Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold240
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: 472780
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
File 4 of 4
Found at i:398663 original size:31 final size:31
Alignment explanation
Indices: 398625--398698 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 31
398615 TACAAGGAAA
398625 AATGTATCGATACATTTAGGTTAAAACCCAG
1 AATGTATCGATACATTTAGGTTAAAACCCAG
* *
398656 AATGTATCGATAGATTTGGGTTAAAACCCAG
1 AATGTATCGATACATTTAGGTTAAAACCCAG
398687 AATGTATCGATA
1 AATGTATCGATA
398699 TAATGAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (31 bp):
AATGTATCGATACATTTAGGTTAAAACCCAG
Found at i:398709 original size:82 final size:83
Alignment explanation
Indices: 398571--398723 Score: 254
Period size: 82 Copynumber: 1.9 Consensus size: 83
398561 CATACATTGA
* *
398571 AGAATGTATTGATACATTTGGGTTAAAAACCTAGAATGTATCGATACAAGGAAAAATGTATCGAT
1 AGAATGTATCGATACATTTGGGTTAAAAACCCAGAATGTATCGATACAAGGAAAAATGTATCGAT
398636 ACATTTAGGTTAAAACCC
66 ACATTTAGGTTAAAACCC
* * *
398654 AGAATGTATCGATAGATTTGGGTT-AAAACCCAGAATGTATCGATATAATGAAAAATGTATCGAT
1 AGAATGTATCGATACATTTGGGTTAAAAACCCAGAATGTATCGATACAAGGAAAAATGTATCGAT
398718 ACATTT
66 ACATTT
398724 TTTTCTAGAA
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
82 43 0.66
83 22 0.34
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (83 bp):
AGAATGTATCGATACATTTGGGTTAAAAACCCAGAATGTATCGATACAAGGAAAAATGTATCGAT
ACATTTAGGTTAAAACCC
Found at i:398803 original size:20 final size:20
Alignment explanation
Indices: 398759--398831 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
398749 GACATGGTCT
* **
398759 TGTATCAATACATTTTAGACA
1 TGTATCAATACA-TTCACTCA
398780 TGTATCGAA-ACATTCACTCA
1 TGTATC-AATACATTCACTCA
**
398800 TGTATCAATACATTCACTTT
1 TGTATCAATACATTCACTCA
*
398820 TGTATCCATACA
1 TGTATCAATACA
398832 AATTGTAGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.05
20 31 0.70
21 9 0.20
22 2 0.05
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (20 bp):
TGTATCAATACATTCACTCA
Found at i:399628 original size:41 final size:42
Alignment explanation
Indices: 399578--399689 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
399568 TGATGTCACC
* *
399578 AACTAGTGTGGGTTTTAAAAAGAAAAAAG-AAAGGGTGCCAC-
1 AACTTGTGTGGGCTTTAAAAAG-AAAAAGCAAAGGGTGCCACT
* * * *
399619 CATTTGTGTGGGCTTAAAGAAAGAAAAAGCAAGGGGTGCCACT
1 AACTTGTGTGGGCTTTAA-AAAGAAAAAGCAAAGGGTGCCACT
*
399662 AACTTGTGTGGGCTTTAAAAAGGAAAAG
1 AACTTGTGTGGGCTTTAAAAAGAAAAAG
399690 ACGTCTTGCT
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
41 19 0.33
42 24 0.41
43 15 0.26
ACGTcount: A:0.39, C:0.11, G:0.29, T:0.21
Consensus pattern (42 bp):
AACTTGTGTGGGCTTTAAAAAGAAAAAGCAAAGGGTGCCACT
Found at i:399688 original size:43 final size:41
Alignment explanation
Indices: 399577--399688 Score: 127
Period size: 41 Copynumber: 2.7 Consensus size: 41
399567 ATGATGTCAC
* * *
399577 CAACTAGTGTGGGTTTTAAAAAGAAAAAAGAAAGGGTGCCA
1 CAACTTGTGTGGGCTTTAAAAAGGAAAAAGAAAGGGTGCCA
* * * *
399618 CCATTTGTGTGGGC-TTAAAGAAAGAAAAAGCAAGGGGTGCCA
1 CAACTTGTGTGGGCTTTAAA-AAGGAAAAAG-AAAGGGTGCCA
399660 CTAACTTGTGTGGGCTTTAAAAAGGAAAA
1 C-AACTTGTGTGGGCTTTAAAAAGGAAAA
399689 GACGTCTTGC
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
40 5 0.09
41 18 0.32
42 11 0.19
43 18 0.32
44 5 0.09
ACGTcount: A:0.39, C:0.12, G:0.28, T:0.21
Consensus pattern (41 bp):
CAACTTGTGTGGGCTTTAAAAAGGAAAAAGAAAGGGTGCCA
Found at i:399750 original size:62 final size:62
Alignment explanation
Indices: 399653--400301 Score: 682
Period size: 62 Copynumber: 10.5 Consensus size: 62
399643 AAAAGCAAGG
* * * *
399653 GGTGCCACTAACTTGTGTGGGCTTTAAAAAGGAAAAGACGTCTTGCTCTTTAAGGACTAAAA
1 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCATCCTGCTCTTTAAGGACTAAAA
* * * * * *
399715 GGTGCTACCAACATGTATGGGCTTTAAAAAGGAAAATGCATCATGCTCTTTGAGGACTAAAA
1 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCATCCTGCTCTTTAAGGACTAAAA
* * * * *
399777 GGTGCGATCAACTTATGTGGGCTTTAGAAAGGAAAAGGCATCATGCTCTTTGAA-GACTAAAA
1 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCATCCTGCTCTTT-AAGGACTAAAA
* ** ** * * *
399839 TGTGCCACCAACTTGTGTGGGCTTTAAAATCGAAAAGGTGTCCTACCCTTTAAGGATTAAAA
1 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCATCCTGCTCTTTAAGGACTAAAA
* * * * * *
399901 GGTGCCACCAACTTATGTGGTCTTT-AAAAGGAAAAGGAAAGCTGTCCAGCTCTTTGAGGACCAA
1 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAA-G---GC-ATCCTGCTCTTTAAGGACTAA
399965 AA
61 AA
* * *
399967 GATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAGGCATCCTACTCTTTAAGGACTAAAA
1 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCATCCTGCTCTTTAAGGACTAAAA
* * * * **
400029 GGCGCCACCAACTTGTGTGAGCTTTAAAAAAGAAAAGGCATCCTACTCTTTGGGGACTAAAA
1 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCATCCTGCTCTTTAAGGACTAAAA
* * * * * * * * *
400091 AGTGCTACCAACGTATGTGGACTTTAAAAAGGAAAAGGCGTCCTTCTCTTTGAGGACCAAAA
1 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCATCCTGCTCTTTAAGGACTAAAA
* * *
400153 GGTGCCACCAACTTGTGTGGGCTTGAAAAAGGAAAAAGCATCCTGCTCATTGAA-GACTAAAA
1 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCATCCTGCTC-TTTAAGGACTAAAA
* * ** *
400215 TGTGCCACCAATTTGTGTGGGCTTTAAAAA--AAATTG--TCCTACTCTTTAAGGACTAAAA
1 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCATCCTGCTCTTTAAGGACTAAAA
*
400273 AGTGCCACCAACTTGTGTGGGCTTTAAAA
1 GGTGCCACCAACTTGTGTGGGCTTTAAAA
400302 GGAGGTGCTA
Statistics
Matches: 487, Mismatches: 90, Indels: 24
0.81 0.15 0.04
Matches are distributed among these distances:
57 4 0.01
58 42 0.09
60 4 0.01
61 10 0.02
62 370 0.76
63 6 0.01
65 1 0.00
66 40 0.08
67 10 0.02
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (62 bp):
GGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCATCCTGCTCTTTAAGGACTAAAA
Found at i:400155 original size:252 final size:246
Alignment explanation
Indices: 399653--400301 Score: 716
Period size: 252 Copynumber: 2.6 Consensus size: 246
399643 AAAAGCAAGG
* * * * ** *
399653 GGTGCCACTAACTTGTGTGGGCTTTAAAAAGG-AAAAGACGTCTTGCTCTTTAAGGACTAAAAGG
1 GGTGCCACCAACTTATGTGGGCTTGAAAAAGGAAAAAG-CATCCAGCTCTTTGAGGACTAAAA-G
* * * * * *
399717 TGCTACCAACATGTATGGGCTTTAAAAAGGAAAATGCATCATGCTCTTTGAGGACTAAAAGGTGC
64 TGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAATGCATCCTACTCTTTAAGGACTAAAAGGTGC
* * * * * * *
399782 GATCAACTTATGTGGGCTTTAGAAAGGAAAAGGCATCATGCTCTTTGAAGACTAAAATGTGCCAC
128 CACCAACTTGTGTGGGCTTTAAAAAAGAAAAGGCATCATACTCTTTGAAGACTAAAAAGTGCCAC
* * * * * **
399847 CAACTTGTGTGGGCTTTAAAATCGAAAAGGTGTCCTACCCTTTAAGGATTAAAA
193 CAACGTATGTGGACTTTAAAAACGAAAAGGCGTCCTACCCTTTAAGGACCAAAA
* * * *
399901 GGTGCCACCAACTTATGTGGTCTT-TAAAAGGAAAAGGAAAGCTGTCCAGCTCTTTGAGGACCAA
1 GGTGCCACCAACTTATGTGGGCTTGAAAAAGG--AA--AAAGC-ATCCAGCTCTTTGAGGACTAA
*
399965 AAGATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAGGCATCCTACTCTTTAAGGACTAAAAG
61 AAG-TGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAATGCATCCTACTCTTTAAGGACTAAAAG
* * * **
400030 GCGCCACCAACTTGTGTGAGCTTTAAAAAAGAAAAGGCATCCTACTCTTTGGGGACTAAAAAGTG
124 GTGCCACCAACTTGTGTGGGCTTTAAAAAAGAAAAGGCATCATACTCTTTGAAGACTAAAAAGTG
* * * * *
400095 CTACCAACGTATGTGGACTTTAAAAAGGAAAAGGCGTCCTTCTCTTTGAGGACCAAAA
189 CCACCAACGTATGTGGACTTTAAAAACGAAAAGGCGTCCTACCCTTTAAGGACCAAAA
* * * *
400153 GGTGCCACCAACTTGTGTGGGCTTGAAAAAGGAAAAAGCATCCTGCTCATTGAAGACTAAAATGT
1 GGTGCCACCAACTTATGTGGGCTTGAAAAAGGAAAAAGCATCCAGCTCTTTGAGGACTAAAA-GT
* *
400218 GCCACCAATTTGTGTGGGCTTTAAAA--AAAATTG--TCCTACTCTTTAAGGACTAAAAAGTGCC
65 GCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-TGCATCCTACTCTTTAAGGACTAAAAGGTGCC
400279 ACCAACTTGTGTGGGCTTTAAAA
129 ACCAACTTGTGTGGGCTTTAAAA
400302 GGAGGTGCTA
Statistics
Matches: 338, Mismatches: 53, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
244 48 0.14
245 4 0.01
246 1 0.00
247 10 0.03
248 61 0.18
249 6 0.02
250 1 0.00
251 4 0.01
252 197 0.58
253 6 0.02
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (246 bp):
GGTGCCACCAACTTATGTGGGCTTGAAAAAGGAAAAAGCATCCAGCTCTTTGAGGACTAAAAGTG
CCACCAACTTGTGTGGGCTTTAAAAGGAAAATGCATCCTACTCTTTAAGGACTAAAAGGTGCCAC
CAACTTGTGTGGGCTTTAAAAAAGAAAAGGCATCATACTCTTTGAAGACTAAAAAGTGCCACCAA
CGTATGTGGACTTTAAAAACGAAAAGGCGTCCTACCCTTTAAGGACCAAAA
Found at i:400242 original size:314 final size:305
Alignment explanation
Indices: 399654--400304 Score: 768
Period size: 314 Copynumber: 2.1 Consensus size: 305
399644 AAAGCAAGGG
* * * * *
399654 GTGCCACTAACTTGTGTGGGCTTTAAAAAGGAAAAGACGTCTTGCTCTTTAAGGACTAAAAGGTG
1 GTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGACATCCTACTCTTTAAGGACTAAAAGGCG
* * * * * *
399719 CTACCAACATGTATGGGCTTTAAAAAGGAAAATGCATCATGCTCTTTGAGGACTAAAAGGTGCGA
65 CCACCAACATGTATGAGCTTTAAAAAAGAAAAGGCATCATACTCTTTGAGGACTAAAAAGTGCGA
* * * * * *
399784 TCAACTTATGTGGGCTTTAGAAAGGAAAAGGCATCATGCTCTTTGAAGACTAAAATGTGCCACCA
130 CCAACGTATGTGGACTTTAAAAAGGAAAAGGCATCATGCTCTTTGAAGACCAAAAGGTGCCACCA
* * * ** * * *
399849 ACTTGTGTGGGCTTTAAAATCGAAAAGGTGTCCTACCCTTTAAGGATTAAAAGGTGCCACCAACT
195 ACTTGTGTGGGCTTGAAAAACGAAAAAGCATCCTACCATTGAAGGACTAAAAGGTGCCACCAACT
* *
399914 TATGTGGTCTTTAAAAGGAAAAGGAAAGCTGTCC-AGCTCTTTGAGGACC-AAAA
260 TATGTGGGCTTT---A--AAAA--AAA-CTGTCCTA-CTCTTTAAGGACCAAAAA
*
399967 GATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAGGCATCCTACTCTTTAAGGACTAAAAGGC
1 G-TGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGACATCCTACTCTTTAAGGACTAAAAGGC
* * * * *
400032 GCCACCAACTTGTGTGAGCTTTAAAAAAGAAAAGGCATCCTACTCTTTGGGGACTAAAAAGTGCT
64 GCCACCAACATGTATGAGCTTTAAAAAAGAAAAGGCATCATACTCTTTGAGGACTAAAAAGTGCG
* * * *
400097 ACCAACGTATGTGGACTTTAAAAAGGAAAAGGCGTCCTTCTCTTTGAGGACCAAAAGGTGCCACC
129 ACCAACGTATGTGGACTTTAAAAAGGAAAAGGCATCATGCTCTTTGAAGACCAAAAGGTGCCACC
* * *
400162 AACTTGTGTGGGCTTGAAAAAGGAAAAAGCATCCTGCTCATTGAA-GACTAAAATGTGCCACCAA
194 AACTTGTGTGGGCTTGAAAAACGAAAAAGCATCCTAC-CATTGAAGGACTAAAAGGTGCCACCAA
* * * *
400226 TTTGTGTGGGCTTTAAAAAAAATTGTCCTACTCTTTAAGGACTAAAAA
258 CTTATGTGGGCTTTAAAAAAAACTGTCCTACTCTTTAAGGACCAAAAA
400274 GTGCCACCAACTTGTGTGGGCTTTAAAAGGA
1 GTGCCACCAACTTGTGTGGGCTTTAAAAGGA
400305 GGTGCTAAGA
Statistics
Matches: 289, Mismatches: 45, Indels: 16
0.83 0.13 0.05
Matches are distributed among these distances:
305 7 0.02
306 39 0.13
307 9 0.03
309 4 0.01
311 1 0.00
313 1 0.00
314 223 0.77
315 5 0.02
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.25
Consensus pattern (305 bp):
GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACATCCTACTCTTTAAGGACTAAAAGGCGC
CACCAACATGTATGAGCTTTAAAAAAGAAAAGGCATCATACTCTTTGAGGACTAAAAAGTGCGAC
CAACGTATGTGGACTTTAAAAAGGAAAAGGCATCATGCTCTTTGAAGACCAAAAGGTGCCACCAA
CTTGTGTGGGCTTGAAAAACGAAAAAGCATCCTACCATTGAAGGACTAAAAGGTGCCACCAACTT
ATGTGGGCTTTAAAAAAAACTGTCCTACTCTTTAAGGACCAAAAA
Found at i:407452 original size:20 final size:20
Alignment explanation
Indices: 407424--407462 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
407414 CTATGTATCG
*
407424 ATACAATGTATCTATACAAT
1 ATACAATGTATCGATACAAT
*
407444 ATACCATGTATCGATACAA
1 ATACAATGTATCGATACAA
407463 ACAGTAGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.31
Consensus pattern (20 bp):
ATACAATGTATCGATACAAT
Found at i:407508 original size:18 final size:19
Alignment explanation
Indices: 407485--407523 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
407475 TAGCTACTGC
407485 CAATTT-CATGTATCGATA
1 CAATTTCCATGTATCGATA
407503 CAATTTGCCATGTATCGATA
1 CAATTT-CCATGTATCGATA
407523 C
1 C
407524 CAAGATCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
20 13 0.68
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (19 bp):
CAATTTCCATGTATCGATA
Found at i:409978 original size:33 final size:30
Alignment explanation
Indices: 409902--409978 Score: 75
Period size: 33 Copynumber: 2.4 Consensus size: 30
409892 AAAACCATTT
409902 TTGATGAAGATTTTGATGAAAAATGAAAAGAA
1 TTGATGAA-ATTTTGATGAAAAA-GAAAAGAA
* *
409934 ATGATGTAATTTTGATGAAATTCAA-AAAACGAA
1 TTGATGAAATTTTGATGAAA---AAGAAAA-GAA
409967 TTGATGAAATTT
1 TTGATGAAATTT
409979 GAGATTGAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
31 12 0.32
32 10 0.27
33 13 0.35
34 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.18, T:0.32
Consensus pattern (30 bp):
TTGATGAAATTTTGATGAAAAAGAAAAGAA
Found at i:411479 original size:13 final size:13
Alignment explanation
Indices: 411461--411486 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
411451 CAATTATTTA
411461 TGTATCGATACAT
1 TGTATCGATACAT
411474 TGTATCGATACAT
1 TGTATCGATACAT
411487 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:412234 original size:21 final size:21
Alignment explanation
Indices: 412193--412236 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
412183 CTCCCCTTTG
* *
412193 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
412214 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
412235 TC
1 TC
412237 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:414057 original size:13 final size:13
Alignment explanation
Indices: 414039--414077 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
414029 ATAATCACCC
* *
414039 TGTATCGATATAT
1 TGTATCGATACAA
414052 TGTATCGATACAA
1 TGTATCGATACAA
414065 TGTATCGATACAA
1 TGTATCGATACAA
414078 GGAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:416176 original size:15 final size:15
Alignment explanation
Indices: 416156--416186 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
416146 ATTTCGTTTG
*
416156 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
416171 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
416186 G
1 G
416187 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:418018 original size:21 final size:21
Alignment explanation
Indices: 417989--418033 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
417979 AAGTTTTCAT
*
417989 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
418009 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
418031 TTT
1 TTT
418034 CATCTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:420271 original size:13 final size:13
Alignment explanation
Indices: 420253--420278 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
420243 CAATTATTTG
420253 TGTATCGATACAT
1 TGTATCGATACAT
420266 TGTATCGATACAT
1 TGTATCGATACAT
420279 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:420293 original size:32 final size:33
Alignment explanation
Indices: 420233--420296 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
420223 TACAAGCCAA
*
420233 TGTATCGATACAATTATTTGTGTATCGATACAT
1 TGTATCGATACAATTATTGGTGTATCGATACAT
420266 TGTATCGATAC-A-TACTTGGTGTATCGATACA
1 TGTATCGATACAATTA-TTGGTGTATCGATACA
420297 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 2 0.07
32 16 0.55
33 11 0.38
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATTATTGGTGTATCGATACAT
Found at i:421241 original size:293 final size:293
Alignment explanation
Indices: 420738--421271 Score: 899
Period size: 293 Copynumber: 1.8 Consensus size: 293
420728 CTTCCCGCAG
* *
420738 ATATGTACTCTGCCTCGATTGTGGATAATGCAACACTATTTTGTTTCTTAGAAAACCATGATATG
1 ATATGTACTCCGCCTCGATTGTGGATAATGCAACACTATTTTATTTCTTAGAAAACCATGATATG
* * * *
420803 AGCATATTACCAAGAAATTGACAAGTATCAGAGTGCTTTTTCTATCTATCTTACAACCACCAAAA
66 AGCATATTACCAAGAAATTGACAAGTACCAAAATGCTTTTTCTATCTATCTCACAACCACCAAAA
*** * * * * *
420868 TCTGTATCCGAGTAAGCATGTAAGGCTAGGGAGGATTCTTTAGGGTACTATAATCCTAAGTTGGG
131 TCCACATCCAAGTAAGCATGTAAGGCTAGAGAAGATTCTTTAGGGTACCACAATCCTAAGTTGGG
*
420933 AGTGTCTCGTAAATACTT-AAAATCCTTTTTACAGCTAGTAAGTGATCCTCTAACTGTTGTTTTA
196 AGTGTCTCCTAAATACTTAAAAATCCTTTTTACAGCTAGTAAGTGATCCTCTAACTGTTGTTTTA
420997 TCCACAAGACTTGCGCACAACACCTTCCTGAAA
261 TCCACAAGACTTGCGCACAACACCTTCCTGAAA
* *
421030 ATATGTACTCCGCCTCGGTTGTGGATAATGCAACACTATTTTATTTCTTGGAAAACCATGATATG
1 ATATGTACTCCGCCTCGATTGTGGATAATGCAACACTATTTTATTTCTTAGAAAACCATGATATG
421095 AGCATATTACCAAGAAATTGACAAGTACCGAAAATGCTTTTTCTATCTATCTCACAACCACCAAA
66 AGCATATTACCAAGAAATTGACAAGTACC-AAAATGCTTTTTCTATCTATCTCACAACCACCAAA
421160 ATCCACATCCAAGTAAGCATGTAAGGCTAGAGAAGATTCTTTAGGGTACCACAATCCTAAGTTGG
130 ATCCACATCCAAGTAAGCATGTAAGGCTAGAGAAGATTCTTTAGGGTACCACAATCCTAAGTTGG
421225 GAGTGTCTCCTAAATACTTAAAAATCCTTTTTACAGCTAGTAAGTGA
195 GAGTGTCTCCTAAATACTTAAAAATCCTTTTTACAGCTAGTAAGTGA
421272 GACTCCCTAG
Statistics
Matches: 223, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
292 89 0.40
293 107 0.48
294 27 0.12
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (293 bp):
ATATGTACTCCGCCTCGATTGTGGATAATGCAACACTATTTTATTTCTTAGAAAACCATGATATG
AGCATATTACCAAGAAATTGACAAGTACCAAAATGCTTTTTCTATCTATCTCACAACCACCAAAA
TCCACATCCAAGTAAGCATGTAAGGCTAGAGAAGATTCTTTAGGGTACCACAATCCTAAGTTGGG
AGTGTCTCCTAAATACTTAAAAATCCTTTTTACAGCTAGTAAGTGATCCTCTAACTGTTGTTTTA
TCCACAAGACTTGCGCACAACACCTTCCTGAAA
Found at i:423922 original size:21 final size:21
Alignment explanation
Indices: 423898--423944 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
423888 ACCATCTTGC
423898 AATTCAATTATCTTCTTTTCT
1 AATTCAATTATCTTCTTTTCT
* *
423919 AATTCACTTATTTTCTTTTCT
1 AATTCAATTATCTTCTTTTCT
423940 AATTC
1 AATTC
423945 TTCTTCTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTCAATTATCTTCTTTTCT
Found at i:423954 original size:21 final size:21
Alignment explanation
Indices: 423910--423958 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
423900 TTCAATTATC
*
423910 TTCTTTTCTAATTCACTTATT
1 TTCTTTTCTAATTCACTTACT
*
423931 TTCTTTTCTAATTCTTCTT-CT
1 TTCTTTTCTAATTC-ACTTACT
423952 TTCTTTT
1 TTCTTTT
423959 TAGGCACATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.67
Consensus pattern (21 bp):
TTCTTTTCTAATTCACTTACT
Found at i:426555 original size:3 final size:3
Alignment explanation
Indices: 426540--426577 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
426530 AACCATCAAA
*
426540 GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
426578 AGTTGACTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.37, C:0.00, G:0.34, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:428169 original size:20 final size:20
Alignment explanation
Indices: 428144--428218 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
428134 TTTTACCTAG
*
428144 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTCA
* * *
428164 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
428184 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
428204 ATGTATCAATACATT
1 ATGTATCGATACATT
428219 CTGTCTTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:432101 original size:20 final size:20
Alignment explanation
Indices: 432068--432141 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
432058 TTTTACCCAG
*
432068 ATGTATCAATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
432088 ATATATCGAGACATGTTTGA
1 ATGTATCGATACATTTTTCA
* *
432108 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
432128 ATGTATCGATACAT
1 ATGTATCGATACAT
432142 CTAGTTAAAA
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:440337 original size:27 final size:27
Alignment explanation
Indices: 440302--441186 Score: 1322
Period size: 28 Copynumber: 32.2 Consensus size: 27
440292 ACTGTGACCT
* *
440302 CTTTAAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
440329 CTTTTAAGTCCATAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
440356 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
440384 CTTTTAAGTCCACAACTCCATGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
440411 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
440439 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
440467 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
440495 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
440523 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
440551 CTTTTAAAGTCCACAACTTCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
440579 CTTTTAAGTCCACAAGTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
440606 CTTTTAAGTCCACAAGTCCGTGGCACG
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
440633 CTTTTAAGTCCACAAGTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
440660 CTTTTAAGTCCACAAGTCCGTGGCACG
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
440687 CTTTTAAGTCCACAAGTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
440714 CTTTTAAGTCCATAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
440742 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
440770 CTTTTAAGTCCACAACTTCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
440797 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
440825 CTTTTAAGTCCACAACTCCGTGGCA-C
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
440851 CTTTGAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
440878 CTTTTAAAGTCCACAACTCCGTGGCATCC
1 CTTTT-AAGTCCACAACTCCGTGGCA-CC
* * *
440907 CTTTTAAGTTCACGACTCCGCGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
440934 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
440961 CTTTTAAAGTCCACAACTCCGTGGCCTCC
1 CTTTT-AAGTCCACAACTCCGTGG-CACC
*
440990 CTTTTAAGTCCACAACTTCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
441017 CTTTTAAGTCCATAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
441044 CTTTTAAGTCCATAACTCCGAGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
441072 CTTTTAAGTCCACAACTCTGTGGTACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
441099 CTTTTAAAGTCCACAACTCCGTGGCACT
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
441127 CTTTTAAAGTCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* **
441155 CTTTTAAGTTCACAACTTTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
441182 CTTTT
1 CTTTT
441187 CAATGCCCAC
Statistics
Matches: 800, Mismatches: 47, Indels: 22
0.92 0.05 0.03
Matches are distributed among these distances:
26 25 0.03
27 346 0.43
28 414 0.52
29 15 0.02
ACGTcount: A:0.23, C:0.34, G:0.15, T:0.28
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:440442 original size:83 final size:82
Alignment explanation
Indices: 440303--441186 Score: 1355
Period size: 83 Copynumber: 10.7 Consensus size: 82
440293 CTGTGACCTC
* *
440303 TTTAAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCATAACTCCGTGGCACCCTTTTAAAGTCC
1 TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCC
440368 ACAACTCCGTGGCACCCT
65 ACAACTCCGTGGCACCCT
*
440386 TTT-AAGTCCACAACTCCATGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTC
1 TTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AAGTC
440450 CACAACTCCGTGGCACCCT
64 CACAACTCCGTGGCACCCT
440469 TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTC
1 TTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AAGTC
440534 CACAACTCCGTGGCACCCT
64 CACAACTCCGTGGCACCCT
* *
440553 TTTAAAGTCCACAACTTCGTGGCACCCTTTTAAGTCCACAAGTCCGTGGCACCCTTTTAAGTCCA
1 TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
* *
440618 CAAGTCCGTGGCACGCT
66 CAACTCCGTGGCACCCT
* * *
440635 TTT-AAGTCCACAAGTCCGTGGCACCCTTTTAAGTCCACAAGTCCGTGGCACGCTTTTAAGTCCA
1 TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
* *
440699 CAAGTCTGTGGCACCCT
66 CAACTCCGTGGCACCCT
*
440716 TTT-AAGTCCATAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTC
1 TTTAAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
*
440780 CACAACTTCGTGGCACCCT
64 CACAACTCCGTGGCACCCT
*
440799 TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCTTTGAAGTCCA
1 TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
440863 CAACTCCGTGGCACCCT
66 CAACTCCGTGGCACCCT
* * *
440880 TTTAAAGTCCACAACTCCGTGGCATCCCTTTTAAGTTCACGACTCCGCGGCACCCTTTTAAGTCC
1 TTTAAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
440945 ACAACTCCGTGGCACCCT
65 ACAACTCCGTGGCACCCT
* *
440963 TTTAAAGTCCACAACTCCGTGGCCTCCCTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAGTCC
1 TTTAAAGTCCACAACTCCGTGG-CACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
441028 ATAACTCCGTGGCACCCT
65 ACAACTCCGTGGCACCCT
* * * * *
441046 TTT-AAGTCCATAACTCCGAGGCATCTCTTTTAAGTCCACAACTCTGTGGTACCCTTTTAAAGTC
1 TTTAAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTC
*
441110 CACAACTCCGTGGCACTCT
64 CACAACTCCGTGGCACCCT
* * **
441129 TTTAAAGTCCACAACTCTGTGGCACCCTTTTAAGTTCACAACTTTGTGGCACCCTTTT
1 TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
441187 CAATGCCCAC
Statistics
Matches: 741, Mismatches: 49, Indels: 22
0.91 0.06 0.03
Matches are distributed among these distances:
81 147 0.20
82 146 0.20
83 302 0.41
84 146 0.20
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.28
Consensus pattern (82 bp):
TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
CAACTCCGTGGCACCCT
Found at i:441222 original size:28 final size:28
Alignment explanation
Indices: 441184--441789 Score: 399
Period size: 28 Copynumber: 20.5 Consensus size: 28
441174 GTGGCACCCT
* *
441184 TTTCAATGCCCACACA-TTAGTGGCATCA
1 TTTCAAAGCCCACA-AGTCAGTGGCATCA
*
441212 TTTCAAAGCCCACAAGTCAGTGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCA
* * *
441240 TTTCAAAGCCCTCACAATTCGGTGGCAGCCCA
1 TTTCAAAG-CC-CACAAGTCAGTGGCA--TCA
* * *
441272 TTTCAAAGCCCACAAGACGGTGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCA
* *
441300 TTTCAAAGCCCACACAAGTCAGTGGCACCT
1 TTTCAAAG-CC-CACAAGTCAGTGGCATCA
*
441330 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
1 TTTCAAAG-CC-CACAAGTCAGTGGC-A-TCA
* ** *
441362 TTTGAAAGCCCATACAAGTTGGCGGCAACTCA
1 TTTCAAAGCCC--ACAAGTCAGTGGC-A-TCA
** *
441394 TTTCAAAGCCCACACAAGTTGGTGGCAACCTA
1 TTTCAAAG-CC-CACAAGTCAGTGGC-ATC-A
** *
441426 TTTCAAAGCCCACACAAGTTGGTGACAACTCA
1 TTTCAAAG-CC-CACAAGTCAGTGGC-A-TCA
* * *
441458 TTTGAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAG-CC-CACAAGTCAGTGGC-A-TCA
* * *
441490 TTTTAAAGTCCACACAAGGT-GGTGGCAACCCA
1 TTTCAAAG-CC-CACAA-GTCAGTGGC-A-TCA
* * *
441522 TTTCAAAGCCCACACAAGTCGGTGGCGTCT
1 TTTCAAAG-CC-CACAAGTCAGTGGCATCA
* *
441552 TTTCAAAGCCCACAAGTCAGTGGTATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCA
* *
441580 TTTCAAAGCCCACAAGTCAGTGGTATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCA
* * * *
441608 TTTCAATGTCCACAAGTCGGTGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCA
* * *
441636 TTTCAAAGCCCACAAGTCAATGGTATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCA
* * * *
441664 TTTCCAAGCCCACAAGTTAGTGGCAACT
1 TTTCAAAGCCCACAAGTCAGTGGCATCA
* * * *
441692 TTTCAAAGCCCACGAGTTAGTGGCAACT
1 TTTCAAAGCCCACAAGTCAGTGGCATCA
* *
441720 TTTCAAAGCCCACGAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCA
*
441748 TTTCAAAGCCCACAAGTTAGTGGCATC-
1 TTTCAAAGCCCACAAGTCAGTGGCATCA
441775 TCTTCAAAGCCCACA
1 T-TTCAAAGCCCACA
441790 GAAGTTAGTG
Statistics
Matches: 498, Mismatches: 62, Indels: 36
0.84 0.10 0.06
Matches are distributed among these distances:
27 2 0.00
28 240 0.48
29 6 0.01
30 76 0.15
31 8 0.02
32 160 0.32
33 5 0.01
34 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCA
Found at i:441242 original size:56 final size:58
Alignment explanation
Indices: 441182--441802 Score: 465
Period size: 56 Copynumber: 10.5 Consensus size: 58
441172 TTGTGGCACC
*
441182 CTTTTCAATGCCCACAC-A-TTAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCAAAGCCCACACAAGTTAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCAT
* * * * *
441238 CTTTTCAAAGCCCTCACAA-TTCGGTGGCAGCCCATTTCAAAGCCCACAAGACGGTGGCAT
1 CTTTTCAAAGCCCACACAAGTT-AGTGGCA--TCATTTCAAAGCCCACAAGTCAGTGGCAT
* * * *
441298 CTTTTCAAAGCCCACACAAGTCAGTGGCACCTTTTCAAAGCCCACACAAGTCGGTGGCAACT
1 CTTTTCAAAGCCCACACAAGTTAGTGGCATCATTTCAAAG-CC-CACAAGTCAGTGGC-A-T
* * * * * ** *
441360 CATTTGAAAGCCCATACAAGTTGGCGGCAACTCATTTCAAAGCCCACACAAGTTGGTGGCAAC
1 CTTTTCAAAGCCCACACAAGTTAGTGGC-A-TCATTTCAAAG-CC-CACAAGTCAGTGGC-AT
* * * * *
441423 CTATTTCAAAGCCCACACAAGTTGGTGACAACTCATTTGAAAGCCCACACAAGTCGGTGGCAACC
1 CT-TTTCAAAGCCCACACAAGTTAGTGGC-A-TCATTTCAAAG-CC-CACAAGTCAGTGGC-A-T
* * * * * *
441488 CATTTT-AAAGTCCACACAAGGTGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCGT
1 C-TTTTCAAAGCCCACACAAGTTAGTGGC-A-TCATTTCAAAG-CC-CACAAGTCAGTGGCAT
* * * *
441550 CTTTTCAAAG-CC-CACAAGTCAGTGGTATCCTTTCAAAGCCCACAAGTCAGTGGTAT
1 CTTTTCAAAGCCCACACAAGTTAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCAT
* * * ** * * *
441606 CCTTTCAATG-TC-CACAAGTCGGTGGCATCTTTTCAAAGCCCACAAGTCAATGGTAT
1 CTTTTCAAAGCCCACACAAGTTAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCAT
* * * * * *
441662 CTTTTCCAAG-CC-CACAAGTTAGTGGCAACTTTTCAAAGCCCACGAGTTAGTGGCAA
1 CTTTTCAAAGCCCACACAAGTTAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCAT
* * * *
441718 CTTTTCAAAG-CC-CACGAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCAT
1 CTTTTCAAAGCCCACACAAGTTAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCAT
* *
441774 CTCTTCAAAGCCCACAGAAGTTAGTGGCA
1 CTTTTCAAAGCCCACACAAGTTAGTGGCA
441803 CCTTTTTTTA
Statistics
Matches: 474, Mismatches: 74, Indels: 32
0.82 0.13 0.06
Matches are distributed among these distances:
56 179 0.38
57 7 0.01
58 37 0.08
59 3 0.01
60 73 0.15
61 8 0.02
62 28 0.06
63 2 0.00
64 131 0.28
65 5 0.01
66 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (58 bp):
CTTTTCAAAGCCCACACAAGTTAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCAT
Found at i:441281 original size:32 final size:32
Alignment explanation
Indices: 441210--441547 Score: 365
Period size: 32 Copynumber: 10.9 Consensus size: 32
441200 TTAGTGGCAT
* *
441210 CATTTCAAAG-CC-CACAAGTCAGTGGC-A-T
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
* * * *
441238 CTTTTCAAAGCCCTCACAATTCGGTGGCAGCC
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
* *
441270 CATTTCAAAG-CC-CACAAGACGGTGGC-A-T
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
* *
441298 CTTTTCAAAGCCCACACAAGTCAGTGGC-A-C
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
* *
441328 CTTTTCAAAGCCCACACAAGTCGGTGGCAACT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
* * * * *
441360 CATTTGAAAGCCCATACAAGTTGGCGGCAACT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
*
441392 CATTTCAAAGCCCACACAAGTTGGTGGCAACC
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
* * * *
441424 TATTTCAAAGCCCACACAAGTTGGTGACAACT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
*
441456 CATTTGAAAGCCCACACAAGTCGGTGGCAACC
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
* *
441488 CATTTTAAAGTCCACACAAGGT-GGTGGCAACC
1 CATTTCAAAGCCCACACAA-GTCGGTGGCAACC
441520 CATTTCAAAGCCCACACAAGTCGGTGGC
1 CATTTCAAAGCCCACACAAGTCGGTGGC
441548 GTCTTTTCAA
Statistics
Matches: 263, Mismatches: 37, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
28 18 0.07
29 4 0.02
30 64 0.24
31 5 0.02
32 170 0.65
33 2 0.01
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (32 bp):
CATTTCAAAGCCCACACAAGTCGGTGGCAACC
Found at i:441407 original size:64 final size:64
Alignment explanation
Indices: 441184--441565 Score: 395
Period size: 64 Copynumber: 6.2 Consensus size: 64
441174 GTGGCACCCT
* * * *
441184 TTTCAATGCCCACAC-A-TTAGTGGC-A-TCATTTCAAAG-CC-CACAAGTCAGTGGC-A-TCT
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCATTTCAAAGCCCACACAAGTCGGTGGCAACTCA
* * * * *
441240 TTTCAAAGCCCTCACAA-TTCGGTGGCAGCCCATTTCAAAG-CC-CACAAGACGGTGGC-A-TCT
1 TTTCAAAGCCCACACAAGTT-GGTGGCAACTCATTTCAAAGCCCACACAAGTCGGTGGCAACTCA
** *
441300 TTTCAAAGCCCACACAAGTCAGTGGC-AC-CTTTTCAAAGCCCACACAAGTCGGTGGCAACTCA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCATTTCAAAGCCCACACAAGTCGGTGGCAACTCA
* * * *
441362 TTTGAAAGCCCATACAAGTTGGCGGCAACTCATTTCAAAGCCCACACAAGTTGGTGGCAAC-CTA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCATTTCAAAGCCCACACAAGTCGGTGGCAACTC-A
* * *
441426 TTTCAAAGCCCACACAAGTTGGTGACAACTCATTTGAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCATTTCAAAGCCCACACAAGTCGGTGGCAACTCA
* * * * * *
441490 TTTTAAAGTCCACACAAGGTGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGC--GTCT
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCATTTCAAAGCCCACACAAGTCGGTGGCAACTCA
441552 TTTCAAAGCCCACA
1 TTTCAAAGCCCACA
441566 AGTCAGTGGT
Statistics
Matches: 275, Mismatches: 38, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
56 13 0.05
57 3 0.01
58 14 0.05
59 3 0.01
60 62 0.23
61 2 0.01
62 36 0.13
63 3 0.01
64 138 0.50
65 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (64 bp):
TTTCAAAGCCCACACAAGTTGGTGGCAACTCATTTCAAAGCCCACACAAGTCGGTGGCAACTCA
Found at i:441456 original size:96 final size:93
Alignment explanation
Indices: 441209--441794 Score: 444
Period size: 84 Copynumber: 6.6 Consensus size: 93
441199 ATTAGTGGCA
* * * * *
441209 TCATTTCAAAG-CC-CACAAGTCAGTGGCATCTTTTCAAAGCCCTCACAATTCGGTGGCAGCCCA
1 TCATTTCAAAGCCCACACAAGTCAGTGGCACCTTTTCAAAGCCCACACAAGTCGGTGGCAACTCA
* *
441272 TTTCAAAGCCC-ACAAGACGGTGGC-A-
66 TTTGAAAGCCCAACAAGTCGGTGGCAAC
*
441297 TCTTTTCAAAGCCCACACAAGTCAGTGGCACCTTTTCAAAGCCCACACAAGTCGGTGGCAACTCA
1 TCATTTCAAAGCCCACACAAGTCAGTGGCACCTTTTCAAAGCCCACACAAGTCGGTGGCAACTCA
* *
441362 TTTGAAAGCCCATACAAGTTGGCGGCAAC
66 TTTGAAAGCCCA-ACAAGTCGGTGGCAAC
** * *
441391 TCATTTCAAAGCCCACACAAGTTGGTGGCAACCTATTTCAAAGCCCACACAAGTTGGTGACAACT
1 TCATTTCAAAGCCCACACAAGTCAGTGGC-ACCT-TTTCAAAGCCCACACAAGTCGGTGGCAACT
441456 CATTTGAAAGCCCACACAAGTCGGTGGCAAC
64 CATTTGAAAGCCCA-ACAAGTCGGTGGCAAC
* * * * * *
441487 CCATTTTAAAGTCCACACAAGGT-GGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGC--G
1 TCATTTCAAAGCCCACACAA-GTCAGTGGC-A-CCTTTTCAAAGCCCACACAAGTCGGTGGCAAC
* * * *
441549 TCTTTTCAAAGCCC-ACAAGTCAGTGG-TA-
63 TCATTTGAAAGCCCAACAAGTCGGTGGCAAC
* * * *
441577 TCCTTTCAAAG-CC-CACAAGTCAGTGGTATCC-TTTCAATG-TC-CACAAGTCGGTGGC-A-TC
1 TCATTTCAAAGCCCACACAAGTCAGTGGCA-CCTTTTCAAAGCCCACACAAGTCGGTGGCAACTC
* * ** *
441635 TTTTCAAAGCCC-ACAAGTCAATGG-TA-
65 ATTTGAAAGCCCAACAAGTCGGTGGCAAC
* * * * * **
441661 TCTTTTCCAAG-CC-CACAAGTTAGTGGCAACTTTTCAAAG-CC-CACGAGTTAGTGGCAACT--
1 TCATTTCAAAGCCCACACAAGTCAGTGGCACCTTTTCAAAGCCCACACAAGTCGGTGGCAACTCA
* * *
441720 TTTCAAAGCCC-ACGAGTCAGTGGC-A-
66 TTTGAAAGCCCAACAAGTCGGTGGCAAC
* * * * *
441745 TCCTTTCAAAG-CC-CACAAGTTAGTGGCATCTCTTCAAAGCCCACAGAAGT
1 TCATTTCAAAGCCCACACAAGTCAGTGGCACCTTTTCAAAGCCCACACAAGT
441795 TAGTGGCACC
Statistics
Matches: 424, Mismatches: 56, Indels: 38
0.82 0.11 0.07
Matches are distributed among these distances:
83 1 0.00
84 141 0.33
85 4 0.01
86 13 0.03
87 5 0.01
88 19 0.04
89 4 0.01
90 63 0.15
91 1 0.00
92 21 0.05
93 1 0.00
94 38 0.09
95 4 0.01
96 105 0.25
97 4 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (93 bp):
TCATTTCAAAGCCCACACAAGTCAGTGGCACCTTTTCAAAGCCCACACAAGTCGGTGGCAACTCA
TTTGAAAGCCCAACAAGTCGGTGGCAAC
Found at i:441935 original size:45 final size:45
Alignment explanation
Indices: 441884--442084 Score: 158
Period size: 45 Copynumber: 4.3 Consensus size: 45
441874 AAATCCGATA
* *
441884 TCGCTGGCATTGAATCAACATATTGGCACCTTTATTAGCTCAATG
1 TCGCTGGCCTTGAATCAACACATTGGCACCTTTATTAGCTCAATG
* *
441929 TCGCTGGCCTTGAATCAGCACA-T-G-ATCCATTTTCCCTTAGCTCAATG
1 TCGCTGGCCTTGAATCAACACATTGGCA-CC--TTT--ATTAGCTCAATG
* * * * *
441976 TTGCTGGCCTTGAATTAGCACATTGTC-CACTTTATTAGCCCAATG
1 TCGCTGGCCTTGAATCAACACATTGGCAC-CTTTATTAGCTCAATG
* * * *
442021 TCGCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCCTTAGTTCAATG
1 TCGCTGGCCTTGAATCAACACATTGG--CACCTTT--ATTAGCTCAATG
*
442070 TCACTGGCCTTGAAT
1 TCGCTGGCCTTGAAT
442085 TGGCACATTA
Statistics
Matches: 125, Mismatches: 17, Indels: 24
0.75 0.10 0.14
Matches are distributed among these distances:
42 1 0.01
43 3 0.02
44 1 0.01
45 55 0.44
47 38 0.30
48 3 0.02
49 24 0.19
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (45 bp):
TCGCTGGCCTTGAATCAACACATTGGCACCTTTATTAGCTCAATG
Found at i:441982 original size:47 final size:47
Alignment explanation
Indices: 441918--442093 Score: 223
Period size: 47 Copynumber: 3.7 Consensus size: 47
441908 GGCACCTTTA
441918 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACA-TGATCCATTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTG-TCCATTTTCCC
* * * *
441965 TTAGCTCAATGTTGCTGGCCTTGAATTAGCACATTGTCCACTTT--A
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCATTTTCCC
*
442010 TTAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATT-GTCCA-TTTTCCC
* * **
442059 TTAGTTCAATGTCACTGGCCTTGAATTGGCACATT
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATT
442094 AGCAATCCTC
Statistics
Matches: 110, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
45 32 0.29
46 5 0.05
47 41 0.37
48 2 0.02
49 30 0.27
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (47 bp):
TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCATTTTCCC
Found at i:442043 original size:92 final size:94
Alignment explanation
Indices: 441913--442093 Score: 294
Period size: 94 Copynumber: 1.9 Consensus size: 94
441903 ATATTGGCAC
*
441913 CTTTATTAGCTCAATGTCGCTGGCCTTGAATCAGCACA-TGATCCA-TTTTCCCTTAGCTCAATG
1 CTTTATTAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGATCCACTTTTCCCTTAGCTCAATG
**
441976 TTGCTGGCCTTGAATTAGCACATTGTCCA
66 TCACTGGCCTTGAATTAGCACATTGTCCA
* *
442005 CTTTATTAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCCTTAGTTCAATG
1 CTTTATTAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGATCCACTTTTCCCTTAGCTCAATG
*
442070 TCACTGGCCTTGAATTGGCACATT
66 TCACTGGCCTTGAATTAGCACATT
442094 AGCAATCCTC
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
92 37 0.46
93 6 0.07
94 38 0.47
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.35
Consensus pattern (94 bp):
CTTTATTAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGATCCACTTTTCCCTTAGCTCAATG
TCACTGGCCTTGAATTAGCACATTGTCCA
Found at i:442502 original size:20 final size:20
Alignment explanation
Indices: 442471--442536 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
442461 TTTTACCCAG
442471 ATGTATCAATACATTTTTCA
1 ATGTATCAATACATTTTTCA
* * * *
442491 ATATATCGATACATGTTTGA
1 ATGTATCAATACATTTTTCA
* *
442511 ATGTATCAATATATTCTTCA
1 ATGTATCAATACATTTTTCA
442531 ATGTAT
1 ATGTAT
442537 TGATACATCT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (20 bp):
ATGTATCAATACATTTTTCA
Found at i:449936 original size:19 final size:19
Alignment explanation
Indices: 449912--449960 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
449902 AAACAGTAAC
449912 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
* *
449931 TGTATCAATAGATAAGTGT
1 TGTATCGATACATAAGTGT
449950 TGTATCGATAC
1 TGTATCGATAC
449961 CATGTATCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:461618 original size:52 final size:52
Alignment explanation
Indices: 461540--461668 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
461530 CGAAATATGA
* *
461540 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
*
461592 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
461644 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
461669 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:461681 original size:52 final size:51
Alignment explanation
Indices: 461540--461688 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 51
461530 CGAAATATGA
*
461540 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* *
461592 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
461644 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
461689 ATGTATTGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 87 0.98
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:461769 original size:20 final size:19
Alignment explanation
Indices: 461740--461777 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
461730 GCAGTAGCTT
461740 AAATTGTATCGATACAAAA
1 AAATTGTATCGATACAAAA
461759 AAATATGTATCGATACAAA
1 AAAT-TGTATCGATACAAA
461778 TCGTTGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (19 bp):
AAATTGTATCGATACAAAA
Found at i:462145 original size:22 final size:21
Alignment explanation
Indices: 462111--462183 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 21
462101 TCTTTCGTAC
*
462111 CAAAAATAA-TAAATAAATAAAA
1 CAAAAAAAACTAAA-AAA-AAAA
462133 -AAAAAAAACTAAAAAAAAAA
1 CAAAAAAAACTAAAAAAAAAA
* *
462153 CTAAAAAAAACCAAAAAACAAA
1 C-AAAAAAAACTAAAAAAAAAA
*
462175 CAAACAAAA
1 CAAAAAAAA
462184 TTAGAAGGGT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
20 4 0.09
21 17 0.39
22 23 0.52
ACGTcount: A:0.81, C:0.11, G:0.00, T:0.08
Consensus pattern (21 bp):
CAAAAAAAACTAAAAAAAAAA
Found at i:462178 original size:11 final size:12
Alignment explanation
Indices: 462131--462162 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
462121 AAATAAATAA
462131 AAAAAAAAAACT
1 AAAAAAAAAACT
462143 AAAAAAAAAACT
1 AAAAAAAAAACT
462155 AAAAAAAA
1 AAAAAAAA
462163 CCAAAAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.88, C:0.06, G:0.00, T:0.06
Consensus pattern (12 bp):
AAAAAAAAAACT
Found at i:463508 original size:28 final size:28
Alignment explanation
Indices: 463475--464311 Score: 943
Period size: 28 Copynumber: 29.5 Consensus size: 28
463465 ATACGACCCT
* *
463475 TTTCAAAGCCCATAAGTCAGTGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
463503 TTTCAAAGCCCACACGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
463531 TTTCGAAGCCCAGAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
463559 TTTCGAAGCCCACAAGTCAGTGGTACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
463587 TTTTCAAAGCCCACAAGTTAGTGGCATACCC
1 -TTTCAAAGCCCACAAGTCAGTGGCAT--CC
* *
463618 TTTCAAAGCCCACAAGTCGGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
463646 TTTCAAACCCCACAAGACAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
463674 TTTCAAAGCCCACAAGT-AGTGGCATCA
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
**
463701 TTTCAAAGCCCACAAGTCAGTGGCACTTT
1 TTTCAAAGCCCACAAGTCAGTGGCA-TCC
* * *
463730 TTTCCAAGCCCATAAGTTAGTGGCATACCC
1 TTTCAAAGCCCACAAGTCAGTGGCAT--CC
*
463760 TTTCAAAGCCCACAAGTCGGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
463787 TTTTCAAAGCCCACAAGACAGTGGTATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
463816 TTTCAAAGCCCACAAGTCAATGGCATCA
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
463844 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
463872 TATTCAAAGCCCACAAGTCA---ACACCC
1 T-TTCAAAGCCCACAAGTCAGTGGCATCC
* * *
463898 TTTCAAACCCCACAAGACAGTGGTATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
463926 TTTCAAAGCCCACAAGTCAGTGGCATCA
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
463954 TTTCAAAGCCCACAAGTCAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
463981 TTATTCAAAGCCCACAAGTCAGTGGCATCA
1 -T-TTCAAAGCCCACAAGTCAGTGGCATCC
*
464011 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
464039 TTTTCAAAGCCCATAAGTCAATGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
*
464068 TTTCAAAGCCCACAAGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * *
464096 TTTTAAATCCCACAAGTTAGTGGCATCA
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
464124 TTTCAAAGCCCACAAGTCAGTGGCATCA
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
464152 TTTCAAAGTCCACAAGTTAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *** * * *
464179 ATTTTAAAATGCATAAGTTAGTGGCATCA
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
464208 TTTCAAAGCCCACAAGTCAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
464235 ATTTCAAAACCCACAAGTAAATGGCATACCC
1 -TTTCAAAGCCCACAAGTCAGTGGCAT--CC
* *
464266 TTTCAAAGCCCACACAAGTCGGTGGCAACTCT
1 TTTCAAAG-CC-CACAAGTCAGTGGC-A-TCC
464298 TTTCAAAGCCCACA
1 TTTCAAAGCCCACA
464312 CAAGTTAGTG
Statistics
Matches: 687, Mismatches: 95, Indels: 52
0.82 0.11 0.06
Matches are distributed among these distances:
25 16 0.02
26 6 0.01
27 31 0.05
28 432 0.63
29 116 0.17
30 56 0.08
31 8 0.01
32 20 0.03
33 1 0.00
34 1 0.00
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.23
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:463760 original size:142 final size:142
Alignment explanation
Indices: 463470--464324 Score: 1021
Period size: 142 Copynumber: 6.0 Consensus size: 142
463460 TGTCAATACG
* * * *
463470 ACCCTTTTCAAAGCCCATAAGTCAGTGGCATCTTTTCAAAGCCCACACGTTAGTGGCATCCTTTC
1 ACCC-TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC
* * * * * *
463535 GAAGCCCAGAAGTCAGTGGCATCCTTTCGAAGCCCACAAGTCAGTGGTACCCTTTTCAAAGCCCA
65 AAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
463600 CAAGTTAGTGGCA
130 CAAGTTAGTGGCA
* * * *
463613 TACCCTTTCAAAGCCCACAAGTCGGTGGCACCCTTTCAAACCCCACAAGACAGTGGCATCCTTTC
1 -ACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC
* *
463678 AAAGCCCACAAGT-AGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCACTTTTTTCCAAGCCCA
65 AAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
*
463742 TAAGTTAGTGGCA
130 CAAGTTAGTGGCA
* * *
463755 TACCCTTTCAAAGCCCACAAGTCGGTGGCA-CCTTTTCAAAGCCCACAAGACAGTGGTATCCTTT
1 -ACCCTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGCATCCTTT
* * *
463819 CAAAGCCCACAAGTCAATGGCATCATTTCAAAGCCCACAAGTCAGTGGCACCCTATTCAAAGCCC
64 CAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCC
* *
463884 ACAAGTCA---AC-
129 ACAAGTTAGTGGCA
* * * *
463894 ACCCTTTCAAACCCCACAAGACAGTGGTATCCTTTCAAAGCCCACAAGTCAGTGGCATCATTTCA
1 ACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCA
* * *
463959 AAGCCCACAAGTCAGTGGCACCTTATTCAAAGCCCACAAGTCAGTGGCA-TCATTTCAAAGCCCA
66 AAGCCCACAAGTCAGTGGCATCAT-TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
*
464023 CAAGTCAGTGGC-
130 CAAGTTAGTGGCA
* * * *
464035 ACCCTTTTCAAAGCCCATAAGTCAATGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTT
1 ACCC-TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC
* * * *
464100 AAATCCCACAAGTTAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCA-TCATTTCAAAGTCCA
65 AAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
464164 CAAGTTAGTGGC-
130 CAAGTTAGTGGCA
* * *** * * *
464176 ACCATTTTAAAATGCATAAGTTAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCA-CCATTTC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTC
* * * * *
464240 AAAACCCACAAGTAAATGGCATACCCTTTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAA
65 AAAGCCCACAAGTCAGTGGCAT--CATTTCAAAG-CC-CACAAGTCAGTGGC-ACTCTTTTCAAA
464305 GCCCACACAAGTTAGTGGCA
125 G-CC-CACAAGTTAGTGGCA
464325 CATTTTTTTA
Statistics
Matches: 621, Mismatches: 72, Indels: 31
0.86 0.10 0.04
Matches are distributed among these distances:
138 95 0.15
139 28 0.05
140 68 0.11
141 59 0.10
142 212 0.34
143 116 0.19
144 17 0.03
145 1 0.00
146 10 0.02
147 1 0.00
148 14 0.02
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.23
Consensus pattern (142 bp):
ACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCA
AAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCAC
AAGTTAGTGGCA
Found at i:465218 original size:20 final size:20
Alignment explanation
Indices: 465193--465297 Score: 84
Period size: 20 Copynumber: 4.8 Consensus size: 20
465183 TTTTACCCAG
465193 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
465213 ATGTATCGATACATTCTGTCTTTTACCCAA
1 ATGTATCGATACA-----T-TTTT---C-A
* * *
465243 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
465263 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
465283 ATGTATCGATACATT
1 ATGTATCGATACATT
465298 CTATCTTTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
20 45 0.66
24 2 0.03
25 2 0.03
26 4 0.06
29 1 0.01
30 14 0.21
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:465266 original size:50 final size:50
Alignment explanation
Indices: 465183--465279 Score: 158
Period size: 50 Copynumber: 1.9 Consensus size: 50
465173 AAAGTCACAT
* * *
465183 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTGTC
1 TTTTACCCAAATGTATCGATACATGTATCAATGTATCGATACATTCTGTC
*
465233 TTTTACCCAAATGTATCGATACATGTATGAATGTATCGATACATTCT
1 TTTTACCCAAATGTATCGATACATGTATCAATGTATCGATACATTCT
465280 TCAATGTATC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (50 bp):
TTTTACCCAAATGTATCGATACATGTATCAATGTATCGATACATTCTGTC
Found at i:465306 original size:70 final size:71
Alignment explanation
Indices: 465193--465347 Score: 249
Period size: 71 Copynumber: 2.2 Consensus size: 71
465183 TTTTACCCAG
* *
465193 ATGTATCGATACATTTTTCAATGTATCGATACATTCTGTC-TTTTACCCAAATGTATCGATACAT
1 ATGTATCGATACATTCTTCAATGTATCGATACATTCTATCTTTTTACCCAAATGTATCGATACAT
465257 GTATGA
66 GTATGA
*
465263 ATGTATCGATACATTCTTCAATGTATCGATACATTCTATCTTTTTACCCAGATGTATCGATACAT
1 ATGTATCGATACATTCTTCAATGTATCGATACATTCTATCTTTTTACCCAAATGTATCGATACAT
* * *
465328 TTTTTA
66 GTATGA
465334 ATGTATCGATACAT
1 ATGTATCGATACAT
465348 CTAGTTAAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
70 38 0.49
71 40 0.51
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (71 bp):
ATGTATCGATACATTCTTCAATGTATCGATACATTCTATCTTTTTACCCAAATGTATCGATACAT
GTATGA
Found at i:472256 original size:14 final size:14
Alignment explanation
Indices: 472237--472264 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
472227 TACACAAAGT
472237 ATGTATCGATACAC
1 ATGTATCGATACAC
472251 ATGTATCGATACAC
1 ATGTATCGATACAC
472265 CAAACATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (14 bp):
ATGTATCGATACAC
Done.