTTGTATGAATATTGTAATGTGAGGATATATTGTAATATTGTAATT
1 --TTTTGTATGAATATTGTAAT-T----TTGTA-TG-AATATTGTAATT
466679 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
466700 ATTTTATAAT
Statistics
Matches: 310, Mismatches: 33, Indels: 80
0.73 0.08 0.19
Matches are distributed among these distances:
38 17 0.05
39 6 0.02
40 9 0.03
41 51 0.16
42 24 0.08
43 21 0.07
44 5 0.02
45 2 0.01
46 3 0.01
47 23 0.07
48 49 0.16
49 77 0.25
50 8 0.03
51 4 0.01
52 3 0.01
53 8 0.03
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.54
Consensus pattern (40 bp):
TTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATT
Found at i:466547 original size:70 final size:69
Alignment explanation
Indices: 466397--466575 Score: 204
Period size: 70 Copynumber: 2.6 Consensus size: 69
466387 ATTAGTAATT
* * ** *
466397 TTTTGTATGAATATTGTAA---TTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATA
1 TTTTGTATGAATATTG-AATTTTTTTGTATGAATATTGT-AATTTTGTACATGAATATTATAATA
*
466459 TTATAG
64 TTATAA
* *
466465 TTTTGTATGAATATTGCAATTTTTTTGCATGAATATTGTAATTTTGTACATGAATATTATAATTT
1 TTTTGTATGAATATTG-AATTTTTTTGTATGAATATTGTAATTTTGTACATGAATATTATAATAT
*
466530 TGTAA
65 TATAA
*
466535 TTTTGTATGAATATT-ATATTTTTTTGTATGAATGTTGTAAT
1 TTTTGTATGAATATTGA-ATTTTTTTGTATGAATATTGTAAT
466576 ATTATAATTT
Statistics
Matches: 95, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
68 19 0.20
69 22 0.23
70 39 0.41
71 15 0.16
ACGTcount: A:0.31, C:0.02, G:0.13, T:0.54
Consensus pattern (69 bp):
TTTTGTATGAATATTGAATTTTTTTGTATGAATATTGTAATTTTGTACATGAATATTATAATATT
ATAA
Found at i:466566 original size:48 final size:48
Alignment explanation
Indices: 466487--466693 Score: 208
Period size: 48 Copynumber: 4.3 Consensus size: 48
466477 ATTGCAATTT
* * * * ** * *
466487 TTTTGCATGAATATTGTAATTTTGTACATGAATATTATAATTTTGTAA
1 TTTTGTATGAATATTATATTTTTTTGTATGAATATTGTAATATTGTAA
* *
466535 TTTTGTATGAATATTATATTTTTTTGTATGAATGTTGTAATATTATAA
1 TTTTGTATGAATATTATATTTTTTTGTATGAATATTGTAATATTGTAA
466583 TTTTGTATGAATATTGCA-ATTTTTTTGTATGAATATTGTAATATTGTAA
1 TTTTGTATGAATATT--ATATTTTTTTGTATGAATATTGTAATATTGTAA
* * * *
466632 TTTTGTATGAATATTGTA---ATGTG-AGGATATATTGTAATATTGTAA
1 TTTTGTATGAATATTATATTTTTTTGTATGA-ATATTGTAATATTGTAA
466677 TTTTTTGTATGAATATT
1 --TTTTGTATGAATATT
466694 GTAATTATTT
Statistics
Matches: 137, Mismatches: 16, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
44 3 0.02
45 20 0.15
47 15 0.11
48 54 0.39
49 44 0.32
50 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.53
Consensus pattern (48 bp):
TTTTGTATGAATATTATATTTTTTTGTATGAATATTGTAATATTGTAA
Found at i:466592 original size:118 final size:119
Alignment explanation
Indices: 466410--466630 Score: 390
Period size: 118 Copynumber: 1.9 Consensus size: 119
466400 TGTATGAATA
*
466410 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAGTTTTGTATGA
1 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATGA
*
466475 ATATTGCAATTTTTTTGCATGAATATTGTAATTTTGTACATGAATATTATAATT
66 ATATTGCAATTTTTTTGCATGAATATTGTAATATTGTACATGAATATTATAATT
* *
466529 TTGTAATTTTGTATGAATATTAT-ATTTTTTTGTATGAATGTTGTAATATTATAATTTTGTATGA
1 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATGA
*
466593 ATATTGCAATTTTTTTGTATGAATATTGTAATATTGTA
66 ATATTGCAATTTTTTTGCATGAATATTGTAATATTGTA
466631 ATTTTGTATG
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
118 74 0.76
119 23 0.24
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (119 bp):
TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATGA
ATATTGCAATTTTTTTGCATGAATATTGTAATATTGTACATGAATATTATAATT
Found at i:466597 original size:19 final size:19
Alignment explanation
Indices: 466573--466630 Score: 53
Period size: 22 Copynumber: 2.9 Consensus size: 19
466563 TGAATGTTGT
466573 AATATTATAATTTTGTATG
1 AATATTATAATTTTGTATG
**
466592 AATATTGCAATTTTTTTGTATG
1 AATATT---ATAATTTTGTATG
* *
466614 AATATTGTAATATTGTA
1 AATATTATAATTTTGTA
466631 ATTTTGTATG
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
19 13 0.43
22 17 0.57
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (19 bp):
AATATTATAATTTTGTATG
Found at i:466651 original size:19 final size:19
Alignment explanation
Indices: 466271--466533 Score: 136
Period size: 19 Copynumber: 13.5 Consensus size: 19
466261 TTTAGATTAG
*
466271 AATTTTGTATGAATATTTT
1 AATTTTGTATGAATATTGT
*
466290 AAATTTTTTGTATGAATATTAT
1 -AA--TTTTGTATGAATATTGT
*
466312 AATTTTTTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
466331 AATGTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
466350 AATTATTTTAT-AATTAAATTTGT
1 AATT-TTGTATGAA-T--A-TTGT
* * *
466373 -ATTTATAGTTTTGGAT-TAGT
1 AATTT-T-G-TATGAATATTGT
466393 AATTTTTTGTATGAATATTGT
1 AA--TTTTGTATGAATATTGT
*
466414 AATTTTGTATGAATATTAT
1 AATTTTGTATGAATATTGT
466433 AAATTTT-T-TG--TA-TG-
1 -AATTTTGTATGAATATTGT
* *
466447 AATATTG--T-AATATTAT
1 AATTTTGTATGAATATTGT
* *
466463 AGTTTTGTATGAATATTGC
1 AATTTTGTATGAATATTGT
*
466482 AATTTTTTTGCATGAATATTGT
1 AA---TTTTGTATGAATATTGT
*
466504 AATTTTGTACATGAATATTAT
1 AATTTTGT--ATGAATATTGT
466525 AATTTTGTA
1 AATTTTGTA
466534 ATTTTGTATG
Statistics
Matches: 187, Mismatches: 27, Indels: 59
0.68 0.10 0.22
Matches are distributed among these distances:
13 6 0.03
14 2 0.01
15 2 0.01
16 7 0.04
18 3 0.02
19 67 0.36
20 22 0.12
21 28 0.15
22 39 0.21
23 7 0.04
24 3 0.02
25 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.54
Consensus pattern (19 bp):
AATTTTGTATGAATATTGT
Found at i:466672 original size:118 final size:119
Alignment explanation
Indices: 466397--466651 Score: 371
Period size: 118 Copynumber: 2.2 Consensus size: 119
466387 ATTAGTAATT
466397 TTTTGTATGAATATTGTAATTTTGTATGAATATTATAA-A-TTTTTTGTATGAATATTGTAATAT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATT-TAATATTTTTTTGTATGAATATTGTAATAT
* *
466460 TATAGTTTTGTATGAATATTGCAATTTTTTTGCATGAATATTGTAATTTTGTACA
65 TATAATTTTGTATGAATATTGCAATTTTTTTGCATGAATATTGTAATATTGTACA
* * *
466515 TGAATAT-TAT-AATTTTGTAATTTTGTATGAATA-TT-ATATTTTTTTGTATGAATGTTGTAAT
1 T---TTTGTATGAATATTGTAATTTTGTATGAATATTTAATATTTTTTTGTATGAATATTGTAAT
*
466576 ATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTGTA-A
63 ATTATAATTTTGTATGAATATTGCAATTTTTTTGCATGAATATTGTAATATTGTACA
466632 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
466652 GTGAGGATAT
Statistics
Matches: 122, Mismatches: 8, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
114 2 0.02
115 3 0.02
116 11 0.09
117 4 0.03
118 75 0.61
119 22 0.18
120 3 0.02
121 2 0.02
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (119 bp):
TTTTGTATGAATATTGTAATTTTGTATGAATATTTAATATTTTTTTGTATGAATATTGTAATATT
ATAATTTTGTATGAATATTGCAATTTTTTTGCATGAATATTGTAATATTGTACA
Found at i:466892 original size:38 final size:38
Alignment explanation
Indices: 466847--466928 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
466837 CATATAAAGT
466847 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
*
466885 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
466923 TTATAA
1 TTATAA
466929 CTGACTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
Found at i:467006 original size:15 final size:15
Alignment explanation
Indices: 466965--467006 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
466955 GTTAACTCAT
*
466965 TTAATTTTTATATAA
1 TTAAATTTTATATAA
*
466980 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
466996 TTAAATTTTAT
1 TTAAATTTTAT
467007 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:468286 original size:16 final size:18
Alignment explanation
Indices: 468265--468301 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
468255 CCTAATTTTT
468265 TTCTTTT-TT-TCCTTCC
1 TTCTTTTCTTCTCCTTCC
*
468281 TTCTTTTCTTCTGCTTCC
1 TTCTTTTCTTCTCCTTCC
468299 TTC
1 TTC
468302 CTTCTTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 9 0.50
ACGTcount: A:0.00, C:0.32, G:0.03, T:0.65
Consensus pattern (18 bp):
TTCTTTTCTTCTCCTTCC
Found at i:468315 original size:18 final size:18
Alignment explanation
Indices: 468265--468316 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 18
468255 CCTAATTTTT
468265 TTCTT-TTT-TTCCTTCC
1 TTCTTCTTTCTTCCTTCC
468281 TTCTTTTCTTCTGCTTCCTTCC
1 TTC--TTCTT-T-CTTCCTTCC
468303 TTCTTCTTTCTTCC
1 TTCTTCTTTCTTCC
468317 GTTTTTGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
16 3 0.10
18 7 0.23
19 3 0.10
20 6 0.20
22 11 0.37
ACGTcount: A:0.00, C:0.35, G:0.02, T:0.63
Consensus pattern (18 bp):
TTCTTCTTTCTTCCTTCC
Found at i:468422 original size:27 final size:27
Alignment explanation
Indices: 468373--468475 Score: 129
Period size: 27 Copynumber: 3.8 Consensus size: 27
468363 AAAATCACAG
*
468373 CATTGGCGCCTTCTA-ATATGGCACCAC
1 CATTGGCGCCTCCTAGATA-GGCACCAC
468400 CATTGGCGCCTCCTAGATAGGCACCAC
1 CATTGGCGCCTCCTAGATAGGCACCAC
* * *
468427 CATTGGCGCCTCCCAAATAGGCACCTC
1 CATTGGCGCCTCCTAGATAGGCACCAC
*
468454 CGTTGGCGCCTTCC-AGATAGGC
1 CATTGGCGCC-TCCTAGATAGGC
468476 GCCAATACTA
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
27 62 0.91
28 6 0.09
ACGTcount: A:0.20, C:0.36, G:0.22, T:0.21
Consensus pattern (27 bp):
CATTGGCGCCTCCTAGATAGGCACCAC
Found at i:468991 original size:6 final size:7
Alignment explanation
Indices: 468958--468989 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
468948 ATAAAAATAT
468958 ATTTTT-
1 ATTTTTA
468964 ATTTTTA
1 ATTTTTA
468971 ATTTTTA
1 ATTTTTA
468978 ATTTTTA
1 ATTTTTA
468985 ATTTT
1 ATTTT
468990 AAAATACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
ATTTTTA
Found at i:469042 original size:20 final size:21
Alignment explanation
Indices: 468998--469042 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
468988 TTAAAATACT
* *
468998 TTTAAAATAAATTTTTTTATT
1 TTTAAAATAAATTTTTTAATG
469019 TTTAAAAT-AATTTTTTAATG
1 TTTAAAATAAATTTTTTAATG
469039 TTTA
1 TTTA
469043 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTAAAATAAATTTTTTAATG
Found at i:470182 original size:8 final size:9
Alignment explanation
Indices: 470163--470196 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
470153 TTAATTTTTG
470163 AAAATTTAA
1 AAAATTTAA
470172 AAAATTTAA
1 AAAATTTAA
*
470181 AAAAATTATA
1 AAAATTTA-A
470191 AAAATT
1 AAAATT
470197 ATTTTTAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATTTAA
Found at i:474490 original size:30 final size:29
Alignment explanation
Indices: 474433--474495 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
474423 CGCGGAAAAT
474433 GGCCCATTCCGGTAAATAATTAAAAAACC
1 GGCCCATTCCGGTAAATAATTAAAAAACC
* *
474462 GGCCCATTTCGGTAAAT-TTTGAAAAAAACC
1 GGCCCATTCCGGTAAATAATT--AAAAAACC
474492 GGCC
1 GGCC
474496 TTTTTTGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 2 0.07
29 16 0.53
30 12 0.40
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (29 bp):
GGCCCATTCCGGTAAATAATTAAAAAACC
Found at i:474617 original size:25 final size:26
Alignment explanation
Indices: 474563--474632 Score: 124
Period size: 25 Copynumber: 2.7 Consensus size: 26
474553 AAAAATAAAA
474563 ATTTACCAAAATATTATAACTTTTTTT
1 ATTTACCAAAATA-TATAACTTTTTTT
474590 ATTTACCAAAATATATAA-TTTTTTT
1 ATTTACCAAAATATATAACTTTTTTT
474615 ATTTACCAAAATATATAA
1 ATTTACCAAAATATATAA
474633 AAAAACTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
25 25 0.58
26 5 0.12
27 13 0.30
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTTACCAAAATATATAACTTTTTTT
Found at i:474793 original size:4 final size:4
Alignment explanation
Indices: 474784--474930 Score: 106
Period size: 4 Copynumber: 36.0 Consensus size: 4
474774 GAAGGAGAGG
* * * *
474784 GAAA GAAA GAAA GAAA GAGA GAAA GAAA GGAA GAAA GGAGAG GGAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA
* * *
474834 G-AA -AAA GAAG GAAA GAAA GGGAAA G-GA GAAGA GAAA AAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA --GAAA GAAA GAA-A GAAA GAAA GAAA GAAA
* *
474882 G-AA GAAGA GAAG GAAAA GAGAA GAAA -AAA GAAA GAAA GAAG GAAA GAAA
1 GAAA GAA-A GAAA G-AAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
474931 AGGAAAGGAG
Statistics
Matches: 112, Mismatches: 18, Indels: 26
0.72 0.12 0.17
Matches are distributed among these distances:
3 12 0.11
4 77 0.69
5 18 0.16
6 5 0.04
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:474875 original size:26 final size:27
Alignment explanation
Indices: 474845--474955 Score: 99
Period size: 26 Copynumber: 4.2 Consensus size: 27
474835 AAAAAGAAGG
474845 AAAGAAAGGGAAAGGAGAAGAGAA-AA
1 AAAGAAAGGGAAAGGAGAAGAGAAGAA
* *
474871 AAAGAAA--GAAAGAAGAAGAGAAGGA
1 AAAGAAAGGGAAAGGAGAAGAGAAGAA
** *
474896 AAAGAGAAGAAAAAAGA-AAGA-AAGAA
1 AAAGA-AAGGGAAAGGAGAAGAGAAGAA
*
474922 GGAAAGAAAAGGAAAGGAGAAGAGAA-AA
1 --AAAGAAAGGGAAAGGAGAAGAGAAGAA
474950 AAAGAA
1 AAAGAA
474956 GAAGAAGAAG
Statistics
Matches: 67, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
24 14 0.21
25 6 0.09
26 19 0.28
27 11 0.16
28 15 0.22
29 2 0.03
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (27 bp):
AAAGAAAGGGAAAGGAGAAGAGAAGAA
Found at i:474886 original size:3 final size:3
Alignment explanation
Indices: 474880--474972 Score: 53
Period size: 3 Copynumber: 33.3 Consensus size: 3
474870 AAAAGAAAGA
474880 AAG AAG AAG -AG AAGG AA- AAG -AG AAG AA- AA- AAG AAAG AAAG AAG
1 AAG AAG AAG AAG AA-G AAG AAG AAG AAG AAG AAG AAG -AAG -AAG AAG
* * * *
474923 GA- AAG AA- AAG GA- AAG GAG AAG -AG AA- AAA AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
474966 AAG AAG A
1 AAG AAG A
474973 GGGAAGGAAG
Statistics
Matches: 72, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
2 18 0.25
3 44 0.61
4 10 0.14
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:474915 original size:81 final size:81
Alignment explanation
Indices: 474775--474997 Score: 248
Period size: 79 Copynumber: 2.8 Consensus size: 81
474765 GGGAGGGCAG
* * * ***
474775 AAGGAG-AGGGAAAGAAAGAAAGAAAGAGAGAA-AGAAAGGAAGAA-AGGAGAGGGAAGAAAGAA
1 AAGGAGAAGAGAAAAAAAGAAAGAAAGA-AGAAGAG-AAGGAA-AAGAGAAGAAAAAAGAAAGAA
*
474837 AAAGAAGGAAAGAAAGGGA
63 AAAGAAGGAAAGAAAAGGA
474856 AAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAGAAGGAAAAGAGAAGAAAAAAGAAAG--AAA
1 AAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAGAAGGAAAAGAGAAGAAAAAAGAAAGAAAAA
474919 GAAGGAAAGAAAAGGA
66 GAAGGAAAGAAAAGGA
** *
474935 AAGGAGAAGAGAAAAAAAG-AAG-AAGAAGAAGAAGAAGAGGGAAG-GAAGGAAAAA-AAAGAAA
1 AAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAG-AGAAG-GAAAAGAGAAGAAAAAAGAAAGAAA
474996 AA
64 AA
474998 AATGTAATTT
Statistics
Matches: 125, Mismatches: 10, Indels: 16
0.83 0.07 0.11
Matches are distributed among these distances:
77 13 0.10
78 17 0.14
79 44 0.35
80 2 0.02
81 28 0.22
82 21 0.17
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (81 bp):
AAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAGAAGGAAAAGAGAAGAAAAAAGAAAGAAAAA
GAAGGAAAGAAAAGGA
Found at i:474944 original size:16 final size:15
Alignment explanation
Indices: 474793--474967 Score: 60
Period size: 14 Copynumber: 12.4 Consensus size: 15
474783 GGAAAGAAAG
474793 AAAGAAA-GAG-AG-
1 AAAGAAAGGAGAAGA
474805 AAAGAAA-G-GAAGA
1 AAAGAAAGGAGAAGA
* *
474818 AAGGAGAGG-GAAG-
1 AAAGAAAGGAGAAGA
* *
474831 AAAGAAA-AAGAAGG
1 AAAGAAAGGAGAAGA
474845 AAAGAAAGG-GAA-A
1 AAAGAAAGGAGAAGA
** *
474858 GGAG-AA-GAGAAAA
1 AAAGAAAGGAGAAGA
474871 AAAGAAA-GA-AAGA
1 AAAGAAAGGAGAAGA
*
474884 AGAAGAGAAGGAAAAGA
1 A-AAGA-AAGGAGAAGA
* **
474901 GAAGAAAAAAGAA-A
1 AAAGAAAGGAGAAGA
474915 GAAAG-AAGGA-AAGA
1 -AAAGAAAGGAGAAGA
474929 AAAGGAAAGGAGAAGA
1 AAA-GAAAGGAGAAGA
* *
474945 GAAAAAAAGAAGAAGA
1 -AAAGAAAGGAGAAGA
474961 AGAAGAA
1 A-AAGAA
474968 GAAGAGGGAA
Statistics
Matches: 121, Mismatches: 22, Indels: 36
0.68 0.12 0.20
Matches are distributed among these distances:
11 2 0.02
12 15 0.12
13 28 0.23
14 29 0.24
15 16 0.13
16 24 0.20
17 7 0.06
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AAAGAAAGGAGAAGA
Found at i:474948 original size:34 final size:33
Alignment explanation
Indices: 474784--474973 Score: 107
Period size: 34 Copynumber: 5.8 Consensus size: 33
474774 GAAGGAGAGG
*
474784 GAAAGAA-AGAAAGAAAGAGAGAA-AGAAAGGAA
1 GAAAGAAGAGAAAGAAA-AGAGAAGAGAAAGAAA
* * * *
474816 GAAAGGAGAGGGAAG-AAAGA-AAAAGAAGGAAA
1 GAAAGAAGA-GAAAGAAAAGAGAAGAGAAAGAAA
* *
474848 GAAAG--G-GAAAGGAGAAGAGAA-AAAAAGAAA
1 GAAAGAAGAGAAA-GAAAAGAGAAGAGAAAGAAA
*
474878 GAAAGAAGAAGAGAAGGAAAAGAGAAGAAAAAAGAAA
1 GAAAGAAG-AGA-AA-GAAAAGAGAAG-AGAAAGAAA
474915 GAAAGAAG-GAAAGAAAAG-GAAAGGAGAAGAGAAA
1 GAAAGAAGAGAAAGAAAAGAG-AA-GAGAA-AGAAA
* *
474949 AAAAGAAGA-AGAAGAAGA-AGAAGAG
1 GAAAGAAGAGA-AAGAAAAGAGAAGAG
474974 GGAAGGAAGG
Statistics
Matches: 127, Mismatches: 12, Indels: 37
0.72 0.07 0.21
Matches are distributed among these distances:
28 3 0.02
29 1 0.01
30 17 0.13
31 4 0.03
32 23 0.18
33 17 0.13
34 24 0.19
35 21 0.17
37 17 0.13
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (33 bp):
GAAAGAAGAGAAAGAAAAGAGAAGAGAAAGAAA
Found at i:474988 original size:37 final size:40
Alignment explanation
Indices: 474778--474989 Score: 151
Period size: 41 Copynumber: 5.3 Consensus size: 40
474768 AGGGCAGAAG
* * *
474778 GAGAGGGAAAGAAAGAAAGAAAGAGAGAAAGAA-AGGAAGAAA
1 GAGAAGGAAA-AAAGAAAGAAAGA-AG-AAGAAGAAGAGGAAA
* * *
474820 GGAGAGGGAAGAAAG-AA-AAAGAAGGA-AAGAA-AGGGAAA
1 -GAGAAGGAAAAAAGAAAGAAAGAAGAAGAAGAAGA-GGAAA
*
474858 GGAGAAGAGAAAAAAAGAAAGAAAGAAGAAG-AGAAG-GAAAA
1 -GAGAAG-G-AAAAAAGAAAGAAAGAAGAAGAAGAAGAGGAAA
* *
474899 GAGAA-GAAAAAAGAAAGAAAGAAGGA-AAGAAAAGGAAA
1 GAGAAGGAAAAAAGAAAGAAAGAAGAAGAAGAAGAGGAAA
*
474937 GGAGAAGAGAAAAAA-AGAAG-AAGAAGAAGAAGAAGAGGGAA
1 -GAGAAG-GAAAAAAGA-AAGAAAGAAGAAGAAGAAGAGGAAA
474978 G-GAAGGAAAAAA
1 GAGAAGGAAAAAA
474990 AAGAAAAAAA
Statistics
Matches: 140, Mismatches: 14, Indels: 35
0.74 0.07 0.19
Matches are distributed among these distances:
37 26 0.19
38 24 0.17
39 12 0.09
40 25 0.18
41 28 0.20
42 16 0.11
43 9 0.06
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (40 bp):
GAGAAGGAAAAAAGAAAGAAAGAAGAAGAAGAAGAGGAAA
Found at i:475074 original size:14 final size:13
Alignment explanation
Indices: 475051--475088 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
475041 TATTTAAAAT
475051 TTATGTTATTTCA
1 TTATGTTATTTCA
475064 TTATAGTTATTTCA
1 TTAT-GTTATTTCA
*
475078 TTATTTTATTT
1 TTATGTTATTT
475089 AGCATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (13 bp):
TTATGTTATTTCA
Found at i:480954 original size:3 final size:3
Alignment explanation
Indices: 480946--480980 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
480936 TCTTAATACT
480946 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
480981 TAATAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:480985 original size:3 final size:3
Alignment explanation
Indices: 480979--481016 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
480969 CAACAACAAC
*
480979 AAT AAT AAT AAT AAT AAT AAT AAT AAT ACT AACT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT A
481017 CTATTATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:481315 original size:54 final size:54
Alignment explanation
Indices: 481231--481333 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
481221 ATAATACGAG
**
481231 TGGTGCCGCCAATTAGTATGGCACCATTGGTGCCGCCAATGGCATTGGCACCAT
1 TGGTGCCGCCAATTAGTATGGCACCATTGGTGCCGCCAATCCCATTGGCACCAT
* * *
481285 TGGTGCCGCCAA-TGGTTTTGGCACCTTTGGTGCCGCCAATCCCATTGGC
1 TGGTGCCGCCAATTAG-TATGGCACCATTGGTGCCGCCAATCCCATTGGC
481334 GTGACCAGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 2 0.05
54 41 0.95
ACGTcount: A:0.17, C:0.29, G:0.28, T:0.26
Consensus pattern (54 bp):
TGGTGCCGCCAATTAGTATGGCACCATTGGTGCCGCCAATCCCATTGGCACCAT
Found at i:481332 original size:27 final size:27
Alignment explanation
Indices: 481231--481333 Score: 127
Period size: 27 Copynumber: 3.8 Consensus size: 27
481221 ATAATACGAG
* *
481231 TGGTGCCGCCAATTAGTA-TGGCACCAT
1 TGGTGCCGCCAA-TGGCATTGGCACCAT
481258 TGGTGCCGCCAATGGCATTGGCACCAT
1 TGGTGCCGCCAATGGCATTGGCACCAT
** *
481285 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGCATTGGCACCAT
**
481312 TGGTGCCGCCAATCCCATTGGC
1 TGGTGCCGCCAATGGCATTGGC
481334 GTGACCAGTT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
26 3 0.05
27 63 0.95
ACGTcount: A:0.17, C:0.29, G:0.28, T:0.26
Consensus pattern (27 bp):
TGGTGCCGCCAATGGCATTGGCACCAT
Found at i:481415 original size:25 final size:25
Alignment explanation
Indices: 481387--481436 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
481377 TTTTTTTGGT
**
481387 TTTTTTGATATATTTTGGTAAATAA
1 TTTTTTGATATATTTTAATAAATAA
*
481412 TTTTTTTATATATTTTAATAAATAA
1 TTTTTTGATATATTTTAATAAATAA
481437 ATAAAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (25 bp):
TTTTTTGATATATTTTAATAAATAA
Found at i:488723 original size:24 final size:25
Alignment explanation
Indices: 488662--488723 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
488652 GACACACCAT
488662 AGCTCGTATGAGCTTACCGATATTC
1 AGCTCGTATGAGCTTACCGATATTC
* * *
488687 AGCTCGGAGGAGCTTACCG-TTTATC
1 AGCTCGTATGAGCTTACCGATAT-TC
488712 -GCTCGTATGAGC
1 AGCTCGTATGAGC
488724 ATACATGTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 12 0.39
25 19 0.61
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGATATTC
Found at i:490545 original size:17 final size:15
Alignment explanation
Indices: 490515--490548 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
490505 TAACTTTAGA
490515 AAGTTATTTTTTTAT
1 AAGTTATTTTTTTAT
490530 AAGTGTATTATTTTTAT
1 AAGT-TATT-TTTTTAT
490547 AA
1 AA
490549 TATAGCACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 4 0.24
17 9 0.53
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (15 bp):
AAGTTATTTTTTTAT
Found at i:497706 original size:5 final size:6
Alignment explanation
Indices: 497691--497715 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
497681 CATATTTTTA
497691 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
497716 TCAATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:497868 original size:29 final size:31
Alignment explanation
Indices: 497825--497905 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
497815 AAATTGAATC
497825 AAATCAAAATTTCATGTA-AAAAAT-TACATA
1 AAATCAAAA-TTCATGTATAAAAATCTACATA
* * *
497855 AAATCAAAATTCATGCATAAAACTCTACATC
1 AAATCAAAATTCATGTATAAAAATCTACATA
**
497886 GGATCAAAATTCATGTATAA
1 AAATCAAAATTCATGTATAA
497906 TTTTAAGATT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
29 7 0.16
30 14 0.33
31 22 0.51
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (31 bp):
AAATCAAAATTCATGTATAAAAATCTACATA
Found at i:501700 original size:14 final size:14
Alignment explanation
Indices: 501683--501745 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 14
501673 TAAATATACG
501683 TATTTAATTATTTA
1 TATTTAATTATTTA
*
501697 TATTT-ATTCATATA
1 TATTTAATT-ATTTA
*
501711 -ATTT-ATTATTTT
1 TATTTAATTATTTA
* *
501723 TAATAAATTATTTAA
1 TATTTAATTATTT-A
501738 TATTTAAT
1 TATTTAAT
501746 AGTAATTTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
12 3 0.08
13 12 0.32
14 16 0.43
15 6 0.16
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTTAATTATTTA
Found at i:501778 original size:16 final size:17
Alignment explanation
Indices: 501742--501778 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
501732 ATTTAATATT
*
501742 TAATAGTAATTTTTAAA
1 TAATAATAATTTTTAAA
501759 -AATAATAA-TTTTAAA
1 TAATAATAATTTTTAAA
501774 TAATA
1 TAATA
501779 TTATTCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
TAATAATAATTTTTAAA
Found at i:503302 original size:4 final size:4
Alignment explanation
Indices: 503255--503317 Score: 56
Period size: 4 Copynumber: 15.8 Consensus size: 4
503245 AATTATTTCT
* * * * * *
503255 TTTA TTTT TTTA -TTA GTTA TTTA TATA TATA TTTG TTGTT TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TTTA
503303 TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTT
503318 TAAACAAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
3 3 0.06
4 43 0.88
5 3 0.06
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:512016 original size:32 final size:35
Alignment explanation
Indices: 511970--512036 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 35
511960 GTTAATTATA
*
511970 ATAATATTTAATATT-T-AATATATT-AATAACGT
1 ATAATATTTAATATTATCAATAAATTAAATAACGT
512002 ATAAT-TTTACATATTATCAATAAATTAAATAACGT
1 ATAATATTTA-ATATTATCAATAAATTAAATAACGT
512037 TGCATCTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 4 0.13
32 10 0.33
33 1 0.03
34 7 0.23
35 8 0.27
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (35 bp):
ATAATATTTAATATTATCAATAAATTAAATAACGT
Found at i:514880 original size:6 final size:6
Alignment explanation
Indices: 514871--514896 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
514861 CTTAATTCTA
514871 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
514897 AAAACCCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:518308 original size:3 final size:3
Alignment explanation
Indices: 518294--518337 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
518284 GAGTTGATAA
*
518294 TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
518338 GCAACCACTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:519578 original size:61 final size:60
Alignment explanation
Indices: 519491--519604 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
519481 AATATTCAAC
* *
519491 AAATATAGCCCTCAATGTTTACAAAAAAAATT-ATTTTAGTTTGAATTCTAAAAAAGTTAAT
1 AAATATAGCCCTCAATGTTTAC--AAAAAATTCAATTTAGTTTCAATTCTAAAAAAGTTAAT
* * *
519552 AAATTTAGCCCTCAAAT-TTTATAAAAATTTCAATTTAGTTTCAATTCTAAAAA
1 AAATATAGCCCTC-AATGTTTACAAAAAATTCAATTTAGTTTCAATTCTAAAAA
519605 TTTTAATGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
59 7 0.15
60 20 0.43
61 16 0.35
62 3 0.07
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (60 bp):
AAATATAGCCCTCAATGTTTACAAAAAATTCAATTTAGTTTCAATTCTAAAAAAGTTAAT
Found at i:531977 original size:12 final size:12
Alignment explanation
Indices: 531960--531994 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
531950 AAATGATGAT
*
531960 ATGTATGTATGC
1 ATGTATGCATGC
531972 ATGTATGCATGC
1 ATGTATGCATGC
*
531984 ATGCATGCATG
1 ATGTATGCATG
531995 TATTCCTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (12 bp):
ATGTATGCATGC
Found at i:536563 original size:18 final size:19
Alignment explanation
Indices: 536520--536569 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
536510 AACTATATTA
536520 AAAAATATTTTATTAATTTTT
1 AAAAATA-TTTA-TAATTTTT
*
536541 -TAAATATTTAT-ATTTTT
1 AAAAATATTTATAATTTTT
536558 AAAAATATTTAT
1 AAAAATATTTAT
536570 CAATAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 6 0.23
18 11 0.42
19 4 0.15
20 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AAAAATATTTATAATTTTT
Found at i:545188 original size:21 final size:21
Alignment explanation
Indices: 545164--545207 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
545154 TATTTTCTAT
*
545164 AATTTTTTTA-ATATTATTATA
1 AATTTTTTTATATAATATT-TA
545185 AATTTTTTTATATAATATTTA
1 AATTTTTTTATATAATATTTA
545206 AA
1 AA
545208 ACTACCCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AATTTTTTTATATAATATTTA
Found at i:547092 original size:16 final size:16
Alignment explanation
Indices: 547071--547122 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
547061 TTTGGTTCGC
547071 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
547087 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* * *
547103 TGTAATGGAATAGATG
1 TGTATTGGATTAGAGG
547119 TGTA
1 TGTA
547123 ATAGCAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:547169 original size:45 final size:44
Alignment explanation
Indices: 547103--547197 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 44
547093 GGATTAGAGG
* * *
547103 TGTAATGGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
547148 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
547192 TGTAAT
1 TGTAAT
547198 AGAGGTGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.41
45 26 0.59
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:547380 original size:18 final size:17
Alignment explanation
Indices: 547359--547393 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
547349 TTATTATTTA
*
547359 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
547377 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
547394 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:547387 original size:28 final size:27
Alignment explanation
Indices: 547317--547389 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
547307 TTTATTATCA
*
547317 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
547345 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
547372 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
547390 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:547527 original size:18 final size:17
Alignment explanation
Indices: 547506--547540 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
547496 TTATTATTAA
*
547506 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
547524 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
547541 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:547552 original size:147 final size:149
Alignment explanation
Indices: 547278--547552 Score: 500
Period size: 147 Copynumber: 1.9 Consensus size: 149
547268 ATGATTATTG
*
547278 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
*
547343 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
547408 AGAAATTTGTTTTGGTAAA
131 AGAAATTTGTTTTGGTAAA
* *
547427 TTATT-TTATTTAAATTTTAATAAGATTA-TTAATATCAATAATAAATAATTTACTCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
547490 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
547553 ATATTCTTAT
Statistics
Matches: 122, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
147 94 0.77
148 23 0.19
149 5 0.04
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (149 bp):
TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
AGAAATTTGTTTTGGTAAA
Found at i:547648 original size:18 final size:17
Alignment explanation
Indices: 547608--547660 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
547598 AAATATAAAT
547608 TAAAATA-ATAA-TT-A
1 TAAAATATATAATTTAA
*
547622 TTAAATATAT--TTTAA
1 TAAAATATATAATTTAA
547637 TTAAAATATATAATTTAA
1 -TAAAATATATAATTTAA
547655 TAAAAT
1 TAAAAT
547661 TCTAATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.26
15 3 0.10
16 9 0.29
17 6 0.19
18 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATATATAATTTAA
Found at i:547718 original size:60 final size:59
Alignment explanation
Indices: 547534--547720 Score: 157
Period size: 60 Copynumber: 3.1 Consensus size: 59
547524 ATATAATTTA
*
547534 ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTC-TAATAA-TAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
* * ** * * * ** * * * *
547595 GTAAAATAT-AAATTAA-AATAATAATTAT-TAAATATATTTTAATTAAAATATATAAT-TT
1 ATAAAAT-TCTAA-TAATAAT-ATTCTTATATGAATTTACTAAAATCATAATATATGATACT
547653 AATAAAATTCTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
1 -ATAAAATTCTAATAAT-AATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
547714 ATAAAAT
1 ATAAAAT
547721 ATAATTTGAA
Statistics
Matches: 91, Mismatches: 26, Indels: 19
0.67 0.19 0.14
Matches are distributed among these distances:
58 5 0.05
59 37 0.41
60 38 0.42
61 10 0.11
62 1 0.01
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (59 bp):
ATAAAATTCTAATAATAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
Found at i:547719 original size:119 final size:120
Alignment explanation
Indices: 547486--547780 Score: 495
Period size: 119 Copynumber: 2.5 Consensus size: 120
547476 TTACTCATAT
*
547486 TTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTAAA-ATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
* * *
547551 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA
65 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
547607 TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC-TAATAATC
1 TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATC
*
547671 AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAT
66 AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
* *
547726 TTGAAATAATTAA-TATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 TTAAAATAA-TAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
547781 TAAAATAATT
Statistics
Matches: 166, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
119 108 0.65
120 53 0.32
121 5 0.03
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (120 bp):
TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATC
AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
Found at i:553063 original size:36 final size:36
Alignment explanation
Indices: 552999--553072 Score: 98
Period size: 38 Copynumber: 2.1 Consensus size: 36
552989 TTGTTTTTTT
552999 ATTTATTTTATATAAAAATAAGAAAAAATTATAATATA
1 ATTTATTTTATATAAAAATAAGAAAAAATTA-AAT-TA
**
553037 ATTTATTTTATA-AAAAATAA-TCAAAATTAAATTA
1 ATTTATTTTATATAAAAATAAGAAAAAATTAAATTA
553071 AT
1 AT
553073 GCTTAATCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 4 0.12
35 3 0.09
36 7 0.21
37 8 0.24
38 12 0.35
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (36 bp):
ATTTATTTTATATAAAAATAAGAAAAAATTAAATTA
Found at i:553305 original size:22 final size:22
Alignment explanation
Indices: 553277--553320 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
553267 CAAAAAAAAA
* *
553277 ATTGTTGTTTTCTTATTGTTTT
1 ATTGTTGTTTTCTCACTGTTTT
553299 ATTGTTGTTTTCTCACTGTTTT
1 ATTGTTGTTTTCTCACTGTTTT
553321 GTTATCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.09, G:0.14, T:0.68
Consensus pattern (22 bp):
ATTGTTGTTTTCTCACTGTTTT
Found at i:557487 original size:265 final size:265
Alignment explanation
Indices: 557014--557544 Score: 1035
Period size: 265 Copynumber: 2.0 Consensus size: 265
557004 GCTTTTTGGG
557014 TTCATGGATTTTCAGTTTTTACTTACTAATTACCATCACATGTTACGAGAATAAATTTGTTATGA
1 TTCATGGATTTTCAGTTTTTACTTACTAATTACCATCACATGTTACGAGAATAAATTTGTTATGA
*
557079 TGTTTATAACAAGATGTTACAGCTTTCCTTCATGTTTTTTGTTGATTCGTAATCTTCCATATAAG
66 TGTTTATAACAAGATGTTACAGCTTTCCTTCATGTTTTTTGTTGATTCGTAATCTTACATATAAG
557144 TTGATGGTTTTAAGTGTGCCTAATTTATTTGTTTTAGATGGCTATGATTTCTTAATTTCTATTTT
131 TTGATGGTTTTAAGTGTGCCTAATTTATTTGTTTTAGATGGCTATGATTTCTTAATTTCTATTTT
557209 TGTTCACTCTTTATCCTTAGTTAAAAATATTTGTGGCTTGCAGGCGAGAGCTGGTCTAGATTATG
196 TGTTCACTCTTTATCCTTAGTTAAAAATATTTGTGGCTTGCAGGCGAGAGCTGGTCTAGATTATG
557274 AATCC
261 AATCC
557279 TTCATGGATTTTCAGTTTTTACTTACTAATTACCATCACATGTTACGAGAATAAATTTGTTATGA
1 TTCATGGATTTTCAGTTTTTACTTACTAATTACCATCACATGTTACGAGAATAAATTTGTTATGA
557344 TGTTTATAACAAGATGTTACAGCTTTCCTTCATGTTTTTTGTTGATTCGTAATCTTACATATAAG
66 TGTTTATAACAAGATGTTACAGCTTTCCTTCATGTTTTTTGTTGATTCGTAATCTTACATATAAG
557409 TTGATGGTTTTAAGTGTGCCTAATTTATTTGTTTTAGATGGCTATGATTTCTTAATTTCTATTTT
131 TTGATGGTTTTAAGTGTGCCTAATTTATTTGTTTTAGATGGCTATGATTTCTTAATTTCTATTTT
* *
557474 TGTTCTCTCTTTATCCTTGGTTAAAAATATTTGTGGCTTGCAGGCGAGAGCTGGTCTAGATTATG
196 TGTTCACTCTTTATCCTTAGTTAAAAATATTTGTGGCTTGCAGGCGAGAGCTGGTCTAGATTATG
557539 AATCC
261 AATCC
557544 T
1 T
557545 CATATGGGAA
Statistics
Matches: 263, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
265 263 1.00
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.46
Consensus pattern (265 bp):
TTCATGGATTTTCAGTTTTTACTTACTAATTACCATCACATGTTACGAGAATAAATTTGTTATGA
TGTTTATAACAAGATGTTACAGCTTTCCTTCATGTTTTTTGTTGATTCGTAATCTTACATATAAG
TTGATGGTTTTAAGTGTGCCTAATTTATTTGTTTTAGATGGCTATGATTTCTTAATTTCTATTTT
TGTTCACTCTTTATCCTTAGTTAAAAATATTTGTGGCTTGCAGGCGAGAGCTGGTCTAGATTATG
AATCC
Found at i:558700 original size:3 final size:3
Alignment explanation
Indices: 558692--558724 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
558682 AGGCTCTGCC
558692 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
558725 GCAGCGCCCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:567787 original size:23 final size:22
Alignment explanation
Indices: 567742--567788 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
567732 CGAAAATATA
*
567742 TTAAATATATATATTTTTATTT
1 TTAAATATATATAGTTTTATTT
*
567764 TTAAA-ATATACTAGTTTTAGTT
1 TTAAATATATA-TAGTTTTATTT
567786 TTA
1 TTA
567789 TTTTAAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (22 bp):
TTAAATATATATAGTTTTATTT
Found at i:567944 original size:92 final size:93
Alignment explanation
Indices: 567837--568017 Score: 319
Period size: 93 Copynumber: 2.0 Consensus size: 93
567827 AACAATTAAT
* *
567837 ACAATTAACAATTAATAATTTGATAT-ATTTGATAATTTTACTAACAATTAATACAATTAACAAT
1 ACAATTAACAATTAATAATTTGATATAATTTGATAATTTTAATAACAATTAATACAATTAAAAAT
567901 TAATAATTTTACTAACAAAATGTTAGTA
66 TAATAATTTTACTAACAAAATGTTAGTA
*
567929 ACAATTAAGAATTAATAATTTGATATAATTTGATAATTTTAATAACAATTAATACAATTAAAAAT
1 ACAATTAACAATTAATAATTTGATATAATTTGATAATTTTAATAACAATTAATACAATTAAAAAT
*
567994 TAATAATTTTACTTACAAAATGTT
66 TAATAATTTTACTAACAAAATGTT
568018 GATTGGTACA
Statistics
Matches: 84, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
92 25 0.30
93 59 0.70
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (93 bp):
ACAATTAACAATTAATAATTTGATATAATTTGATAATTTTAATAACAATTAATACAATTAAAAAT
TAATAATTTTACTAACAAAATGTTAGTA
Found at i:568040 original size:93 final size:92
Alignment explanation
Indices: 567849--568052 Score: 281
Period size: 93 Copynumber: 2.2 Consensus size: 92
567839 AATTAACAAT
* *
567849 TAATAATTTGATAT-ATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTAC
1 TAATAATTTGATATAATTTGATAATTTTAATAACAATTAATACAATTAAAAATTAATAATTTTAC
* *
567913 TAACAAAATGTTAGTAACAATTAAGAAT
66 TAACAAAATGTTAGTAACAA-TAAAAAA
567941 TAATAATTTGATATAATTTGATAATTTTAATAACAATTAATACAATTAAAAATTAATAATTTTAC
1 TAATAATTTGATATAATTTGATAATTTTAATAACAATTAATACAATTAAAAATTAATAATTTTAC
*
568006 TTACAAAATGTTGATTGGT-ACAA-AAAAAA
66 TAACAAAATGTT-A---GTAACAATAAAAAA
*
568035 T-ATAATTTGATACAATTT
1 TAATAATTTGATATAATTT
568053 TAATAACAAT
Statistics
Matches: 101, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
92 14 0.14
93 75 0.74
94 6 0.06
96 4 0.04
97 2 0.02
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (92 bp):
TAATAATTTGATATAATTTGATAATTTTAATAACAATTAATACAATTAAAAATTAATAATTTTAC
TAACAAAATGTTAGTAACAATAAAAAA
Found at i:568067 original size:16 final size:16
Alignment explanation
Indices: 568048--568088 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
568038 AATTTGATAC
568048 AATTTTAATAACAATT
1 AATTTTAATAACAATT
*
568064 AATTTTGATAACAATT
1 AATTTTAATAACAATT
*
568080 AGTTTTAAT
1 AATTTTAAT
568089 TTTAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (16 bp):
AATTTTAATAACAATT
Found at i:568090 original size:22 final size:23
Alignment explanation
Indices: 568062--568123 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
568052 TTAATAACAA
* * *
568062 TTAATTTTGATAACAAT-TAGTT
1 TTAATTTTAATAAAAATATAATT
568084 TTAATTTTAATAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
568107 TTAATTTTAATTAAAAA
1 TTAATTTTAA-TAAAAA
568124 ATAGGCCGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 15 0.43
23 14 0.40
24 6 0.17
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:568262 original size:20 final size:20
Alignment explanation
Indices: 568237--568274 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
568227 AGCCTCCTTG
568237 TATAAATATCCCATCATTAC
1 TATAAATATCCCATCATTAC
*
568257 TATAAATATCCCCTCATT
1 TATAAATATCCCATCATT
568275 CTTCAACTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (20 bp):
TATAAATATCCCATCATTAC
Found at i:568479 original size:22 final size:22
Alignment explanation
Indices: 568438--568480 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
568428 GGGAAAATGA
568438 TTTTTAGAAAATAACTTATTTAT
1 TTTTTAGAAAATAAC-TATTTAT
568461 TTTTTAGAAAACTAA-TATTT
1 TTTTTAGAAAA-TAACTATTT
568481 TCTAGTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 11 0.58
24 3 0.16
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTTTAGAAAATAACTATTTAT
Found at i:573394 original size:24 final size:24
Alignment explanation
Indices: 573362--573411 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
573352 GTAAAAGTAT
573362 CATGGAGGTACTTGTATTAGGAGA
1 CATGGAGGTACTTGTATTAGGAGA
573386 CATGGAGGTACTTGTATTAGGAGA
1 CATGGAGGTACTTGTATTAGGAGA
573410 CA
1 CA
573412 GATTATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.10, G:0.32, T:0.28
Consensus pattern (24 bp):
CATGGAGGTACTTGTATTAGGAGA
Found at i:574455 original size:24 final size:24
Alignment explanation
Indices: 574423--574472 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
574413 GTAAAAGTAT
574423 CATGGAGGTACTTGTATTAGGAGA
1 CATGGAGGTACTTGTATTAGGAGA
574447 CATGGAGGTACTTGTATTAGGAGA
1 CATGGAGGTACTTGTATTAGGAGA
574471 CA
1 CA
574473 GATTATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.10, G:0.32, T:0.28
Consensus pattern (24 bp):
CATGGAGGTACTTGTATTAGGAGA
Found at i:580679 original size:20 final size:22
Alignment explanation
Indices: 580651--580695 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
580641 GTATGAAAGC
*
580651 ATATTTTTATATGTAAGTATAT
1 ATATTTATATATGTAAGTATAT
580673 ATATTTATATATGTAAGTATAT
1 ATATTTATATATGTAAGTATAT
580695 A
1 A
580696 ATAAAGGCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
ATATTTATATATGTAAGTATAT
Found at i:580757 original size:63 final size:61
Alignment explanation
Indices: 580617--580758 Score: 162
Period size: 63 Copynumber: 2.3 Consensus size: 61
580607 TGAAAGTATA
* * * *
580617 TATATATGTATATATAATAAAGGCGTATGAAAGCATATTTTTATATGTAAGTATATATATT
1 TATATATGTATATATAATAAAGGCGTATGAAAGCATATTTTTACATGTAAGTATAAAAATG
* *
580678 TATATATGTAAGTATATAATAAAGGCGTATGAAAGCATATTTATGTACATGT-ATTTTAAAAAAT
1 TATATATGT-A-TATATAATAAAGGCGTATGAAAGCATATTT-T-TACATGTAAGTAT-AAAAAT
580742 G
61 G
580743 TATATA-GATATATATA
1 TATATATG-TATATATA
580759 GATGTGCAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
61 9 0.13
62 1 0.01
63 36 0.52
64 6 0.09
65 17 0.25
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.40
Consensus pattern (61 bp):
TATATATGTATATATAATAAAGGCGTATGAAAGCATATTTTTACATGTAAGTATAAAAATG
Found at i:580975 original size:3 final size:3
Alignment explanation
Indices: 580967--580998 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
580957 AAAAAGGGAA
580967 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
580999 GCTAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:590505 original size:31 final size:31
Alignment explanation
Indices: 590465--590529 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
590455 ATGACCTGCT
* * * *
590465 ACCCTGGATTGCCCGACGACGATGGCTTACC
1 ACCCCGGATTACCCGACAACGATGGCCTACC
590496 ACCCCGGATTACCCGACAACGATGGCCTACC
1 ACCCCGGATTACCCGACAACGATGGCCTACC
590527 ACC
1 ACC
590530 AGGTTGTCCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.40, G:0.22, T:0.15
Consensus pattern (31 bp):
ACCCCGGATTACCCGACAACGATGGCCTACC
Found at i:598006 original size:29 final size:30
Alignment explanation
Indices: 597971--598044 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 30
597961 AGACATTTTA
*
597971 TAAAAATACATGTACCACATTAAATATTT-
1 TAAAAATATATGTACCACATTAAATATTTG
* **
598000 TCAAAATATAAATACCACATTAAATATTTG
1 TAAAAATATATGTACCACATTAAATATTTG
598030 TAAAAATATATGTAC
1 TAAAAATATATGTAC
598045 AAAATGTAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 25 0.68
30 12 0.32
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.34
Consensus pattern (30 bp):
TAAAAATATATGTACCACATTAAATATTTG
Found at i:598872 original size:29 final size:31
Alignment explanation
Indices: 598811--598872 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 31
598801 ACAATTTAAT
* **
598811 TTGGTCATTTTGAATTTTTGTATTTTTTGAA
1 TTGGTCATTTTGAATTTCTGTATTTTTCAAA
*
598842 TTGGTCATTTT-TA-TTCTGTATTTTTCAAA
1 TTGGTCATTTTGAATTTCTGTATTTTTCAAA
598871 TT
1 TT
598873 TTAAACTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 15 0.56
30 1 0.04
31 11 0.41
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (31 bp):
TTGGTCATTTTGAATTTCTGTATTTTTCAAA
Found at i:601846 original size:23 final size:23
Alignment explanation
Indices: 601806--601850 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
601796 ATAGAAAAAG
*
601806 ATATATATGCAACGATATATATT
1 ATATATATGAAACGATATATATT
601829 ATATATTATGAAAC-ATATATAT
1 ATATA-TATGAAACGATATATAT
601851 ATTAATATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (23 bp):
ATATATATGAAACGATATATATT
Found at i:603906 original size:41 final size:41
Alignment explanation
Indices: 603861--604189 Score: 169
Period size: 41 Copynumber: 7.3 Consensus size: 41
603851 CTATATTTAA
603861 ATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACT
1 ATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACT
* * * ** *
603902 ATTTTTTTAATATTATACATATATTCATTTACGTATGTAAGCTATATTTA-A
1 ATTTTATTAATA--ATA-A-AT-TT-A-TAACTTAAATAAG---TA-TTACT
603953 ATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACT
1 ATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACT
* * * ** *
603994 ATTTTTTTAATATTATACATATATTCATTTACGTATGTAAGCTATATTTA-A
1 ATTTTATTAATA--ATA-A-AT-TT-A-TAACTTAAATAAG---TA-TTACT
604045 ATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACT
1 ATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACT
* * * ** *
604086 ATTTTTTTAATATTATACATATATTCATTTACGTATGTAAGCTATATTTA-A
1 ATTTTATTAATA--ATA-A-AT-TT-A-TAACTTAAATAAG---TA-TTACT
604137 ATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACT
1 ATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACT
*
604178 ATTTTTTTAATA
1 ATTTTATTAATA
604190 TTATACATAT
Statistics
Matches: 215, Mismatches: 37, Indels: 72
0.66 0.11 0.22
Matches are distributed among these distances:
40 9 0.04
41 50 0.23
43 9 0.04
44 30 0.14
45 9 0.04
46 12 0.06
47 9 0.04
48 30 0.14
49 9 0.04
51 39 0.18
52 9 0.04
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (41 bp):
ATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACT
Found at i:603989 original size:92 final size:92
Alignment explanation
Indices: 603832--604209 Score: 756
Period size: 92 Copynumber: 4.1 Consensus size: 92
603822 GTTTAAAAGC
603832 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
603897 TTACTATTTTTTTAATATTATACATAT
66 TTACTATTTTTTTAATATTATACATAT
603924 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
603989 TTACTATTTTTTTAATATTATACATAT
66 TTACTATTTTTTTAATATTATACATAT
604016 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
604081 TTACTATTTTTTTAATATTATACATAT
66 TTACTATTTTTTTAATATTATACATAT
604108 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
604173 TTACTATTTTTTTAATATTATACATAT
66 TTACTATTTTTTTAATATTATACATAT
604200 ATTCATTTAC
1 ATTCATTTAC
604210 NNNNNNNNNN
Statistics
Matches: 286, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 286 1.00
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (92 bp):
ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
TTACTATTTTTTTAATATTATACATAT
Found at i:607583 original size:66 final size:65
Alignment explanation
Indices: 607476--607646 Score: 218
Period size: 66 Copynumber: 2.6 Consensus size: 65
607466 GAGCAAATTA
* * * * *
607476 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCTA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
607540 G
65 G
* *
607541 CTACAACTTAAAGCAGATGCAGTAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
607606 G
65 G
* * *
607607 CAGCAACTTAAAGCAGATGCGGCAGCAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
607647 CGGCAGCGAG
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 2 0.02
66 86 0.93
67 4 0.04
ACGTcount: A:0.41, C:0.18, G:0.27, T:0.14
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:607690 original size:21 final size:21
Alignment explanation
Indices: 607617--607725 Score: 119
Period size: 21 Copynumber: 5.2 Consensus size: 21
607607 CAGCAACTTA
* * * *
607617 AAGCAGATGCGGCAGCAAGAG
1 AAGCAGAGGCTGCAGCGAGGG
* *
607638 AAGCAGAGGCGGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
* *
607659 AAGTACAGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
** *
607680 AAGCAGAGGCTAAAGTGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
607701 AAGCAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
607722 AAGC
1 AAGC
607726 CGAGCAGCGT
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 74 1.00
ACGTcount: A:0.34, C:0.17, G:0.43, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:608115 original size:43 final size:42
Alignment explanation
Indices: 608081--608479 Score: 216
Period size: 43 Copynumber: 9.3 Consensus size: 42
608071 AGGTGTTGGC
* * *
608081 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGAT-ATGGT
* ** *
608124 CTTTAGCGGCGTTTGTAGAAAAAGCGCCACTAAAGATCATGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGAT-ATGGT
** *
608167 CTTTAGCGGCGTTTGTGGGGAAAACGCCGCTAAAGAT-TAGGTT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATAT-GG-T
* * * * *
608210 CTTTAGTGGCGTTTTGTTGTCGAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCG-TTTGTGGTCAAAGCGCCGCTAAAGAT-ATGGT
* ** *
608254 CTATT-GCGGCGTTTGAGGGGAAAGTGCCGCTAAAGAT-TAGGTT
1 CT-TTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATAT-GG-T
* * * * * *
608297 CTTTCGTGGCGTTTGTGATCAAAGTGCCGCTATAGATTAGGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGA-TATGGT
* * *** * ** *
608340 -TTATTGCGGCGTTTGAGAAAAAAACGCCGCTAAAGACCCTGAT
1 CTT-TAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGA-TATGGT
* ** * * * *
608383 CTTTAGCGGCGCTTGT-CCCAAAAACGCCGCTAAAGGTCTTAGT
1 CTTTAGCGGCGTTTGTGGTC-AAAGCGCCGCTAAAGAT-ATGGT
* * *
608426 CTTCAGCGGCGTTTGTGCT-AGAAGCGCCGCTAAAGATCAGGGT
1 CTTTAGCGGCGTTTGTGGTCA-AAGCGCCGCTAAAGAT-ATGGT
608469 CTTTAGCGGCG
1 CTTTAGCGGCG
608480 CATTCATTAG
Statistics
Matches: 269, Mismatches: 70, Indels: 34
0.72 0.19 0.09
Matches are distributed among these distances:
41 1 0.00
42 9 0.03
43 221 0.82
44 34 0.13
45 4 0.01
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (42 bp):
CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATATGGT
Found at i:608195 original size:86 final size:85
Alignment explanation
Indices: 608081--608479 Score: 293
Period size: 86 Copynumber: 4.6 Consensus size: 85
608071 AGGTGTTGGC
* * ** *
608081 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTAGAAAA
1 CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGT-GAAAA
*
608146 AGCGCCACTAAAGATCATGGT
65 AGCGCCGCTAAAGATCATGGT
* * * * ***
608167 CTTTAGCGGCGTTTGTGGGGAAAACGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTTGTCG
1 CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCG-TTTG-TGAAA
* *
608232 AAGCGCCGCTATAGATCAGGGT
64 AAGCGCCGCTAAAGATCATGGT
* * * * * * *
608254 CTATT-GCGGCGTTTGAGGGGAAAGTGCCGCTAAAGATTAGGTTCTTTCGTGGCGTTTGTGATCA
1 CT-TTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTGA-AA
* * * *
608318 AAGTGCCGCTATAGATTAGGGT
64 AAGCGCCGCTAAAGATCATGGT
* * *** * * ** * * *
608340 -TTATTGCGGCGTTTGAGAAAAAAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTGTCCCAA
1 CTT-TAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGT--GAA
* * *
608404 AAA-CGCCGCTAAAGGTCTTAGT
63 AAAGCGCCGCTAAAGATCATGGT
* **
608426 CTTCAGCGGCGTTTGT-GCTAGAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCG
1 CTTTAGCGGCGTTTGTGGGGA-AAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCG
608480 CATTCATTAG
Statistics
Matches: 248, Mismatches: 55, Indels: 20
0.77 0.17 0.06
Matches are distributed among these distances:
84 1 0.00
85 5 0.02
86 162 0.65
87 76 0.31
88 4 0.02
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (85 bp):
CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTGAAAAA
GCGCCGCTAAAGATCATGGT
Found at i:608326 original size:130 final size:129
Alignment explanation
Indices: 608081--608337 Score: 304
Period size: 130 Copynumber: 2.0 Consensus size: 129
608071 AGGTGTTGGC
608081 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTAGAAAA
1 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTAGAAAA
* *
608146 AGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGGGGAAAACGCCGCTAAAGATTAGGTT
66 AGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGAGCAAAACGCCGCTAAAGATTAGGTT
* * * * *
608210 CTTTAGTGGCGTTTTGTTGTCGAAGCGCCGCTATAGATCAGGGTCTATT-GCGGCGTTTG-AGGG
1 CTTTAGTGGCGTTTT-TGGTCAAAGCGCCGCTAAAGATAAGGGTCT-TTAGCGGCGTTTGTA-GA
* * * * * * * ** *
608273 GAAAGTGCCGCTAAAGATTA-GGTTCTTTCGTGGCGTTTGTGATCAAAGTGCCGCTATAGATTAG
63 AAAAGCGCCACTAAAGATCATGG-TCTTTAGCGGCGTTTGTGAGCAAAACGCCGCTAAAGATTAG
608337 G
127 G
608338 GTTTATTGCG
Statistics
Matches: 107, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
129 18 0.17
130 87 0.81
131 2 0.02
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.30
Consensus pattern (129 bp):
CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTAGAAAA
AGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGAGCAAAACGCCGCTAAAGATTAGGTT
Found at i:608351 original size:130 final size:129
Alignment explanation
Indices: 608081--608479 Score: 292
Period size: 130 Copynumber: 3.1 Consensus size: 129
608071 AGGTGTTGGC
*
608081 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTAGAAAA
1 CTTTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTAGAAAA
* *
608146 AGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGGGGAAAACGCCGCTAAAGATTAGGTT
66 AGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGAGCAAAACGCCGCTAAAGATTAGGTT
* * * * * *
608210 CTTTAGTGGCGTTTTGTTGTCGAAGCGCCGCTATAGATCAGGGTCTATT-GCGGCGTTTG-AGGG
1 CTTTAGCGGCGTTTT-TGGTCAAAGCGCCGCTAAAGATAAGGGTCT-TTAGCGGCGTTTGTA-GA
* * * * * * * ** *
608273 GAAAGTGCCGCTAAAGATTA-GGTTCTTTCGTGGCGTTTGTGATCAAAGTGCCGCTATAGATTAG
63 AAAAGCGCCACTAAAGATCATGG-TCTTTAGCGGCGTTTGTGAGCAAAACGCCGCTAAAGATTA-
608337 GGTT
126 GGTT
** *** * **** * * **
608341 -TATT-GCGGCGTTTGAGAAAAAAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTGTCCCAA
1 CT-TTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGT-AGAA
* * * * * * *
608404 AAA-CGCCGCTAAAGGTCTTAGTCTTCAGCGGCGTTTGT--GCTAGAAGCGCCGCTAAAGATCAG
64 AAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGAGC-A-AAACGCCGCTAAAGATTAG
*
608466 GGT
127 GTT
608469 CTTTAGCGGCG
1 CTTTAGCGGCG
608480 CATTCATTAG
Statistics
Matches: 207, Mismatches: 49, Indels: 28
0.73 0.17 0.10
Matches are distributed among these distances:
127 1 0.00
128 8 0.04
129 92 0.44
130 98 0.47
131 8 0.04
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (129 bp):
CTTTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTAGAAAA
AGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGAGCAAAACGCCGCTAAAGATTAGGTT
Found at i:608868 original size:3 final size:3
Alignment explanation
Indices: 608862--608891 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
608852 AACAATAGGG
608862 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
608892 AGTTCACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Done.